Daily Papers

Fluorescence Lifetime Imaging (FLI) is a critical molecular imaging modality that provides unique information about the tissue microenvironment, which is invaluable for biomedical applications. FLI operates by acquiring and analyzing photon time-of-arrival histograms to extract quantitative parameters associated with temporal fluorescence decay. These histograms are influenced by the intrinsic properties of the fluorophore, instrument parameters, time-of-flight distributions associated with pixel-wise variations in the topographic and optical characteristics of the sample. Recent advancements in Deep Learning (DL) have enabled improved fluorescence lifetime parameter estimation. However, existing models are primarily designed for planar surface samples, limiting their applicability in translational scenarios involving complex surface profiles, such as in-vivo whole-animal or imaged guided surgical applications. To address this limitation, we present MFliNet (Macroscopic FLI Network), a novel DL architecture that integrates the Instrument Response Function (IRF) as an additional input alongside experimental photon time-of-arrival histograms. Leveraging the capabilities of a Differential Transformer encoder-decoder architecture, MFliNet effectively focuses on critical input features, such as variations in photon time-of-arrival distributions. We evaluate MFliNet using rigorously designed tissue-mimicking phantoms and preclinical in-vivo cancer xenograft models. Our results demonstrate the model's robustness and suitability for complex macroscopic FLI applications, offering new opportunities for advanced biomedical imaging in diverse and challenging settings.

Semiconductor lasers have been rapidly evolving to meet the demands of next-generation optical networks. This imposes much more stringent requirements on the laser reliability, which are dominated by degradation mechanisms (e.g., sudden degradation) limiting the semiconductor laser lifetime. Physics-based approaches are often used to characterize the degradation behavior analytically, yet explicit domain knowledge and accurate mathematical models are required. Building such models can be very challenging due to a lack of a full understanding of the complex physical processes inducing the degradation under various operating conditions. To overcome the aforementioned limitations, we propose a new data-driven approach, extracting useful insights from the operational monitored data to predict the degradation trend without requiring any specific knowledge or using any physical model. The proposed approach is based on an unsupervised technique, a conditional variational autoencoder, and validated using vertical-cavity surface-emitting laser (VCSEL) and tunable edge emitting laser reliability data. The experimental results confirm that our model (i) achieves a good degradation prediction and generalization performance by yielding an F1 score of 95.3%, (ii) outperforms several baseline ML based anomaly detection techniques, and (iii) helps to shorten the aging tests by early predicting the failed devices before the end of the test and thereby saving costs

Practical identifiability is a critical concern in data-driven modeling of mathematical systems. In this paper, we propose a novel framework for practical identifiability analysis to evaluate parameter identifiability in mathematical models of biological systems. Starting with a rigorous mathematical definition of practical identifiability, we demonstrate its equivalence to the invertibility of the Fisher Information Matrix. Our framework establishes the relationship between practical identifiability and coordinate identifiability, introducing a novel metric that simplifies and accelerates the evaluation of parameter identifiability compared to the profile likelihood method. Additionally, we introduce new regularization terms to address non-identifiable parameters, enabling uncertainty quantification and improving model reliability. To guide experimental design, we present an optimal data collection algorithm that ensures all model parameters are practically identifiable. Applications to Hill functions, neural networks, and dynamic biological models demonstrate the feasibility and efficiency of the proposed computational framework in uncovering critical biological processes and identifying key observable variables.

We study the problem of estimating the time delay between two signals representing delayed, irregularly sampled and noisy versions of the same underlying pattern. We propose and demonstrate an evolutionary algorithm for the (hyper)parameter estimation of a kernel-based technique in the context of an astronomical problem, namely estimating the time delay between two gravitationally lensed signals from a distant quasar. Mixed types (integer and real) are used to represent variables within the evolutionary algorithm. We test the algorithm on several artificial data sets, and also on real astronomical observations of quasar Q0957+561. By carrying out a statistical analysis of the results we present a detailed comparison of our method with the most popular methods for time delay estimation in astrophysics. Our method yields more accurate and more stable time delay estimates: for Q0957+561, we obtain 419.6 days for the time delay between images A and B. Our methodology can be readily applied to current state-of-the-art optical monitoring data in astronomy, but can also be applied in other disciplines involving similar time series data.

Fluorescence labeling is the standard approach to reveal cellular structures and other subcellular constituents for microscopy images. However, this invasive procedure may perturb or even kill the cells and the procedure itself is highly time-consuming and complex. Recently, in silico labeling has emerged as a promising alternative, aiming to use machine learning models to directly predict the fluorescently labeled images from label-free microscopy. In this paper, we propose a deep learning-based in silico labeling method for the Light My Cells challenge. Built upon pix2pix, our proposed method can be trained using the partially labeled datasets with an adaptive loss. Moreover, we explore the effectiveness of several training strategies to handle different input modalities, such as training them together or separately. The results show that our method achieves promising performance for in silico labeling. Our code is available at https://github.com/MedICL-VU/LightMyCells.

We present a low-cost ultraviolet to infrared absolute quantum efficiency detector characterization system developed using commercial off-the-shelf components. The key components of the experiment include a light source,a regulated power supply, a monochromator, an integrating sphere, and a calibrated photodiode. We provide a step-by-step procedure to construct the photon and quantum efficiency transfer curves of imaging sensors. We present results for the GSENSE 2020 BSI CMOS sensor and the Sony IMX 455 BSI CMOS sensor. As a reference for similar characterizations, we provide a list of parts and associated costs along with images of our setup.

We introduce a general, flexible, parametric survival modelling framework which encompasses key shapes of hazard function (constant, increasing, decreasing, up-then-down, down-then-up), various common survival distributions (log-logistic, Burr type XII, Weibull, Gompertz), and includes defective distributions (i.e., cure models). This generality is achieved using four basic distributional parameters: two scale-type parameters and two shape parameters. Generalising to covariate dependence, the scale-type regression components correspond to accelerated failure time (AFT) and proportional hazards (PH) models. Therefore, this general formulation unifies the most popular survival models which allows us to consider the practical value of possible modelling choices for survival data. Furthermore, in line with our proposed flexible baseline distribution, we advocate the use of multi-parameter regression in which more than one distributional parameter depends on covariates - rather than the usual convention of having a single covariate-dependent (scale) parameter. While many choices are available, we suggest introducing covariates through just one or other of the two scale parameters, which covers AFT and PH models, in combination with a `power' shape parameter, which allows for more complex non-AFT/non-PH effects, while the other shape parameter remains covariate-independent, and handles automatic selection of the baseline distribution. We explore inferential issues in simulations, both with and without a covariate, with particular focus on evidence concerning the need, or otherwise, to include both AFT and PH parameters. We illustrate the efficacy of our modelling framework by investigating differences between treatment groups using data from a lung cancer study and a melanoma study. Censoring is accommodated throughout.

Solid-state quantum emitters have emerged as a leading quantum memory for quantum networking applications. However, standard optical characterization techniques are neither efficient nor repeatable at scale. In this work, we introduce and demonstrate spectroscopic techniques that enable large-scale, automated characterization of color centers. We first demonstrate the ability to track color centers by registering them to a fabricated machine-readable global coordinate system, enabling systematic comparison of the same color center sites over many experiments. We then implement resonant photoluminescence excitation in a widefield cryogenic microscope to parallelize resonant spectroscopy, achieving two orders of magnitude speed-up over confocal microscopy. Finally, we demonstrate automated chip-scale characterization of color centers and devices at room temperature, imaging thousands of microscope fields of view. These tools will enable accelerated identification of useful quantum emitters at chip-scale, enabling advances in scaling up color center platforms for quantum information applications, materials science, and device design and characterization.

A model to investigate Thermally Stimulated Depolarization Current (TSDC) peak parameters using the dipole-dipole interaction concept is proposed by the author in this work. The proposed model describe the (TSDC) peak successfully since it gives a significant peak parameters (i.e. Activation energy (E) and the per-exponential factor (\tau_0) in addition to the dipole-dipole interaction strength parameter (di). Application of this model to determine the peak parameters of polyvinyl chloride(PVC) polymer is presented . The results show how the model fit the experimental thermal sampling data. Finally the results are compared to the well know techniques; the initial rise method (IR), the half width method (HW) in addition to the Cowell and Woods analysis.

X-ray observing facilities, such as the Chandra X-ray Observatory and the eROSITA, have detected millions of astronomical sources associated with high-energy phenomena. The arrival of photons as a function of time follows a Poisson process and can vary by orders-of-magnitude, presenting obstacles for common tasks such as source classification, physical property derivation, and anomaly detection. Previous work has either failed to directly capture the Poisson nature of the data or only focuses on Poisson rate function reconstruction. In this work, we present Poisson Process AutoDecoder (PPAD). PPAD is a neural field decoder that maps fixed-length latent features to continuous Poisson rate functions across energy band and time via unsupervised learning. PPAD reconstructs the rate function and yields a representation at the same time. We demonstrate the efficacy of PPAD via reconstruction, regression, classification and anomaly detection experiments using the Chandra Source Catalog.

Accurately measuring the cycle lifetime of commercial lithium-ion batteries is crucial for performance and technology development. We introduce a novel hybrid approach combining a physics-based equation with a self-attention model to predict the cycle lifetimes of commercial lithium iron phosphate graphite cells via early-cycle data. After fitting capacity loss curves to this physics-based equation, we then use a self-attention layer to reconstruct entire battery capacity loss curves. Our model exhibits comparable performances to existing models while predicting more information: the entire capacity loss curve instead of cycle life. This provides more robustness and interpretability: our model does not need to be retrained for a different notion of end-of-life and is backed by physical intuition.

Intracellular lasers are emerging as powerful biosensors for multiplexed tracking and precision sensing of cells and their microenvironment. This sensing capacity is enabled by quantifying their narrow-linewidth emission spectra, which is presently challenging to do at high speeds. In this work, we demonstrate rapid snapshot hyperspectral imaging of intracellular lasers. Using integral field mapping with a microlens array and a diffraction grating, we obtain images of the spatial and spectral intensity distribution from a single camera acquisition. We demonstrate widefield hyperspectral imaging over a 3times3 mm^2 field of view and volumetric imaging over 250times250times800 mum^3 volumes with a spatial resolution of 5 mum and a spectral resolution of less than 0.8 nm. We evaluate the performance and outline the challenges and strengths of snapshot methods in the context of characterising the emission from intracellular lasers. This method offers new opportunities for a diverse range of applications, including high-throughput and long-term biosensing with intracellular lasers.

Bayesian parameter inference is useful to improve Li-ion battery diagnostics and can help formulate battery aging models. However, it is computationally intensive and cannot be easily repeated for multiple cycles, multiple operating conditions, or multiple replicate cells. To reduce the computational cost of Bayesian calibration, numerical solvers for physics-based models can be replaced with faster surrogates. A physics-informed neural network (PINN) is developed as a surrogate for the pseudo-2D (P2D) battery model calibration. For the P2D surrogate, additional training regularization was needed as compared to the PINN single-particle model (SPM) developed in Part I. Both the PINN SPM and P2D surrogate models are exercised for parameter inference and compared to data obtained from a direct numerical solution of the governing equations. A parameter inference study highlights the ability to use these PINNs to calibrate scaling parameters for the cathode Li diffusion and the anode exchange current density. By realizing computational speed-ups of 2250x for the P2D model, as compared to using standard integrating methods, the PINN surrogates enable rapid state-of-health diagnostics. In the low-data availability scenario, the testing error was estimated to 2mV for the SPM surrogate and 10mV for the P2D surrogate which could be mitigated with additional data.

Practitioners frequently aim to infer an unobserved population trajectory using sample snapshots at multiple time points. For instance, in single-cell sequencing, scientists would like to learn how gene expression evolves over time. But sequencing any cell destroys that cell. So we cannot access any cell's full trajectory, but we can access snapshot samples from many cells. Stochastic differential equations are commonly used to analyze systems with full individual-trajectory access; since here we have only sample snapshots, these methods are inapplicable. The deep learning community has recently explored using Schr\"odinger bridges (SBs) and their extensions to estimate these dynamics. However, these methods either (1) interpolate between just two time points or (2) require a single fixed reference dynamic within the SB, which is often just set to be Brownian motion. But learning piecewise from adjacent time points can fail to capture long-term dependencies. And practitioners are typically able to specify a model class for the reference dynamic but not the exact values of the parameters within it. So we propose a new method that (1) learns the unobserved trajectories from sample snapshots across multiple time points and (2) requires specification only of a class of reference dynamics, not a single fixed one. In particular, we suggest an iterative projection method inspired by Schr\"odinger bridges; we alternate between learning a piecewise SB on the unobserved trajectories and using the learned SB to refine our best guess for the dynamics within the reference class. We demonstrate the advantages of our method via a well-known simulated parametric model from ecology, simulated and real data from systems biology, and real motion-capture data.

Automatic analysis of the enormous sets of images is a critical task in life sciences. This faces many challenges such as: algorithms are highly parameterized, significant human input is intertwined, and lacking a standard meta-visualization approach. This paper proposes an alternative iterative approach for optimizing input parameters, saving time by minimizing the user involvement, and allowing for understanding the workflow of algorithms and discovering new ones. The main focus is on developing an interactive visualization technique that enables users to analyze the relationships between sampled input parameters and corresponding output. This technique is implemented as a prototype called Veni Vidi Vici, or "I came, I saw, I conquered." This strategy is inspired by the mathematical formulas of numbering computable functions and is developed atop ImageJ, a scientific image processing program. A case study is presented to investigate the proposed framework. Finally, the paper explores some potential future issues in the application of the proposed approach in parameter space analysis in visualization.

Traditional fluorescence staining is phototoxic to live cells, slow, and expensive; thus, the subcellular structure prediction (SSP) from transmitted light (TL) images is emerging as a label-free, faster, low-cost alternative. However, existing approaches utilize 3D networks for one-to-one voxel level dense prediction, which necessitates a frequent and time-consuming Z-axis imaging process. Moreover, 3D convolutions inevitably lead to significant computation and GPU memory overhead. Therefore, we propose an efficient framework, SparseSSP, predicting fluorescent intensities within the target voxel grid in an efficient paradigm instead of relying entirely on 3D topologies. In particular, SparseSSP makes two pivotal improvements to prior works. First, SparseSSP introduces a one-to-many voxel mapping paradigm, which permits the sparse TL slices to reconstruct the subcellular structure. Secondly, we propose a hybrid dimensions topology, which folds the Z-axis information into channel features, enabling the 2D network layers to tackle SSP under low computational cost. We conduct extensive experiments to validate the effectiveness and advantages of SparseSSP on diverse sparse imaging ratios, and our approach achieves a leading performance compared to pure 3D topologies. SparseSSP reduces imaging frequencies compared to previous dense-view SSP (i.e., the number of imaging is reduced up to 87.5% at most), which is significant in visualizing rapid biological dynamics on low-cost devices and samples.

To plan and optimize energy storage demands that account for Li-ion battery aging dynamics, techniques need to be developed to diagnose battery internal states accurately and rapidly. This study seeks to reduce the computational resources needed to determine a battery's internal states by replacing physics-based Li-ion battery models -- such as the single-particle model (SPM) and the pseudo-2D (P2D) model -- with a physics-informed neural network (PINN) surrogate. The surrogate model makes high-throughput techniques, such as Bayesian calibration, tractable to determine battery internal parameters from voltage responses. This manuscript is the first of a two-part series that introduces PINN surrogates of Li-ion battery models for parameter inference (i.e., state-of-health diagnostics). In this first part, a method is presented for constructing a PINN surrogate of the SPM. A multi-fidelity hierarchical training, where several neural nets are trained with multiple physics-loss fidelities is shown to significantly improve the surrogate accuracy when only training on the governing equation residuals. The implementation is made available in a companion repository (https://github.com/NREL/pinnstripes). The techniques used to develop a PINN surrogate of the SPM are extended in Part II for the PINN surrogate for the P2D battery model, and explore the Bayesian calibration capabilities of both surrogates.

The PRObabilistic Value-Added Bright Galaxy Survey (PROVABGS) catalog will provide measurements of galaxy properties, such as stellar mass (M_*), star formation rate ({rm SFR}), stellar metallicity (Z_{rm MW}), and stellar age (t_{rm age, MW}), for >10 million galaxies of the DESI Bright Galaxy Survey. Full posterior distributions of the galaxy properties will be inferred using state-of-the-art Bayesian spectral energy distribution (SED) modeling of DESI spectroscopy and Legacy Surveys photometry. In this work, we present the SED model, Bayesian inference framework, and methodology of PROVABGS. Furthermore, we apply the PROVABGS SED modeling on realistic synthetic DESI spectra and photometry, constructed using the L-GALAXIES semi-analytic model. We compare the inferred galaxy properties to the true galaxy properties of the simulation using a hierarchical Bayesian framework to quantify accuracy and precision. Overall, we accurately infer the true M_*, {rm SFR}, Z_{rm MW}, and t_{rm age, MW} of the simulated galaxies. However, the priors on galaxy properties induced by the SED model have a significant impact on the posteriors. They impose a {rm SFR}{>}10^{-1} M_odot/{rm yr} lower bound on {rm SFR}, a {sim}0.3 dex bias on log Z_{rm MW} for galaxies with low spectral signal-to-noise, and t_{rm age, MW} < 8,{rm Gyr} upper bound on stellar age. This work also demonstrates that a joint analysis of spectra and photometry significantly improves the constraints on galaxy properties over photometry alone and is necessary to mitigate the impact of the priors. With the methodology presented and validated in this work, PROVABGS will maximize information extracted from DESI observations and provide a probabilistic value-added galaxy catalog that will extend current galaxy studies to new regimes and unlock cutting-edge probabilistic analyses.

Diffusion models suffer from slow sample generation at inference time. Therefore, developing a principled framework for fast deterministic/stochastic sampling for a broader class of diffusion models is a promising direction. We propose two complementary frameworks for accelerating sample generation in pre-trained models: Conjugate Integrators and Splitting Integrators. Conjugate integrators generalize DDIM, mapping the reverse diffusion dynamics to a more amenable space for sampling. In contrast, splitting-based integrators, commonly used in molecular dynamics, reduce the numerical simulation error by cleverly alternating between numerical updates involving the data and auxiliary variables. After extensively studying these methods empirically and theoretically, we present a hybrid method that leads to the best-reported performance for diffusion models in augmented spaces. Applied to Phase Space Langevin Diffusion [Pandey & Mandt, 2023] on CIFAR-10, our deterministic and stochastic samplers achieve FID scores of 2.11 and 2.36 in only 100 network function evaluations (NFE) as compared to 2.57 and 2.63 for the best-performing baselines, respectively. Our code and model checkpoints will be made publicly available at https://github.com/mandt-lab/PSLD.

A class of generative models that unifies flow-based and diffusion-based methods is introduced. These models extend the framework proposed in Albergo & Vanden-Eijnden (2023), enabling the use of a broad class of continuous-time stochastic processes called `stochastic interpolants' to bridge any two arbitrary probability density functions exactly in finite time. These interpolants are built by combining data from the two prescribed densities with an additional latent variable that shapes the bridge in a flexible way. The time-dependent probability density function of the stochastic interpolant is shown to satisfy a first-order transport equation as well as a family of forward and backward Fokker-Planck equations with tunable diffusion coefficient. Upon consideration of the time evolution of an individual sample, this viewpoint immediately leads to both deterministic and stochastic generative models based on probability flow equations or stochastic differential equations with an adjustable level of noise. The drift coefficients entering these models are time-dependent velocity fields characterized as the unique minimizers of simple quadratic objective functions, one of which is a new objective for the score of the interpolant density. We show that minimization of these quadratic objectives leads to control of the likelihood for generative models built upon stochastic dynamics, while likelihood control for deterministic dynamics is more stringent. We also discuss connections with other methods such as score-based diffusion models, stochastic localization processes, probabilistic denoising techniques, and rectifying flows. In addition, we demonstrate that stochastic interpolants recover the Schr\"odinger bridge between the two target densities when explicitly optimizing over the interpolant. Finally, algorithmic aspects are discussed and the approach is illustrated on numerical examples.

This paper will discuss the microphysical simulation of interactions in liquid xenon, the active detector medium in many leading rare-event searches for new physics, and describe experimental observables useful for understanding detector performance. The scintillation and ionization yield distributions for signal and background will be presented using the Noble Element Simulation Technique (NEST), which is a toolkit based on experimental data and simple, empirical formulae, which mimic previous microphysics modeling, but are guided by data. The NEST models for light and charge production as a function of the particle type, energy, and electric field will be reviewed, as well as models for energy resolution and final pulse areas. NEST will be compared to other models or sets of models, and vetted against real data, with several specific examples pulled from XENON, ZEPLIN, LUX, LZ, PandaX, and table-top experiments used for calibrations.

High Power Laser's (HPL) optimal performance is essential for the success of a wide variety of experimental tasks related to light-matter interactions. Traditionally, HPL parameters are optimised in an automated fashion relying on black-box numerical methods. However, these can be demanding in terms of computational resources and usually disregard transient and complex dynamics. Model-free Deep Reinforcement Learning (DRL) offers a promising alternative framework for optimising HPL performance since it allows to tune the control parameters as a function of system states subject to nonlinear temporal dynamics without requiring an explicit dynamics model of those. Furthermore, DRL aims to find an optimal control policy rather than a static parameter configuration, particularly suitable for dynamic processes involving sequential decision-making. This is particularly relevant as laser systems are typically characterised by dynamic rather than static traits. Hence the need for a strategy to choose the control applied based on the current context instead of one single optimal control configuration. This paper investigates the potential of DRL in improving the efficiency and safety of HPL control systems. We apply this technique to optimise the temporal profile of laser pulses in the L1 pump laser hosted at the ELI Beamlines facility. We show how to adapt DRL to the setting of spectral phase control by solely tuning dispersion coefficients of the spectral phase and reaching pulses similar to transform limited with full-width at half-maximum (FWHM) of ca1.6 ps.

The lack of freely available standardized datasets represents an aggravating factor during the development and testing the performance of novel computational techniques in exposure assessment and dosimetry research. This hinders progress as researchers are required to generate numerical data (field, power and temperature distribution) anew using simulation software for each exposure scenario. Other than being time consuming, this approach is highly susceptible to errors that occur during the configuration of the electromagnetic model. To address this issue, in this paper, the limited available data on the incident power density and resultant maximum temperature rise on the skin surface considering various steady-state exposure scenarios at 10-90 GHz have been statistically modeled. The synthetic data have been sampled from the fitted statistical multivariate distribution with respect to predetermined dosimetric constraints. We thus present a comprehensive and open-source dataset compiled of the high-fidelity numerical data considering various exposures to a realistic source. Furthermore, different surrogate models for predicting maximum temperature rise on the skin surface were fitted based on the synthetic dataset. All surrogate models were tested on the originally available data where satisfactory predictive performance has been demonstrated. A simple technique of combining quadratic polynomial and tensor-product spline surrogates, each operating on its own cluster of data, has achieved the lowest mean absolute error of 0.058 {\deg}C. Therefore, overall experimental results indicate the validity of the proposed synthetic dataset.

Many hybrid quantum-classical algorithms for the application of ground state energy estimation in quantum chemistry involve estimating the expectation value of a molecular Hamiltonian with respect to a quantum state through measurements on a quantum device. To guide the selection of measurement methods designed for this observable estimation problem, we propose a benchmark called CSHOREBench (Common States and Hamiltonians for ObseRvable Estimation Benchmark) that assesses the performance of these methods against a set of common molecular Hamiltonians and common states encountered during the runtime of hybrid quantum-classical algorithms. In CSHOREBench, we account for resource utilization of a quantum computer through measurements of a prepared state, and a classical computer through computational runtime spent in proposing measurements and classical post-processing of acquired measurement outcomes. We apply CSHOREBench considering a variety of measurement methods on Hamiltonians of size up to 16 qubits. Our discussion is aided by using the framework of decision diagrams which provides an efficient data structure for various randomized methods and illustrate how to derandomize distributions on decision diagrams. In numerical simulations, we find that the methods of decision diagrams and derandomization are the most preferable. In experiments on IBM quantum devices against small molecules, we observe that decision diagrams reduces the number of measurements made by classical shadows by more than 80%, that made by locally biased classical shadows by around 57%, and consistently require fewer quantum measurements along with lower classical computational runtime than derandomization. Furthermore, CSHOREBench is empirically efficient to run when considering states of random quantum ansatz with fixed depth.

We incorporate discrete and continuous time Markov processes as building blocks into probabilistic graphical models with latent and observed variables. We introduce the automatic Backward Filtering Forward Guiding (BFFG) paradigm (Mider et al., 2021) for programmable inference on latent states and model parameters. Our starting point is a generative model, a forward description of the probabilistic process dynamics. We backpropagate the information provided by observations through the model to transform the generative (forward) model into a pre-conditional model guided by the data. It approximates the actual conditional model with known likelihood-ratio between the two. The backward filter and the forward change of measure are suitable to be incorporated into a probabilistic programming context because they can be formulated as a set of transformation rules. The guided generative model can be incorporated in different approaches to efficiently sample latent states and parameters conditional on observations. We show applicability in a variety of settings, including Markov chains with discrete state space, interacting particle systems, state space models, branching diffusions and Gamma processes.

This study developed a novel method for detecting hypernuclear events recorded in nuclear emulsion sheets using machine learning techniques. The artificial neural network-based object detection model was trained on surrogate images created through Monte Carlo simulations and image-style transformations using generative adversarial networks. The performance of the proposed model was evaluated using alpha-decay events obtained from the J-PARC E07 emulsion data. The model achieved approximately twice the detection efficiency of conventional image processing and reduced the time spent on manual visual inspection by approximately 1/17. The established method was successfully applied to the detection of hypernuclear events. This approach is a state-of-the-art tool for discovering rare events recorded in nuclear emulsion sheets without any real data for training.

Recent space-borne and ground-based observations provide photometric measurements as time series. The effect of interstellar dust extinction in the near-infrared range is only 10% of that measured in the V band. However, the sensitivity of the light curve shape to the physical parameters in the near-infrared is much lower. So, interpreting these types of data sets requires new approaches like the different large-scale surveys, which create similar problems with big data. Using a selected data set, we provide a method for applying routines implemented in R to extract most information of measurements to determine physical parameters, which can also be used in automatic classification schemes and pipeline processing. We made a multivariate classification of 131 Cepheid light curves (LC) in J, H, and K colors, where all the LCs were represented in 20D parameter space in these colors separately. Performing a Principal Component Analysis (PCA), we got an orthogonal coordinate system and squared Euclidean distances between LCs, with 6 significant eigenvalues, reducing the 20-dimension to 6. We also estimated the optimal number of partitions of similar objects and found it to be equal to 7 in each color; their dependence on the period, absolute magnitude, amplitude, and metallicity are also discussed. We computed the Spearman rank correlations, showing that periods and absolute magnitudes correlate with the first three PCs significantly. The first two PC are also found to have a relationship with the amplitude, but the metallicity effects are only marginal. The method shown can be generalized and implemented in unsupervised classification schemes and analysis of mixed and biased samples. The analysis of our Classical Cepheid near-infrared LC sample showed that the J, H, K curves are insufficient for determination of stellar metallicity, with mass being the key factor shaping them.

Battery Life Prediction (BLP), which relies on time series data produced by battery degradation tests, is crucial for battery utilization, optimization, and production. Despite impressive advancements, this research area faces three key challenges. Firstly, the limited size of existing datasets impedes insights into modern battery life data. Secondly, most datasets are restricted to small-capacity lithium-ion batteries tested under a narrow range of diversity in labs, raising concerns about the generalizability of findings. Thirdly, inconsistent and limited benchmarks across studies obscure the effectiveness of baselines and leave it unclear if models popular in other time series fields are effective for BLP. To address these challenges, we propose BatteryLife, a comprehensive dataset and benchmark for BLP. BatteryLife integrates 16 datasets, offering a 2.4 times sample size compared to the previous largest dataset, and provides the most diverse battery life resource with batteries from 8 formats, 80 chemical systems, 12 operating temperatures, and 646 charge/discharge protocols, including both laboratory and industrial tests. Notably, BatteryLife is the first to release battery life datasets of zinc-ion batteries, sodium-ion batteries, and industry-tested large-capacity lithium-ion batteries. With the comprehensive dataset, we revisit the effectiveness of baselines popular in this and other time series fields. Furthermore, we propose CyclePatch, a plug-in technique that can be employed in a series of neural networks. Extensive benchmarking of 18 methods reveals that models popular in other time series fields can be unsuitable for BLP, and CyclePatch consistently improves model performance establishing state-of-the-art benchmarks. Moreover, BatteryLife evaluates model performance across aging conditions and domains. BatteryLife is available at https://github.com/Ruifeng-Tan/BatteryLife.

Semiconductor lasers, one of the key components for optical communication systems, have been rapidly evolving to meet the requirements of next generation optical networks with respect to high speed, low power consumption, small form factor etc. However, these demands have brought severe challenges to the semiconductor laser reliability. Therefore, a great deal of attention has been devoted to improving it and thereby ensuring reliable transmission. In this paper, a predictive maintenance framework using machine learning techniques is proposed for real-time heath monitoring and prognosis of semiconductor laser and thus enhancing its reliability. The proposed approach is composed of three stages: i) real-time performance degradation prediction, ii) degradation detection, and iii) remaining useful life (RUL) prediction. First of all, an attention based gated recurrent unit (GRU) model is adopted for real-time prediction of performance degradation. Then, a convolutional autoencoder is used to detect the degradation or abnormal behavior of a laser, given the predicted degradation performance values. Once an abnormal state is detected, a RUL prediction model based on attention-based deep learning is utilized. Afterwards, the estimated RUL is input for decision making and maintenance planning. The proposed framework is validated using experimental data derived from accelerated aging tests conducted for semiconductor tunable lasers. The proposed approach achieves a very good degradation performance prediction capability with a small root mean square error (RMSE) of 0.01, a good anomaly detection accuracy of 94.24% and a better RUL estimation capability compared to the existing ML-based laser RUL prediction models.

We present a web-based software tool, the Virtual Quantum Optics Laboratory (VQOL), that may be used for designing and executing realistic simulations of quantum optics experiments. A graphical user interface allows one to rapidly build and configure a variety of different optical experiments, while the runtime environment provides unique capabilities for visualization and analysis. All standard linear optical components are available as well as sources of thermal, coherent, and entangled Gaussian states. A unique aspect of VQOL is the introduction of non-Gaussian measurements using detectors modeled as deterministic devices that "click" when the amplitude of the light falls above a given threshold. We describe the underlying theoretical models and provide several illustrative examples. We find that VQOL provides a a faithful representation of many experimental quantum optics phenomena and may serve as both a useful instructional tool for students as well as a valuable research tool for practitioners.

Despite the variety of available computational approaches, state-of-the-art methods for calculating excitation energies such as time-dependent density functional theory (TDDFT), are computationally demanding and thus limited to moderate system sizes. Here, we introduce a new variation of constrained DFT (CDFT), wherein the constraint corresponds to a particular transition (T), or combination of transitions, between occupied and virtual orbitals, rather than a region of the simulation space as in traditional CDFT. We compare T-CDFT with TDDFT and DeltaSCF results for the low lying excited states (S_{1} and T_{1}) of a set of gas phase acene molecules and OLED emitters, as well as with reference results from the literature. At the PBE level of theory, T-CDFT outperforms DeltaSCF for both classes of molecules, while also proving to be more robust. For the local excitations seen in the acenes, T-CDFT and TDDFT perform equally well. For the charge-transfer (CT)-like excitations seen in the OLED molecules, T-CDFT also performs well, in contrast to the severe energy underestimation seen with TDDFT. In other words, T-CDFT is equally applicable to both local excitations and CT states, providing more reliable excitation energies at a much lower computational cost than TDDFT. T-CDFT is designed for large systems and has been implemented in the linear scaling BigDFT code. It is therefore ideally suited for exploring the effects of explicit environments on excitation energies, paving the way for future simulations of excited states in complex realistic morphologies, such as those which occur in OLED materials.

State of health (SOH) is a crucial indicator for assessing the degradation level of batteries that cannot be measured directly but requires estimation. Accurate SOH estimation enhances detection, control, and feedback for Li-ion batteries, allowing for safe and efficient energy management and guiding the development of new-generation batteries. Despite the significant progress in data-driven SOH estimation, the time and resource-consuming degradation experiments for generating lifelong training data pose a challenge in establishing one large model capable of handling diverse types of Li-ion batteries, e.g., cross-chemistry, cross-manufacturer, and cross-capacity. Hence, this paper utilizes the strong generalization capability of large language model (LLM) to proposes a novel framework for adaptable SOH estimation across diverse batteries. To match the real scenario where unlabeled data sequentially arrives in use with distribution shifts, the proposed model is modified by a test-time training technique to ensure estimation accuracy even at the battery's end of life. The validation results demonstrate that the proposed framework achieves state-of-the-art accuracy on four widely recognized datasets collected from 62 batteries. Furthermore, we analyze the theoretical challenges of cross-battery estimation and provide a quantitative explanation of the effectiveness of our method.

The binding energies of the five bound rotational levels J=0-4 in the highest vibrational level v=14 in the X^1Sigma_g^+ ground electronic state of H_2 were measured in a three-step ultraviolet-laser experiment. Two-photon UV-photolysis of H_2S produced population in these high-lying bound states, that were subsequently interrogated at high precision via Doppler-free spectroscopy of the F^1Sigma_g^+ - X^1Sigma_g^+ system. A third UV-laser was used for detection through auto-ionizing resonances. The experimentally determined binding energies were found to be in excellent agreement with calculations based on non-adiabatic perturbation theory, also including relativistic and quantum electrodynamical contributions. The s-wave scattering length of the H + H system is derived from the binding energy of the last bound J=0 level via a direct semi-empirical approach, yielding a value of a_s = 0.2724(5) a_0, in good agreement with a result from a previously followed theoretical approach. The subtle effect of the malpha^4 relativity contribution to a_s was found to be significant. In a similar manner a value for the p-wave scattering volume is determined via the J=1 binding energy yielding a_p = -134.0000(6) a_0^3. The binding energy of the last bound state in H_2, the (v=14, J=4) level, is determined at 0.023(4) cm^{-1}, in good agreement with calculation. The effect of the hyperfine substructure caused by the two hydrogen atoms at large internuclear separation, giving rise to three distinct dissociation limits, is discussed.

In recent years, the demand for hyperspectral imaging devices has grown significantly, driven by their ability of capturing high-resolution spectral information. Among the several possible optical designs for acquiring hyperspectral images, there is a growing interest in interferometric spectral imaging systems based on division of aperture. These systems have the advantage of capturing snapshot acquisitions while maintaining a compact design. However, they require a careful calibration to operate properly. In this work, we present the interferometer response characterization algorithm (IRCA), a robust three-step procedure designed to characterize the transmittance response of multi-aperture imaging spectrometers based on the interferometry of Fabry-Perot. Additionally, we propose a formulation of the image formation model for such devices suitable to estimate the parameters of interest by considering the model under various regimes of finesse. The proposed algorithm processes the image output obtained from a set of monochromatic light sources and refines the results using nonlinear regression after an ad-hoc initialization. Through experimental analysis conducted on four different prototypes from the Image SPectrometer On Chip (ImSPOC) family, we validate the performance of our approach for characterization. The associated source code for this paper is available at https://github.com/danaroth83/irca.

Generating novel molecules with out-of-distribution properties is a major challenge in molecular discovery. While supervised learning methods generate high-quality molecules similar to those in a dataset, they struggle to generalize to out-of-distribution properties. Reinforcement learning can explore new chemical spaces but often conducts 'reward-hacking' and generates non-synthesizable molecules. In this work, we address this problem by integrating a state-of-the-art supervised learning method, STGG+, in an active learning loop. Our approach iteratively generates, evaluates, and fine-tunes STGG+ to continuously expand its knowledge. We denote this approach STGG+AL. We apply STGG+AL to the design of organic pi-functional materials, specifically two challenging tasks: 1) generating highly absorptive molecules characterized by high oscillator strength and 2) designing absorptive molecules with reasonable oscillator strength in the near-infrared (NIR) range. The generated molecules are validated and rationalized in-silico with time-dependent density functional theory. Our results demonstrate that our method is highly effective in generating novel molecules with high oscillator strength, contrary to existing methods such as reinforcement learning (RL) methods. We open-source our active-learning code along with our Conjugated-xTB dataset containing 2.9 million pi-conjugated molecules and the function for approximating the oscillator strength and absorption wavelength (based on sTDA-xTB).

Confocal fluorescence microscopy is one of the most accessible and widely used imaging techniques for the study of biological processes. Scanning confocal microscopy allows the capture of high-quality images from 3D samples, yet suffers from well-known limitations such as photobleaching and phototoxicity of specimens caused by intense light exposure, which limits its use in some applications, especially for living cells. Cellular damage can be alleviated by changing imaging parameters to reduce light exposure, often at the expense of image quality. Machine/deep learning methods for single-image super-resolution (SISR) can be applied to restore image quality by upscaling lower-resolution (LR) images to produce high-resolution images (HR). These SISR methods have been successfully applied to photo-realistic images due partly to the abundance of publicly available data. In contrast, the lack of publicly available data partly limits their application and success in scanning confocal microscopy. In this paper, we introduce a large scanning confocal microscopy dataset named SR-CACO-2 that is comprised of low- and high-resolution image pairs marked for three different fluorescent markers. It allows the evaluation of performance of SISR methods on three different upscaling levels (X2, X4, X8). SR-CACO-2 contains the human epithelial cell line Caco-2 (ATCC HTB-37), and it is composed of 22 tiles that have been translated in the form of 9,937 image patches for experiments with SISR methods. Given the new SR-CACO-2 dataset, we also provide benchmarking results for 15 state-of-the-art methods that are representative of the main SISR families. Results show that these methods have limited success in producing high-resolution textures, indicating that SR-CACO-2 represents a challenging problem. Our dataset, code and pretrained weights are available: https://github.com/sbelharbi/sr-caco-2.

Magnetic resonance imaging (MRI) is a cornerstone of modern medical imaging. However, long image acquisition times, the need for qualitative expert analysis, and the lack of (and difficulty extracting) quantitative indicators that are sensitive to tissue health have curtailed widespread clinical and research studies. While recent machine learning methods for MRI reconstruction and analysis have shown promise for reducing this burden, these techniques are primarily validated with imperfect image quality metrics, which are discordant with clinically-relevant measures that ultimately hamper clinical deployment and clinician trust. To mitigate this challenge, we present the Stanford Knee MRI with Multi-Task Evaluation (SKM-TEA) dataset, a collection of quantitative knee MRI (qMRI) scans that enables end-to-end, clinically-relevant evaluation of MRI reconstruction and analysis tools. This 1.6TB dataset consists of raw-data measurements of ~25,000 slices (155 patients) of anonymized patient MRI scans, the corresponding scanner-generated DICOM images, manual segmentations of four tissues, and bounding box annotations for sixteen clinically relevant pathologies. We provide a framework for using qMRI parameter maps, along with image reconstructions and dense image labels, for measuring the quality of qMRI biomarker estimates extracted from MRI reconstruction, segmentation, and detection techniques. Finally, we use this framework to benchmark state-of-the-art baselines on this dataset. We hope our SKM-TEA dataset and code can enable a broad spectrum of research for modular image reconstruction and image analysis in a clinically informed manner. Dataset access, code, and benchmarks are available at https://github.com/StanfordMIMI/skm-tea.

In physics and engineering literature, the distribution of the excursion-above-zero time distribution (exceedance distribution) for a stationary Gaussian process has been approximated by a stationary switching process with independently distributed switching times. The approach matched the covariance of the clipped Gaussian process with the one for the stationary switching process and the distribution of the latter was used as the so-called independent interval approximation (IIA). The approach successfully assessed the persistency exponent for many physically important processes but left an unanswered question when such an approach leads to a mathematically meaningful and proper exceedance distribution. Here we address this question by proposing an alternative matching of the expected values of the clipped Slepian process and the corresponding switched process initiated at the origin. The method has allowed resolving the mathematical correctness of the matching method for a large subclass of the Gaussian processes with monotonic covariance, for which we provide a sufficient condition for the validity of the IIA. Within this class, the IIA produces a valid distribution for the excursion time and is represented in an explicit stochastic form that connects directly to the covariance of the underlying Gaussian process. We compare the excursion level distributions as well as the corresponding persistency exponents obtained through the IIA method with numerically computed exact distributions, and the simulated distribution for several important Gaussian models. We also argue that for stationary Gaussian processes with a non-monotonic covariance, the IIA fails and should not be used.

We present Mantis Shrimp, a multi-survey deep learning model for photometric redshift estimation that fuses ultra-violet (GALEX), optical (PanSTARRS), and infrared (UnWISE) imagery. Machine learning is now an established approach for photometric redshift estimation, with generally acknowledged higher performance in areas with a high density of spectroscopically identified galaxies over template-based methods. Multiple works have shown that image-based convolutional neural networks can outperform tabular-based color/magnitude models. In comparison to tabular models, image models have additional design complexities: it is largely unknown how to fuse inputs from different instruments which have different resolutions or noise properties. The Mantis Shrimp model estimates the conditional density estimate of redshift using cutout images. The density estimates are well calibrated and the point estimates perform well in the distribution of available spectroscopically confirmed galaxies with (bias = 1e-2), scatter (NMAD = 2.44e-2) and catastrophic outlier rate (eta=17.53%). We find that early fusion approaches (e.g., resampling and stacking images from different instruments) match the performance of late fusion approaches (e.g., concatenating latent space representations), so that the design choice ultimately is left to the user. Finally, we study how the models learn to use information across bands, finding evidence that our models successfully incorporates information from all surveys. The applicability of our model to the analysis of large populations of galaxies is limited by the speed of downloading cutouts from external servers; however, our model could be useful in smaller studies such as generating priors over redshift for stellar population synthesis.

Hoffmann et al. (2022) propose three methods for estimating a compute-optimal scaling law. We attempt to replicate their third estimation procedure, which involves fitting a parametric loss function to a reconstruction of data from their plots. We find that the reported estimates are inconsistent with their first two estimation methods, fail at fitting the extracted data, and report implausibly narrow confidence intervals--intervals this narrow would require over 600,000 experiments, while they likely only ran fewer than 500. In contrast, our rederivation of the scaling law using the third approach yields results that are compatible with the findings from the first two estimation procedures described by Hoffmann et al.

This paper presents a data-driven, task-specific paradigm for experimental design, to shorten acquisition time, reduce costs, and accelerate the deployment of imaging devices. Current approaches in experimental design focus on model-parameter estimation and require specification of a particular model, whereas in imaging, other tasks may drive the design. Furthermore, such approaches often lead to intractable optimization problems in real-world imaging applications. Here we present a new paradigm for experimental design that simultaneously optimizes the design (set of image channels) and trains a machine-learning model to execute a user-specified image-analysis task. The approach obtains data densely-sampled over the measurement space (many image channels) for a small number of acquisitions, then identifies a subset of channels of prespecified size that best supports the task. We propose a method: TADRED for TAsk-DRiven Experimental Design in imaging, to identify the most informative channel-subset whilst simultaneously training a network to execute the task given the subset. Experiments demonstrate the potential of TADRED in diverse imaging applications: several clinically-relevant tasks in magnetic resonance imaging; and remote sensing and physiological applications of hyperspectral imaging. Results show substantial improvement over classical experimental design, two recent application-specific methods within the new paradigm, and state-of-the-art approaches in supervised feature selection. We anticipate further applications of our approach. Code is available: https://github.com/sbb-gh/experimental-design-multichannel

A dynamical model based on a phenomenological charm quark-nucleon(c-N) potential v_{cN} and the Pomeron-exchange mechanism is constructed to investigate the J/Psi photo-production on the nucleon from threshold to invariant mass W=300 GeV. The J/Psi-N potential,V_{J/Psi N}(r),is constructed by folding v_{cN} into the wavefunction Phi_{J/Psi}(cc) of J/Psi within a Constituent Quark Model(CQM) of Ref.[43]. A photo-production amplitude is also generated by v_{cN} by a cc-loop integration over the gammarightarrow cc vertex function and Phi_{J/Psi}(cc). No commonly used Vector Meson Dominance assumption is used to define this photo-production amplitude which is needed to describe the data near the threshold. The potential v_{cN}(r) is parameterized in a form such that the predicted V_{J/Psi N}(r) at large distances has the same Yukawa potential form extracted from a Lattice QCD(LQCD) calculation of Ref.[18]. The parameters of v_{cN} are determined by fitting the total cross section data of JLab by performing calculations that include J/Psi-N final state interactions(FSI). The resulting differential cross sections are found in good agreements with the data. It is shown that the FSI effects dominate the cross section in the very near threshold region, allowing for sensitive testing of the predicted J/Psi-N scattering amplitudes. By imposing the constraints of J/Psi-N potential extracted from the LQCD calculation, we have obtained three J/Psi-N potentials which fit the JLab data equally well. The resulting J/Psi-N scattering lengths are in the range of a=(-0.05 fm sim -0.25 fm). With the determined v_{cN}(r) and the wavefunctions generated from the same CQM, the constructed model is used to predict the cross sections of photo-production of eta_c(1S) and Psi(2S) mesons for future experimental tests.

We present Monte Carlo (MC) simulation results from a study of a compact plastic-scintillator detector suitable for imaging fast neutrons in the 1 -- 10 MeV energy range: the miniTimeCube (mTC). Originally designed for antineutrino detection, the mTC consists of 24 MultiChannel Plate (MCP) photodetectors surrounding a 13 cm cube of boron-doped plastic scintillator. Our simulation results show that waveform digitization of 1536 optically sensitive channels surrounding the scintillator should allow for spatiotemporal determination of individual neutron-proton scatters in the detector volume to thicksim100 picoseconds and thicksim5 mm. A Bayesian estimation framework is presented for multiple-scatter reconstruction, and is used to estimate the incoming direction and energy of simulated individual neutrons. Finally, we show how populations of reconstructed neutrons can be used to estimate the direction and energy spectrum of nearby simulated neutron sources.

We develop a framework for non-asymptotic analysis of deterministic samplers used for diffusion generative modeling. Several recent works have analyzed stochastic samplers using tools like Girsanov's theorem and a chain rule variant of the interpolation argument. Unfortunately, these techniques give vacuous bounds when applied to deterministic samplers. We give a new operational interpretation for deterministic sampling by showing that one step along the probability flow ODE can be expressed as two steps: 1) a restoration step that runs gradient ascent on the conditional log-likelihood at some infinitesimally previous time, and 2) a degradation step that runs the forward process using noise pointing back towards the current iterate. This perspective allows us to extend denoising diffusion implicit models to general, non-linear forward processes. We then develop the first polynomial convergence bounds for these samplers under mild conditions on the data distribution.

We present griz light curves of 251 Type Ia Supernovae (SNe Ia) from the first 3 years of the Dark Energy Survey Supernova Program's (DES-SN) spectroscopically classified sample. The photometric pipeline described in this paper produces the calibrated fluxes and associated uncertainties used in the cosmological parameter analysis (Brout et al. 2018-SYS, DES Collaboration et al. 2018) by employing a scene modeling approach that simultaneously forward models a variable transient flux and temporally constant host galaxy. We inject artificial point sources onto DECam images to test the accuracy of our photometric method. Upon comparison of input and measured artificial supernova fluxes, we find flux biases peak at 3 mmag. We require corrections to our photometric uncertainties as a function of host galaxy surface brightness at the transient location, similar to that seen by the DES Difference Imaging Pipeline used to discover transients. The public release of the light curves can be found at https://des.ncsa.illinois.edu/releases/sn.

Elucidating quantum coherence effects and geometrical factors for efficient energy transfer in photosynthesis has the potential to uncover non-classical design principles for advanced organic materials. We study energy transfer in a linear light-harvesting model to reveal that dimerized geometries with strong electronic coherences within donor and acceptor pairs exhibit significantly improved efficiency, which is in marked contrast to predictions of the classical F\"orster theory. We reveal that energy tuning due to coherent delocalization of photoexcitations is mainly responsible for the efficiency optimization. This coherence-assisted energy-tuning mechanism also explains the energetics and chlorophyll arrangements in the widely-studied Fenna-Matthews-Olson complex. We argue that a clustered network with rapid energy relaxation among donors and resonant energy transfer from donor to acceptor states provides a basic formula for constructing efficient light-harvesting systems, and the general principles revealed here can be generalized to larger systems and benefit future innovation of efficient molecular light-harvesting materials.

Harmonic retrieval techniques are the foundation of radio channel sounding, estimation and modeling. This paper introduces a Deep Learning approach for two-dimensional spectral estimation from frequency and time samples of a radio channel transfer function. Our work can estimate two-dimensional parameters from a signal containing an unknown number of paths. In contrast to existing deep learning-based methods, the signal parameters are not estimated via classification but instead in a quasi-grid-free manner. This alleviates the bias, spectral leakage, and ghost targets that grid-based approaches inherently produce. The proposed architecture also reliably estimates the number of spectral components in the measurement. Hence, the architecture jointly solves the model order selection problem and the parameter estimation task. Additionally, we propose a multi-channel windowing of the data during preprocessing, increasing the resulting estimator's robustness. We verify the performance compared to existing harmonic retrieval methods and also show how it can be integrated into an existing maximum likelihood estimator for efficient initialization of a gradient-based iteration.

PROTACs are a promising therapeutic modality that harnesses the cell's built-in degradation machinery to degrade specific proteins. Despite their potential, developing new PROTACs is challenging and requires significant domain expertise, time, and cost. Meanwhile, machine learning has transformed drug design and development. In this work, we present a strategy for curating open-source PROTAC data and an open-source deep learning tool for predicting the degradation activity of novel PROTAC molecules. The curated dataset incorporates important information such as pDC_{50}, D_{max}, E3 ligase type, POI amino acid sequence, and experimental cell type. Our model architecture leverages learned embeddings from pretrained machine learning models, in particular for encoding protein sequences and cell type information. We assessed the quality of the curated data and the generalization ability of our model architecture against new PROTACs and targets via three tailored studies, which we recommend other researchers to use in evaluating their degradation activity models. In each study, three models predict protein degradation in a majority vote setting, reaching a top test accuracy of 82.6% and 0.848 ROC AUC, and a test accuracy of 61% and 0.615 ROC AUC when generalizing to novel protein targets. Our results are not only comparable to state-of-the-art models for protein degradation prediction, but also part of an open-source implementation which is easily reproducible and less computationally complex than existing approaches.

Conventional diffusion models typically relies on a fixed forward process, which implicitly defines complex marginal distributions over latent variables. This can often complicate the reverse process' task in learning generative trajectories, and results in costly inference for diffusion models. To address these limitations, we introduce Neural Flow Diffusion Models (NFDM), a novel framework that enhances diffusion models by supporting a broader range of forward processes beyond the fixed linear Gaussian. We also propose a novel parameterization technique for learning the forward process. Our framework provides an end-to-end, simulation-free optimization objective, effectively minimizing a variational upper bound on the negative log-likelihood. Experimental results demonstrate NFDM's strong performance, evidenced by state-of-the-art likelihood estimation. Furthermore, we investigate NFDM's capacity for learning generative dynamics with specific characteristics, such as deterministic straight lines trajectories. This exploration underscores NFDM's versatility and its potential for a wide range of applications.

Inverse problems aim to determine parameters from observations, a crucial task in engineering and science. Lately, generative models, especially diffusion models, have gained popularity in this area for their ability to produce realistic solutions and their good mathematical properties. Despite their success, an important drawback of diffusion models is their sensitivity to the choice of variance schedule, which controls the dynamics of the diffusion process. Fine-tuning this schedule for specific applications is crucial but time-costly and does not guarantee an optimal result. We propose a novel approach for learning the schedule as part of the training process. Our method supports probabilistic conditioning on data, provides high-quality solutions, and is flexible, proving able to adapt to different applications with minimum overhead. This approach is tested in two unrelated inverse problems: super-resolution microscopy and quantitative phase imaging, yielding comparable or superior results to previous methods and fine-tuned diffusion models. We conclude that fine-tuning the schedule by experimentation should be avoided because it can be learned during training in a stable way that yields better results.

We here propose a machine learning approach for monitoring particle detectors in real-time. The goal is to assess the compatibility of incoming experimental data with a reference dataset, characterising the data behaviour under normal circumstances, via a likelihood-ratio hypothesis test. The model is based on a modern implementation of kernel methods, nonparametric algorithms that can learn any continuous function given enough data. The resulting approach is efficient and agnostic to the type of anomaly that may be present in the data. Our study demonstrates the effectiveness of this strategy on multivariate data from drift tube chamber muon detectors.

We introduce a new family of physics-inspired generative models termed PFGM++ that unifies diffusion models and Poisson Flow Generative Models (PFGM). These models realize generative trajectories for N dimensional data by embedding paths in N{+}D dimensional space while still controlling the progression with a simple scalar norm of the D additional variables. The new models reduce to PFGM when D{=}1 and to diffusion models when D{to}infty. The flexibility of choosing D allows us to trade off robustness against rigidity as increasing D results in more concentrated coupling between the data and the additional variable norms. We dispense with the biased large batch field targets used in PFGM and instead provide an unbiased perturbation-based objective similar to diffusion models. To explore different choices of D, we provide a direct alignment method for transferring well-tuned hyperparameters from diffusion models (D{to} infty) to any finite D values. Our experiments show that models with finite D can be superior to previous state-of-the-art diffusion models on CIFAR-10/FFHQ 64{times}64 datasets, with FID scores of 1.91/2.43 when D{=}2048/128. In class-conditional setting, D{=}2048 yields current state-of-the-art FID of 1.74 on CIFAR-10. In addition, we demonstrate that models with smaller D exhibit improved robustness against modeling errors. Code is available at https://github.com/Newbeeer/pfgmpp

We apply a complex network approach to analyse the time series of five solar parameters, and propose an strategy to predict the number of sunspots for the next solar maximum, and when will this maximum will occur. The approach is based on the Visibility Graph (VG) algorithm, and a slightly modified version of it, the Horizontal Visibility Graph (HVG), which map a time series into a complex network. Various network metrics exhibit either an exponential or a scale-free behavior, and we find that the evolution of the characteristic decay exponents is consistent with variations of the sunspots number along solar cycles. During solar minimum, the sunspots number and the solar index time series have characteristic decay exponents that correlate well with the next maximum sunspots number, suggesting that they may be good precursors of the intensity of the next solar maximum. Based on this observation, we find that, based on current data, the algorithm predicts a number of 179 sunspots for cycle 25. Combining this with the Hathaway function, adjusted to yield such maximum sunspots number, we find that the maximum for solar cycle 25 will occur in December 2024/January 2025.

In this work, we aim to estimate the stellar parameters of the primary (Aa) by performing asteroseismic analysis on its period-spacing pattern. We use the C-3PO neural network to perform asteroseismic modelling of the g-mode period-spacing pattern of Aa, discussing the interplay of this information with external constraints from spectroscopy (T_{rm eff} and log(g)) and eclipse modelling (R). To estimate the level of uncertainty due to different frequency extraction and pattern identification processes, we consider four different variations on the period-spacing patterns. To better understand the correlations between and the uncertainty structure of our parameter estimates, we also employed a classical, parameter-based MCMC grid search on four different stellar grids. The best-fitting, externally constrained model to the period-spacing pattern arrives at estimates of the stellar properties for Aa of: M=1.51 pm 0.05 M_odot, X_c =0.43 pm 0.04, R=1.66 pm 0.1 R_odot, f_{rm ov}=0.010, Omega_c=1.58 pm 0.01 d^{-1} with rigid rotation to within the measurement errors, log(T_{rm eff})=3.856 pm 0.008 dex, log(g)=4.18 pm 0.04 dex, and log(L)=0.809 pm 0.005 dex, which agree well with previous measurements from eclipse modelling, spectroscopy, and the Gaia DR3 luminosity. We find that the near-core properties of the best-fitting asteroseismic models are consistent with external constraints from eclipse modelling and spectroscopy. Aa appears to be a typical example of a gamma Dor star, fitting well within existing populations. We find that Aa is quasi-rigidly rotating to within the uncertainties, and note that the asteroseismic age estimate for Aa (1100 pm 100 Myr) is considerably older than the young (35 Myr) age implied by previous isochrone fits to the B binary in the literature. Our MCMC parameter-based grid-search agrees well with our pattern-modelling approach.

Diffusion models have exhibited excellent performance in various domains. The probability flow ordinary differential equation (ODE) of diffusion models (i.e., diffusion ODEs) is a particular case of continuous normalizing flows (CNFs), which enables deterministic inference and exact likelihood evaluation. However, the likelihood estimation results by diffusion ODEs are still far from those of the state-of-the-art likelihood-based generative models. In this work, we propose several improved techniques for maximum likelihood estimation for diffusion ODEs, including both training and evaluation perspectives. For training, we propose velocity parameterization and explore variance reduction techniques for faster convergence. We also derive an error-bounded high-order flow matching objective for finetuning, which improves the ODE likelihood and smooths its trajectory. For evaluation, we propose a novel training-free truncated-normal dequantization to fill the training-evaluation gap commonly existing in diffusion ODEs. Building upon these techniques, we achieve state-of-the-art likelihood estimation results on image datasets (2.56 on CIFAR-10, 3.43/3.69 on ImageNet-32) without variational dequantization or data augmentation.

Bayesian optimization (BO) has established itself as a leading strategy for efficiently optimizing expensive-to-evaluate functions. Existing BO methods mostly rely on Gaussian process (GP) surrogate models and are not applicable to (doubly-stochastic) Gaussian Cox processes, where the observation process is modulated by a latent intensity function modeled as a GP. In this paper, we propose a novel maximum a posteriori inference of Gaussian Cox processes. It leverages the Laplace approximation and change of kernel technique to transform the problem into a new reproducing kernel Hilbert space, where it becomes more tractable computationally. It enables us to obtain both a functional posterior of the latent intensity function and the covariance of the posterior, thus extending existing works that often focus on specific link functions or estimating the posterior mean. Using the result, we propose a BO framework based on the Gaussian Cox process model and further develop a Nystr\"om approximation for efficient computation. Extensive evaluations on various synthetic and real-world datasets demonstrate significant improvement over state-of-the-art inference solutions for Gaussian Cox processes, as well as effective BO with a wide range of acquisition functions designed through the underlying Gaussian Cox process model.

The coupling of the angular jitter of the spacecraft and their sub-assemblies with the optical bench and the telescope into the interferometric length readout will be a major noise source in the LISA mission. We refer to this noise as tilt-to-length (TTL) coupling. It will be reduced directly by realignments, and the residual noise will then be subtracted in post-processing. The success of these mitigation strategies depends on an accurate computation of the TTL coupling coefficients. We present here a thorough analysis of the accuracy of the coefficient estimation under different jitter characteristics, angular readout noise levels, and gravitational wave sources. We analyze in which cases the estimates degrade using two estimators, the common least squares estimator and the instrumental variables estimator. Our investigations show that angular readout noise leads to a bias of the least squares estimator, depending on the TTL coupling coefficients, jitter and readout noise level, while the instrumental variable estimator is not biased. We present an equation that predicts the estimation bias of the least squares method due to angular readout noise.

The simulation of the metabolism in mammalian cells becomes a severe problem if spatial distributions must be taken into account. Especially the cytoplasm has a very complex geometric structure which cannot be handled by standard discretization techniques. In the present paper we propose a homogenization technique for computing effective diffusion constants. This is accomplished by using a two-step strategy. The first step consists of an analytic homogenization from the smallest to an intermediate scale. The homogenization error is estimated by comparing the analytic diffusion constant with a numerical estimate obtained by using real cell geometries. The second step consists of a random homogenization. Since no analytical solution is known to this homogenization problem, a numerical approximation algorithm is proposed. Although rather expensive this algorithm provides a reasonable estimate of the homogenized diffusion constant.

The last decade has witnessed a rapid growth of the field of exoplanet discovery and characterisation. However, several big challenges remain, many of which could be addressed using machine learning methodology. For instance, the most prolific method for detecting exoplanets and inferring several of their characteristics, transit photometry, is very sensitive to the presence of stellar spots. The current practice in the literature is to identify the effects of spots visually and correct for them manually or discard the affected data. This paper explores a first step towards fully automating the efficient and precise derivation of transit depths from transit light curves in the presence of stellar spots. The methods and results we present were obtained in the context of the 1st Machine Learning Challenge organized for the European Space Agency's upcoming Ariel mission. We first present the problem, the simulated Ariel-like data and outline the Challenge while identifying best practices for organizing similar challenges in the future. Finally, we present the solutions obtained by the top-5 winning teams, provide their code and discuss their implications. Successful solutions either construct highly non-linear (w.r.t. the raw data) models with minimal preprocessing -deep neural networks and ensemble methods- or amount to obtaining meaningful statistics from the light curves, constructing linear models on which yields comparably good predictive performance.

Posterior sampling has been shown to be a powerful Bayesian approach for solving imaging inverse problems. The recent plug-and-play unadjusted Langevin algorithm (PnP-ULA) has emerged as a promising method for Monte Carlo sampling and minimum mean squared error (MMSE) estimation by combining physical measurement models with deep-learning priors specified using image denoisers. However, the intricate relationship between the sampling distribution of PnP-ULA and the mismatched data-fidelity and denoiser has not been theoretically analyzed. We address this gap by proposing a posterior-L2 pseudometric and using it to quantify an explicit error bound for PnP-ULA under mismatched posterior distribution. We numerically validate our theory on several inverse problems such as sampling from Gaussian mixture models and image deblurring. Our results suggest that the sensitivity of the sampling distribution of PnP-ULA to a mismatch in the measurement model and the denoiser can be precisely characterized.

Despite the recent advances in the field of computational Schr\"odinger Bridges (SB), most existing SB solvers are still heavy-weighted and require complex optimization of several neural networks. It turns out that there is no principal solver which plays the role of simple-yet-effective baseline for SB just like, e.g., k-means method in clustering, logistic regression in classification or Sinkhorn algorithm in discrete optimal transport. We address this issue and propose a novel fast and simple SB solver. Our development is a smart combination of two ideas which recently appeared in the field: (a) parameterization of the Schr\"odinger potentials with sum-exp quadratic functions and (b) viewing the log-Schr\"odinger potentials as the energy functions. We show that combined together these ideas yield a lightweight, simulation-free and theoretically justified SB solver with a simple straightforward optimization objective. As a result, it allows solving SB in moderate dimensions in a matter of minutes on CPU without a painful hyperparameter selection. Our light solver resembles the Gaussian mixture model which is widely used for density estimation. Inspired by this similarity, we also prove an important theoretical result showing that our light solver is a universal approximator of SBs. Furthemore, we conduct the analysis of the generalization error of our light solver. The code for our solver can be found at https://github.com/ngushchin/LightSB

Markov jump processes are continuous-time stochastic processes which describe dynamical systems evolving in discrete state spaces. These processes find wide application in the natural sciences and machine learning, but their inference is known to be far from trivial. In this work we introduce a methodology for zero-shot inference of Markov jump processes (MJPs), on bounded state spaces, from noisy and sparse observations, which consists of two components. First, a broad probability distribution over families of MJPs, as well as over possible observation times and noise mechanisms, with which we simulate a synthetic dataset of hidden MJPs and their noisy observation process. Second, a neural network model that processes subsets of the simulated observations, and that is trained to output the initial condition and rate matrix of the target MJP in a supervised way. We empirically demonstrate that one and the same (pretrained) model can infer, in a zero-shot fashion, hidden MJPs evolving in state spaces of different dimensionalities. Specifically, we infer MJPs which describe (i) discrete flashing ratchet systems, which are a type of Brownian motors, and the conformational dynamics in (ii) molecular simulations, (iii) experimental ion channel data and (iv) simple protein folding models. What is more, we show that our model performs on par with state-of-the-art models which are finetuned to the target datasets.

Strongly lensed variable quasars can serve as precise cosmological probes, provided that time delays between the image fluxes can be accurately measured. A number of methods have been proposed to address this problem. In this paper, we explore in detail a new approach based on kernel regression estimates, which is able to estimate a single time delay given several datasets for the same quasar. We develop realistic artificial data sets in order to carry out controlled experiments to test of performance of this new approach. We also test our method on real data from strongly lensed quasar Q0957+561 and compare our estimates against existing results.

This paper presents a differentially private approach to Kaplan-Meier estimation that achieves accurate survival probability estimates while safeguarding individual privacy. The Kaplan-Meier estimator is widely used in survival analysis to estimate survival functions over time, yet applying it to sensitive datasets, such as clinical records, risks revealing private information. To address this, we introduce a novel algorithm that applies time-indexed Laplace noise, dynamic clipping, and smoothing to produce a privacy-preserving survival curve while maintaining the cumulative structure of the Kaplan-Meier estimator. By scaling noise over time, the algorithm accounts for decreasing sensitivity as fewer individuals remain at risk, while dynamic clipping and smoothing prevent extreme values and reduce fluctuations, preserving the natural shape of the survival curve. Our results, evaluated on the NCCTG lung cancer dataset, show that the proposed method effectively lowers root mean squared error (RMSE) and enhances accuracy across privacy budgets (epsilon). At epsilon = 10, the algorithm achieves an RMSE as low as 0.04, closely approximating non-private estimates. Additionally, membership inference attacks reveal that higher epsilon values (e.g., epsilon geq 6) significantly reduce influential points, particularly at higher thresholds, lowering susceptibility to inference attacks. These findings confirm that our approach balances privacy and utility, advancing privacy-preserving survival analysis.

Blazars, a class of active galactic nuclei (AGN) powered by supermassive black holes, are known for their remarkable variability across multiple timescales and wavelengths. With advancements in both ground- and space-based telescopes, our understanding of AGN central engines has significantly improved. However, the mechanisms driving this variability remain elusive, and continue to fascinate both theorists and observers alike. The primary objective of this study is to constrain the X-ray variability properties of the TeV blazar PKS 2155-304. We conduct a comprehensive X-ray spectral and timing analysis, focusing on both long-term and intra-day variability. This analysis uses data from 22 epochs of XMM-Newton EPIC-pn observations, collected over 15 years (2000-2014). To investigate the variability of the source, we applied both timing and spectral analyses. For the timing analysis, we estimated fractional variability, variability amplitude, minimum variability timescales, flux distribution, and power spectral density (PSD). In the spectral analysis, we fitted the X-ray spectra using power-law, log-parabola, and broken power-law (BPL) models to determine the best-fitting parameters. Additionally, we studied the hardness ratio (HR). We observed moderate intra-day variability in most of the light curves. Seven out of the twenty-two observations showed a clear bimodal flux distribution, indicating the presence of two distinct flux states. Our analysis revealed a variable power-law PSD slope. Most HR plots did not show significant variation with flux, except for one observation (OBSID 0124930501), where HR increased with flux (Count/s). The fitted X-ray spectra favored the BPL model for the majority of observations. The findings of this work shed light on the intraday variability of blazars, providing insights into the non-thermal jet processes that drive the observed flux variations.

The Diffusion models, widely used for image generation, face significant challenges related to their broad applicability due to prolonged inference times and high memory demands. Efficient Post-Training Quantization (PTQ) is crucial to address these issues. However, unlike traditional models, diffusion models critically rely on the time-step for the multi-round denoising. Typically, each time-step is encoded into a hypersensitive temporal feature by several modules. Despite this, existing PTQ methods do not optimize these modules individually. Instead, they employ unsuitable reconstruction objectives and complex calibration methods, leading to significant disturbances in the temporal feature and denoising trajectory, as well as reduced compression efficiency. To address these challenges, we introduce a novel quantization framework that includes three strategies: 1) TIB-based Maintenance: Based on our innovative Temporal Information Block (TIB) definition, Temporal Information-aware Reconstruction (TIAR) and Finite Set Calibration (FSC) are developed to efficiently align original temporal features. 2) Cache-based Maintenance: Instead of indirect and complex optimization for the related modules, pre-computing and caching quantized counterparts of temporal features are developed to minimize errors. 3) Disturbance-aware Selection: Employ temporal feature errors to guide a fine-grained selection between the two maintenance strategies for further disturbance reduction. This framework preserves most of the temporal information and ensures high-quality end-to-end generation. Extensive testing on various datasets, diffusion models and hardware confirms our superior performance and acceleration..

Quantum systems of infinite dimension, such as bosonic oscillators, provide vast resources for quantum sensing. Yet, a general theory on how to manipulate such bosonic modes for sensing beyond parameter estimation is unknown. We present a general algorithmic framework, quantum signal processing interferometry (QSPI), for quantum sensing at the fundamental limits of quantum mechanics by generalizing Ramsey-type interferometry. Our QSPI sensing protocol relies on performing nonlinear polynomial transformations on the oscillator's quadrature operators by generalizing quantum signal processing (QSP) from qubits to hybrid qubit-oscillator systems. We use our QSPI sensing framework to make efficient binary decisions on a displacement channel in the single-shot limit. Theoretical analysis suggests the sensing accuracy, given a single-shot qubit measurement, scales inversely with the sensing time or circuit depth of the algorithm. We further concatenate a series of such binary decisions to perform parameter estimation in a bit-by-bit fashion. Numerical simulations are performed to support these statements. Our QSPI protocol offers a unified framework for quantum sensing using continuous-variable bosonic systems beyond parameter estimation and establishes a promising avenue toward efficient and scalable quantum control and quantum sensing schemes beyond the NISQ era.

In this paper we introduce the concept of what we call "NUDAR" (NeUtrino Direction and Ranging), making the point that measurements of the observed energy and direction vectors can be employed to passively deduce the exact three-dimensional location and thermal power of geophysical and anthropogenic neutrino sources from even a single detector. We present the most precise background estimates to date, all handled in full three dimensions, as functions of depth and geographical location. For the present calculations, we consider a hypothetical 138 kiloton detector which can be transported to an ocean site and deployed to an operational depth. We present a Bayesian estimation framework to incorporate any a priori knowledge of the reactor that we are trying to detect, as well as the estimated uncertainty in the background and the oscillation parameters. Most importantly, we fully employ the knowledge of the reactor spectrum and the distance-dependent effects of neutrino oscillations on such spectra. The latter, in particular, makes possible determination of range from one location, given adequate signal statistics. Further, we explore the rich potential of improving detection with even modest improvements in individual neutrino direction determination. We conclude that a 300 MWth reactor can indeed be geolocated, and its operating power estimated with one or two detectors in the hundred kiloton class at ranges out to a few hundred kilometers. We note that such detectors would have natural and non-interfering utility for scientific studies of geo-neutrinos, neutrino oscillations, and astrophysical neutrinos. This motivates the development of cost effective methods of constructing and deploying such next generation detectors.

Diffusion Probabilistic Models (DPM) have shown remarkable efficacy in the synthesis of high-quality images. However, their inference process characteristically requires numerous, potentially hundreds, of iterative steps, which could exaggerate the problem of exposure bias due to the training and inference discrepancy. Previous work has attempted to mitigate this issue by perturbing inputs during training, which consequently mandates the retraining of the DPM. In this work, we conduct a systematic study of exposure bias in DPM and, intriguingly, we find that the exposure bias could be alleviated with a novel sampling method that we propose, without retraining the model. We empirically and theoretically show that, during inference, for each backward time step t and corresponding state x_t, there might exist another time step t_s which exhibits superior coupling with x_t. Based on this finding, we introduce a sampling method named Time-Shift Sampler. Our framework can be seamlessly integrated to existing sampling algorithms, such as DDPM, DDIM and other high-order solvers, inducing merely minimal additional computations. Experimental results show our method brings significant and consistent improvements in FID scores on different datasets and sampling methods. For example, integrating Time-Shift Sampler to F-PNDM yields a FID=3.88, achieving 44.49\% improvements as compared to F-PNDM, on CIFAR-10 with 10 sampling steps, which is more performant than the vanilla DDIM with 100 sampling steps. Our code is available at https://github.com/Mingxiao-Li/TS-DPM.

Simulating rare events, such as the transformation of a reactant into a product in a chemical reaction typically requires enhanced sampling techniques that rely on heuristically chosen collective variables (CVs). We propose using differentiable simulations (DiffSim) for the discovery and enhanced sampling of chemical transformations without a need to resort to preselected CVs, using only a distance metric. Reaction path discovery and estimation of the biasing potential that enhances the sampling are merged into a single end-to-end problem that is solved by path-integral optimization. This is achieved by introducing multiple improvements over standard DiffSim such as partial backpropagation and graph mini-batching making DiffSim training stable and efficient. The potential of DiffSim is demonstrated in the successful discovery of transition paths for the Muller-Brown model potential as well as a benchmark chemical system - alanine dipeptide.

Knowledge of mixtures' phase equilibria is crucial in nature and technical chemistry. Phase equilibria calculations of mixtures require activity coefficients. However, experimental data on activity coefficients is often limited due to high cost of experiments. For an accurate and efficient prediction of activity coefficients, machine learning approaches have been recently developed. However, current machine learning approaches still extrapolate poorly for activity coefficients of unknown molecules. In this work, we introduce the SMILES-to-Properties-Transformer (SPT), a natural language processing network to predict binary limiting activity coefficients from SMILES codes. To overcome the limitations of available experimental data, we initially train our network on a large dataset of synthetic data sampled from COSMO-RS (10 Million data points) and then fine-tune the model on experimental data (20 870 data points). This training strategy enables SPT to accurately predict limiting activity coefficients even for unknown molecules, cutting the mean prediction error in half compared to state-of-the-art models for activity coefficient predictions such as COSMO-RS, UNIFAC, and improving on recent machine learning approaches.

Wavefront shaping is a technique for directing light through turbid media. The theoretical aspects of wavefront shaping are well understood, and under near-ideal experimental conditions, accurate predictions for the expected signal enhancement can be given. In practice, however, there are many experimental factors that negatively affect the outcome of the experiment. Here, we present a comprehensive overview of these experimental factors, including the effect of sample scattering properties, noise, and response of the spatial light modulator. We present simple means to identify experimental imperfections and to minimize their negative effect on the outcome of the experiment. This paper is accompanied by Python code for automatically quantifying experimental problems using the OpenWFS framework for running and simulating wavefront shaping experiments.

Recently, pre-trained foundation models have enabled significant advancements in multiple fields. In molecular machine learning, however, where datasets are often hand-curated, and hence typically small, the lack of datasets with labeled features, and codebases to manage those datasets, has hindered the development of foundation models. In this work, we present seven novel datasets categorized by size into three distinct categories: ToyMix, LargeMix and UltraLarge. These datasets push the boundaries in both the scale and the diversity of supervised labels for molecular learning. They cover nearly 100 million molecules and over 3000 sparsely defined tasks, totaling more than 13 billion individual labels of both quantum and biological nature. In comparison, our datasets contain 300 times more data points than the widely used OGB-LSC PCQM4Mv2 dataset, and 13 times more than the quantum-only QM1B dataset. In addition, to support the development of foundational models based on our proposed datasets, we present the Graphium graph machine learning library which simplifies the process of building and training molecular machine learning models for multi-task and multi-level molecular datasets. Finally, we present a range of baseline results as a starting point of multi-task and multi-level training on these datasets. Empirically, we observe that performance on low-resource biological datasets show improvement by also training on large amounts of quantum data. This indicates that there may be potential in multi-task and multi-level training of a foundation model and fine-tuning it to resource-constrained downstream tasks.

We present cosmological analysis of 12 nearby (z<0.06) Type IIP supernovae (SNe IIP) observed with the ROTSE-IIIb telescope. To achieve precise photometry, we present a new image differencing technique that is implemented for the first time on the ROTSE SN photometry pipeline. With this method, we find up to a 20\% increase in the detection efficiency and significant reduction in residual RMS scatter of the SN lightcurves when compared to the previous pipeline performance. We use the published optical spectra and broadband photometry of well studied SNe IIP to establish temporal models for ejecta velocity and photospheric temperature evolution for our SNe IIP population. This study yields measurements that are competitive to other methods even when the data are limited to a single epoch during the photospheric phase of SNe IIP. Using the fully reduced ROTSE photometry and optical spectra, we apply these models to the respective photometric epochs for each SN in the ROTSE IIP sample. This facilitates the use of the Expanding Photosphere Method (EPM) to obtain distance estimates to their respective host galaxies. We then perform cosmological parameter fitting using these EPM distances from which we measure the Hubble constant to be 72.9^{+5.7}_{-4.3}~{rm kms^{-1}~Mpc^{-1}}, which is consistent with the standard Lambda CDM model values derived using other independent techniques.

Diffusion models have recently achieved success in solving Bayesian inverse problems with learned data priors. Current methods build on top of the diffusion sampling process, where each denoising step makes small modifications to samples from the previous step. However, this process struggles to correct errors from earlier sampling steps, leading to worse performance in complicated nonlinear inverse problems, such as phase retrieval. To address this challenge, we propose a new method called Decoupled Annealing Posterior Sampling (DAPS) that relies on a novel noise annealing process. Specifically, we decouple consecutive steps in a diffusion sampling trajectory, allowing them to vary considerably from one another while ensuring their time-marginals anneal to the true posterior as we reduce noise levels. This approach enables the exploration of a larger solution space, improving the success rate for accurate reconstructions. We demonstrate that DAPS significantly improves sample quality and stability across multiple image restoration tasks, particularly in complicated nonlinear inverse problems. For example, we achieve a PSNR of 30.72dB on the FFHQ 256 dataset for phase retrieval, which is an improvement of 9.12dB compared to existing methods.

In this paper, a mathematical model is developed to describe the evolution of the concentration of compounds through a gas chromatography column. The model couples mass balances and kinetic equations for all components. Both single and multiple-component cases are considered with constant or variable velocity. Non-dimensionalisation indicates the small effect of diffusion. The system where diffusion is neglected is analysed using Laplace transforms. In the multiple-component case, it is demonstrated that the competition between the compounds is negligible and the equations may be decoupled. This reduces the problem to solving a single integral equation to determine the concentration profile for all components (since they are scaled versions of each other). For a given analyte, we then only two parameters need to be fitted to the data. To verify this approach, the full governing equations are also solved numerically using the finite difference method and a global adaptive quadrature method to integrate the Laplace transformation. Comparison with the Laplace solution verifies the high degree of accuracy of the simpler Laplace form. The Laplace solution is then verified against experimental data from BTEX chromatography. This novel method, which involves solving a single equation and fitting parameters in pairs for individual components, is highly efficient. It is significantly faster and simpler than the full numerical solution and avoids the computationally expensive methods that would normally be used to fit all curves at the same time.

Human face aging is irreversible process causing changes in human face characteristics such us hair whitening, muscles drop and wrinkles. Due to the importance of human face aging in biometrics systems, age estimation became an attractive area for researchers. This paper presents a novel method to estimate the age from face images, using binarized statistical image features (BSIF) and local binary patterns (LBP)histograms as features performed by support vector regression (SVR) and kernel ridge regression (KRR). We applied our method on FG-NET and PAL datasets. Our proposed method has shown superiority to that of the state-of-the-art methods when using the whole PAL database.

We reanalyze the spectral lag data for GRB 160625B using frequentist inference in order to constrain the energy scale (E_{QG}) of Lorentz Invariance Violation (LIV). For this purpose, we use profile likelihood to deal with the astrophysical nuisance parameters. This is in contrast to Bayesian inference implemented in previous works, where marginalization was carried out over the nuisance parameters. We show that with profile likelihood, we do not find a global minimum for chi^2 as a function of E_{QG} below the Planck scale for both linear and quadratic models of LIV, whereas bounded credible intervals were previously obtained using Bayesian inference. Therefore, we can set one-sided lower limits in a straightforward manner. We find that E_{QG} geq 2.55 times 10^{16} GeV and E_{QG} geq 1.85 times 10^7 GeV at 95\% c.l., for linear and quadratic LIV, respectively. Therefore, this is the first proof-of-principles application of profile likelihood method to the analysis of GRB spectral lag data to constrain LIV.

With the increasing availability of wearable devices, photoplethysmography (PPG) has emerged as a promising non-invasive tool for monitoring human hemodynamics. We propose a deep learning framework to estimate vascular age (AI-vascular age) from PPG signals, incorporating a distribution-aware loss to address biases caused by imbalanced data. The model was developed using data from the UK Biobank (UKB), with 98,672 participants in the development cohort and 113,559 participants (144,683 data pairs) for clinical evaluation. After adjusting for key confounders, individuals with a vascular age gap (AI-vascular age minus calendar age) exceeding 9 years had a significantly higher risk of major adverse cardiovascular and cerebrovascular events (MACCE) (HR = 2.37, p < 0.005) and secondary outcomes, including diabetes (HR = 2.69, p < 0.005), hypertension (HR = 2.88, p < 0.005), coronary heart disease (HR = 2.20, p < 0.005), heart failure (HR = 2.15, p < 0.005), myocardial infarction (HR = 2.51, p < 0.005), stroke (HR = 2.55, p < 0.005), and all-cause mortality (HR = 2.51, p < 0.005). Conversely, participants with a vascular age gap below -9 years exhibited a significantly lower incidence of these outcomes. We further evaluated the longitudinal applicability of AI-vascular age using serial PPG data from the UKB, demonstrating its value in risk stratification by leveraging AI-vascular age at two distinct time points to predict future MACCE incidence. External validation was performed on a MIMIC-III-derived cohort (n = 2,343), where each one-year increase in vascular age gap was significantly associated with elevated in-hospital mortality risk (OR = 1.02, p < 0.005). In conclusion, our study establishes AI-vascular age as a novel, non-invasive digital biomarker for cardiovascular health assessment.

Bessel functions are critical in scientific computing for applications such as machine learning, protein structure modeling, and robotics. However, currently, available routines lack precision or fail for certain input ranges, such as when the order v is large, and GPU-specific implementations are limited. We address the precision limitations of current numerical implementations while dramatically improving the runtime. We propose two novel algorithms for computing the logarithm of modified Bessel functions of the first and second kinds by computing intermediate values on a logarithmic scale. Our algorithms are robust and never have issues with underflows or overflows while having relative errors on the order of machine precision, even for inputs where existing libraries fail. In C++/CUDA, our algorithms have median and maximum speedups of 45x and 6150x for GPU and 17x and 3403x for CPU, respectively, over the ranges of inputs and third-party libraries tested. Compared to SciPy, the algorithms have median and maximum speedups of 77x and 300x for GPU and 35x and 98x for CPU, respectively, over the tested inputs. The ability to robustly compute a solution and the low relative errors allow us to fit von Mises-Fisher, vMF, distributions to high-dimensional neural network features. This is, e.g., relevant for uncertainty quantification in metric learning. We obtain image feature data by processing CIFAR10 training images with the convolutional layers of a pre-trained ResNet50. We successfully fit vMF distributions to 2048-, 8192-, and 32768-dimensional image feature data using our algorithms. Our approach provides fast and accurate results while existing implementations in SciPy and mpmath fail to fit successfully. Our approach is readily implementable on GPUs, and we provide a fast open-source implementation alongside this paper.

The present work investigates two properties of level crossings of a stationary Gaussian process X(t) with autocorrelation function R_X(tau). We show firstly that if R_X(tau) admits finite second and fourth derivatives at the origin, the length of up-excursions above a large negative level -gamma is asymptotically exponential as -gamma to -infty. Secondly, assuming that R_X(tau) admits a finite second derivative at the origin and some defined properties, we derive the mean number of crossings as well as the length of successive excursions above two subsequent large levels. The asymptotic results are shown to be effective even for moderate values of crossing level. An application of the developed results is proposed to derive the probability of successive excursions above adjacent levels during a time window.

Enhancing the visibility in extreme low-light environments is a challenging task. Under nearly lightless condition, existing image denoising methods could easily break down due to significantly low SNR. In this paper, we systematically study the noise statistics in the imaging pipeline of CMOS photosensors, and formulate a comprehensive noise model that can accurately characterize the real noise structures. Our novel model considers the noise sources caused by digital camera electronics which are largely overlooked by existing methods yet have significant influence on raw measurement in the dark. It provides a way to decouple the intricate noise structure into different statistical distributions with physical interpretations. Moreover, our noise model can be used to synthesize realistic training data for learning-based low-light denoising algorithms. In this regard, although promising results have been shown recently with deep convolutional neural networks, the success heavily depends on abundant noisy clean image pairs for training, which are tremendously difficult to obtain in practice. Generalizing their trained models to images from new devices is also problematic. Extensive experiments on multiple low-light denoising datasets -- including a newly collected one in this work covering various devices -- show that a deep neural network trained with our proposed noise formation model can reach surprisingly-high accuracy. The results are on par with or sometimes even outperform training with paired real data, opening a new door to real-world extreme low-light photography.

We study the problem of estimating the distribution of the return of a policy using an offline dataset that is not generated from the policy, i.e., distributional offline policy evaluation (OPE). We propose an algorithm called Fitted Likelihood Estimation (FLE), which conducts a sequence of Maximum Likelihood Estimation (MLE) and has the flexibility of integrating any state-of-the-art probabilistic generative models as long as it can be trained via MLE. FLE can be used for both finite-horizon and infinite-horizon discounted settings where rewards can be multi-dimensional vectors. Our theoretical results show that for both finite-horizon and infinite-horizon discounted settings, FLE can learn distributions that are close to the ground truth under total variation distance and Wasserstein distance, respectively. Our theoretical results hold under the conditions that the offline data covers the test policy's traces and that the supervised learning MLE procedures succeed. Experimentally, we demonstrate the performance of FLE with two generative models, Gaussian mixture models and diffusion models. For the multi-dimensional reward setting, FLE with diffusion models is capable of estimating the complicated distribution of the return of a test policy.

Parameter inference, i.e. inferring the posterior distribution of the parameters of a statistical model given some data, is a central problem to many scientific disciplines. Generative models can be used as an alternative to Markov Chain Monte Carlo methods for conducting posterior inference, both in likelihood-based and simulation-based problems. However, assessing the accuracy of posteriors encoded in generative models is not straightforward. In this paper, we introduce `Tests of Accuracy with Random Points' (TARP) coverage testing as a method to estimate coverage probabilities of generative posterior estimators. Our method differs from previously-existing coverage-based methods, which require posterior evaluations. We prove that our approach is necessary and sufficient to show that a posterior estimator is accurate. We demonstrate the method on a variety of synthetic examples, and show that TARP can be used to test the results of posterior inference analyses in high-dimensional spaces. We also show that our method can detect inaccurate inferences in cases where existing methods fail.

LSST and Euclid must address the daunting challenge of analyzing the unprecedented volumes of imaging and spectroscopic data that these next-generation instruments will generate. A promising approach to overcoming this challenge involves rapid, automatic image processing using appropriately trained Deep Learning (DL) algorithms. However, reliable application of DL requires large, accurately labeled samples of training data. Galaxy Zoo Express (GZX) is a recent experiment that simulated using Bayesian inference to dynamically aggregate binary responses provided by citizen scientists via the Zooniverse crowd-sourcing platform in real time. The GZX approach enables collaboration between human and machine classifiers and provides rapidly generated, reliably labeled datasets, thereby enabling online training of accurate machine classifiers. We present selected results from GZX and show how the Bayesian aggregation engine it uses can be extended to efficiently provide object-localization and bounding-box annotations of two-dimensional data with quantified reliability. DL algorithms that are trained using these annotations will facilitate numerous panchromatic data modeling tasks including morphological classification and substructure detection in direct imaging, as well as decontamination and emission line identification for slitless spectroscopy. Effectively combining the speed of modern computational analyses with the human capacity to extrapolate from few examples will be critical if the potential of forthcoming large-scale surveys is to be realized.

Temporal point processes (TPP) are a natural tool for modeling event-based data. Among all TPP models, Hawkes processes have proven to be the most widely used, mainly due to their adequate modeling for various applications, particularly when considering exponential or non-parametric kernels. Although non-parametric kernels are an option, such models require large datasets. While exponential kernels are more data efficient and relevant for specific applications where events immediately trigger more events, they are ill-suited for applications where latencies need to be estimated, such as in neuroscience. This work aims to offer an efficient solution to TPP inference using general parametric kernels with finite support. The developed solution consists of a fast ell_2 gradient-based solver leveraging a discretized version of the events. After theoretically supporting the use of discretization, the statistical and computational efficiency of the novel approach is demonstrated through various numerical experiments. Finally, the method's effectiveness is evaluated by modeling the occurrence of stimuli-induced patterns from brain signals recorded with magnetoencephalography (MEG). Given the use of general parametric kernels, results show that the proposed approach leads to an improved estimation of pattern latency than the state-of-the-art.

Retrosynthesis planning is a fundamental challenge in chemistry which aims at designing reaction pathways from commercially available starting materials to a target molecule. Each step in multi-step retrosynthesis planning requires accurate prediction of possible precursor molecules given the target molecule and confidence estimates to guide heuristic search algorithms. We model single-step retrosynthesis planning as a distribution learning problem in a discrete state space. First, we introduce the Markov Bridge Model, a generative framework aimed to approximate the dependency between two intractable discrete distributions accessible via a finite sample of coupled data points. Our framework is based on the concept of a Markov bridge, a Markov process pinned at its endpoints. Unlike diffusion-based methods, our Markov Bridge Model does not need a tractable noise distribution as a sampling proxy and directly operates on the input product molecules as samples from the intractable prior distribution. We then address the retrosynthesis planning problem with our novel framework and introduce RetroBridge, a template-free retrosynthesis modeling approach that achieves state-of-the-art results on standard evaluation benchmarks.

Important classes of active matter systems can be modeled using kinetic theories. However, kinetic theories can be high dimensional and challenging to simulate. Reduced-order representations based on tracking only low-order moments of the kinetic model serve as an efficient alternative, but typically require closure assumptions to model unrepresented higher-order moments. In this study, we present a learning framework based on neural networks that exploit rotational symmetries in the closure terms to learn accurate closure models directly from kinetic simulations. The data-driven closures demonstrate excellent a-priori predictions comparable to the state-of-the-art Bingham closure. We provide a systematic comparison between different neural network architectures and demonstrate that nonlocal effects can be safely ignored to model the closure terms. We develop an active learning strategy that enables accurate prediction of the closure terms across the entire parameter space using a single neural network without the need for retraining. We also propose a data-efficient training procedure based on time-stepping constraints and a differentiable pseudo-spectral solver, which enables the learning of stable closures suitable for a-posteriori inference. The coarse-grained simulations equipped with data-driven closure models faithfully reproduce the mean velocity statistics, scalar order parameters, and velocity power spectra observed in simulations of the kinetic theory. Our differentiable framework also facilitates the estimation of parameters in coarse-grained descriptions conditioned on data.

Temporal Point Processes (TPP) are probabilistic generative frameworks. They model discrete event sequences localized in continuous time. Generally, real-life events reveal descriptive information, known as marks. Marked TPPs model time and marks of the event together for practical relevance. Conditioned on past events, marked TPPs aim to learn the joint distribution of the time and the mark of the next event. For simplicity, conditionally independent TPP models assume time and marks are independent given event history. They factorize the conditional joint distribution of time and mark into the product of individual conditional distributions. This structural limitation in the design of TPP models hurt the predictive performance on entangled time and mark interactions. In this work, we model the conditional inter-dependence of time and mark to overcome the limitations of conditionally independent models. We construct a multivariate TPP conditioning the time distribution on the current event mark in addition to past events. Besides the conventional intensity-based models for conditional joint distribution, we also draw on flexible intensity-free TPP models from the literature. The proposed TPP models outperform conditionally independent and dependent models in standard prediction tasks. Our experimentation on various datasets with multiple evaluation metrics highlights the merit of the proposed approach.

The assumption that response and predictor belong to the same statistical unit may be violated in practice. Unbiased estimation and recovery of true label ordering based on unlabeled data are challenging tasks and have attracted increasing attentions in the recent literature. In this paper, we present a relatively complete analysis of label permutation problem for the generalized linear model with multivariate responses. The theory is established under different scenarios, with knowledge of true parameters, with partial knowledge of underlying label permutation matrix and without any knowledge. Our results remove the stringent conditions required by the current literature and are further extended to the missing observation setting which has never been considered in the field of label permutation problem. On computational side, we propose two methods, "maximum likelihood estimation" algorithm and "two-step estimation" algorithm, to accommodate for different settings. When the proportion of permuted labels is moderate, both methods work effectively. Multiple numerical experiments are provided and corroborate our theoretical findings.

[This paper was initially published in PHME conference in 2016, selected for further publication in International Journal of Prognostics and Health Management.] This paper describes an Autoregressive Partially-hidden Markov model (ARPHMM) for fault detection and prognostics of equipments based on sensors' data. It is a particular dynamic Bayesian network that allows to represent the dynamics of a system by means of a Hidden Markov Model (HMM) and an autoregressive (AR) process. The Markov chain assumes that the system is switching back and forth between internal states while the AR process ensures a temporal coherence on sensor measurements. A sound learning procedure of standard ARHMM based on maximum likelihood allows to iteratively estimate all parameters simultaneously. This paper suggests a modification of the learning procedure considering that one may have prior knowledge about the structure which becomes partially hidden. The integration of the prior is based on the Theory of Weighted Distributions which is compatible with the Expectation-Maximization algorithm in the sense that the convergence properties are still satisfied. We show how to apply this model to estimate the remaining useful life based on health indicators. The autoregressive parameters can indeed be used for prediction while the latent structure can be used to get information about the degradation level. The interest of the proposed method for prognostics and health assessment is demonstrated on CMAPSS datasets.

Battery degradation remains a critical challenge in the pursuit of green technologies and sustainable energy solutions. Despite significant research efforts, predicting battery capacity loss accurately remains a formidable task due to its complex nature, influenced by both aging and cycling behaviors. To address this challenge, we introduce a novel general-purpose model for battery degradation prediction and synthesis, DiffBatt. Leveraging an innovative combination of conditional and unconditional diffusion models with classifier-free guidance and transformer architecture, DiffBatt achieves high expressivity and scalability. DiffBatt operates as a probabilistic model to capture uncertainty in aging behaviors and a generative model to simulate battery degradation. The performance of the model excels in prediction tasks while also enabling the generation of synthetic degradation curves, facilitating enhanced model training by data augmentation. In the remaining useful life prediction task, DiffBatt provides accurate results with a mean RMSE of 196 cycles across all datasets, outperforming all other models and demonstrating superior generalizability. This work represents an important step towards developing foundational models for battery degradation.

Diffusion models have demonstrated impressive generative capabilities, but their exposure bias problem, described as the input mismatch between training and sampling, lacks in-depth exploration. In this paper, we systematically investigate the exposure bias problem in diffusion models by first analytically modelling the sampling distribution, based on which we then attribute the prediction error at each sampling step as the root cause of the exposure bias issue. Furthermore, we discuss potential solutions to this issue and propose an intuitive metric for it. Along with the elucidation of exposure bias, we propose a simple, yet effective, training-free method called Epsilon Scaling to alleviate the exposure bias. We show that Epsilon Scaling explicitly moves the sampling trajectory closer to the vector field learned in the training phase by scaling down the network output (Epsilon), mitigating the input mismatch between training and sampling. Experiments on various diffusion frameworks (ADM, DDPM/DDIM, EDM, LDM), unconditional and conditional settings, and deterministic vs. stochastic sampling verify the effectiveness of our method. Remarkably, our ADM-ES, as a SOTA stochastic sampler, obtains 2.17 FID on CIFAR-10 under 100-step unconditional generation. The code is available at https://github.com/forever208/ADM-ES and https://github.com/forever208/EDM-ES.

The early prediction of battery life (EPBL) is vital for enhancing the efficiency and extending the lifespan of lithium batteries. Traditional models with fixed architectures often encounter underfitting or overfitting issues due to the diverse data distributions in different EPBL tasks. An interpretable deep learning model of flexible parallel neural network (FPNN) is proposed, which includes an InceptionBlock, a 3D convolutional neural network (CNN), a 2D CNN, and a dual-stream network. The proposed model effectively extracts electrochemical features from video-like formatted data using the 3D CNN and achieves advanced multi-scale feature abstraction through the InceptionBlock. The FPNN can adaptively adjust the number of InceptionBlocks to flexibly handle tasks of varying complexity in EPBL. The test on the MIT dataset shows that the FPNN model achieves outstanding predictive accuracy in EPBL tasks, with MAPEs of 2.47%, 1.29%, 1.08%, and 0.88% when the input cyclic data volumes are 10, 20, 30, and 40, respectively. The interpretability of the FPNN is mainly reflected in its flexible unit structure and parameter selection: its diverse branching structure enables the model to capture features at different scales, thus allowing the machine to learn informative features. The approach presented herein provides an accurate, adaptable, and comprehensible solution for early life prediction of lithium batteries, opening new possibilities in the field of battery health monitoring.

In recent years, machine learning models like DALL-E, Craiyon, and Stable Diffusion have gained significant attention for their ability to generate high-resolution images from concise descriptions. Concurrently, quantum computing is showing promising advances, especially with quantum machine learning which capitalizes on quantum mechanics to meet the increasing computational requirements of traditional machine learning algorithms. This paper explores the integration of quantum machine learning and variational quantum circuits to augment the efficacy of diffusion-based image generation models. Specifically, we address two challenges of classical diffusion models: their low sampling speed and the extensive parameter requirements. We introduce two quantum diffusion models and benchmark their capabilities against their classical counterparts using MNIST digits, Fashion MNIST, and CIFAR-10. Our models surpass the classical models with similar parameter counts in terms of performance metrics FID, SSIM, and PSNR. Moreover, we introduce a consistency model unitary single sampling architecture that combines the diffusion procedure into a single step, enabling a fast one-step image generation.

Recently, efficient fine-tuning of large-scale pre-trained models has attracted increasing research interests, where linear probing (LP) as a fundamental module is involved in exploiting the final representations for task-dependent classification. However, most of the existing methods focus on how to effectively introduce a few of learnable parameters, and little work pays attention to the commonly used LP module. In this paper, we propose a novel Moment Probing (MP) method to further explore the potential of LP. Distinguished from LP which builds a linear classification head based on the mean of final features (e.g., word tokens for ViT) or classification tokens, our MP performs a linear classifier on feature distribution, which provides the stronger representation ability by exploiting richer statistical information inherent in features. Specifically, we represent feature distribution by its characteristic function, which is efficiently approximated by using first- and second-order moments of features. Furthermore, we propose a multi-head convolutional cross-covariance (MHC^3) to compute second-order moments in an efficient and effective manner. By considering that MP could affect feature learning, we introduce a partially shared module to learn two recalibrating parameters (PSRP) for backbones based on MP, namely MP_{+}. Extensive experiments on ten benchmarks using various models show that our MP significantly outperforms LP and is competitive with counterparts at less training cost, while our MP_{+} achieves state-of-the-art performance.

Biological processes, functions, and properties are intricately linked to the ensemble of protein conformations, rather than being solely determined by a single stable conformation. In this study, we have developed P2DFlow, a generative model based on SE(3) flow matching, to predict the structural ensembles of proteins. We specifically designed a valuable prior for the flow process and enhanced the model's ability to distinguish each intermediate state by incorporating an additional dimension to describe the ensemble data, which can reflect the physical laws governing the distribution of ensembles, so that the prior knowledge can effectively guide the generation process. When trained and evaluated on the MD datasets of ATLAS, P2DFlow outperforms other baseline models on extensive experiments, successfully capturing the observable dynamic fluctuations as evidenced in crystal structure and MD simulations. As a potential proxy agent for protein molecular simulation, the high-quality ensembles generated by P2DFlow could significantly aid in understanding protein functions across various scenarios. Code is available at https://github.com/BLEACH366/P2DFlow

We consider the problem of linear estimation, and establish an extension of the Gauss-Markov theorem, in which the bias operator is allowed to be non-zero but bounded with respect to a matrix norm of Schatten type. We derive simple and explicit formulas for the optimal estimator in the cases of Nuclear and Spectral norms (with the Frobenius case recovering ridge regression). Additionally, we analytically derive the generalization error in multiple random matrix ensembles, and compare with Ridge regression. Finally, we conduct an extensive simulation study, in which we show that the cross-validated Nuclear and Spectral regressors can outperform Ridge in several circumstances.

The interdiffusion coefficients are estimated either following the Wagner's method expressed with respect to the composition (mol or atomic fraction) normalized variable after considering the molar volume variation or the den Broeder's method expressed with respect to the concentration (composition divided by the molar volume) normalized variable. On the other hand, the relations for estimation of the intrinsic diffusion coefficients of components as established by van Loo and integrated diffusion coefficients in a phase with narrow homogeneity range as established by Wagner are currently available with respect to the composition normalized variable only. In this study, we have first derived the relation proposed by den Broeder following the line of treatment proposed by Wagner. Further, the relations for estimation of the intrinsic diffusion coefficients of the components and integrated interdiffusion coefficient are established with respect to the concentration normalized variable, which were not available earlier. The veracity of these methods is examined based on the estimation of data in Ni-Pd, Ni-Al and Cu-Sn systems. Our analysis indicates that both the approaches are logically correct and there is small difference in the estimated data in these systems although a higher difference could be found in other systems. The integrated interdiffusion coefficients with respect to the concentration (or concentration normalized variable) can only be estimated considering the ideal molar volume variation. This might be drawback in certain practical systems.

Addressing the critical theme of recycling electronic waste (E-waste), this contribution is dedicated to developing advanced automated data processing pipelines as a basis for decision-making and process control. Aligning with the broader goals of the circular economy and the United Nations (UN) Sustainable Development Goals (SDG), our work leverages non-invasive analysis methods utilizing RGB and hyperspectral imaging data to provide both quantitative and qualitative insights into the E-waste stream composition for optimizing recycling efficiency. In this paper, we introduce 'PCB-Vision'; a pioneering RGB-hyperspectral printed circuit board (PCB) benchmark dataset, comprising 53 RGB images of high spatial resolution paired with their corresponding high spectral resolution hyperspectral data cubes in the visible and near-infrared (VNIR) range. Grounded in open science principles, our dataset provides a comprehensive resource for researchers through high-quality ground truths, focusing on three primary PCB components: integrated circuits (IC), capacitors, and connectors. We provide extensive statistical investigations on the proposed dataset together with the performance of several state-of-the-art (SOTA) models, including U-Net, Attention U-Net, Residual U-Net, LinkNet, and DeepLabv3+. By openly sharing this multi-scene benchmark dataset along with the baseline codes, we hope to foster transparent, traceable, and comparable developments of advanced data processing across various scientific communities, including, but not limited to, computer vision and remote sensing. Emphasizing our commitment to supporting a collaborative and inclusive scientific community, all materials, including code, data, ground truth, and masks, will be accessible at https://github.com/hifexplo/PCBVision.

We present final natural system optical (ugriBV) and near-infrared (YJH) photometry of 134 supernovae (SNe) with probable white dwarf progenitors that were observed in 2004-2009 as part of the first stage of the Carnegie Supernova Project (CSP-I). The sample consists of 123 Type Ia SNe, 5 Type Iax SNe, 2 super-Chandrasekhar SN candidates, 2 Type Ia SNe interacting with circumstellar matter, and 2 SN 2006bt-like events. The redshifts of the objects range from z = 0.0037 to 0.0835; the median redshift is 0.0241. For 120 (90%) of these SNe, near-infrared photometry was obtained. Average optical extinction coefficients and color terms are derived and demonstrated to be stable during the five CSP-I observing campaigns. Measurements of the CSP-I near-infrared bandpasses are also described, and near-infrared color terms are estimated through synthetic photometry of stellar atmosphere models. Optical and near-infrared magnitudes of local sequences of tertiary standard stars for each supernova are given, and a new calibration of Y-band magnitudes of the Persson et al. (1998) standards in the CSP-I natural system is presented.

Diffusion models have impressive image generation capability, but low-quality generations still exist, and their identification remains challenging due to the lack of a proper sample-wise metric. To address this, we propose BayesDiff, a pixel-wise uncertainty estimator for generations from diffusion models based on Bayesian inference. In particular, we derive a novel uncertainty iteration principle to characterize the uncertainty dynamics in diffusion, and leverage the last-layer Laplace approximation for efficient Bayesian inference. The estimated pixel-wise uncertainty can not only be aggregated into a sample-wise metric to filter out low-fidelity images but also aids in augmenting successful generations and rectifying artifacts in failed generations in text-to-image tasks. Extensive experiments demonstrate the efficacy of BayesDiff and its promise for practical applications.

In this work, we obtain the error estimate of the rotation parameter beta from the core bounce phase of the characteristic gravitational wave signal of a rapidly rotating core collapse supernova (CCSN). We quantify the error with asymptotic expansions of the covariance of a Maximum Likelihood Estimator (MLE) in terms of inverse powers of Signal-Noise Ratio (SNR), this method has been previously applied to parameter estimation for compact binary coalescences. When the second order of this expansion is negligible, it indicates that the first order is a good approximation of the error that will have a matching filter approach when estimating beta. The analysis indicates that we should be able to resolve the presence of rotation for the galactic and nearby extragalactic progenitors. We show that the estimation error Delta beta can be as small as a few percent and is larger for small values of beta.

The state of health (SOH) of a Li-ion battery is a critical parameter that determines the remaining capacity and the remaining lifetime of the battery. In this paper, we propose SambaMixer a novel structured state space model (SSM) for predicting the state of health of Li-ion batteries. The proposed SSM is based on the MambaMixer architecture, which is designed to handle multi-variate time signals. We evaluate our model on the NASA battery discharge dataset and show that our model outperforms the state-of-the-art on this dataset. We further introduce a novel anchor-based resampling method which ensures time signals are of the expected length while also serving as augmentation technique. Finally, we condition prediction on the sample time and the cycle time difference using positional encodings to improve the performance of our model and to learn recuperation effects. Our results proof that our model is able to predict the SOH of Li-ion batteries with high accuracy and robustness.

The dynamics of biomolecules are crucial for our understanding of their functioning in living systems. However, current 3D imaging techniques, such as cryogenic electron microscopy (cryo-EM), require freezing the sample, which limits the observation of their conformational changes in real time. The innovative liquid-phase electron microscopy (liquid-phase EM) technique allows molecules to be placed in the native liquid environment, providing a unique opportunity to observe their dynamics. In this paper, we propose TEMPOR, a Temporal Electron MicroscoPy Object Reconstruction algorithm for liquid-phase EM that leverages an implicit neural representation (INR) and a dynamical variational auto-encoder (DVAE) to recover time series of molecular structures. We demonstrate its advantages in recovering different motion dynamics from two simulated datasets, 7bcq and Cas9. To our knowledge, our work is the first attempt to directly recover 3D structures of a temporally-varying particle from liquid-phase EM movies. It provides a promising new approach for studying molecules' 3D dynamics in structural biology.

Isotopic substitution in molecular systems can affect fundamental molecular properties including the energy position and spacing of electronic, vibrational and rotational levels, thus modifying the dynamics associated to their coherent superposition. In extreme ultraviolet spectroscopy, the photoelectron leaving the molecule after the absorption of a single photon can trigger an ultrafast nuclear motion in the cation, which can lead, eventually, to molecular fragmentation. This dynamics depends on the mass of the constituents of the cation, thus showing, in general, a significant isotopic dependence. In time-resolved attosecond photoelectron interferometry, the absorption of the extreme ultraviolet photon is accompanied by the exchange of an additional quantum of energy (typically in the infrared spectral range) with the photoelectron-photoion system, offering the opportunity to investigate in time the influence of isotopic substitution on the characteristics of the photoionisation dynamics. Here we show that attosecond photoelectron interferometry is sensitive to isotopic substitution by investigating the two-color photoionisation spectra measured in a mixture of methane (CH_4) and deuteromethane (CD_4). The isotopic dependence manifests itself in the modification of the amplitude and contrast of the oscillations of the photoelectron peaks generated in the two-color field with the two isotopologues. The observed effects are interpreted considering the differences in the time evolution of the nuclear autocorrelation functions in the two molecules.

The theories of offline and online reinforcement learning, despite having evolved in parallel, have begun to show signs of the possibility for a unification, with algorithms and analysis techniques for one setting often having natural counterparts in the other. However, the notion of density ratio modeling, an emerging paradigm in offline RL, has been largely absent from online RL, perhaps for good reason: the very existence and boundedness of density ratios relies on access to an exploratory dataset with good coverage, but the core challenge in online RL is to collect such a dataset without having one to start. In this work we show -- perhaps surprisingly -- that density ratio-based algorithms have online counterparts. Assuming only the existence of an exploratory distribution with good coverage, a structural condition known as coverability (Xie et al., 2023), we give a new algorithm (GLOW) that uses density ratio realizability and value function realizability to perform sample-efficient online exploration. GLOW addresses unbounded density ratios via careful use of truncation, and combines this with optimism to guide exploration. GLOW is computationally inefficient; we complement it with a more efficient counterpart, HyGLOW, for the Hybrid RL setting (Song et al., 2022) wherein online RL is augmented with additional offline data. HyGLOW is derived as a special case of a more general meta-algorithm that provides a provable black-box reduction from hybrid RL to offline RL, which may be of independent interest.

We present a systematic study of the BVRI colours of novae over the course of their eruptions. Where possible, interstellar reddening was measured using the equivalent widths of Diffuse Interstellar Bands (DIBs). Some novae lack spectra with sufficient resolution and signal-to-noise ratios; therefore, we supplement as necessary with 3D and 2D dust maps. Utilising only novae with DIB- or 3D-map-based E(B-V), we find an average intrinsic (B-V)_0 colour of novae at V-band light curve peak of 0.18 with a standard deviation of 0.31, based on a sample of 23 novae. When the light curve has declined by 2 magnitudes (t_2), we find an average (B-V)_0 = -0.02 with a standard deviation of 0.19. These average colours are consistent with previous findings, although the spreads are larger than previously found due to more accurate reddening estimates. We also examined the intrinsic (R-I)_0 and (V-R)_0 colours across our sample. These colours behave similarly to (B-V)_0, except that the (V-R)_0 colour gets redder after peak, likely due to the contributions of emission line flux. We searched for correlations between nova colours and t_2, peak V-band absolute magnitude, and GeV gamma-ray luminosity, but find no statistically significant correlations. Nova colours can therefore be used as standard "crayons" to estimate interstellar reddening from photometry alone, with 0.2--0.3 mag uncertainty. We present a novel Bayesian strategy for estimating distances to Galactic novae based on these E(B-V) measurements, independent of assumptions about luminosity, built using 3D dust maps and a stellar mass model of the Milky Way.

High-throughput screening techniques are commonly used to obtain large quantities of data in many fields of biology. It is well known that artifacts arising from variability in the technical execution of different experimental batches within such screens confound these observations and can lead to invalid biological conclusions. It is therefore necessary to account for these batch effects when analyzing outcomes. In this paper we describe RxRx1, a biological dataset designed specifically for the systematic study of batch effect correction methods. The dataset consists of 125,510 high-resolution fluorescence microscopy images of human cells under 1,138 genetic perturbations in 51 experimental batches across 4 cell types. Visual inspection of the images alone clearly demonstrates significant batch effects. We propose a classification task designed to evaluate the effectiveness of experimental batch correction methods on these images and examine the performance of a number of correction methods on this task. Our goal in releasing RxRx1 is to encourage the development of effective experimental batch correction methods that generalize well to unseen experimental batches. The dataset can be downloaded at https://rxrx.ai.

Galaxy clusters selected based on overdensities of galaxies in photometric surveys provide the largest cluster samples. Yet modeling the selection function of such samples is complicated by non-cluster members projected along the line of sight (projection effects) and the potential detection of unvirialized objects (contamination). We empirically constrain the magnitude of these effects by cross-matching galaxy clusters selected in the Dark Energy survey data with the \rdmpr, algorithm with significant detections in three South Pole Telescope surveys (SZ, pol-ECS, pol-500d). For matched clusters, we augment the \rdmpr,catalog by the SPT detection significance. For unmatched objects we use the SPT detection threshold as an upper limit on the SZe signature. Using a Bayesian population model applied to the collected multi-wavelength data, we explore various physically motivated models to describe the relationship between observed richness and halo mass. Our analysis reveals the limitations of a simple lognormal scatter model in describing the data. We rule out significant contamination by unvirialized objects at the high-richness end of the sample. While dedicated simulations offer a well-fitting calibration of projection effects, our findings suggest the presence of redshift-dependent trends that these simulations may not have captured. Our findings highlight that modeling the selection function of optically detected clusters remains a complicated challenge, requiring a combination of simulation and data-driven approaches.

Computational microscopy, in which hardware and algorithms of an imaging system are jointly designed, shows promise for making imaging systems that cost less, perform more robustly, and collect new types of information. Often, the performance of computational imaging systems, especially those that incorporate machine learning, is sample-dependent. Thus, standardized datasets are an essential tool for comparing the performance of different approaches. Here, we introduce the Berkeley Single Cell Computational Microscopy (BSCCM) dataset, which contains over ~12,000,000 images of 400,000 of individual white blood cells. The dataset contains images captured with multiple illumination patterns on an LED array microscope and fluorescent measurements of the abundance of surface proteins that mark different cell types. We hope this dataset will provide a valuable resource for the development and testing of new algorithms in computational microscopy and computer vision with practical biomedical applications.

Full quantum tomography of high-dimensional quantum systems is experimentally infeasible due to the exponential scaling of the number of required measurements on the number of qubits in the system. However, several ideas were proposed recently for predicting the limited number of features for these states, or estimating the expectation values of operators, without the need for full state reconstruction. These ideas go under the general name of shadow tomography. Here we provide an experimental demonstration of property estimation based on classical shadows proposed in [H.-Y. Huang, R. Kueng, J. Preskill. Nat. Phys. https://doi.org/10.1038/s41567-020-0932-7 (2020)] and study its performance in the quantum optical experiment with high-dimensional spatial states of photons. We show on experimental data how this procedure outperforms conventional state reconstruction in fidelity estimation from a limited number of measurements.

We present subarcsecond-resolution ALMA mosaics of the Orion Bar PDR in [CI] 609 um, C2H (4-3), and C18O (3-2) emission lines, complemented by JWST images of H2 and aromatic infrared band (AIB) emission. The rim of the Bar shows very corrugated structures made of small-scale H2 dissociation fronts (DFs). The [CI] 609 um emission peaks very close (~0.002 pc) to the main H2-emitting DFs, suggesting the presence of gas density gradients. These DFs are also bright and remarkably similar in C2H emission, which traces 'hydrocarbon radical peaks' characterized by very high C2H abundances, reaching up to several x10^-7. The high abundance of C2H and of related hydrocarbon radicals, such as CH3, CH2, and CH, can be attributed to gas-phase reactions driven by elevated temperatures, the presence of C+ and C, and the reactivity of FUV-pumped H2. The hydrocarbon radical peaks roughly coincide with maxima of the 3.4/3.3 um AIB intensity ratio, a proxy for the aliphatic-to-aromatic content of PAHs. This implies that the conditions triggering the formation of simple hydrocarbons also favor the formation (and survival) of PAHs with aliphatic side groups, potentially via the contribution of bottom-up processes in which abundant hydrocarbon radicals react in situ with PAHs. Ahead of the DFs, in the atomic PDR zone (where [H]>>[H2]), the AIB emission is brightest, but small PAHs and carbonaceous grains undergo photo-processing due to the stronger FUV field. Our detection of trace amounts of C2H in this zone may result from the photoerosion of these species. This study provides a spatially resolved view of the chemical stratification of key carbon carriers in a PDR. Overall, both bottom-up and top-down processes appear to link simple hydrocarbon molecules with PAHs in molecular clouds; however, the exact chemical pathways and their relative contributions remain to be quantified.

We revisit quantum phase estimation algorithms for the purpose of obtaining the energy levels of many-body Hamiltonians and pay particular attention to the statistical analysis of their outputs. We introduce the mean phase direction of the parent distribution associated with eigenstate inputs as a new post-processing tool. By connecting it with the unknown phase, we find that if used as its direct estimator, it exceeds the accuracy of the standard majority rule using one less bit of resolution, making evident that it can also be inverted to provide unbiased estimation. Moreover, we show how to directly use this quantity to accurately find the energy levels when the initialized state is an eigenstate of the simulated propagator during the whole time evolution, which allows for shallower algorithms. We then use IBM Q hardware to carry out the digital quantum simulation of three toy models: a two-level system, a two-spin Ising model and a two-site Hubbard model at half-filling. Methodologies are provided to implement Trotterization and reduce the variability of results in noisy intermediate scale quantum computers.

In molecular dynamics (MD) simulations, rare events, such as protein folding, are typically studied by means of enhanced sampling techniques, most of which rely on the definition of a collective variable (CV) along which the acceleration occurs. Obtaining an expressive CV is crucial, but often hindered by the lack of information about the particular event, e.g., the transition from unfolded to folded conformation. We propose a simulation-free data augmentation strategy using physics-inspired metrics to generate geodesic interpolations resembling protein folding transitions, thereby improving sampling efficiency without true transition state samples. Leveraging interpolation progress parameters, we introduce a regression-based learning scheme for CV models, which outperforms classifier-based methods when transition state data is limited and noisy

Advanced generative model (e.g., diffusion model) derived from simplified continuity assumptions of data distribution, though showing promising progress, has been difficult to apply directly to geometry generation applications due to the multi-modality and noise-sensitive nature of molecule geometry. This work introduces Geometric Bayesian Flow Networks (GeoBFN), which naturally fits molecule geometry by modeling diverse modalities in the differentiable parameter space of distributions. GeoBFN maintains the SE-(3) invariant density modeling property by incorporating equivariant inter-dependency modeling on parameters of distributions and unifying the probabilistic modeling of different modalities. Through optimized training and sampling techniques, we demonstrate that GeoBFN achieves state-of-the-art performance on multiple 3D molecule generation benchmarks in terms of generation quality (90.87% molecule stability in QM9 and 85.6% atom stability in GEOM-DRUG. GeoBFN can also conduct sampling with any number of steps to reach an optimal trade-off between efficiency and quality (e.g., 20-times speedup without sacrificing performance).

We present microlux, which is a Jax-based code that can compute the binary microlensing light curve and its derivatives both efficiently and accurately. The key feature of microlux is the implementation of a modified version of the adaptive sampling algorithm that was originally proposed by V. Bozza to account for the finite-source effect most efficiently. The efficiency and accuracy of microlux have been verified across the relevant parameter space for binary microlensing. As a differentiable code, microlux makes it possible to apply gradient-based algorithms to the search and posterior estimation of the microlensing modeling. As an example, we use microlux to model a real microlensing event and infer the model posterior via both Fisher information matrix and Hamiltonian Monte Carlo, neither of which would have been possible without the access to accurate model gradients.

We present a novel variational framework for performing inference in (neural) stochastic differential equations (SDEs) driven by Markov-approximate fractional Brownian motion (fBM). SDEs offer a versatile tool for modeling real-world continuous-time dynamic systems with inherent noise and randomness. Combining SDEs with the powerful inference capabilities of variational methods, enables the learning of representative function distributions through stochastic gradient descent. However, conventional SDEs typically assume the underlying noise to follow a Brownian motion (BM), which hinders their ability to capture long-term dependencies. In contrast, fractional Brownian motion (fBM) extends BM to encompass non-Markovian dynamics, but existing methods for inferring fBM parameters are either computationally demanding or statistically inefficient. In this paper, building upon the Markov approximation of fBM, we derive the evidence lower bound essential for efficient variational inference of posterior path measures, drawing from the well-established field of stochastic analysis. Additionally, we provide a closed-form expression to determine optimal approximation coefficients. Furthermore, we propose the use of neural networks to learn the drift, diffusion and control terms within our variational posterior, leading to the variational training of neural-SDEs. In this framework, we also optimize the Hurst index, governing the nature of our fractional noise. Beyond validation on synthetic data, we contribute a novel architecture for variational latent video prediction,-an approach that, to the best of our knowledge, enables the first variational neural-SDE application to video perception.

Graph Neural Networks (GNNs) have been widely adopted for drug discovery with molecular graphs. Nevertheless, current GNNs are mainly good at leveraging short-range interactions (SRI) but struggle to capture long-range interactions (LRI), both of which are crucial for determining molecular properties. To tackle this issue, we propose a method that implicitly projects all original atoms into a few Neural Atoms, which abstracts the collective information of atomic groups within a molecule. Specifically, we explicitly exchange the information among neural atoms and project them back to the atoms' representations as an enhancement. With this mechanism, neural atoms establish the communication channels among distant nodes, effectively reducing the interaction scope of arbitrary node pairs into a single hop. To provide an inspection of our method from a physical perspective, we reveal its connection with the traditional LRI calculation method, Ewald Summation. We conduct extensive experiments on three long-range graph benchmarks, covering both graph-level and link-level tasks on molecular graphs. We empirically justify that our method can be equipped with an arbitrary GNN and help to capture LRI.

Model selection/optimization in conformal inference is challenging, since it may break the exchangeability between labeled and unlabeled data. We study this problem in the context of conformal selection, which uses conformal p-values to select ``interesting'' instances with large unobserved labels from a pool of unlabeled data, while controlling the FDR in finite sample. For validity, existing solutions require the model choice to be independent of the data used to construct the p-values and calibrate the selection set. However, when presented with many model choices and limited labeled data, it is desirable to (i) select the best model in a data-driven manner, and (ii) mitigate power loss due to sample splitting. This paper presents OptCS, a general framework that allows valid statistical testing (selection) after flexible data-driven model optimization. We introduce general conditions under which OptCS constructs valid conformal p-values despite substantial data reuse and handles complex p-value dependencies to maintain finite-sample FDR control via a novel multiple testing procedure. We instantiate this general recipe to propose three FDR-controlling procedures, each optimizing the models differently: (i) selecting the most powerful one among multiple pre-trained candidate models, (ii) using all data for model fitting without sample splitting, and (iii) combining full-sample model fitting and selection. We demonstrate the efficacy of our methods via simulation studies and real applications in drug discovery and alignment of large language models in radiology report generation.

We model and study the processes of excitation, absorption, and transfer in various networks. The model consists of a harmonic oscillator representing a single-mode radiation field, a qubit acting as an antenna, a network through which the excitation propagates, and a qubit at the end serving as a sink. We investigate how off-resonant excitations can be optimally absorbed and transmitted through the network. Three strategies are considered: optimising network energies, adjusting the couplings between the radiation field, the antenna, and the network, or introducing and optimising driving fields at the start and end of the network. These strategies are tested on three different types of network with increasing complexity: nearest-neighbour and star configurations, and one associated with the Fenna-Matthews-Olson complex. The results show that, among the various strategies, the introduction of driving fields is the most effective, leading to a significant increase in the probability of reaching the sink in a given time. This result remains stable across networks of varying dimensionalities and types, and the driving process requires only a few parameters to be effective.

This work introduces a diffusion model for molecule generation in 3D that is equivariant to Euclidean transformations. Our E(3) Equivariant Diffusion Model (EDM) learns to denoise a diffusion process with an equivariant network that jointly operates on both continuous (atom coordinates) and categorical features (atom types). In addition, we provide a probabilistic analysis which admits likelihood computation of molecules using our model. Experimentally, the proposed method significantly outperforms previous 3D molecular generative methods regarding the quality of generated samples and efficiency at training time.

This work derives methods for performing nonparametric, nonasymptotic statistical inference for population means under the constraint of local differential privacy (LDP). Given bounded observations (X_1, dots, X_n) with mean mu^star that are privatized into (Z_1, dots, Z_n), we present confidence intervals (CI) and time-uniform confidence sequences (CS) for mu^star when only given access to the privatized data. To achieve this, we introduce a nonparametric and sequentially interactive generalization of Warner's famous ``randomized response'' mechanism, satisfying LDP for arbitrary bounded random variables, and then provide CIs and CSs for their means given access to the resulting privatized observations. For example, our results yield private analogues of Hoeffding's inequality in both fixed-time and time-uniform regimes. We extend these Hoeffding-type CSs to capture time-varying (non-stationary) means, and conclude by illustrating how these methods can be used to conduct private online A/B tests.

Recently, diffusion probabilistic models (DPMs) have achieved promising results in diverse generative tasks. A typical DPM framework includes a forward process that gradually diffuses the data distribution and a reverse process that recovers the data distribution from time-dependent data scores. In this work, we observe that the stochastic reverse process of data scores is a martingale, from which concentration bounds and the optional stopping theorem for data scores can be derived. Then, we discover a simple way for calibrating an arbitrary pretrained DPM, with which the score matching loss can be reduced and the lower bounds of model likelihood can consequently be increased. We provide general calibration guidelines under various model parametrizations. Our calibration method is performed only once and the resulting models can be used repeatedly for sampling. We conduct experiments on multiple datasets to empirically validate our proposal. Our code is at https://github.com/thudzj/Calibrated-DPMs.

The 100 MW cryogenic liquid oxygen/hydrogen multi-injector combustor BKD operated by the DLR Institute of Space Propulsion is a research platform that allows the study of thermoacoustic instabilities under realistic conditions, representative of small upper stage rocket engines. We use data from BKD experimental campaigns in which the static chamber pressure and fuel-oxidizer ratio are varied such that the first tangential mode of the combustor is excited under some conditions. We train an autoregressive Bayesian neural network model to forecast the amplitude of the dynamic pressure time series, inputting multiple sensor measurements (injector pressure/ temperature measurements, static chamber pressure, high-frequency dynamic pressure measurements, high-frequency OH* chemiluminescence measurements) and future flow rate control signals. The Bayesian nature of our algorithms allows us to work with a dataset whose size is restricted by the expense of each experimental run, without making overconfident extrapolations. We find that the networks are able to accurately forecast the evolution of the pressure amplitude and anticipate instability events on unseen experimental runs 500 milliseconds in advance. We compare the predictive accuracy of multiple models using different combinations of sensor inputs. We find that the high-frequency dynamic pressure signal is particularly informative. We also use the technique of integrated gradients to interpret the influence of different sensor inputs on the model prediction. The negative log-likelihood of data points in the test dataset indicates that predictive uncertainties are well-characterized by our Bayesian model and simulating a sensor failure event results as expected in a dramatic increase in the epistemic component of the uncertainty.

We introduce the FRactional-Order graph Neural Dynamical network (FROND), a new continuous graph neural network (GNN) framework. Unlike traditional continuous GNNs that rely on integer-order differential equations, FROND employs the Caputo fractional derivative to leverage the non-local properties of fractional calculus. This approach enables the capture of long-term dependencies in feature updates, moving beyond the Markovian update mechanisms in conventional integer-order models and offering enhanced capabilities in graph representation learning. We offer an interpretation of the node feature updating process in FROND from a non-Markovian random walk perspective when the feature updating is particularly governed by a diffusion process. We demonstrate analytically that oversmoothing can be mitigated in this setting. Experimentally, we validate the FROND framework by comparing the fractional adaptations of various established integer-order continuous GNNs, demonstrating their consistently improved performance and underscoring the framework's potential as an effective extension to enhance traditional continuous GNNs. The code is available at https://github.com/zknus/ICLR2024-FROND.

Diffusion models have been recently studied as powerful generative inverse problem solvers, owing to their high quality reconstructions and the ease of combining existing iterative solvers. However, most works focus on solving simple linear inverse problems in noiseless settings, which significantly under-represents the complexity of real-world problems. In this work, we extend diffusion solvers to efficiently handle general noisy (non)linear inverse problems via approximation of the posterior sampling. Interestingly, the resulting posterior sampling scheme is a blended version of diffusion sampling with the manifold constrained gradient without a strict measurement consistency projection step, yielding a more desirable generative path in noisy settings compared to the previous studies. Our method demonstrates that diffusion models can incorporate various measurement noise statistics such as Gaussian and Poisson, and also efficiently handle noisy nonlinear inverse problems such as Fourier phase retrieval and non-uniform deblurring. Code available at https://github.com/DPS2022/diffusion-posterior-sampling

While score-based generative models are the model of choice across diverse domains, there are limited tools available for controlling inference-time behavior in a principled manner, e.g. for composing multiple pretrained models. Existing classifier-free guidance methods use a simple heuristic to mix conditional and unconditional scores to approximately sample from conditional distributions. However, such methods do not approximate the intermediate distributions, necessitating additional 'corrector' steps. In this work, we provide an efficient and principled method for sampling from a sequence of annealed, geometric-averaged, or product distributions derived from pretrained score-based models. We derive a weighted simulation scheme which we call Feynman-Kac Correctors (FKCs) based on the celebrated Feynman-Kac formula by carefully accounting for terms in the appropriate partial differential equations (PDEs). To simulate these PDEs, we propose Sequential Monte Carlo (SMC) resampling algorithms that leverage inference-time scaling to improve sampling quality. We empirically demonstrate the utility of our methods by proposing amortized sampling via inference-time temperature annealing, improving multi-objective molecule generation using pretrained models, and improving classifier-free guidance for text-to-image generation. Our code is available at https://github.com/martaskrt/fkc-diffusion.

Persistent homology (PH) provides topological descriptors for geometric data, such as weighted graphs, which are interpretable, stable to perturbations, and invariant under, e.g., relabeling. Most applications of PH focus on the one-parameter case -- where the descriptors summarize the changes in topology of data as it is filtered by a single quantity of interest -- and there is now a wide array of methods enabling the use of one-parameter PH descriptors in data science, which rely on the stable vectorization of these descriptors as elements of a Hilbert space. Although the multiparameter PH (MPH) of data that is filtered by several quantities of interest encodes much richer information than its one-parameter counterpart, the scarceness of stability results for MPH descriptors has so far limited the available options for the stable vectorization of MPH. In this paper, we aim to bring together the best of both worlds by showing how the interpretation of signed barcodes -- a recent family of MPH descriptors -- as signed measures leads to natural extensions of vectorization strategies from one parameter to multiple parameters. The resulting feature vectors are easy to define and to compute, and provably stable. While, as a proof of concept, we focus on simple choices of signed barcodes and vectorizations, we already see notable performance improvements when comparing our feature vectors to state-of-the-art topology-based methods on various types of data.

Visible-light cameras can capture subtle physiological biomarkers without physical contact with the subject. We present the Multi-Site Physiological Monitoring (MSPM) dataset, which is the first dataset collected to support the study of simultaneous camera-based vital signs estimation from multiple locations on the body. MSPM enables research on remote photoplethysmography (rPPG), respiration rate, and pulse transit time (PTT); it contains ground-truth measurements of pulse oximetry (at multiple body locations) and blood pressure using contacting sensors. We provide thorough experiments demonstrating the suitability of MSPM to support research on rPPG, respiration rate, and PTT. Cross-dataset rPPG experiments reveal that MSPM is a challenging yet high quality dataset, with intra-dataset pulse rate mean absolute error (MAE) below 4 beats per minute (BPM), and cross-dataset pulse rate MAE below 2 BPM in certain cases. Respiration experiments find a MAE of 1.09 breaths per minute by extracting motion features from the chest. PTT experiments find that across the pairs of different body sites, there is high correlation between remote PTT and contact-measured PTT, which facilitates the possibility for future camera-based PTT research.

There is a growing gap between the impressive results of deep image generative models and classical algorithms that offer theoretical guarantees. The former suffer from mode collapse or memorization issues, limiting their application to scientific data. The latter require restrictive assumptions such as log-concavity to escape the curse of dimensionality. We partially bridge this gap by introducing conditionally strongly log-concave (CSLC) models, which factorize the data distribution into a product of conditional probability distributions that are strongly log-concave. This factorization is obtained with orthogonal projectors adapted to the data distribution. It leads to efficient parameter estimation and sampling algorithms, with theoretical guarantees, although the data distribution is not globally log-concave. We show that several challenging multiscale processes are conditionally log-concave using wavelet packet orthogonal projectors. Numerical results are shown for physical fields such as the varphi^4 model and weak lensing convergence maps with higher resolution than in previous works.

Generative tasks about molecules, including but not limited to molecule generation, are crucial for drug discovery and material design, and have consistently attracted significant attention. In recent years, diffusion models have emerged as an impressive class of deep generative models, sparking extensive research and leading to numerous studies on their application to molecular generative tasks. Despite the proliferation of related work, there remains a notable lack of up-to-date and systematic surveys in this area. Particularly, due to the diversity of diffusion model formulations, molecular data modalities, and generative task types, the research landscape is challenging to navigate, hindering understanding and limiting the area's growth. To address this, this paper conducts a comprehensive survey of diffusion model-based molecular generative methods. We systematically review the research from the perspectives of methodological formulations, data modalities, and task types, offering a novel taxonomy. This survey aims to facilitate understanding and further flourishing development in this area. The relevant papers are summarized at: https://github.com/AzureLeon1/awesome-molecular-diffusion-models.

Diffusion-based image restoration (IR) methods aim to use diffusion models to recover high-quality (HQ) images from degraded images and achieve promising performance. Due to the inherent property of diffusion models, most of these methods need long serial sampling chains to restore HQ images step-by-step. As a result, it leads to expensive sampling time and high computation costs. Moreover, such long sampling chains hinder understanding the relationship between the restoration results and the inputs since it is hard to compute the gradients in the whole chains. In this work, we aim to rethink the diffusion-based IR models through a different perspective, i.e., a deep equilibrium (DEQ) fixed point system. Specifically, we derive an analytical solution by modeling the entire sampling chain in diffusion-based IR models as a joint multivariate fixed point system. With the help of the analytical solution, we are able to conduct single-image sampling in a parallel way and restore HQ images without training. Furthermore, we compute fast gradients in DEQ and found that initialization optimization can boost performance and control the generation direction. Extensive experiments on benchmarks demonstrate the effectiveness of our proposed method on typical IR tasks and real-world settings. The code and models will be made publicly available.

We introduce the framework of model space into quantum imaginary time evolution (QITE) to enable stable estimation of ground and excited states using a quantum computer. Model-space QITE (MSQITE) propagates a model space to the exact one by retaining its orthogonality, and hence is able to describe multiple states simultaneously. The quantum Lanczos (QLanczos) algorithm is extended to MSQITE to accelerate the convergence. The present scheme is found to outperform both the standard QLanczos and the recently proposed folded-spectrum QITE in simulating excited states. Moreover, we demonstrate that spin contamination can be effectively removed by shifting the imaginary time propagator, and thus excited states with a particular spin quantum number are efficiently captured without falling into the different spin states that have lower energies. We also investigate how different levels of the unitary approximation employed in MSQITE can affect the results. The effectiveness of the algorithm over QITE is demonstrated by noise simulations for the H4 model system.

Large-scale recordings of neural activity are providing new opportunities to study neural population dynamics. A powerful method for analyzing such high-dimensional measurements is to deploy an algorithm to learn the low-dimensional latent dynamics. LFADS (Latent Factor Analysis via Dynamical Systems) is a deep learning method for inferring latent dynamics from high-dimensional neural spiking data recorded simultaneously in single trials. This method has shown a remarkable performance in modeling complex brain signals with an average inference latency in milliseconds. As our capacity of simultaneously recording many neurons is increasing exponentially, it is becoming crucial to build capacity for deploying low-latency inference of the computing algorithms. To improve the real-time processing ability of LFADS, we introduce an efficient implementation of the LFADS models onto Field Programmable Gate Arrays (FPGA). Our implementation shows an inference latency of 41.97 mus for processing the data in a single trial on a Xilinx U55C.

Biophysical modeling, particularly involving partial differential equations (PDEs), offers significant potential for tailoring disease treatment protocols to individual patients. However, the inverse problem-solving aspect of these models presents a substantial challenge, either due to the high computational requirements of model-based approaches or the limited robustness of deep learning (DL) methods. We propose a novel framework that leverages the unique strengths of both approaches in a synergistic manner. Our method incorporates a DL ensemble for initial parameter estimation, facilitating efficient downstream evolutionary sampling initialized with this DL-based prior. We showcase the effectiveness of integrating a rapid deep-learning algorithm with a high-precision evolution strategy in estimating brain tumor cell concentrations from magnetic resonance images. The DL-Prior plays a pivotal role, significantly constraining the effective sampling-parameter space. This reduction results in a fivefold convergence acceleration and a Dice-score of 95%

Advancements in space telescopes have opened new avenues for gathering vast amounts of data on exoplanet atmosphere spectra. However, accurately extracting chemical and physical properties from these spectra poses significant challenges due to the non-linear nature of the underlying physics. This paper presents novel machine learning models developed by the AstroAI team for the Ariel Data Challenge 2023, where one of the models secured the top position among 293 competitors. Leveraging Normalizing Flows, our models predict the posterior probability distribution of atmospheric parameters under different atmospheric assumptions. Moreover, we introduce an alternative model that exhibits higher performance potential than the winning model, despite scoring lower in the challenge. These findings highlight the need to reevaluate the evaluation metric and prompt further exploration of more efficient and accurate approaches for exoplanet atmosphere spectra analysis. Finally, we present recommendations to enhance the challenge and models, providing valuable insights for future applications on real observational data. These advancements pave the way for more effective and timely analysis of exoplanet atmospheric properties, advancing our understanding of these distant worlds.

Learning curve extrapolation aims to predict model performance in later epochs of training, based on the performance in earlier epochs. In this work, we argue that, while the inherent uncertainty in the extrapolation of learning curves warrants a Bayesian approach, existing methods are (i) overly restrictive, and/or (ii) computationally expensive. We describe the first application of prior-data fitted neural networks (PFNs) in this context. A PFN is a transformer, pre-trained on data generated from a prior, to perform approximate Bayesian inference in a single forward pass. We propose LC-PFN, a PFN trained to extrapolate 10 million artificial right-censored learning curves generated from a parametric prior proposed in prior art using MCMC. We demonstrate that LC-PFN can approximate the posterior predictive distribution more accurately than MCMC, while being over 10 000 times faster. We also show that the same LC-PFN achieves competitive performance extrapolating a total of 20 000 real learning curves from four learning curve benchmarks (LCBench, NAS-Bench-201, Taskset, and PD1) that stem from training a wide range of model architectures (MLPs, CNNs, RNNs, and Transformers) on 53 different datasets with varying input modalities (tabular, image, text, and protein data). Finally, we investigate its potential in the context of model selection and find that a simple LC-PFN based predictive early stopping criterion obtains 2 - 6x speed-ups on 45 of these datasets, at virtually no overhead.

The reliability with Machine Learning (ML) techniques in novel materials discovery often depend on the quality of the dataset, in addition to the relevant features used in describing the material. In this regard, the current study presents and validates a newly processed materials dataset that can be utilized for benchmark ML analysis, as it relates to the prediction and classification of deterministic target properties. Originally, the dataset was extracted from the Open Quantum Materials Database (OQMD) and contains a robust 16,323 samples of ABX3 inorganic perovskite structures. The dataset is tabular in form and is preprocessed to include sixty-one generalized input features that broadly describes the physicochemical, stability/geometrical, and Density Functional Theory (DFT) target properties associated with the elemental ionic sites in a three-dimensional ABX3 polyhedral. For validation, four different ML models are employed to predict three distinctive target properties, namely: formation energy, energy band gap, and crystal system. On experimentation, the best accuracy measurements are reported at 0.013 eV/atom MAE, 0.216 eV MAE, and 85% F1, corresponding to the formation energy prediction, band gap prediction and crystal system multi-classification, respectively. Moreover, the realized results are compared with previous literature and as such, affirms the resourcefulness of the current dataset for future benchmark materials analysis via ML techniques. The preprocessed dataset and source codes are openly available to download from github.com/chenebuah/ML_abx3_dataset.

Large-Area Picosecond Photo-Detectors (LAPPDs) show great potential for expanding the performance envelope of Micro-Channel Plates (MCPs) to areas of up to 20 x 20 cm and larger. Such scaling introduces new challenges, including how to meet the electronics readout burden of ever larger area MCPs. One solution is to replace the traditional grid anode used for readout with a microwave stripline anode, thus allowing the channel count to scale with MCP width rather than area. However, stripline anodes introduce new issues not commonly dealt with in grid-anodes, especially as their length increases. One of these issues is the near simultaneous arrival of multiple photons on the detector, creating possible confusion about how to reconstruct their arrival times and positions. We propose a maximum a posteriori solution to the problem and verify its performance in simulated scintillator and water-Cherenkov detectors.

We present a method to convert certain single photon sources into devices capable of emitting large strings of photonic cluster state in a controlled and pulsed "on demand" manner. Such sources would greatly reduce the resources required to achieve linear optical quantum computation. Standard spin errors, such as dephasing, are shown to affect only 1 or 2 of the emitted photons at a time. This allows for the use of standard fault tolerance techniques, and shows that the photonic machine gun can be fired for arbitrarily long times. Using realistic parameters for current quantum dot sources, we conclude high entangled-photon emission rates are achievable, with Pauli-error rates per photon of less than 0.2%. For quantum dot sources the method has the added advantage of alleviating the problematic issues of obtaining identical photons from independent, non-identical quantum dots, and of exciton dephasing.

We apply a Gaussian process method to the extreme gamma-ray flares of 3C 454.3 and 3C 279 to discover the variable patterns and then to investigate the physical origins of the giant flares. The kernels of stochastically driven damped simple harmonic oscillator (SHO), the damped random-walk (DRW), and Matrm ern-3/2 are respectively used to describe the adaptive-binning gamma-ray light curves of the two flares. Our findings show that both the extreme gamma-ray flares of 3C 454.3 and 3C 279 clearly prefer the SHO kernel in the over-damped mode and the Matrm ern-3/2 kernel over the DRW kernel. The resulted SHO and Matrm ern-3/2 power spectral densities (PSDs) are the same for each object, with the index changing from -4 at high frequencies to 0 at low frequencies. The patterns of the two flares are both approaching the critical damping mode with the quality factor Q approx 0.4 (i.e., the damping ratio eta approx 1.25), but with slightly different damping timescales. The characteristic timescale (corresponding to the broken frequency in the PSD) for 3C 454.3 is 2-3 days and 3-5 days for 3C 279. The variable patterns found here suggest that once the system responds to the energy injection disturbance, the release of the energy in the system is finished abruptly. The obtained timescale provides a constraint on the size of energy dissipation region for each source.

This article presents a review about the main CERN n\_TOF contributions to the field of neutron-capture experiments of interest for s-process nucleosynthesis studies over the last 25 years, with special focus on the measurement of radioactive isotopes. A few recent capture experiments on stable isotopes of astrophysical interest are also discussed. Results on s-process branching nuclei are appropriate to illustrate how advances in detection systems and upgrades in the facility have enabled increasingly challenging experiments and, as a consequence, have led to a better understanding and modeling of the s-process mechanism of nucleosynthesis. New endeavors combining radioactive-ion beams from ISOLDE for the production of radioisotopically pure samples for activation experiments at the new NEAR facility at n\_TOF are briefly discussed. On the basis of these new exciting results, also current limitations of state-of-the-art TOF and activation techniques will be depicted, thereby showing the pressing need for further upgrades and enhancements on both facilities and detection systems. A brief account of the potential technique based on inverse kinematics for direct neutron-capture measurements is also presented.

Diffusion probabilistic models (DPMs) have exhibited excellent performance for high-fidelity image generation while suffering from inefficient sampling. Recent works accelerate the sampling procedure by proposing fast ODE solvers that leverage the specific ODE form of DPMs. However, they highly rely on specific parameterization during inference (such as noise/data prediction), which might not be the optimal choice. In this work, we propose a novel formulation towards the optimal parameterization during sampling that minimizes the first-order discretization error of the ODE solution. Based on such formulation, we propose DPM-Solver-v3, a new fast ODE solver for DPMs by introducing several coefficients efficiently computed on the pretrained model, which we call empirical model statistics. We further incorporate multistep methods and a predictor-corrector framework, and propose some techniques for improving sample quality at small numbers of function evaluations (NFE) or large guidance scales. Experiments show that DPM-Solver-v3 achieves consistently better or comparable performance in both unconditional and conditional sampling with both pixel-space and latent-space DPMs, especially in 5sim10 NFEs. We achieve FIDs of 12.21 (5 NFE), 2.51 (10 NFE) on unconditional CIFAR10, and MSE of 0.55 (5 NFE, 7.5 guidance scale) on Stable Diffusion, bringing a speed-up of 15\%sim30\% compared to previous state-of-the-art training-free methods. Code is available at https://github.com/thu-ml/DPM-Solver-v3.

Accurate and timely detection of plant stress is essential for yield protection, allowing better-targeted intervention strategies. Recent advances in remote sensing and deep learning have shown great potential for rapid non-invasive detection of plant stress in a fully automated and reproducible manner. However, the existing models always face several challenges: 1) computational inefficiency and the misclassifications between the different stresses with similar symptoms; and 2) the poor interpretability of the host-stress interaction. In this work, we propose a novel fast Fourier Convolutional Neural Network (FFDNN) for accurate and explainable detection of two plant stresses with similar symptoms (i.e. Wheat Yellow Rust And Nitrogen Deficiency). Specifically, unlike the existing CNN models, the main components of the proposed model include: 1) a fast Fourier convolutional block, a newly fast Fourier transformation kernel as the basic perception unit, to substitute the traditional convolutional kernel to capture both local and global responses to plant stress in various time-scale and improve computing efficiency with reduced learning parameters in Fourier domain; 2) Capsule Feature Encoder to encapsulate the extracted features into a series of vector features to represent part-to-whole relationship with the hierarchical structure of the host-stress interactions of the specific stress. In addition, in order to alleviate over-fitting, a photochemical vegetation indices-based filter is placed as pre-processing operator to remove the non-photochemical noises from the input Sentinel-2 time series.

In this study we explore the optimization of laser pulse duration to obtain the shortest possible pulse. We do this by employing a feedback loop between a pulse shaper and pulse duration measurements. We apply to this problem several iterative algorithms including gradient descent, Bayesian Optimization and genetic algorithms, using a simulation of the actual laser represented via a semi-physical model of the laser based on the process of linear and non-linear phase accumulation.

This paper studies generative flow networks (GFlowNets) to sample objects from the Boltzmann energy distribution via a sequence of actions. In particular, we focus on improving GFlowNet with partial inference: training flow functions with the evaluation of the intermediate states or transitions. To this end, the recently developed forward-looking GFlowNet reparameterizes the flow functions based on evaluating the energy of intermediate states. However, such an evaluation of intermediate energies may (i) be too expensive or impossible to evaluate and (ii) even provide misleading training signals under large energy fluctuations along the sequence of actions. To resolve this issue, we propose learning energy decompositions for GFlowNets (LED-GFN). Our main idea is to (i) decompose the energy of an object into learnable potential functions defined on state transitions and (ii) reparameterize the flow functions using the potential functions. In particular, to produce informative local credits, we propose to regularize the potential to change smoothly over the sequence of actions. It is also noteworthy that training GFlowNet with our learned potential can preserve the optimal policy. We empirically verify the superiority of LED-GFN in five problems including the generation of unstructured and maximum independent sets, molecular graphs, and RNA sequences.

Interrogating the evolution of biological changes at early stages of life requires longitudinal profiling of molecules, such as DNA methylation, which can be challenging with children. We introduce a probabilistic and longitudinal machine learning framework based on multi-mean Gaussian processes (GPs), accounting for individual and gene correlations across time. This method provides future predictions of DNA methylation status at different individual ages while accounting for uncertainty. Our model is trained on a birth cohort of children with methylation profiled at ages 0-4, and we demonstrated that the status of methylation sites for each child can be accurately predicted at ages 5-7. We show that methylation profiles predicted by multi-mean GPs can be used to estimate other phenotypes, such as epigenetic age, and enable comparison to other health measures of interest. This approach encourages epigenetic studies to move towards longitudinal design for investigating epigenetic changes during development, ageing and disease progression.

In this work we take a Category Theoretic perspective on the relationship between probabilistic modeling and function approximation. We begin by defining two extensions of function composition to stochastic process subordination: one based on the co-Kleisli category under the comonad (Omega x -) and one based on the parameterization of a category with a Lawvere theory. We show how these extensions relate to the category Stoch and other Markov Categories. Next, we apply the Para construction to extend stochastic processes to parameterized statistical models and we define a way to compose the likelihood functions of these models. We conclude with a demonstration of how the Maximum Likelihood Estimation procedure defines an identity-on-objects functor from the category of statistical models to the category of Learners. Code to accompany this paper can be found at https://github.com/dshieble/Categorical_Stochastic_Processes_and_Likelihood

Understanding and interpreting dynamics of functional materials in situ is a grand challenge in physics and materials science due to the difficulty of experimentally probing materials at varied length and time scales. X-ray photon correlation spectroscopy (XPCS) is uniquely well-suited for characterizing materials dynamics over wide-ranging time scales, however spatial and temporal heterogeneity in material behavior can make interpretation of experimental XPCS data difficult. In this work we have developed an unsupervised deep learning (DL) framework for automated classification and interpretation of relaxation dynamics from experimental data without requiring any prior physical knowledge of the system behavior. We demonstrate how this method can be used to rapidly explore large datasets to identify samples of interest, and we apply this approach to directly correlate bulk properties of a model system to microscopic dynamics. Importantly, this DL framework is material and process agnostic, marking a concrete step towards autonomous materials discovery.

We study the optimisation problem associated with Gaussian process regression using squared loss. The most common approach to this problem is to apply an exact solver, such as conjugate gradient descent, either directly, or to a reduced-order version of the problem. Recently, driven by successes in deep learning, stochastic gradient descent has gained traction as an alternative. In this paper, we show that when done rightx2014by which we mean using specific insights from the optimisation and kernel communitiesx2014this approach is highly effective. We thus introduce a particular stochastic dual gradient descent algorithm, that may be implemented with a few lines of code using any deep learning framework. We explain our design decisions by illustrating their advantage against alternatives with ablation studies and show that the new method is highly competitive. Our evaluations on standard regression benchmarks and a Bayesian optimisation task set our approach apart from preconditioned conjugate gradients, variational Gaussian process approximations, and a previous version of stochastic gradient descent for Gaussian processes. On a molecular binding affinity prediction task, our method places Gaussian process regression on par in terms of performance with state-of-the-art graph neural networks.

Although data diffusion embeddings are ubiquitous in unsupervised learning and have proven to be a viable technique for uncovering the underlying intrinsic geometry of data, diffusion embeddings are inherently limited due to their discrete nature. To this end, we propose neural FIM, a method for computing the Fisher information metric (FIM) from point cloud data - allowing for a continuous manifold model for the data. Neural FIM creates an extensible metric space from discrete point cloud data such that information from the metric can inform us of manifold characteristics such as volume and geodesics. We demonstrate Neural FIM's utility in selecting parameters for the PHATE visualization method as well as its ability to obtain information pertaining to local volume illuminating branching points and cluster centers embeddings of a toy dataset and two single-cell datasets of IPSC reprogramming and PBMCs (immune cells).

About 90% of the computing resources available to the LHCb experiment has been spent to produce simulated data samples for Run 2 of the Large Hadron Collider at CERN. The upgraded LHCb detector will be able to collect larger data samples, requiring many more simulated events to analyze the data to be collected in Run 3. Simulation is a key necessity of analysis to interpret signal, reject background and measure efficiencies. The needed simulation will far exceed the pledged resources, requiring an evolution in technologies and techniques to produce these simulated data samples. In this contribution, we discuss Lamarr, a Gaudi-based framework to speed-up the simulation production parameterizing both the detector response and the reconstruction algorithms of the LHCb experiment. Deep Generative Models powered by several algorithms and strategies are employed to effectively parameterize the high-level response of the single components of the LHCb detector, encoding within neural networks the experimental errors and uncertainties introduced in the detection and reconstruction phases. Where possible, models are trained directly on real data, statistically subtracting any background components by applying appropriate reweighing procedures. Embedding Lamarr in the general LHCb Gauss Simulation framework allows to combine its execution with any of the available generators in a seamless way. The resulting software package enables a simulation process independent of the detailed simulation used to date.

The illumination of the accretion disks is frequently studied assuming that the incident X-ray flux is a point-like source. The approach is referred as lamppost model.The most recent computations of the X-ray reprocessing by the disk take into account the departure from the simple lamppost models. However, in computations of the incident flux thermalization and subsequent re-emission in the optical-UV band the lamppost approximation is most frequently assumed. We test if the UV-optical reverberation mapping and time delay measurements are sensitive to this assumption. We assume that the incident radiation originates from a region extended along the symmetry axis. To model this, we adopt a simple setup by representing the emission as two lamps irradiating the disk simultaneously from two different heights. We then compare the resulting predictions with those obtained for a single lamppost located at an intermediate height. We show at the basis of the transfer function that the deviation of the wavelength-dependent delay curve shows at most a difference of 20% in comparison to a single lamppost, assuming the black hole mass of 10^8 M_{odot}, Eddington ratio 1, and the location of the lamps at 5 and 100 rg. The maximum deviation happens for the lamp luminosity ratio sim3. When simulating light curves for a two-lamp setup and a standard lamppost with the same black hole mass and a sampling rate of 0.1 days, we find no measurable differences in the ICCF profiles between the two setups. Larger black hole mass and considerably lower Eddington ratio would allow to see larger differences between a single lamppost and a two-lampost model. UV/optical reverberation mapping is not very sensitive to the vertical extension of the corona.

Modeling the interaction between proteins and ligands and accurately predicting their binding structures is a critical yet challenging task in drug discovery. Recent advancements in deep learning have shown promise in addressing this challenge, with sampling-based and regression-based methods emerging as two prominent approaches. However, these methods have notable limitations. Sampling-based methods often suffer from low efficiency due to the need for generating multiple candidate structures for selection. On the other hand, regression-based methods offer fast predictions but may experience decreased accuracy. Additionally, the variation in protein sizes often requires external modules for selecting suitable binding pockets, further impacting efficiency. In this work, we propose FABind, an end-to-end model that combines pocket prediction and docking to achieve accurate and fast protein-ligand binding. FABind incorporates a unique ligand-informed pocket prediction module, which is also leveraged for docking pose estimation. The model further enhances the docking process by incrementally integrating the predicted pocket to optimize protein-ligand binding, reducing discrepancies between training and inference. Through extensive experiments on benchmark datasets, our proposed FABind demonstrates strong advantages in terms of effectiveness and efficiency compared to existing methods. Our code is available at https://github.com/QizhiPei/FABind

Catalyst discovery and optimization is key to solving many societal and energy challenges including solar fuels synthesis, long-term energy storage, and renewable fertilizer production. Despite considerable effort by the catalysis community to apply machine learning models to the computational catalyst discovery process, it remains an open challenge to build models that can generalize across both elemental compositions of surfaces and adsorbate identity/configurations, perhaps because datasets have been smaller in catalysis than related fields. To address this we developed the OC20 dataset, consisting of 1,281,040 Density Functional Theory (DFT) relaxations (~264,890,000 single point evaluations) across a wide swath of materials, surfaces, and adsorbates (nitrogen, carbon, and oxygen chemistries). We supplemented this dataset with randomly perturbed structures, short timescale molecular dynamics, and electronic structure analyses. The dataset comprises three central tasks indicative of day-to-day catalyst modeling and comes with pre-defined train/validation/test splits to facilitate direct comparisons with future model development efforts. We applied three state-of-the-art graph neural network models (CGCNN, SchNet, Dimenet++) to each of these tasks as baseline demonstrations for the community to build on. In almost every task, no upper limit on model size was identified, suggesting that even larger models are likely to improve on initial results. The dataset and baseline models are both provided as open resources, as well as a public leader board to encourage community contributions to solve these important tasks.

We propose algorithms for approximate filtering and smoothing in high-dimensional Factorial hidden Markov models. The approximation involves discarding, in a principled way, likelihood factors according to a notion of locality in a factor graph associated with the emission distribution. This allows the exponential-in-dimension cost of exact filtering and smoothing to be avoided. We prove that the approximation accuracy, measured in a local total variation norm, is "dimension-free" in the sense that as the overall dimension of the model increases the error bounds we derive do not necessarily degrade. A key step in the analysis is to quantify the error introduced by localizing the likelihood function in a Bayes' rule update. The factorial structure of the likelihood function which we exploit arises naturally when data have known spatial or network structure. We demonstrate the new algorithms on synthetic examples and a London Underground passenger flow problem, where the factor graph is effectively given by the train network.

Advancements in neural machinery have led to a wide range of algorithmic solutions for molecular property prediction. Two classes of models in particular have yielded promising results: neural networks applied to computed molecular fingerprints or expert-crafted descriptors, and graph convolutional neural networks that construct a learned molecular representation by operating on the graph structure of the molecule. However, recent literature has yet to clearly determine which of these two methods is superior when generalizing to new chemical space. Furthermore, prior research has rarely examined these new models in industry research settings in comparison to existing employed models. In this paper, we benchmark models extensively on 19 public and 16 proprietary industrial datasets spanning a wide variety of chemical endpoints. In addition, we introduce a graph convolutional model that consistently matches or outperforms models using fixed molecular descriptors as well as previous graph neural architectures on both public and proprietary datasets. Our empirical findings indicate that while approaches based on these representations have yet to reach the level of experimental reproducibility, our proposed model nevertheless offers significant improvements over models currently used in industrial workflows.

As host to two accreting planets, PDS 70 provides a unique opportunity to probe the chemical complexity of atmosphere-forming material. We present ALMA Band 6 observations of the PDS~70 disk and report the first chemical inventory of the system. With a spatial resolution of 0.4''-0.5'' (sim50 au), 12 species are detected, including CO isotopologues and formaldehyde, small hydrocarbons, HCN and HCO+ isotopologues, and S-bearing molecules. SO and CH3OH are not detected. All lines show a large cavity at the center of the disk, indicative of the deep gap carved by the massive planets. The radial profiles of the line emission are compared to the (sub-)mm continuum and infrared scattered light intensity profiles. Different molecular transitions peak at different radii, revealing the complex interplay between density, temperature and chemistry in setting molecular abundances. Column densities and optical depth profiles are derived for all detected molecules, and upper limits obtained for the non detections. Excitation temperature is obtained for H2CO. Deuteration and nitrogen fractionation profiles from the hydro-cyanide lines show radially increasing fractionation levels. Comparison of the disk chemical inventory to grids of chemical models from the literature strongly suggests a disk molecular layer hosting a carbon to oxygen ratio C/O>1, thus providing for the first time compelling evidence of planets actively accreting high C/O ratio gas at present time.

We investigate the fidelity of Grover's search algorithm by implementing it on an open quantum system. In particular, we study with what accuracy one can estimate that the algorithm would deliver the searched state. In reality, every system has some influence of its environment. We include the environmental effects on the system dynamics by using a recently reported fluctuation-regulated quantum master equation (FRQME). The FRQME indicates that in addition to the regular relaxation due to system-environment coupling, the applied drive also causes dissipation in the system dynamics. As a result, the fidelity is found to depend on both the drive-induced dissipative terms and the relaxation terms and we find that there exists a competition between them, leading to an optimum value of the drive amplitude for which the fidelity becomes maximum. For efficient implementation of the search algorithm, precise knowledge of this optimum drive amplitude is essential.

Molecular dynamics (MD) is a powerful technique for studying microscopic phenomena, but its computational cost has driven significant interest in the development of deep learning-based surrogate models. We introduce generative modeling of molecular trajectories as a paradigm for learning flexible multi-task surrogate models of MD from data. By conditioning on appropriately chosen frames of the trajectory, we show such generative models can be adapted to diverse tasks such as forward simulation, transition path sampling, and trajectory upsampling. By alternatively conditioning on part of the molecular system and inpainting the rest, we also demonstrate the first steps towards dynamics-conditioned molecular design. We validate the full set of these capabilities on tetrapeptide simulations and show that our model can produce reasonable ensembles of protein monomers. Altogether, our work illustrates how generative modeling can unlock value from MD data towards diverse downstream tasks that are not straightforward to address with existing methods or even MD itself. Code is available at https://github.com/bjing2016/mdgen.

Imaging under extremely low-light conditions presents a significant challenge and is an ill-posed problem due to the low signal-to-noise ratio (SNR) caused by minimal photon capture. Previously, diffusion models have been used for multiple kinds of generative tasks and image-to-image tasks, however, these models work as a post-processing step. These diffusion models are trained on processed images and learn on processed images. However, such approaches are often not well-suited for extremely low-light tasks. Unlike the task of low-light image enhancement or image-to-image enhancement, we tackle the task of learning the entire image-processing pipeline, from the RAW image to a processed image. For this task, a traditional image processing pipeline often consists of multiple specialized parts that are overly reliant on the downstream tasks. Unlike these, we develop a new generative ISP that relies on fine-tuning latent diffusion models on RAW images and generating processed long-exposure images which allows for the apt use of the priors from large text-to-image generation models. We evaluate our approach on popular end-to-end low-light datasets for which we see promising results and set a new SoTA on the See-in-Dark (SID) dataset. Furthermore, with this work, we hope to pave the way for more generative and diffusion-based image processing and other problems on RAW data.

Connecting optimal transport and variational inference, we present a principled and systematic framework for sampling and generative modelling centred around divergences on path space. Our work culminates in the development of the Controlled Monte Carlo Diffusion sampler (CMCD) for Bayesian computation, a score-based annealing technique that crucially adapts both forward and backward dynamics in a diffusion model. On the way, we clarify the relationship between the EM-algorithm and iterative proportional fitting (IPF) for Schr{\"o}dinger bridges, deriving as well a regularised objective that bypasses the iterative bottleneck of standard IPF-updates. Finally, we show that CMCD has a strong foundation in the Jarzinsky and Crooks identities from statistical physics, and that it convincingly outperforms competing approaches across a wide array of experiments.

The singlet-doublet vector-like fermion dark matter model has been extensively studied in the literature over the past decade. An important parameter in this model is the singlet-doublet mixing angle (sintheta). All the previous studies have primarily focused on annihilation and co-annihilation processes for obtaining the correct dark matter relic density, assuming that the singlet and doublet components decouple at the same epoch. In this work, we demonstrate that this assumption holds only for larger mixing angles with a dependency on the mass of the dark matter. However, it badly fails for the mixing angle sintheta<0.05. We present a systematic study of the parameter space of the singlet-doublet dark matter relic, incorporating annihilation, co-annihilation, and, for the first time, co-scattering processes. Additionally, the freeze-in parameter space is also explored. We found that due to the inclusion of co-scattering processes, the correct relic density parameter space is shifted towards the detection sensitivity range of the LHC and MATHUSLA via displaced vertex signatures.

In this work we present a new method for the estimation of Mutual Information (MI) between random variables. Our approach is based on an original interpretation of the Girsanov theorem, which allows us to use score-based diffusion models to estimate the Kullback Leibler divergence between two densities as a difference between their score functions. As a by-product, our method also enables the estimation of the entropy of random variables. Armed with such building blocks, we present a general recipe to measure MI, which unfolds in two directions: one uses conditional diffusion process, whereas the other uses joint diffusion processes that allow simultaneous modelling of two random variables. Our results, which derive from a thorough experimental protocol over all the variants of our approach, indicate that our method is more accurate than the main alternatives from the literature, especially for challenging distributions. Furthermore, our methods pass MI self-consistency tests, including data processing and additivity under independence, which instead are a pain-point of existing methods.

Brain tumor growth is unique to each glioma patient and extends beyond what is visible in imaging scans, infiltrating surrounding brain tissue. Understanding these hidden patient-specific progressions is essential for effective therapies. Current treatment plans for brain tumors, such as radiotherapy, typically involve delineating a uniform margin around the visible tumor on pre-treatment scans to target this invisible tumor growth. This "one size fits all" approach is derived from population studies and often fails to account for the nuances of individual patient conditions. We present the GliODIL framework, which infers the full spatial distribution of tumor cell concentration from available multi-modal imaging, leveraging a Fisher-Kolmogorov type physics model to describe tumor growth. This is achieved through the newly introduced method of Optimizing the Discrete Loss (ODIL), where both data and physics-based constraints are softly assimilated into the solution. Our test dataset comprises 152 glioblastoma patients with pre-treatment imaging and post-treatment follow-ups for tumor recurrence monitoring. By blending data-driven techniques with physics-based constraints, GliODIL enhances recurrence prediction in radiotherapy planning, challenging traditional uniform margins and strict adherence to the Fisher-Kolmogorov partial differential equation (PDE) model, which is adapted for complex cases.

Novel machine learning methods for tabular data generation are often developed on small datasets which do not match the scale required for scientific applications. We investigate a recent proposal to use XGBoost as the function approximator in diffusion and flow-matching models on tabular data, which proved to be extremely memory intensive, even on tiny datasets. In this work, we conduct a critical analysis of the existing implementation from an engineering perspective, and show that these limitations are not fundamental to the method; with better implementation it can be scaled to datasets 370x larger than previously used. Our efficient implementation also unlocks scaling models to much larger sizes which we show directly leads to improved performance on benchmark tasks. We also propose algorithmic improvements that can further benefit resource usage and model performance, including multi-output trees which are well-suited to generative modeling. Finally, we present results on large-scale scientific datasets derived from experimental particle physics as part of the Fast Calorimeter Simulation Challenge. Code is available at https://github.com/layer6ai-labs/calo-forest.

Motivation: Ab initio protein docking represents a major challenge for optimizing a noisy and costly "black box"-like function in a high-dimensional space. Despite progress in this field, there is no docking method available for rigorous uncertainty quantification (UQ) of its solution quality (e.g. interface RMSD or iRMSD). Results: We introduce a novel algorithm, Bayesian Active Learning (BAL), for optimization and UQ of such black-box functions and flexible protein docking. BAL directly models the posterior distribution of the global optimum (or native structures for protein docking) with active sampling and posterior estimation iteratively feeding each other. Furthermore, we use complex normal modes to represent a homogeneous Euclidean conformation space suitable for high-dimension optimization and construct funnel-like energy models for encounter complexes. Over a protein docking benchmark set and a CAPRI set including homology docking, we establish that BAL significantly improve against both starting points by rigid docking and refinements by particle swarm optimization, providing for one third targets a top-3 near-native prediction. BAL also generates tight confidence intervals with half range around 25% of iRMSD and confidence level at 85%. Its estimated probability of a prediction being native or not achieves binary classification AUROC at 0.93 and AUPRC over 0.60 (compared to 0.14 by chance); and also found to help ranking predictions. To the best of our knowledge, this study represents the first uncertainty quantification solution for protein docking, with theoretical rigor and comprehensive assessment. Source codes are available at https://github.com/Shen-Lab/BAL.

The polarization of an X-ray beam that produces electrons with velocity components perpendicular to the beam generates an azimuthal distribution of the ejected electrons. We present methods for simulating and for analyzing the angular dependence of electron detections which enable us to derive simple analytical expressions for useful statistical properties of observable data. The derivations are verified by simulations. While we confirm the results of previous work on this topic, we provide an extension needed for analytical treatment of the full range of possible polarization amplitudes.

Computational catalysis is playing an increasingly significant role in the design of catalysts across a wide range of applications. A common task for many computational methods is the need to accurately compute the minimum binding energy - the adsorption energy - for an adsorbate and a catalyst surface of interest. Traditionally, the identification of low energy adsorbate-surface configurations relies on heuristic methods and researcher intuition. As the desire to perform high-throughput screening increases, it becomes challenging to use heuristics and intuition alone. In this paper, we demonstrate machine learning potentials can be leveraged to identify low energy adsorbate-surface configurations more accurately and efficiently. Our algorithm provides a spectrum of trade-offs between accuracy and efficiency, with one balanced option finding the lowest energy configuration, within a 0.1 eV threshold, 86.33% of the time, while achieving a 1331x speedup in computation. To standardize benchmarking, we introduce the Open Catalyst Dense dataset containing nearly 1,000 diverse surfaces and 85,658 unique configurations.

Recently, various methods have been proposed to address the inconsistency issue of DDIM inversion to enable image editing, such as EDICT [36] and Null-text inversion [22]. However, the above methods introduce considerable computational overhead. In this paper, we propose a new technique, named bi-directional integration approximation (BDIA), to perform exact diffusion inversion with neglible computational overhead. Suppose we would like to estimate the next diffusion state z_{i-1} at timestep t_i with the historical information (i,z_i) and (i+1,z_{i+1}). We first obtain the estimated Gaussian noise boldsymbol{epsilon}(z_i,i), and then apply the DDIM update procedure twice for approximating the ODE integration over the next time-slot [t_i, t_{i-1}] in the forward manner and the previous time-slot [t_i, t_{t+1}] in the backward manner. The DDIM step for the previous time-slot is used to refine the integration approximation made earlier when computing z_i. A nice property of BDIA-DDIM is that the update expression for z_{i-1} is a linear combination of (z_{i+1}, z_i, boldsymbol{epsilon}(z_i,i)). This allows for exact backward computation of z_{i+1} given (z_i, z_{i-1}), thus leading to exact diffusion inversion. It is demonstrated with experiments that (round-trip) BDIA-DDIM is particularly effective for image editing. Our experiments further show that BDIA-DDIM produces markedly better image sampling qualities than DDIM for text-to-image generation. BDIA can also be applied to improve the performance of other ODE solvers in addition to DDIM. In our work, it is found that applying BDIA to the EDM sampling procedure produces consistently better performance over four pre-trained models.

Neutron tagging in Gadolinium-doped water may play a significant role in reducing backgrounds from atmospheric neutrinos in next generation proton-decay searches using megaton-scale Water Cherenkov detectors. Similar techniques might also be useful in the detection of supernova neutrinos. Accurate determination of neutron tagging efficiencies will require a detailed understanding of the number of neutrons produced by neutrino interactions in water as a function of momentum transferred. We propose the Atmospheric Neutrino Neutron Interaction Experiment (ANNIE), designed to measure the neutron yield of atmospheric neutrino interactions in gadolinium-doped water. An innovative aspect of the ANNIE design is the use of precision timing to localize interaction vertices in the small fiducial volume of the detector. We propose to achieve this by using early production of LAPPDs (Large Area Picosecond Photodetectors). This experiment will be a first application of these devices demonstrating their feasibility for Water Cherenkov neutrino detectors.

Neutron tagging in Gadolinium-doped water may play a significant role in reducing backgrounds from atmospheric neutrinos in next generation proton-decay searches using megaton-scale Water Cherenkov detectors. Similar techniques might also be useful in the detection of supernova neutrinos. Accurate determination of neutron tagging efficiencies will require a detailed understanding of the number of neutrons produced by neutrino interactions in water as a function of momentum transferred. We propose the Atmospheric Neutrino Neutron Interaction Experiment (ANNIE), designed to measure the neutron yield of atmospheric neutrino interactions in gadolinium-doped water. An innovative aspect of the ANNIE design is the use of precision timing to localize interaction vertices in the small fiducial volume of the detector. We propose to achieve this by using early production of LAPPDs (Large Area Picosecond Photodetectors). This experiment will be a first application of these devices demonstrating their feasibility for Water Cherenkov neutrino detectors.

A great deal of effort has been devoted to reducing the risk of spurious scientific discoveries, from the use of sophisticated validation techniques, to deep statistical methods for controlling the false discovery rate in multiple hypothesis testing. However, there is a fundamental disconnect between the theoretical results and the practice of data analysis: the theory of statistical inference assumes a fixed collection of hypotheses to be tested, or learning algorithms to be applied, selected non-adaptively before the data are gathered, whereas in practice data is shared and reused with hypotheses and new analyses being generated on the basis of data exploration and the outcomes of previous analyses. In this work we initiate a principled study of how to guarantee the validity of statistical inference in adaptive data analysis. As an instance of this problem, we propose and investigate the question of estimating the expectations of m adaptively chosen functions on an unknown distribution given n random samples. We show that, surprisingly, there is a way to estimate an exponential in n number of expectations accurately even if the functions are chosen adaptively. This gives an exponential improvement over standard empirical estimators that are limited to a linear number of estimates. Our result follows from a general technique that counter-intuitively involves actively perturbing and coordinating the estimates, using techniques developed for privacy preservation. We give additional applications of this technique to our question.

Discrete diffusion models with absorbing processes have shown promise in language modeling. The key quantities to be estimated are the ratios between the marginal probabilities of two transitive states at all timesteps, called the concrete score. In this paper, we reveal that the concrete score in absorbing diffusion can be expressed as conditional probabilities of clean data, multiplied by a time-dependent scalar in an analytic form. Motivated by this finding, we propose reparameterized absorbing discrete diffusion (RADD), a dedicated diffusion model without time-condition that characterizes the time-independent conditional probabilities. Besides its simplicity, RADD can reduce the number of function evaluations (NFEs) by caching the output of the time-independent network when the noisy sample remains unchanged in a sampling interval. Empirically, RADD is up to 3.5 times faster while achieving similar performance with the strongest baseline. Built upon the new perspective of conditional distributions, we further unify absorbing discrete diffusion and any-order autoregressive models (AO-ARMs), showing that the upper bound on the negative log-likelihood for the diffusion model can be interpreted as an expected negative log-likelihood for AO-ARMs. Further, our RADD models achieve SOTA performance among diffusion models on 5 zero-shot language modeling benchmarks (measured by perplexity) at the GPT-2 scale. Our code is available at https://github.com/ML-GSAI/RADD.

Solar irradiance and its variations in the ultraviolet (UV) control the photochemistry in Earth's atmosphere and influence Earth's climate. The variability of Mg II h and k core-to-wing ratio, also known as the Mg II index, is highly correlated with the solar UV irradiance variability. Because of this, Mg II index is routinely used as a proxy for solar UV irradiance variability, which can help to get insights into the influence of solar UV irradiance variability on Earth's climate. Measurements of the Mg II index, however, have only been carried out since 1978 and do not cover the climate relevant timescales longer than a few decades. Here we present a model to calculate the Mg II index and its variability based on the well-established SATIRE (Spectral And Total Irradiance REconstruction) model. We demonstrate that our model calculations yield an excellent agreement with the observed Mg II index variations, both on the solar activity cycle and on the solar rotation timescales. Using this model, we synthesize Mg II index timeseries on climate relevant timescales of decades and longer. Here we present the timeseries of the Mg II index spanning nearly three centuries.

Introduction: Blood vessels can be non-invasively visualized from a digital fundus image (DFI). Several studies have shown an association between cardiovascular risk and vascular features obtained from DFI. Recent advances in computer vision and image segmentation enable automatising DFI blood vessel segmentation. There is a need for a resource that can automatically compute digital vasculature biomarkers (VBM) from these segmented DFI. Methods: In this paper, we introduce a Python Vasculature BioMarker toolbox, denoted PVBM. A total of 11 VBMs were implemented. In particular, we introduce new algorithmic methods to estimate tortuosity and branching angles. Using PVBM, and as a proof of usability, we analyze geometric vascular differences between glaucomatous patients and healthy controls. Results: We built a fully automated vasculature biomarker toolbox based on DFI segmentations and provided a proof of usability to characterize the vascular changes in glaucoma. For arterioles and venules, all biomarkers were significant and lower in glaucoma patients compared to healthy controls except for tortuosity, venular singularity length and venular branching angles. Conclusion: We have automated the computation of 11 VBMs from retinal blood vessel segmentation. The PVBM toolbox is made open source under a GNU GPL 3 license and is available on physiozoo.com (following publication).

Given the existence of various forward and inverse problems in combustion studies and applications that necessitate distinct methods for resolution, a framework to solve them in a unified way is critically needed. A promising approach is the integration of machine learning methods with governing equations of combustion systems, which exhibits superior generality and few-shot learning ability compared to purely data-driven methods. In this work, the FlamePINN-1D framework is proposed to solve the forward and inverse problems of 1D laminar flames based on physics-informed neural networks. Three cases with increasing complexity have been tested: Case 1 are freely-propagating premixed (FPP) flames with simplified physical models, while Case 2 and Case 3 are FPP and counterflow premixed (CFP) flames with detailed models, respectively. For forward problems, FlamePINN-1D aims to solve the flame fields and infer the unknown eigenvalues (such as laminar flame speeds) under the constraints of governing equations and boundary conditions. For inverse problems, FlamePINN-1D aims to reconstruct the continuous fields and infer the unknown parameters (such as transport and chemical kinetics parameters) from noisy sparse observations of the flame. Our results strongly validate these capabilities of FlamePINN-1D across various flames and working conditions. Compared to traditional methods, FlamePINN-1D is differentiable and mesh-free, exhibits no discretization errors, and is easier to implement for inverse problems. The inverse problem results also indicate the possibility of optimizing chemical mechanisms from measurements of laboratory 1D flames. Furthermore, some proposed strategies, such as hard constraints and thin-layer normalization, are proven to be essential for the robust learning of FlamePINN-1D. The code for this paper is partially available at https://github.com/CAME-THU/FlamePINN-1D.

In this paper we tackle the problem of generating conformers of a molecule in 3D space given its molecular graph. We parameterize these conformers as continuous functions that map elements from the molecular graph to points in 3D space. We then formulate the problem of learning to generate conformers as learning a distribution over these functions using a diffusion generative model, called Molecular Conformer Fields (MCF). Our approach is simple and scalable, and achieves state-of-the-art performance on challenging molecular conformer generation benchmarks while making no assumptions about the explicit structure of molecules (e.g. modeling torsional angles). MCF represents an advance in extending diffusion models to handle complex scientific problems in a conceptually simple, scalable and effective manner.

One straightforward metric to evaluate a survival prediction model is based on the Mean Absolute Error (MAE) -- the average of the absolute difference between the time predicted by the model and the true event time, over all subjects. Unfortunately, this is challenging because, in practice, the test set includes (right) censored individuals, meaning we do not know when a censored individual actually experienced the event. In this paper, we explore various metrics to estimate MAE for survival datasets that include (many) censored individuals. Moreover, we introduce a novel and effective approach for generating realistic semi-synthetic survival datasets to facilitate the evaluation of metrics. Our findings, based on the analysis of the semi-synthetic datasets, reveal that our proposed metric (MAE using pseudo-observations) is able to rank models accurately based on their performance, and often closely matches the true MAE -- in particular, is better than several alternative methods.

Approximate inference in Gaussian process (GP) models with non-conjugate likelihoods gets entangled with the learning of the model hyperparameters. We improve hyperparameter learning in GP models and focus on the interplay between variational inference (VI) and the learning target. While VI's lower bound to the marginal likelihood is a suitable objective for inferring the approximate posterior, we show that a direct approximation of the marginal likelihood as in Expectation Propagation (EP) is a better learning objective for hyperparameter optimization. We design a hybrid training procedure to bring the best of both worlds: it leverages conjugate-computation VI for inference and uses an EP-like marginal likelihood approximation for hyperparameter learning. We compare VI, EP, Laplace approximation, and our proposed training procedure and empirically demonstrate the effectiveness of our proposal across a wide range of data sets.

Finding the mode of a high dimensional probability distribution D is a fundamental algorithmic problem in statistics and data analysis. There has been particular interest in efficient methods for solving the problem when D is represented as a mixture model or kernel density estimate, although few algorithmic results with worst-case approximation and runtime guarantees are known. In this work, we significantly generalize a result of (LeeLiMusco:2021) on mode approximation for Gaussian mixture models. We develop randomized dimensionality reduction methods for mixtures involving a broader class of kernels, including the popular logistic, sigmoid, and generalized Gaussian kernels. As in Lee et al.'s work, our dimensionality reduction results yield quasi-polynomial algorithms for mode finding with multiplicative accuracy (1-epsilon) for any epsilon > 0. Moreover, when combined with gradient descent, they yield efficient practical heuristics for the problem. In addition to our positive results, we prove a hardness result for box kernels, showing that there is no polynomial time algorithm for finding the mode of a kernel density estimate, unless P = NP. Obtaining similar hardness results for kernels used in practice (like Gaussian or logistic kernels) is an interesting future direction.