Daily Papers

This work studies the generalization issue of face anti-spoofing (FAS) models on domain gaps, such as image resolution, blurriness and sensor variations. Most prior works regard domain-specific signals as a negative impact, and apply metric learning or adversarial losses to remove them from feature representation. Though learning a domain-invariant feature space is viable for the training data, we show that the feature shift still exists in an unseen test domain, which backfires on the generalizability of the classifier. In this work, instead of constructing a domain-invariant feature space, we encourage domain separability while aligning the live-to-spoof transition (i.e., the trajectory from live to spoof) to be the same for all domains. We formulate this FAS strategy of separability and alignment (SA-FAS) as a problem of invariant risk minimization (IRM), and learn domain-variant feature representation but domain-invariant classifier. We demonstrate the effectiveness of SA-FAS on challenging cross-domain FAS datasets and establish state-of-the-art performance.

Direct Alignment Algorithms (DAAs) simplify language model alignment by replacing reinforcement learning (RL) and reward modeling (RM) in Reinforcement Learning from Human Feedback (RLHF) with direct policy optimization. DAAs can be classified by their ranking losses (pairwise vs. pointwise), by the rewards used in those losses (e.g., likelihood ratios of policy and reference policy, or odds ratios), or by whether a Supervised Fine-Tuning (SFT) phase is required (two-stage vs. one-stage). We first show that one-stage methods underperform two-stage methods. To address this, we incorporate an explicit SFT phase and introduce the beta parameter, controlling the strength of preference optimization, into single-stage ORPO and ASFT. These modifications improve their performance in Alpaca Eval 2 by +3.46 (ORPO) and +8.27 (ASFT), matching two-stage methods like DPO. Further analysis reveals that the key factor is whether the approach uses pairwise or pointwise objectives, rather than the specific implicit reward or loss function. These results highlight the importance of careful evaluation to avoid premature claims of performance gains or overall superiority in alignment algorithms.

We introduce Baichuan Alignment, a detailed analysis of the alignment techniques employed in the Baichuan series of models. This represents the industry's first comprehensive account of alignment methodologies, offering valuable insights for advancing AI research. We investigate the critical components that enhance model performance during the alignment process, including optimization methods, data strategies, capability enhancements, and evaluation processes. The process spans three key stages: Prompt Augmentation System (PAS), Supervised Fine-Tuning (SFT), and Preference Alignment. The problems encountered, the solutions applied, and the improvements made are thoroughly recorded. Through comparisons across well-established benchmarks, we highlight the technological advancements enabled by Baichuan Alignment. Baichuan-Instruct is an internal model, while Qwen2-Nova-72B and Llama3-PBM-Nova-70B are instruct versions of the Qwen2-72B and Llama-3-70B base models, optimized through Baichuan Alignment. Baichuan-Instruct demonstrates significant improvements in core capabilities, with user experience gains ranging from 17% to 28%, and performs exceptionally well on specialized benchmarks. In open-source benchmark evaluations, both Qwen2-Nova-72B and Llama3-PBM-Nova-70B consistently outperform their respective official instruct versions across nearly all datasets. This report aims to clarify the key technologies behind the alignment process, fostering a deeper understanding within the community. Llama3-PBM-Nova-70B model is available at https://huggingface.co/PKU-Baichuan-MLSystemLab/Llama3-PBM-Nova-70B.

In the evolving landscape of computer vision, foundation models have emerged as pivotal tools, exhibiting exceptional adaptability to a myriad of tasks. Among these, the Segment Anything Model (SAM) by Meta AI has distinguished itself in image segmentation. However, SAM, like its counterparts, encounters limitations in specific niche applications, prompting a quest for enhancement strategies that do not compromise its inherent capabilities. This paper introduces ASAM, a novel methodology that amplifies SAM's performance through adversarial tuning. We harness the potential of natural adversarial examples, inspired by their successful implementation in natural language processing. By utilizing a stable diffusion model, we augment a subset (1%) of the SA-1B dataset, generating adversarial instances that are more representative of natural variations rather than conventional imperceptible perturbations. Our approach maintains the photorealism of adversarial examples and ensures alignment with original mask annotations, thereby preserving the integrity of the segmentation task. The fine-tuned ASAM demonstrates significant improvements across a diverse range of segmentation tasks without necessitating additional data or architectural modifications. The results of our extensive evaluations confirm that ASAM establishes new benchmarks in segmentation tasks, thereby contributing to the advancement of foundational models in computer vision. Our project page is in https://asam2024.github.io/.

This paper proposes an unsupervised method that leverages topological characteristics of data manifolds to estimate class separability of the data without requiring labels. Experiments conducted in this paper on several datasets demonstrate a clear correlation and consistency between the class separability estimated by the proposed method with supervised metrics like Fisher Discriminant Ratio~(FDR) and cross-validation of a classifier, which both require labels. This can enable implementing learning paradigms aimed at learning from both labeled and unlabeled data, like semi-supervised and transductive learning. This would be particularly useful when we have limited labeled data and a relatively large unlabeled dataset that can be used to enhance the learning process. The proposed method is implemented for language model fine-tuning with automated stopping criterion by monitoring class separability of the embedding-space manifold in an unsupervised setting. The proposed methodology has been first validated on synthetic data, where the results show a clear consistency between class separability estimated by the proposed method and class separability computed by FDR. The method has been also implemented on both public and internal data. The results show that the proposed method can effectively aid -- without the need for labels -- a decision on when to stop or continue the fine-tuning of a language model and which fine-tuning iteration is expected to achieve a maximum classification performance through quantification of the class separability of the embedding manifold.

As Facial Recognition System(FRS) is widely applied in areas such as access control and mobile payments due to its convenience and high accuracy. The security of facial recognition is also highly regarded. The Face anti-spoofing system(FAS) for face recognition is an important component used to enhance the security of face recognition systems. Traditional FAS used images containing identity information to detect spoofing traces, however there is a risk of privacy leakage during the transmission and storage of these images. Besides, the encryption and decryption of these privacy-sensitive data takes too long compared to inference time by FAS model. To address the above issues, we propose a face anti-spoofing algorithm based on facial skin patches leveraging pure facial skin patch images as input, which contain no privacy information, no encryption or decryption is needed for these images. We conduct experiments on several public datasets, the results prove that our algorithm has demonstrated superiority in both accuracy and speed.

Segment anything model (SAM) is a prompt-guided vision foundation model for cutting out the object of interest from its background. Since Meta research team released the SA project, SAM has attracted significant attention due to its impressive zero-shot transfer performance and high versatility of being compatible with other models for advanced vision applications like image editing with fine-grained control. Many of such use cases need to be run on resource-constraint edge devices, like mobile Apps. In this work, we aim to make SAM mobile-friendly by replacing the heavyweight image encoder with a lightweight one. A naive way to train such a new SAM as in the original SAM paper leads to unsatisfactory performance, especially when limited training sources are available. We find that this is mainly caused by the coupled optimization of the image encoder and mask decoder, motivated by which we propose decoupled distillation. Concretely, we distill the knowledge from the image encoder ViT-H in the original SAM to a lightweight image encoder, which can be automatically compatible with the mask decoder in the original SAM. The training can be completed on a single GPU within less than one day, and the resulting lightweight SAM is termed MobileSAM which is more than 60 times smaller yet performs on par with the original SAM. For inference speed, MobileSAM runs around 10ms per image: 8ms on the image encoder and 2ms on the mask decoder. With superior performance and a higher versatility, our MobileSAM is 7 times smaller and 4 times faster than the concurrent FastSAM, making it more suitable for mobile applications. The code for MobileSAM project is provided at https://github.com/ChaoningZhang/MobileSAM

Reinforcement Learning with Human Feedback (RLHF) and its variants have made huge strides toward the effective alignment of large language models (LLMs) to follow instructions and reflect human values. More recently, Direct Alignment Algorithms (DAAs) have emerged in which the reward modeling stage of RLHF is skipped by characterizing the reward directly as a function of the policy being learned. Examples include Direct Preference Optimization (DPO) and Simple Preference Optimization (SimPO). These methods often suffer from likelihood displacement, a phenomenon by which the probabilities of preferred responses are often reduced undesirably. In this paper, we argue that, for DAAs the reward (function) shape matters. We introduce AlphaPO, a new DAA method that leverages an alpha-parameter to help change the shape of the reward function beyond the standard log reward. AlphaPO helps maintain fine-grained control over likelihood displacement and over-optimization. Compared to SimPO, one of the best performing DAAs, AlphaPO leads to about 7\% to 10\% relative improvement in alignment performance for the instruct versions of Mistral-7B and Llama3-8B. The analysis and results presented highlight the importance of the reward shape, and how one can systematically change it to affect training dynamics, as well as improve alignment performance.

We present a novel unified bilevel optimization-based framework, PARL, formulated to address the recently highlighted critical issue of policy alignment in reinforcement learning using utility or preference-based feedback. We identify a major gap within current algorithmic designs for solving policy alignment due to a lack of precise characterization of the dependence of the alignment objective on the data generated by policy trajectories. This shortfall contributes to the sub-optimal performance observed in contemporary algorithms. Our framework addressed these concerns by explicitly parameterizing the distribution of the upper alignment objective (reward design) by the lower optimal variable (optimal policy for the designed reward). Interestingly, from an optimization perspective, our formulation leads to a new class of stochastic bilevel problems where the stochasticity at the upper objective depends upon the lower-level variable. To demonstrate the efficacy of our formulation in resolving alignment issues in RL, we devised an algorithm named A-PARL to solve PARL problem, establishing sample complexity bounds of order O(1/T). Our empirical results substantiate that the proposed PARL can address the alignment concerns in RL by showing significant improvements (up to 63\% in terms of required samples) for policy alignment in large-scale environments of the Deepmind control suite and Meta world tasks.

Sparse autoencoders (SAEs) are a promising approach to extracting features from neural networks, enabling model interpretability as well as causal interventions on model internals. SAEs generate sparse feature representations using a sparsifying activation function that implicitly defines a set of token-feature matches. We frame the token-feature matching as a resource allocation problem constrained by a total sparsity upper bound. For example, TopK SAEs solve this allocation problem with the additional constraint that each token matches with at most k features. In TopK SAEs, the k active features per token constraint is the same across tokens, despite some tokens being more difficult to reconstruct than others. To address this limitation, we propose two novel SAE variants, Feature Choice SAEs and Mutual Choice SAEs, which each allow for a variable number of active features per token. Feature Choice SAEs solve the sparsity allocation problem under the additional constraint that each feature matches with at most m tokens. Mutual Choice SAEs solve the unrestricted allocation problem where the total sparsity budget can be allocated freely between tokens and features. Additionally, we introduce a new auxiliary loss function, aux_zipf_loss, which generalises the aux_k_loss to mitigate dead and underutilised features. Our methods result in SAEs with fewer dead features and improved reconstruction loss at equivalent sparsity levels as a result of the inherent adaptive computation. More accurate and scalable feature extraction methods provide a path towards better understanding and more precise control of foundation models.

We present a new table structure recognition (TSR) approach, called TSRFormer, to robustly recognizing the structures of complex tables with geometrical distortions from various table images. Unlike previous methods, we formulate table separation line prediction as a line regression problem instead of an image segmentation problem and propose a new two-stage DETR based separator prediction approach, dubbed Separator REgression TRansformer (SepRETR), to predict separation lines from table images directly. To make the two-stage DETR framework work efficiently and effectively for the separation line prediction task, we propose two improvements: 1) A prior-enhanced matching strategy to solve the slow convergence issue of DETR; 2) A new cross attention module to sample features from a high-resolution convolutional feature map directly so that high localization accuracy is achieved with low computational cost. After separation line prediction, a simple relation network based cell merging module is used to recover spanning cells. With these new techniques, our TSRFormer achieves state-of-the-art performance on several benchmark datasets, including SciTSR, PubTabNet and WTW. Furthermore, we have validated the robustness of our approach to tables with complex structures, borderless cells, large blank spaces, empty or spanning cells as well as distorted or even curved shapes on a more challenging real-world in-house dataset.

In the field of antibody engineering, an essential task is to design a novel antibody whose paratopes bind to a specific antigen with correct epitopes. Understanding antibody structure and its paratope can facilitate a mechanistic understanding of its function. Therefore, antibody structure prediction from its sequence alone has always been a highly valuable problem for de novo antibody design. AlphaFold2, a breakthrough in the field of structural biology, provides a solution to predict protein structure based on protein sequences and computationally expensive coevolutionary multiple sequence alignments (MSAs). However, the computational efficiency and undesirable prediction accuracy of antibodies, especially on the complementarity-determining regions (CDRs) of antibodies limit their applications in the industrially high-throughput drug design. To learn an informative representation of antibodies, we employed a deep antibody language model (ALM) on curated sequences from the observed antibody space database via a transformer model. We also developed a novel model named xTrimoABFold to predict antibody structure from antibody sequence based on the pretrained ALM as well as efficient evoformers and structural modules. The model was trained end-to-end on the antibody structures in PDB by minimizing the ensemble loss of domain-specific focal loss on CDR and the frame-aligned point loss. xTrimoABFold outperforms AlphaFold2 and other protein language model based SOTAs, e.g., OmegaFold, HelixFold-Single, and IgFold with a large significant margin (30+\% improvement on RMSD) while performing 151 times faster than AlphaFold2. To the best of our knowledge, xTrimoABFold achieved state-of-the-art antibody structure prediction. Its improvement in both accuracy and efficiency makes it a valuable tool for de novo antibody design and could make further improvements in immuno-theory.

Despite substantial advances, single-image super-resolution (SISR) is always in a dilemma to reconstruct high-quality images with limited information from one input image, especially in realistic scenarios. In this paper, we establish a large-scale real-world burst super-resolution dataset, i.e., RealBSR, to explore the faithful reconstruction of image details from multiple frames. Furthermore, we introduce a Federated Burst Affinity network (FBAnet) to investigate non-trivial pixel-wise displacements among images under real-world image degradation. Specifically, rather than using pixel-wise alignment, our FBAnet employs a simple homography alignment from a structural geometry aspect and a Federated Affinity Fusion (FAF) strategy to aggregate the complementary information among frames. Those fused informative representations are fed to a Transformer-based module of burst representation decoding. Besides, we have conducted extensive experiments on two versions of our datasets, i.e., RealBSR-RAW and RealBSR-RGB. Experimental results demonstrate that our FBAnet outperforms existing state-of-the-art burst SR methods and also achieves visually-pleasant SR image predictions with model details. Our dataset, codes, and models are publicly available at https://github.com/yjsunnn/FBANet.

Population-based search has recently emerged as a possible alternative to Reinforcement Learning (RL) for black-box neural architecture search (NAS). It performs well in practice even though it is not theoretically well understood. In particular, whereas traditional population-based search methods such as evolutionary algorithms (EAs) draw much power from crossover operations, it is difficult to take advantage of them in NAS. The main obstacle is believed to be the permutation problem: The mapping between genotype and phenotype in traditional graph representations is many-to-one, leading to a disruptive effect of standard crossover. This paper presents the first theoretical analysis of the behaviors of mutation, crossover and RL in black-box NAS, and proposes a new crossover operator based on the shortest edit path (SEP) in graph space. The SEP crossover is shown theoretically to overcome the permutation problem, and as a result, have a better expected improvement compared to mutation, standard crossover and RL. Further, it empirically outperform these other methods on state-of-the-art NAS benchmarks. The SEP crossover therefore allows taking full advantage of population-based search in NAS, and the underlying theory can serve as a foundation for deeper understanding of black-box NAS methods in general.

Recent years have witnessed a surge in the development of protein foundation models, significantly improving performance in protein prediction and generative tasks ranging from 3D structure prediction and protein design to conformational dynamics. However, the capabilities and limitations associated with these models remain poorly understood due to the absence of a unified evaluation framework. To fill this gap, we introduce ProteinBench, a holistic evaluation framework designed to enhance the transparency of protein foundation models. Our approach consists of three key components: (i) A taxonomic classification of tasks that broadly encompass the main challenges in the protein domain, based on the relationships between different protein modalities; (ii) A multi-metric evaluation approach that assesses performance across four key dimensions: quality, novelty, diversity, and robustness; and (iii) In-depth analyses from various user objectives, providing a holistic view of model performance. Our comprehensive evaluation of protein foundation models reveals several key findings that shed light on their current capabilities and limitations. To promote transparency and facilitate further research, we release the evaluation dataset, code, and a public leaderboard publicly for further analysis and a general modular toolkit. We intend for ProteinBench to be a living benchmark for establishing a standardized, in-depth evaluation framework for protein foundation models, driving their development and application while fostering collaboration within the field.

The Segmentation Anything Model (SAM) requires labor-intensive data labeling. We present Unsupervised SAM (UnSAM) for promptable and automatic whole-image segmentation that does not require human annotations. UnSAM utilizes a divide-and-conquer strategy to "discover" the hierarchical structure of visual scenes. We first leverage top-down clustering methods to partition an unlabeled image into instance/semantic level segments. For all pixels within a segment, a bottom-up clustering method is employed to iteratively merge them into larger groups, thereby forming a hierarchical structure. These unsupervised multi-granular masks are then utilized to supervise model training. Evaluated across seven popular datasets, UnSAM achieves competitive results with the supervised counterpart SAM, and surpasses the previous state-of-the-art in unsupervised segmentation by 11% in terms of AR. Moreover, we show that supervised SAM can also benefit from our self-supervised labels. By integrating our unsupervised pseudo masks into SA-1B's ground-truth masks and training UnSAM with only 1% of SA-1B, a lightly semi-supervised UnSAM can often segment entities overlooked by supervised SAM, exceeding SAM's AR by over 6.7% and AP by 3.9% on SA-1B.

Protein design, a grand challenge of the day, involves optimization on a fitness landscape, and leading methods adopt a model-based approach where a model is trained on a training set (protein sequences and fitness) and proposes candidates to explore next. These methods are challenged by sparsity of high-fitness samples in the training set, a problem that has been in the literature. A less recognized but equally important problem stems from the distribution of training samples in the design space: leading methods are not designed for scenarios where the desired optimum is in a region that is not only poorly represented in training data, but also relatively far from the highly represented low-fitness regions. We show that this problem of "separation" in the design space is a significant bottleneck in existing model-based optimization tools and propose a new approach that uses a novel VAE as its search model to overcome the problem. We demonstrate its advantage over prior methods in robustly finding improved samples, regardless of the imbalance and separation between low- and high-fitness training samples. Our comprehensive benchmark on real and semi-synthetic protein datasets as well as solution design for physics-informed neural networks, showcases the generality of our approach in discrete and continuous design spaces. Our implementation is available at https://github.com/sabagh1994/PGVAE.

Existing zero-shot skeleton-based action recognition methods utilize projection networks to learn a shared latent space of skeleton features and semantic embeddings. The inherent imbalance in action recognition datasets, characterized by variable skeleton sequences yet constant class labels, presents significant challenges for alignment. To address the imbalance, we propose SA-DVAE -- Semantic Alignment via Disentangled Variational Autoencoders, a method that first adopts feature disentanglement to separate skeleton features into two independent parts -- one is semantic-related and another is irrelevant -- to better align skeleton and semantic features. We implement this idea via a pair of modality-specific variational autoencoders coupled with a total correction penalty. We conduct experiments on three benchmark datasets: NTU RGB+D, NTU RGB+D 120 and PKU-MMD, and our experimental results show that SA-DAVE produces improved performance over existing methods. The code is available at https://github.com/pha123661/SA-DVAE.

Consistency and reliability are crucial for conducting AI research. Many famous research fields, such as object detection, have been compared and validated with solid benchmark frameworks. After AlphaFold2, the protein folding task has entered a new phase, and many methods are proposed based on the component of AlphaFold2. The importance of a unified research framework in protein folding contains implementations and benchmarks to consistently and fairly compare various approaches. To achieve this, we present Solvent, an protein folding framework that supports significant components of state-of-th-arts models in the manner of off-the-shelf interface Solvent contains different models implemented in a unified codebase and supports training and evaluation for defined models on the same dataset. We benchmark well-known algorithms and their components and provide experiments that give helpful insights into the protein structure modeling field. We hope that Solvent will increase the reliability and consistency of proposed models and gives efficiency in both speed and costs, resulting in acceleration on protein folding modeling research. The code is available at https://github.com/kakaobrain/solvent, and the project will continue to be developed.

Image-text matching plays a critical role in bridging the vision and language, and great progress has been made by exploiting the global alignment between image and sentence, or local alignments between regions and words. However, how to make the most of these alignments to infer more accurate matching scores is still underexplored. In this paper, we propose a novel Similarity Graph Reasoning and Attention Filtration (SGRAF) network for image-text matching. Specifically, the vector-based similarity representations are firstly learned to characterize the local and global alignments in a more comprehensive manner, and then the Similarity Graph Reasoning (SGR) module relying on one graph convolutional neural network is introduced to infer relation-aware similarities with both the local and global alignments. The Similarity Attention Filtration (SAF) module is further developed to integrate these alignments effectively by selectively attending on the significant and representative alignments and meanwhile casting aside the interferences of non-meaningful alignments. We demonstrate the superiority of the proposed method with achieving state-of-the-art performances on the Flickr30K and MSCOCO datasets, and the good interpretability of SGR and SAF modules with extensive qualitative experiments and analyses.

Decompilation transforms compiled code back into a high-level programming language for analysis when source code is unavailable. Previous work has primarily focused on enhancing decompilation performance by increasing the scale of model parameters or training data for pre-training. Based on the characteristics of the decompilation task, we propose two methods: (1) Without fine-tuning, the Self-Constructed Context Decompilation (sc^2dec) method recompiles the LLM's decompilation results to construct pairs for in-context learning, helping the model improve decompilation performance. (2) Fine-grained Alignment Enhancement (FAE), which meticulously aligns assembly code with source code at the statement level by leveraging debugging information, is employed during the fine-tuning phase to achieve further improvements in decompilation. By integrating these two methods, we achieved a Re-Executability performance improvement of approximately 7.35\% on the Decompile-Eval benchmark, establishing a new state-of-the-art performance of 55.03\%.

Alignment is the most critical step in building large language models (LLMs) that meet human needs. With the rapid development of LLMs gradually surpassing human capabilities, traditional alignment methods based on human-annotation are increasingly unable to meet the scalability demands. Therefore, there is an urgent need to explore new sources of automated alignment signals and technical approaches. In this paper, we systematically review the recently emerging methods of automated alignment, attempting to explore how to achieve effective, scalable, automated alignment once the capabilities of LLMs exceed those of humans. Specifically, we categorize existing automated alignment methods into 4 major categories based on the sources of alignment signals and discuss the current status and potential development of each category. Additionally, we explore the underlying mechanisms that enable automated alignment and discuss the essential factors that make automated alignment technologies feasible and effective from the fundamental role of alignment.

Multiple Sequence Alignment (MSA) plays a pivotal role in unveiling the evolutionary trajectories of protein families. The accuracy of protein structure predictions is often compromised for protein sequences that lack sufficient homologous information to construct high quality MSA. Although various methods have been proposed to generate virtual MSA under these conditions, they fall short in comprehensively capturing the intricate coevolutionary patterns within MSA or require guidance from external oracle models. Here we introduce MSAGPT, a novel approach to prompt protein structure predictions via MSA generative pretraining in the low MSA regime. MSAGPT employs a simple yet effective 2D evolutionary positional encoding scheme to model complex evolutionary patterns. Endowed by this, its flexible 1D MSA decoding framework facilitates zero or few shot learning. Moreover, we demonstrate that leveraging the feedback from AlphaFold2 can further enhance the model capacity via Rejective Fine tuning (RFT) and Reinforcement Learning from AF2 Feedback (RLAF). Extensive experiments confirm the efficacy of MSAGPT in generating faithful virtual MSA to enhance the structure prediction accuracy. The transfer learning capabilities also highlight its great potential for facilitating other protein tasks.

Cryo-electron microscopy (cryo-EM) is a technique for reconstructing the 3-dimensional (3D) structure of biomolecules (especially large protein complexes and molecular assemblies). As the resolution increases to the near-atomic scale, building protein structures de novo from cryo-EM maps becomes possible. Recently, recognition-based de novo building methods have shown the potential to streamline this process. However, it cannot build a complete structure due to the low signal-to-noise ratio (SNR) problem. At the same time, AlphaFold has led to a great breakthrough in predicting protein structures. This has inspired us to combine fragment recognition and structure prediction methods to build a complete structure. In this paper, we propose a new method named FFF that bridges protein structure prediction and protein structure recognition with flexible fitting. First, a multi-level recognition network is used to capture various structural features from the input 3D cryo-EM map. Next, protein structural fragments are generated using pseudo peptide vectors and a protein sequence alignment method based on these extracted features. Finally, a complete structural model is constructed using the predicted protein fragments via flexible fitting. Based on our benchmark tests, FFF outperforms the baseline methods for building complete protein structures.

The recent advancements in large language models (LLMs) and pre-trained vision models have accelerated the development of vision-language large models (VLLMs), enhancing the interaction between visual and linguistic modalities. Despite their notable success across various domains, VLLMs face challenges in modality alignment, which can lead to issues like hallucinations and unsafe content generation. Current alignment techniques often rely on coarse feedback and external datasets, limiting scalability and performance. In this paper, we propose FiSAO (Fine-Grained Self-Alignment Optimization), a novel self-alignment method that utilizes the model's own visual encoder as a fine-grained verifier to improve vision-language alignment without the need for additional data. By leveraging token-level feedback from the vision encoder, FiSAO significantly improves vision-language alignment, even surpassing traditional preference tuning methods that require additional data. Through both theoretical analysis and experimental validation, we demonstrate that FiSAO effectively addresses the misalignment problem in VLLMs, marking the first instance of token-level rewards being applied to such models.

Misalignment between model predictions and intended usage can be detrimental for the deployment of computer vision models. The issue is exacerbated when the task involves complex structured outputs, as it becomes harder to design procedures which address this misalignment. In natural language processing, this is often addressed using reinforcement learning techniques that align models with a task reward. We adopt this approach and show its surprising effectiveness across multiple computer vision tasks, such as object detection, panoptic segmentation, colorization and image captioning. We believe this approach has the potential to be widely useful for better aligning models with a diverse range of computer vision tasks.

This work introduces a new framework, ProtoSAM, for one-shot medical image segmentation. It combines the use of prototypical networks, known for few-shot segmentation, with SAM - a natural image foundation model. The method proposed creates an initial coarse segmentation mask using the ALPnet prototypical network, augmented with a DINOv2 encoder. Following the extraction of an initial mask, prompts are extracted, such as points and bounding boxes, which are then input into the Segment Anything Model (SAM). State-of-the-art results are shown on several medical image datasets and demonstrate automated segmentation capabilities using a single image example (one shot) with no need for fine-tuning of the foundation model. Our code is available at: https://github.com/levayz/ProtoSAM

Large-scale Protein Language Models (PLMs) have improved performance in protein prediction tasks, ranging from 3D structure prediction to various function predictions. In particular, AlphaFold, a ground-breaking AI system, could potentially reshape structural biology. However, the utility of the PLM module in AlphaFold, Evoformer, has not been explored beyond structure prediction. In this paper, we investigate the representation ability of three popular PLMs: ESM-1b (single sequence), MSA-Transformer (multiple sequence alignment) and Evoformer (structural), with a special focus on Evoformer. Specifically, we aim to answer the following key questions: (i) Does the Evoformer trained as part of AlphaFold produce representations amenable to predicting protein function? (ii) If yes, can Evoformer replace ESM-1b and MSA-Transformer? (ii) How much do these PLMs rely on evolution-related protein data? In this regard, are they complementary to each other? We compare these models by empirical study along with new insights and conclusions. All code and datasets for reproducibility are available at https://github.com/elttaes/Revisiting-PLMs.

The emergence of Vision Language Models (VLMs) has brought unprecedented advances in understanding multimodal information. The combination of textual and visual semantics in VLMs is highly complex and diverse, making the safety alignment of these models challenging. Furthermore, due to the limited study on the safety alignment of VLMs, there is a lack of large-scale, high-quality datasets. To address these limitations, we propose a Safety Preference Alignment dataset for Vision Language Models named SPA-VL. In terms of breadth, SPA-VL covers 6 harmfulness domains, 13 categories, and 53 subcategories, and contains 100,788 samples of the quadruple (question, image, chosen response, rejected response). In terms of depth, the responses are collected from 12 open- (e.g., QwenVL) and closed-source (e.g., Gemini) VLMs to ensure diversity. The experimental results indicate that models trained with alignment techniques on the SPA-VL dataset exhibit substantial improvements in harmlessness and helpfulness while maintaining core capabilities. SPA-VL, as a large-scale, high-quality, and diverse dataset, represents a significant milestone in ensuring that VLMs achieve both harmlessness and helpfulness. We have made our code https://github.com/EchoseChen/SPA-VL-RLHF and SPA-VL dataset url https://huggingface.co/datasets/sqrti/SPA-VL publicly available.

Recently, State Space Models (SSMs), with Mamba as a prime example, have shown great promise for long-range dependency modeling with linear complexity. Then, Vision Mamba and the subsequent architectures are presented successively, and they perform well on visual tasks. The crucial step of applying Mamba to visual tasks is to construct 2D visual features in sequential manners. To effectively organize and construct visual features within the 2D image space through 1D selective scan, we propose a novel Multi-Head Scan (MHS) module. The embeddings extracted from the preceding layer are projected into multiple lower-dimensional subspaces. Subsequently, within each subspace, the selective scan is performed along distinct scan routes. The resulting sub-embeddings, obtained from the multi-head scan process, are then integrated and ultimately projected back into the high-dimensional space. Moreover, we incorporate a Scan Route Attention (SRA) mechanism to enhance the module's capability to discern complex structures. To validate the efficacy of our module, we exclusively substitute the 2D-Selective-Scan (SS2D) block in VM-UNet with our proposed module, and we train our models from scratch without using any pre-trained weights. The results indicate a significant improvement in performance while reducing the parameters of the original VM-UNet. The code for this study is publicly available at https://github.com/PixDeep/MHS-VM.

Understanding and mitigating the potential risks associated with foundation models (FMs) hinges on developing effective interpretability methods. Sparse Autoencoders (SAEs) have emerged as a promising tool for disentangling FM representations, but they struggle to capture rare, yet crucial concepts in the data. We introduce Specialized Sparse Autoencoders (SSAEs), designed to illuminate these elusive dark matter features by focusing on specific subdomains. We present a practical recipe for training SSAEs, demonstrating the efficacy of dense retrieval for data selection and the benefits of Tilted Empirical Risk Minimization as a training objective to improve concept recall. Our evaluation of SSAEs on standard metrics, such as downstream perplexity and L_0 sparsity, show that they effectively capture subdomain tail concepts, exceeding the capabilities of general-purpose SAEs. We showcase the practical utility of SSAEs in a case study on the Bias in Bios dataset, where SSAEs achieve a 12.5\% increase in worst-group classification accuracy when applied to remove spurious gender information. SSAEs provide a powerful new lens for peering into the inner workings of FMs in subdomains.

Vector databases manage large collections of embedding vectors. As AI applications are growing rapidly, so are the number of embeddings that need to be stored and indexed. The Faiss library is dedicated to vector similarity search, a core functionality of vector databases. Faiss is a toolkit of indexing methods and related primitives used to search, cluster, compress and transform vectors. This paper first describes the tradeoff space of vector search, then the design principles of Faiss in terms of structure, approach to optimization and interfacing. We benchmark key features of the library and discuss a few selected applications to highlight its broad applicability.

Modern alignment techniques based on human preferences, such as RLHF and DPO, typically employ divergence regularization relative to the reference model to ensure training stability. However, this often limits the flexibility of models during alignment, especially when there is a clear distributional discrepancy between the preference data and the reference model. In this paper, we focus on the alignment of recent text-to-image diffusion models, such as Stable Diffusion XL (SDXL), and find that this "reference mismatch" is indeed a significant problem in aligning these models due to the unstructured nature of visual modalities: e.g., a preference for a particular stylistic aspect can easily induce such a discrepancy. Motivated by this observation, we propose a novel and memory-friendly preference alignment method for diffusion models that does not depend on any reference model, coined margin-aware preference optimization (MaPO). MaPO jointly maximizes the likelihood margin between the preferred and dispreferred image sets and the likelihood of the preferred sets, simultaneously learning general stylistic features and preferences. For evaluation, we introduce two new pairwise preference datasets, which comprise self-generated image pairs from SDXL, Pick-Style and Pick-Safety, simulating diverse scenarios of reference mismatch. Our experiments validate that MaPO can significantly improve alignment on Pick-Style and Pick-Safety and general preference alignment when used with Pick-a-Pic v2, surpassing the base SDXL and other existing methods. Our code, models, and datasets are publicly available via https://mapo-t2i.github.io

Visual clustering is a common perceptual task in scatterplots that supports diverse analytics tasks (e.g., cluster identification). However, even with the same scatterplot, the ways of perceiving clusters (i.e., conducting visual clustering) can differ due to the differences among individuals and ambiguous cluster boundaries. Although such perceptual variability casts doubt on the reliability of data analysis based on visual clustering, we lack a systematic way to efficiently assess this variability. In this research, we study perceptual variability in conducting visual clustering, which we call Cluster Ambiguity. To this end, we introduce CLAMS, a data-driven visual quality measure for automatically predicting cluster ambiguity in monochrome scatterplots. We first conduct a qualitative study to identify key factors that affect the visual separation of clusters (e.g., proximity or size difference between clusters). Based on study findings, we deploy a regression module that estimates the human-judged separability of two clusters. Then, CLAMS predicts cluster ambiguity by analyzing the aggregated results of all pairwise separability between clusters that are generated by the module. CLAMS outperforms widely-used clustering techniques in predicting ground truth cluster ambiguity. Meanwhile, CLAMS exhibits performance on par with human annotators. We conclude our work by presenting two applications for optimizing and benchmarking data mining techniques using CLAMS. The interactive demo of CLAMS is available at clusterambiguity.dev.

We propose AffineGlue, a method for joint two-view feature matching and robust estimation that reduces the combinatorial complexity of the problem by employing single-point minimal solvers. AffineGlue selects potential matches from one-to-many correspondences to estimate minimal models. Guided matching is then used to find matches consistent with the model, suffering less from the ambiguities of one-to-one matches. Moreover, we derive a new minimal solver for homography estimation, requiring only a single affine correspondence (AC) and a gravity prior. Furthermore, we train a neural network to reject ACs that are unlikely to lead to a good model. AffineGlue is superior to the SOTA on real-world datasets, even when assuming that the gravity direction points downwards. On PhotoTourism, the AUC@10{\deg} score is improved by 6.6 points compared to the SOTA. On ScanNet, AffineGlue makes SuperPoint and SuperGlue achieve similar accuracy as the detector-free LoFTR.

Recent AI advances have enabled multi-modal systems to model and translate diverse information spaces. Extending beyond text and vision, we introduce OneProt, a multi-modal AI for proteins that integrates structural, sequence, alignment, and binding site data. Using the ImageBind framework, OneProt aligns the latent spaces of modality encoders along protein sequences. It demonstrates strong performance in retrieval tasks and surpasses state-of-the-art methods in various downstream tasks, including metal ion binding classification, gene-ontology annotation, and enzyme function prediction. This work expands multi-modal capabilities in protein models, paving the way for applications in drug discovery, biocatalytic reaction planning, and protein engineering.

We revisit the weakly supervised cross-modal face-name alignment task; that is, given an image and a caption, we label the faces in the image with the names occurring in the caption. Whereas past approaches have learned the latent alignment between names and faces by uncertainty reasoning over a set of images and their respective captions, in this paper, we rely on appropriate loss functions to learn the alignments in a neural network setting and propose SECLA and SECLA-B. SECLA is a Symmetry-Enhanced Contrastive Learning-based Alignment model that can effectively maximize the similarity scores between corresponding faces and names in a weakly supervised fashion. A variation of the model, SECLA-B, learns to align names and faces as humans do, that is, learning from easy to hard cases to further increase the performance of SECLA. More specifically, SECLA-B applies a two-stage learning framework: (1) Training the model on an easy subset with a few names and faces in each image-caption pair. (2) Leveraging the known pairs of names and faces from the easy cases using a bootstrapping strategy with additional loss to prevent forgetting and learning new alignments at the same time. We achieve state-of-the-art results for both the augmented Labeled Faces in the Wild dataset and the Celebrity Together dataset. In addition, we believe that our methods can be adapted to other multimodal news understanding tasks.

Current LLM alignment techniques use pairwise human preferences at a sample level, and as such, they do not imply an alignment on the distributional level. We propose in this paper Alignment via Optimal Transport (AOT), a novel method for distributional preference alignment of LLMs. AOT aligns LLMs on unpaired preference data by making the reward distribution of the positive samples stochastically dominant in the first order on the distribution of negative samples. We introduce a convex relaxation of this first-order stochastic dominance and cast it as an optimal transport problem with a smooth and convex cost. Thanks to the one-dimensional nature of the resulting optimal transport problem and the convexity of the cost, it has a closed-form solution via sorting on empirical measures. We fine-tune LLMs with this AOT objective, which enables alignment by penalizing the violation of the stochastic dominance of the reward distribution of the positive samples on the reward distribution of the negative samples. We analyze the sample complexity of AOT by considering the dual of the OT problem and show that it converges at the parametric rate. Empirically, we show on a diverse set of alignment datasets and LLMs that AOT leads to state-of-the-art models in the 7B family of models when evaluated with Open LLM Benchmarks and AlpacaEval.

Recent advances in synthetic methods enable designing subunits that self-assemble into structures with well-defined sizes and architectures, but yields are frequently suppressed by the formation of off-target metastable structures. Increasing the complexity (number of distinct inter-subunit interaction types) can inhibit off-target structures, but leads to slower kinetics and higher synthesis costs. Here, we use icosahedral shells formed of programmable triangular subunits as a model system, and identify design principles that produce the highest target yield at the lowest complexity. We use a symmetry-based construction to create a range of design complexities, starting from the maximal symmetry Caspar-Klug assembly up to the fully addressable, zero-symmetry assembly. Kinetic Monte Carlo simulations reveal that the most prominent defects leading to off-target assemblies are a class of disclinations. We derive symmetry-based rules for identifying the optimal (lowest-complexity, highest-symmetry) design that inhibits these disclinations, leading to robust, high-fidelity assembly of targets with arbitrarily large sizes. Optimal complexity varies non-monotonically with target size, with `magic' sizes appearing for high-symmetry designs in which symmetry axes do not intersect vertices of the triangular net. The optimal designs at magic sizes require 12 times fewer inequivalent interaction-types than the (minimal symmetry) fully addressable construction.

Contrastive Analysis is a sub-field of Representation Learning that aims at separating common factors of variation between two datasets, a background (i.e., healthy subjects) and a target (i.e., diseased subjects), from the salient factors of variation, only present in the target dataset. Despite their relevance, current models based on Variational Auto-Encoders have shown poor performance in learning semantically-expressive representations. On the other hand, Contrastive Representation Learning has shown tremendous performance leaps in various applications (classification, clustering, etc.). In this work, we propose to leverage the ability of Contrastive Learning to learn semantically expressive representations well adapted for Contrastive Analysis. We reformulate it under the lens of the InfoMax Principle and identify two Mutual Information terms to maximize and one to minimize. We decompose the first two terms into an Alignment and a Uniformity term, as commonly done in Contrastive Learning. Then, we motivate a novel Mutual Information minimization strategy to prevent information leakage between common and salient distributions. We validate our method, called SepCLR, on three visual datasets and three medical datasets, specifically conceived to assess the pattern separation capability in Contrastive Analysis. Code available at https://github.com/neurospin-projects/2024_rlouiset_sep_clr.

Face anti-spoofing (FAS) based on domain generalization (DG) has been recently studied to improve the generalization on unseen scenarios. Previous methods typically rely on domain labels to align the distribution of each domain for learning domain-invariant representations. However, artificial domain labels are coarse-grained and subjective, which cannot reflect real domain distributions accurately. Besides, such domain-aware methods focus on domain-level alignment, which is not fine-grained enough to ensure that learned representations are insensitive to domain styles. To address these issues, we propose a novel perspective for DG FAS that aligns features on the instance level without the need for domain labels. Specifically, Instance-Aware Domain Generalization framework is proposed to learn the generalizable feature by weakening the features' sensitivity to instance-specific styles. Concretely, we propose Asymmetric Instance Adaptive Whitening to adaptively eliminate the style-sensitive feature correlation, boosting the generalization. Moreover, Dynamic Kernel Generator and Categorical Style Assembly are proposed to first extract the instance-specific features and then generate the style-diversified features with large style shifts, respectively, further facilitating the learning of style-insensitive features. Extensive experiments and analysis demonstrate the superiority of our method over state-of-the-art competitors. Code will be publicly available at https://github.com/qianyuzqy/IADG.

Large language models (LLMs) have shown remarkable abilities in diverse natural language processing (NLP) tasks. The LLMs generally undergo supervised fine-tuning (SFT) followed by preference alignment to be usable in downstream applications. However, this sequential training pipeline leads to alignment tax that degrades the LLM performance. This paper introduces PAFT, a new PArallel training paradigm for effective LLM Fine-Tuning, which independently performs SFT and preference alignment (e.g., DPO and ORPO, etc.) with the same pre-trained model on respective datasets. The model produced by SFT and the model from preference alignment are then merged into a final model by parameter fusing for use in downstream applications. This work reveals important findings that preference alignment like DPO naturally results in a sparse model while SFT leads to a natural dense model which needs to be sparsified for effective model merging. This paper introduces an effective interference resolution which reduces the redundancy by sparsifying the delta parameters. The LLM resulted from the new training paradigm achieved Rank #1 on the HuggingFace Open LLM Leaderboard. Comprehensive evaluation shows the effectiveness of the parallel training paradigm.

Multi-modal foundation models combining vision and language models such as Flamingo or GPT-4 have recently gained enormous interest. Alignment of foundation models is used to prevent models from providing toxic or harmful output. While malicious users have successfully tried to jailbreak foundation models, an equally important question is if honest users could be harmed by malicious third-party content. In this paper we show that imperceivable attacks on images in order to change the caption output of a multi-modal foundation model can be used by malicious content providers to harm honest users e.g. by guiding them to malicious websites or broadcast fake information. This indicates that countermeasures to adversarial attacks should be used by any deployed multi-modal foundation model.

Stereo image super-resolution aims at enhancing the quality of super-resolution results by utilizing the complementary information provided by binocular systems. To obtain reasonable performance, most methods focus on finely designing modules, loss functions, and etc. to exploit information from another viewpoint. This has the side effect of increasing system complexity, making it difficult for researchers to evaluate new ideas and compare methods. This paper inherits a strong and simple image restoration model, NAFNet, for single-view feature extraction and extends it by adding cross attention modules to fuse features between views to adapt to binocular scenarios. The proposed baseline for stereo image super-resolution is noted as NAFSSR. Furthermore, training/testing strategies are proposed to fully exploit the performance of NAFSSR. Extensive experiments demonstrate the effectiveness of our method. In particular, NAFSSR outperforms the state-of-the-art methods on the KITTI 2012, KITTI 2015, Middlebury, and Flickr1024 datasets. With NAFSSR, we won 1st place in the NTIRE 2022 Stereo Image Super-resolution Challenge. Codes and models will be released at https://github.com/megvii-research/NAFNet.

The success of AI assistants based on Language Models (LLMs) hinges on Reinforcement Learning from Human Feedback (RLHF) to comprehend and align with user intentions. However, traditional alignment algorithms, such as PPO, are hampered by complex annotation and training requirements. This reliance limits the applicability of RLHF and hinders the development of professional assistants tailored to diverse human preferences. In this work, we introduce Linear Alignment, a novel algorithm that aligns language models with human preferences in one single inference step, eliminating the reliance on data annotation and model training. Linear alignment incorporates a new parameterization for policy optimization under divergence constraints, which enables the extraction of optimal policy in a closed-form manner and facilitates the direct estimation of the aligned response. Extensive experiments on both general and personalized preference datasets demonstrate that linear alignment significantly enhances the performance and efficiency of LLM alignment across diverse scenarios. Our code and dataset will be published on https://github.com/Wizardcoast/Linear_Alignment.git.

Radiologists play a crucial role by translating medical images into medical reports. However, the field faces staffing shortages and increasing workloads. While automated approaches using vision-language models (VLMs) show promise as assistants, they require exceptionally high accuracy. Most current VLMs in radiology rely solely on supervised fine-tuning (SFT). Meanwhile, in the general domain, additional preference fine-tuning has become standard practice. The challenge in radiology lies in the prohibitive cost of obtaining radiologist feedback. We propose a scalable automated preference alignment technique for VLMs in radiology, focusing on chest X-ray (CXR) report generation. Our method leverages publicly available datasets with an LLM-as-a-Judge mechanism, eliminating the need for additional expert radiologist feedback. We evaluate and benchmark five direct alignment algorithms (DAAs). Our results show up to a 57.4% improvement in average GREEN scores, a LLM-based metric for evaluating CXR reports, and a 9.2% increase in an average across six metrics (domain specific and general), compared to the SFT baseline. We study reward overoptimization via length exploitation, with reports lengthening by up to 3.2x. To assess a potential alignment tax, we benchmark on six additional diverse tasks, finding no significant degradations. A reader study involving four board-certified radiologists indicates win rates of up to 0.62 over the SFT baseline, while significantly penalizing verbosity. Our analysis provides actionable insights for the development of VLMs in high-stakes fields like radiology.

The design of novel protein structures remains a challenge in protein engineering for applications across biomedicine and chemistry. In this line of work, a diffusion model over rigid bodies in 3D (referred to as frames) has shown success in generating novel, functional protein backbones that have not been observed in nature. However, there exists no principled methodological framework for diffusion on SE(3), the space of orientation preserving rigid motions in R3, that operates on frames and confers the group invariance. We address these shortcomings by developing theoretical foundations of SE(3) invariant diffusion models on multiple frames followed by a novel framework, FrameDiff, for learning the SE(3) equivariant score over multiple frames. We apply FrameDiff on monomer backbone generation and find it can generate designable monomers up to 500 amino acids without relying on a pretrained protein structure prediction network that has been integral to previous methods. We find our samples are capable of generalizing beyond any known protein structure.

Predicting which proteins interact together from amino-acid sequences is an important task. We develop a method to pair interacting protein sequences which leverages the power of protein language models trained on multiple sequence alignments, such as MSA Transformer and the EvoFormer module of AlphaFold. We formulate the problem of pairing interacting partners among the paralogs of two protein families in a differentiable way. We introduce a method called DiffPALM that solves it by exploiting the ability of MSA Transformer to fill in masked amino acids in multiple sequence alignments using the surrounding context. MSA Transformer encodes coevolution between functionally or structurally coupled amino acids. We show that it captures inter-chain coevolution, while it was trained on single-chain data, which means that it can be used out-of-distribution. Relying on MSA Transformer without fine-tuning, DiffPALM outperforms existing coevolution-based pairing methods on difficult benchmarks of shallow multiple sequence alignments extracted from ubiquitous prokaryotic protein datasets. It also outperforms an alternative method based on a state-of-the-art protein language model trained on single sequences. Paired alignments of interacting protein sequences are a crucial ingredient of supervised deep learning methods to predict the three-dimensional structure of protein complexes. DiffPALM substantially improves the structure prediction of some eukaryotic protein complexes by AlphaFold-Multimer, without significantly deteriorating any of those we tested. It also achieves competitive performance with using orthology-based pairing.

Understanding how features evolve across layers in deep neural networks is a fundamental challenge in mechanistic interpretability, particularly due to polysemanticity and feature superposition. While Sparse Autoencoders (SAEs) have been used to extract interpretable features from individual layers, aligning these features across layers has remained an open problem. In this paper, we introduce SAE Match, a novel, data-free method for aligning SAE features across different layers of a neural network. Our approach involves matching features by minimizing the mean squared error between the folded parameters of SAEs, a technique that incorporates activation thresholds into the encoder and decoder weights to account for differences in feature scales. Through extensive experiments on the Gemma 2 language model, we demonstrate that our method effectively captures feature evolution across layers, improving feature matching quality. We also show that features persist over several layers and that our approach can approximate hidden states across layers. Our work advances the understanding of feature dynamics in neural networks and provides a new tool for mechanistic interpretability studies.

Recent years have witnessed remarkable progress made in large language models (LLMs). Such advancements, while garnering significant attention, have concurrently elicited various concerns. The potential of these models is undeniably vast; however, they may yield texts that are imprecise, misleading, or even detrimental. Consequently, it becomes paramount to employ alignment techniques to ensure these models to exhibit behaviors consistent with human values. This survey endeavors to furnish an extensive exploration of alignment methodologies designed for LLMs, in conjunction with the extant capability research in this domain. Adopting the lens of AI alignment, we categorize the prevailing methods and emergent proposals for the alignment of LLMs into outer and inner alignment. We also probe into salient issues including the models' interpretability, and potential vulnerabilities to adversarial attacks. To assess LLM alignment, we present a wide variety of benchmarks and evaluation methodologies. After discussing the state of alignment research for LLMs, we finally cast a vision toward the future, contemplating the promising avenues of research that lie ahead. Our aspiration for this survey extends beyond merely spurring research interests in this realm. We also envision bridging the gap between the AI alignment research community and the researchers engrossed in the capability exploration of LLMs for both capable and safe LLMs.

Sparse autoencoders (SAEs) have lately been used to uncover interpretable latent features in large language models. Here, we explore their potential for decomposing latent representations in complex and high-dimensional biological data, where the underlying variables are often unknown. On simulated data we show that generative hidden variables can be captured in learned representations in the form of superpositions. The degree to which they are learned depends on the completeness of the representations. Superpositions, however, are not identifiable if these generative variables are unknown. SAEs can to some extent recover these variables, yielding interpretable features. Applied to single-cell multi-omics data, we show that an SAE can uncover key biological processes such as carbon dioxide transport and ion homeostasis, which are crucial for red blood cell differentiation and immune function. Our findings highlight how SAEs can be used in advancing interpretability in biological and other scientific domains.

We present PlainMamba: a simple non-hierarchical state space model (SSM) designed for general visual recognition. The recent Mamba model has shown how SSMs can be highly competitive with other architectures on sequential data and initial attempts have been made to apply it to images. In this paper, we further adapt the selective scanning process of Mamba to the visual domain, enhancing its ability to learn features from two-dimensional images by (i) a continuous 2D scanning process that improves spatial continuity by ensuring adjacency of tokens in the scanning sequence, and (ii) direction-aware updating which enables the model to discern the spatial relations of tokens by encoding directional information. Our architecture is designed to be easy to use and easy to scale, formed by stacking identical PlainMamba blocks, resulting in a model with constant width throughout all layers. The architecture is further simplified by removing the need for special tokens. We evaluate PlainMamba on a variety of visual recognition tasks including image classification, semantic segmentation, object detection, and instance segmentation. Our method achieves performance gains over previous non-hierarchical models and is competitive with hierarchical alternatives. For tasks requiring high-resolution inputs, in particular, PlainMamba requires much less computing while maintaining high performance. Code and models are available at https://github.com/ChenhongyiYang/PlainMamba

Image registration is important for medical imaging, the estimation of the spatial transformation between different images. Many previous studies have used learning-based methods for coarse-to-fine registration to efficiently perform 3D image registration. The coarse-to-fine approach, however, is limited when dealing with the different motions of nearby objects. Here we propose a novel Motion-Aware (MA) structure that captures the different motions in a region. The MA structure incorporates a novel Residual Aligner (RA) module which predicts the multi-head displacement field used to disentangle the different motions of multiple neighbouring objects. Compared with other deep learning methods, the network based on the MA structure and RA module achieve one of the most accurate unsupervised inter-subject registration on the 9 organs of assorted sizes in abdominal CT scans, with the highest-ranked registration of the veins (Dice Similarity Coefficient / Average surface distance: 62\%/4.9mm for the vena cava and 34\%/7.9mm for the portal and splenic vein), with a half-sized structure and more efficient computation. Applied to the segmentation of lungs in chest CT scans, the new network achieves results which were indistinguishable from the best-ranked networks (94\%/3.0mm). Additionally, the theorem on predicted motion pattern and the design of MA structure are validated by further analysis.

Face anti-spoofing (FAS) is indispensable for a face recognition system. Many texture-driven countermeasures were developed against presentation attacks (PAs), but the performance against unseen domains or unseen spoofing types is still unsatisfactory. Instead of exhaustively collecting all the spoofing variations and making binary decisions of live/spoof, we offer a new perspective on the FAS task to distinguish between normal and abnormal movements of live and spoof presentations. We propose Geometry-Aware Interaction Network (GAIN), which exploits dense facial landmarks with spatio-temporal graph convolutional network (ST-GCN) to establish a more interpretable and modularized FAS model. Additionally, with our cross-attention feature interaction mechanism, GAIN can be easily integrated with other existing methods to significantly boost performance. Our approach achieves state-of-the-art performance in the standard intra- and cross-dataset evaluations. Moreover, our model outperforms state-of-the-art methods by a large margin in the cross-dataset cross-type protocol on CASIA-SURF 3DMask (+10.26% higher AUC score), exhibiting strong robustness against domain shifts and unseen spoofing types.

The field of bioinformatics has seen significant progress, making the cross-modal text-molecule retrieval task increasingly vital. This task focuses on accurately retrieving molecule structures based on textual descriptions, by effectively aligning textual descriptions and molecules to assist researchers in identifying suitable molecular candidates. However, many existing approaches overlook the details inherent in molecule sub-structures. In this work, we introduce the Optimal TRansport-based Multi-grained Alignments model (ORMA), a novel approach that facilitates multi-grained alignments between textual descriptions and molecules. Our model features a text encoder and a molecule encoder. The text encoder processes textual descriptions to generate both token-level and sentence-level representations, while molecules are modeled as hierarchical heterogeneous graphs, encompassing atom, motif, and molecule nodes to extract representations at these three levels. A key innovation in ORMA is the application of Optimal Transport (OT) to align tokens with motifs, creating multi-token representations that integrate multiple token alignments with their corresponding motifs. Additionally, we employ contrastive learning to refine cross-modal alignments at three distinct scales: token-atom, multitoken-motif, and sentence-molecule, ensuring that the similarities between correctly matched text-molecule pairs are maximized while those of unmatched pairs are minimized. To our knowledge, this is the first attempt to explore alignments at both the motif and multi-token levels. Experimental results on the ChEBI-20 and PCdes datasets demonstrate that ORMA significantly outperforms existing state-of-the-art (SOTA) models.

Multiple sequence alignments (MSAs) of proteins encode rich biological information and have been workhorses in bioinformatic methods for tasks like protein design and protein structure prediction for decades. Recent breakthroughs like AlphaFold2 that use transformers to attend directly over large quantities of raw MSAs have reaffirmed their importance. Generation of MSAs is highly computationally intensive, however, and no datasets comparable to those used to train AlphaFold2 have been made available to the research community, hindering progress in machine learning for proteins. To remedy this problem, we introduce OpenProteinSet, an open-source corpus of more than 16 million MSAs, associated structural homologs from the Protein Data Bank, and AlphaFold2 protein structure predictions. We have previously demonstrated the utility of OpenProteinSet by successfully retraining AlphaFold2 on it. We expect OpenProteinSet to be broadly useful as training and validation data for 1) diverse tasks focused on protein structure, function, and design and 2) large-scale multimodal machine learning research.

The current paradigm for safety alignment of large language models (LLMs) follows a one-size-fits-all approach: the model refuses to interact with any content deemed unsafe by the model provider. This approach lacks flexibility in the face of varying social norms across cultures and regions. In addition, users may have diverse safety needs, making a model with static safety standards too restrictive to be useful, as well as too costly to be re-aligned. We propose Controllable Safety Alignment (CoSA), a framework designed to adapt models to diverse safety requirements without re-training. Instead of aligning a fixed model, we align models to follow safety configs -- free-form natural language descriptions of the desired safety behaviors -- that are provided as part of the system prompt. To adjust model safety behavior, authorized users only need to modify such safety configs at inference time. To enable that, we propose CoSAlign, a data-centric method for aligning LLMs to easily adapt to diverse safety configs. Furthermore, we devise a novel controllability evaluation protocol that considers both helpfulness and configured safety, summarizing them into CoSA-Score, and construct CoSApien, a human-authored benchmark that consists of real-world LLM use cases with diverse safety requirements and corresponding evaluation prompts. We show that CoSAlign leads to substantial gains of controllability over strong baselines including in-context alignment. Our framework encourages better representation and adaptation to pluralistic human values in LLMs, and thereby increasing their practicality.

The Segment Anything Model (SAM) has recently gained popularity in the field of image segmentation due to its impressive capabilities in various segmentation tasks and its prompt-based interface. However, recent studies and individual experiments have shown that SAM underperforms in medical image segmentation, since the lack of the medical specific knowledge. This raises the question of how to enhance SAM's segmentation capability for medical images. In this paper, instead of fine-tuning the SAM model, we propose the Medical SAM Adapter (Med-SA), which incorporates domain-specific medical knowledge into the segmentation model using a light yet effective adaptation technique. In Med-SA, we propose Space-Depth Transpose (SD-Trans) to adapt 2D SAM to 3D medical images and Hyper-Prompting Adapter (HyP-Adpt) to achieve prompt-conditioned adaptation. We conduct comprehensive evaluation experiments on 17 medical image segmentation tasks across various image modalities. Med-SA outperforms several state-of-the-art (SOTA) medical image segmentation methods, while updating only 2\% of the parameters. Our code is released at https://github.com/KidsWithTokens/Medical-SAM-Adapter.

Aligning foundation models is essential for their safe and trustworthy deployment. However, traditional fine-tuning methods are computationally intensive and require updating billions of model parameters. A promising alternative, alignment via decoding, adjusts the response distribution directly without model updates to maximize a target reward r, thus providing a lightweight and adaptable framework for alignment. However, principled decoding methods rely on oracle access to an optimal Q-function (Q^*), which is often unavailable in practice. Hence, prior SoTA methods either approximate this Q^* using Q^{pi_{sft}} (derived from the reference SFT model) or rely on short-term rewards, resulting in sub-optimal decoding performance. In this work, we propose Transfer Q^*, which implicitly estimates the optimal value function for a target reward r through a baseline model rho_{BL} aligned with a baseline reward rho_{BL} (which can be different from the target reward r). Theoretical analyses of Transfer Q^* provide a rigorous characterization of its optimality, deriving an upper bound on the sub-optimality gap and identifying a hyperparameter to control the deviation from the pre-trained reference SFT model based on user needs. Our approach significantly reduces the sub-optimality gap observed in prior SoTA methods and demonstrates superior empirical performance across key metrics such as coherence, diversity, and quality in extensive tests on several synthetic and real datasets.

Large Language Models (LLMs) are nowadays expected to generate content aligned with human preferences. Current work focuses on alignment at model training time, through techniques such as Reinforcement Learning with Human Feedback (RLHF). However, it is unclear if such methods are an effective choice to teach alignment objectives to the model. First, the inability to incorporate multiple, custom rewards and reliance on a model developer's view of universal and static principles are key limitations. Second, the residual gaps in model training and the reliability of such approaches are also questionable (e.g. susceptibility to jail-breaking even after safety training). To address these, we propose DeAL, a framework that allows the user to customize reward functions and enables Decoding-time Alignment of LLMs (DeAL). At its core, we view decoding as a heuristic-guided search process and facilitate the use of a wide variety of alignment objectives. Our experiments with programmatic constraints such as keyword and length constraints (studied widely in the pre-LLM era) and abstract objectives such as harmlessness and helpfulness (proposed in the post-LLM era) show that we can DeAL with fine-grained trade-offs, improve adherence to alignment objectives, and address residual gaps in LLMs. Lastly, while DeAL can be effectively paired with RLHF and prompting techniques, its generality makes decoding slower, an optimization we leave for future work.

With the rapid development of large language models (LLMs), they are not only used as general-purpose AI assistants but are also customized through further fine-tuning to meet the requirements of different applications. A pivotal factor in the success of current LLMs is the alignment process. Current alignment methods, such as supervised fine-tuning (SFT) and reinforcement learning from human feedback (RLHF), focus on training-time alignment and are often complex and cumbersome to implement. Therefore, we develop InferAligner, a novel inference-time alignment method that utilizes cross-model guidance for harmlessness alignment. InferAligner utilizes safety steering vectors extracted from safety-aligned model to modify the activations of the target model when responding to harmful inputs, thereby guiding the target model to provide harmless responses. Experimental results show that our method can be very effectively applied to domain-specific models in finance, medicine, and mathematics, as well as to multimodal large language models (MLLMs) such as LLaVA. It significantly diminishes the Attack Success Rate (ASR) of both harmful instructions and jailbreak attacks, while maintaining almost unchanged performance in downstream tasks.

Multimedia summarization with multimodal output (MSMO) is a recently explored application in language grounding. It plays an essential role in real-world applications, i.e., automatically generating cover images and titles for news articles or providing introductions to online videos. However, existing methods extract features from the whole video and article and use fusion methods to select the representative one, thus usually ignoring the critical structure and varying semantics. In this work, we propose a Semantics-Consistent Cross-domain Summarization (SCCS) model based on optimal transport alignment with visual and textual segmentation. In specific, our method first decomposes both video and article into segments in order to capture the structural semantics, respectively. Then SCCS follows a cross-domain alignment objective with optimal transport distance, which leverages multimodal interaction to match and select the visual and textual summary. We evaluated our method on three recent multimodal datasets and demonstrated the effectiveness of our method in producing high-quality multimodal summaries.

Grouping is inherently ambiguous due to the multiple levels of granularity in which one can decompose a scene -- should the wheels of an excavator be considered separate or part of the whole? We present Group Anything with Radiance Fields (GARField), an approach for decomposing 3D scenes into a hierarchy of semantically meaningful groups from posed image inputs. To do this we embrace group ambiguity through physical scale: by optimizing a scale-conditioned 3D affinity feature field, a point in the world can belong to different groups of different sizes. We optimize this field from a set of 2D masks provided by Segment Anything (SAM) in a way that respects coarse-to-fine hierarchy, using scale to consistently fuse conflicting masks from different viewpoints. From this field we can derive a hierarchy of possible groupings via automatic tree construction or user interaction. We evaluate GARField on a variety of in-the-wild scenes and find it effectively extracts groups at many levels: clusters of objects, objects, and various subparts. GARField inherently represents multi-view consistent groupings and produces higher fidelity groups than the input SAM masks. GARField's hierarchical grouping could have exciting downstream applications such as 3D asset extraction or dynamic scene understanding. See the project website at https://www.garfield.studio/

In this paper, we propose a new class of metric for table structure recognition (TSR) evaluation, called grid table similarity (GriTS). Unlike prior metrics, GriTS evaluates the correctness of a predicted table directly in its natural form as a matrix. To create a similarity measure between matrices, we generalize the two-dimensional largest common substructure (2D-LCS) problem, which is NP-hard, to the 2D most similar substructures (2D-MSS) problem and propose a polynomial-time heuristic for solving it. This algorithm produces both an upper and a lower bound on the true similarity between matrices. We show using evaluation on a large real-world dataset that in practice there is almost no difference between these bounds. We compare GriTS to other metrics and empirically validate that matrix similarity exhibits more desirable behavior than alternatives for TSR performance evaluation. Finally, GriTS unifies all three subtasks of cell topology recognition, cell location recognition, and cell content recognition within the same framework, which simplifies the evaluation and enables more meaningful comparisons across different types of TSR approaches. Code will be released at https://github.com/microsoft/table-transformer.

Fine-tuning large pretrained language models on a limited training corpus usually suffers from poor generalization. Prior works show that the recently-proposed sharpness-aware minimization (SAM) optimization method can improve the model generalization. However, SAM adds a perturbation to each model parameter equally (but not all parameters contribute equally to the optimization of training), which we argue is sub-optimal and will lead to excessive computation. In this paper, we propose a novel optimization procedure, namely FSAM, which introduces a Fisher mask to improve the efficiency and performance of SAM. In short, instead of adding perturbation to all parameters, FSAM uses the Fisher information to identity the important parameters and formulates a Fisher mask to obtain the sparse perturbation, i.e., making the optimizer focus on these important parameters. Experiments on various tasks in GLUE and SuperGLUE benchmarks show that FSAM consistently outperforms the vanilla SAM by 0.67~1.98 average score among four different pretrained models. We also empirically show that FSAM works well in other complex scenarios, e.g., fine-tuning on generation tasks or limited training data. Encouragingly, when training data is limited, FSAM improves the SAM by a large margin, i.e., up to 15.1.

The effects of ligand binding on protein structures and their in vivo functions carry numerous implications for modern biomedical research and biotechnology development efforts such as drug discovery. Although several deep learning (DL) methods and benchmarks designed for protein-ligand docking have recently been introduced, to date no prior works have systematically studied the behavior of the latest docking and structure prediction methods within the broadly applicable context of (1) using predicted (apo) protein structures for docking (e.g., for applicability to new proteins); (2) binding multiple (cofactor) ligands concurrently to a given target protein (e.g., for enzyme design); and (3) having no prior knowledge of binding pockets (e.g., for generalization to unknown pockets). To enable a deeper understanding of docking methods' real-world utility, we introduce PoseBench, the first comprehensive benchmark for broadly applicable protein-ligand docking. PoseBench enables researchers to rigorously and systematically evaluate DL methods for apo-to-holo protein-ligand docking and protein-ligand structure prediction using both primary ligand and multi-ligand benchmark datasets, the latter of which we introduce for the first time to the DL community. Empirically, using PoseBench, we find that (1) DL co-folding methods generally outperform comparable conventional and DL docking baselines, yet popular methods such as AlphaFold 3 are still challenged by prediction targets with novel protein sequences; (2) certain DL co-folding methods are highly sensitive to their input multiple sequence alignments, while others are not; and (3) DL methods struggle to strike a balance between structural accuracy and chemical specificity when predicting novel or multi-ligand protein targets. Code, data, tutorials, and benchmark results are available at https://github.com/BioinfoMachineLearning/PoseBench.

Identity-consistent video generation seeks to synthesize videos that are guided by both textual prompts and reference images of entities. Current approaches typically utilize cross-attention layers to integrate the appearance of the entity, which predominantly captures semantic attributes, resulting in compromised fidelity of entities. Moreover, these methods necessitate iterative fine-tuning for each new entity encountered, thereby limiting their applicability. To address these challenges, we introduce VideoAssembler, a novel end-to-end framework for identity-consistent video generation that can conduct inference directly when encountering new entities. VideoAssembler is adept at producing videos that are not only flexible with respect to the input reference entities but also responsive to textual conditions. Additionally, by modulating the quantity of input images for the entity, VideoAssembler enables the execution of tasks ranging from image-to-video generation to sophisticated video editing. VideoAssembler comprises two principal components: the Reference Entity Pyramid (REP) encoder and the Entity-Prompt Attention Fusion (EPAF) module. The REP encoder is designed to infuse comprehensive appearance details into the denoising stages of the stable diffusion model. Concurrently, the EPAF module is utilized to integrate text-aligned features effectively. Furthermore, to mitigate the challenge of scarce data, we present a methodology for the preprocessing of training data. Our evaluation of the VideoAssembler framework on the UCF-101, MSR-VTT, and DAVIS datasets indicates that it achieves good performances in both quantitative and qualitative analyses (346.84 in FVD and 48.01 in IS on UCF-101). Our project page is at https://gulucaptain.github.io/videoassembler/.