Daily Papers

This paper presents the development of a prototype Automatic Speech Recognition (ASR) system specifically designed for Bengali biomedical data. Recent advancements in Bengali ASR are encouraging, but a lack of domain-specific data limits the creation of practical healthcare ASR models. This project bridges this gap by developing an ASR system tailored for Bengali medical terms like symptoms, severity levels, and diseases, encompassing two major dialects: Bengali and Sylheti. We train and evaluate two popular ASR frameworks on a comprehensive 46-hour Bengali medical corpus. Our core objective is to create deployable health-domain ASR systems for digital health applications, ultimately increasing accessibility for non-technical users in the healthcare sector.

Multilingual automatic speech recognition (ASR) in the medical domain serves as a foundational task for various downstream applications such as speech translation, spoken language understanding, and voice-activated assistants. This technology enhances patient care by enabling efficient communication across language barriers, alleviating specialized workforce shortages, and facilitating improved diagnosis and treatment, particularly during pandemics. In this work, we introduce MultiMed, a collection of small-to-large end-to-end ASR models for the medical domain, spanning five languages: Vietnamese, English, German, French, and Mandarin Chinese, together with the corresponding real-world ASR dataset. To our best knowledge, MultiMed stands as the largest and the first multilingual medical ASR dataset, in terms of total duration, number of speakers, diversity of diseases, recording conditions, speaker roles, unique medical terms, accents, and ICD-10 codes. Secondly, we establish the empirical baselines, present the first reproducible study of multilinguality in medical ASR, conduct a layer-wise ablation study for end-to-end ASR training, and provide the first linguistic analysis for multilingual medical ASR. All code, data, and models are available online https://github.com/leduckhai/MultiMed/tree/master/MultiMed

In today's interconnected globe, moving abroad is more and more prevalent, whether it's for employment, refugee resettlement, or other causes. Language difficulties between natives and immigrants present a common issue on a daily basis, especially in medical domain. This can make it difficult for patients and doctors to communicate during anamnesis or in the emergency room, which compromises patient care. The goal of the HYKIST Project is to develop a speech translation system to support patient-doctor communication with ASR and MT. ASR systems have recently displayed astounding performance on particular tasks for which enough quantities of training data are available, such as LibriSpeech. Building a good model is still difficult due to a variety of speaking styles, acoustic and recording settings, and a lack of in-domain training data. In this thesis, we describe our efforts to construct ASR systems for a conversational telephone speech recognition task in the medical domain for Vietnamese language to assist emergency room contact between doctors and patients across linguistic barriers. In order to enhance the system's performance, we investigate various training schedules and data combining strategies. We also examine how best to make use of the little data that is available. The use of publicly accessible models like XLSR-53 is compared to the use of customized pre-trained models, and both supervised and unsupervised approaches are utilized using wav2vec 2.0 as architecture.

Language barriers present a great challenge in our increasingly connected and global world. Especially within the medical domain, e.g. hospital or emergency room, communication difficulties and delays may lead to malpractice and non-optimal patient care. In the HYKIST project, we consider patient-physician communication, more specifically between a German-speaking physician and an Arabic- or Vietnamese-speaking patient. Currently, a doctor can call the Triaphon service to get assistance from an interpreter in order to help facilitate communication. The HYKIST goal is to support the usually non-professional bilingual interpreter with an automatic speech translation system to improve patient care and help overcome language barriers. In this work, we present our ASR system development efforts for this conversational telephone speech translation task in the medical domain for two languages pairs, data collection, various acoustic model architectures and dialect-induced difficulties.

Due to privacy restrictions, there's a shortage of publicly available speech recognition datasets in the medical domain. In this work, we present VietMed - a Vietnamese speech recognition dataset in the medical domain comprising 16h of labeled medical speech, 1000h of unlabeled medical speech and 1200h of unlabeled general-domain speech. To our best knowledge, VietMed is by far the world's largest public medical speech recognition dataset in 7 aspects: total duration, number of speakers, diseases, recording conditions, speaker roles, unique medical terms and accents. VietMed is also by far the largest public Vietnamese speech dataset in terms of total duration. Additionally, we are the first to present a medical ASR dataset covering all ICD-10 disease groups and all accents within a country. Moreover, we release the first public large-scale pre-trained models for Vietnamese ASR, w2v2-Viet and XLSR-53-Viet, along with the first public large-scale fine-tuned models for medical ASR. Even without any medical data in unsupervised pre-training, our best pre-trained model XLSR-53-Viet generalizes very well to the medical domain by outperforming state-of-the-art XLSR-53, from 51.8% to 29.6% WER on test set (a relative reduction of more than 40%). All code, data and models are made publicly available here: https://github.com/leduckhai/MultiMed.

Africa has a very low doctor-to-patient ratio. At very busy clinics, doctors could see 30+ patients per day -- a heavy patient burden compared with developed countries -- but productivity tools such as clinical automatic speech recognition (ASR) are lacking for these overworked clinicians. However, clinical ASR is mature, even ubiquitous, in developed nations, and clinician-reported performance of commercial clinical ASR systems is generally satisfactory. Furthermore, the recent performance of general domain ASR is approaching human accuracy. However, several gaps exist. Several publications have highlighted racial bias with speech-to-text algorithms and performance on minority accents lags significantly. To our knowledge, there is no publicly available research or benchmark on accented African clinical ASR, and speech data is non-existent for the majority of African accents. We release AfriSpeech, 200hrs of Pan-African English speech, 67,577 clips from 2,463 unique speakers across 120 indigenous accents from 13 countries for clinical and general domain ASR, a benchmark test set, with publicly available pre-trained models with SOTA performance on the AfriSpeech benchmark.

A user-generated text on social media enables health workers to keep track of information, identify possible outbreaks, forecast disease trends, monitor emergency cases, and ascertain disease awareness and response to official health correspondence. This exchange of health information on social media has been regarded as an attempt to enhance public health surveillance (PHS). Despite its potential, the technology is still in its early stages and is not ready for widespread application. Advancements in pretrained language models (PLMs) have facilitated the development of several domain-specific PLMs and a variety of downstream applications. However, there are no PLMs for social media tasks involving PHS. We present and release PHS-BERT, a transformer-based PLM, to identify tasks related to public health surveillance on social media. We compared and benchmarked the performance of PHS-BERT on 25 datasets from different social medial platforms related to 7 different PHS tasks. Compared with existing PLMs that are mainly evaluated on limited tasks, PHS-BERT achieved state-of-the-art performance on all 25 tested datasets, showing that our PLM is robust and generalizable in the common PHS tasks. By making PHS-BERT available, we aim to facilitate the community to reduce the computational cost and introduce new baselines for future works across various PHS-related tasks.

Advancements in deep neural networks have allowed automatic speech recognition (ASR) systems to attain human parity on several publicly available clean speech datasets. However, even state-of-the-art ASR systems experience performance degradation when confronted with adverse conditions, as a well-trained acoustic model is sensitive to variations in the speech domain, e.g., background noise. Intuitively, humans address this issue by relying on their linguistic knowledge: the meaning of ambiguous spoken terms is usually inferred from contextual cues thereby reducing the dependency on the auditory system. Inspired by this observation, we introduce the first open-source benchmark to utilize external large language models (LLMs) for ASR error correction, where N-best decoding hypotheses provide informative elements for true transcription prediction. This approach is a paradigm shift from the traditional language model rescoring strategy that can only select one candidate hypothesis as the output transcription. The proposed benchmark contains a novel dataset, HyPoradise (HP), encompassing more than 334,000 pairs of N-best hypotheses and corresponding accurate transcriptions across prevalent speech domains. Given this dataset, we examine three types of error correction techniques based on LLMs with varying amounts of labeled hypotheses-transcription pairs, which gains a significant word error rate (WER) reduction. Experimental evidence demonstrates the proposed technique achieves a breakthrough by surpassing the upper bound of traditional re-ranking based methods. More surprisingly, LLM with reasonable prompt and its generative capability can even correct those tokens that are missing in N-best list. We make our results publicly accessible for reproducible pipelines with released pre-trained models, thus providing a new evaluation paradigm for ASR error correction with LLMs.

Electronic health record (EHR) systems are used extensively throughout the healthcare domain. However, data interchangeability between EHR systems is limited due to the use of different coding standards across systems. Existing methods of mapping coding standards based on manual human experts mapping, dictionary mapping, symbolic NLP and classification are unscalable and cannot accommodate large scale EHR datasets. In this work, we present Text2Node, a cross-domain mapping system capable of mapping medical phrases to concepts in a large taxonomy (such as SNOMED CT). The system is designed to generalize from a limited set of training samples and map phrases to elements of the taxonomy that are not covered by training data. As a result, our system is scalable, robust to wording variants between coding systems and can output highly relevant concepts when no exact concept exists in the target taxonomy. Text2Node operates in three main stages: first, the lexicon is mapped to word embeddings; second, the taxonomy is vectorized using node embeddings; and finally, the mapping function is trained to connect the two embedding spaces. We compared multiple algorithms and architectures for each stage of the training, including GloVe and FastText word embeddings, CNN and Bi-LSTM mapping functions, and node2vec for node embeddings. We confirmed the robustness and generalisation properties of Text2Node by mapping ICD-9-CM Diagnosis phrases to SNOMED CT and by zero-shot training at comparable accuracy. This system is a novel methodological contribution to the task of normalizing and linking phrases to a taxonomy, advancing data interchangeability in healthcare. When applied, the system can use electronic health records to generate an embedding that incorporates taxonomical medical knowledge to improve clinical predictive models.

Disease risk prediction has attracted increasing attention in the field of modern healthcare, especially with the latest advances in artificial intelligence (AI). Electronic health records (EHRs), which contain heterogeneous patient information, are widely used in disease risk prediction tasks. One challenge of applying AI models for risk prediction lies in generating interpretable evidence to support the prediction results while retaining the prediction ability. In order to address this problem, we propose the method of jointly embedding words and labels whereby attention modules learn the weights of words from medical notes according to their relevance to the names of risk prediction labels. This approach boosts interpretability by employing an attention mechanism and including the names of prediction tasks in the model. However, its application is only limited to the handling of textual inputs such as medical notes. In this paper, we propose a label dependent attention model LDAM to 1) improve the interpretability by exploiting Clinical-BERT (a biomedical language model pre-trained on a large clinical corpus) to encode biomedically meaningful features and labels jointly; 2) extend the idea of joint embedding to the processing of time-series data, and develop a multi-modal learning framework for integrating heterogeneous information from medical notes and time-series health status indicators. To demonstrate our method, we apply LDAM to the MIMIC-III dataset to predict different disease risks. We evaluate our method both quantitatively and qualitatively. Specifically, the predictive power of LDAM will be shown, and case studies will be carried out to illustrate its interpretability.

Curated datasets for healthcare are often limited due to the need of human annotations from experts. In this paper, we present MedEval, a multi-level, multi-task, and multi-domain medical benchmark to facilitate the development of language models for healthcare. MedEval is comprehensive and consists of data from several healthcare systems and spans 35 human body regions from 8 examination modalities. With 22,779 collected sentences and 21,228 reports, we provide expert annotations at multiple levels, offering a granular potential usage of the data and supporting a wide range of tasks. Moreover, we systematically evaluated 10 generic and domain-specific language models under zero-shot and finetuning settings, from domain-adapted baselines in healthcare to general-purposed state-of-the-art large language models (e.g., ChatGPT). Our evaluations reveal varying effectiveness of the two categories of language models across different tasks, from which we notice the importance of instruction tuning for few-shot usage of large language models. Our investigation paves the way toward benchmarking language models for healthcare and provides valuable insights into the strengths and limitations of adopting large language models in medical domains, informing their practical applications and future advancements.

Summaries generated from medical conversations can improve recall and understanding of care plans for patients and reduce documentation burden for doctors. Recent advancements in automatic speech recognition (ASR) and natural language understanding (NLU) offer potential solutions to generate these summaries automatically, but rigorous quantitative baselines for benchmarking research in this domain are lacking. In this paper, we bridge this gap for two tasks: classifying utterances from medical conversations according to (i) the SOAP section and (ii) the speaker role. Both are fundamental building blocks along the path towards an end-to-end, automated SOAP note for medical conversations. We provide details on a dataset that contains human and ASR transcriptions of medical conversations and corresponding machine learning optimized SOAP notes. We then present a systematic analysis in which we adapt an existing deep learning architecture to the two aforementioned tasks. The results suggest that modelling context in a hierarchical manner, which captures both word and utterance level context, yields substantial improvements on both classification tasks. Additionally, we develop and analyze a modular method for adapting our model to ASR output.

Although recent advances in scaling large language models (LLMs) have resulted in improvements on many NLP tasks, it remains unclear whether these models trained primarily with general web text are the right tool in highly specialized, safety critical domains such as clinical text. Recent results have suggested that LLMs encode a surprising amount of medical knowledge. This raises an important question regarding the utility of smaller domain-specific language models. With the success of general-domain LLMs, is there still a need for specialized clinical models? To investigate this question, we conduct an extensive empirical analysis of 12 language models, ranging from 220M to 175B parameters, measuring their performance on 3 different clinical tasks that test their ability to parse and reason over electronic health records. As part of our experiments, we train T5-Base and T5-Large models from scratch on clinical notes from MIMIC III and IV to directly investigate the efficiency of clinical tokens. We show that relatively small specialized clinical models substantially outperform all in-context learning approaches, even when finetuned on limited annotated data. Further, we find that pretraining on clinical tokens allows for smaller, more parameter-efficient models that either match or outperform much larger language models trained on general text. We release the code and the models used under the PhysioNet Credentialed Health Data license and data use agreement.

Healthcare systems continuously generate vast amounts of electronic health records (EHRs), commonly stored in the Fast Healthcare Interoperability Resources (FHIR) standard. Despite the wealth of information in these records, their complexity and volume make it difficult for users to retrieve and interpret crucial health insights. Recent advances in Large Language Models (LLMs) offer a solution, enabling semantic question answering (QA) over medical data, allowing users to interact with their health records more effectively. However, ensuring privacy and compliance requires edge and private deployments of LLMs. This paper proposes a novel approach to semantic QA over EHRs by first identifying the most relevant FHIR resources for a user query (Task1) and subsequently answering the query based on these resources (Task2). We explore the performance of privately hosted, fine-tuned LLMs, evaluating them against benchmark models such as GPT-4 and GPT-4o. Our results demonstrate that fine-tuned LLMs, while 250x smaller in size, outperform GPT-4 family models by 0.55% in F1 score on Task1 and 42% on Meteor Task in Task2. Additionally, we examine advanced aspects of LLM usage, including sequential fine-tuning, model self-evaluation (narcissistic evaluation), and the impact of training data size on performance. The models and datasets are available here: https://huggingface.co/genloop

The deployment of large language models (LLMs) within the healthcare sector has sparked both enthusiasm and apprehension. These models exhibit the remarkable capability to provide proficient responses to free-text queries, demonstrating a nuanced understanding of professional medical knowledge. This comprehensive survey delves into the functionalities of existing LLMs designed for healthcare applications, elucidating the trajectory of their development, starting from traditional Pretrained Language Models (PLMs) to the present state of LLMs in healthcare sector. First, we explore the potential of LLMs to amplify the efficiency and effectiveness of diverse healthcare applications, particularly focusing on clinical language understanding tasks. These tasks encompass a wide spectrum, ranging from named entity recognition and relation extraction to natural language inference, multi-modal medical applications, document classification, and question-answering. Additionally, we conduct an extensive comparison of the most recent state-of-the-art LLMs in the healthcare domain, while also assessing the utilization of various open-source LLMs and highlighting their significance in healthcare applications. Furthermore, we present the essential performance metrics employed to evaluate LLMs in the biomedical domain, shedding light on their effectiveness and limitations. Finally, we summarize the prominent challenges and constraints faced by large language models in the healthcare sector, offering a holistic perspective on their potential benefits and shortcomings. This review provides a comprehensive exploration of the current landscape of LLMs in healthcare, addressing their role in transforming medical applications and the areas that warrant further research and development.

Masked Language Models (MLMs) have proven to be effective for second-pass rescoring in Automatic Speech Recognition (ASR) systems. In this work, we propose Masked Audio Text Encoder (MATE), a multi-modal masked language model rescorer which incorporates acoustic representations into the input space of MLM. We adopt contrastive learning for effectively aligning the modalities by learning shared representations. We show that using a multi-modal rescorer is beneficial for domain generalization of the ASR system when target domain data is unavailable. MATE reduces word error rate (WER) by 4%-16% on in-domain, and 3%-7% on out-of-domain datasets, over the text-only baseline. Additionally, with very limited amount of training data (0.8 hours), MATE achieves a WER reduction of 8%-23% over the first-pass baseline.

We propose Samba ASR, the first state-of-the-art Automatic Speech Recognition (ASR) model leveraging the novel Mamba architecture as both encoder and decoder, built on the foundation of state-space models (SSMs). Unlike transformer-based ASR models, which rely on self-attention mechanisms to capture dependencies, Samba ASR effectively models both local and global temporal dependencies using efficient state-space dynamics, achieving remarkable performance gains. By addressing the limitations of transformers, such as quadratic scaling with input length and difficulty in handling long-range dependencies, Samba ASR achieves superior accuracy and efficiency. Experimental results demonstrate that Samba ASR surpasses existing open-source transformer-based ASR models across various standard benchmarks, establishing it as the new state of the art in ASR. Extensive evaluations on benchmark datasets show significant improvements in Word Error Rate (WER), with competitive performance even in low-resource scenarios. Furthermore, the computational efficiency and parameter optimization of the Mamba architecture make Samba ASR a scalable and robust solution for diverse ASR tasks. Our contributions include: A new Samba ASR architecture demonstrating the superiority of SSMs over transformer-based models for speech sequence processing. A comprehensive evaluation on public benchmarks showcasing state-of-the-art performance. An analysis of computational efficiency, robustness to noise, and sequence generalization. This work highlights the viability of Mamba SSMs as a transformer-free alternative for efficient and accurate ASR. By leveraging state-space modeling advancements, Samba ASR sets a new benchmark for ASR performance and future research.

The ability of large language models (LLMs) to follow natural language instructions with human-level fluency suggests many opportunities in healthcare to reduce administrative burden and improve quality of care. However, evaluating LLMs on realistic text generation tasks for healthcare remains challenging. Existing question answering datasets for electronic health record (EHR) data fail to capture the complexity of information needs and documentation burdens experienced by clinicians. To address these challenges, we introduce MedAlign, a benchmark dataset of 983 natural language instructions for EHR data. MedAlign is curated by 15 clinicians (7 specialities), includes clinician-written reference responses for 303 instructions, and provides 276 longitudinal EHRs for grounding instruction-response pairs. We used MedAlign to evaluate 6 general domain LLMs, having clinicians rank the accuracy and quality of each LLM response. We found high error rates, ranging from 35% (GPT-4) to 68% (MPT-7B-Instruct), and an 8.3% drop in accuracy moving from 32k to 2k context lengths for GPT-4. Finally, we report correlations between clinician rankings and automated natural language generation metrics as a way to rank LLMs without human review. We make MedAlign available under a research data use agreement to enable LLM evaluations on tasks aligned with clinician needs and preferences.

Electronic health records (EHRs) contain vast amounts of complex data, but harmonizing and processing this information remains a challenging and costly task requiring significant clinical expertise. While large language models (LLMs) have shown promise in various healthcare applications, their potential for abstracting medical concepts from EHRs remains largely unexplored. We introduce EHRmonize, a framework leveraging LLMs to abstract medical concepts from EHR data. Our study uses medication data from two real-world EHR databases to evaluate five LLMs on two free-text extraction and six binary classification tasks across various prompting strategies. GPT-4o's with 10-shot prompting achieved the highest performance in all tasks, accompanied by Claude-3.5-Sonnet in a subset of tasks. GPT-4o achieved an accuracy of 97% in identifying generic route names, 82% for generic drug names, and 100% in performing binary classification of antibiotics. While EHRmonize significantly enhances efficiency, reducing annotation time by an estimated 60%, we emphasize that clinician oversight remains essential. Our framework, available as a Python package, offers a promising tool to assist clinicians in EHR data abstraction, potentially accelerating healthcare research and improving data harmonization processes.

Pre-trained language models (PLMs), such as BERT and GPT, have revolutionized the field of NLP, not only in the general domain but also in the biomedical domain. Most prior efforts in building biomedical PLMs have resorted simply to domain adaptation and focused mainly on English. In this work we introduce eHealth, a Chinese biomedical PLM built from scratch with a new pre-training framework. This new framework pre-trains eHealth as a discriminator through both token- and sequence-level discrimination. The former is to detect input tokens corrupted by a generator and recover their original identities from plausible candidates, while the latter is to further distinguish corruptions of a same original sequence from those of others. As such, eHealth can learn language semantics at both token and sequence levels. Extensive experiments on 11 Chinese biomedical language understanding tasks of various forms verify the effectiveness and superiority of our approach. We release the pre-trained model at https://github.com/PaddlePaddle/Research/tree/master/KG/eHealth and will also release the code later.

Electronic health records (EHR) contain narrative notes that provide extensive details on the medical condition and management of patients. Natural language processing (NLP) of clinical notes can use observed frequencies of clinical terms as predictive features for downstream applications such as clinical decision making and patient trajectory prediction. However, due to the vast number of highly similar and related clinical concepts, a more effective modeling strategy is to represent clinical terms as semantic embeddings via representation learning and use the low dimensional embeddings as feature vectors for predictive modeling. To achieve efficient representation, fine-tuning pretrained language models with biomedical knowledge graphs may generate better embeddings for biomedical terms than those from standard language models alone. These embeddings can effectively discriminate synonymous pairs of from those that are unrelated. However, they often fail to capture different degrees of similarity or relatedness for concepts that are hierarchical in nature. To overcome this limitation, we propose HiPrBERT, a novel biomedical term representation model trained on additionally complied data that contains hierarchical structures for various biomedical terms. We modify an existing contrastive loss function to extract information from these hierarchies. Our numerical experiments demonstrate that HiPrBERT effectively learns the pair-wise distance from hierarchical information, resulting in a substantially more informative embeddings for further biomedical applications

In this work, we propose a method to create domain-sensitive speech recognition models that utilize textual domain information by conditioning its generation on a given text prompt. This is accomplished by fine-tuning a pre-trained, end-to-end model (Whisper) to learn from demonstrations with prompt examples. We show that this ability can be generalized to different domains and even various prompt contexts, with our model gaining a Word Error Rate (WER) reduction of up to 33% on unseen datasets from various domains, such as medical conversation, air traffic control communication, and financial meetings. Considering the limited availability of audio-transcript pair data, we further extend our method to text-only fine-tuning to achieve domain sensitivity as well as domain adaptation. We demonstrate that our text-only fine-tuned model can also attend to various prompt contexts, with the model reaching the most WER reduction of 29% on the medical conversation dataset.

Large Language Models (LLMs) have shown the potential to significantly contribute to patient care, diagnostics, and administrative processes. Emerging biomedical LLMs address healthcare-specific challenges, including privacy demands and computational constraints. However, evaluation of these models has primarily been limited to non-clinical tasks, which do not reflect the complexity of practical clinical applications. Additionally, there has been no thorough comparison between biomedical and general-domain LLMs for clinical tasks. To fill this gap, we present the Clinical Language Understanding Evaluation (CLUE), a benchmark tailored to evaluate LLMs on real-world clinical tasks. CLUE includes two novel datasets derived from MIMIC IV discharge letters and four existing tasks designed to test the practical applicability of LLMs in healthcare settings. Our evaluation covers several biomedical and general domain LLMs, providing insights into their clinical performance and applicability. CLUE represents a step towards a standardized approach to evaluating and developing LLMs in healthcare to align future model development with the real-world needs of clinical application. We publish our evaluation and data generation scripts: https://github.com/dadaamin/CLUE

While Automatic Speech Recognition (ASR) systems are widely used in many real-world applications, they often do not generalize well to new domains and need to be finetuned on data from these domains. However, target-domain data usually are not readily available in many scenarios. In this paper, we propose a new strategy for adapting ASR models to new target domains without any text or speech from those domains. To accomplish this, we propose a novel data synthesis pipeline that uses a Large Language Model (LLM) to generate a target domain text corpus, and a state-of-the-art controllable speech synthesis model to generate the corresponding speech. We propose a simple yet effective in-context instruction finetuning strategy to increase the effectiveness of LLM in generating text corpora for new domains. Experiments on the SLURP dataset show that the proposed method achieves an average relative word error rate improvement of 28% on unseen target domains without any performance drop in source domains.

Pretrained language models have been used in various natural language processing applications. In the mental health domain, domain-specific language models are pretrained and released, which facilitates the early detection of mental health conditions. Social posts, e.g., on Reddit, are usually long documents. However, there are no domain-specific pretrained models for long-sequence modeling in the mental health domain. This paper conducts domain-specific continued pretraining to capture the long context for mental health. Specifically, we train and release MentalXLNet and MentalLongformer based on XLNet and Longformer. We evaluate the mental health classification performance and the long-range ability of these two domain-specific pretrained models. Our models are released in HuggingFace.

In health, most large language model (LLM) research has focused on clinical tasks. However, mobile and wearable devices, which are rarely integrated into such tasks, provide rich, longitudinal data for personal health monitoring. Here we present Personal Health Large Language Model (PH-LLM), fine-tuned from Gemini for understanding and reasoning over numerical time-series personal health data. We created and curated three datasets that test 1) production of personalized insights and recommendations from sleep patterns, physical activity, and physiological responses, 2) expert domain knowledge, and 3) prediction of self-reported sleep outcomes. For the first task we designed 857 case studies in collaboration with domain experts to assess real-world scenarios in sleep and fitness. Through comprehensive evaluation of domain-specific rubrics, we observed that Gemini Ultra 1.0 and PH-LLM are not statistically different from expert performance in fitness and, while experts remain superior for sleep, fine-tuning PH-LLM provided significant improvements in using relevant domain knowledge and personalizing information for sleep insights. We evaluated PH-LLM domain knowledge using multiple choice sleep medicine and fitness examinations. PH-LLM achieved 79% on sleep and 88% on fitness, exceeding average scores from a sample of human experts. Finally, we trained PH-LLM to predict self-reported sleep quality outcomes from textual and multimodal encoding representations of wearable data, and demonstrate that multimodal encoding is required to match performance of specialized discriminative models. Although further development and evaluation are necessary in the safety-critical personal health domain, these results demonstrate both the broad knowledge and capabilities of Gemini models and the benefit of contextualizing physiological data for personal health applications as done with PH-LLM.

Social determinants of health (SDoH) have an important impact on patient outcomes but are incompletely collected from the electronic health records (EHR). This study researched the ability of large language models to extract SDoH from free text in EHRs, where they are most commonly documented, and explored the role of synthetic clinical text for improving the extraction of these scarcely documented, yet extremely valuable, clinical data. 800 patient notes were annotated for SDoH categories, and several transformer-based models were evaluated. The study also experimented with synthetic data generation and assessed for algorithmic bias. Our best-performing models were fine-tuned Flan-T5 XL (macro-F1 0.71) for any SDoH, and Flan-T5 XXL (macro-F1 0.70). The benefit of augmenting fine-tuning with synthetic data varied across model architecture and size, with smaller Flan-T5 models (base and large) showing the greatest improvements in performance (delta F1 +0.12 to +0.23). Model performance was similar on the in-hospital system dataset but worse on the MIMIC-III dataset. Our best-performing fine-tuned models outperformed zero- and few-shot performance of ChatGPT-family models for both tasks. These fine-tuned models were less likely than ChatGPT to change their prediction when race/ethnicity and gender descriptors were added to the text, suggesting less algorithmic bias (p<0.05). At the patient-level, our models identified 93.8% of patients with adverse SDoH, while ICD-10 codes captured 2.0%. Our method can effectively extracted SDoH information from clinic notes, performing better compare to GPT zero- and few-shot settings. These models could enhance real-world evidence on SDoH and aid in identifying patients needing social support.

Automatically classifying electronic health records (EHRs) into diagnostic codes has been challenging to the NLP community. State-of-the-art methods treated this problem as a multilabel classification problem and proposed various architectures to model this problem. However, these systems did not leverage the superb performance of pretrained language models, which achieved superb performance on natural language understanding tasks. Prior work has shown that pretrained language models underperformed on this task with the regular finetuning scheme. Therefore, this paper aims at analyzing the causes of the underperformance and developing a framework for automatic ICD coding with pretrained language models. We spotted three main issues through the experiments: 1) large label space, 2) long input sequences, and 3) domain mismatch between pretraining and fine-tuning. We propose PLMICD, a framework that tackles the challenges with various strategies. The experimental results show that our proposed framework can overcome the challenges and achieves state-of-the-art performance in terms of multiple metrics on the benchmark MIMIC data. The source code is available at https://github.com/MiuLab/PLM-ICD

This paper introduces FT Speech, a new speech corpus created from the recorded meetings of the Danish Parliament, otherwise known as the Folketing (FT). The corpus contains over 1,800 hours of transcribed speech by a total of 434 speakers. It is significantly larger in duration, vocabulary, and amount of spontaneous speech than the existing public speech corpora for Danish, which are largely limited to read-aloud and dictation data. We outline design considerations, including the preprocessing methods and the alignment procedure. To evaluate the quality of the corpus, we train automatic speech recognition systems on the new resource and compare them to the systems trained on the Danish part of Sprakbanken, the largest public ASR corpus for Danish to date. Our baseline results show that we achieve a 14.01 WER on the new corpus. A combination of FT Speech with in-domain language data provides comparable results to models trained specifically on Sprakbanken, showing that FT Speech transfers well to this data set. Interestingly, our results demonstrate that the opposite is not the case. This shows that FT Speech provides a valuable resource for promoting research on Danish ASR with more spontaneous speech.

Despite the remarkable progress in the development of predictive models for healthcare, applying these algorithms on a large scale has been challenging. Algorithms trained on a particular task, based on specific data formats available in a set of medical records, tend to not generalize well to other tasks or databases in which the data fields may differ. To address this challenge, we propose General Healthcare Predictive Framework (GenHPF), which is applicable to any EHR with minimal preprocessing for multiple prediction tasks. GenHPF resolves heterogeneity in medical codes and schemas by converting EHRs into a hierarchical textual representation while incorporating as many features as possible. To evaluate the efficacy of GenHPF, we conduct multi-task learning experiments with single-source and multi-source settings, on three publicly available EHR datasets with different schemas for 12 clinically meaningful prediction tasks. Our framework significantly outperforms baseline models that utilize domain knowledge in multi-source learning, improving average AUROC by 1.2%P in pooled learning and 2.6%P in transfer learning while also showing comparable results when trained on a single EHR dataset. Furthermore, we demonstrate that self-supervised pretraining using multi-source datasets is effective when combined with GenHPF, resulting in a 0.6%P AUROC improvement compared to models without pretraining. By eliminating the need for preprocessing and feature engineering, we believe that this work offers a solid framework for multi-task and multi-source learning that can be leveraged to speed up the scaling and usage of predictive algorithms in healthcare.

This paper is dedicated to the design and evaluation of the first AMR parser tailored for clinical notes. Our objective was to facilitate the precise transformation of the clinical notes into structured AMR expressions, thereby enhancing the interpretability and usability of clinical text data at scale. Leveraging the colon cancer dataset from the Temporal Histories of Your Medical Events (THYME) corpus, we adapted a state-of-the-art AMR parser utilizing continuous training. Our approach incorporates data augmentation techniques to enhance the accuracy of AMR structure predictions. Notably, through this learning strategy, our parser achieved an impressive F1 score of 88% on the THYME corpus's colon cancer dataset. Moreover, our research delved into the efficacy of data required for domain adaptation within the realm of clinical notes, presenting domain adaptation data requirements for AMR parsing. This exploration not only underscores the parser's robust performance but also highlights its potential in facilitating a deeper understanding of clinical narratives through structured semantic representations.

We address a challenging and practical task of labeling questions in speech in real time during telephone calls to emergency medical services in English, which embeds within a broader decision support system for emergency call-takers. We propose a novel multimodal approach to real-time sequence labeling in speech. Our model treats speech and its own textual representation as two separate modalities or views, as it jointly learns from streamed audio and its noisy transcription into text via automatic speech recognition. Our results show significant gains of jointly learning from the two modalities when compared to text or audio only, under adverse noise and limited volume of training data. The results generalize to medical symptoms detection where we observe a similar pattern of improvements with multimodal learning.

The image-based multimodal automatic speech recognition (ASR) model enhances speech recognition performance by incorporating audio-related image. However, some works suggest that introducing image information to model does not help improving ASR performance. In this paper, we propose a novel approach effectively utilizing audio-related image information and set up VHASR, a multimodal speech recognition system that uses vision as hotwords to strengthen the model's speech recognition capability. Our system utilizes a dual-stream architecture, which firstly transcribes the text on the two streams separately, and then combines the outputs. We evaluate the proposed model on four datasets: Flickr8k, ADE20k, COCO, and OpenImages. The experimental results show that VHASR can effectively utilize key information in images to enhance the model's speech recognition ability. Its performance not only surpasses unimodal ASR, but also achieves SOTA among existing image-based multimodal ASR.

Recent large language models (LLMs) in the general domain, such as ChatGPT, have shown remarkable success in following instructions and producing human-like responses. However, such language models have not been learned individually and carefully for the medical domain, resulting in poor diagnostic accuracy and inability to give correct recommendations for medical diagnosis, medications, etc. To address this issue, we collected more than 700 diseases and their corresponding symptoms, recommended medications, and required medical tests, and then generated 5K doctor-patient conversations. By fine-tuning models of doctor-patient conversations, these models emerge with great potential to understand patients' needs, provide informed advice, and offer valuable assistance in a variety of medical-related fields. The integration of these advanced language models into healthcare can revolutionize the way healthcare professionals and patients communicate, ultimately improving the overall quality of care and patient outcomes. In addition, we will open all source code, datasets and model weights to advance the further development of dialogue models in the medical field. In addition, the training data, code, and weights of this project are available at: https://github.com/Kent0n-Li/ChatDoctor.

Intent is defined for understanding spoken language in existing works. Both textual features and acoustic features involved in medical speech contain intent, which is important for symptomatic diagnosis. In this paper, we propose a medical speech classification model named DRSC that automatically learns to disentangle intent and content representations from textual-acoustic data for classification. The intent representations of the text domain and the Mel-spectrogram domain are extracted via intent encoders, and then the reconstructed text feature and the Mel-spectrogram feature are obtained through two exchanges. After combining the intent from two domains into a joint representation, the integrated intent representation is fed into a decision layer for classification. Experimental results show that our model obtains an average accuracy rate of 95% in detecting 25 different medical symptoms.

In natural language processing applied to the clinical domain, utilizing large language models has emerged as a promising avenue for error detection and correction on clinical notes, a knowledge-intensive task for which annotated data is scarce. This paper presents MedReAct'N'MedReFlex, which leverages a suite of four LLM-based medical agents. The MedReAct agent initiates the process by observing, analyzing, and taking action, generating trajectories to guide the search to target a potential error in the clinical notes. Subsequently, the MedEval agent employs five evaluators to assess the targeted error and the proposed correction. In cases where MedReAct's actions prove insufficient, the MedReFlex agent intervenes, engaging in reflective analysis and proposing alternative strategies. Finally, the MedFinalParser agent formats the final output, preserving the original style while ensuring the integrity of the error correction process. One core component of our method is our RAG pipeline based on our ClinicalCorp corpora. Among other well-known sources containing clinical guidelines and information, we preprocess and release the open-source MedWiki dataset for clinical RAG application. Our results demonstrate the central role of our RAG approach with ClinicalCorp leveraged through the MedReAct'N'MedReFlex framework. It achieved the ninth rank on the MEDIQA-CORR 2024 final leaderboard.

This paper presents our efforts to build a robust ASR model for the shared task Automatic Speech Recognition for spontaneous and prepared speech & Speech Emotion Recognition in Portuguese (SE&R 2022). The goal of the challenge is to advance the ASR research for the Portuguese language, considering prepared and spontaneous speech in different dialects. Our method consist on fine-tuning an ASR model in a domain-specific approach, applying gain normalization and selective noise insertion. The proposed method improved over the strong baseline provided on the test set in 3 of the 4 tracks available

Question answering (QA) systems have gained explosive attention in recent years. However, QA tasks in Vietnamese do not have many datasets. Significantly, there is mostly no dataset in the medical domain. Therefore, we built a Vietnamese Healthcare Question Answering dataset (ViHealthQA), including 10,015 question-answer passage pairs for this task, in which questions from health-interested users were asked on prestigious health websites and answers from highly qualified experts. This paper proposes a two-stage QA system based on Sentence-BERT (SBERT) using multiple negatives ranking (MNR) loss combined with BM25. Then, we conduct diverse experiments with many bag-of-words models to assess our system's performance. With the obtained results, this system achieves better performance than traditional methods.

Recent advances in natural language processing (NLP) can be largely attributed to the advent of pre-trained language models such as BERT and RoBERTa. While these models demonstrate remarkable performance on general datasets, they can struggle in specialized domains such as medicine, where unique domain-specific terminologies, domain-specific abbreviations, and varying document structures are common. This paper explores strategies for adapting these models to domain-specific requirements, primarily through continuous pre-training on domain-specific data. We pre-trained several German medical language models on 2.4B tokens derived from translated public English medical data and 3B tokens of German clinical data. The resulting models were evaluated on various German downstream tasks, including named entity recognition (NER), multi-label classification, and extractive question answering. Our results suggest that models augmented by clinical and translation-based pre-training typically outperform general domain models in medical contexts. We conclude that continuous pre-training has demonstrated the ability to match or even exceed the performance of clinical models trained from scratch. Furthermore, pre-training on clinical data or leveraging translated texts have proven to be reliable methods for domain adaptation in medical NLP tasks.

Recently, the increasing demand for superior medical services has highlighted the discrepancies in the medical infrastructure. With big data, especially texts, forming the foundation of medical services, there is an exigent need for effective natural language processing (NLP) solutions tailored to the healthcare domain. Conventional approaches leveraging pre-trained models present promising results in this domain and current large language models (LLMs) offer advanced foundation for medical text processing. However, most medical LLMs are trained only with supervised fine-tuning (SFT), even though it efficiently empowers LLMs to understand and respond to medical instructions but is ineffective in learning domain knowledge and aligning with human preference. Another engineering barrier that prevents current medical LLM from better text processing ability is their restricted context length (e.g., 2,048 tokens), making it hard for the LLMs to process long context, which is frequently required in the medical domain. In this work, we propose ChiMed-GPT, a new benchmark LLM designed explicitly for Chinese medical domain, with enlarged context length to 4,096 tokens and undergoes a comprehensive training regime with pre-training, SFT, and RLHF. Evaluations on real-world tasks including information extraction, question answering, and dialogue generation demonstrate ChiMed-GPT's superior performance over general domain LLMs. Furthermore, we analyze possible biases through prompting ChiMed-GPT to perform attitude scales regarding discrimination of patients, so as to contribute to further responsible development of LLMs in the medical domain. The code and model are released at https://github.com/synlp/ChiMed-GPT.

End-to-end automatic speech recognition (E2E ASR) systems often suffer from mistranscription of domain-specific phrases, such as named entities, sometimes leading to catastrophic failures in downstream tasks. A family of fast and lightweight named entity correction (NEC) models for ASR have recently been proposed, which normally build on phonetic-level edit distance algorithms and have shown impressive NEC performance. However, as the named entity (NE) list grows, the problems of phonetic confusion in the NE list are exacerbated; for example, homophone ambiguities increase substantially. In view of this, we proposed a novel Description Augmented Named entity CorrEctoR (dubbed DANCER), which leverages entity descriptions to provide additional information to facilitate mitigation of phonetic confusion for NEC on ASR transcription. To this end, an efficient entity description augmented masked language model (EDA-MLM) comprised of a dense retrieval model is introduced, enabling MLM to adapt swiftly to domain-specific entities for the NEC task. A series of experiments conducted on the AISHELL-1 and Homophone datasets confirm the effectiveness of our modeling approach. DANCER outperforms a strong baseline, the phonetic edit-distance-based NEC model (PED-NEC), by a character error rate (CER) reduction of about 7% relatively on AISHELL-1 for named entities. More notably, when tested on Homophone that contain named entities of high phonetic confusion, DANCER offers a more pronounced CER reduction of 46% relatively over PED-NEC for named entities.

Automatic speech recognition (ASR) allows transcribing the communications between air traffic controllers (ATCOs) and aircraft pilots. The transcriptions are used later to extract ATC named entities, e.g., aircraft callsigns. One common challenge is speech activity detection (SAD) and speaker diarization (SD). In the failure condition, two or more segments remain in the same recording, jeopardizing the overall performance. We propose a system that combines SAD and a BERT model to perform speaker change detection and speaker role detection (SRD) by chunking ASR transcripts, i.e., SD with a defined number of speakers together with SRD. The proposed model is evaluated on real-life public ATC databases. Our BERT SD model baseline reaches up to 10% and 20% token-based Jaccard error rate (JER) in public and private ATC databases. We also achieved relative improvements of 32% and 7.7% in JERs and SD error rate (DER), respectively, compared to VBx, a well-known SD system.

Automatic speech recognition (ASR) systems are designed to transcribe spoken language into written text and find utility in a variety of applications including voice assistants and transcription services. However, it has been observed that state-of-the-art ASR systems which deliver impressive benchmark results, struggle with speakers of certain regions or demographics due to variation in their speech properties. In this work, we describe the curation of a massive speech dataset of 8740 hours consisting of sim9.8K technical lectures in the English language along with their transcripts delivered by instructors representing various parts of Indian demography. The dataset is sourced from the very popular NPTEL MOOC platform. We use the curated dataset to measure the existing disparity in YouTube Automatic Captions and OpenAI Whisper model performance across the diverse demographic traits of speakers in India. While there exists disparity due to gender, native region, age and speech rate of speakers, disparity based on caste is non-existent. We also observe statistically significant disparity across the disciplines of the lectures. These results indicate the need of more inclusive and robust ASR systems and more representational datasets for disparity evaluation in them.

Large language models have exhibited exceptional performance on various Natural Language Processing (NLP) tasks, leveraging techniques such as the pre-training, and instruction fine-tuning. Despite these advances, their effectiveness in medical applications is limited, due to challenges such as factual inaccuracies, reasoning abilities, and lack grounding in real-world experience. In this study, we present ClinicalGPT, a language model explicitly designed and optimized for clinical scenarios. By incorporating extensive and diverse real-world data, such as medical records, domain-specific knowledge, and multi-round dialogue consultations in the training process, ClinicalGPT is better prepared to handle multiple clinical task. Furthermore, we introduce a comprehensive evaluation framework that includes medical knowledge question-answering, medical exams, patient consultations, and diagnostic analysis of medical records. Our results demonstrate that ClinicalGPT significantly outperforms other models in these tasks, highlighting the effectiveness of our approach in adapting large language models to the critical domain of healthcare.

Large Language Models (LLMs) have demonstrated remarkable versatility in recent years, offering potential applications across specialized domains such as healthcare and medicine. Despite the availability of various open-source LLMs tailored for health contexts, adapting general-purpose LLMs to the medical domain presents significant challenges. In this paper, we introduce BioMistral, an open-source LLM tailored for the biomedical domain, utilizing Mistral as its foundation model and further pre-trained on PubMed Central. We conduct a comprehensive evaluation of BioMistral on a benchmark comprising 10 established medical question-answering (QA) tasks in English. We also explore lightweight models obtained through quantization and model merging approaches. Our results demonstrate BioMistral's superior performance compared to existing open-source medical models and its competitive edge against proprietary counterparts. Finally, to address the limited availability of data beyond English and to assess the multilingual generalization of medical LLMs, we automatically translated and evaluated this benchmark into 7 other languages. This marks the first large-scale multilingual evaluation of LLMs in the medical domain. Datasets, multilingual evaluation benchmarks, scripts, and all the models obtained during our experiments are freely released.

The performance of automated speech recognition (ASR) systems is well known to differ for varied application domains. At the same time, vendors and research groups typically report ASR quality results either for limited use simplistic domains (audiobooks, TED talks), or proprietary datasets. To fill this gap, we provide an open-source 10-hour ASR system evaluation dataset NTR MediaSpeech for 4 languages: Spanish, French, Turkish and Arabic. The dataset was collected from the official youtube channels of media in the respective languages, and manually transcribed. We estimate that the WER of the dataset is under 5%. We have benchmarked many ASR systems available both commercially and freely, and provide the benchmark results. We also open-source baseline QuartzNet models for each language.

This work presents biomedical and clinical language models for Spanish by experimenting with different pretraining choices, such as masking at word and subword level, varying the vocabulary size and testing with domain data, looking for better language representations. Interestingly, in the absence of enough clinical data to train a model from scratch, we applied mixed-domain pretraining and cross-domain transfer approaches to generate a performant bio-clinical model suitable for real-world clinical data. We evaluated our models on Named Entity Recognition (NER) tasks for biomedical documents and challenging hospital discharge reports. When compared against the competitive mBERT and BETO models, we outperform them in all NER tasks by a significant margin. Finally, we studied the impact of the model's vocabulary on the NER performances by offering an interesting vocabulary-centric analysis. The results confirm that domain-specific pretraining is fundamental to achieving higher performances in downstream NER tasks, even within a mid-resource scenario. To the best of our knowledge, we provide the first biomedical and clinical transformer-based pretrained language models for Spanish, intending to boost native Spanish NLP applications in biomedicine. Our best models are freely available in the HuggingFace hub: https://huggingface.co/BSC-TeMU.

In Natural Language Processing (NLP), Machine Reading Comprehension (MRC) is the task of answering a question based on a given context. To handle questions in the medical domain, modern language models such as BioBERT, SciBERT and even ChatGPT are trained on vast amounts of in-domain medical corpora. However, in-domain pre-training is expensive in terms of time and resources. In this paper, we propose a resource-efficient approach for injecting domain knowledge into a model without relying on such domain-specific pre-training. Knowledge graphs are powerful resources for accessing medical information. Building on existing work, we introduce a method using Multi-Layer Perceptrons (MLPs) for aligning and integrating embeddings extracted from medical knowledge graphs with the embedding spaces of pre-trained language models (LMs). The aligned embeddings are fused with open-domain LMs BERT and RoBERTa that are fine-tuned for two MRC tasks, span detection (COVID-QA) and multiple-choice questions (PubMedQA). We compare our method to prior techniques that rely on a vocabulary overlap for embedding alignment and show how our method circumvents this requirement to deliver better performance. On both datasets, our method allows BERT/RoBERTa to either perform on par (occasionally exceeding) with stronger domain-specific models or show improvements in general over prior techniques. With the proposed approach, we signal an alternative method to in-domain pre-training to achieve domain proficiency.

While holding great promise for improving and facilitating healthcare, large language models (LLMs) struggle to produce up-to-date responses on evolving topics due to outdated knowledge or hallucination. Retrieval-augmented generation (RAG) is a pivotal innovation that improves the accuracy and relevance of LLM responses by integrating LLMs with a search engine and external sources of knowledge. However, the quality of RAG responses can be largely impacted by the rank and density of key information in the retrieval results, such as the "lost-in-the-middle" problem. In this work, we aim to improve the robustness and reliability of the RAG workflow in the medical domain. Specifically, we propose a map-reduce strategy, BriefContext, to combat the "lost-in-the-middle" issue without modifying the model weights. We demonstrated the advantage of the workflow with various LLM backbones and on multiple QA datasets. This method promises to improve the safety and reliability of LLMs deployed in healthcare domains.

Question Answering on Electronic Health Records (EHR-QA) has a significant impact on the healthcare domain, and it is being actively studied. Previous research on structured EHR-QA focuses on converting natural language queries into query language such as SQL or SPARQL (NLQ2Query), so the problem scope is limited to pre-defined data types by the specific query language. In order to expand the EHR-QA task beyond this limitation to handle multi-modal medical data and solve complex inference in the future, more primitive systemic language is needed. In this paper, we design the program-based model (NLQ2Program) for EHR-QA as the first step towards the future direction. We tackle MIMICSPARQL*, the graph-based EHR-QA dataset, via a program-based approach in a semi-supervised manner in order to overcome the absence of gold programs. Without the gold program, our proposed model shows comparable performance to the previous state-of-the-art model, which is an NLQ2Query model (0.9% gain). In addition, for a reliable EHR-QA model, we apply the uncertainty decomposition method to measure the ambiguity in the input question. We empirically confirmed data uncertainty is most indicative of the ambiguity in the input question.

Pre-trained transformer language models (LMs) have in recent years become the dominant paradigm in applied NLP. These models have achieved state-of-the-art performance on tasks such as information extraction, question answering, sentiment analysis, document classification and many others. In the biomedical domain, significant progress has been made in adapting this paradigm to NLP tasks that require the integration of domain-specific knowledge as well as statistical modelling of language. In particular, research in this area has focused on the question of how best to construct LMs that take into account not only the patterns of token distribution in medical text, but also the wealth of structured information contained in terminology resources such as the UMLS. This work contributes a data-centric paradigm for enriching the language representations of biomedical transformer-encoder LMs by extracting text sequences from the UMLS. This allows for graph-based learning objectives to be combined with masked-language pre-training. Preliminary results from experiments in the extension of pre-trained LMs as well as training from scratch show that this framework improves downstream performance on multiple biomedical and clinical Named Entity Recognition (NER) tasks.

Speech recognition applications cover a range of different audio and text distributions, with different speaking styles, background noise, transcription punctuation and character casing. However, many speech recognition systems require dataset-specific tuning (audio filtering, punctuation removal and normalisation of casing), therefore assuming a-priori knowledge of both the audio and text distributions. This tuning requirement can lead to systems failing to generalise to other datasets and domains. To promote the development of multi-domain speech systems, we introduce the End-to-end Speech Benchmark (ESB) for evaluating the performance of a single automatic speech recognition (ASR) system across a broad set of speech datasets. Benchmarked systems must use the same data pre- and post-processing algorithm across datasets - assuming the audio and text data distributions are a-priori unknown. We compare a series of state-of-the-art (SoTA) end-to-end (E2E) systems on this benchmark, demonstrating how a single speech system can be applied and evaluated on a wide range of data distributions. We find E2E systems to be effective across datasets: in a fair comparison, E2E systems achieve within 2.6% of SoTA systems tuned to a specific dataset. Our analysis reveals that transcription artefacts, such as punctuation and casing, pose difficulties for ASR systems and should be included in evaluation. We believe E2E benchmarking over a range of datasets promotes the research of multi-domain speech recognition systems. ESB is available at https://huggingface.co/esb.

Whilst there has been growing progress in Entity Linking (EL) for general language, existing datasets fail to address the complex nature of health terminology in layman's language. Meanwhile, there is a growing need for applications that can understand the public's voice in the health domain. To address this we introduce a new corpus called COMETA, consisting of 20k English biomedical entity mentions from Reddit expert-annotated with links to SNOMED CT, a widely-used medical knowledge graph. Our corpus satisfies a combination of desirable properties, from scale and coverage to diversity and quality, that to the best of our knowledge has not been met by any of the existing resources in the field. Through benchmark experiments on 20 EL baselines from string- to neural-based models we shed light on the ability of these systems to perform complex inference on entities and concepts under 2 challenging evaluation scenarios. Our experimental results on COMETA illustrate that no golden bullet exists and even the best mainstream techniques still have a significant performance gap to fill, while the best solution relies on combining different views of data.

Large language models (LLMs) hold immense promise to serve complex health information needs but also have the potential to introduce harm and exacerbate health disparities. Reliably evaluating equity-related model failures is a critical step toward developing systems that promote health equity. In this work, we present resources and methodologies for surfacing biases with potential to precipitate equity-related harms in long-form, LLM-generated answers to medical questions and then conduct an empirical case study with Med-PaLM 2, resulting in the largest human evaluation study in this area to date. Our contributions include a multifactorial framework for human assessment of LLM-generated answers for biases, and EquityMedQA, a collection of seven newly-released datasets comprising both manually-curated and LLM-generated questions enriched for adversarial queries. Both our human assessment framework and dataset design process are grounded in an iterative participatory approach and review of possible biases in Med-PaLM 2 answers to adversarial queries. Through our empirical study, we find that the use of a collection of datasets curated through a variety of methodologies, coupled with a thorough evaluation protocol that leverages multiple assessment rubric designs and diverse rater groups, surfaces biases that may be missed via narrower evaluation approaches. Our experience underscores the importance of using diverse assessment methodologies and involving raters of varying backgrounds and expertise. We emphasize that while our framework can identify specific forms of bias, it is not sufficient to holistically assess whether the deployment of an AI system promotes equitable health outcomes. We hope the broader community leverages and builds on these tools and methods towards realizing a shared goal of LLMs that promote accessible and equitable healthcare for all.

The delayed access to specialized psychiatric assessments and care for patients at risk of suicidal tendencies in emergency departments creates a notable gap in timely intervention, hindering the provision of adequate mental health support during critical situations. To address this, we present a non-invasive, speech-based approach for automatic suicide risk assessment. For our study, we have collected a novel dataset of speech recordings from 20 patients from which we extract three sets of features, including wav2vec, interpretable speech and acoustic features, and deep learning-based spectral representations. We proceed by conducting a binary classification to assess suicide risk in a leave-one-subject-out fashion. Our most effective speech model achieves a balanced accuracy of 66.2,%. Moreover, we show that integrating our speech model with a series of patients' metadata, such as the history of suicide attempts or access to firearms, improves the overall result. The metadata integration yields a balanced accuracy of 94.4,%, marking an absolute improvement of 28.2,%, demonstrating the efficacy of our proposed approaches for automatic suicide risk assessment in emergency medicine.

Recently, Large Language Models (LLMs) have showcased remarkable capabilities in natural language understanding. While demonstrating proficiency in everyday conversations and question-answering situations, these models frequently struggle in domains that require precision, such as medical applications, due to their lack of domain-specific knowledge. In this paper, we describe the procedure for building a powerful, open-source language model specifically designed for medicine applications, termed as PMC-LLaMA. Our contributions are threefold: (i) we systematically investigate the process of adapting a general-purpose foundation language model towards medical domain, this involves data-centric knowledge injection through the integration of 4.8M biomedical academic papers and 30K medical textbooks, as well as comprehensive fine-tuning for alignment with domain-specific instructions; (ii) we contribute a large-scale, comprehensive dataset for instruction tuning. This dataset encompasses medical question-answering (QA), rationale for reasoning, and conversational dialogues, comprising a total of 202M tokens; (iii) we conduct thorough ablation studies to demonstrate the effectiveness of each proposed component. While evaluating on various public medical question-answering benchmarks, our lightweight PMCLLaMA, which consists of only 13 billion parameters, exhibits superior performance, even surpassing ChatGPT. All models, codes, datasets can be found in https://github.com/chaoyi-wu/PMC-LLaMA.

Retrieval-augmented generation (RAG) has emerged as a promising approach to enhance the performance of large language models (LLMs) in knowledge-intensive tasks such as those from medical domain. However, the sensitive nature of the medical domain necessitates a completely accurate and trustworthy system. While existing RAG benchmarks primarily focus on the standard retrieve-answer setting, they overlook many practical scenarios that measure crucial aspects of a reliable medical system. This paper addresses this gap by providing a comprehensive evaluation framework for medical question-answering (QA) systems in a RAG setting for these situations, including sufficiency, integration, and robustness. We introduce Medical Retrieval-Augmented Generation Benchmark (MedRGB) that provides various supplementary elements to four medical QA datasets for testing LLMs' ability to handle these specific scenarios. Utilizing MedRGB, we conduct extensive evaluations of both state-of-the-art commercial LLMs and open-source models across multiple retrieval conditions. Our experimental results reveals current models' limited ability to handle noise and misinformation in the retrieved documents. We further analyze the LLMs' reasoning processes to provides valuable insights and future directions for developing RAG systems in this critical medical domain.

Multimodal foundation models, such as Gemini and ChatGPT, have revolutionized human-machine interactions by seamlessly integrating various forms of data. Developing a universal spoken language model that comprehends a wide range of natural language instructions is critical for bridging communication gaps and facilitating more intuitive interactions. However, the absence of a comprehensive evaluation benchmark poses a significant challenge. We present Dynamic-SUPERB Phase-2, an open and evolving benchmark for the comprehensive evaluation of instruction-based universal speech models. Building upon the first generation, this second version incorporates 125 new tasks contributed collaboratively by the global research community, expanding the benchmark to a total of 180 tasks, making it the largest benchmark for speech and audio evaluation. While the first generation of Dynamic-SUPERB was limited to classification tasks, Dynamic-SUPERB Phase-2 broadens its evaluation capabilities by introducing a wide array of novel and diverse tasks, including regression and sequence generation, across speech, music, and environmental audio. Evaluation results indicate that none of the models performed well universally. SALMONN-13B excelled in English ASR, while WavLLM demonstrated high accuracy in emotion recognition, but current models still require further innovations to handle a broader range of tasks. We will soon open-source all task data and the evaluation pipeline.

Spoken Named Entity Recognition (NER) aims to extracting named entities from speech and categorizing them into types like person, location, organization, etc. In this work, we present VietMed-NER - the first spoken NER dataset in the medical domain. To our best knowledge, our real-world dataset is the largest spoken NER dataset in the world in terms of the number of entity types, featuring 18 distinct types. Secondly, we present baseline results using various state-of-the-art pre-trained models: encoder-only and sequence-to-sequence. We found that pre-trained multilingual models XLM-R outperformed all monolingual models on both reference text and ASR output. Also in general, encoders perform better than sequence-to-sequence models for the NER task. By simply translating, the transcript is applicable not just to Vietnamese but to other languages as well. All code, data and models are made publicly available here: https://github.com/leduckhai/MultiMed

Large language models (LLMs), such as GPT-4, have demonstrated remarkable capabilities across a wide range of tasks, including health applications. In this paper, we study how LLMs can be used to scale biomedical knowledge curation. We find that while LLMs already possess decent competency in structuring biomedical text, by distillation into a task-specific student model through self-supervised learning, substantial gains can be attained over out-of-box LLMs, with additional advantages such as cost, efficiency, and white-box model access. We conduct a case study on adverse drug event (ADE) extraction, which is an important area for improving care. On standard ADE extraction evaluation, a GPT-3.5 distilled PubMedBERT model attained comparable accuracy as supervised state-of-the-art models without using any labeled data. Despite being over 1,000 times smaller, the distilled model outperformed its teacher GPT-3.5 by over 6 absolute points in F1 and GPT-4 by over 5 absolute points. Ablation studies on distillation model choice (e.g., PubMedBERT vs BioGPT) and ADE extraction architecture shed light on best practice for biomedical knowledge extraction. Similar gains were attained by distillation for other standard biomedical knowledge extraction tasks such as gene-disease associations and protected health information, further illustrating the promise of this approach.

Linking clinical narratives to standardized vocabularies and coding systems is a key component of unlocking the information in medical text for analysis. However, many domains of medical concepts lack well-developed terminologies that can support effective coding of medical text. We present a framework for developing natural language processing (NLP) technologies for automated coding of under-studied types of medical information, and demonstrate its applicability via a case study on physical mobility function. Mobility is a component of many health measures, from post-acute care and surgical outcomes to chronic frailty and disability, and is coded in the International Classification of Functioning, Disability, and Health (ICF). However, mobility and other types of functional activity remain under-studied in medical informatics, and neither the ICF nor commonly-used medical terminologies capture functional status terminology in practice. We investigated two data-driven paradigms, classification and candidate selection, to link narrative observations of mobility to standardized ICF codes, using a dataset of clinical narratives from physical therapy encounters. Recent advances in language modeling and word embedding were used as features for established machine learning models and a novel deep learning approach, achieving a macro F-1 score of 84% on linking mobility activity reports to ICF codes. Both classification and candidate selection approaches present distinct strengths for automated coding in under-studied domains, and we highlight that the combination of (i) a small annotated data set; (ii) expert definitions of codes of interest; and (iii) a representative text corpus is sufficient to produce high-performing automated coding systems. This study has implications for the ongoing growth of NLP tools for a variety of specialized applications in clinical care and research.

Large language models (LLMs) have demonstrated remarkable success in NLP tasks. However, there is a paucity of studies that attempt to evaluate their performances on social media-based health-related natural language processing tasks, which have traditionally been difficult to achieve high scores in. We benchmarked one supervised classic machine learning model based on Support Vector Machines (SVMs), three supervised pretrained language models (PLMs) based on RoBERTa, BERTweet, and SocBERT, and two LLM based classifiers (GPT3.5 and GPT4), across 6 text classification tasks. We developed three approaches for leveraging LLMs for text classification: employing LLMs as zero-shot classifiers, us-ing LLMs as annotators to annotate training data for supervised classifiers, and utilizing LLMs with few-shot examples for augmentation of manually annotated data. Our comprehensive experiments demonstrate that employ-ing data augmentation using LLMs (GPT-4) with relatively small human-annotated data to train lightweight supervised classification models achieves superior results compared to training with human-annotated data alone. Supervised learners also outperform GPT-4 and GPT-3.5 in zero-shot settings. By leveraging this data augmentation strategy, we can harness the power of LLMs to develop smaller, more effective domain-specific NLP models. LLM-annotated data without human guidance for training light-weight supervised classification models is an ineffective strategy. However, LLM, as a zero-shot classifier, shows promise in excluding false negatives and potentially reducing the human effort required for data annotation. Future investigations are imperative to explore optimal training data sizes and the optimal amounts of augmented data.

Recent research has demonstrated that training a linear connector between speech foundation encoders and large language models (LLMs) enables this architecture to achieve strong ASR capabilities. Despite the impressive results, it remains unclear whether these simple approaches are robust enough across different scenarios and speech conditions, such as domain shifts and different speech perturbations. In this paper, we address these questions by conducting various ablation experiments using a recent and widely adopted approach called SLAM-ASR. We present novel empirical findings that offer insights on how to effectively utilize the SLAM-ASR architecture across a wide range of settings. Our main findings indicate that the SLAM-ASR exhibits poor performance in cross-domain evaluation settings. Additionally, speech perturbations within in-domain data, such as changes in speed or the presence of additive noise, can significantly impact performance. Our findings offer critical insights for fine-tuning and configuring robust LLM-based ASR models, tailored to different data characteristics and computational resources.

Automatic speech recognition (ASR) on low resource languages improves the access of linguistic minorities to technological advantages provided by artificial intelligence (AI). In this paper, we address the problem of data scarcity for the Hong Kong Cantonese language by creating a new Cantonese dataset. Our dataset, Multi-Domain Cantonese Corpus (MDCC), consists of 73.6 hours of clean read speech paired with transcripts, collected from Cantonese audiobooks from Hong Kong. It comprises philosophy, politics, education, culture, lifestyle and family domains, covering a wide range of topics. We also review all existing Cantonese datasets and analyze them according to their speech type, data source, total size and availability. We further conduct experiments with Fairseq S2T Transformer, a state-of-the-art ASR model, on the biggest existing dataset, Common Voice zh-HK, and our proposed MDCC, and the results show the effectiveness of our dataset. In addition, we create a powerful and robust Cantonese ASR model by applying multi-dataset learning on MDCC and Common Voice zh-HK.

The digitization of healthcare has facilitated the sharing and re-using of medical data but has also raised concerns about confidentiality and privacy. HIPAA (Health Insurance Portability and Accountability Act) mandates removing re-identifying information before the dissemination of medical records. Thus, effective and efficient solutions for de-identifying medical data, especially those in free-text forms, are highly needed. While various computer-assisted de-identification methods, including both rule-based and learning-based, have been developed and used in prior practice, such solutions still lack generalizability or need to be fine-tuned according to different scenarios, significantly imposing restrictions in wider use. The advancement of large language models (LLM), such as ChatGPT and GPT-4, have shown great potential in processing text data in the medical domain with zero-shot in-context learning, especially in the task of privacy protection, as these models can identify confidential information by their powerful named entity recognition (NER) capability. In this work, we developed a novel GPT4-enabled de-identification framework (``DeID-GPT") to automatically identify and remove the identifying information. Compared to existing commonly used medical text data de-identification methods, our developed DeID-GPT showed the highest accuracy and remarkable reliability in masking private information from the unstructured medical text while preserving the original structure and meaning of the text. This study is one of the earliest to utilize ChatGPT and GPT-4 for medical text data processing and de-identification, which provides insights for further research and solution development on the use of LLMs such as ChatGPT/GPT-4 in healthcare. Codes and benchmarking data information are available at https://github.com/yhydhx/ChatGPT-API.

The evolution of speech technology has been spurred by the rapid increase in dataset sizes. Traditional speech models generally depend on a large amount of labeled training data, which is scarce for low-resource languages. This paper presents GigaSpeech 2, a large-scale, multi-domain, multilingual speech recognition corpus. It is designed for low-resource languages and does not rely on paired speech and text data. GigaSpeech 2 comprises about 30,000 hours of automatically transcribed speech, including Thai, Indonesian, and Vietnamese, gathered from unlabeled YouTube videos. We also introduce an automated pipeline for data crawling, transcription, and label refinement. Specifically, this pipeline uses Whisper for initial transcription and TorchAudio for forced alignment, combined with multi-dimensional filtering for data quality assurance. A modified Noisy Student Training is developed to further refine flawed pseudo labels iteratively, thus enhancing model performance. Experimental results on our manually transcribed evaluation set and two public test sets from Common Voice and FLEURS confirm our corpus's high quality and broad applicability. Notably, ASR models trained on GigaSpeech 2 can reduce the word error rate for Thai, Indonesian, and Vietnamese on our challenging and realistic YouTube test set by 25% to 40% compared to the Whisper large-v3 model, with merely 10% model parameters. Furthermore, our ASR models trained on Gigaspeech 2 yield superior performance compared to commercial services. We believe that our newly introduced corpus and pipeline will open a new avenue for low-resource speech recognition and significantly facilitate research in this area.

We introduce the largest transcribed Arabic speech corpus, QASR, collected from the broadcast domain. This multi-dialect speech dataset contains 2,000 hours of speech sampled at 16kHz crawled from Aljazeera news channel. The dataset is released with lightly supervised transcriptions, aligned with the audio segments. Unlike previous datasets, QASR contains linguistically motivated segmentation, punctuation, speaker information among others. QASR is suitable for training and evaluating speech recognition systems, acoustics- and/or linguistics- based Arabic dialect identification, punctuation restoration, speaker identification, speaker linking, and potentially other NLP modules for spoken data. In addition to QASR transcription, we release a dataset of 130M words to aid in designing and training a better language model. We show that end-to-end automatic speech recognition trained on QASR reports a competitive word error rate compared to the previous MGB-2 corpus. We report baseline results for downstream natural language processing tasks such as named entity recognition using speech transcript. We also report the first baseline for Arabic punctuation restoration. We make the corpus available for the research community.

Extracting patient information from unstructured text is a critical task in health decision-support and clinical research. Large language models (LLMs) have shown the potential to accelerate clinical curation via few-shot in-context learning, in contrast to supervised learning which requires much more costly human annotations. However, despite drastic advances in modern LLMs such as GPT-4, they still struggle with issues regarding accuracy and interpretability, especially in mission-critical domains such as health. Here, we explore a general mitigation framework using self-verification, which leverages the LLM to provide provenance for its own extraction and check its own outputs. This is made possible by the asymmetry between verification and generation, where the latter is often much easier than the former. Experimental results show that our method consistently improves accuracy for various LLMs in standard clinical information extraction tasks. Additionally, self-verification yields interpretations in the form of a short text span corresponding to each output, which makes it very efficient for human experts to audit the results, paving the way towards trustworthy extraction of clinical information in resource-constrained scenarios. To facilitate future research in this direction, we release our code and prompts.

The advancement in healthcare has shifted focus toward patient-centric approaches, particularly in self-care and patient education, facilitated by access to Electronic Health Records (EHR). However, medical jargon in EHRs poses significant challenges in patient comprehension. To address this, we introduce a new task of automatically generating lay definitions, aiming to simplify complex medical terms into patient-friendly lay language. We first created the README dataset, an extensive collection of over 50,000 unique (medical term, lay definition) pairs and 300,000 mentions, each offering context-aware lay definitions manually annotated by domain experts. We have also engineered a data-centric Human-AI pipeline that synergizes data filtering, augmentation, and selection to improve data quality. We then used README as the training data for models and leveraged a Retrieval-Augmented Generation method to reduce hallucinations and improve the quality of model outputs. Our extensive automatic and human evaluations demonstrate that open-source mobile-friendly models, when fine-tuned with high-quality data, are capable of matching or even surpassing the performance of state-of-the-art closed-source large language models like ChatGPT. This research represents a significant stride in closing the knowledge gap in patient education and advancing patient-centric healthcare solutions.

Large language models (LLMs) are transforming the ways the general public accesses and consumes information. Their influence is particularly pronounced in pivotal sectors like healthcare, where lay individuals are increasingly appropriating LLMs as conversational agents for everyday queries. While LLMs demonstrate impressive language understanding and generation proficiencies, concerns regarding their safety remain paramount in these high-stake domains. Moreover, the development of LLMs is disproportionately focused on English. It remains unclear how these LLMs perform in the context of non-English languages, a gap that is critical for ensuring equity in the real-world use of these systems.This paper provides a framework to investigate the effectiveness of LLMs as multi-lingual dialogue systems for healthcare queries. Our empirically-derived framework XlingEval focuses on three fundamental criteria for evaluating LLM responses to naturalistic human-authored health-related questions: correctness, consistency, and verifiability. Through extensive experiments on four major global languages, including English, Spanish, Chinese, and Hindi, spanning three expert-annotated large health Q&A datasets, and through an amalgamation of algorithmic and human-evaluation strategies, we found a pronounced disparity in LLM responses across these languages, indicating a need for enhanced cross-lingual capabilities. We further propose XlingHealth, a cross-lingual benchmark for examining the multilingual capabilities of LLMs in the healthcare context. Our findings underscore the pressing need to bolster the cross-lingual capacities of these models, and to provide an equitable information ecosystem accessible to all.

Electronic Health Records (EHRs) hold immense potential for advancing healthcare, offering rich, longitudinal data that combines structured information with valuable insights from unstructured clinical notes. However, the unstructured nature of clinical text poses significant challenges for secondary applications. Traditional methods for structuring EHR free-text data, such as rule-based systems and multi-stage pipelines, are often limited by their time-consuming configurations and inability to adapt across clinical notes from diverse healthcare settings. Few systems provide a comprehensive attribute extraction for terminologies. While giant large language models (LLMs) like GPT-4 and LLaMA 405B excel at structuring tasks, they are slow, costly, and impractical for large-scale use. To overcome these limitations, we introduce GENIE, a Generative Note Information Extraction system that leverages LLMs to streamline the structuring of unstructured clinical text into usable data with standardized format. GENIE processes entire paragraphs in a single pass, extracting entities, assertion statuses, locations, modifiers, values, and purposes with high accuracy. Its unified, end-to-end approach simplifies workflows, reduces errors, and eliminates the need for extensive manual intervention. Using a robust data preparation pipeline and fine-tuned small scale LLMs, GENIE achieves competitive performance across multiple information extraction tasks, outperforming traditional tools like cTAKES and MetaMap and can handle extra attributes to be extracted. GENIE strongly enhances real-world applicability and scalability in healthcare systems. By open-sourcing the model and test data, we aim to encourage collaboration and drive further advancements in EHR structurization.

Large-scale language models (LLMs) have achieved remarkable success across various language tasks but suffer from hallucinations and temporal misalignment. To mitigate these shortcomings, Retrieval-augmented generation (RAG) has been utilized to provide external knowledge to facilitate the answer generation. However, applying such models to the medical domain faces several challenges due to the lack of domain-specific knowledge and the intricacy of real-world scenarios. In this study, we explore LLMs with RAG framework for knowledge-intensive tasks in the medical field. To evaluate the capabilities of LLMs, we introduce MedicineQA, a multi-round dialogue benchmark that simulates the real-world medication consultation scenario and requires LLMs to answer with retrieved evidence from the medicine database. MedicineQA contains 300 multi-round question-answering pairs, each embedded within a detailed dialogue history, highlighting the challenge posed by this knowledge-intensive task to current LLMs. We further propose a new Distill-Retrieve-Read framework instead of the previous Retrieve-then-Read. Specifically, the distillation and retrieval process utilizes a tool calling mechanism to formulate search queries that emulate the keyword-based inquiries used by search engines. With experimental results, we show that our framework brings notable performance improvements and surpasses the previous counterparts in the evidence retrieval process in terms of evidence retrieval accuracy. This advancement sheds light on applying RAG to the medical domain.

We present a novel approach to personalized sleep health management using few-shot Chain-of-Thought (CoT) distillation, enabling small-scale language models (> 2B parameters) to rival the performance of large language models (LLMs) in specialized health domains. Our method simultaneously distills problem-solving strategies, long-tail expert knowledge, and personalized recommendation capabilities from larger models into more efficient, compact models. Unlike existing systems, our approach offers three key functionalities: generating personalized sleep health recommendations, supporting user-specific follow-up inquiries, and providing responses to domain-specific knowledge questions. We focus on sleep health due to its measurability via wearable devices and its impact on overall well-being. Our experimental setup, involving GPT-4o for data synthesis, Qwen-max for instruction set creation, and Qwen2.5 1.5B for model distillation, demonstrates significant improvements over baseline small-scale models in penalization, reasoning, and knowledge application. Experiments using 100 simulated sleep reports and 1,000 domain-specific questions shows our model achieves comparable performance to larger models while maintaining efficiency for real-world deployment. This research not only advances AI-driven health management but also provides a novel approach to leveraging LLM capabilities in resource-constrained environments, potentially enhancing the accessibility of personalized healthcare solutions.

In the era of digital healthcare, the huge volumes of textual information generated every day in hospitals constitute an essential but underused asset that could be exploited with task-specific, fine-tuned biomedical language representation models, improving patient care and management. For such specialized domains, previous research has shown that fine-tuning models stemming from broad-coverage checkpoints can largely benefit additional training rounds over large-scale in-domain resources. However, these resources are often unreachable for less-resourced languages like Italian, preventing local medical institutions to employ in-domain adaptation. In order to reduce this gap, our work investigates two accessible approaches to derive biomedical language models in languages other than English, taking Italian as a concrete use-case: one based on neural machine translation of English resources, favoring quantity over quality; the other based on a high-grade, narrow-scoped corpus natively written in Italian, thus preferring quality over quantity. Our study shows that data quantity is a harder constraint than data quality for biomedical adaptation, but the concatenation of high-quality data can improve model performance even when dealing with relatively size-limited corpora. The models published from our investigations have the potential to unlock important research opportunities for Italian hospitals and academia. Finally, the set of lessons learned from the study constitutes valuable insights towards a solution to build biomedical language models that are generalizable to other less-resourced languages and different domain settings.

This paper proposes a chatbot framework that adopts a hybrid model which consists of a knowledge graph and a text similarity model. Based on this chatbot framework, we build HHH, an online question-and-answer (QA) Healthcare Helper system for answering complex medical questions. HHH maintains a knowledge graph constructed from medical data collected from the Internet. HHH also implements a novel text representation and similarity deep learning model, Hierarchical BiLSTM Attention Model (HBAM), to find the most similar question from a large QA dataset. We compare HBAM with other state-of-the-art language models such as bidirectional encoder representation from transformers (BERT) and Manhattan LSTM Model (MaLSTM). We train and test the models with a subset of the Quora duplicate questions dataset in the medical area. The experimental results show that our model is able to achieve a superior performance than these existing methods.

Recent proprietary large language models (LLMs), such as GPT-4, have achieved a milestone in tackling diverse challenges in the biomedical domain, ranging from multiple-choice questions to long-form generations. To address challenges that still cannot be handled with the encoded knowledge of LLMs, various retrieval-augmented generation (RAG) methods have been developed by searching documents from the knowledge corpus and appending them unconditionally or selectively to the input of LLMs for generation. However, when applying existing methods to different domain-specific problems, poor generalization becomes apparent, leading to fetching incorrect documents or making inaccurate judgments. In this paper, we introduce Self-BioRAG, a framework reliable for biomedical text that specializes in generating explanations, retrieving domain-specific documents, and self-reflecting generated responses. We utilize 84k filtered biomedical instruction sets to train Self-BioRAG that can assess its generated explanations with customized reflective tokens. Our work proves that domain-specific components, such as a retriever, domain-related document corpus, and instruction sets are necessary for adhering to domain-related instructions. Using three major medical question-answering benchmark datasets, experimental results of Self-BioRAG demonstrate significant performance gains by achieving a 7.2% absolute improvement on average over the state-of-the-art open-foundation model with a parameter size of 7B or less. Overall, we analyze that Self-BioRAG finds the clues in the question, retrieves relevant documents if needed, and understands how to answer with information from retrieved documents and encoded knowledge as a medical expert does. We release our data and code for training our framework components and model weights (7B and 13B) to enhance capabilities in biomedical and clinical domains.

Large Language Models (LLMs), particularly those similar to ChatGPT, have significantly influenced the field of Natural Language Processing (NLP). While these models excel in general language tasks, their performance in domain-specific downstream tasks such as biomedical and clinical Named Entity Recognition (NER), Relation Extraction (RE), and Medical Natural Language Inference (NLI) is still evolving. In this context, our study investigates the potential of instruction tuning for biomedical language processing, applying this technique to two general LLMs of substantial scale. We present a comprehensive, instruction-based model trained on a dataset that consists of approximately 200,000 instruction-focused samples. This dataset represents a carefully curated compilation of existing data, meticulously adapted and reformatted to align with the specific requirements of our instruction-based tasks. This initiative represents an important step in utilising such models to achieve results on par with specialised encoder-only models like BioBERT and BioClinicalBERT for various classical biomedical NLP tasks. Our work includes an analysis of the dataset's composition and its impact on model performance, providing insights into the intricacies of instruction tuning. By sharing our codes, models, and the distinctively assembled instruction-based dataset, we seek to encourage ongoing research and development in this area.

The meaningful use of electronic health records (EHR) continues to progress in the digital era with clinical decision support systems augmented by artificial intelligence. A priority in improving provider experience is to overcome information overload and reduce the cognitive burden so fewer medical errors and cognitive biases are introduced during patient care. One major type of medical error is diagnostic error due to systematic or predictable errors in judgment that rely on heuristics. The potential for clinical natural language processing (cNLP) to model diagnostic reasoning in humans with forward reasoning from data to diagnosis and potentially reduce the cognitive burden and medical error has not been investigated. Existing tasks to advance the science in cNLP have largely focused on information extraction and named entity recognition through classification tasks. We introduce a novel suite of tasks coined as Diagnostic Reasoning Benchmarks, DR.BENCH, as a new benchmark for developing and evaluating cNLP models with clinical diagnostic reasoning ability. The suite includes six tasks from ten publicly available datasets addressing clinical text understanding, medical knowledge reasoning, and diagnosis generation. DR.BENCH is the first clinical suite of tasks designed to be a natural language generation framework to evaluate pre-trained language models. Experiments with state-of-the-art pre-trained generative language models using large general domain models and models that were continually trained on a medical corpus demonstrate opportunities for improvement when evaluated in DR. BENCH. We share DR. BENCH as a publicly available GitLab repository with a systematic approach to load and evaluate models for the cNLP community.

Healthcare monitoring is crucial for early detection, timely intervention, and the ongoing management of health conditions, ultimately improving individuals' quality of life. Recent research shows that Large Language Models (LLMs) have demonstrated impressive performance in supporting healthcare tasks. However, existing LLM-based healthcare solutions typically rely on cloud-based systems, which raise privacy concerns and increase the risk of personal information leakage. As a result, there is growing interest in running these models locally on devices like mobile phones and wearables to protect users' privacy. Small Language Models (SLMs) are potential candidates to solve privacy and computational issues, as they are more efficient and better suited for local deployment. However, the performance of SLMs in healthcare domains has not yet been investigated. This paper examines the capability of SLMs to accurately analyze health data, such as steps, calories, sleep minutes, and other vital statistics, to assess an individual's health status. Our results show that, TinyLlama, which has 1.1 billion parameters, utilizes 4.31 GB memory, and has 0.48s latency, showing the best performance compared other four state-of-the-art (SOTA) SLMs on various healthcare applications. Our results indicate that SLMs could potentially be deployed on wearable or mobile devices for real-time health monitoring, providing a practical solution for efficient and privacy-preserving healthcare.

Recent breakthroughs in NLP largely increased the presence of ASR systems in our daily lives. However, for many low-resource languages, ASR models still need to be improved due in part to the difficulty of acquiring pertinent data. This project aims to help advance research in ASR models for Swiss German dialects, by providing insights about the performance of state-of-the-art ASR models on recently published Swiss German speech datasets. We propose a novel loss that takes into account the semantic distance between the predicted and the ground-truth labels. We outperform current state-of-the-art results by fine-tuning OpenAI's Whisper model on Swiss-German datasets.

Hotword customization is one of the concerned issues remained in ASR field - it is of value to enable users of ASR systems to customize names of entities, persons and other phrases to obtain better experience. The past few years have seen effective modeling strategies for ASR contextualization developed, but they still exhibit space for improvement about training stability and the invisible activation process. In this paper we propose Semantic-Augmented Contextual-Paraformer (SeACo-Paraformer) a novel NAR based ASR system with flexible and effective hotword customization ability. It possesses the advantages of AED-based model's accuracy, NAR model's efficiency, and explicit customization capacity of superior performance. Through extensive experiments with 50,000 hours of industrial big data, our proposed model outperforms strong baselines in customization. Besides, we explore an efficient way to filter large-scale incoming hotwords for further improvement. The industrial models compared, source codes and two hotword test sets are all open source.

We present HealthGPT, a powerful Medical Large Vision-Language Model (Med-LVLM) that integrates medical visual comprehension and generation capabilities within a unified autoregressive paradigm. Our bootstrapping philosophy is to progressively adapt heterogeneous comprehension and generation knowledge to pre-trained large language models (LLMs). This is achieved through a novel heterogeneous low-rank adaptation (H-LoRA) technique, which is complemented by a tailored hierarchical visual perception approach and a three-stage learning strategy. To effectively learn the HealthGPT, we devise a comprehensive medical domain-specific comprehension and generation dataset called VL-Health. Experimental results demonstrate exceptional performance and scalability of HealthGPT in medical visual unified tasks. Our project can be accessed at https://github.com/DCDmllm/HealthGPT.

The Norwegian Parliamentary Speech Corpus (NPSC) is a speech dataset with recordings of meetings from Stortinget, the Norwegian parliament. It is the first, publicly available dataset containing unscripted, Norwegian speech designed for training of automatic speech recognition (ASR) systems. The recordings are manually transcribed and annotated with language codes and speakers, and there are detailed metadata about the speakers. The transcriptions exist in both normalized and non-normalized form, and non-standardized words are explicitly marked and annotated with standardized equivalents. To test the usefulness of this dataset, we have compared an ASR system trained on the NPSC with a baseline system trained on only manuscript-read speech. These systems were tested on an independent dataset containing spontaneous, dialectal speech. The NPSC-trained system performed significantly better, with a 22.9% relative improvement in word error rate (WER). Moreover, training on the NPSC is shown to have a "democratizing" effect in terms of dialects, as improvements are generally larger for dialects with higher WER from the baseline system.

Clinical natural language processing requires methods that can address domain-specific challenges, such as complex medical terminology and clinical contexts. Recently, large language models (LLMs) have shown promise in this domain. Yet, their direct deployment can lead to privacy issues and are constrained by resources. To address this challenge, we delve into synthetic clinical text generation using LLMs for clinical NLP tasks. We propose an innovative, resource-efficient approach, ClinGen, which infuses knowledge into the process. Our model involves clinical knowledge extraction and context-informed LLM prompting. Both clinical topics and writing styles are drawn from external domain-specific knowledge graphs and LLMs to guide data generation. Our extensive empirical study across 7 clinical NLP tasks and 16 datasets reveals that ClinGen consistently enhances performance across various tasks, effectively aligning the distribution of real datasets and significantly enriching the diversity of generated training instances. We will publish our code and all the generated data in https://github.com/ritaranx/ClinGen.

Respiratory audio, such as coughing and breathing sounds, has predictive power for a wide range of healthcare applications, yet is currently under-explored. The main problem for those applications arises from the difficulty in collecting large labeled task-specific data for model development. Generalizable respiratory acoustic foundation models pretrained with unlabeled data would offer appealing advantages and possibly unlock this impasse. However, given the safety-critical nature of healthcare applications, it is pivotal to also ensure openness and replicability for any proposed foundation model solution. To this end, we introduce OPERA, an OPEn Respiratory Acoustic foundation model pretraining and benchmarking system, as the first approach answering this need. We curate large-scale respiratory audio datasets (~136K samples, 440 hours), pretrain three pioneering foundation models, and build a benchmark consisting of 19 downstream respiratory health tasks for evaluation. Our pretrained models demonstrate superior performance (against existing acoustic models pretrained with general audio on 16 out of 19 tasks) and generalizability (to unseen datasets and new respiratory audio modalities). This highlights the great promise of respiratory acoustic foundation models and encourages more studies using OPERA as an open resource to accelerate research on respiratory audio for health. The system is accessible from https://github.com/evelyn0414/OPERA.

User-generated data sources have gained significance in uncovering Adverse Drug Reactions (ADRs), with an increasing number of discussions occurring in the digital world. However, the existing clinical corpora predominantly revolve around scientific articles in English. This work presents a multilingual corpus of texts concerning ADRs gathered from diverse sources, including patient fora, social media, and clinical reports in German, French, and Japanese. Our corpus contains annotations covering 12 entity types, four attribute types, and 13 relation types. It contributes to the development of real-world multilingual language models for healthcare. We provide statistics to highlight certain challenges associated with the corpus and conduct preliminary experiments resulting in strong baselines for extracting entities and relations between these entities, both within and across languages.

In this study, we investigate the potential of Large Language Models to complement biomedical knowledge graphs in the training of semantic models for the biomedical and clinical domains. Drawing on the wealth of the UMLS knowledge graph and harnessing cutting-edge Large Language Models, we propose a new state-of-the-art approach for obtaining high-fidelity representations of biomedical concepts and sentences, consisting of three steps: an improved contrastive learning phase, a novel self-distillation phase, and a weight averaging phase. Through rigorous evaluations via the extensive BioLORD testing suite and diverse downstream tasks, we demonstrate consistent and substantial performance improvements over the previous state of the art (e.g. +2pts on MedSTS, +2.5pts on MedNLI-S, +6.1pts on EHR-Rel-B). Besides our new state-of-the-art biomedical model for English, we also distill and release a multilingual model compatible with 50+ languages and finetuned on 7 European languages. Many clinical pipelines can benefit from our latest models. Our new multilingual model enables a range of languages to benefit from our advancements in biomedical semantic representation learning, opening a new avenue for bioinformatics researchers around the world. As a result, we hope to see BioLORD-2023 becoming a precious tool for future biomedical applications.

Hospital information systems (HIS) have become an essential part of healthcare institutions and now incorporate prescribing support software. Prescription support software allows for structured information capture, which improves the safety, appropriateness and efficiency of prescriptions and reduces the number of adverse drug events (ADEs). However, such a system increases the amount of time physicians spend at a computer entering information instead of providing medical care. In addition, any new visiting clinician must learn to manage complex interfaces since each HIS has its own interfaces. In this paper, we present a natural language interface for e-prescribing software in the form of a spoken dialogue system accessible on a smartphone. This system allows prescribers to record their prescriptions verbally, a form of interaction closer to their usual practice. The system extracts the formal representation of the prescription ready to be checked by the prescribing software and uses the dialogue to request mandatory information, correct errors or warn of particular situations. Since, to the best of our knowledge, there is no existing voice-based prescription dialogue system, we present the system developed in a low-resource environment, focusing on dialogue modeling, semantic extraction and data augmentation. The system was evaluated in the wild with 55 participants. This evaluation showed that our system has an average prescription time of 66.15 seconds for physicians and 35.64 seconds for other experts, and a task success rate of 76\% for physicians and 72\% for other experts. All evaluation data were recorded and annotated to form PxCorpus, the first spoken drug prescription corpus that has been made fully available to the community (https://doi.org/10.5281/zenodo.6524162).

We present a machine sound dataset to benchmark domain generalization techniques for anomalous sound detection (ASD). Domain shifts are differences in data distributions that can degrade the detection performance, and handling them is a major issue for the application of ASD systems. While currently available datasets for ASD tasks assume that occurrences of domain shifts are known, in practice, they can be difficult to detect. To handle such domain shifts, domain generalization techniques that perform well regardless of the domains should be investigated. In this paper, we present the first ASD dataset for the domain generalization techniques, called MIMII DG. The dataset consists of five machine types and three domain shift scenarios for each machine type. The dataset is dedicated to the domain generalization task with features such as multiple different values for parameters that cause domain shifts and introduction of domain shifts that can be difficult to detect, such as shifts in the background noise. Experimental results using two baseline systems indicate that the dataset reproduces domain shift scenarios and is useful for benchmarking domain generalization techniques.

Recent work on self-supervised pre-training focus on leveraging large-scale unlabeled speech data to build robust end-to-end (E2E) acoustic models (AM) that can be later fine-tuned on downstream tasks e.g., automatic speech recognition (ASR). Yet, few works investigated the impact on performance when the data properties substantially differ between the pre-training and fine-tuning phases, termed domain shift. We target this scenario by analyzing the robustness of Wav2Vec 2.0 and XLS-R models on downstream ASR for a completely unseen domain, air traffic control (ATC) communications. We benchmark these two models on several open-source and challenging ATC databases with signal-to-noise ratio between 5 and 20 dB. Relative word error rate (WER) reductions between 20% to 40% are obtained in comparison to hybrid-based ASR baselines by only fine-tuning E2E acoustic models with a smaller fraction of labeled data. We analyze WERs on the low-resource scenario and gender bias carried by one ATC dataset.

Large language models (LLMs) are typically trained on general source data for various domains, but a recent surge in domain-specific LLMs has shown their potential to outperform general-purpose models in domain-specific tasks (e.g., biomedicine). Although domain-specific pre-training enhances efficiency and leads to smaller models, the computational costs of training these LLMs remain high, posing budgeting challenges. We introduce MediSwift, a suite of biomedical LMs that leverage sparse pre-training on domain-specific biomedical text data. By inducing up to 75% weight sparsity during the pre-training phase, MediSwift achieves a 2-2.5x reduction in training FLOPs. Notably, all sparse pre-training was performed on the Cerebras CS-2 system, which is specifically designed to realize the acceleration benefits from unstructured weight sparsity, thereby significantly enhancing the efficiency of the MediSwift models. Through subsequent dense fine-tuning and strategic soft prompting, MediSwift models outperform existing LLMs up to 7B parameters on biomedical tasks, setting new benchmarks w.r.t efficiency-accuracy on tasks such as PubMedQA. Our results show that sparse pre-training, along with dense fine-tuning and soft prompting, offers an effective method for creating high-performing, computationally efficient models in specialized domains.

Since the emergence of the Transformer architecture, language model development has increased, driven by their promising potential. However, releasing these models into production requires properly understanding their behavior, particularly in sensitive domains such as medicine. Despite this need, the medical literature still lacks technical assessments of pre-trained language models, which are especially valuable in resource-constrained settings in terms of computational power or limited budget. To address this gap, we provide a comprehensive survey of language models in the medical domain. In addition, we selected a subset of these models for thorough evaluation, focusing on classification and text generation tasks. Our subset encompasses 53 models, ranging from 110 million to 13 billion parameters, spanning the three families of Transformer-based models and from diverse knowledge domains. This study employs a series of approaches for text classification together with zero-shot prompting instead of model training or fine-tuning, which closely resembles the limited resource setting in which many users of language models find themselves. Encouragingly, our findings reveal remarkable performance across various tasks and datasets, underscoring the latent potential of certain models to contain medical knowledge, even without domain specialization. Consequently, our study advocates for further exploration of model applications in medical contexts, particularly in resource-constrained settings. The code is available on https://github.com/anpoc/Language-models-in-medicine.

Named entity recognition (NER) stands as a fundamental and pivotal task within the realm of Natural Language Processing. Particularly within the domain of Biomedical Method NER, this task presents notable challenges, stemming from the continual influx of domain-specific terminologies in scholarly literature. Current research in Biomedical Method (BioMethod) NER suffers from a scarcity of resources, primarily attributed to the intricate nature of methodological concepts, which necessitate a profound understanding for precise delineation. In this study, we propose a novel dataset for biomedical method entity recognition, employing an automated BioMethod entity recognition and information retrieval system to assist human annotation. Furthermore, we comprehensively explore a range of conventional and contemporary open-domain NER methodologies, including the utilization of cutting-edge large-scale language models (LLMs) customised to our dataset. Our empirical findings reveal that the large parameter counts of language models surprisingly inhibit the effective assimilation of entity extraction patterns pertaining to biomedical methods. Remarkably, the approach, leveraging the modestly sized ALBERT model (only 11MB), in conjunction with conditional random fields (CRF), achieves state-of-the-art (SOTA) performance.

DIHARD III was the third in a series of speaker diarization challenges intended to improve the robustness of diarization systems to variability in recording equipment, noise conditions, and conversational domain. Speaker diarization was evaluated under two speech activity conditions (diarization from a reference speech activity vs. diarization from scratch) and 11 diverse domains. The domains span a range of recording conditions and interaction types, including read audio-books, meeting speech, clinical interviews, web videos, and, for the first time, conversational telephone speech. A total of 30 organizations (forming 21teams) from industry and academia submitted 499 valid system outputs. The evaluation results indicate that speaker diarization has improved markedly since DIHARD I, particularly for two-party interactions, but that for many domains (e.g., web video) the problem remains far from solved.

Spoken language understanding (SLU) tasks are usually solved by first transcribing an utterance with automatic speech recognition (ASR) and then feeding the output to a text-based model. Recent advances in self-supervised representation learning for speech data have focused on improving the ASR component. We investigate whether representation learning for speech has matured enough to replace ASR in SLU. We compare learned speech features from wav2vec 2.0, state-of-the-art ASR transcripts, and the ground truth text as input for a novel speech-based named entity recognition task, a cardiac arrest detection task on real-world emergency calls and two existing SLU benchmarks. We show that learned speech features are superior to ASR transcripts on three classification tasks. For machine translation, ASR transcripts are still the better choice. We highlight the intrinsic robustness of wav2vec 2.0 representations to out-of-vocabulary words as key to better performance.

While Automatic Speech Recognition (ASR) models have shown significant advances with the introduction of unsupervised or self-supervised training techniques, these improvements are still only limited to a subsection of languages and speakers. Transfer learning enables the adaptation of large-scale multilingual models to not only low-resource languages but also to more specific speaker groups. However, fine-tuning on data from new domains is usually accompanied by a decrease in performance on the original domain. Therefore, in our experiments, we examine how well the performance of large-scale ASR models can be approximated for smaller domains, with our own dataset of German Senior Voice Commands (SVC-de), and how much of the general speech recognition performance can be preserved by selectively freezing parts of the model during training. To further increase the robustness of the ASR model to vocabulary and speakers outside of the fine-tuned domain, we apply Experience Replay for continual learning. By adding only a fraction of data from the original domain, we are able to reach Word-Error-Rates (WERs) below 5\% on the new domain, while stabilizing performance for general speech recognition at acceptable WERs.

This technical report introduces a Named Clinical Entity Recognition Benchmark for evaluating language models in healthcare, addressing the crucial natural language processing (NLP) task of extracting structured information from clinical narratives to support applications like automated coding, clinical trial cohort identification, and clinical decision support. The leaderboard provides a standardized platform for assessing diverse language models, including encoder and decoder architectures, on their ability to identify and classify clinical entities across multiple medical domains. A curated collection of openly available clinical datasets is utilized, encompassing entities such as diseases, symptoms, medications, procedures, and laboratory measurements. Importantly, these entities are standardized according to the Observational Medical Outcomes Partnership (OMOP) Common Data Model, ensuring consistency and interoperability across different healthcare systems and datasets, and a comprehensive evaluation of model performance. Performance of models is primarily assessed using the F1-score, and it is complemented by various assessment modes to provide comprehensive insights into model performance. The report also includes a brief analysis of models evaluated to date, highlighting observed trends and limitations. By establishing this benchmarking framework, the leaderboard aims to promote transparency, facilitate comparative analyses, and drive innovation in clinical entity recognition tasks, addressing the need for robust evaluation methods in healthcare NLP.

Advances in natural language processing techniques, such as named entity recognition and normalization to widely used standardized terminologies like UMLS or SNOMED-CT, along with the digitalization of electronic health records, have significantly advanced clinical text analysis. This study presents ClinLinker, a novel approach employing a two-phase pipeline for medical entity linking that leverages the potential of in-domain adapted language models for biomedical text mining: initial candidate retrieval using a SapBERT-based bi-encoder and subsequent re-ranking with a cross-encoder, trained by following a contrastive-learning strategy to be tailored to medical concepts in Spanish. This methodology, focused initially on content in Spanish, substantially outperforming multilingual language models designed for the same purpose. This is true even for complex scenarios involving heterogeneous medical terminologies and being trained on a subset of the original data. Our results, evaluated using top-k accuracy at 25 and other top-k metrics, demonstrate our approach's performance on two distinct clinical entity linking Gold Standard corpora, DisTEMIST (diseases) and MedProcNER (clinical procedures), outperforming previous benchmarks by 40 points in DisTEMIST and 43 points in MedProcNER, both normalized to SNOMED-CT codes. These findings highlight our approach's ability to address language-specific nuances and set a new benchmark in entity linking, offering a potent tool for enhancing the utility of digital medical records. The resulting system is of practical value, both for large scale automatic generation of structured data derived from clinical records, as well as for exhaustive extraction and harmonization of predefined clinical variables of interest.

Since the rise of large language models (LLMs), the domain adaptation has been one of the hot topics in various domains. Many medical LLMs trained with English medical dataset have made public recently. However, Japanese LLMs in medical domain still lack its research. Here we utilize multiple 70B-parameter LLMs for the first time and show that instruction tuning using Japanese medical question-answering dataset significantly improves the ability of Japanese LLMs to solve Japanese medical license exams, surpassing 50\% in accuracy. In particular, the Japanese-centric models exhibit a more significant leap in improvement through instruction tuning compared to their English-centric counterparts. This underscores the importance of continual pretraining and the adjustment of the tokenizer in our local language. We also examine two slightly different prompt formats, resulting in non-negligible performance improvement.

The utilization of large language models (LLMs) in the Healthcare domain has generated both excitement and concern due to their ability to effectively respond to freetext queries with certain professional knowledge. This survey outlines the capabilities of the currently developed LLMs for Healthcare and explicates their development process, with the aim of providing an overview of the development roadmap from traditional Pretrained Language Models (PLMs) to LLMs. Specifically, we first explore the potential of LLMs to enhance the efficiency and effectiveness of various Healthcare applications highlighting both the strengths and limitations. Secondly, we conduct a comparison between the previous PLMs and the latest LLMs, as well as comparing various LLMs with each other. Then we summarize related Healthcare training data, training methods, optimization strategies, and usage. Finally, the unique concerns associated with deploying LLMs in Healthcare settings are investigated, particularly regarding fairness, accountability, transparency and ethics. Our survey provide a comprehensive investigation from perspectives of both computer science and Healthcare specialty. Besides the discussion about Healthcare concerns, we supports the computer science community by compiling a collection of open source resources, such as accessible datasets, the latest methodologies, code implementations, and evaluation benchmarks in the Github. Summarily, we contend that a significant paradigm shift is underway, transitioning from PLMs to LLMs. This shift encompasses a move from discriminative AI approaches to generative AI approaches, as well as a shift from model-centered methodologies to datacentered methodologies.

Mental health is a critical issue in modern society, and mental disorders could sometimes turn to suicidal ideation without adequate treatment. Early detection of mental disorders and suicidal ideation from social content provides a potential way for effective social intervention. Recent advances in pretrained contextualized language representations have promoted the development of several domain-specific pretrained models and facilitated several downstream applications. However, there are no existing pretrained language models for mental healthcare. This paper trains and release two pretrained masked language models, i.e., MentalBERT and MentalRoBERTa, to benefit machine learning for the mental healthcare research community. Besides, we evaluate our trained domain-specific models and several variants of pretrained language models on several mental disorder detection benchmarks and demonstrate that language representations pretrained in the target domain improve the performance of mental health detection tasks.

Incremental learning is one paradigm to enable model building and updating at scale with streaming data. For end-to-end automatic speech recognition (ASR) tasks, the absence of human annotated labels along with the need for privacy preserving policies for model building makes it a daunting challenge. Motivated by these challenges, in this paper we use a cloud based framework for production systems to demonstrate insights from privacy preserving incremental learning for automatic speech recognition (ILASR). By privacy preserving, we mean, usage of ephemeral data which are not human annotated. This system is a step forward for production levelASR models for incremental/continual learning that offers near real-time test-bed for experimentation in the cloud for end-to-end ASR, while adhering to privacy-preserving policies. We show that the proposed system can improve the production models significantly(3%) over a new time period of six months even in the absence of human annotated labels with varying levels of weak supervision and large batch sizes in incremental learning. This improvement is 20% over test sets with new words and phrases in the new time period. We demonstrate the effectiveness of model building in a privacy-preserving incremental fashion for ASR while further exploring the utility of having an effective teacher model and use of large batch sizes.

Clinical Natural Language Processing (NLP) has become an emerging technology in healthcare that leverages a large amount of free-text data in electronic health records (EHRs) to improve patient care, support clinical decisions, and facilitate clinical and translational science research. Recently, deep learning has achieved state-of-the-art performance in many clinical NLP tasks. However, training deep learning models usually requires large annotated datasets, which are normally not publicly available and can be time-consuming to build in clinical domains. Working with smaller annotated datasets is typical in clinical NLP and therefore, ensuring that deep learning models perform well is crucial for the models to be used in real-world applications. A widely adopted approach is fine-tuning existing Pre-trained Language Models (PLMs), but these attempts fall short when the training dataset contains only a few annotated samples. Few-Shot Learning (FSL) has recently been investigated to tackle this problem. Siamese Neural Network (SNN) has been widely utilized as an FSL approach in computer vision, but has not been studied well in NLP. Furthermore, the literature on its applications in clinical domains is scarce. In this paper, we propose two SNN-based FSL approaches for clinical NLP, including Pre-Trained SNN (PT-SNN) and SNN with Second-Order Embeddings (SOE-SNN). We evaluated the proposed approaches on two clinical tasks, namely clinical text classification and clinical named entity recognition. We tested three few-shot settings including 4-shot, 8-shot, and 16-shot learning. Both clinical NLP tasks were benchmarked using three PLMs, including BERT,BioBERT, and BioClinicalBERT. The experimental results verified the effectiveness of the proposed SNN-based FSL approaches in both NLP tasks.

Large language models (LLMs) demonstrate remarkable medical expertise, but data privacy concerns impede their direct use in healthcare environments. Although offering improved data privacy protection, domain-specific small language models (SLMs) often underperform LLMs, emphasizing the need for methods that reduce this performance gap while alleviating privacy concerns. In this paper, we present a simple yet effective method that harnesses LLMs' medical proficiency to boost SLM performance in medical tasks under privacy-restricted scenarios. Specifically, we mitigate patient privacy issues by extracting keywords from medical data and prompting the LLM to generate a medical knowledge-intensive context by simulating clinicians' thought processes. This context serves as additional input for SLMs, augmenting their decision-making capabilities. Our method significantly enhances performance in both few-shot and full training settings across three medical knowledge-intensive tasks, achieving up to a 22.57% increase in absolute accuracy compared to SLM fine-tuning without context, and sets new state-of-the-art results in two medical tasks within privacy-restricted scenarios. Further out-of-domain testing and experiments in two general domain datasets showcase its generalizability and broad applicability.

The exponential surge in online health information, coupled with its increasing use by non-experts, highlights the pressing need for advanced Health Information Retrieval models that consider not only topical relevance but also the factual accuracy of the retrieved information, given the potential risks associated with health misinformation. To this aim, this paper introduces a solution driven by Retrieval-Augmented Generation (RAG), which leverages the capabilities of generative Large Language Models (LLMs) to enhance the retrieval of health-related documents grounded in scientific evidence. In particular, we propose a three-stage model: in the first stage, the user's query is employed to retrieve topically relevant passages with associated references from a knowledge base constituted by scientific literature. In the second stage, these passages, alongside the initial query, are processed by LLMs to generate a contextually relevant rich text (GenText). In the last stage, the documents to be retrieved are evaluated and ranked both from the point of view of topical relevance and factual accuracy by means of their comparison with GenText, either through stance detection or semantic similarity. In addition to calculating factual accuracy, GenText can offer a layer of explainability for it, aiding users in understanding the reasoning behind the retrieval. Experimental evaluation of our model on benchmark datasets and against baseline models demonstrates its effectiveness in enhancing the retrieval of both topically relevant and factually accurate health information, thus presenting a significant step forward in the health misinformation mitigation problem.

Mental health disorders are one of the most serious diseases in the world. Most people with such a disease lack access to adequate care, which highlights the importance of training models for the diagnosis and treatment of mental health disorders. However, in the mental health domain, privacy concerns limit the accessibility of personalized treatment data, making it challenging to build powerful models. In this paper, we introduce MentalArena, a self-play framework to train language models by generating domain-specific personalized data, where we obtain a better model capable of making a personalized diagnosis and treatment (as a therapist) and providing information (as a patient). To accurately model human-like mental health patients, we devise Symptom Encoder, which simulates a real patient from both cognition and behavior perspectives. To address intent bias during patient-therapist interactions, we propose Symptom Decoder to compare diagnosed symptoms with encoded symptoms, and dynamically manage the dialogue between patient and therapist according to the identified deviations. We evaluated MentalArena against 6 benchmarks, including biomedicalQA and mental health tasks, compared to 6 advanced models. Our models, fine-tuned on both GPT-3.5 and Llama-3-8b, significantly outperform their counterparts, including GPT-4o. We hope that our work can inspire future research on personalized care. Code is available in https://github.com/Scarelette/MentalArena/tree/main

There is an increasing interest in developing artificial intelligence (AI) systems to process and interpret electronic health records (EHRs). Natural language processing (NLP) powered by pretrained language models is the key technology for medical AI systems utilizing clinical narratives. However, there are few clinical language models, the largest of which trained in the clinical domain is comparatively small at 110 million parameters (compared with billions of parameters in the general domain). It is not clear how large clinical language models with billions of parameters can help medical AI systems utilize unstructured EHRs. In this study, we develop from scratch a large clinical language model - GatorTron - using >90 billion words of text (including >82 billion words of de-identified clinical text) and systematically evaluate it on 5 clinical NLP tasks including clinical concept extraction, medical relation extraction, semantic textual similarity, natural language inference (NLI), and medical question answering (MQA). We examine how (1) scaling up the number of parameters and (2) scaling up the size of the training data could benefit these NLP tasks. GatorTron models scale up the clinical language model from 110 million to 8.9 billion parameters and improve 5 clinical NLP tasks (e.g., 9.6% and 9.5% improvement in accuracy for NLI and MQA), which can be applied to medical AI systems to improve healthcare delivery. The GatorTron models are publicly available at: https://catalog.ngc.nvidia.com/orgs/nvidia/teams/clara/models/gatortron_og.

Recently, Automatic Speech Recognition (ASR), a system that converts audio into text, has caught a lot of attention in the machine learning community. Thus, a lot of publicly available models were released in HuggingFace. However, most of these ASR models are available in English; only a minority of the models are available in Thai. Additionally, most of the Thai ASR models are closed-sourced, and the performance of existing open-sourced models lacks robustness. To address this problem, we train a new ASR model on a pre-trained XLSR-Wav2Vec model with the Thai CommonVoice corpus V8 and train a trigram language model to boost the performance of our ASR model. We hope that our models will be beneficial to individuals and the ASR community in Thailand.

Identifying disease phenotypes from electronic health records (EHRs) is critical for numerous secondary uses. Manually encoding physician knowledge into rules is particularly challenging for rare diseases due to inadequate EHR coding, necessitating review of clinical notes. Large language models (LLMs) offer promise in text understanding but may not efficiently handle real-world clinical documentation. We propose a zero-shot LLM-based method enriched by retrieval-augmented generation and MapReduce, which pre-identifies disease-related text snippets to be used in parallel as queries for the LLM to establish diagnosis. We show that this method as applied to pulmonary hypertension (PH), a rare disease characterized by elevated arterial pressures in the lungs, significantly outperforms physician logic rules (F_1 score of 0.62 vs. 0.75). This method has the potential to enhance rare disease cohort identification, expanding the scope of robust clinical research and care gap identification.

Interactions with virtual assistants typically start with a predefined trigger phrase followed by the user command. To make interactions with the assistant more intuitive, we explore whether it is feasible to drop the requirement that users must begin each command with a trigger phrase. We explore this task in three ways: First, we train classifiers using only acoustic information obtained from the audio waveform. Second, we take the decoder outputs of an automatic speech recognition (ASR) system, such as 1-best hypotheses, as input features to a large language model (LLM). Finally, we explore a multimodal system that combines acoustic and lexical features, as well as ASR decoder signals in an LLM. Using multimodal information yields relative equal-error-rate improvements over text-only and audio-only models of up to 39% and 61%. Increasing the size of the LLM and training with low-rank adaption leads to further relative EER reductions of up to 18% on our dataset.

Foundation Models (FMs) trained on Electronic Health Records (EHRs) have achieved state-of-the-art results on numerous clinical prediction tasks. However, most existing EHR FMs have context windows of <1k tokens. This prevents them from modeling full patient EHRs which can exceed 10k's of events. Recent advancements in subquadratic long-context architectures (e.g., Mamba) offer a promising solution. However, their application to EHR data has not been well-studied. We address this gap by presenting the first systematic evaluation of the effect of context length on modeling EHR data. We find that longer context models improve predictive performance -- our Mamba-based model surpasses the prior state-of-the-art on 9/14 tasks on the EHRSHOT prediction benchmark. For clinical applications, however, model performance alone is insufficient -- robustness to the unique properties of EHR is crucial. Thus, we also evaluate models across three previously underexplored properties of EHR data: (1) the prevalence of "copy-forwarded" diagnoses which creates artificial repetition of tokens within EHR sequences; (2) the irregular time intervals between EHR events which can lead to a wide range of timespans within a context window; and (3) the natural increase in disease complexity over time which makes later tokens in the EHR harder to predict than earlier ones. Stratifying our EHRSHOT results, we find that higher levels of each property correlate negatively with model performance, but that longer context models are more robust to more extreme levels of these properties. Our work highlights the potential for using long-context architectures to model EHR data, and offers a case study for identifying new challenges in modeling sequential data motivated by domains outside of natural language. We release our models and code at: https://github.com/som-shahlab/long_context_clues

This review paper explores recent advances in deep learning approaches for non-invasive cognitive impairment detection. We examine various non-invasive indicators of cognitive decline, including speech and language, facial, and motoric mobility. The paper provides an overview of relevant datasets, feature-extracting techniques, and deep-learning architectures applied to this domain. We have analyzed the performance of different methods across modalities and observed that speech and language-based methods generally achieved the highest detection performance. Studies combining acoustic and linguistic features tended to outperform those using a single modality. Facial analysis methods showed promise for visual modalities but were less extensively studied. Most papers focused on binary classification (impaired vs. non-impaired), with fewer addressing multi-class or regression tasks. Transfer learning and pre-trained language models emerged as popular and effective techniques, especially for linguistic analysis. Despite significant progress, several challenges remain, including data standardization and accessibility, model explainability, longitudinal analysis limitations, and clinical adaptation. Lastly, we propose future research directions, such as investigating language-agnostic speech analysis methods, developing multi-modal diagnostic systems, and addressing ethical considerations in AI-assisted healthcare. By synthesizing current trends and identifying key obstacles, this review aims to guide further development of deep learning-based cognitive impairment detection systems to improve early diagnosis and ultimately patient outcomes.

Indigenous languages are a fundamental legacy in the development of human communication, embodying the unique identity and culture of local communities of America. The Second AmericasNLP Competition Track 1 of NeurIPS 2022 proposed developing automatic speech recognition (ASR) systems for five indigenous languages: Quechua, Guarani, Bribri, Kotiria, and Wa'ikhana. In this paper, we propose a reliable ASR model for each target language by crawling speech corpora spanning diverse sources and applying data augmentation methods that resulted in the winning approach in this competition. To achieve this, we systematically investigated the impact of different hyperparameters by a Bayesian search on the performance of the language models, specifically focusing on the variants of the Wav2vec2.0 XLS-R model: 300M and 1B parameters. Moreover, we performed a global sensitivity analysis to assess the contribution of various hyperparametric configurations to the performances of our best models. Importantly, our results show that freeze fine-tuning updates and dropout rate are more vital parameters than the total number of epochs of lr. Additionally, we liberate our best models -- with no other ASR model reported until now for two Wa'ikhana and Kotiria -- and the many experiments performed to pave the way to other researchers to continue improving ASR in minority languages. This insight opens up interesting avenues for future work, allowing for the advancement of ASR techniques in the preservation of minority indigenous and acknowledging the complexities involved in this important endeavour.

Integrating named entity recognition (NER) with automatic speech recognition (ASR) can significantly enhance transcription accuracy and informativeness. In this paper, we introduce WhisperNER, a novel model that allows joint speech transcription and entity recognition. WhisperNER supports open-type NER, enabling recognition of diverse and evolving entities at inference. Building on recent advancements in open NER research, we augment a large synthetic dataset with synthetic speech samples. This allows us to train WhisperNER on a large number of examples with diverse NER tags. During training, the model is prompted with NER labels and optimized to output the transcribed utterance along with the corresponding tagged entities. To evaluate WhisperNER, we generate synthetic speech for commonly used NER benchmarks and annotate existing ASR datasets with open NER tags. Our experiments demonstrate that WhisperNER outperforms natural baselines on both out-of-domain open type NER and supervised finetuning.

Nowadays the medical domain is receiving more and more attention in applications involving Artificial Intelligence. Clinicians have to deal with an enormous amount of unstructured textual data to make a conclusion about patients' health in their everyday life. Argument mining helps to provide a structure to such data by detecting argumentative components in the text and classifying the relations between them. However, as it is the case for many tasks in Natural Language Processing in general and in medical text processing in particular, the large majority of the work on computational argumentation has been done only for English. This is also the case with the only dataset available for argumentation in the medical domain, namely, the annotated medical data of abstracts of Randomized Controlled Trials (RCT) from the MEDLINE database. In order to mitigate the lack of annotated data for other languages, we empirically investigate several strategies to perform argument mining and classification in medical texts for a language for which no annotated data is available. This project shows that automatically translating and project annotations from English to a target language (Spanish) is an effective way to generate annotated data without manual intervention. Furthermore, our experiments demonstrate that the translation and projection approach outperforms zero-shot cross-lingual approaches using a large masked multilingual language model. Finally, we show how the automatically generated data in Spanish can also be used to improve results in the original English evaluation setting.

Many large language models (LLMs) for medicine have largely been evaluated on short texts, and their ability to handle longer sequences such as a complete electronic health record (EHR) has not been systematically explored. Assessing these models on long sequences is crucial since prior work in the general domain has demonstrated performance degradation of LLMs on longer texts. Motivated by this, we introduce LongBoX, a collection of seven medical datasets in text-to-text format, designed to investigate model performance on long sequences. Preliminary experiments reveal that both medical LLMs (e.g., BioGPT) and strong general domain LLMs (e.g., FLAN-T5) struggle on this benchmark. We further evaluate two techniques designed for long-sequence handling: (i) local-global attention, and (ii) Fusion-in-Decoder (FiD). Our results demonstrate mixed results with long-sequence handling - while scores on some datasets increase, there is substantial room for improvement. We hope that LongBoX facilitates the development of more effective long-sequence techniques for the medical domain. Data and source code are available at https://github.com/Mihir3009/LongBoX.

This paper proposes a simple yet effective way of regularising the encoder-decoder-based automatic speech recognition (ASR) models that enhance the robustness of the model and improve the generalisation to out-of-domain scenarios. The proposed approach is dubbed as Decoder-Centric Regularisation in Encoder-Decoder (DeCRED) architecture for ASR, where auxiliary classifier(s) is introduced in layers of the decoder module. Leveraging these classifiers, we propose two decoding strategies that re-estimate the next token probabilities. Using the recent E-branchformer architecture, we build strong ASR systems that obtained competitive WERs as compared to Whisper-medium and outperformed OWSM v3; while relying only on a fraction of training data and model size. On top of such a strong baseline, we show that DeCRED can further improve the results and, moreover, generalise much better to out-of-domain scenarios, where we show an absolute reduction of 2.7 and 2.9 WERs on AMI and Gigaspeech datasets, respectively. We provide extensive analysis and accompanying experiments that support the benefits of the proposed regularisation scheme.

Predicting disease trajectories from electronic health records (EHRs) is a complex task due to major challenges such as data non-stationarity, high granularity of medical codes, and integration of multimodal data. EHRs contain both structured data, such as diagnostic codes, and unstructured data, such as clinical notes, which hold essential information often overlooked. Current models, primarily based on structured data, struggle to capture the complete medical context of patients, resulting in a loss of valuable information. To address this issue, we propose an approach that integrates unstructured clinical notes into transformer-based deep learning models for sequential disease prediction. This integration enriches the representation of patients' medical histories, thereby improving the accuracy of diagnosis predictions. Experiments on MIMIC-IV datasets demonstrate that the proposed approach outperforms traditional models relying solely on structured data.

Automatic Speech Recognition (ASR) systems predominantly cater to monolingual inputs and struggle with the complexity introduced by mixed language audio. In this paper, we present a novel Multi-Agent Data Generation Framework (MADGF) to address this challenge. We finetune the open-source multilingual ASR model, Whisper, utilizing our generated Mixed Cantonese and English (MCE) audio dataset, Which achieved an impressive Mix Error Rate (MER) of 14.28%, 35.13% lower than the original model. Meanwhile, single language recognition ability is not affected, 12.6% Character Error Rate (CER) in Common voice zh-HK, 14.8% Word Error Rate (WER) in Common voice en. However, these metrics do not encompass all aspects critical to the ASR systems. Hence, we propose a novel evaluation metric called Fidelity to the Original Audio, Accuracy, and Latency (FAL).

Recent advances in automatic speech recognition (ASR) often rely on large speech foundation models for generating high-quality transcriptions. However, these models can be impractical due to limited computing resources. The situation is even more severe in terms of more realistic or difficult scenarios, such as code-switching ASR (CS-ASR). To address this, we present a framework for developing more efficient models for CS-ASR through knowledge distillation using realistic speech-only data. Our proposed method, Leave No Knowledge Behind During Knowledge Distillation (K^2D), leverages both the teacher model's knowledge and additional insights from a small auxiliary model. We evaluate our approach on two in-domain and two out-domain datasets, demonstrating that K^2D is effective. By conducting K^2D on the unlabeled realistic data, we have successfully obtained a 2-time smaller model with 5-time faster generation speed while outperforming the baseline methods and the teacher model on all the testing sets. We have made our model publicly available on Hugging Face (https://huggingface.co/andybi7676/k2d-whisper.zh-en).

Speech datasets available in the public domain are often underutilized because of challenges in discoverability and interoperability. A comprehensive framework has been designed to survey, catalog, and curate available speech datasets, which allows replicable evaluation of automatic speech recognition (ASR) systems. A case study focused on the Polish language was conducted; the framework was applied to curate more than 24 datasets and evaluate 25 combinations of ASR systems and models. This research constitutes the most extensive comparison to date of both commercial and free ASR systems for the Polish language. It draws insights from 600 system-model-test set evaluations, marking a significant advancement in both scale and comprehensiveness. The results of surveys and performance comparisons are available as interactive dashboards (https://huggingface.co/spaces/amu-cai/pl-asr-leaderboard) along with curated datasets (https://huggingface.co/datasets/amu-cai/pl-asr-bigos-v2, https://huggingface.co/datasets/pelcra/pl-asr-pelcra-for-bigos) and the open challenge call (https://poleval.pl/tasks/task3). Tools used for evaluation are open-sourced (https://github.com/goodmike31/pl-asr-bigos-tools), facilitating replication and adaptation for other languages, as well as continuous expansion with new datasets and systems.

As people increasingly prioritize their health, the speed and breadth of health information dissemination on the internet have also grown. At the same time, the presence of false health information (health rumors) intermingled with genuine content poses a significant potential threat to public health. However, current research on Chinese health rumors still lacks a large-scale, public, and open-source dataset of health rumor information, as well as effective and reliable rumor detection methods. This paper addresses this gap by constructing a dataset containing 1.12 million health-related rumors (HealthRCN) through web scraping of common health-related questions and a series of data processing steps. HealthRCN is the largest known dataset of Chinese health information rumors to date. Based on this dataset, we propose retrieval-augmented large language models for Chinese health rumor detection and explainability (HRDE). This model leverages retrieved relevant information to accurately determine whether the input health information is a rumor and provides explanatory responses, effectively aiding users in verifying the authenticity of health information. In evaluation experiments, we compared multiple models and found that HRDE outperformed them all, including GPT-4-1106-Preview, in rumor detection accuracy and answer quality. HRDE achieved an average accuracy of 91.04% and an F1 score of 91.58%.

Self-supervised learning (SSL) is a powerful tool that allows learning of underlying representations from unlabeled data. Transformer based models such as wav2vec 2.0 and HuBERT are leading the field in the speech domain. Generally these models are fine-tuned on a small amount of labeled data for a downstream task such as Automatic Speech Recognition (ASR). This involves re-training the majority of the model for each task. Adapters are small lightweight modules which are commonly used in Natural Language Processing (NLP) to adapt pre-trained models to new tasks. In this paper we propose applying adapters to wav2vec 2.0 to reduce the number of parameters required for downstream ASR tasks, and increase scalability of the model to multiple tasks or languages. Using adapters we can perform ASR while training fewer than 10% of parameters per task compared to full fine-tuning with little degradation of performance. Ablations show that applying adapters into just the top few layers of the pre-trained network gives similar performance to full transfer, supporting the theory that higher pre-trained layers encode more phonemic information, and further optimizing efficiency.

Automatic Speech Recognition (ASR) has witnessed a profound research interest. Recent breakthroughs have given ASR systems different prospects such as faithfully transcribing spoken language, which is a pivotal advancement in building conversational agents. However, there is still an imminent challenge of accurately discerning context-dependent words and phrases. In this work, we propose a novel approach for enhancing contextual recognition within ASR systems via semantic lattice processing leveraging the power of deep learning models in accurately delivering spot-on transcriptions across a wide variety of vocabularies and speaking styles. Our solution consists of using Hidden Markov Models and Gaussian Mixture Models (HMM-GMM) along with Deep Neural Networks (DNN) models integrating both language and acoustic modeling for better accuracy. We infused our network with the use of a transformer-based model to properly rescore the word lattice achieving remarkable capabilities with a palpable reduction in Word Error Rate (WER). We demonstrate the effectiveness of our proposed framework on the LibriSpeech dataset with empirical analyses.

ASR Error Detection (AED) models aim to post-process the output of Automatic Speech Recognition (ASR) systems, in order to detect transcription errors. Modern approaches usually use text-based input, comprised solely of the ASR transcription hypothesis, disregarding additional signals from the ASR model. Instead, we propose to utilize the ASR system's word-level confidence scores for improving AED performance. Specifically, we add an ASR Confidence Embedding (ACE) layer to the AED model's encoder, allowing us to jointly encode the confidence scores and the transcribed text into a contextualized representation. Our experiments show the benefits of ASR confidence scores for AED, their complementary effect over the textual signal, as well as the effectiveness and robustness of ACE for combining these signals. To foster further research, we publish a novel AED dataset consisting of ASR outputs on the LibriSpeech corpus with annotated transcription errors.

Recently, multilingual artificial intelligence assistants, exemplified by ChatGPT, have gained immense popularity. As a crucial gateway to human-computer interaction, multilingual automatic speech recognition (ASR) has also garnered significant attention, as evidenced by systems like Whisper. However, the proprietary nature of the training data has impeded researchers' efforts to study multilingual ASR. This paper introduces MSR-86K, an evolving, large-scale multilingual corpus for speech recognition research. The corpus is derived from publicly accessible videos on YouTube, comprising 15 languages and a total of 86,300 hours of transcribed ASR data. We also introduce how to use the MSR-86K corpus and other open-source corpora to train a robust multilingual ASR model that is competitive with Whisper. MSR-86K will be publicly released on HuggingFace, and we believe that such a large corpus will pave new avenues for research in multilingual ASR.

In this paper, we present an encoder-decoder model leveraging Flan-T5 for post-Automatic Speech Recognition (ASR) Generative Speech Error Correction (GenSEC), and we refer to it as FlanEC. We explore its application within the GenSEC framework to enhance ASR outputs by mapping n-best hypotheses into a single output sentence. By utilizing n-best lists from ASR models, we aim to improve the linguistic correctness, accuracy, and grammaticality of final ASR transcriptions. Specifically, we investigate whether scaling the training data and incorporating diverse datasets can lead to significant improvements in post-ASR error correction. We evaluate FlanEC using the HyPoradise dataset, providing a comprehensive analysis of the model's effectiveness in this domain. Furthermore, we assess the proposed approach under different settings to evaluate model scalability and efficiency, offering valuable insights into the potential of instruction-tuned encoder-decoder models for this task.

Despite improvements to the generalization performance of automated speech recognition (ASR) models, specializing ASR models for downstream tasks remains a challenging task, primarily due to reduced data availability (necessitating increased data collection), and rapidly shifting data distributions (requiring more frequent model fine-tuning). In this work, we investigate the potential of leveraging external knowledge, particularly through off-policy key-value stores generated with text-to-speech methods, to allow for flexible post-training adaptation to new data distributions. In our approach, audio embeddings captured from text-to-speech, along with semantic text embeddings, are used to bias ASR via an approximate k-nearest-neighbor (KNN) based attentive fusion step. Our experiments on LibiriSpeech and in-house voice assistant/search datasets show that the proposed approach can reduce domain adaptation time by up to 1K GPU-hours while providing up to 3% WER improvement compared to a fine-tuning baseline, suggesting a promising approach for adapting production ASR systems in challenging zero and few-shot scenarios.

As opposed to general English, many concepts in biomedical terminology have been designed in recent history by biomedical professionals with the goal of being precise and concise. This is often achieved by concatenating meaningful biomedical morphemes to create new semantic units. Nevertheless, most modern biomedical language models (LMs) are pre-trained using standard domain-specific tokenizers derived from large scale biomedical corpus statistics without explicitly leveraging the agglutinating nature of biomedical language. In this work, we first find that standard open-domain and biomedical tokenizers are largely unable to segment biomedical terms into meaningful components. Therefore, we hypothesize that using a tokenizer which segments biomedical terminology more accurately would enable biomedical LMs to improve their performance on downstream biomedical NLP tasks, especially ones which involve biomedical terms directly such as named entity recognition (NER) and entity linking. Surprisingly, we find that pre-training a biomedical LM using a more accurate biomedical tokenizer does not improve the entity representation quality of a language model as measured by several intrinsic and extrinsic measures such as masked language modeling prediction (MLM) accuracy as well as NER and entity linking performance. These quantitative findings, along with a case study which explores entity representation quality more directly, suggest that the biomedical pre-training process is quite robust to instances of sub-optimal tokenization.

This paper introduces GigaSpeech, an evolving, multi-domain English speech recognition corpus with 10,000 hours of high quality labeled audio suitable for supervised training, and 40,000 hours of total audio suitable for semi-supervised and unsupervised training. Around 40,000 hours of transcribed audio is first collected from audiobooks, podcasts and YouTube, covering both read and spontaneous speaking styles, and a variety of topics, such as arts, science, sports, etc. A new forced alignment and segmentation pipeline is proposed to create sentence segments suitable for speech recognition training, and to filter out segments with low-quality transcription. For system training, GigaSpeech provides five subsets of different sizes, 10h, 250h, 1000h, 2500h, and 10000h. For our 10,000-hour XL training subset, we cap the word error rate at 4% during the filtering/validation stage, and for all our other smaller training subsets, we cap it at 0%. The DEV and TEST evaluation sets, on the other hand, are re-processed by professional human transcribers to ensure high transcription quality. Baseline systems are provided for popular speech recognition toolkits, namely Athena, ESPnet, Kaldi and Pika.

In this paper, we consider enhancing medical visual-language pre-training (VLP) with domain-specific knowledge, by exploiting the paired image-text reports from the radiological daily practice. In particular, we make the following contributions: First, unlike existing works that directly process the raw reports, we adopt a novel triplet extraction module to extract the medical-related information, avoiding unnecessary complexity from language grammar and enhancing the supervision signals; Second, we propose a novel triplet encoding module with entity translation by querying a knowledge base, to exploit the rich domain knowledge in medical field, and implicitly build relationships between medical entities in the language embedding space; Third, we propose to use a Transformer-based fusion model for spatially aligning the entity description with visual signals at the image patch level, enabling the ability for medical diagnosis; Fourth, we conduct thorough experiments to validate the effectiveness of our architecture, and benchmark on numerous public benchmarks, e.g., ChestX-ray14, RSNA Pneumonia, SIIM-ACR Pneumothorax, COVIDx CXR-2, COVID Rural, and EdemaSeverity. In both zero-shot and fine-tuning settings, our model has demonstrated strong performance compared with the former methods on disease classification and grounding.

Generative Error Correction (GEC) has emerged as a powerful post-processing method to enhance the performance of Automatic Speech Recognition (ASR) systems. However, we show that GEC models struggle to generalize beyond the specific types of errors encountered during training, limiting their ability to correct new, unseen errors at test time, particularly in out-of-domain (OOD) scenarios. This phenomenon amplifies with named entities (NEs), where, in addition to insufficient contextual information or knowledge about the NEs, novel NEs keep emerging. To address these issues, we propose DARAG (Data- and Retrieval-Augmented Generative Error Correction), a novel approach designed to improve GEC for ASR in in-domain (ID) and OOD scenarios. We augment the GEC training dataset with synthetic data generated by prompting LLMs and text-to-speech models, thereby simulating additional errors from which the model can learn. For OOD scenarios, we simulate test-time errors from new domains similarly and in an unsupervised fashion. Additionally, to better handle named entities, we introduce retrieval-augmented correction by augmenting the input with entities retrieved from a database. Our approach is simple, scalable, and both domain- and language-agnostic. We experiment on multiple datasets and settings, showing that DARAG outperforms all our baselines, achieving 8\% -- 30\% relative WER improvements in ID and 10\% -- 33\% improvements in OOD settings.

Mental distress like depression and anxiety contribute to the largest proportion of the global burden of diseases. Automated diagnosis systems of such disorders, empowered by recent innovations in Artificial Intelligence, can pave the way to reduce the sufferings of the affected individuals. Development of such systems requires information-rich and balanced corpora. In this work, we introduce a novel mental distress analysis audio dataset DEPAC, labeled based on established thresholds on depression and anxiety standard screening tools. This large dataset comprises multiple speech tasks per individual, as well as relevant demographic information. Alongside, we present a feature set consisting of hand-curated acoustic and linguistic features, which were found effective in identifying signs of mental illnesses in human speech. Finally, we justify the quality and effectiveness of our proposed audio corpus and feature set in predicting depression severity by comparing the performance of baseline machine learning models built on this dataset with baseline models trained on other well-known depression corpora.

Advances in large language models (LLMs) provide new opportunities in healthcare for improved patient care, clinical decision-making, and enhancement of physician and administrator workflows. However, the potential of these models importantly depends on their ability to generalize effectively across clinical environments and populations, a challenge often underestimated in early development. To better understand reasons for these challenges and inform mitigation approaches, we evaluated ClinicLLM, an LLM trained on [HOSPITAL]'s clinical notes, analyzing its performance on 30-day all-cause readmission prediction focusing on variability across hospitals and patient characteristics. We found poorer generalization particularly in hospitals with fewer samples, among patients with government and unspecified insurance, the elderly, and those with high comorbidities. To understand reasons for lack of generalization, we investigated sample sizes for fine-tuning, note content (number of words per note), patient characteristics (comorbidity level, age, insurance type, borough), and health system aspects (hospital, all-cause 30-day readmission, and mortality rates). We used descriptive statistics and supervised classification to identify features. We found that, along with sample size, patient age, number of comorbidities, and the number of words in notes are all important factors related to generalization. Finally, we compared local fine-tuning (hospital specific), instance-based augmented fine-tuning and cluster-based fine-tuning for improving generalization. Among these, local fine-tuning proved most effective, increasing AUC by 0.25% to 11.74% (most helpful in settings with limited data). Overall, this study provides new insights for enhancing the deployment of large language models in the societally important domain of healthcare, and improving their performance for broader populations.

The integration of Large Language Models (LLMs) into healthcare promises to transform medical diagnostics, research, and patient care. Yet, the progression of medical LLMs faces obstacles such as complex training requirements, rigorous evaluation demands, and the dominance of proprietary models that restrict academic exploration. Transparent, comprehensive access to LLM resources is essential for advancing the field, fostering reproducibility, and encouraging innovation in healthcare AI. We present Hippocrates, an open-source LLM framework specifically developed for the medical domain. In stark contrast to previous efforts, it offers unrestricted access to its training datasets, codebase, checkpoints, and evaluation protocols. This open approach is designed to stimulate collaborative research, allowing the community to build upon, refine, and rigorously evaluate medical LLMs within a transparent ecosystem. Also, we introduce Hippo, a family of 7B models tailored for the medical domain, fine-tuned from Mistral and LLaMA2 through continual pre-training, instruction tuning, and reinforcement learning from human and AI feedback. Our models outperform existing open medical LLMs models by a large-margin, even surpassing models with 70B parameters. Through Hippocrates, we aspire to unlock the full potential of LLMs not just to advance medical knowledge and patient care but also to democratize the benefits of AI research in healthcare, making them available across the globe.

The advancement of natural language processing (NLP) systems in healthcare hinges on language model ability to interpret the intricate information contained within clinical notes. This process often requires integrating information from various time points in a patient's medical history. However, most earlier clinical language models were pretrained with a context length limited to roughly one clinical document. In this study, We introduce ClinicalMamba, a specialized version of the Mamba language model, pretrained on a vast corpus of longitudinal clinical notes to address the unique linguistic characteristics and information processing needs of the medical domain. ClinicalMamba, with 130 million and 2.8 billion parameters, demonstrates a superior performance in modeling clinical language across extended text lengths compared to Mamba and clinical Llama. With few-shot learning, ClinicalMamba achieves notable benchmarks in speed and accuracy, outperforming existing clinical language models and general domain large models like GPT-4 in longitudinal clinical notes information extraction tasks.

In recent years, the application of Large Language Models (LLMs) in healthcare has shown significant promise in improving the accessibility and dissemination of medical knowledge. This paper presents a detailed study of various LLMs trained on the MedQuAD medical question-answering dataset, with a focus on identifying the most effective model for providing accurate medical information. Among the models tested, the Sentence-t5 combined with Mistral 7B demonstrated superior performance, achieving a precision score of 0.762. This model's enhanced capabilities are attributed to its advanced pretraining techniques, robust architecture, and effective prompt construction methodologies. By leveraging these strengths, the Sentence-t5 + Mistral 7B model excels in understanding and generating precise medical answers. Our findings highlight the potential of integrating sophisticated LLMs in medical contexts to facilitate efficient and accurate medical knowledge retrieval, thus significantly enhancing patient education and support.

The usage of automatic speech recognition (ASR) systems are becoming omnipresent ranging from personal assistant to chatbots, home, and industrial automation systems, etc. Modern robots are also equipped with ASR capabilities for interacting with humans as speech is the most natural interaction modality. However, ASR in robots faces additional challenges as compared to a personal assistant. Being an embodied agent, a robot must recognize the physical entities around it and therefore reliably recognize the speech containing the description of such entities. However, current ASR systems are often unable to do so due to limitations in ASR training, such as generic datasets and open-vocabulary modeling. Also, adverse conditions during inference, such as noise, accented, and far-field speech makes the transcription inaccurate. In this work, we present a method to incorporate a robot's visual information into an ASR system and improve the recognition of a spoken utterance containing a visible entity. Specifically, we propose a new decoder biasing technique to incorporate the visual context while ensuring the ASR output does not degrade for incorrect context. We achieve a 59% relative reduction in WER from an unmodified ASR system.

The utilization of clinical reports for various secondary purposes, including health research and treatment monitoring, is crucial for enhancing patient care. Natural Language Processing (NLP) tools have emerged as valuable assets for extracting and processing relevant information from these reports. However, the availability of specialized language models for the clinical domain in Spanish has been limited. In this paper, we introduce EriBERTa, a bilingual domain-specific language model pre-trained on extensive medical and clinical corpora. We demonstrate that EriBERTa outperforms previous Spanish language models in the clinical domain, showcasing its superior capabilities in understanding medical texts and extracting meaningful information. Moreover, EriBERTa exhibits promising transfer learning abilities, allowing for knowledge transfer from one language to another. This aspect is particularly beneficial given the scarcity of Spanish clinical data.

Non-linguistic filler words, such as "uh" or "um", are prevalent in spontaneous speech and serve as indicators for expressing hesitation or uncertainty. Previous works for detecting certain non-linguistic filler words are highly dependent on transcriptions from a well-established commercial automatic speech recognition (ASR) system. However, certain ASR systems are not universally accessible from many aspects, e.g., budget, target languages, and computational power. In this work, we investigate filler word detection system that does not depend on ASR systems. We show that, by using the structured state space sequence model (S4) and neural semi-Markov conditional random fields (semi-CRFs), we achieve an absolute F1 improvement of 6.4% (segment level) and 3.1% (event level) on the PodcastFillers dataset. We also conduct a qualitative analysis on the detected results to analyze the limitations of our proposed system.

With the advent of Vision-Language Models (VLMs), medical artificial intelligence (AI) has experienced significant technological progress and paradigm shifts. This survey provides an extensive review of recent advancements in Medical Vision-Language Models (Med-VLMs), which integrate visual and textual data to enhance healthcare outcomes. We discuss the foundational technology behind Med-VLMs, illustrating how general models are adapted for complex medical tasks, and examine their applications in healthcare. The transformative impact of Med-VLMs on clinical practice, education, and patient care is highlighted, alongside challenges such as data scarcity, narrow task generalization, interpretability issues, and ethical concerns like fairness, accountability, and privacy. These limitations are exacerbated by uneven dataset distribution, computational demands, and regulatory hurdles. Rigorous evaluation methods and robust regulatory frameworks are essential for safe integration into healthcare workflows. Future directions include leveraging large-scale, diverse datasets, improving cross-modal generalization, and enhancing interpretability. Innovations like federated learning, lightweight architectures, and Electronic Health Record (EHR) integration are explored as pathways to democratize access and improve clinical relevance. This review aims to provide a comprehensive understanding of Med-VLMs' strengths and limitations, fostering their ethical and balanced adoption in healthcare.

The remarkable capabilities of Large Language Models (LLMs) make them increasingly compelling for adoption in real-world healthcare applications. However, the risks associated with using LLMs in medical applications have not been systematically characterized. We propose using five key principles for safe and trustworthy medical AI: Truthfulness, Resilience, Fairness, Robustness, and Privacy, along with ten specific aspects. Under this comprehensive framework, we introduce a novel MedGuard benchmark with 1,000 expert-verified questions. Our evaluation of 11 commonly used LLMs shows that the current language models, regardless of their safety alignment mechanisms, generally perform poorly on most of our benchmarks, particularly when compared to the high performance of human physicians. Despite recent reports indicate that advanced LLMs like ChatGPT can match or even exceed human performance in various medical tasks, this study underscores a significant safety gap, highlighting the crucial need for human oversight and the implementation of AI safety guardrails.

Research on language technology for the development of medical applications is currently a hot topic in Natural Language Understanding and Generation. Thus, a number of large language models (LLMs) have recently been adapted to the medical domain, so that they can be used as a tool for mediating in human-AI interaction. While these LLMs display competitive performance on automated medical texts benchmarks, they have been pre-trained and evaluated with a focus on a single language (English mostly). This is particularly true of text-to-text models, which typically require large amounts of domain-specific pre-training data, often not easily accessible for many languages. In this paper, we address these shortcomings by compiling, to the best of our knowledge, the largest multilingual corpus for the medical domain in four languages, namely English, French, Italian and Spanish. This new corpus has been used to train Medical mT5, the first open-source text-to-text multilingual model for the medical domain. Additionally, we present two new evaluation benchmarks for all four languages with the aim of facilitating multilingual research in this domain. A comprehensive evaluation shows that Medical mT5 outperforms both encoders and similarly sized text-to-text models for the Spanish, French, and Italian benchmarks, while being competitive with current state-of-the-art LLMs in English.

High-quality data labeling from specific domains is costly and human time-consuming. In this work, we propose a self-supervised domain adaptation method, based upon an iterative pseudo-forced alignment algorithm. The produced alignments are employed to customize an end-to-end Automatic Speech Recognition (ASR) and iteratively refined. The algorithm is fed with frame-wise character posteriors produced by a seed ASR, trained with out-of-domain data, and optimized throughout a Connectionist Temporal Classification (CTC) loss. The alignments are computed iteratively upon a corpus of broadcast TV. The process is repeated by reducing the quantity of text to be aligned or expanding the alignment window until finding the best possible audio-text alignment. The starting timestamps, or temporal anchors, are produced uniquely based on the confidence score of the last aligned utterance. This score is computed with the paths of the CTC-alignment matrix. With this methodology, no human-revised text references are required. Alignments from long audio files with low-quality transcriptions, like TV captions, are filtered out by confidence score and ready for further ASR adaptation. The obtained results, on both the Spanish RTVE2022 and CommonVoice databases, underpin the feasibility of using CTC-based systems to perform: highly accurate audio-text alignments, domain adaptation and semi-supervised training of end-to-end ASR.

In this work we introduce Labrador, a pre-trained Transformer model for laboratory data. Labrador and BERT were pre-trained on a corpus of 100 million lab test results from electronic health records (EHRs) and evaluated on various downstream outcome prediction tasks. Both models demonstrate mastery of the pre-training task but neither consistently outperform XGBoost on downstream supervised tasks. Our ablation studies reveal that transfer learning shows limited effectiveness for BERT and achieves marginal success with Labrador. We explore the reasons for the failure of transfer learning and suggest that the data generating process underlying each patient cannot be characterized sufficiently using labs alone, among other factors. We encourage future work to focus on joint modeling of multiple EHR data categories and to include tree-based baselines in their evaluations.

This paper presents the Esethu Framework, a sustainable data curation framework specifically designed to empower local communities and ensure equitable benefit-sharing from their linguistic resources. This framework is supported by the Esethu license, a novel community-centric data license. As a proof of concept, we introduce the Vuk'uzenzele isiXhosa Speech Dataset (ViXSD), an open-source corpus developed under the Esethu Framework and License. The dataset, containing read speech from native isiXhosa speakers enriched with demographic and linguistic metadata, demonstrates how community-driven licensing and curation principles can bridge resource gaps in automatic speech recognition (ASR) for African languages while safeguarding the interests of data creators. We describe the framework guiding dataset development, outline the Esethu license provisions, present the methodology for ViXSD, and present ASR experiments validating ViXSD's usability in building and refining voice-driven applications for isiXhosa.

This study explores voice cloning to generate synthetic speech replicating the unique patterns of individuals with dysarthria. Using the TORGO dataset, we address data scarcity and privacy challenges in speech-language pathology. Our contributions include demonstrating that voice cloning preserves dysarthric speech characteristics, analyzing differences between real and synthetic data, and discussing implications for diagnostics, rehabilitation, and communication. We cloned voices from dysarthric and control speakers using a commercial platform, ensuring gender-matched synthetic voices. A licensed speech-language pathologist (SLP) evaluated a subset for dysarthria, speaker gender, and synthetic indicators. The SLP correctly identified dysarthria in all cases and speaker gender in 95% but misclassified 30% of synthetic samples as real, indicating high realism. Our results suggest synthetic speech effectively captures disordered characteristics and that voice cloning has advanced to produce high-quality data resembling real speech, even to trained professionals. This has critical implications for healthcare, where synthetic data can mitigate data scarcity, protect privacy, and enhance AI-driven diagnostics. By enabling the creation of diverse, high-quality speech datasets, voice cloning can improve generalizable models, personalize therapy, and advance assistive technologies for dysarthria. We publicly release our synthetic dataset to foster further research and collaboration, aiming to develop robust models that improve patient outcomes in speech-language pathology.

In this study, we provide solutions to two practical yet overlooked scenarios in federated learning for electronic health records (EHRs): firstly, we introduce EHRFL, a framework that facilitates federated learning across healthcare institutions with distinct medical coding systems and database schemas using text-based linearization of EHRs. Secondly, we focus on a scenario where a single healthcare institution initiates federated learning to build a model tailored for itself, in which the number of clients must be optimized in order to reduce expenses incurred by the host. For selecting participating clients, we present a novel precision-based method, leveraging data latents to identify suitable participants for the institution. Our empirical results show that EHRFL effectively enables federated learning across hospitals with different EHR systems. Furthermore, our results demonstrate the efficacy of our precision-based method in selecting reduced number of participating clients without compromising model performance, resulting in lower operational costs when constructing institution-specific models. We believe this work lays a foundation for the broader adoption of federated learning on EHRs.

With increasingly more powerful compute capabilities and resources in today's devices, traditionally compute-intensive automatic speech recognition (ASR) has been moving from the cloud to devices to better protect user privacy. However, it is still challenging to implement on-device ASR on resource-constrained devices, such as smartphones, smart wearables, and other smart home automation devices. In this paper, we propose a series of model architecture adaptions, neural network graph transformations, and numerical optimizations to fit an advanced Conformer based end-to-end streaming ASR system on resource-constrained devices without accuracy degradation. We achieve over 5.26 times faster than realtime (0.19 RTF) speech recognition on smart wearables while minimizing energy consumption and achieving state-of-the-art accuracy. The proposed methods are widely applicable to other transformer-based server-free AI applications. In addition, we provide a complete theory on optimal pre-normalizers that numerically stabilize layer normalization in any Lp-norm using any floating point precision.

Self-supervised learning (SSL) has achieved great success in speech-related tasks, driven by advancements in speech encoder architectures and the expansion of datasets. While Transformer and Conformer architectures have dominated SSL backbones, encoders like Zipformer, which excel in automatic speech recognition (ASR), remain unexplored in SSL. Concurrently, inefficiencies in data processing within existing SSL training frameworks, such as fairseq, pose challenges in managing the growing volumes of training data. To address these issues, we propose k2SSL, an open-source framework that offers faster, more memory-efficient, and better-performing self-supervised speech representation learning, with a focus on downstream ASR tasks. The optimized HuBERT and proposed Zipformer-based SSL systems exhibit substantial reductions in both training time and memory usage during SSL training. Experiments on LibriSpeech and Libri-Light demonstrate that Zipformer-based SSL systems significantly outperform comparable HuBERT and WavLM systems, achieving a relative WER reduction on dev-other/test-other of up to 34.8%/32.4% compared to HuBERT Base after supervised fine-tuning, along with a 3.5x pre-training speedup in total GPU hours.

Clinical diagnosis prediction models, when provided with a patient's medical history, aim to detect potential diseases early, facilitating timely intervention and improving prognostic outcomes. However, the inherent scarcity of patient data and large disease candidate space often pose challenges in developing satisfactory models for this intricate task. The exploration of leveraging Large Language Models (LLMs) for encapsulating clinical decision processes has been limited. We introduce MERA, a clinical diagnosis prediction model that bridges pertaining natural language knowledge with medical practice. We apply hierarchical contrastive learning on a disease candidate ranking list to alleviate the large decision space issue. With concept memorization through fine-tuning, we bridge the natural language clinical knowledge with medical codes. Experimental results on MIMIC-III and IV datasets show that MERA achieves the state-of-the-art diagnosis prediction performance and dramatically elevates the diagnosis prediction capabilities of generative LMs.

Despite the proven effectiveness of Transformer neural networks across multiple domains, their performance with Electronic Health Records (EHR) can be nuanced. The unique, multidimensional sequential nature of EHR data can sometimes make even simple linear models with carefully engineered features more competitive. Thus, the advantages of Transformers, such as efficient transfer learning and improved scalability are not always fully exploited in EHR applications. Addressing these challenges, we introduce SANSformer, an attention-free sequential model designed with specific inductive biases to cater for the unique characteristics of EHR data. In this work, we aim to forecast the demand for healthcare services, by predicting the number of patient visits to healthcare facilities. The challenge amplifies when dealing with divergent patient subgroups, like those with rare diseases, which are characterized by unique health trajectories and are typically smaller in size. To address this, we employ a self-supervised pretraining strategy, Generative Summary Pretraining (GSP), which predicts future summary statistics based on past health records of a patient. Our models are pretrained on a health registry of nearly one million patients, then fine-tuned for specific subgroup prediction tasks, showcasing the potential to handle the multifaceted nature of EHR data. In evaluation, SANSformer consistently surpasses robust EHR baselines, with our GSP pretraining method notably amplifying model performance, particularly within smaller patient subgroups. Our results illuminate the promising potential of tailored attention-free models and self-supervised pretraining in refining healthcare utilization predictions across various patient demographics.

Medical Dialogue Generation serves a critical role in telemedicine by facilitating the dissemination of medical expertise to patients. Existing studies focus on incorporating textual representations, which have limited their ability to represent the semantics of text, such as ignoring important medical entities. To enhance the model's understanding of the textual semantics and the medical knowledge including entities and relations, we introduce the use of Abstract Meaning Representations (AMR) to construct graphical representations that delineate the roles of language constituents and medical entities within the dialogues. In this paper, We propose a novel framework that models dialogues between patients and healthcare professionals using AMR graphs, where the neural networks incorporate textual and graphical knowledge with a dual attention mechanism. Experimental results show that our framework outperforms strong baseline models in medical dialogue generation, demonstrating the effectiveness of AMR graphs in enhancing the representations of medical knowledge and logical relationships. Furthermore, to support future research in this domain, we provide the corresponding source code at https://github.com/Bernard-Yang/MedDiaAMR.

Large-language models have recently demonstrated impressive zero-shot capabilities in a variety of natural language tasks such as summarization, dialogue generation, and question-answering. Despite many promising applications in clinical medicine, adoption of these models in real-world settings has been largely limited by their tendency to generate incorrect and sometimes even toxic statements. In this study, we develop Almanac, a large language model framework augmented with retrieval capabilities for medical guideline and treatment recommendations. Performance on a novel dataset of clinical scenarios (n = 130) evaluated by a panel of 5 board-certified and resident physicians demonstrates significant increases in factuality (mean of 18% at p-value < 0.05) across all specialties, with improvements in completeness and safety. Our results demonstrate the potential for large language models to be effective tools in the clinical decision-making process, while also emphasizing the importance of careful testing and deployment to mitigate their shortcomings.

While large language models (LLMs) have achieved state-of-the-art performance on a wide range of medical question answering (QA) tasks, they still face challenges with hallucinations and outdated knowledge. Retrieval-augmented generation (RAG) is a promising solution and has been widely adopted. However, a RAG system can involve multiple flexible components, and there is a lack of best practices regarding the optimal RAG setting for various medical purposes. To systematically evaluate such systems, we propose the Medical Information Retrieval-Augmented Generation Evaluation (MIRAGE), a first-of-its-kind benchmark including 7,663 questions from five medical QA datasets. Using MIRAGE, we conducted large-scale experiments with over 1.8 trillion prompt tokens on 41 combinations of different corpora, retrievers, and backbone LLMs through the MedRAG toolkit introduced in this work. Overall, MedRAG improves the accuracy of six different LLMs by up to 18% over chain-of-thought prompting, elevating the performance of GPT-3.5 and Mixtral to GPT-4-level. Our results show that the combination of various medical corpora and retrievers achieves the best performance. In addition, we discovered a log-linear scaling property and the "lost-in-the-middle" effects in medical RAG. We believe our comprehensive evaluations can serve as practical guidelines for implementing RAG systems for medicine.

Depression is a critical concern in global mental health, prompting extensive research into AI-based detection methods. Among various AI technologies, Large Language Models (LLMs) stand out for their versatility in mental healthcare applications. However, their primary limitation arises from their exclusive dependence on textual input, which constrains their overall capabilities. Furthermore, the utilization of LLMs in identifying and analyzing depressive states is still relatively untapped. In this paper, we present an innovative approach to integrating acoustic speech information into the LLMs framework for multimodal depression detection. We investigate an efficient method for depression detection by integrating speech signals into LLMs utilizing Acoustic Landmarks. By incorporating acoustic landmarks, which are specific to the pronunciation of spoken words, our method adds critical dimensions to text transcripts. This integration also provides insights into the unique speech patterns of individuals, revealing the potential mental states of individuals. Evaluations of the proposed approach on the DAIC-WOZ dataset reveal state-of-the-art results when compared with existing Audio-Text baselines. In addition, this approach is not only valuable for the detection of depression but also represents a new perspective in enhancing the ability of LLMs to comprehend and process speech signals.

Advances in machine learning have made it possible to perform various text and speech processing tasks, including automatic speech recognition (ASR), in an end-to-end (E2E) manner. Since typical E2E approaches require large amounts of training data and resources, leveraging pre-trained foundation models instead of training from scratch is gaining attention. Although there have been attempts to use pre-trained speech and language models in ASR, most of them are limited to using either. This paper explores the potential of integrating a pre-trained speech representation model with a large language model (LLM) for E2E ASR. The proposed model enables E2E ASR by generating text tokens in an autoregressive manner via speech representations as speech prompts, taking advantage of the vast knowledge provided by the LLM. Furthermore, the proposed model can incorporate remarkable developments for LLM utilization, such as inference optimization and parameter-efficient domain adaptation. Experimental results show that the proposed model achieves performance comparable to modern E2E ASR models.

We propose a bearing health management framework leveraging large language models (BearLLM), a novel multimodal model that unifies multiple bearing-related tasks by processing user prompts and vibration signals. Specifically, we introduce a prior knowledge-enhanced unified vibration signal representation to handle various working conditions across multiple datasets. This involves adaptively sampling the vibration signals based on the sampling rate of the sensor, incorporating the frequency domain to unify input dimensions, and using a fault-free reference signal as an auxiliary input. To extract features from vibration signals, we first train a fault classification network, then convert and align the extracted features into word embedding, and finally concatenate these with text embedding as input to an LLM. To evaluate the performance of the proposed method, we constructed the first large-scale multimodal bearing health management (MBHM) dataset, including paired vibration signals and textual descriptions. With our unified vibration signal representation, BearLLM using one set of pre-trained weights achieves state-of-the-art performance on nine publicly available fault diagnosis benchmarks, outperforming specific methods designed for individual datasets. We provide a dataset, our model, and code to inspire future research on building more capable industrial multimodal models (https://github.com/hatton613/BearLLM).

Foundation models (FMs) have exhibited remarkable performance across a wide range of downstream tasks in many domains. Nevertheless, general-purpose FMs often face challenges when confronted with domain-specific problems, due to their limited access to the proprietary training data in a particular domain. In biomedicine, there are various biological modalities, such as molecules, proteins, and cells, which are encoded by the language of life and exhibit significant modality gaps with human natural language. In this paper, we introduce BioMedGPT, an open multimodal generative pre-trained transformer (GPT) for biomedicine, to bridge the gap between the language of life and human natural language. BioMedGPT allows users to easily ``communicate'' with diverse biological modalities through free text, which is the first of its kind. BioMedGPT aligns different biological modalities with natural language via a large generative language model, namely, BioMedGPT-LM. We publish BioMedGPT-10B, which unifies the feature spaces of molecules, proteins, and natural language via encoding and alignment. Through fine-tuning, BioMedGPT-10B outperforms or is on par with human and significantly larger general-purpose foundation models on the biomedical QA task. It also demonstrates promising performance in the molecule QA and protein QA tasks, which could greatly accelerate the discovery of new drugs and therapeutic targets. In addition, BioMedGPT-LM-7B is the first large generative language model based on Llama2 in the biomedical domain, therefore is commercial friendly. Both BioMedGPT-10B and BioMedGPT-LM-7B are open-sourced to the research community. In addition, we publish the datasets that are meticulously curated for the alignment of multi-modalities, i.e., PubChemQA and UniProtQA. All the models, codes, and datasets are available at https://github.com/PharMolix/OpenBioMed.

The increasing use of tools and solutions based on Large Language Models (LLMs) for various tasks in the medical domain has become a prominent trend. Their use in this highly critical and sensitive domain has thus raised important questions about their robustness, especially in response to variations in input, and the reliability of the generated outputs. This study addresses these questions by constructing a textual dataset based on the ICD-10-CM code descriptions, widely used in US hospitals and containing many clinical terms, and their easily reproducible rephrasing. We then benchmarked existing embedding models, either generalist or specialized in the clinical domain, in a semantic search task where the goal was to correctly match the rephrased text to the original description. Our results showed that generalist models performed better than clinical models, suggesting that existing clinical specialized models are more sensitive to small changes in input that confuse them. The highlighted problem of specialized models may be due to the fact that they have not been trained on sufficient data, and in particular on datasets that are not diverse enough to have a reliable global language understanding, which is still necessary for accurate handling of medical documents.

Pretraining large neural language models, such as BERT, has led to impressive gains on many natural language processing (NLP) tasks. However, most pretraining efforts focus on general domain corpora, such as newswire and Web. A prevailing assumption is that even domain-specific pretraining can benefit by starting from general-domain language models. In this paper, we challenge this assumption by showing that for domains with abundant unlabeled text, such as biomedicine, pretraining language models from scratch results in substantial gains over continual pretraining of general-domain language models. To facilitate this investigation, we compile a comprehensive biomedical NLP benchmark from publicly-available datasets. Our experiments show that domain-specific pretraining serves as a solid foundation for a wide range of biomedical NLP tasks, leading to new state-of-the-art results across the board. Further, in conducting a thorough evaluation of modeling choices, both for pretraining and task-specific fine-tuning, we discover that some common practices are unnecessary with BERT models, such as using complex tagging schemes in named entity recognition (NER). To help accelerate research in biomedical NLP, we have released our state-of-the-art pretrained and task-specific models for the community, and created a leaderboard featuring our BLURB benchmark (short for Biomedical Language Understanding & Reasoning Benchmark) at https://aka.ms/BLURB.

Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder that often emerges in early childhood. ASD assessment typically involves an observation protocol including note-taking and ratings of child's social behavior conducted by a trained clinician. A robust machine learning (ML) model that is capable of labeling adult and child audio has the potential to save significant time and labor in manual coding children's behaviors. This may assist clinicians capture events of interest, better communicate events with parents, and educate new clinicians. In this study, we leverage the self-supervised learning model, Wav2Vec 2.0 (W2V2), pretrained on 4300h of home recordings of children under 5 years old, to build a unified system that performs both speaker diarization (SD) and vocalization classification (VC) tasks. We apply this system to two-channel audio recordings of brief 3-5 minute clinician-child interactions using the Rapid-ABC corpus. We propose a novel technique by introducing auxiliary features extracted from W2V2-based automatic speech recognition (ASR) system for children under 4 years old to improve children's VC task. We test our proposed method of improving children's VC task on two corpora (Rapid-ABC and BabbleCor) and observe consistent improvements. Furthermore, we reach, or perhaps outperform, the state-of-the-art performance of BabbleCor.

In the ongoing wave of impact driven by large language models (LLMs) like ChatGPT, the adaptation of LLMs to medical domain has emerged as a crucial research frontier. Since mainstream LLMs tend to be designed for general-purpose applications, constructing a medical LLM through domain adaptation is a huge challenge. While instruction-tuning is used to fine-tune some LLMs, its precise roles in domain adaptation remain unknown. Here we show the contribution of LoRA-based instruction-tuning to performance in Japanese medical question-answering tasks. In doing so, we employ a multifaceted evaluation for multiple-choice questions, including scoring based on "Exact match" and "Gestalt distance" in addition to the conventional accuracy. Our findings suggest that LoRA-based instruction-tuning can partially incorporate domain-specific knowledge into LLMs, with larger models demonstrating more pronounced effects. Furthermore, our results underscore the potential of adapting English-centric models for Japanese applications in domain adaptation, while also highlighting the persisting limitations of Japanese-centric models. This initiative represents a pioneering effort in enabling medical institutions to fine-tune and operate models without relying on external services.

Audio-visual speech recognition has received a lot of attention due to its robustness against acoustic noise. Recently, the performance of automatic, visual, and audio-visual speech recognition (ASR, VSR, and AV-ASR, respectively) has been substantially improved, mainly due to the use of larger models and training sets. However, accurate labelling of datasets is time-consuming and expensive. Hence, in this work, we investigate the use of automatically-generated transcriptions of unlabelled datasets to increase the training set size. For this purpose, we use publicly-available pre-trained ASR models to automatically transcribe unlabelled datasets such as AVSpeech and VoxCeleb2. Then, we train ASR, VSR and AV-ASR models on the augmented training set, which consists of the LRS2 and LRS3 datasets as well as the additional automatically-transcribed data. We demonstrate that increasing the size of the training set, a recent trend in the literature, leads to reduced WER despite using noisy transcriptions. The proposed model achieves new state-of-the-art performance on AV-ASR on LRS2 and LRS3. In particular, it achieves a WER of 0.9% on LRS3, a relative improvement of 30% over the current state-of-the-art approach, and outperforms methods that have been trained on non-publicly available datasets with 26 times more training data.

This work presents a seemingly simple but effective technique to improve low-resource ASR systems for phonetic languages. By identifying sets of acoustically similar graphemes in these languages, we first reduce the output alphabet of the ASR system using linguistically meaningful reductions and then reconstruct the original alphabet using a standalone module. We demonstrate that this lessens the burden and improves the performance of low-resource end-to-end ASR systems (because only reduced-alphabet predictions are needed) and that it is possible to design a very simple but effective reconstruction module that recovers sequences in the original alphabet from sequences in the reduced alphabet. We present a finite state transducer-based reconstruction module that operates on the 1-best ASR hypothesis in the reduced alphabet. We demonstrate the efficacy of our proposed technique using ASR systems for two Indian languages, Gujarati and Telugu. With access to only 10 hrs of speech data, we obtain relative WER reductions of up to 7% compared to systems that do not use any reduction.

Electronic Health Records (EHRs) are integral for storing comprehensive patient medical records, combining structured data (e.g., medications) with detailed clinical notes (e.g., physician notes). These elements are essential for straightforward data retrieval and provide deep, contextual insights into patient care. However, they often suffer from discrepancies due to unintuitive EHR system designs and human errors, posing serious risks to patient safety. To address this, we developed EHRCon, a new dataset and task specifically designed to ensure data consistency between structured tables and unstructured notes in EHRs. EHRCon was crafted in collaboration with healthcare professionals using the MIMIC-III EHR dataset, and includes manual annotations of 3,943 entities across 105 clinical notes checked against database entries for consistency. EHRCon has two versions, one using the original MIMIC-III schema, and another using the OMOP CDM schema, in order to increase its applicability and generalizability. Furthermore, leveraging the capabilities of large language models, we introduce CheckEHR, a novel framework for verifying the consistency between clinical notes and database tables. CheckEHR utilizes an eight-stage process and shows promising results in both few-shot and zero-shot settings. The code is available at https://github.com/dustn1259/EHRCon.

Pretrained language models have served as important backbones for natural language processing. Recently, in-domain pretraining has been shown to benefit various domain-specific downstream tasks. In the biomedical domain, natural language generation (NLG) tasks are of critical importance, while understudied. Approaching natural language understanding (NLU) tasks as NLG achieves satisfying performance in the general domain through constrained language generation or language prompting. We emphasize the lack of in-domain generative language models and the unsystematic generative downstream benchmarks in the biomedical domain, hindering the development of the research community. In this work, we introduce the generative language model BioBART that adapts BART to the biomedical domain. We collate various biomedical language generation tasks including dialogue, summarization, entity linking, and named entity recognition. BioBART pretrained on PubMed abstracts has enhanced performance compared to BART and set strong baselines on several tasks. Furthermore, we conduct ablation studies on the pretraining tasks for BioBART and find that sentence permutation has negative effects on downstream tasks.

Current voice assistants typically use the best hypothesis yielded by their Automatic Speech Recognition (ASR) module as input to their Natural Language Understanding (NLU) module, thereby losing helpful information that might be stored in lower-ranked ASR hypotheses. We explore the change in performance of NLU associated tasks when utilizing five-best ASR hypotheses when compared to status quo for two language datasets, German and Portuguese. To harvest information from the ASR five-best, we leverage extractive summarization and joint extractive-abstractive summarization models for Domain Classification (DC) experiments while using a sequence-to-sequence model with a pointer generator network for Intent Classification (IC) and Named Entity Recognition (NER) multi-task experiments. For the DC full test set, we observe significant improvements of up to 7.2% and 15.5% in micro-averaged F1 scores, for German and Portuguese, respectively. In cases where the best ASR hypothesis was not an exact match to the transcribed utterance (mismatched test set), we see improvements of up to 6.7% and 8.8% micro-averaged F1 scores, for German and Portuguese, respectively. For IC and NER multi-task experiments, when evaluating on the mismatched test set, we see improvements across all domains in German and in 17 out of 19 domains in Portuguese (improvements based on change in SeMER scores). Our results suggest that the use of multiple ASR hypotheses, as opposed to one, can lead to significant performance improvements in the DC task for these non-English datasets. In addition, it could lead to significant improvement in the performance of IC and NER tasks in cases where the ASR model makes mistakes.

Medical dialogue systems (MDS) aim to provide patients with medical services, such as diagnosis and prescription. Since most patients cannot precisely describe their symptoms, dialogue understanding is challenging for MDS. Previous studies mainly addressed this by extracting the mentioned medical entities as critical dialogue history information. In this work, we argue that it is also essential to capture the transitions of the medical entities and the doctor's dialogue acts in each turn, as they help the understanding of how the dialogue flows and enhance the prediction of the entities and dialogue acts to be adopted in the following turn. Correspondingly, we propose a Dual Flow enhanced Medical (DFMed) dialogue generation framework. It extracts the medical entities and dialogue acts used in the dialogue history and models their transitions with an entity-centric graph flow and a sequential act flow, respectively. We employ two sequential models to encode them and devise an interweaving component to enhance their interactions. Experiments on two datasets demonstrate that our method exceeds baselines in both automatic and manual evaluations.

Biomedical data is inherently multimodal, consisting of electronic health records, medical imaging, digital pathology, genome sequencing, wearable sensors, and more. The application of artificial intelligence tools to these multifaceted sensing technologies has the potential to revolutionize the prognosis, diagnosis, and management of human health and disease. However, current approaches to biomedical AI typically only train and evaluate with one or a small set of medical modalities and tasks. This limitation hampers the development of comprehensive tools that can leverage the rich interconnected information across many heterogeneous biomedical sensors. To address this challenge, we present MultiMed, a benchmark designed to evaluate and enable large-scale learning across a wide spectrum of medical modalities and tasks. MultiMed consists of 2.56 million samples across ten medical modalities such as medical reports, pathology, genomics, and protein data, and is structured into eleven challenging tasks, including disease prognosis, protein structure prediction, and medical question answering. Using MultiMed, we conduct comprehensive experiments benchmarking state-of-the-art unimodal, multimodal, and multitask models. Our analysis highlights the advantages of training large-scale medical models across many related modalities and tasks. Moreover, MultiMed enables studies of generalization across related medical concepts, robustness to real-world noisy data and distribution shifts, and novel modality combinations to improve prediction performance. MultiMed will be publicly available and regularly updated and welcomes inputs from the community.

The integration of Large Language Models (LLMs) into healthcare applications offers promising advancements in medical diagnostics, treatment recommendations, and patient care. However, the susceptibility of LLMs to adversarial attacks poses a significant threat, potentially leading to harmful outcomes in delicate medical contexts. This study investigates the vulnerability of LLMs to two types of adversarial attacks in three medical tasks. Utilizing real-world patient data, we demonstrate that both open-source and proprietary LLMs are susceptible to manipulation across multiple tasks. This research further reveals that domain-specific tasks demand more adversarial data in model fine-tuning than general domain tasks for effective attack execution, especially for more capable models. We discover that while integrating adversarial data does not markedly degrade overall model performance on medical benchmarks, it does lead to noticeable shifts in fine-tuned model weights, suggesting a potential pathway for detecting and countering model attacks. This research highlights the urgent need for robust security measures and the development of defensive mechanisms to safeguard LLMs in medical applications, to ensure their safe and effective deployment in healthcare settings.