Daily Papers

Numerous biological and physical processes can be modeled as systems of interacting entities evolving continuously over time, e.g. the dynamics of communicating cells or physical particles. Learning the dynamics of such systems is essential for predicting the temporal evolution of populations across novel samples and unseen environments. Flow-based models allow for learning these dynamics at the population level - they model the evolution of the entire distribution of samples. However, current flow-based models are limited to a single initial population and a set of predefined conditions which describe different dynamics. We argue that multiple processes in natural sciences have to be represented as vector fields on the Wasserstein manifold of probability densities. That is, the change of the population at any moment in time depends on the population itself due to the interactions between samples. In particular, this is crucial for personalized medicine where the development of diseases and their respective treatment response depends on the microenvironment of cells specific to each patient. We propose Meta Flow Matching (MFM), a practical approach to integrating along these vector fields on the Wasserstein manifold by amortizing the flow model over the initial populations. Namely, we embed the population of samples using a Graph Neural Network (GNN) and use these embeddings to train a Flow Matching model. This gives MFM the ability to generalize over the initial distributions unlike previously proposed methods. We demonstrate the ability of MFM to improve prediction of individual treatment responses on a large scale multi-patient single-cell drug screen dataset.

Disease progression simulation is a crucial area of research that has significant implications for clinical diagnosis, prognosis, and treatment. One major challenge in this field is the lack of continuous medical imaging monitoring of individual patients over time. To address this issue, we develop a novel framework termed Progressive Image Editing (PIE) that enables controlled manipulation of disease-related image features, facilitating precise and realistic disease progression simulation. Specifically, we leverage recent advancements in text-to-image generative models to simulate disease progression accurately and personalize it for each patient. We theoretically analyze the iterative refining process in our framework as a gradient descent with an exponentially decayed learning rate. To validate our framework, we conduct experiments in three medical imaging domains. Our results demonstrate the superiority of PIE over existing methods such as Stable Diffusion Walk and Style-Based Manifold Extrapolation based on CLIP score (Realism) and Disease Classification Confidence (Alignment). Our user study collected feedback from 35 veteran physicians to assess the generated progressions. Remarkably, 76.2% of the feedback agrees with the fidelity of the generated progressions. To our best knowledge, PIE is the first of its kind to generate disease progression images meeting real-world standards. It is a promising tool for medical research and clinical practice, potentially allowing healthcare providers to model disease trajectories over time, predict future treatment responses, and improve patient outcomes.

Medical benchmark datasets significantly contribute to developing Large Language Models (LLMs) for medical knowledge extraction, diagnosis, summarization, and other uses. Yet, current benchmarks are mainly derived from exam questions given to medical students or cases described in the medical literature, lacking the complexity of real-world patient cases that deviate from classic textbook abstractions. These include rare diseases, uncommon presentations of common diseases, and unexpected treatment responses. Here, we construct Clinically Uncommon Patient Cases and Diagnosis Dataset (CUPCase) based on 3,562 real-world case reports from BMC, including diagnoses in open-ended textual format and as multiple-choice options with distractors. Using this dataset, we evaluate the ability of state-of-the-art LLMs, including both general-purpose and Clinical LLMs, to identify and correctly diagnose a patient case, and test models' performance when only partial information about cases is available. Our findings show that general-purpose GPT-4o attains the best performance in both the multiple-choice task (average accuracy of 87.9%) and the open-ended task (BERTScore F1 of 0.764), outperforming several LLMs with a focus on the medical domain such as Meditron-70B and MedLM-Large. Moreover, GPT-4o was able to maintain 87% and 88% of its performance with only the first 20% of tokens of the case presentation in multiple-choice and free text, respectively, highlighting the potential of LLMs to aid in early diagnosis in real-world cases. CUPCase expands our ability to evaluate LLMs for clinical decision support in an open and reproducible manner.

Foundation models are reshaping computational pathology by enabling transfer learning, where models pre-trained on vast datasets can be adapted for downstream diagnostic, prognostic, and therapeutic response tasks. Despite these advances, foundation models are still limited in their ability to encode the entire gigapixel whole-slide images without additional training and often lack complementary multimodal data. Here, we introduce Threads, a slide-level foundation model capable of generating universal representations of whole-slide images of any size. Threads was pre-trained using a multimodal learning approach on a diverse cohort of 47,171 hematoxylin and eosin (H&E)-stained tissue sections, paired with corresponding genomic and transcriptomic profiles - the largest such paired dataset to be used for foundation model development to date. This unique training paradigm enables Threads to capture the tissue's underlying molecular composition, yielding powerful representations applicable to a wide array of downstream tasks. In extensive benchmarking across 54 oncology tasks, including clinical subtyping, grading, mutation prediction, immunohistochemistry status determination, treatment response prediction, and survival prediction, Threads outperformed all baselines while demonstrating remarkable generalizability and label efficiency. It is particularly well suited for predicting rare events, further emphasizing its clinical utility. We intend to make the model publicly available for the broader community.

This article details the advances made to a system that uses artificial intelligence to identify alarming student responses. This system is built into our assessment platform to assess whether a student's response indicates they are a threat to themselves or others. Such responses may include details concerning threats of violence, severe depression, suicide risks, and descriptions of abuse. Driven by advances in natural language processing, the latest model is a fine-tuned language model trained on a large corpus consisting of student responses and supplementary texts. We demonstrate that the use of a language model delivers a substantial improvement in accuracy over the previous iterations of this system.

Dynamic treatment regimes (DTRs) are personalized, adaptive, multi-stage treatment plans that adapt treatment decisions both to an individual's initial features and to intermediate outcomes and features at each subsequent stage, which are affected by decisions in prior stages. Examples include personalized first- and second-line treatments of chronic conditions like diabetes, cancer, and depression, which adapt to patient response to first-line treatment, disease progression, and individual characteristics. While existing literature mostly focuses on estimating the optimal DTR from offline data such as from sequentially randomized trials, we study the problem of developing the optimal DTR in an online manner, where the interaction with each individual affect both our cumulative reward and our data collection for future learning. We term this the DTR bandit problem. We propose a novel algorithm that, by carefully balancing exploration and exploitation, is guaranteed to achieve rate-optimal regret when the transition and reward models are linear. We demonstrate our algorithm and its benefits both in synthetic experiments and in a case study of adaptive treatment of major depressive disorder using real-world data.

The recent advancements in artificial intelligence highlight the potential of language models in psychological health support. While models trained on data from mental health service platform have achieved preliminary success, challenges persist in areas such as data scarcity, quality, and ensuring a solid foundation in psychological techniques. To address these challenges, this study introduces a novel approach to enhance the precision and efficacy of psychological support through large language models. Specifically, we design a specific prompt derived from principles of Cognitive Behavioral Therapy (CBT) and have generated the CBT QA dataset, specifically for Chinese psychological health Q&A based on CBT structured intervention strategies. Unlike previous methods, our dataset emphasizes professional and structured response. Utilizing this dataset, we fine-tuned the large language model, giving birth to CBT-LLM, the large-scale language model specifically designed for Cognitive Behavioral Therapy techniques. Empirical evaluations demonstrate that CBT-LLM excels in generating structured, professional, and highly relevant responses in psychological health support tasks, showcasing its practicality and quality. The model is available on Hugging Face: https://huggingface.co/Hongbin37/CBT-LLM.

Inspire therapy is an FDA-approved internal neurostimulation treatment for obstructive sleep apnea. However, not all patients respond to this therapy, posing a challenge even for experienced otolaryngologists to determine candidacy. This paper makes the first attempt to leverage both machine learning and deep learning techniques in discerning patient responsiveness to Inspire therapy using medical data and videos captured through Drug-Induced Sleep Endoscopy (DISE), an essential procedure for Inspire therapy. To achieve this, we gathered and annotated three datasets from 127 patients. Two of these datasets comprise endoscopic videos focused on the Base of the Tongue and Velopharynx. The third dataset composes the patient's clinical information. By utilizing these datasets, we benchmarked and compared the performance of six deep learning models and five classical machine learning algorithms. The results demonstrate the potential of employing machine learning and deep learning techniques to determine a patient's eligibility for Inspire therapy, paving the way for future advancements in this field.

Automated scoring engines are increasingly being used to score the free-form text responses that students give to questions. Such engines are not designed to appropriately deal with responses that a human reader would find alarming such as those that indicate an intention to self-harm or harm others, responses that allude to drug abuse or sexual abuse or any response that would elicit concern for the student writing the response. Our neural network models have been designed to help identify these anomalous responses from a large collection of typical responses that students give. The responses identified by the neural network can be assessed for urgency, severity, and validity more quickly by a team of reviewers than otherwise possible. Given the anomalous nature of these types of responses, our goal is to maximize the chance of flagging these responses for review given the constraint that only a fixed percentage of responses can viably be assessed by a team of reviewers.

As mental health issues globally escalate, there is a tremendous need for advanced digital support systems. We introduce MentalAgora, a novel framework employing large language models enhanced by interaction between multiple agents for tailored mental health support. This framework operates through three stages: strategic debating, tailored counselor creation, and response generation, enabling the dynamic customization of responses based on individual user preferences and therapeutic needs. We conduct experiments utilizing a high-quality evaluation dataset TherapyTalk crafted with mental health professionals, shwoing that MentalAgora generates expert-aligned and user preference-enhanced responses. Our evaluations, including experiments and user studies, demonstrate that MentalAgora aligns with professional standards and effectively meets user preferences, setting a new benchmark for digital mental health interventions.

The way people respond to messaging from public health organizations on social media can provide insight into public perceptions on critical health issues, especially during a global crisis such as COVID-19. It could be valuable for high-impact organizations such as the US Centers for Disease Control and Prevention (CDC) or the World Health Organization (WHO) to understand how these perceptions impact reception of messaging on health policy recommendations. We collect two datasets of public health messages and their responses from Twitter relating to COVID-19 and Vaccines, and introduce a predictive method which can be used to explore the potential reception of such messages. Specifically, we harness a generative model (GPT-2) to directly predict probable future responses and demonstrate how it can be used to optimize expected reception of important health guidance. Finally, we introduce a novel evaluation scheme with extensive statistical testing which allows us to conclude that our models capture the semantics and sentiment found in actual public health responses.

Combination therapies have become the standard of care for diseases such as cancer, tuberculosis, malaria and HIV. However, the combinatorial set of available multi-drug treatments creates a challenge in identifying effective combination therapies available in a situation. To assist medical professionals in identifying beneficial drug-combinations, we construct an expert-annotated dataset for extracting information about the efficacy of drug combinations from the scientific literature. Beyond its practical utility, the dataset also presents a unique NLP challenge, as the first relation extraction dataset consisting of variable-length relations. Furthermore, the relations in this dataset predominantly require language understanding beyond the sentence level, adding to the challenge of this task. We provide a promising baseline model and identify clear areas for further improvement. We release our dataset, code, and baseline models publicly to encourage the NLP community to participate in this task.

The Russian Drug Reaction Corpus (RuDReC) is a new partially annotated corpus of consumer reviews in Russian about pharmaceutical products for the detection of health-related named entities and the effectiveness of pharmaceutical products. The corpus itself consists of two parts, the raw one and the labelled one. The raw part includes 1.4 million health-related user-generated texts collected from various Internet sources, including social media. The labelled part contains 500 consumer reviews about drug therapy with drug- and disease-related information. Labels for sentences include health-related issues or their absence. The sentences with one are additionally labelled at the expression level for identification of fine-grained subtypes such as drug classes and drug forms, drug indications, and drug reactions. Further, we present a baseline model for named entity recognition (NER) and multi-label sentence classification tasks on this corpus. The macro F1 score of 74.85% in the NER task was achieved by our RuDR-BERT model. For the sentence classification task, our model achieves the macro F1 score of 68.82% gaining 7.47% over the score of BERT model trained on Russian data. We make the RuDReC corpus and pretrained weights of domain-specific BERT models freely available at https://github.com/cimm-kzn/RuDReC

Given the dominance of dense retrievers that do not generalize well beyond their training dataset distributions, domain-specific test sets are essential in evaluating retrieval. There are few test datasets for retrieval systems intended for use by healthcare providers in a point-of-care setting. To fill this gap we have collaborated with medical professionals to create CURE, an ad-hoc retrieval test dataset for passage ranking with 2000 queries spanning 10 medical domains with a monolingual (English) and two cross-lingual (French/Spanish -> English) conditions. In this paper, we describe how CURE was constructed and provide baseline results to showcase its effectiveness as an evaluation tool. CURE is published with a Creative Commons Attribution Non Commercial 4.0 license and can be accessed on Hugging Face.

Background: Rapid advancements in natural language processing have led to the development of large language models with the potential to revolutionize mental health care. These models have shown promise in assisting clinicians and providing support to individuals experiencing various psychological challenges. Objective: This study aims to compare the performance of two large language models, GPT-4 and Chat-GPT, in responding to a set of 18 psychological prompts, to assess their potential applicability in mental health care settings. Methods: A blind methodology was employed, with a clinical psychologist evaluating the models' responses without knowledge of their origins. The prompts encompassed a diverse range of mental health topics, including depression, anxiety, and trauma, to ensure a comprehensive assessment. Results: The results demonstrated a significant difference in performance between the two models (p > 0.05). GPT-4 achieved an average rating of 8.29 out of 10, while Chat-GPT received an average rating of 6.52. The clinical psychologist's evaluation suggested that GPT-4 was more effective at generating clinically relevant and empathetic responses, thereby providing better support and guidance to potential users. Conclusions: This study contributes to the growing body of literature on the applicability of large language models in mental health care settings. The findings underscore the importance of continued research and development in the field to optimize these models for clinical use. Further investigation is necessary to understand the specific factors underlying the performance differences between the two models and to explore their generalizability across various populations and mental health conditions.

In the pharmaceutical industry, the use of artificial intelligence (AI) has seen consistent growth over the past decade. This rise is attributed to major advancements in statistical machine learning methodologies, computational capabilities and the increased availability of large datasets. AI techniques are applied throughout different stages of drug development, ranging from drug discovery to post-marketing benefit-risk assessment. Kolluri et al. provided a review of several case studies that span these stages, featuring key applications such as protein structure prediction, success probability estimation, subgroup identification, and AI-assisted clinical trial monitoring. From a regulatory standpoint, there was a notable uptick in submissions incorporating AI components in 2021. The most prevalent therapeutic areas leveraging AI were oncology (27%), psychiatry (15%), gastroenterology (12%), and neurology (11%). The paradigm of personalized or precision medicine has gained significant traction in recent research, partly due to advancements in AI techniques hamburg2010path. This shift has had a transformative impact on the pharmaceutical industry. Departing from the traditional "one-size-fits-all" model, personalized medicine incorporates various individual factors, such as environmental conditions, lifestyle choices, and health histories, to formulate customized treatment plans. By utilizing sophisticated machine learning algorithms, clinicians and researchers are better equipped to make informed decisions in areas such as disease prevention, diagnosis, and treatment selection, thereby optimizing health outcomes for each individual.

Applying large language models (LLMs) to assist in psycho-counseling is an emerging and meaningful approach, driven by the significant gap between patient needs and the availability of mental health support. However, current LLMs struggle to consistently provide effective responses to client speeches, largely due to the lack of supervision from high-quality real psycho-counseling data, whose content is typically inaccessible due to client privacy concerns. Furthermore, the quality of therapists' responses in available sessions can vary significantly based on their professional training and experience. Assessing the quality of therapists' responses remains an open challenge. In this work, we address these challenges by first proposing a set of professional and comprehensive principles to evaluate therapists' responses to client speeches. Using these principles, we create a preference dataset, PsychoCounsel-Preference, which contains 36k high-quality preference comparison pairs. This dataset aligns with the preferences of professional psychotherapists, providing a robust foundation for evaluating and improving LLMs in psycho-counseling. Experiments on reward modeling and preference learning demonstrate that PsychoCounsel-Preference is an excellent resource for LLMs to acquire essential skills for responding to clients in a counseling session. Our best-aligned model, PsychoCounsel-Llama3-8B, achieves an impressive win rate of 87% against GPT-4o. We release PsychoCounsel-Preference, PsychoCounsel-Llama3-8B and the reward model PsychoCounsel Llama3-8B-Reward to facilitate the research of psycho-counseling with LLMs at: https://hf.co/Psychotherapy-LLM.

We test whether Large Language Models (LLMs) can be used to simulate human participants in social-science studies. To do this, we run replications of 14 studies from the Many Labs 2 replication project with OpenAI's text-davinci-003 model, colloquially known as GPT3.5. Based on our pre-registered analyses, we find that among the eight studies we could analyse, our GPT sample replicated 37.5% of the original results and 37.5% of the Many Labs 2 results. However, we were unable to analyse the remaining six studies due to an unexpected phenomenon we call the "correct answer" effect. Different runs of GPT3.5 answered nuanced questions probing political orientation, economic preference, judgement, and moral philosophy with zero or near-zero variation in responses: with the supposedly "correct answer." In one exploratory follow-up study, we found that a "correct answer" was robust to changing the demographic details that precede the prompt. In another, we found that most but not all "correct answers" were robust to changing the order of answer choices. One of our most striking findings occurred in our replication of the Moral Foundations Theory survey results, where we found GPT3.5 identifying as a political conservative in 99.6% of the cases, and as a liberal in 99.3% of the cases in the reverse-order condition. However, both self-reported 'GPT conservatives' and 'GPT liberals' showed right-leaning moral foundations. Our results cast doubts on the validity of using LLMs as a general replacement for human participants in the social sciences. Our results also raise concerns that a hypothetical AI-led future may be subject to a diminished diversity-of-thought.

Despite growing interest in using large language models (LLMs) in healthcare, current explorations do not assess the real-world utility and safety of LLMs in clinical settings. Our objective was to determine whether two LLMs can serve information needs submitted by physicians as questions to an informatics consultation service in a safe and concordant manner. Sixty six questions from an informatics consult service were submitted to GPT-3.5 and GPT-4 via simple prompts. 12 physicians assessed the LLM responses' possibility of patient harm and concordance with existing reports from an informatics consultation service. Physician assessments were summarized based on majority vote. For no questions did a majority of physicians deem either LLM response as harmful. For GPT-3.5, responses to 8 questions were concordant with the informatics consult report, 20 discordant, and 9 were unable to be assessed. There were 29 responses with no majority on "Agree", "Disagree", and "Unable to assess". For GPT-4, responses to 13 questions were concordant, 15 discordant, and 3 were unable to be assessed. There were 35 responses with no majority. Responses from both LLMs were largely devoid of overt harm, but less than 20% of the responses agreed with an answer from an informatics consultation service, responses contained hallucinated references, and physicians were divided on what constitutes harm. These results suggest that while general purpose LLMs are able to provide safe and credible responses, they often do not meet the specific information need of a given question. A definitive evaluation of the usefulness of LLMs in healthcare settings will likely require additional research on prompt engineering, calibration, and custom-tailoring of general purpose models.

How do we most effectively treat a disease or condition? Ideally, we could consult a database of evidence gleaned from clinical trials to answer such questions. Unfortunately, no such database exists; clinical trial results are instead disseminated primarily via lengthy natural language articles. Perusing all such articles would be prohibitively time-consuming for healthcare practitioners; they instead tend to depend on manually compiled systematic reviews of medical literature to inform care. NLP may speed this process up, and eventually facilitate immediate consult of published evidence. The Evidence Inference dataset was recently released to facilitate research toward this end. This task entails inferring the comparative performance of two treatments, with respect to a given outcome, from a particular article (describing a clinical trial) and identifying supporting evidence. For instance: Does this article report that chemotherapy performed better than surgery for five-year survival rates of operable cancers? In this paper, we collect additional annotations to expand the Evidence Inference dataset by 25\%, provide stronger baseline models, systematically inspect the errors that these make, and probe dataset quality. We also release an abstract only (as opposed to full-texts) version of the task for rapid model prototyping. The updated corpus, documentation, and code for new baselines and evaluations are available at http://evidence-inference.ebm-nlp.com/.

To effectively optimize and personalize treatments, it is necessary to investigate the heterogeneity of treatment effects. With the wide range of users being treated over many online controlled experiments, the typical approach of manually investigating each dimension of heterogeneity becomes overly cumbersome and prone to subjective human biases. We need an efficient way to search through thousands of experiments with hundreds of target covariates and hundreds of breakdown dimensions. In this paper, we propose a systematic paradigm for detecting, surfacing and characterizing heterogeneous treatment effects. First, we detect if treatment effect variation is present in an experiment, prior to specifying any breakdowns. Second, we surface the most relevant dimensions for heterogeneity. Finally, we characterize the heterogeneity beyond just the conditional average treatment effects (CATE) by studying the conditional distributions of the estimated individual treatment effects. We show the effectiveness of our methods using simulated data and empirical studies.

Inferring unbiased treatment effects has received widespread attention in the machine learning community. In recent years, our community has proposed numerous solutions in standard settings, high-dimensional treatment settings, and even longitudinal settings. While very diverse, the solution has mostly relied on neural networks for inference and simultaneous correction of assignment bias. New approaches typically build on top of previous approaches by proposing new (or refined) architectures and learning algorithms. However, the end result -- a neural-network-based inference machine -- remains unchallenged. In this paper, we introduce a different type of solution in the longitudinal setting: a closed-form ordinary differential equation (ODE). While we still rely on continuous optimization to learn an ODE, the resulting inference machine is no longer a neural network. Doing so yields several advantages such as interpretability, irregular sampling, and a different set of identification assumptions. Above all, we consider the introduction of a completely new type of solution to be our most important contribution as it may spark entirely new innovations in treatment effects in general. We facilitate this by formulating our contribution as a framework that can transform any ODE discovery method into a treatment effects method.

Recent advances in Natural Language Processing (NLP), and specifically automated Question Answering (QA) systems, have demonstrated both impressive linguistic fluency and a pernicious tendency to reflect social biases. In this study, we introduce Q-Pain, a dataset for assessing bias in medical QA in the context of pain management, one of the most challenging forms of clinical decision-making. Along with the dataset, we propose a new, rigorous framework, including a sample experimental design, to measure the potential biases present when making treatment decisions. We demonstrate its use by assessing two reference Question-Answering systems, GPT-2 and GPT-3, and find statistically significant differences in treatment between intersectional race-gender subgroups, thus reaffirming the risks posed by AI in medical settings, and the need for datasets like ours to ensure safety before medical AI applications are deployed.

Clinical question answering systems have the potential to provide clinicians with relevant and timely answers to their questions. Nonetheless, despite the advances that have been made, adoption of these systems in clinical settings has been slow. One issue is a lack of question-answering datasets which reflect the real-world needs of health professionals. In this work, we present RealMedQA, a dataset of realistic clinical questions generated by humans and an LLM. We describe the process for generating and verifying the QA pairs and assess several QA models on BioASQ and RealMedQA to assess the relative difficulty of matching answers to questions. We show that the LLM is more cost-efficient for generating "ideal" QA pairs. Additionally, we achieve a lower lexical similarity between questions and answers than BioASQ which provides an additional challenge to the top two QA models, as per the results. We release our code and our dataset publicly to encourage further research.

There is a significant gap between patient needs and available mental health support today. In this paper, we aim to thoroughly examine the potential of using Large Language Models (LLMs) to assist professional psychotherapy. To this end, we propose a new benchmark, CBT-BENCH, for the systematic evaluation of cognitive behavioral therapy (CBT) assistance. We include three levels of tasks in CBT-BENCH: I: Basic CBT knowledge acquisition, with the task of multiple-choice questions; II: Cognitive model understanding, with the tasks of cognitive distortion classification, primary core belief classification, and fine-grained core belief classification; III: Therapeutic response generation, with the task of generating responses to patient speech in CBT therapy sessions. These tasks encompass key aspects of CBT that could potentially be enhanced through AI assistance, while also outlining a hierarchy of capability requirements, ranging from basic knowledge recitation to engaging in real therapeutic conversations. We evaluated representative LLMs on our benchmark. Experimental results indicate that while LLMs perform well in reciting CBT knowledge, they fall short in complex real-world scenarios requiring deep analysis of patients' cognitive structures and generating effective responses, suggesting potential future work.

Millions of users come to online peer counseling platforms to seek support on diverse topics ranging from relationship stress to anxiety. However, studies show that online peer support groups are not always as effective as expected largely due to users' negative experiences with unhelpful counselors. Peer counselors are key to the success of online peer counseling platforms, but most of them often do not have systematic ways to receive guidelines or supervision. In this work, we introduce CARE: an interactive AI-based tool to empower peer counselors through automatic suggestion generation. During the practical training stage, CARE helps diagnose which specific counseling strategies are most suitable in the given context and provides tailored example responses as suggestions. Counselors can choose to select, modify, or ignore any suggestion before replying to the support seeker. Building upon the Motivational Interviewing framework, CARE utilizes large-scale counseling conversation data together with advanced natural language generation techniques to achieve these functionalities. We demonstrate the efficacy of CARE by performing both quantitative evaluations and qualitative user studies through simulated chats and semi-structured interviews. We also find that CARE especially helps novice counselors respond better in challenging situations.

Clinical monitoring of metastatic disease to the brain can be a laborious and time-consuming process, especially in cases involving multiple metastases when the assessment is performed manually. The Response Assessment in Neuro-Oncology Brain Metastases (RANO-BM) guideline, which utilizes the unidimensional longest diameter, is commonly used in clinical and research settings to evaluate response to therapy in patients with brain metastases. However, accurate volumetric assessment of the lesion and surrounding peri-lesional edema holds significant importance in clinical decision-making and can greatly enhance outcome prediction. The unique challenge in performing segmentations of brain metastases lies in their common occurrence as small lesions. Detection and segmentation of lesions that are smaller than 10 mm in size has not demonstrated high accuracy in prior publications. The brain metastases challenge sets itself apart from previously conducted MICCAI challenges on glioma segmentation due to the significant variability in lesion size. Unlike gliomas, which tend to be larger on presentation scans, brain metastases exhibit a wide range of sizes and tend to include small lesions. We hope that the BraTS-METS dataset and challenge will advance the field of automated brain metastasis detection and segmentation.

Problem: Effective patient-centered communication is a core competency for physicians. However, both seasoned providers and medical trainees report decreased confidence in leading conversations on sensitive topics such as goals of care or end-of-life discussions. The significant administrative burden and the resources required to provide dedicated training in leading difficult conversations has been a long-standing problem in medical education. Approach: In this work, we present a novel educational tool designed to facilitate interactive, real-time simulations of difficult conversations in a video-based format through the use of multimodal generative artificial intelligence (AI). Leveraging recent advances in language modeling, computer vision, and generative audio, this tool creates realistic, interactive scenarios with avatars, or "synthetic patients." These synthetic patients interact with users throughout various stages of medical care using a custom-built video chat application, offering learners the chance to practice conversations with patients from diverse belief systems, personalities, and ethnic backgrounds. Outcomes: While the development of this platform demanded substantial upfront investment in labor, it offers a highly-realistic simulation experience with minimal financial investment. For medical trainees, this educational tool can be implemented within programs to simulate patient-provider conversations and can be incorporated into existing palliative care curriculum to provide a scalable, high-fidelity simulation environment for mastering difficult conversations. Next Steps: Future developments will explore enhancing the authenticity of these encounters by working with patients to incorporate their histories and personalities, as well as employing the use of AI-generated evaluations to offer immediate, constructive feedback to learners post-simulation.

We present a corpus of 5,000 richly annotated abstracts of medical articles describing clinical randomized controlled trials. Annotations include demarcations of text spans that describe the Patient population enrolled, the Interventions studied and to what they were Compared, and the Outcomes measured (the `PICO' elements). These spans are further annotated at a more granular level, e.g., individual interventions within them are marked and mapped onto a structured medical vocabulary. We acquired annotations from a diverse set of workers with varying levels of expertise and cost. We describe our data collection process and the corpus itself in detail. We then outline a set of challenging NLP tasks that would aid searching of the medical literature and the practice of evidence-based medicine.

Wider access to therapeutic care is one of the biggest challenges in mental health treatment. Due to institutional barriers, some people seeking mental health support have turned to large language models (LLMs) for personalized therapy, even though these models are largely unsanctioned and untested. We investigate the potential and limitations of using LLMs as providers of evidence-based therapy by using mixed methods clinical metrics. Using HELPERT, a prompt run on a large language model using the same process and training as a comparative group of peer counselors, we replicated publicly accessible mental health conversations rooted in Cognitive Behavioral Therapy (CBT) to compare session dynamics and counselor's CBT-based behaviors between original peer support sessions and their reconstructed HELPERT sessions. Two licensed, CBT-trained clinical psychologists evaluated the sessions using the Cognitive Therapy Rating Scale and provided qualitative feedback. Our findings show that the peer sessions are characterized by empathy, small talk, therapeutic alliance, and shared experiences but often exhibit therapist drift. Conversely, HELPERT reconstructed sessions exhibit minimal therapist drift and higher adherence to CBT methods but display a lack of collaboration, empathy, and cultural understanding. Through CTRS ratings and psychologists' feedback, we highlight the importance of human-AI collaboration for scalable mental health. Our work outlines the ethical implication of imparting human-like subjective qualities to LLMs in therapeutic settings, particularly the risk of deceptive empathy, which may lead to unrealistic patient expectations and potential harm.

Ensuring the accuracy of responses provided by large language models (LLMs) is crucial, particularly in clinical settings where incorrect information may directly impact patient health. To address this challenge, we construct K-QA, a dataset containing 1,212 patient questions originating from real-world conversations held on K Health (an AI-driven clinical platform). We employ a panel of in-house physicians to answer and manually decompose a subset of K-QA into self-contained statements. Additionally, we formulate two NLI-based evaluation metrics approximating recall and precision: (1) comprehensiveness, measuring the percentage of essential clinical information in the generated answer and (2) hallucination rate, measuring the number of statements from the physician-curated response contradicted by the LLM answer. Finally, we use K-QA along with these metrics to evaluate several state-of-the-art models, as well as the effect of in-context learning and medically-oriented augmented retrieval schemes developed by the authors. Our findings indicate that in-context learning improves the comprehensiveness of the models, and augmented retrieval is effective in reducing hallucinations. We make K-QA available to to the community to spur research into medically accurate NLP applications.

Great research interests have been attracted to devise AI services that are able to provide mental health support. However, the lack of corpora is a main obstacle to this research, particularly in Chinese language. In this paper, we propose PsyQA, a Chinese dataset of psychological health support in the form of question and answer pair. PsyQA is crawled from a Chinese mental health service platform, and contains 22K questions and 56K long and well-structured answers. Based on the psychological counseling theories, we annotate a portion of answer texts with typical strategies for providing support, and further present in-depth analysis of both lexical features and strategy patterns in the counseling answers. We also evaluate the performance of generating counseling answers with the generative pretrained models. Results show that utilizing strategies enhances the fluency and helpfulness of generated answers, but there is still a large space for future research.

Objective: Using natural language processing (NLP) to find sentences that state treatment plans in a clinical note, would automate plan extraction and would further enable their use in tools that help providers and care managers. However, as in the most NLP tasks on clinical text, creating gold standard to train and test NLP models is tedious and expensive. Fortuitously, sometimes but not always clinical notes contain sections with a heading that identifies the section as a plan. Leveraging contents of such labeled sections as a noisy training data, we assessed accuracy of NLP models trained with the data. Methods: We used common variations of plan headings and rule-based heuristics to find plan sections with headings in clinical notes, and we extracted sentences from them and formed a noisy training data of plan sentences. We trained Support Vector Machine (SVM) and Convolutional Neural Network (CNN) models with the data. We measured accuracy of the trained models on the noisy dataset using ten-fold cross validation and separately on a set-aside manually annotated dataset. Results: About 13% of 117,730 clinical notes contained treatment plans sections with recognizable headings in the 1001 longitudinal patient records that were obtained from Cleveland Clinic under an IRB approval. We were able to extract and create a noisy training data of 13,492 plan sentences from the clinical notes. CNN achieved best F measures, 0.91 and 0.97 in the cross-validation and set-aside evaluation experiments respectively. SVM slightly underperformed with F measures of 0.89 and 0.96 in the same experiments. Conclusion: Our study showed that the training supervised learning models using noisy plan sentences was effective in identifying them in all clinical notes. More broadly, sections with informal headings in clinical notes can be a good source for generating effective training data.

Randomized controlled trials (RCTs) are considered the gold standard for estimating the average treatment effect (ATE) of interventions. One use of RCTs is to study the causes of global poverty -- a subject explicitly cited in the 2019 Nobel Memorial Prize awarded to Duflo, Banerjee, and Kremer "for their experimental approach to alleviating global poverty." Because the ATE is a population summary, anti-poverty experiments often seek to unpack the effect variation around the ATE by conditioning (CATE) on tabular variables such as age and ethnicity that were measured during the RCT data collection. Although such variables are key to unpacking CATE, using only such variables may fail to capture historical, geographical, or neighborhood-specific contributors to effect variation, as tabular RCT data are often only observed near the time of the experiment. In global poverty research, when the location of the experiment units is approximately known, satellite imagery can provide a window into such factors important for understanding heterogeneity. However, there is no method that specifically enables applied researchers to analyze CATE from images. In this paper, using a deep probabilistic modeling framework, we develop such a method that estimates latent clusters of images by identifying images with similar treatment effects distributions. Our interpretable image CATE model also includes a sensitivity factor that quantifies the importance of image segments contributing to the effect cluster prediction. We compare the proposed methods against alternatives in simulation; also, we show how the model works in an actual RCT, estimating the effects of an anti-poverty intervention in northern Uganda and obtaining a posterior predictive distribution over effects for the rest of the country where no experimental data was collected. We make all models available in open-source software.

This paper introduces the "CIVICS: Culturally-Informed & Values-Inclusive Corpus for Societal impacts" dataset, designed to evaluate the social and cultural variation of Large Language Models (LLMs) across multiple languages and value-sensitive topics. We create a hand-crafted, multilingual dataset of value-laden prompts which address specific socially sensitive topics, including LGBTQI rights, social welfare, immigration, disability rights, and surrogacy. CIVICS is designed to generate responses showing LLMs' encoded and implicit values. Through our dynamic annotation processes, tailored prompt design, and experiments, we investigate how open-weight LLMs respond to value-sensitive issues, exploring their behavior across diverse linguistic and cultural contexts. Using two experimental set-ups based on log-probabilities and long-form responses, we show social and cultural variability across different LLMs. Specifically, experiments involving long-form responses demonstrate that refusals are triggered disparately across models, but consistently and more frequently in English or translated statements. Moreover, specific topics and sources lead to more pronounced differences across model answers, particularly on immigration, LGBTQI rights, and social welfare. As shown by our experiments, the CIVICS dataset aims to serve as a tool for future research, promoting reproducibility and transparency across broader linguistic settings, and furthering the development of AI technologies that respect and reflect global cultural diversities and value pluralism. The CIVICS dataset and tools will be made available upon publication under open licenses; an anonymized version is currently available at https://huggingface.co/CIVICS-dataset.

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

In psychotherapy, therapeutic outcome assessment, or treatment outcome evaluation, is essential for enhancing mental health care by systematically evaluating therapeutic processes and outcomes. Existing large language model approaches often focus on therapist-centered, single-session evaluations, neglecting the client's subjective experience and longitudinal progress across multiple sessions. To address these limitations, we propose IPAEval, a client-Informed Psychological Assessment-based Evaluation framework that automates treatment outcome evaluations from the client's perspective using clinical interviews. IPAEval integrates cross-session client-contextual assessment and session-focused client-dynamics assessment to provide a comprehensive understanding of therapeutic progress. Experiments on our newly developed TheraPhase dataset demonstrate that IPAEval effectively tracks symptom severity and treatment outcomes over multiple sessions, outperforming previous single-session models and validating the benefits of items-aware reasoning mechanisms.

Providing high quality explanations for AI predictions based on machine learning is a challenging and complex task. To work well it requires, among other factors: selecting a proper level of generality/specificity of the explanation; considering assumptions about the familiarity of the explanation beneficiary with the AI task under consideration; referring to specific elements that have contributed to the decision; making use of additional knowledge (e.g. expert evidence) which might not be part of the prediction process; and providing evidence supporting negative hypothesis. Finally, the system needs to formulate the explanation in a clearly interpretable, and possibly convincing, way. Given these considerations, ANTIDOTE fosters an integrated vision of explainable AI, where low-level characteristics of the deep learning process are combined with higher level schemes proper of the human argumentation capacity. ANTIDOTE will exploit cross-disciplinary competences in deep learning and argumentation to support a broader and innovative view of explainable AI, where the need for high-quality explanations for clinical cases deliberation is critical. As a first result of the project, we publish the Antidote CasiMedicos dataset to facilitate research on explainable AI in general, and argumentation in the medical domain in particular.

Adverse Drug Reactions (ADRs) from psychiatric medications are the leading cause of hospitalizations among mental health patients. With healthcare systems and online communities facing limitations in resolving ADR-related issues, Large Language Models (LLMs) have the potential to fill this gap. Despite the increasing capabilities of LLMs, past research has not explored their capabilities in detecting ADRs related to psychiatric medications or in providing effective harm reduction strategies. To address this, we introduce the Psych-ADR benchmark and the Adverse Drug Reaction Response Assessment (ADRA) framework to systematically evaluate LLM performance in detecting ADR expressions and delivering expert-aligned mitigation strategies. Our analyses show that LLMs struggle with understanding the nuances of ADRs and differentiating between types of ADRs. While LLMs align with experts in terms of expressed emotions and tone of the text, their responses are more complex, harder to read, and only 70.86% aligned with expert strategies. Furthermore, they provide less actionable advice by a margin of 12.32% on average. Our work provides a comprehensive benchmark and evaluation framework for assessing LLMs in strategy-driven tasks within high-risk domains.

Existing datasets that contain boolean questions, such as BoolQ and TYDI QA , provide the user with a YES/NO response to the question. However, a one word response is not sufficient for an explainable system. We promote explainability by releasing a new set of annotations marking the evidence in existing TyDi QA and BoolQ datasets. We show that our annotations can be used to train a model that extracts improved evidence spans compared to models that rely on existing resources. We confirm our findings with a user study which shows that our extracted evidence spans enhance the user experience. We also provide further insight into the challenges of answering boolean questions, such as passages containing conflicting YES and NO answers, and varying degrees of relevance of the predicted evidence.

Documentation burden is a major contributor to clinician burnout, which is rising nationally and is an urgent threat to our ability to care for patients. Artificial intelligence (AI) chatbots, such as ChatGPT, could reduce clinician burden by assisting with documentation. Although many hospitals are actively integrating such systems into electronic medical record systems, AI chatbots utility and impact on clinical decision-making have not been studied for this intended use. We are the first to examine the utility of large language models in assisting clinicians draft responses to patient questions. In our two-stage cross-sectional study, 6 oncologists responded to 100 realistic synthetic cancer patient scenarios and portal messages developed to reflect common medical situations, first manually, then with AI assistance. We find AI-assisted responses were longer, less readable, but provided acceptable drafts without edits 58% of time. AI assistance improved efficiency 77% of time, with low harm risk (82% safe). However, 7.7% unedited AI responses could severely harm. In 31% cases, physicians thought AI drafts were human-written. AI assistance led to more patient education recommendations, fewer clinical actions than manual responses. Results show promise for AI to improve clinician efficiency and patient care through assisting documentation, if used judiciously. Monitoring model outputs and human-AI interaction remains crucial for safe implementation.

Visual question answering is a task of predicting the answer to a question about an image. Given that different people can provide different answers to a visual question, we aim to better understand why with answer groundings. We introduce the first dataset that visually grounds each unique answer to each visual question, which we call VQAAnswerTherapy. We then propose two novel problems of predicting whether a visual question has a single answer grounding and localizing all answer groundings. We benchmark modern algorithms for these novel problems to show where they succeed and struggle. The dataset and evaluation server can be found publicly at https://vizwiz.org/tasks-and-datasets/vqa-answer-therapy/.

Substance use disorders (SUDs) are a growing concern globally, necessitating enhanced understanding of the problem and its trends through data-driven research. Social media are unique and important sources of information about SUDs, particularly since the data in such sources are often generated by people with lived experiences. In this paper, we introduce Reddit-Impacts, a challenging Named Entity Recognition (NER) dataset curated from subreddits dedicated to discussions on prescription and illicit opioids, as well as medications for opioid use disorder. The dataset specifically concentrates on the lesser-studied, yet critically important, aspects of substance use--its clinical and social impacts. We collected data from chosen subreddits using the publicly available Application Programming Interface for Reddit. We manually annotated text spans representing clinical and social impacts reported by people who also reported personal nonmedical use of substances including but not limited to opioids, stimulants and benzodiazepines. Our objective is to create a resource that can enable the development of systems that can automatically detect clinical and social impacts of substance use from text-based social media data. The successful development of such systems may enable us to better understand how nonmedical use of substances affects individual health and societal dynamics, aiding the development of effective public health strategies. In addition to creating the annotated data set, we applied several machine learning models to establish baseline performances. Specifically, we experimented with transformer models like BERT, and RoBERTa, one few-shot learning model DANN by leveraging the full training dataset, and GPT-3.5 by using one-shot learning, for automatic NER of clinical and social impacts. The dataset has been made available through the 2024 SMM4H shared tasks.

This paper presents ChatCounselor, a large language model (LLM) solution designed to provide mental health support. Unlike generic chatbots, ChatCounselor is distinguished by its foundation in real conversations between consulting clients and professional psychologists, enabling it to possess specialized knowledge and counseling skills in the field of psychology. The training dataset, Psych8k, was constructed from 260 in-depth interviews, each spanning an hour. To assess the quality of counseling responses, the counseling Bench was devised. Leveraging GPT-4 and meticulously crafted prompts based on seven metrics of psychological counseling assessment, the model underwent evaluation using a set of real-world counseling questions. Impressively, ChatCounselor surpasses existing open-source models in the counseling Bench and approaches the performance level of ChatGPT, showcasing the remarkable enhancement in model capability attained through high-quality domain-specific data.

In the medical domain, numerous scenarios necessitate the long-form generation ability of large language models (LLMs). Specifically, when addressing patients' questions, it is essential that the model's response conveys factual claims, highlighting the need for an automated method to evaluate those claims. Thus, we introduce MedLFQA, a benchmark dataset reconstructed using long-form question-answering datasets related to the biomedical domain. We use MedLFQA to facilitate the automatic evaluations of factuality. We also propose OLAPH, a simple and novel framework that enables the improvement of factuality through automatic evaluations. The OLAPH framework iteratively trains LLMs to mitigate hallucinations using sampling predictions and preference optimization. In other words, we iteratively set the highest-scoring response as a preferred response derived from sampling predictions and train LLMs to align with the preferred response that improves factuality. We highlight that, even on evaluation metrics not used during training, LLMs trained with our OLAPH framework demonstrate significant performance improvement in factuality. Our findings reveal that a 7B LLM trained with our OLAPH framework can provide long answers comparable to the medical experts' answers in terms of factuality. We believe that our work could shed light on gauging the long-text generation ability of LLMs in the medical domain. Our code and datasets are available at https://github.com/dmis-lab/OLAPH}{https://github.com/dmis-lab/OLAPH.

Online mental health support communities have grown in recent years for providing accessible mental and emotional health support through volunteer counselors. Despite millions of people participating in chat support on these platforms, the clinical effectiveness of these communities on mental health symptoms remains unknown. Furthermore, although volunteers receive some training based on established therapeutic skills studied in face-to-face environments such as active listening and motivational interviewing, it remains understudied how the usage of these skills in this online context affects people's mental health status. In our work, we collaborate with one of the largest online peer support platforms and use both natural language processing and machine learning techniques to measure how one-on-one support chats affect depression and anxiety symptoms. We measure how the techniques and characteristics of support providers, such as using affirmation, empathy, and past experience on the platform, affect support-seekers' mental health changes. We find that online peer support chats improve both depression and anxiety symptoms with a statistically significant but relatively small effect size. Additionally, support providers' techniques such as emphasizing the autonomy of the client lead to better mental health outcomes. However, we also found that some behaviors (e.g. persuading) are actually harmful to depression and anxiety outcomes. Our work provides key understanding for mental health care in the online setting and designing training systems for online support providers.

In recent years, there is strong emphasis on mining medical data using machine learning techniques. A common problem is to obtain a noiseless set of textual documents, with a relevant content for the research question, and developing a Question Answering (QA) model for a specific medical field. The purpose of this paper is to present a new methodology for building a medical dataset and obtain a QA model for analysis of symptoms and impact on daily life for a specific disease domain. The ``Mental Health'' forum was used, a forum dedicated to people suffering from schizophrenia and different mental disorders. Relevant posts of active users, who regularly participate, were extrapolated providing a new method of obtaining low-bias content and without privacy issues. Furthermore, it is shown how to pre-process the dataset to convert it into a QA dataset. The Bidirectional Encoder Representations from Transformers (BERT), DistilBERT, RoBERTa, and BioBERT models were fine-tuned and evaluated via F1-Score, Exact Match, Precision and Recall. Accurate empirical experiments demonstrated the effectiveness of the proposed method for obtaining an accurate dataset for QA model implementation. By fine-tuning the BioBERT QA model, we achieved an F1 score of 0.885, showing a considerable improvement and outperforming the state-of-the-art model for mental disorders domain.

Current medical question answering systems have difficulty processing long, detailed and informally worded questions submitted by patients, called Consumer Health Questions (CHQs). To address this issue, we introduce a medical question understanding and answering system with knowledge grounding and semantic self-supervision. Our system is a pipeline that first summarizes a long, medical, user-written question, using a supervised summarization loss. Then, our system performs a two-step retrieval to return answers. The system first matches the summarized user question with an FAQ from a trusted medical knowledge base, and then retrieves a fixed number of relevant sentences from the corresponding answer document. In the absence of labels for question matching or answer relevance, we design 3 novel, self-supervised and semantically-guided losses. We evaluate our model against two strong retrieval-based question answering baselines. Evaluators ask their own questions and rate the answers retrieved by our baselines and own system according to their relevance. They find that our system retrieves more relevant answers, while achieving speeds 20 times faster. Our self-supervised losses also help the summarizer achieve higher scores in ROUGE, as well as in human evaluation metrics. We release our code to encourage further research.

Concerns about hallucinations in Large Language Models (LLMs) have been raised by researchers, yet their potential in areas where creativity is vital, such as drug discovery, merits exploration. In this paper, we come up with the hypothesis that hallucinations can improve LLMs in drug discovery. To verify this hypothesis, we use LLMs to describe the SMILES string of molecules in natural language and then incorporate these descriptions as part of the prompt to address specific tasks in drug discovery. Evaluated on seven LLMs and five classification tasks, our findings confirm the hypothesis: LLMs can achieve better performance with text containing hallucinations. Notably, Llama-3.1-8B achieves an 18.35% gain in ROC-AUC compared to the baseline without hallucination. Furthermore, hallucinations generated by GPT-4o provide the most consistent improvements across models. Additionally, we conduct empirical analyses and a case study to investigate key factors affecting performance and the underlying reasons. Our research sheds light on the potential use of hallucinations for LLMs and offers new perspectives for future research leveraging LLMs in drug discovery.

This paper introduces a new testbed CLIFT (Clinical Shift) for the clinical domain Question-answering task. The testbed includes 7.5k high-quality question answering samples to provide a diverse and reliable benchmark. We performed a comprehensive experimental study and evaluated several QA deep-learning models under the proposed testbed. Despite impressive results on the original test set, the performance degrades when applied to new test sets, which shows the distribution shift. Our findings emphasize the need for and the potential for increasing the robustness of clinical domain models under distributional shifts. The testbed offers one way to track progress in that direction. It also highlights the necessity of adopting evaluation metrics that consider robustness to natural distribution shifts. We plan to expand the corpus by adding more samples and model results. The full paper and the updated benchmark are available at github.com/openlifescience-ai/clift

In recent years, there have been significant breakthroughs in the field of natural language processing, particularly with the development of large language models (LLMs). These LLMs have showcased remarkable capabilities on various benchmarks. In the healthcare field, the exact role LLMs and other future AI models will play remains unclear. There is a potential for these models in the future to be used as part of adaptive physician training, medical co-pilot applications, and digital patient interaction scenarios. The ability of AI models to participate in medical training and patient care will depend in part on their mastery of the knowledge content of specific medical fields. This study investigated the medical knowledge capability of LLMs, specifically in the context of internal medicine subspecialty multiple-choice test-taking ability. We compared the performance of several open-source LLMs (Koala 7B, Falcon 7B, Stable-Vicuna 13B, and Orca Mini 13B), to GPT-4 and Claude 2 on multiple-choice questions in the field of Nephrology. Nephrology was chosen as an example of a particularly conceptually complex subspecialty field within internal medicine. The study was conducted to evaluate the ability of LLM models to provide correct answers to nephSAP (Nephrology Self-Assessment Program) multiple-choice questions. The overall success of open-sourced LLMs in answering the 858 nephSAP multiple-choice questions correctly was 17.1% - 25.5%. In contrast, Claude 2 answered 54.4% of the questions correctly, whereas GPT-4 achieved a score of 73.3%. We show that current widely used open-sourced LLMs do poorly in their ability for zero-shot reasoning when compared to GPT-4 and Claude 2. The findings of this study potentially have significant implications for the future of subspecialty medical training and patient care.

Despite the potential of Large Language Models (LLMs) in medicine, they may generate responses lacking supporting evidence or based on hallucinated evidence. While Retrieval Augment Generation (RAG) is popular to address this issue, few studies implemented and evaluated RAG in downstream domain-specific applications. We developed a RAG pipeline with 70,000 ophthalmology-specific documents that retrieve relevant documents to augment LLMs during inference time. In a case study on long-form consumer health questions, we systematically evaluated the responses including over 500 references of LLMs with and without RAG on 100 questions with 10 healthcare professionals. The evaluation focuses on factuality of evidence, selection and ranking of evidence, attribution of evidence, and answer accuracy and completeness. LLMs without RAG provided 252 references in total. Of which, 45.3% hallucinated, 34.1% consisted of minor errors, and 20.6% were correct. In contrast, LLMs with RAG significantly improved accuracy (54.5% being correct) and reduced error rates (18.8% with minor hallucinations and 26.7% with errors). 62.5% of the top 10 documents retrieved by RAG were selected as the top references in the LLM response, with an average ranking of 4.9. The use of RAG also improved evidence attribution (increasing from 1.85 to 2.49 on a 5-point scale, P<0.001), albeit with slight decreases in accuracy (from 3.52 to 3.23, P=0.03) and completeness (from 3.47 to 3.27, P=0.17). The results demonstrate that LLMs frequently exhibited hallucinated and erroneous evidence in the responses, raising concerns for downstream applications in the medical domain. RAG substantially reduced the proportion of such evidence but encountered challenges.

In this paper, we release a largest ever medical Question Answering (QA) dataset with 26 million QA pairs. We benchmark many existing approaches in our dataset in terms of both retrieval and generation. Experimental results show that the existing models perform far lower than expected and the released dataset is still challenging in the pre-trained language model era. Moreover, we also experimentally show the benefit of the proposed dataset in many aspects: (i) trained models for other QA datasets in a zero-shot fashion; and (ii) as external knowledge for retrieval-augmented generation (RAG); and (iii) improving existing pre-trained language models by using the QA pairs as a pre-training corpus in continued training manner. We believe that this dataset will not only contribute to medical research but also facilitate both the patients and clinical doctors. See https://github.com/FreedomIntelligence/Huatuo-26M.

This study explores the use of Large language models to analyze therapist remarks in a psychotherapeutic setting. The paper focuses on the application of BERTopic, a machine learning-based topic modeling tool, to the dialogue of two different groups of therapists (classical and modern), which makes it possible to identify and describe a set of topics that consistently emerge across these groups. The paper describes in detail the chosen algorithm for BERTopic, which included creating a vector space from a corpus of therapist remarks, reducing its dimensionality, clustering the space, and creating and optimizing topic representation. Along with the automatic topical modeling by the BERTopic, the research involved an expert assessment of the findings and manual topic structure optimization. The topic modeling results highlighted the most common and stable topics in therapists speech, offering insights into how language patterns in therapy develop and remain stable across different therapeutic styles. This work contributes to the growing field of machine learning in psychotherapy by demonstrating the potential of automated methods to improve both the practice and training of therapists. The study highlights the value of topic modeling as a tool for gaining a deeper understanding of therapeutic dialogue and offers new opportunities for improving therapeutic effectiveness and clinical supervision.

Large language models (LLMs) have shown remarkable progress in encoding clinical knowledge and responding to complex medical queries with appropriate clinical reasoning. However, their applicability in subspecialist or complex medical settings remains underexplored. In this work, we probe the performance of AMIE, a research conversational diagnostic AI system, in the subspecialist domain of breast oncology care without specific fine-tuning to this challenging domain. To perform this evaluation, we curated a set of 50 synthetic breast cancer vignettes representing a range of treatment-naive and treatment-refractory cases and mirroring the key information available to a multidisciplinary tumor board for decision-making (openly released with this work). We developed a detailed clinical rubric for evaluating management plans, including axes such as the quality of case summarization, safety of the proposed care plan, and recommendations for chemotherapy, radiotherapy, surgery and hormonal therapy. To improve performance, we enhanced AMIE with the inference-time ability to perform web search retrieval to gather relevant and up-to-date clinical knowledge and refine its responses with a multi-stage self-critique pipeline. We compare response quality of AMIE with internal medicine trainees, oncology fellows, and general oncology attendings under both automated and specialist clinician evaluations. In our evaluations, AMIE outperformed trainees and fellows demonstrating the potential of the system in this challenging and important domain. We further demonstrate through qualitative examples, how systems such as AMIE might facilitate conversational interactions to assist clinicians in their decision making. However, AMIE's performance was overall inferior to attending oncologists suggesting that further research is needed prior to consideration of prospective uses.

We propose MMLU-SR, a novel dataset designed to measure the true comprehension abilities of Large Language Models (LLMs) by challenging their performance in question-answering tasks with modified terms. We reasoned that an agent that ``truly'' understands a concept can still evaluate it when key terms are replaced by suitably defined alternate terms, and sought to differentiate such comprehension from mere text replacement. In our study, we modified standardized test questions by replacing a key term with a dummy word along with its definition. The key term could be in the context of questions, answers, or both questions and answers. Notwithstanding the high scores achieved by recent popular LLMs on the MMLU leaderboard, we found a substantial reduction in model performance after such replacement, suggesting poor comprehension. This new benchmark provides a rigorous benchmark for testing true model comprehension, and poses a challenge to the broader scientific community.

Language model users often issue queries that lack specification, where the context under which a query was issued -- such as the user's identity, the query's intent, and the criteria for a response to be useful -- is not explicit. For instance, a good response to a subjective query like "What book should I read next?" would depend on the user's preferences, and a good response to an open-ended query like "How do antibiotics work against bacteria?" would depend on the user's expertise. This makes evaluation of responses to such queries an ill-posed task, as evaluators may make arbitrary judgments about the response quality. To remedy this, we present contextualized evaluations, a protocol that synthetically constructs context surrounding an underspecified query and provides it during evaluation. We find that the presence of context can 1) alter conclusions drawn from evaluation, even flipping win rates between model pairs, 2) nudge evaluators to make fewer judgments based on surface-level criteria, like style, and 3) provide new insights about model behavior across diverse contexts. Specifically, our procedure uncovers an implicit bias towards WEIRD contexts in models' "default" responses and we find that models are not equally sensitive to following different contexts, even when they are provided in prompts.

Throughout the course of my Ph.D., I have been designing the user experience (UX) of various machine learning (ML) systems. In this workshop, I share two projects as case studies in which people engage with ML in much more complicated and nuanced ways than the technical HCML work might assume. The first case study describes how cardiology teams in three hospitals used a clinical decision-support system that helps them decide whether and when to implant an artificial heart to a heart failure patient. I demonstrate that physicians cannot draw on their decision-making experience by seeing only patient data on paper. They are also confused by some fundamental premises upon which ML operates. For example, physicians asked: Are ML predictions made based on clinicians' best efforts? Is it ethical to make decisions based on previous patients' collective outcomes? In the second case study, my collaborators and I designed an intelligent text editor, with the goal of improving authors' writing experience with NLP (Natural Language Processing) technologies. We prototyped a number of generative functionalities where the system provides phrase-or-sentence-level writing suggestions upon user request. When writing with the prototype, however, authors shared that they need to "see where the sentence is going two paragraphs later" in order to decide whether the suggestion aligns with their writing; Some even considered adopting machine suggestions as plagiarism, therefore "is simply wrong". By sharing these unexpected and intriguing responses from these real-world ML users, I hope to start a discussion about such previously-unknown complexities and nuances of -- as the workshop proposal states -- "putting ML at the service of people in a way that is accessible, useful, and trustworthy to all".

One way to personalize chatbot interactions is by establishing common ground with the intended reader. A domain where establishing mutual understanding could be particularly impactful is vaccine concerns and misinformation. Vaccine interventions are forms of messaging which aim to answer concerns expressed about vaccination. Tailoring responses in this domain is difficult, since opinions often have seemingly little ideological overlap. We define the task of tailoring vaccine interventions to a Common-Ground Opinion (CGO). Tailoring responses to a CGO involves meaningfully improving the answer by relating it to an opinion or belief the reader holds. In this paper we introduce TAILOR-CGO, a dataset for evaluating how well responses are tailored to provided CGOs. We benchmark several major LLMs on this task; finding GPT-4-Turbo performs significantly better than others. We also build automatic evaluation metrics, including an efficient and accurate BERT model that outperforms finetuned LLMs, investigate how to successfully tailor vaccine messaging to CGOs, and provide actionable recommendations from this investigation. Code and model weights: https://github.com/rickardstureborg/tailor-cgo Dataset: https://huggingface.co/datasets/DukeNLP/tailor-cgo

The recommendation of medication is a vital aspect of intelligent healthcare systems, as it involves prescribing the most suitable drugs based on a patient's specific health needs. Unfortunately, many sophisticated models currently in use tend to overlook the nuanced semantics of medical data, while only relying heavily on identities. Furthermore, these models face significant challenges in handling cases involving patients who are visiting the hospital for the first time, as they lack prior prescription histories to draw upon. To tackle these issues, we harness the powerful semantic comprehension and input-agnostic characteristics of Large Language Models (LLMs). Our research aims to transform existing medication recommendation methodologies using LLMs. In this paper, we introduce a novel approach called Large Language Model Distilling Medication Recommendation (LEADER). We begin by creating appropriate prompt templates that enable LLMs to suggest medications effectively. However, the straightforward integration of LLMs into recommender systems leads to an out-of-corpus issue specific to drugs. We handle it by adapting the LLMs with a novel output layer and a refined tuning loss function. Although LLM-based models exhibit remarkable capabilities, they are plagued by high computational costs during inference, which is impractical for the healthcare sector. To mitigate this, we have developed a feature-level knowledge distillation technique, which transfers the LLM's proficiency to a more compact model. Extensive experiments conducted on two real-world datasets, MIMIC-III and MIMIC-IV, demonstrate that our proposed model not only delivers effective results but also is efficient. To ease the reproducibility of our experiments, we release the implementation code online.

Pir\'a is a reading comprehension dataset focused on the ocean, the Brazilian coast, and climate change, built from a collection of scientific abstracts and reports on these topics. This dataset represents a versatile language resource, particularly useful for testing the ability of current machine learning models to acquire expert scientific knowledge. Despite its potential, a detailed set of baselines has not yet been developed for Pir\'a. By creating these baselines, researchers can more easily utilize Pir\'a as a resource for testing machine learning models across a wide range of question answering tasks. In this paper, we define six benchmarks over the Pir\'a dataset, covering closed generative question answering, machine reading comprehension, information retrieval, open question answering, answer triggering, and multiple choice question answering. As part of this effort, we have also produced a curated version of the original dataset, where we fixed a number of grammar issues, repetitions, and other shortcomings. Furthermore, the dataset has been extended in several new directions, so as to face the aforementioned benchmarks: translation of supporting texts from English into Portuguese, classification labels for answerability, automatic paraphrases of questions and answers, and multiple choice candidates. The results described in this paper provide several points of reference for researchers interested in exploring the challenges provided by the Pir\'a dataset.

The global cost of drug discovery and development exceeds $200 billion annually. The main results of drug discovery and development are the outcomes of clinical trials, which directly influence the regulatory approval of new drug candidates and ultimately affect patient outcomes. Despite their significance, large-scale, high-quality clinical trial outcome data are not readily available to the public. Suppose a large clinical trial outcome dataset is provided; machine learning researchers can potentially develop accurate prediction models using past trials and outcome labels, which could help prioritize and optimize therapeutic programs, ultimately benefiting patients. This paper introduces Clinical Trial Outcome (CTO) dataset, the largest trial outcome dataset with around 479K clinical trials, aggregating outcomes from multiple sources of weakly supervised labels, minimizing the noise from individual sources, and eliminating the need for human annotation. These sources include large language model (LLM) decisions on trial-related documents, news headline sentiments, stock prices of trial sponsors, trial linkages across phases, and other signals such as patient dropout rates and adverse events. CTO's labels show unprecedented agreement with supervised clinical trial outcome labels from test split of the supervised TOP dataset, with a 91 F1.

In this paper, we present the current progress of the project Verif.ai, an open-source scientific generative question-answering system with referenced and verified answers. The components of the system are (1) an information retrieval system combining semantic and lexical search techniques over scientific papers (PubMed), (2) a fine-tuned generative model (Mistral 7B) taking top answers and generating answers with references to the papers from which the claim was derived, and (3) a verification engine that cross-checks the generated claim and the abstract or paper from which the claim was derived, verifying whether there may have been any hallucinations in generating the claim. We are reinforcing the generative model by providing the abstract in context, but in addition, an independent set of methods and models are verifying the answer and checking for hallucinations. Therefore, we believe that by using our method, we can make scientists more productive, while building trust in the use of generative language models in scientific environments, where hallucinations and misinformation cannot be tolerated.

Since the advent of chatbots in the commercial sector, they have been widely employed in the customer service department. Typically, these commercial chatbots are retrieval-based, so they are unable to respond to queries absent in the provided dataset. On the contrary, generative chatbots try to create the most appropriate response, but are mostly unable to create a smooth flow in the customer-bot dialog. Since the client has few options left for continuing after receiving a response, the dialog becomes short. Through our work, we try to maximize the intelligence of a simple conversational agent so it can answer unseen queries, and generate follow-up questions or remarks. We have built a chatbot for a jewelry shop that finds the underlying objective of the customer's query by finding similarity of the input to patterns in the corpus. Our system features an audio input interface for clients, so they may speak to it in natural language. After converting the audio to text, we trained the model to extract the intent of the query, to find an appropriate response and to speak to the client in a natural human voice. To gauge the system's performance, we used performance metrics such as Recall, Precision and F1 score.

Despite end-to-end neural systems making significant progress in the last decade for task-oriented as well as chit-chat based dialogue systems, most dialogue systems rely on hybrid approaches which use a combination of rule-based, retrieval and generative approaches for generating a set of ranked responses. Such dialogue systems need to rely on a fallback mechanism to respond to out-of-domain or novel user queries which are not answerable within the scope of the dialog system. While, dialog systems today rely on static and unnatural responses like "I don't know the answer to that question" or "I'm not sure about that", we design a neural approach which generates responses which are contextually aware with the user query as well as say no to the user. Such customized responses provide paraphrasing ability and contextualization as well as improve the interaction with the user and reduce dialogue monotonicity. Our simple approach makes use of rules over dependency parses and a text-to-text transformer fine-tuned on synthetic data of question-response pairs generating highly relevant, grammatical as well as diverse questions. We perform automatic and manual evaluations to demonstrate the efficacy of the system.

Drug discovery typically consists of multiple steps, including identifying a target protein key to a disease's etiology, validating that interacting with this target could prevent symptoms or cure the disease, discovering a small molecule or biologic therapeutic to interact with it, and optimizing the candidate molecule through a complex landscape of required properties. Drug discovery related tasks often involve prediction and generation while considering multiple entities that potentially interact, which poses a challenge for typical AI models. For this purpose we present MAMMAL - Molecular Aligned Multi-Modal Architecture and Language - a method that we applied to create a versatile multi-task foundation model ibm/biomed.omics.bl.sm.ma-ted-458m that learns from large-scale biological datasets (2 billion samples) across diverse modalities, including proteins, small molecules, and genes. We introduce a prompt syntax that supports a wide range of classification, regression, and generation tasks. It allows combining different modalities and entity types as inputs and/or outputs. Our model handles combinations of tokens and scalars and enables the generation of small molecules and proteins, property prediction, and transcriptomic lab test predictions. We evaluated the model on 11 diverse downstream tasks spanning different steps within a typical drug discovery pipeline, where it reaches new SOTA in 9 tasks and is comparable to SOTA in 2 tasks. This performance is achieved while using a unified architecture serving all tasks, in contrast to the original SOTA performance achieved using tailored architectures. The model code and pretrained weights are publicly available at https://github.com/BiomedSciAI/biomed-multi-alignment and https://huggingface.co/ibm/biomed.omics.bl.sm.ma-ted-458m.

Automatic depression detection from conversational data has gained significant interest in recent years. The DAIC-WOZ dataset, interviews conducted by a human-controlled virtual agent, has been widely used for this task. Recent studies have reported enhanced performance when incorporating interviewer's prompts into the model. In this work, we hypothesize that this improvement might be mainly due to a bias present in these prompts, rather than the proposed architectures and methods. Through ablation experiments and qualitative analysis, we discover that models using interviewer's prompts learn to focus on a specific region of the interviews, where questions about past experiences with mental health issues are asked, and use them as discriminative shortcuts to detect depressed participants. In contrast, models using participant responses gather evidence from across the entire interview. Finally, to highlight the magnitude of this bias, we achieve a 0.90 F1 score by intentionally exploiting it, the highest result reported to date on this dataset using only textual information. Our findings underline the need for caution when incorporating interviewers' prompts into models, as they may inadvertently learn to exploit targeted prompts, rather than learning to characterize the language and behavior that are genuinely indicative of the patient's mental health condition.

Under the pandemic of COVID-19, people experiencing COVID19-related symptoms or exposed to risk factors have a pressing need to consult doctors. Due to hospital closure, a lot of consulting services have been moved online. Because of the shortage of medical professionals, many people cannot receive online consultations timely. To address this problem, we aim to develop a medical dialogue system that can provide COVID19-related consultations. We collected two dialogue datasets -- CovidDialog -- (in English and Chinese respectively) containing conversations between doctors and patients about COVID-19. On these two datasets, we train several dialogue generation models based on Transformer, GPT, and BERT-GPT. Since the two COVID-19 dialogue datasets are small in size, which bear high risk of overfitting, we leverage transfer learning to mitigate data deficiency. Specifically, we take the pretrained models of Transformer, GPT, and BERT-GPT on dialog datasets and other large-scale texts, then finetune them on our CovidDialog tasks. We perform both automatic and human evaluation of responses generated by these models. The results show that the generated responses are promising in being doctor-like, relevant to the conversation history, and clinically informative. The data and code are available at https://github.com/UCSD-AI4H/COVID-Dialogue.

Large datasets are essential for neural modeling of many NLP tasks. Current publicly available open-domain dialogue datasets offer a trade-off between quality (e.g., DailyDialog) and size (e.g., Opensubtitles). We narrow this gap by building a high-quality dataset of 14.8M utterances in English, and smaller datasets in German, Dutch, Spanish, Portuguese, Italian, and Hungarian. We extract and process dialogues from public-domain books made available by Project Gutenberg. We describe our dialogue extraction pipeline, analyze the effects of the various heuristics used, and present an error analysis of extracted dialogues. Finally, we conduct experiments showing that better response quality can be achieved in zero-shot and finetuning settings by training on our data than on the larger but much noisier Opensubtitles dataset. Our open-source pipeline (https://github.com/ricsinaruto/gutenberg-dialog) can be extended to further languages with little additional effort. Researchers can also build their versions of existing datasets by adjusting various trade-off parameters. We also built a web demo for interacting with our models: https://ricsinaruto.github.io/chatbot.html.

Personalized treatment effect estimates are often of interest in high-stakes applications -- thus, before deploying a model estimating such effects in practice, one needs to be sure that the best candidate from the ever-growing machine learning toolbox for this task was chosen. Unfortunately, due to the absence of counterfactual information in practice, it is usually not possible to rely on standard validation metrics for doing so, leading to a well-known model selection dilemma in the treatment effect estimation literature. While some solutions have recently been investigated, systematic understanding of the strengths and weaknesses of different model selection criteria is still lacking. In this paper, instead of attempting to declare a global `winner', we therefore empirically investigate success- and failure modes of different selection criteria. We highlight that there is a complex interplay between selection strategies, candidate estimators and the data used for comparing them, and provide interesting insights into the relative (dis)advantages of different criteria alongside desiderata for the design of further illuminating empirical studies in this context.

Textual health records of cancer patients are usually protracted and highly unstructured, making it very time-consuming for health professionals to get a complete overview of the patient's therapeutic course. As such limitations can lead to suboptimal and/or inefficient treatment procedures, healthcare providers would greatly benefit from a system that effectively summarizes the information of those records. With the advent of deep neural models, this objective has been partially attained for English clinical texts, however, the research community still lacks an effective solution for languages with limited resources. In this paper, we present the approach we developed to extract procedures, drugs, and diseases from oncology health records written in European Portuguese. This project was conducted in collaboration with the Portuguese Institute for Oncology which, besides holding over 10 years of duly protected medical records, also provided oncologist expertise throughout the development of the project. Since there is no annotated corpus for biomedical entity extraction in Portuguese, we also present the strategy we followed in annotating the corpus for the development of the models. The final models, which combined a neural architecture with entity linking, achieved F_1 scores of 88.6, 95.0, and 55.8 per cent in the mention extraction of procedures, drugs, and diseases, respectively.

Previous works on Treatment Effect Estimation (TEE) are not in widespread use because they are predominantly theoretical, where strong parametric assumptions are made but untractable for practical application. Recent work uses multilayer perceptron (MLP) for modeling casual relationships, however, MLPs lag far behind recent advances in ML methodology, which limits their applicability and generalizability. To extend beyond the single domain formulation and towards more realistic learning scenarios, we explore model design spaces beyond MLPs, i.e., transformer backbones, which provide flexibility where attention layers govern interactions among treatments and covariates to exploit structural similarities of potential outcomes for confounding control. Through careful model design, Transformers as Treatment Effect Estimators (TransTEE) is proposed. We show empirically that TransTEE can: (1) serve as a general purpose treatment effect estimator that significantly outperforms competitive baselines in a variety of challenging TEE problems (e.g., discrete, continuous, structured, or dosage-associated treatments) and is applicable to both when covariates are tabular and when they consist of structural data (e.g., texts, graphs); (2) yield multiple advantages: compatibility with propensity score modeling, parameter efficiency, robustness to continuous treatment value distribution shifts, explainable in covariate adjustment, and real-world utility in auditing pre-trained language models

Background: General-purpose large language models that utilize both text and images have not been evaluated on a diverse array of challenging medical cases. Methods: Using 934 cases from the NEJM Image Challenge published between 2005 and 2023, we evaluated the accuracy of the recently released Generative Pre-trained Transformer 4 with Vision model (GPT-4V) compared to human respondents overall and stratified by question difficulty, image type, and skin tone. We further conducted a physician evaluation of GPT-4V on 69 NEJM clinicopathological conferences (CPCs). Analyses were conducted for models utilizing text alone, images alone, and both text and images. Results: GPT-4V achieved an overall accuracy of 61% (95% CI, 58 to 64%) compared to 49% (95% CI, 49 to 50%) for humans. GPT-4V outperformed humans at all levels of difficulty and disagreement, skin tones, and image types; the exception was radiographic images, where performance was equivalent between GPT-4V and human respondents. Longer, more informative captions were associated with improved performance for GPT-4V but similar performance for human respondents. GPT-4V included the correct diagnosis in its differential for 80% (95% CI, 68 to 88%) of CPCs when using text alone, compared to 58% (95% CI, 45 to 70%) of CPCs when using both images and text. Conclusions: GPT-4V outperformed human respondents on challenging medical cases and was able to synthesize information from both images and text, but performance deteriorated when images were added to highly informative text. Overall, our results suggest that multimodal AI models may be useful in medical diagnostic reasoning but that their accuracy may depend heavily on context.

Instrumental variable (IV) methods are used to estimate causal effects in settings with unobserved confounding, where we cannot directly experiment on the treatment variable. Instruments are variables which only affect the outcome indirectly via the treatment variable(s). Most IV applications focus on low-dimensional treatments and crucially require at least as many instruments as treatments. This assumption is restrictive: in the natural sciences we often seek to infer causal effects of high-dimensional treatments (e.g., the effect of gene expressions or microbiota on health and disease), but can only run few experiments with a limited number of instruments (e.g., drugs or antibiotics). In such underspecified problems, the full treatment effect is not identifiable in a single experiment even in the linear case. We show that one can still reliably recover the projection of the treatment effect onto the instrumented subspace and develop techniques to consistently combine such partial estimates from different sets of instruments. We then leverage our combined estimators in an algorithm that iteratively proposes the most informative instruments at each round of experimentation to maximize the overall information about the full causal effect.

State-of-the-art question answering (QA) models exhibit a variety of social biases (e.g., with respect to sex or race), generally explained by similar issues in their training data. However, what has been overlooked so far is that in the critical domain of biomedicine, any unjustified change in model output due to patient demographics is problematic: it results in the unfair treatment of patients. Selecting only questions on biomedical topics whose answers do not depend on ethnicity, sex, or sexual orientation, we ask the following research questions: (RQ1) Do the answers of QA models change when being provided with irrelevant demographic information? (RQ2) Does the answer of RQ1 differ between knowledge graph (KG)-grounded and text-based QA systems? We find that irrelevant demographic information change up to 15% of the answers of a KG-grounded system and up to 23% of the answers of a text-based system, including changes that affect accuracy. We conclude that unjustified answer changes caused by patient demographics are a frequent phenomenon, which raises fairness concerns and should be paid more attention to.

Being able to provide explanations for a model's decision has become a central requirement for the development, deployment, and adoption of machine learning models. However, we are yet to understand what explanation methods can and cannot do. How do upstream factors such as data, model prediction, hyperparameters, and random initialization influence downstream explanations? While previous work raised concerns that explanations (E) may have little relationship with the prediction (Y), there is a lack of conclusive study to quantify this relationship. Our work borrows tools from causal inference to systematically assay this relationship. More specifically, we study the relationship between E and Y by measuring the treatment effect when intervening on their causal ancestors, i.e., on hyperparameters and inputs used to generate saliency-based Es or Ys. Our results suggest that the relationships between E and Y is far from ideal. In fact, the gap between 'ideal' case only increase in higher-performing models -- models that are likely to be deployed. Our work is a promising first step towards providing a quantitative measure of the relationship between E and Y, which could also inform the future development of methods for E with a quantitative metric.

Recent approaches to empathetic response generation incorporate emotion causalities to enhance comprehension of both the user's feelings and experiences. However, these approaches suffer from two critical issues. First, they only consider causalities between the user's emotion and the user's experiences, and ignore those between the user's experiences. Second, they neglect interdependence among causalities and reason them independently. To solve the above problems, we expect to reason all plausible causalities interdependently and simultaneously, given the user's emotion, dialogue history, and future dialogue content. Then, we infuse these causalities into response generation for empathetic responses. Specifically, we design a new model, i.e., the Conditional Variational Graph Auto-Encoder (CVGAE), for the causality reasoning, and adopt a multi-source attention mechanism in the decoder for the causality infusion. We name the whole framework as CARE, abbreviated for CAusality Reasoning for Empathetic conversation. Experimental results indicate that our method achieves state-of-the-art performance.

Clinical trials are fundamental in developing new drugs, medical devices, and treatments. However, they are often time-consuming and have low success rates. Although there have been initial attempts to create large language models (LLMs) for clinical trial design and patient-trial matching, these models remain task-specific and not adaptable to diverse clinical trial tasks. To address this challenge, we propose a clinical trial foundation model named Panacea, designed to handle multiple tasks, including trial search, trial summarization, trial design, and patient-trial matching. We also assemble a large-scale dataset, named TrialAlign, of 793,279 trial documents and 1,113,207 trial-related scientific papers, to infuse clinical knowledge into the model by pre-training. We further curate TrialInstruct, which has 200,866 of instruction data for fine-tuning. These resources enable Panacea to be widely applicable for a range of clinical trial tasks based on user requirements. We evaluated Panacea on a new benchmark, named TrialPanorama, which covers eight clinical trial tasks. Our method performed the best on seven of the eight tasks compared to six cutting-edge generic or medicine-specific LLMs. Specifically, Panacea showed great potential to collaborate with human experts in crafting the design of eligibility criteria, study arms, and outcome measures, in multi-round conversations. In addition, Panacea achieved 14.42% improvement in patient-trial matching, 41.78% to 52.02% improvement in trial search, and consistently ranked at the top for five aspects of trial summarization. Our approach demonstrates the effectiveness of Panacea in clinical trials and establishes a comprehensive resource, including training data, model, and benchmark, for developing clinical trial foundation models, paving the path for AI-based clinical trial development.

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

The increased capabilities of generative AI have dramatically expanded its possible use cases in medicine. We provide a comprehensive overview of generative AI use cases for clinicians, patients, clinical trial organizers, researchers, and trainees. We then discuss the many challenges -- including maintaining privacy and security, improving transparency and interpretability, upholding equity, and rigorously evaluating models -- which must be overcome to realize this potential, and the open research directions they give rise to.

There are various methods for adapting LLMs to different domains. The most common methods are prompting, finetuning, and RAG. In this work, we explore the possibility of adapting a model using one of the PEFT methods - QLoRA. The experiment aims to simulate human responses based on their interviews. The simulation quality is assessed by comparing the quality of the style and the quality of the generated facts.

Natural language processing (NLP) is an area of artificial intelligence that applies information technologies to process the human language, understand it to a certain degree, and use it in various applications. This area has rapidly developed in the last few years and now employs modern variants of deep neural networks to extract relevant patterns from large text corpora. The main objective of this work is to survey the recent use of NLP in the field of pharmacology. As our work shows, NLP is a highly relevant information extraction and processing approach for pharmacology. It has been used extensively, from intelligent searches through thousands of medical documents to finding traces of adversarial drug interactions in social media. We split our coverage into five categories to survey modern NLP methodology, commonly addressed tasks, relevant textual data, knowledge bases, and useful programming libraries. We split each of the five categories into appropriate subcategories, describe their main properties and ideas, and summarize them in a tabular form. The resulting survey presents a comprehensive overview of the area, useful to practitioners and interested observers.

Clinical trial matching is the task of identifying trials for which patients may be potentially eligible. Typically, this task is labor-intensive and requires detailed verification of patient electronic health records (EHRs) against the stringent inclusion and exclusion criteria of clinical trials. This process is manual, time-intensive, and challenging to scale up, resulting in many patients missing out on potential therapeutic options. Recent advancements in Large Language Models (LLMs) have made automating patient-trial matching possible, as shown in multiple concurrent research studies. However, the current approaches are confined to constrained, often synthetic datasets that do not adequately mirror the complexities encountered in real-world medical data. In this study, we present the first, end-to-end large-scale empirical evaluation of clinical trial matching using real-world EHRs. Our study showcases the capability of LLMs to accurately match patients with appropriate clinical trials. We perform experiments with proprietary LLMs, including GPT-4 and GPT-3.5, as well as our custom fine-tuned model called OncoLLM and show that OncoLLM, despite its significantly smaller size, not only outperforms GPT-3.5 but also matches the performance of qualified medical doctors. All experiments were carried out on real-world EHRs that include clinical notes and available clinical trials from a single cancer center in the United States.

Stroke remains a leading cause of global morbidity and mortality, placing a heavy socioeconomic burden. Over the past decade, advances in endovascular reperfusion therapy and the use of CT and MRI imaging for treatment guidance have significantly improved patient outcomes and are now standard in clinical practice. To develop machine learning algorithms that can extract meaningful and reproducible models of brain function for both clinical and research purposes from stroke images - particularly for lesion identification, brain health quantification, and prognosis - large, diverse, and well-annotated public datasets are essential. While only a few datasets with (sub-)acute stroke data were previously available, several large, high-quality datasets have recently been made publicly accessible. However, these existing datasets include only MRI data. In contrast, our dataset is the first to offer comprehensive longitudinal stroke data, including acute CT imaging with angiography and perfusion, follow-up MRI at 2-9 days, as well as acute and longitudinal clinical data up to a three-month outcome. The dataset includes a training dataset of n = 150 and a test dataset of n = 100 scans. Training data is publicly available, while test data will be used exclusively for model validation. We are making this dataset available as part of the 2024 edition of the Ischemic Stroke Lesion Segmentation (ISLES) challenge (https://www.isles-challenge.org/), which continuously aims to establish benchmark methods for acute and sub-acute ischemic stroke lesion segmentation, aiding in creating open stroke imaging datasets and evaluating cutting-edge image processing algorithms.

Complex chemical structures, like drugs, are usually defined by SMILES strings as a sequence of molecules and bonds. These SMILES strings are used in different complex machine learning-based drug-related research and representation works. Escaping from complex representation, in this work, we pose a single question: What if we treat drug SMILES as conventional sentences and engage in text classification for drug classification? Our experiments affirm the possibility with very competitive scores. The study explores the notion of viewing each atom and bond as sentence components, employing basic NLP methods to categorize drug types, proving that complex problems can also be solved with simpler perspectives. The data and code are available here: https://github.com/azminewasi/Drug-Classification-NLP.

We introduce the StatCan Dialogue Dataset consisting of 19,379 conversation turns between agents working at Statistics Canada and online users looking for published data tables. The conversations stem from genuine intents, are held in English or French, and lead to agents retrieving one of over 5000 complex data tables. Based on this dataset, we propose two tasks: (1) automatic retrieval of relevant tables based on a on-going conversation, and (2) automatic generation of appropriate agent responses at each turn. We investigate the difficulty of each task by establishing strong baselines. Our experiments on a temporal data split reveal that all models struggle to generalize to future conversations, as we observe a significant drop in performance across both tasks when we move from the validation to the test set. In addition, we find that response generation models struggle to decide when to return a table. Considering that the tasks pose significant challenges to existing models, we encourage the community to develop models for our task, which can be directly used to help knowledge workers find relevant tables for live chat users.

Online medical consultation (OMC) restricts doctors to gathering patient information solely through inquiries, making the already complex sequential decision-making process of diagnosis even more challenging. Recently, the rapid advancement of large language models has demonstrated a significant potential to transform OMC. However, most studies have primarily focused on improving diagnostic accuracy under conditions of relatively sufficient information, while paying limited attention to the "inquiry" phase of the consultation process. This lack of focus has left the relationship between "inquiry" and "diagnosis" insufficiently explored. In this paper, we first extract real patient interaction strategies from authentic doctor-patient conversations and use these strategies to guide the training of a patient simulator that closely mirrors real-world behavior. By inputting medical records into our patient simulator to simulate patient responses, we conduct extensive experiments to explore the relationship between "inquiry" and "diagnosis" in the consultation process. Experimental results demonstrate that inquiry and diagnosis adhere to the Liebig's law: poor inquiry quality limits the effectiveness of diagnosis, regardless of diagnostic capability, and vice versa. Furthermore, the experiments reveal significant differences in the inquiry performance of various models. To investigate this phenomenon, we categorize the inquiry process into four types: (1) chief complaint inquiry; (2) specification of known symptoms; (3) inquiry about accompanying symptoms; and (4) gathering family or medical history. We analyze the distribution of inquiries across the four types for different models to explore the reasons behind their significant performance differences. We plan to open-source the weights and related code of our patient simulator at https://github.com/LIO-H-ZEN/PatientSimulator.

We propose DISC-MedLLM, a comprehensive solution that leverages Large Language Models (LLMs) to provide accurate and truthful medical response in end-to-end conversational healthcare services. To construct high-quality Supervised Fine-Tuning (SFT) datasets, we employ three strategies: utilizing medical knowledge-graphs, reconstructing real-world dialogues, and incorporating human-guided preference rephrasing. These datasets are instrumental in training DISC-MedLLM, surpassing existing medical LLMs in both single-turn and multi-turn consultation scenarios. Extensive experimental results demonstrate the effectiveness of the proposed model in bridging the gap between general language models and real-world medical consultation. Additionally, we release the constructed dataset and model weights to further contribute to research and development. Further details and resources can be found at https://github.com/FudanDISC/DISC-MedLLM

To assess the effectiveness of any medical intervention, researchers must conduct a time-intensive and highly manual literature review. NLP systems can help to automate or assist in parts of this expensive process. In support of this goal, we release MS^2 (Multi-Document Summarization of Medical Studies), a dataset of over 470k documents and 20k summaries derived from the scientific literature. This dataset facilitates the development of systems that can assess and aggregate contradictory evidence across multiple studies, and is the first large-scale, publicly available multi-document summarization dataset in the biomedical domain. We experiment with a summarization system based on BART, with promising early results. We formulate our summarization inputs and targets in both free text and structured forms and modify a recently proposed metric to assess the quality of our system's generated summaries. Data and models are available at https://github.com/allenai/ms2

The past year has seen rapid acceleration in the development of large language models (LLMs). However, without proper steering and safeguards, LLMs will readily follow malicious instructions, provide unsafe advice, and generate toxic content. We introduce SimpleSafetyTests (SST) as a new test suite for rapidly and systematically identifying such critical safety risks. The test suite comprises 100 test prompts across five harm areas that LLMs, for the vast majority of applications, should refuse to comply with. We test 11 open-access and open-source LLMs and four closed-source LLMs, and find critical safety weaknesses. While some of the models do not give a single unsafe response, most give unsafe responses to more than 20% of the prompts, with over 50% unsafe responses in the extreme. Prepending a safety-emphasising system prompt substantially reduces the occurrence of unsafe responses, but does not completely stop them from happening. Trained annotators labelled every model response to SST (n = 3,000). We use these annotations to evaluate five AI safety filters (which assess whether a models' response is unsafe given a prompt) as a way of automatically evaluating models' performance on SST. The filters' performance varies considerably. There are also differences across the five harm areas, and on the unsafe versus safe responses. The widely-used Perspective API has 72% accuracy and a newly-created zero-shot prompt to OpenAI's GPT-4 performs best with 89% accuracy. Content Warning: This paper contains prompts and responses that relate to child abuse, suicide, self-harm and eating disorders, scams and fraud, illegal items, and physical harm.

This paper presents a dataset with over 3.3M threads and 134.5M posts from the Politically Incorrect board (/pol/) of the imageboard forum 4chan, posted over a period of almost 3.5 years (June 2016-November 2019). To the best of our knowledge, this represents the largest publicly available 4chan dataset, providing the community with an archive of posts that have been permanently deleted from 4chan and are otherwise inaccessible. We augment the data with a set of additional labels, including toxicity scores and the named entities mentioned in each post. We also present a statistical analysis of the dataset, providing an overview of what researchers interested in using it can expect, as well as a simple content analysis, shedding light on the most prominent discussion topics, the most popular entities mentioned, and the toxicity level of each post. Overall, we are confident that our work will motivate and assist researchers in studying and understanding 4chan, as well as its role on the greater Web. For instance, we hope this dataset may be used for cross-platform studies of social media, as well as being useful for other types of research like natural language processing. Finally, our dataset can assist qualitative work focusing on in-depth case studies of specific narratives, events, or social theories.

Current approaches to empathetic response generation view the set of emotions expressed in the input text as a flat structure, where all the emotions are treated uniformly. We argue that empathetic responses often mimic the emotion of the user to a varying degree, depending on its positivity or negativity and content. We show that the consideration of this polarity-based emotion clusters and emotional mimicry results in improved empathy and contextual relevance of the response as compared to the state-of-the-art. Also, we introduce stochasticity into the emotion mixture that yields emotionally more varied empathetic responses than the previous work. We demonstrate the importance of these factors to empathetic response generation using both automatic- and human-based evaluations. The implementation of MIME is publicly available at https://github.com/declare-lab/MIME.

Ambiguous questions are a challenge for Question Answering models, as they require answers that cover multiple interpretations of the original query. To this end, these models are required to generate long-form answers that often combine conflicting pieces of information. Although recent advances in the field have shown strong capabilities in generating fluent responses, certain research questions remain unanswered. Does model/data scaling improve the answers' quality? Do automated metrics align with human judgment? To what extent do these models ground their answers in evidence? In this study, we aim to thoroughly investigate these aspects, and provide valuable insights into the limitations of the current approaches. To aid in reproducibility and further extension of our work, we open-source our code at https://github.com/din0s/ambig_lfqa.

Humans often refer to personal narratives, life experiences, and events to make a conversation more engaging and rich. While persona-grounded dialog models are able to generate responses that follow a given persona, they often miss out on stating detailed experiences or events related to a persona, often leaving conversations shallow and dull. In this work, we equip dialog models with 'background stories' related to a persona by leveraging fictional narratives from existing story datasets (e.g. ROCStories). Since current dialog datasets do not contain such narratives as responses, we perform an unsupervised adaptation of a retrieved story for generating a dialog response using a gradient-based rewriting technique. Our proposed method encourages the generated response to be fluent (i.e., highly likely) with the dialog history, minimally different from the retrieved story to preserve event ordering and consistent with the original persona. We demonstrate that our method can generate responses that are more diverse, and are rated more engaging and human-like by human evaluators, compared to outputs from existing dialog models.

Background: Health datasets from clinical sources do not reflect the breadth and diversity of disease in the real world, impacting research, medical education, and artificial intelligence (AI) tool development. Dermatology is a suitable area to develop and test a new and scalable method to create representative health datasets. Methods: We used Google Search advertisements to invite contributions to an open access dataset of images of dermatology conditions, demographic and symptom information. With informed contributor consent, we describe and release this dataset containing 10,408 images from 5,033 contributions from internet users in the United States over 8 months starting March 2023. The dataset includes dermatologist condition labels as well as estimated Fitzpatrick Skin Type (eFST) and Monk Skin Tone (eMST) labels for the images. Results: We received a median of 22 submissions/day (IQR 14-30). Female (66.72%) and younger (52% < age 40) contributors had a higher representation in the dataset compared to the US population, and 32.6% of contributors reported a non-White racial or ethnic identity. Over 97.5% of contributions were genuine images of skin conditions. Dermatologist confidence in assigning a differential diagnosis increased with the number of available variables, and showed a weaker correlation with image sharpness (Spearman's P values <0.001 and 0.01 respectively). Most contributions were short-duration (54% with onset < 7 days ago ) and 89% were allergic, infectious, or inflammatory conditions. eFST and eMST distributions reflected the geographical origin of the dataset. The dataset is available at github.com/google-research-datasets/scin . Conclusion: Search ads are effective at crowdsourcing images of health conditions. The SCIN dataset bridges important gaps in the availability of representative images of common skin conditions.

This paper introduces MedMCQA, a new large-scale, Multiple-Choice Question Answering (MCQA) dataset designed to address real-world medical entrance exam questions. More than 194k high-quality AIIMS \& NEET PG entrance exam MCQs covering 2.4k healthcare topics and 21 medical subjects are collected with an average token length of 12.77 and high topical diversity. Each sample contains a question, correct answer(s), and other options which requires a deeper language understanding as it tests the 10+ reasoning abilities of a model across a wide range of medical subjects \& topics. A detailed explanation of the solution, along with the above information, is provided in this study.

Answer sentence selection is the task of identifying sentences that contain the answer to a given question. This is an important problem in its own right as well as in the larger context of open domain question answering. We propose a novel approach to solving this task via means of distributed representations, and learn to match questions with answers by considering their semantic encoding. This contrasts prior work on this task, which typically relies on classifiers with large numbers of hand-crafted syntactic and semantic features and various external resources. Our approach does not require any feature engineering nor does it involve specialist linguistic data, making this model easily applicable to a wide range of domains and languages. Experimental results on a standard benchmark dataset from TREC demonstrate that---despite its simplicity---our model matches state of the art performance on the answer sentence selection task.

We present CovidQA, the beginnings of a question answering dataset specifically designed for COVID-19, built by hand from knowledge gathered from Kaggle's COVID-19 Open Research Dataset Challenge. To our knowledge, this is the first publicly available resource of its type, and intended as a stopgap measure for guiding research until more substantial evaluation resources become available. While this dataset, comprising 124 question-article pairs as of the present version 0.1 release, does not have sufficient examples for supervised machine learning, we believe that it can be helpful for evaluating the zero-shot or transfer capabilities of existing models on topics specifically related to COVID-19. This paper describes our methodology for constructing the dataset and presents the effectiveness of a number of baselines, including term-based techniques and various transformer-based models. The dataset is available at http://covidqa.ai/

Recent researches of large language models(LLM), which is pre-trained on massive general-purpose corpora, have achieved breakthroughs in responding human queries. However, these methods face challenges including limited data insufficiency to support extensive pre-training and can not align responses with users' instructions. To address these issues, we introduce a medical instruction dataset, CMedINS, containing six medical instructions derived from actual medical tasks, which effectively fine-tunes LLM in conjunction with other data. Subsequently, We launch our medical model, IIMedGPT, employing an efficient preference alignment method, Direct preference Optimization(DPO). The results show that our final model outperforms existing medical models in medical dialogue.Datsets, Code and model checkpoints will be released upon acceptance.

Perception of toxicity evolves over time and often differs between geographies and cultural backgrounds. Similarly, black-box commercially available APIs for detecting toxicity, such as the Perspective API, are not static, but frequently retrained to address any unattended weaknesses and biases. We evaluate the implications of these changes on the reproducibility of findings that compare the relative merits of models and methods that aim to curb toxicity. Our findings suggest that research that relied on inherited automatic toxicity scores to compare models and techniques may have resulted in inaccurate findings. Rescoring all models from HELM, a widely respected living benchmark, for toxicity with the recent version of the API led to a different ranking of widely used foundation models. We suggest caution in applying apples-to-apples comparisons between studies and lay recommendations for a more structured approach to evaluating toxicity over time. Code and data are available at https://github.com/for-ai/black-box-api-challenges.

We assessed the performance of commercial Large Language Models (LLMs) GPT-3.5-Turbo and GPT-4 on tasks from the 2023 BioASQ challenge. In Task 11b Phase B, which is focused on answer generation, both models demonstrated competitive abilities with leading systems. Remarkably, they achieved this with simple zero-shot learning, grounded with relevant snippets. Even without relevant snippets, their performance was decent, though not on par with the best systems. Interestingly, the older and cheaper GPT-3.5-Turbo system was able to compete with GPT-4 in the grounded Q&A setting on factoid and list answers. In Task 11b Phase A, focusing on retrieval, query expansion through zero-shot learning improved performance, but the models fell short compared to other systems. The code needed to rerun these experiments is available through GitHub.

We present WeaverBird, an intelligent dialogue system designed specifically for the finance domain. Our system harnesses a large language model of GPT architecture that has been tuned using extensive corpora of finance-related text. As a result, our system possesses the capability to understand complex financial queries, such as "How should I manage my investments during inflation?", and provide informed responses. Furthermore, our system incorporates a local knowledge base and a search engine to retrieve relevant information. The final responses are conditioned on the search results and include proper citations to the sources, thus enjoying an enhanced credibility. Through a range of finance-related questions, we have demonstrated the superior performance of our system compared to other models. To experience our system firsthand, users can interact with our live demo at https://weaverbird.ttic.edu, as well as watch our 2-min video illustration at https://www.youtube.com/watch?v=fyV2qQkX6Tc.

Large Language Model (LLM)-based applications are graduating from research prototypes to products serving millions of users, influencing how people write and consume information. A prominent example is the appearance of Answer Engines: LLM-based generative search engines supplanting traditional search engines. Answer engines not only retrieve relevant sources to a user query but synthesize answer summaries that cite the sources. To understand these systems' limitations, we first conducted a study with 21 participants, evaluating interactions with answer vs. traditional search engines and identifying 16 answer engine limitations. From these insights, we propose 16 answer engine design recommendations, linked to 8 metrics. An automated evaluation implementing our metrics on three popular engines (You.com, Perplexity.ai, BingChat) quantifies common limitations (e.g., frequent hallucination, inaccurate citation) and unique features (e.g., variation in answer confidence), with results mirroring user study insights. We release our Answer Engine Evaluation benchmark (AEE) to facilitate transparent evaluation of LLM-based applications.

Understanding the reason for emotional support response is crucial for establishing connections between users and emotional support dialogue systems. Previous works mostly focus on generating better responses but ignore interpretability, which is extremely important for constructing reliable dialogue systems. To empower the system with better interpretability, we propose an emotional support response generation scheme, named Emotion-Focused and Strategy-Driven Chain-of-Thought (ESCoT), mimicking the process of identifying, understanding, and regulating emotions. Specially, we construct a new dataset with ESCoT in two steps: (1) Dialogue Generation where we first generate diverse conversation situations, then enhance dialogue generation using richer emotional support strategies based on these situations; (2) Chain Supplement where we focus on supplementing selected dialogues with elements such as emotion, stimuli, appraisal, and strategy reason, forming the manually verified chains. Additionally, we further develop a model to generate dialogue responses with better interpretability. We also conduct extensive experiments and human evaluations to validate the effectiveness of the proposed ESCoT and generated dialogue responses. Our data and code are available at https://github.com/TeigenZhang/ESCoT{https://github.com/TeigenZhang/ESCoT}.

We discuss an algorithm which produces the meaning of a sentence given meanings of its words, and its resemblance to quantum teleportation. In fact, this protocol was the main source of inspiration for this algorithm which has many applications in the area of Natural Language Processing.

The challenge of replicating research results has posed a significant impediment to the field of molecular biology. The advent of modern intelligent systems has led to notable progress in various domains. Consequently, we embarked on an investigation of intelligent monitoring systems as a means of tackling the issue of the reproducibility crisis. Specifically, we first curate a comprehensive multimodal dataset, named ProBio, as an initial step towards this objective. This dataset comprises fine-grained hierarchical annotations intended for the purpose of studying activity understanding in BioLab. Next, we devise two challenging benchmarks, transparent solution tracking and multimodal action recognition, to emphasize the unique characteristics and difficulties associated with activity understanding in BioLab settings. Finally, we provide a thorough experimental evaluation of contemporary video understanding models and highlight their limitations in this specialized domain to identify potential avenues for future research. We hope ProBio with associated benchmarks may garner increased focus on modern AI techniques in the realm of molecular biology.

The detection of depression through non-verbal cues has gained significant attention. Previous research predominantly centred on identifying depression within the confines of controlled laboratory environments, often with the supervision of psychologists or counsellors. Unfortunately, datasets generated in such controlled settings may struggle to account for individual behaviours in real-life situations. In response to this limitation, we present the Extended D-vlog dataset, encompassing a collection of 1, 261 YouTube vlogs. Additionally, the emergence of large language models (LLMs) like GPT3.5, and GPT4 has sparked interest in their potential they can act like mental health professionals. Yet, the readiness of these LLM models to be used in real-life settings is still a concern as they can give wrong responses that can harm the users. We introduce a virtual agent serving as an initial contact for mental health patients, offering Cognitive Behavioral Therapy (CBT)-based responses. It comprises two core functions: 1. Identifying depression in individuals, and 2. Delivering CBT-based therapeutic responses. Our Mistral model achieved impressive scores of 70.1% and 30.9% for distortion assessment and classification, along with a Bert score of 88.7%. Moreover, utilizing the TVLT model on our Multimodal Extended D-vlog Dataset yielded outstanding results, with an impressive F1-score of 67.8%

In natural human-to-human conversations, participants often receive feedback signals from one another based on their follow-up reactions. These reactions can include verbal responses, facial expressions, changes in emotional state, and other non-verbal cues. Similarly, in human-machine interactions, the machine can leverage the user's follow-up utterances as feedback signals to assess whether it has appropriately addressed the user's request. Therefore, we propose using the likelihood of follow-up utterances as rewards to differentiate preferred responses from less favored ones, without relying on human or commercial LLM-based preference annotations. Our proposed reward mechanism, ``Follow-up Likelihood as Reward" (FLR), matches the performance of strong reward models trained on large-scale human or GPT-4 annotated data on 8 pairwise-preference and 4 rating-based benchmarks. Building upon the FLR mechanism, we propose to automatically mine preference data from the online generations of a base policy model. The preference data are subsequently used to boost the helpfulness of the base model through direct alignment from preference (DAP) methods, such as direct preference optimization (DPO). Lastly, we demonstrate that fine-tuning the language model that provides follow-up likelihood with natural language feedback significantly enhances FLR's performance on reward modeling benchmarks and effectiveness in aligning the base policy model's helpfulness.

Recent research on large language models (LLMs) has primarily focused on their adaptation and application in specialized domains. The application of LLMs in the medical field is mainly concentrated on tasks such as the automation of medical report generation, summarization, diagnostic reasoning, and question-and-answer interactions between doctors and patients. The challenge of becoming a good teacher is more formidable than that of becoming a good student, and this study pioneers the application of LLMs in the field of medical education. In this work, we investigate the extent to which LLMs can generate medical qualification exam questions and corresponding answers based on few-shot prompts. Utilizing a real-world Chinese dataset of elderly chronic diseases, we tasked the LLMs with generating open-ended questions and answers based on a subset of sampled admission reports across eight widely used LLMs, including ERNIE 4, ChatGLM 4, Doubao, Hunyuan, Spark 4, Qwen, Llama 3, and Mistral. Furthermore, we engaged medical experts to manually evaluate these open-ended questions and answers across multiple dimensions. The study found that LLMs, after using few-shot prompts, can effectively mimic real-world medical qualification exam questions, whereas there is room for improvement in the correctness, evidence-based statements, and professionalism of the generated answers. Moreover, LLMs also demonstrate a decent level of ability to correct and rectify reference answers. Given the immense potential of artificial intelligence in the medical field, the task of generating questions and answers for medical qualification exams aimed at medical students, interns and residents can be a significant focus of future research.

Advances in foundation modeling have reshaped computational pathology. However, the increasing number of available models and lack of standardized benchmarks make it increasingly complex to assess their strengths, limitations, and potential for further development. To address these challenges, we introduce a new suite of software tools for whole-slide image processing, foundation model benchmarking, and curated publicly available tasks. We anticipate that these resources will promote transparency, reproducibility, and continued progress in the field.

Developing the required technology to assist medical experts in their everyday activities is currently a hot topic in the Artificial Intelligence research field. Thus, a number of large language models (LLMs) and automated benchmarks have recently been proposed with the aim of facilitating information extraction in Evidence-Based Medicine (EBM) using natural language as a tool for mediating in human-AI interaction. The most representative benchmarks are limited to either multiple-choice or long-form answers and are available only in English. In order to address these shortcomings, in this paper we present a new dataset which, unlike previous work: (i) includes not only explanatory arguments for the correct answer, but also arguments to reason why the incorrect answers are not correct; (ii) the explanations are written originally by medical doctors to answer questions from the Spanish Residency Medical Exams. Furthermore, this new benchmark allows us to setup a novel extractive task which consists of identifying the explanation of the correct answer written by medical doctors. An additional benefit of our setting is that we can leverage the extractive QA paradigm to automatically evaluate performance of LLMs without resorting to costly manual evaluation by medical experts. Comprehensive experimentation with language models for Spanish shows that sometimes multilingual models fare better than monolingual ones, even outperforming models which have been adapted to the medical domain. Furthermore, results across the monolingual models are mixed, with supposedly smaller and inferior models performing competitively. In any case, the obtained results show that our novel dataset and approach can be an effective technique to help medical practitioners in identifying relevant evidence-based explanations for medical questions.

The Mental Health Question Answer (MHQA) task requires the seeker and supporter to complete the support process in one-turn dialogue. Given the richness of help-seeker posts, supporters must thoroughly understand the content and provide logical, comprehensive, and well-structured responses. Previous works in MHQA mostly focus on single-agent approaches based on the cognitive element of Cognitive Behavioral Therapy (CBT), but they overlook the interactions among various CBT elements, such as emotion and cognition. This limitation hinders the models' ability to thoroughly understand the distress of help-seekers. To address this, we propose a framework named Multi-Agent Deductive Planning (MADP), which is based on the interactions between the various psychological elements of CBT. This method guides Large Language Models (LLMs) to achieve a deeper understanding of the seeker's context and provide more personalized assistance based on individual circumstances. Furthermore, we construct a new dataset based on the MADP framework and use it to fine-tune LLMs, resulting in a specialized model named MADP-LLM. We conduct extensive experiments, including comparisons with multiple LLMs, human evaluations, and automatic evaluations, to validate the effectiveness of the MADP framework and MADP-LLM.

We, team AImsterdam, summarize our submission to the fastMRI challenge (Zbontar et al., 2018). Our approach builds on recent advances in invertible learning to infer models as presented in Putzky and Welling (2019). Both, our single-coil and our multi-coil model share the same basic architecture.

According to the World Health Organization (WHO), suicide was the fourth leading cause of death in the world for individuals aged 15 to 29 in 2019. Given the rapid increase in mental health issues, providing psychological support is both crucial and urgent. In this paper: (1) we propose S\'olo Esc\'uchame, the first open-source Spanish emotional assistance chatbot, based on LLaMA-2-7b-Chat. (2) We introduced the HEAR (Hispanic Emotional Accompaniment Responses) dataset, compiled from multiple English sources translated into Spanish, as well as generic data generated using ChatGPT-3.5-Turbo. Finally, (3) we propose an evaluation metric based on two semi-automatic assessment methods. Our system outperforms a range of state-of-the-art models in providing psychological assistance in Spanish. Our models and datasets are publicly available to facilitate reproducibility.

Over the past two years, EleutherAI has established itself as a radically novel initiative aimed at both promoting open-source research and conducting research in a transparent, openly accessible and collaborative manner. EleutherAI's approach to research goes beyond transparency: by doing research entirely in public, anyone in the world can observe and contribute at every stage. Our work has been received positively and has resulted in several high-impact projects in Natural Language Processing and other fields. In this paper, we describe our experience doing public-facing machine learning research, the benefits we believe this approach brings, and the pitfalls we have encountered.

Recent advances in generative models, including large language models (LLMs), vision language models (VLMs), and diffusion models, have accelerated the field of natural language and image processing in medicine and marked a significant paradigm shift in how biomedical models can be developed and deployed. While these models are highly adaptable to new tasks, scaling and evaluating their usage presents new challenges not addressed in previous frameworks. In particular, the ability of these models to produce useful outputs with little to no specialized training data ("zero-" or "few-shot" approaches), as well as the open-ended nature of their outputs, necessitate the development of new guidelines for robust reporting of clinical generative model research. In response to gaps in standards and best practices for the development of clinical AI tools identified by US Executive Order 141103 and several emerging national networks for clinical AI evaluation, we begin to formalize some of these guidelines by building on the original MI-CLAIM checklist. The new checklist, MI-CLAIM-GEN (Table 1), aims to address differences in training, evaluation, interpretability, and reproducibility of new generative models compared to non-generative ("predictive") AI models. This MI-CLAIM-GEN checklist also seeks to clarify cohort selection reporting with unstructured clinical data and adds additional items on alignment with ethical standards for clinical AI research.

A key component of successfully reading a passage of text is the ability to apply knowledge gained from the passage to a new situation. In order to facilitate progress on this kind of reading, we present ROPES, a challenging benchmark for reading comprehension targeting Reasoning Over Paragraph Effects in Situations. We target expository language describing causes and effects (e.g., "animal pollinators increase efficiency of fertilization in flowers"), as they have clear implications for new situations. A system is presented a background passage containing at least one of these relations, a novel situation that uses this background, and questions that require reasoning about effects of the relationships in the background passage in the context of the situation. We collect background passages from science textbooks and Wikipedia that contain such phenomena, and ask crowd workers to author situations, questions, and answers, resulting in a 14,322 question dataset. We analyze the challenges of this task and evaluate the performance of state-of-the-art reading comprehension models. The best model performs only slightly better than randomly guessing an answer of the correct type, at 61.6% F1, well below the human performance of 89.0%.

Within the field of causal inference, we consider the problem of estimating heterogeneous treatment effects from data. We propose and validate a novel approach for learning feature representations to aid the estimation of the conditional average treatment effect or CATE. Our method focuses on an intermediate layer in a neural network trained to predict the outcome from the features. In contrast to previous approaches that encourage the distribution of representations to be treatment-invariant, we leverage a genetic algorithm that optimizes over representations useful for predicting the outcome to select those less useful for predicting the treatment. This allows us to retain information within the features useful for predicting outcome even if that information may be related to treatment assignment. We validate our method on synthetic examples and illustrate its use on a real life dataset.

In the last years, there have been significant developments in the area of Question Answering over Knowledge Graphs (KGQA). Despite all the notable advancements, current KGQA datasets only provide the answers as the direct output result of the formal query, rather than full sentences incorporating question context. For achieving coherent answers sentence with the question's vocabulary, template-based verbalization so are usually employed for a better representation of answers, which in turn require extensive expert intervention. Thus, making way for machine learning approaches; however, there is a scarcity of datasets that empower machine learning models in this area. Hence, we provide the VANiLLa dataset which aims at reducing this gap by offering answers in natural language sentences. The answer sentences in this dataset are syntactically and semantically closer to the question than to the triple fact. Our dataset consists of over 100k simple questions adapted from the CSQA and SimpleQuestionsWikidata datasets and generated using a semi-automatic framework. We also present results of training our dataset on multiple baseline models adapted from current state-of-the-art Natural Language Generation (NLG) architectures. We believe that this dataset will allow researchers to focus on finding suitable methodologies and architectures for answer verbalization.

Recently, the demand for psychological counseling has significantly increased as more individuals express concerns about their mental health. This surge has accelerated efforts to improve the accessibility of counseling by using large language models (LLMs) as counselors. To ensure client privacy, training open-source LLMs faces a key challenge: the absence of realistic counseling datasets. To address this, we introduce Cactus, a multi-turn dialogue dataset that emulates real-life interactions using the goal-oriented and structured approach of Cognitive Behavioral Therapy (CBT). We create a diverse and realistic dataset by designing clients with varied, specific personas, and having counselors systematically apply CBT techniques in their interactions. To assess the quality of our data, we benchmark against established psychological criteria used to evaluate real counseling sessions, ensuring alignment with expert evaluations. Experimental results demonstrate that Camel, a model trained with Cactus, outperforms other models in counseling skills, highlighting its effectiveness and potential as a counseling agent. We make our data, model, and code publicly available.

We present PubMed 200k RCT, a new dataset based on PubMed for sequential sentence classification. The dataset consists of approximately 200,000 abstracts of randomized controlled trials, totaling 2.3 million sentences. Each sentence of each abstract is labeled with their role in the abstract using one of the following classes: background, objective, method, result, or conclusion. The purpose of releasing this dataset is twofold. First, the majority of datasets for sequential short-text classification (i.e., classification of short texts that appear in sequences) are small: we hope that releasing a new large dataset will help develop more accurate algorithms for this task. Second, from an application perspective, researchers need better tools to efficiently skim through the literature. Automatically classifying each sentence in an abstract would help researchers read abstracts more efficiently, especially in fields where abstracts may be long, such as the medical field.

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.

This report describes the training dataset creation and recipe behind the family of arctic-embed text embedding models (a set of five models ranging from 22 to 334 million parameters with weights open-sourced under an Apache-2 license). At the time of their release, each model achieved state-of-the-art retrieval accuracy for models of their size on the MTEB Retrieval leaderboard, with the largest model, arctic-embed-l outperforming closed source embedding models such as Cohere's embed-v3 and Open AI's text-embed-3-large. In addition to the details of our training recipe, we have provided several informative ablation studies, which we believe are the cause of our model performance.

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.

We collected a large dataset consisting of nearly 900 unique participants. For every participant we recorded two 30 second uncompressed videos, synchronized PPG waveforms and a single blood pressure measurement. Gender, age and skin color were also registered for every participant. The dataset includes roughly equal numbers of males and females, as well as participants of all ages. While the skin color distribution could have been more balanced, the dataset contains individuals from every skin color. The data was collected in a diverse set of locations to ensure a wide variety of backgrounds and lighting conditions. In an effort to assist in the research and development of remote vital sign measurement we are now opening up access to this dataset.

Trolling in online communities typically involves disruptive behaviors such as provoking anger and manipulating discussions, leading to a polarized atmosphere and emotional distress. Robust moderation is essential for mitigating these negative impacts and maintaining a healthy and constructive community atmosphere. However, effectively addressing trolls is difficult because their behaviors vary widely and require different response strategies (RSs) to counter them. This diversity makes it challenging to choose an appropriate RS for each specific situation. To address this challenge, our research investigates whether humans have preferred strategies tailored to different types of trolling behaviors. Our findings reveal a correlation between the types of trolling encountered and the preferred RS. In this paper, we introduce a methodology for generating counter-responses to trolls by recommending appropriate RSs, supported by a dataset aligning these strategies with human preferences across various troll contexts. The experimental results demonstrate that our proposed approach guides constructive discussion and reduces the negative effects of trolls, thereby enhancing the online community environment.

Evaluating open-domain dialogue systems is challenging for reasons such as the one-to-many problem, i.e., many appropriate responses other than just the golden response. As of now, automatic evaluation methods need better consistency with humans, while reliable human evaluation can be time- and cost-intensive. To this end, we propose the Reference-Assisted Dialogue Evaluation (RADE) approach under the multi-task learning framework, which leverages the pre-created utterance as reference other than the gold response to relief the one-to-many problem. Specifically, RADE explicitly compares reference and the candidate response to predict their overall scores. Moreover, an auxiliary response generation task enhances prediction via a shared encoder. To support RADE, we extend three datasets with additional rated responses other than just a golden response by human annotation. Experiments on our three datasets and two existing benchmarks demonstrate the effectiveness of our method, where Pearson, Spearman, and Kendall correlations with human evaluation outperform state-of-the-art baselines.

Observational studies require adjustment for confounding factors that are correlated with both the treatment and outcome. In the setting where the observed variables are tabular quantities such as average income in a neighborhood, tools have been developed for addressing such confounding. However, in many parts of the developing world, features about local communities may be scarce. In this context, satellite imagery can play an important role, serving as a proxy for the confounding variables otherwise unobserved. In this paper, we study confounder adjustment in this non-tabular setting, where patterns or objects found in satellite images contribute to the confounder bias. Using the evaluation of anti-poverty aid programs in Africa as our running example, we formalize the challenge of performing causal adjustment with such unstructured data -- what conditions are sufficient to identify causal effects, how to perform estimation, and how to quantify the ways in which certain aspects of the unstructured image object are most predictive of the treatment decision. Via simulation, we also explore the sensitivity of satellite image-based observational inference to image resolution and to misspecification of the image-associated confounder. Finally, we apply these tools in estimating the effect of anti-poverty interventions in African communities from satellite imagery.

People increasingly search online for answers to their medical questions but the rate at which medical questions are asked online significantly exceeds the capacity of qualified people to answer them. This leaves many questions unanswered or inadequately answered. Many of these questions are not unique, and reliable identification of similar questions would enable more efficient and effective question answering schema. COVID-19 has only exacerbated this problem. Almost every government agency and healthcare organization has tried to meet the informational need of users by building online FAQs, but there is no way for people to ask their question and know if it is answered on one of these pages. While many research efforts have focused on the problem of general question similarity, these approaches do not generalize well to domains that require expert knowledge to determine semantic similarity, such as the medical domain. In this paper, we show how a double fine-tuning approach of pretraining a neural network on medical question-answer pairs followed by fine-tuning on medical question-question pairs is a particularly useful intermediate task for the ultimate goal of determining medical question similarity. While other pretraining tasks yield an accuracy below 78.7% on this task, our model achieves an accuracy of 82.6% with the same number of training examples, an accuracy of 80.0% with a much smaller training set, and an accuracy of 84.5% when the full corpus of medical question-answer data is used. We also describe a currently live system that uses the trained model to match user questions to COVID-related FAQs.

Machine learning (ML) holds great potential for accurately forecasting treatment outcomes over time, which could ultimately enable the adoption of more individualized treatment strategies in many practical applications. However, a significant challenge that has been largely overlooked by the ML literature on this topic is the presence of informative sampling in observational data. When instances are observed irregularly over time, sampling times are typically not random, but rather informative -- depending on the instance's characteristics, past outcomes, and administered treatments. In this work, we formalize informative sampling as a covariate shift problem and show that it can prohibit accurate estimation of treatment outcomes if not properly accounted for. To overcome this challenge, we present a general framework for learning treatment outcomes in the presence of informative sampling using inverse intensity-weighting, and propose a novel method, TESAR-CDE, that instantiates this framework using Neural CDEs. Using a simulation environment based on a clinical use case, we demonstrate the effectiveness of our approach in learning under informative sampling.

Existing open-source helpfulness preference datasets do not specify what makes some responses more helpful and others less so. Models trained on these datasets can incidentally learn to model dataset artifacts (e.g. preferring longer but unhelpful responses only due to their length). To alleviate this problem, we collect HelpSteer, a multi-attribute helpfulness dataset annotated for the various aspects that make responses helpful. Specifically, our 37k-sample dataset has annotations for correctness, coherence, complexity, and verbosity in addition to overall helpfulness of responses. Training Llama 2 70B using the HelpSteer dataset with SteerLM technique produces a model that scores 7.54 on MT Bench, which is currently the highest score for open models that do not require training data from more powerful models (e.g. GPT4). We release this dataset with CC-BY-4.0 license at https://huggingface.co/datasets/nvidia/HelpSteer

Depression has proven to be a significant public health issue, profoundly affecting the psychological well-being of individuals. If it remains undiagnosed, depression can lead to severe health issues, which can manifest physically and even lead to suicide. Generally, Diagnosing depression or any other mental disorder involves conducting semi-structured interviews alongside supplementary questionnaires, including variants of the Patient Health Questionnaire (PHQ) by Clinicians and mental health professionals. This approach places significant reliance on the experience and judgment of trained physicians, making the diagnosis susceptible to personal biases. Given that the underlying mechanisms causing depression are still being actively researched, physicians often face challenges in diagnosing and treating the condition, particularly in its early stages of clinical presentation. Recently, significant strides have been made in Artificial neural computing to solve problems involving text, image, and speech in various domains. Our analysis has aimed to leverage these state-of-the-art (SOTA) models in our experiments to achieve optimal outcomes leveraging multiple modalities. The experiments were performed on the Extended Distress Analysis Interview Corpus Wizard of Oz dataset (E-DAIC) corpus presented in the Audio/Visual Emotion Challenge (AVEC) 2019 Challenge. The proposed solutions demonstrate better results achieved by Proprietary and Open-source Large Language Models (LLMs), which achieved a Root Mean Square Error (RMSE) score of 3.98 on Textual Modality, beating the AVEC 2019 challenge baseline results and current SOTA regression analysis architectures. Additionally, the proposed solution achieved an accuracy of 71.43% in the classification task. The paper also includes a novel audio-visual multi-modal network that predicts PHQ-8 scores with an RMSE of 6.51.

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 large-scale dataset, ReCoRD, for machine reading comprehension requiring commonsense reasoning. Experiments on this dataset demonstrate that the performance of state-of-the-art MRC systems fall far behind human performance. ReCoRD represents a challenge for future research to bridge the gap between human and machine commonsense reading comprehension. ReCoRD is available at http://nlp.jhu.edu/record.

Clinical Question Answering (QA) systems enable doctors to quickly access patient information from electronic health records (EHRs). However, training these systems requires significant annotated data, which is limited due to the expertise needed and the privacy concerns associated with clinical data. This paper explores generating Clinical QA data using large language models (LLMs) in a zero-shot setting. We find that naive prompting often results in easy questions that do not reflect the complexity of clinical scenarios. To address this, we propose two prompting strategies: 1) instructing the model to generate questions that do not overlap with the input context, and 2) summarizing the input record using a predefined schema to scaffold question generation. Experiments on two Clinical QA datasets demonstrate that our method generates more challenging questions, significantly improving fine-tuning performance over baselines. We compare synthetic and gold data and find a gap between their training efficacy resulting from the quality of synthetically generated answers.

We introduce MilkQA, a question answering dataset from the dairy domain dedicated to the study of consumer questions. The dataset contains 2,657 pairs of questions and answers, written in the Portuguese language and originally collected by the Brazilian Agricultural Research Corporation (Embrapa). All questions were motivated by real situations and written by thousands of authors with very different backgrounds and levels of literacy, while answers were elaborated by specialists from Embrapa's customer service. Our dataset was filtered and anonymized by three human annotators. Consumer questions are a challenging kind of question that is usually employed as a form of seeking information. Although several question answering datasets are available, most of such resources are not suitable for research on answer selection models for consumer questions. We aim to fill this gap by making MilkQA publicly available. We study the behavior of four answer selection models on MilkQA: two baseline models and two convolutional neural network archictetures. Our results show that MilkQA poses real challenges to computational models, particularly due to linguistic characteristics of its questions and to their unusually longer lengths. Only one of the experimented models gives reasonable results, at the cost of high computational requirements.

We fine-tune GPT-3 to answer long-form questions using a text-based web-browsing environment, which allows the model to search and navigate the web. By setting up the task so that it can be performed by humans, we are able to train models on the task using imitation learning, and then optimize answer quality with human feedback. To make human evaluation of factual accuracy easier, models must collect references while browsing in support of their answers. We train and evaluate our models on ELI5, a dataset of questions asked by Reddit users. Our best model is obtained by fine-tuning GPT-3 using behavior cloning, and then performing rejection sampling against a reward model trained to predict human preferences. This model's answers are preferred by humans 56% of the time to those of our human demonstrators, and 69% of the time to the highest-voted answer from Reddit.

Clinical trial matching is a key process in health delivery and discovery. In practice, it is plagued by overwhelming unstructured data and unscalable manual processing. In this paper, we conduct a systematic study on scaling clinical trial matching using large language models (LLMs), with oncology as the focus area. Our study is grounded in a clinical trial matching system currently in test deployment at a large U.S. health network. Initial findings are promising: out of box, cutting-edge LLMs, such as GPT-4, can already structure elaborate eligibility criteria of clinical trials and extract complex matching logic (e.g., nested AND/OR/NOT). While still far from perfect, LLMs substantially outperform prior strong baselines and may serve as a preliminary solution to help triage patient-trial candidates with humans in the loop. Our study also reveals a few significant growth areas for applying LLMs to end-to-end clinical trial matching, such as context limitation and accuracy, especially in structuring patient information from longitudinal medical records.

People experiencing severe distress increasingly use Large Language Model (LLM) chatbots as mental health support tools. Discussions on social media have described how engagements were lifesaving for some, but evidence suggests that general-purpose LLM chatbots also have notable risks that could endanger the welfare of users if not designed responsibly. In this study, we investigate the lived experiences of people who have used LLM chatbots for mental health support. We build on interviews with 21 individuals from globally diverse backgrounds to analyze how users create unique support roles for their chatbots, fill in gaps in everyday care, and navigate associated cultural limitations when seeking support from chatbots. We ground our analysis in psychotherapy literature around effective support, and introduce the concept of therapeutic alignment, or aligning AI with therapeutic values for mental health contexts. Our study offers recommendations for how designers can approach the ethical and effective use of LLM chatbots and other AI mental health support tools in mental health care.

Is it possible to develop an "AI Pathologist" to pass the board-certified examination of the American Board of Pathology? To achieve this goal, the first step is to create a visual question answering (VQA) dataset where the AI agent is presented with a pathology image together with a question and is asked to give the correct answer. Our work makes the first attempt to build such a dataset. Different from creating general-domain VQA datasets where the images are widely accessible and there are many crowdsourcing workers available and capable of generating question-answer pairs, developing a medical VQA dataset is much more challenging. First, due to privacy concerns, pathology images are usually not publicly available. Second, only well-trained pathologists can understand pathology images, but they barely have time to help create datasets for AI research. To address these challenges, we resort to pathology textbooks and online digital libraries. We develop a semi-automated pipeline to extract pathology images and captions from textbooks and generate question-answer pairs from captions using natural language processing. We collect 32,799 open-ended questions from 4,998 pathology images where each question is manually checked to ensure correctness. To our best knowledge, this is the first dataset for pathology VQA. Our dataset will be released publicly to promote research in medical VQA.

As the field of artificial intelligence progresses, assistive technologies are becoming more widely used across all industries. The healthcare industry is no different, with numerous studies being done to develop assistive tools for healthcare professionals. Automatic diagnostic systems are one such beneficial tool that can assist with a variety of tasks, including collecting patient information, analyzing test results, and diagnosing patients. However, the idea of developing systems that can provide a differential diagnosis has been largely overlooked in most of these research studies. In this study, we propose a transformer-based approach for providing differential diagnoses based on a patient's age, sex, medical history, and symptoms. We use the DDXPlus dataset, which provides differential diagnosis information for patients based on 49 disease types. Firstly, we propose a method to process the tabular patient data from the dataset and engineer them into patient reports to make them suitable for our research. In addition, we introduce two data modification modules to diversify the training data and consequently improve the robustness of the models. We approach the task as a multi-label classification problem and conduct extensive experiments using four transformer models. All the models displayed promising results by achieving over 97% F1 score on the held-out test set. Moreover, we design additional behavioral tests to get a broader understanding of the models. In particular, for one of our test cases, we prepared a custom test set of 100 samples with the assistance of a doctor. The results on the custom set showed that our proposed data modification modules improved the model's generalization capabilities. We hope our findings will provide future researchers with valuable insights and inspire them to develop reliable systems for automatic differential diagnosis.

Large participatory biomedical studies, studies that recruit individuals to join a dataset, are gaining popularity and investment, especially for analysis by modern AI methods. Because they purposively recruit participants, these studies are uniquely able to address a lack of historical representation, an issue that has affected many biomedical datasets. In this work, we define representativeness as the similarity to a target population distribution of a set of attributes and our goal is to mirror the U.S. population across distributions of age, gender, race, and ethnicity. Many participatory studies recruit at several institutions, so we introduce a computational approach to adaptively allocate recruitment resources among sites to improve representativeness. In simulated recruitment of 10,000-participant cohorts from medical centers in the STAR Clinical Research Network, we show that our approach yields a more representative cohort than existing baselines. Thus, we highlight the value of computational modeling in guiding recruitment efforts.

We introduce a large scale MAchine Reading COmprehension dataset, which we name MS MARCO. The dataset comprises of 1,010,916 anonymized questions---sampled from Bing's search query logs---each with a human generated answer and 182,669 completely human rewritten generated answers. In addition, the dataset contains 8,841,823 passages---extracted from 3,563,535 web documents retrieved by Bing---that provide the information necessary for curating the natural language answers. A question in the MS MARCO dataset may have multiple answers or no answers at all. Using this dataset, we propose three different tasks with varying levels of difficulty: (i) predict if a question is answerable given a set of context passages, and extract and synthesize the answer as a human would (ii) generate a well-formed answer (if possible) based on the context passages that can be understood with the question and passage context, and finally (iii) rank a set of retrieved passages given a question. The size of the dataset and the fact that the questions are derived from real user search queries distinguishes MS MARCO from other well-known publicly available datasets for machine reading comprehension and question-answering. We believe that the scale and the real-world nature of this dataset makes it attractive for benchmarking machine reading comprehension and question-answering models.

Recent approaches to empathetic response generation try to incorporate commonsense knowledge or reasoning about the causes of emotions to better understand the user's experiences and feelings. However, these approaches mainly focus on understanding the causalities of context from the user's perspective, ignoring the system's perspective. In this paper, we propose a commonsense-based causality explanation approach for diverse empathetic response generation that considers both the user's perspective (user's desires and reactions) and the system's perspective (system's intentions and reactions). We enhance ChatGPT's ability to reason for the system's perspective by integrating in-context learning with commonsense knowledge. Then, we integrate the commonsense-based causality explanation with both ChatGPT and a T5-based model. Experimental evaluations demonstrate that our method outperforms other comparable methods on both automatic and human evaluations.

Alzheimer's disease (AD) is a degenerative brain disease impairing a person's ability to perform day to day activities. The clinical manifestations of Alzheimer's disease are characterized by heterogeneity in age, disease span, progression rate, impairment of memory and cognitive abilities. Due to these variabilities, personalized care and treatment planning, as well as patient counseling about their individual progression is limited. Recent developments in machine learning to detect hidden patterns in complex, multi-dimensional datasets provides significant opportunities to address this critical need. In this work, we use unsupervised and supervised machine learning approaches for subtype identification and prediction. We apply machine learning methods to the extensive clinical observations available at the Alzheimer's Disease Neuroimaging Initiative (ADNI) data set to identify patient subtypes and to predict disease progression. Our analysis depicts the progression space for the Alzheimer's disease into low, moderate and high disease progression zones. The proposed work will enable early detection and characterization of distinct disease subtypes based on clinical heterogeneity. We anticipate that our models will enable patient counseling, clinical trial design, and ultimately individualized clinical care.

Recent progress in large language models has enabled the deployment of many generative NLP applications. At the same time, it has also led to a misleading public discourse that ``it's all been solved.'' Not surprisingly, this has in turn made many NLP researchers -- especially those at the beginning of their career -- wonder about what NLP research area they should focus on. This document is a compilation of NLP research directions that are rich for exploration, reflecting the views of a diverse group of PhD students in an academic research lab. While we identify many research areas, many others exist; we do not cover those areas that are currently addressed by LLMs but where LLMs lag behind in performance, or those focused on LLM development. We welcome suggestions for other research directions to include: https://bit.ly/nlp-era-llm

The current work addresses a virtual environment with self-replicating agents whose decisions are based on a form of "somatic computation" (soma - body) in which basic emotional responses, taken in parallelism to actual living organisms, are introduced as a way to provide the agents with greater reflexive abilities. The work provides a contribution to the field of Artificial Intelligence (AI) and Artificial Life (ALife) in connection to a neurobiology-based cognitive framework for artificial systems and virtual environments' simulations. The performance of the agents capable of emotional responses is compared with that of self-replicating automata, and the implications of research on emotions and AI, in connection to both virtual agents as well as robots, is addressed regarding possible future directions and applications.

The common toxicity and societal bias in contents generated by large language models (LLMs) necessitate strategies to reduce harm. Present solutions often demand white-box access to the model or substantial training, which is impractical for cutting-edge commercial LLMs. Moreover, prevailing prompting methods depend on external tool feedback and fail to simultaneously lessen toxicity and bias. Motivated by social psychology principles, we propose a novel strategy named perspective-taking prompting (\textsc{PeT)} that inspires LLMs to integrate diverse human perspectives and self-regulate their responses. This self-correction mechanism can significantly diminish toxicity (up to 89%) and bias (up to 73%) in LLMs' responses. Rigorous evaluations and ablation studies are conducted on two commercial LLMs (ChatGPT and GLM) and three open-source LLMs, revealing PeT's superiority in producing less harmful responses, outperforming five strong baselines.

Recent artificial intelligence (AI) systems have reached milestones in "grand challenges" ranging from Go to protein-folding. The capability to retrieve medical knowledge, reason over it, and answer medical questions comparably to physicians has long been viewed as one such grand challenge. Large language models (LLMs) have catalyzed significant progress in medical question answering; Med-PaLM was the first model to exceed a "passing" score in US Medical Licensing Examination (USMLE) style questions with a score of 67.2% on the MedQA dataset. However, this and other prior work suggested significant room for improvement, especially when models' answers were compared to clinicians' answers. Here we present Med-PaLM 2, which bridges these gaps by leveraging a combination of base LLM improvements (PaLM 2), medical domain finetuning, and prompting strategies including a novel ensemble refinement approach. Med-PaLM 2 scored up to 86.5% on the MedQA dataset, improving upon Med-PaLM by over 19% and setting a new state-of-the-art. We also observed performance approaching or exceeding state-of-the-art across MedMCQA, PubMedQA, and MMLU clinical topics datasets. We performed detailed human evaluations on long-form questions along multiple axes relevant to clinical applications. In pairwise comparative ranking of 1066 consumer medical questions, physicians preferred Med-PaLM 2 answers to those produced by physicians on eight of nine axes pertaining to clinical utility (p < 0.001). We also observed significant improvements compared to Med-PaLM on every evaluation axis (p < 0.001) on newly introduced datasets of 240 long-form "adversarial" questions to probe LLM limitations. While further studies are necessary to validate the efficacy of these models in real-world settings, these results highlight rapid progress towards physician-level performance in medical question answering.

As generative large language models (LLMs) grow more performant and prevalent, we must develop comprehensive enough tools to measure and improve their fairness. Different prompt-based datasets can be used to measure social bias across multiple text domains and demographic axes, meaning that testing LLMs on more datasets can potentially help us characterize their biases more fully, and better ensure equal and equitable treatment of marginalized demographic groups. In this work, our focus is two-fold: (1) Benchmarking: a comparison of 6 different prompt-based bias and toxicity metrics across 12 demographic axes and 5 families of generative LLMs. Out of those 6 metrics, AdvPromptSet and HolisticBiasR are novel datasets proposed in the paper. The comparison of those benchmarks gives us insights about the bias and toxicity of the compared models. Therefore, we explore the frequency of demographic terms in common LLM pre-training corpora and how this may relate to model biases. (2) Mitigation: we conduct a comprehensive study of how well 3 bias/toxicity mitigation techniques perform across our suite of measurements. ROBBIE aims to provide insights for practitioners while deploying a model, emphasizing the need to not only measure potential harms, but also understand how they arise by characterizing the data, mitigate harms once found, and balance any trade-offs. We open-source our analysis code in hopes of encouraging broader measurements of bias in future LLMs.

This study investigates the consistency of feedback ratings generated by OpenAI's GPT-4, a state-of-the-art artificial intelligence language model, across multiple iterations, time spans and stylistic variations. The model rated responses to tasks within the Higher Education (HE) subject domain of macroeconomics in terms of their content and style. Statistical analysis was conducted in order to learn more about the interrater reliability, consistency of the ratings across iterations and the correlation between ratings in terms of content and style. The results revealed a high interrater reliability with ICC scores ranging between 0.94 and 0.99 for different timespans, suggesting that GPT-4 is capable of generating consistent ratings across repetitions with a clear prompt. Style and content ratings show a high correlation of 0.87. When applying a non-adequate style the average content ratings remained constant, while style ratings decreased, which indicates that the large language model (LLM) effectively distinguishes between these two criteria during evaluation. The prompt used in this study is furthermore presented and explained. Further research is necessary to assess the robustness and reliability of AI models in various use cases.

There is a lack of benchmarks for evaluating large language models (LLMs) in long-form medical question answering (QA). Most existing medical QA evaluation benchmarks focus on automatic metrics and multiple-choice questions. While valuable, these benchmarks fail to fully capture or assess the complexities of real-world clinical applications where LLMs are being deployed. Furthermore, existing studies on evaluating long-form answer generation in medical QA are primarily closed-source, lacking access to human medical expert annotations, which makes it difficult to reproduce results and enhance existing baselines. In this work, we introduce a new publicly available benchmark featuring real-world consumer medical questions with long-form answer evaluations annotated by medical doctors. We performed pairwise comparisons of responses from various open and closed-source medical and general-purpose LLMs based on criteria such as correctness, helpfulness, harmfulness, and bias. Additionally, we performed a comprehensive LLM-as-a-judge analysis to study the alignment between human judgments and LLMs. Our preliminary results highlight the strong potential of open LLMs in medical QA compared to leading closed models. Code & Data: https://github.com/lavita-ai/medical-eval-sphere

As mental health care systems worldwide struggle to meet demand, there is increasing focus on using language models to infer neuropsychiatric conditions or psychopathological traits from language production. Yet, so far, this research has only delivered solutions with limited clinical applicability, due to insufficient consideration of ethical questions crucial to ensuring the synergy between possible applications and model design. To accelerate progress towards clinically applicable models, our paper charts the ethical landscape of research on language-based inference of psychopathology and provides a practical tool for researchers to navigate it. We identify seven core ethical principles that should guide model development and deployment in this domain, translate them into ELLIPS, an ethical toolkit operationalizing these principles into questions that can guide researchers' choices with respect to data selection, architectures, evaluation, and model deployment, and provide a case study exemplifying its use. With this, we aim to facilitate the emergence of model technology with concrete potential for real-world applicability.

In this study, we present MedS-Bench, a comprehensive benchmark designed to evaluate the performance of large language models (LLMs) in clinical contexts. Unlike existing benchmarks that focus on multiple-choice question answering, MedS-Bench spans 11 high-level clinical tasks, including clinical report summarization, treatment recommendations, diagnosis, named entity recognition, and medical concept explanation, among others. We evaluated six leading LLMs, e.g., MEDITRON, Mistral, InternLM 2, Llama 3, GPT-4, and Claude-3.5 using few-shot prompting, and found that even the most sophisticated models struggle with these complex tasks. To address these limitations, we developed MedS-Ins, a large-scale instruction tuning dataset for medicine. MedS-Ins comprises 58 medically oriented language corpora, totaling 13.5 million samples across 122 tasks. To demonstrate the dataset's utility, we conducted a proof-of-concept experiment by performing instruction tuning on a lightweight, open-source medical language model. The resulting model, MMedIns-Llama 3, significantly outperformed existing models across nearly all clinical tasks. To promote further advancements in the application of LLMs to clinical challenges, we have made the MedS-Ins dataset fully accessible and invite the research community to contribute to its expansion.Additionally, we have launched a dynamic leaderboard for MedS-Bench, which we plan to regularly update the test set to track progress and enhance the adaptation of general LLMs to the medical domain. Leaderboard: https://henrychur.github.io/MedS-Bench/. Github: https://github.com/MAGIC-AI4Med/MedS-Ins.

Background: Social media platforms have become a viable source of medical information, with patients and healthcare professionals using them to share health-related information and track diseases. Similarly, YouTube, the largest video-sharing platform in the world contains vlogs where individuals talk about their illnesses. The aim of our study was to investigate the use of Natural Language Processing (NLP) to identify the spoken content of YouTube vlogs related to the diagnosis of Coronavirus disease of 2019 (COVID-19) for public health screening. Methods: COVID-19 videos on YouTube were searched using relevant keywords. A total of 1000 videos being spoken in English were downloaded out of which 791 were classified as vlogs, 192 were non-vlogs, and 17 were deleted by the channel. The videos were converted into a textual format using Microsoft Streams. The textual data was preprocessed using basic and advanced preprocessing methods. A lexicon of 200 words was created which contained words related to COVID-19. The data was analyzed using topic modeling, word clouds, and lexicon matching. Results: The word cloud results revealed discussions about COVID-19 symptoms like "fever", along with generic terms such as "mask" and "isolation". Lexical analysis demonstrated that in 96.46% of videos, patients discussed generic terms, and in 95.45% of videos, people talked about COVID-19 symptoms. LDA Topic Modeling results also generated topics that successfully captured key themes and content related to our investigation of COVID-19 diagnoses in YouTube vlogs. Conclusion: By leveraging NLP techniques on YouTube vlogs public health practitioners can enhance their ability to mitigate the effects of pandemics and effectively respond to public health challenges.

Legal practice has witnessed a sharp rise in products incorporating artificial intelligence (AI). Such tools are designed to assist with a wide range of core legal tasks, from search and summarization of caselaw to document drafting. But the large language models used in these tools are prone to "hallucinate," or make up false information, making their use risky in high-stakes domains. Recently, certain legal research providers have touted methods such as retrieval-augmented generation (RAG) as "eliminating" (Casetext, 2023) or "avoid[ing]" hallucinations (Thomson Reuters, 2023), or guaranteeing "hallucination-free" legal citations (LexisNexis, 2023). Because of the closed nature of these systems, systematically assessing these claims is challenging. In this article, we design and report on the first preregistered empirical evaluation of AI-driven legal research tools. We demonstrate that the providers' claims are overstated. While hallucinations are reduced relative to general-purpose chatbots (GPT-4), we find that the AI research tools made by LexisNexis (Lexis+ AI) and Thomson Reuters (Westlaw AI-Assisted Research and Ask Practical Law AI) each hallucinate between 17% and 33% of the time. We also document substantial differences between systems in responsiveness and accuracy. Our article makes four key contributions. It is the first to assess and report the performance of RAG-based proprietary legal AI tools. Second, it introduces a comprehensive, preregistered dataset for identifying and understanding vulnerabilities in these systems. Third, it proposes a clear typology for differentiating between hallucinations and accurate legal responses. Last, it provides evidence to inform the responsibilities of legal professionals in supervising and verifying AI outputs, which remains a central open question for the responsible integration of AI into law.

LLMs have demonstrated impressive performance in answering medical questions, such as passing scores on medical licensing examinations. However, medical board exam questions or general clinical questions do not capture the complexity of realistic clinical cases. Moreover, the lack of reference explanations means we cannot easily evaluate the reasoning of model decisions, a crucial component of supporting doctors in making complex medical decisions. To address these challenges, we construct two new datasets: JAMA Clinical Challenge and Medbullets. JAMA Clinical Challenge consists of questions based on challenging clinical cases, while Medbullets comprises USMLE Step 2&3 style clinical questions. Both datasets are structured as multiple-choice question-answering tasks, where each question is accompanied by an expert-written explanation. We evaluate four LLMs on the two datasets using various prompts. Experiments demonstrate that our datasets are harder than previous benchmarks. The inconsistency between automatic and human evaluations of model-generated explanations highlights the need to develop new metrics to support future research on explainable medical QA.

Readers of academic research papers often read with the goal of answering specific questions. Question Answering systems that can answer those questions can make consumption of the content much more efficient. However, building such tools requires data that reflect the difficulty of the task arising from complex reasoning about claims made in multiple parts of a paper. In contrast, existing information-seeking question answering datasets usually contain questions about generic factoid-type information. We therefore present QASPER, a dataset of 5,049 questions over 1,585 Natural Language Processing papers. Each question is written by an NLP practitioner who read only the title and abstract of the corresponding paper, and the question seeks information present in the full text. The questions are then answered by a separate set of NLP practitioners who also provide supporting evidence to answers. We find that existing models that do well on other QA tasks do not perform well on answering these questions, underperforming humans by at least 27 F1 points when answering them from entire papers, motivating further research in document-grounded, information-seeking QA, which our dataset is designed to facilitate.

Teachers and students are increasingly relying on online learning resources to supplement the ones provided in school. This increase in the breadth and depth of available resources is a great thing for students, but only provided they are able to find answers to their queries. Question-answering and information retrieval systems have benefited from public datasets to train and evaluate their algorithms, but most of these datasets have been in English text written by and for adults. We introduce a new public French question-answering dataset collected from Alloprof, a Quebec-based primary and high-school help website, containing 29 349 questions and their explanations in a variety of school subjects from 10 368 students, with more than half of the explanations containing links to other questions or some of the 2 596 reference pages on the website. We also present a case study of this dataset in an information retrieval task. This dataset was collected on the Alloprof public forum, with all questions verified for their appropriateness and the explanations verified both for their appropriateness and their relevance to the question. To predict relevant documents, architectures using pre-trained BERT models were fine-tuned and evaluated. This dataset will allow researchers to develop question-answering, information retrieval and other algorithms specifically for the French speaking education context. Furthermore, the range of language proficiency, images, mathematical symbols and spelling mistakes will necessitate algorithms based on a multimodal comprehension. The case study we present as a baseline shows an approach that relies on recent techniques provides an acceptable performance level, but more work is necessary before it can reliably be used and trusted in a production setting.

There has been a rapidly growing interest in Automatic Symptom Detection (ASD) and Automatic Diagnosis (AD) systems in the machine learning research literature, aiming to assist doctors in telemedicine services. These systems are designed to interact with patients, collect evidence about their symptoms and relevant antecedents, and possibly make predictions about the underlying diseases. Doctors would review the interactions, including the evidence and the predictions, collect if necessary additional information from patients, before deciding on next steps. Despite recent progress in this area, an important piece of doctors' interactions with patients is missing in the design of these systems, namely the differential diagnosis. Its absence is largely due to the lack of datasets that include such information for models to train on. In this work, we present a large-scale synthetic dataset of roughly 1.3 million patients that includes a differential diagnosis, along with the ground truth pathology, symptoms and antecedents for each patient. Unlike existing datasets which only contain binary symptoms and antecedents, this dataset also contains categorical and multi-choice symptoms and antecedents useful for efficient data collection. Moreover, some symptoms are organized in a hierarchy, making it possible to design systems able to interact with patients in a logical way. As a proof-of-concept, we extend two existing AD and ASD systems to incorporate the differential diagnosis, and provide empirical evidence that using differentials as training signals is essential for the efficiency of such systems or for helping doctors better understand the reasoning of those systems.

We introduce "ivrit.ai", a comprehensive Hebrew speech dataset, addressing the distinct lack of extensive, high-quality resources for advancing Automated Speech Recognition (ASR) technology in Hebrew. With over 3,300 speech hours and a over a thousand diverse speakers, ivrit.ai offers a substantial compilation of Hebrew speech across various contexts. It is delivered in three forms to cater to varying research needs: raw unprocessed audio; data post-Voice Activity Detection, and partially transcribed data. The dataset stands out for its legal accessibility, permitting use at no cost, thereby serving as a crucial resource for researchers, developers, and commercial entities. ivrit.ai opens up numerous applications, offering vast potential to enhance AI capabilities in Hebrew. Future efforts aim to expand ivrit.ai further, thereby advancing Hebrew's standing in AI research and technology.

Millions of people participate in online peer-to-peer support sessions, yet there has been little prior research on systematic psychology-based evaluations of fine-grained peer-counselor behavior in relation to client satisfaction. This paper seeks to bridge this gap by mapping peer-counselor chat-messages to motivational interviewing (MI) techniques. We annotate 14,797 utterances from 734 chat conversations using 17 MI techniques and introduce four new interviewing codes such as chit-chat and inappropriate to account for the unique conversational patterns observed on online platforms. We automate the process of labeling peer-counselor responses to MI techniques by fine-tuning large domain-specific language models and then use these automated measures to investigate the behavior of the peer counselors via correlational studies. Specifically, we study the impact of MI techniques on the conversation ratings to investigate the techniques that predict clients' satisfaction with their counseling sessions. When counselors use techniques such as reflection and affirmation, clients are more satisfied. Examining volunteer counselors' change in usage of techniques suggest that counselors learn to use more introduction and open questions as they gain experience. This work provides a deeper understanding of the use of motivational interviewing techniques on peer-to-peer counselor platforms and sheds light on how to build better training programs for volunteer counselors on online platforms.

With COVID-19 having emerged as the most widespread human pandemic disease in a century, the need to control its spread to avoid massive loss of life became more than necessary, and extremely fast. Several vaccines were developed and the task of policy makers was suddenly to convince the reluctant population to be vaccinated by various means. While some countries have chosen a policy of mandatory vaccination or punitive incentives, many states in the United States have adopted various incentives to try to increase vaccination coverage. A study we conducted in recent months quantified the effect of these measures on the proportion of the population vaccinated, using the synthetic control method, by simulating what would have happened without these measures. The aim now is to generalize this study to smaller scales, to improve the results of our previous study, to quantify their robustness and to provide a tool that can be used by policy makers to adapt their behavior in light of the results obtained.

Large Language Models (LLMs) have the potential of facilitating the development of Artificial Intelligence technology to assist medical experts for interactive decision support, which has been demonstrated by their competitive performances in Medical QA. However, while impressive, the required quality bar for medical applications remains far from being achieved. Currently, LLMs remain challenged by outdated knowledge and by their tendency to generate hallucinated content. Furthermore, most benchmarks to assess medical knowledge lack reference gold explanations which means that it is not possible to evaluate the reasoning of LLMs predictions. Finally, the situation is particularly grim if we consider benchmarking LLMs for languages other than English which remains, as far as we know, a totally neglected topic. In order to address these shortcomings, in this paper we present MedExpQA, the first multilingual benchmark based on medical exams to evaluate LLMs in Medical Question Answering. To the best of our knowledge, MedExpQA includes for the first time reference gold explanations written by medical doctors which can be leveraged to establish various gold-based upper-bounds for comparison with LLMs performance. Comprehensive multilingual experimentation using both the gold reference explanations and Retrieval Augmented Generation (RAG) approaches show that performance of LLMs still has large room for improvement, especially for languages other than English. Furthermore, and despite using state-of-the-art RAG methods, our results also demonstrate the difficulty of obtaining and integrating readily available medical knowledge that may positively impact results on downstream evaluations for Medical Question Answering. So far the benchmark is available in four languages, but we hope that this work may encourage further development to other languages.

We present Eir Thai Medical LLM, a large language model with 8 billion parameters, specifically designed to enhance the accuracy of handling medical tasks in the Thai language. This model focuses on providing clear and easy-to-understand answers for both healthcare professionals and patients, thereby improving the efficiency of diagnosis and treatment processes. Human evaluation was conducted to ensure that the model adheres to care standards and provides unbiased answers. To prioritize data security, the model is deployed within the hospital's internal network, ensuring both high security and faster processing speeds. The internal API connection is secured with encryption and strict authentication measures to prevent data leaks and unauthorized access. We evaluated several open-source large language models with 8 billion parameters on four medical benchmarks: MedQA, MedMCQA, PubMedQA, and the medical subset of MMLU. The best-performing baselines were used to develop Eir Thai Medical LLM. Our evaluation employed multiple questioning strategies, including zero-shot, few-shot, chain-of-thought reasoning, and ensemble/self-consistency voting methods. Our model outperformed commercially available Thai-language large language models by more than 10%. In addition, we developed enhanced model testing tailored for clinical use in Thai across 18 clinical tasks, where our model exceeded GPT-4o performance by more than 11%

We present a statistical model for German medical natural language processing trained for named entity recognition (NER) as an open, publicly available model. The work serves as a refined successor to our first GERNERMED model which is substantially outperformed by our work. We demonstrate the effectiveness of combining multiple techniques in order to achieve strong results in entity recognition performance by the means of transfer-learning on pretrained deep language models (LM), word-alignment and neural machine translation. Due to the sparse situation on open, public medical entity recognition models for German texts, this work offers benefits to the German research community on medical NLP as a baseline model. Since our model is based on public English data, its weights are provided without legal restrictions on usage and distribution. The sample code and the statistical model is available at: https://github.com/frankkramer-lab/GERNERMED-pp

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.

Background: Cancer remains one of the leading causes of morbidity and mortality worldwide. Comprehensive datasets that combine histopathological images with genetic and survival data across various tumour sites are essential for advancing computational pathology and personalised medicine. Results: We present SurGen, a dataset comprising 1,020 H&E-stained whole slide images (WSIs) from 843 colorectal cancer cases. The dataset includes detailed annotations for key genetic mutations (KRAS, NRAS, BRAF) and mismatch repair status, as well as survival data for 426 cases. To demonstrate SurGen's practical utility, we conducted a proof-of-concept machine learning experiment predicting mismatch repair status from the WSIs, achieving a test AUROC of 0.8316. These preliminary results underscore the dataset's potential to facilitate research in biomarker discovery, prognostic modelling, and advanced machine learning applications in colorectal cancer. Conclusions: SurGen offers a valuable resource for the scientific community, enabling studies that require high-quality WSIs linked with comprehensive clinical and genetic information on colorectal cancer. Our initial findings affirm the dataset's capacity to advance diagnostic precision and foster the development of personalised treatment strategies in colorectal oncology. Data available online at https://doi.org/10.6019/S-BIAD1285.

While day-to-day questions come with a variety of answer types, the current question-answering (QA) literature has failed to adequately address the answer diversity of questions. To this end, we present GooAQ, a large-scale dataset with a variety of answer types. This dataset contains over 5 million questions and 3 million answers collected from Google. GooAQ questions are collected semi-automatically from the Google search engine using its autocomplete feature. This results in naturalistic questions of practical interest that are nonetheless short and expressed using simple language. GooAQ answers are mined from Google's responses to our collected questions, specifically from the answer boxes in the search results. This yields a rich space of answer types, containing both textual answers (short and long) as well as more structured ones such as collections. We benchmarkT5 models on GooAQ and observe that: (a) in line with recent work, LM's strong performance on GooAQ's short-answer questions heavily benefit from annotated data; however, (b) their quality in generating coherent and accurate responses for questions requiring long responses (such as 'how' and 'why' questions) is less reliant on observing annotated data and mainly supported by their pre-training. We release GooAQ to facilitate further research on improving QA with diverse response types.

Several recent works seek to develop foundation models specifically for medical applications, adapting general-purpose large language models (LLMs) and vision-language models (VLMs) via continued pretraining on publicly available biomedical corpora. These works typically claim that such domain-adaptive pretraining (DAPT) improves performance on downstream medical tasks, such as answering medical licensing exam questions. In this paper, we compare ten public "medical" LLMs and two VLMs against their corresponding base models, arriving at a different conclusion: all medical VLMs and nearly all medical LLMs fail to consistently improve over their base models in the zero-/few-shot prompting and supervised fine-tuning regimes for medical question-answering (QA). For instance, across all tasks and model pairs we consider in the 3-shot setting, medical LLMs only outperform their base models in 22.7% of cases, reach a (statistical) tie in 36.8% of cases, and are significantly worse than their base models in the remaining 40.5% of cases. Our conclusions are based on (i) comparing each medical model head-to-head, directly against the corresponding base model; (ii) optimizing the prompts for each model separately in zero-/few-shot prompting; and (iii) accounting for statistical uncertainty in comparisons. While these basic practices are not consistently adopted in the literature, our ablations show that they substantially impact conclusions. Meanwhile, we find that after fine-tuning on specific QA tasks, medical LLMs can show performance improvements, but the benefits do not carry over to tasks based on clinical notes. Our findings suggest that state-of-the-art general-domain models may already exhibit strong medical knowledge and reasoning capabilities, and offer recommendations to strengthen the conclusions of future studies.

Farmers face several challenges when growing crops like uncertain irrigation, poor soil quality, etc. Especially in India, a major fraction of farmers do not have the knowledge to select appropriate crops and fertilizers. Moreover, crop failure due to disease causes a significant loss to the farmers, as well as the consumers. While there have been recent developments in the automated detection of these diseases using Machine Learning techniques, the utilization of Deep Learning has not been fully explored. Additionally, such models are not easy to use because of the high-quality data used in their training, lack of computational power, and poor generalizability of the models. To this end, we create an open-source easy-to-use web application to address some of these issues which may help improve crop production. In particular, we support crop recommendation, fertilizer recommendation, plant disease prediction, and an interactive news-feed. In addition, we also use interpretability techniques in an attempt to explain the prediction made by our disease detection model.

Temporally dense single-person "small data" have become widely available thanks to mobile apps and wearable sensors. Many caregivers and self-trackers want to use these data to help a specific person change their behavior to achieve desired health outcomes. Ideally, this involves discerning possible causes from correlations using that person's own observational time series data. In this paper, we estimate within-individual average treatment effects of physical activity on sleep duration, and vice-versa. We introduce the model twin randomization (MoTR; "motor") method for analyzing an individual's intensive longitudinal data. Formally, MoTR is an application of the g-formula (i.e., standardization, back-door adjustment) under serial interference. It estimates stable recurring effects, as is done in n-of-1 trials and single case experimental designs. We compare our approach to standard methods (with possible confounding) to show how to use causal inference to make better personalized recommendations for health behavior change, and analyze 222 days of Fitbit sleep and steps data for one of the authors.

As large language models increase in capability, researchers have started to conduct surveys of all kinds on these models with varying scientific motivations. In this work, we examine what we can learn from a model's survey responses on the basis of the well-established American Community Survey (ACS) by the U.S. Census Bureau. Evaluating more than a dozen different models, varying in size from a few hundred million to ten billion parameters, hundreds of thousands of times each on questions from the ACS, we systematically establish two dominant patterns. First, smaller models have a significant position and labeling bias, for example, towards survey responses labeled with the letter "A". This A-bias diminishes, albeit slowly, as model size increases. Second, when adjusting for this labeling bias through randomized answer ordering, models still do not trend toward US population statistics or those of any cognizable population. Rather, models across the board trend toward uniformly random aggregate statistics over survey responses. This pattern is robust to various different ways of prompting the model, including what is the de-facto standard. Our findings demonstrate that aggregate statistics of a language model's survey responses lack the signals found in human populations. This absence of statistical signal cautions about the use of survey responses from large language models at present time.

One of the most widely used methods to evaluate LLMs are Multiple Choice Question (MCQ) tests. MCQ benchmarks enable the testing of LLM knowledge on almost any topic at scale as the results can be processed automatically. To help the LLM answer, a few examples called few shots can be included in the prompt. Moreover, the LLM can be asked to answer the question directly with the selected option or to first provide the reasoning and then the selected answer, which is known as chain of thought. In addition to checking whether the selected answer is correct, the evaluation can look at the LLM-estimated probability of its response as an indication of the confidence of the LLM in the response. In this paper, we study how the LLM confidence in its answer depends on whether the model has been asked to answer directly or to provide the reasoning before answering. The results of the evaluation of questions on a wide range of topics in seven different models show that LLMs are more confident in their answers when they provide reasoning before the answer. This occurs regardless of whether the selected answer is correct. Our hypothesis is that this behavior is due to the reasoning that modifies the probability of the selected answer, as the LLM predicts the answer based on the input question and the reasoning that supports the selection made. Therefore, LLM estimated probabilities seem to have intrinsic limitations that should be understood in order to use them in evaluation procedures. Interestingly, the same behavior has been observed in humans, for whom explaining an answer increases confidence in its correctness.

The proliferation of online misinformation has posed significant threats to public interest. While numerous online users actively participate in the combat against misinformation, many of such responses can be characterized by the lack of politeness and supporting facts. As a solution, text generation approaches are proposed to automatically produce counter-misinformation responses. Nevertheless, existing methods are often trained end-to-end without leveraging external knowledge, resulting in subpar text quality and excessively repetitive responses. In this paper, we propose retrieval augmented response generation for online misinformation (RARG), which collects supporting evidence from scientific sources and generates counter-misinformation responses based on the evidences. In particular, our RARG consists of two stages: (1) evidence collection, where we design a retrieval pipeline to retrieve and rerank evidence documents using a database comprising over 1M academic articles; (2) response generation, in which we align large language models (LLMs) to generate evidence-based responses via reinforcement learning from human feedback (RLHF). We propose a reward function to maximize the utilization of the retrieved evidence while maintaining the quality of the generated text, which yields polite and factual responses that clearly refutes misinformation. To demonstrate the effectiveness of our method, we study the case of COVID-19 and perform extensive experiments with both in- and cross-domain datasets, where RARG consistently outperforms baselines by generating high-quality counter-misinformation responses.

Images are increasingly becoming the currency for documenting biodiversity on the planet, providing novel opportunities for accelerating scientific discoveries in the field of organismal biology, especially with the advent of large vision-language models (VLMs). We ask if pre-trained VLMs can aid scientists in answering a range of biologically relevant questions without any additional fine-tuning. In this paper, we evaluate the effectiveness of 12 state-of-the-art (SOTA) VLMs in the field of organismal biology using a novel dataset, VLM4Bio, consisting of 469K question-answer pairs involving 30K images from three groups of organisms: fishes, birds, and butterflies, covering five biologically relevant tasks. We also explore the effects of applying prompting techniques and tests for reasoning hallucination on the performance of VLMs, shedding new light on the capabilities of current SOTA VLMs in answering biologically relevant questions using images. The code and datasets for running all the analyses reported in this paper can be found at https://github.com/sammarfy/VLM4Bio.

Patient recruitment is challenging for clinical trials. We introduce TrialGPT, an end-to-end framework for zero-shot patient-to-trial matching with large language models. TrialGPT comprises three modules: it first performs large-scale filtering to retrieve candidate trials (TrialGPT-Retrieval); then predicts criterion-level patient eligibility (TrialGPT-Matching); and finally generates trial-level scores (TrialGPT-Ranking). We evaluate TrialGPT on three cohorts of 183 synthetic patients with over 75,000 trial annotations. TrialGPT-Retrieval can recall over 90% of relevant trials using less than 6% of the initial collection. Manual evaluations on 1,015 patient-criterion pairs show that TrialGPT-Matching achieves an accuracy of 87.3% with faithful explanations, close to the expert performance. The TrialGPT-Ranking scores are highly correlated with human judgments and outperform the best-competing models by 43.8% in ranking and excluding trials. Furthermore, our user study reveals that TrialGPT can reduce the screening time by 42.6% in patient recruitment. Overall, these results have demonstrated promising opportunities for patient-to-trial matching with TrialGPT.

Doctors typically write in incomprehensible handwriting, making it difficult for both the general public and some pharmacists to understand the medications they have prescribed. It is not ideal for them to write the prescription quietly and methodically because they will be dealing with dozens of patients every day and will be swamped with work.As a result, their handwriting is illegible. This may result in reports or prescriptions consisting of short forms and cursive writing that a typical person or pharmacist won't be able to read properly, which will cause prescribed medications to be misspelled. However, some individuals are accustomed to writing prescriptions in regional languages because we all live in an area with a diversity of regional languages. It makes analyzing the content much more challenging. So, in this project, we'll use a recognition system to build a tool that can translate the handwriting of physicians in any language. This system will be made into an application which is fully autonomous in functioning. As the user uploads the prescription image the program will pre-process the image by performing image pre-processing, and word segmentations initially before processing the image for training. And it will be done for every language we require the model to detect. And as of the deduction model will be made using deep learning techniques including CNN, RNN, and LSTM, which are utilized to train the model. To match words from various languages that will be written in the system, Unicode will be used. Furthermore, fuzzy search and market basket analysis are employed to offer an end result that will be optimized from the pharmaceutical database and displayed to the user as a structured output.

SberQuAD -- a large scale analog of Stanford SQuAD in the Russian language - is a valuable resource that has not been properly presented to the scientific community. We fill this gap by providing a description, a thorough analysis, and baseline experimental results.

Considerable effort has been dedicated to mitigating toxicity, but existing methods often require drastic modifications to model parameters or the use of computationally intensive auxiliary models. Furthermore, previous approaches have often neglected the crucial factor of language's evolving nature over time. In this work, we present a comprehensive perspective on toxicity mitigation that takes into account its changing nature. We introduce Goodtriever, a flexible methodology that matches the current state-of-the-art toxicity mitigation while achieving 43% relative latency reduction during inference and being more computationally efficient. By incorporating a retrieval-based approach at decoding time, Goodtriever enables toxicity-controlled text generation. Our research advocates for an increased focus on adaptable mitigation techniques, which better reflect the data drift models face when deployed in the wild. Code and data are available at https://github.com/for-ai/goodtriever.

The approval success rate of drug candidates is very low with the majority of failure due to safety and efficacy. Increasingly available high dimensional information on targets, drug molecules and indications provides an opportunity for ML methods to integrate multiple data modalities and better predict clinically promising drug targets. Notably, drug targets with human genetics evidence are shown to have better odds to succeed. However, a recent tensor factorization-based approach found that additional information on targets and indications might not necessarily improve the predictive accuracy. Here we revisit this approach by integrating different types of human genetics evidence collated from publicly available sources to support each target-indication pair. We use Bayesian tensor factorization to show that models incorporating all available human genetics evidence (rare disease, gene burden, common disease) modestly improves the clinical outcome prediction over models using single line of genetics evidence. We provide additional insight into the relative predictive power of different types of human genetics evidence for predicting the success of clinical outcomes.

Hate speech is a harmful form of online expression, often manifesting as derogatory posts. It is a significant risk in digital environments. With the rise of Large Language Models (LLMs), there is concern about their potential to replicate hate speech patterns, given their training on vast amounts of unmoderated internet data. Understanding how LLMs respond to hate speech is crucial for their responsible deployment. However, the behaviour of LLMs towards hate speech has been limited compared. This paper investigates the reactions of seven state-of-the-art LLMs (LLaMA 2, Vicuna, LLaMA 3, Mistral, GPT-3.5, GPT-4, and Gemini Pro) to hate speech. Through qualitative analysis, we aim to reveal the spectrum of responses these models produce, highlighting their capacity to handle hate speech inputs. We also discuss strategies to mitigate hate speech generation by LLMs, particularly through fine-tuning and guideline guardrailing. Finally, we explore the models' responses to hate speech framed in politically correct language.

With the spread of the use of Text2Img diffusion models such as DALL-E 2, Imagen, Mid Journey and Stable Diffusion, one challenge that artists face is selecting the right prompts to achieve the desired artistic output. We present techniques for measuring the effect that specific words and phrases in prompts have, and (in the Appendix) present guidance on the selection of prompts to produce desired effects.

There exist challenges in learning and understanding religions as the presence of complexity and depth of religious doctrines and teachings. Chatbots as question-answering systems can help in solving these challenges. LLM chatbots use NLP techniques to establish connections between topics and accurately respond to complex questions. These capabilities make it perfect to be used in enlightenment on religion as a question answering chatbot. However, LLMs also have a tendency to generate false information, known as hallucination. The responses of the chatbots can include content that insults personal religious beliefs, interfaith conflicts, and controversial or sensitive topics. It needs to avoid such cases without promoting hate speech or offending certain groups of people or their beliefs. This study uses a vector database-based Retrieval Augmented Generation (RAG) approach to enhance the accuracy and transparency of LLMs. Our question-answering system is called as "MufassirQAS". We created a vector database with several open-access books that include Turkish context. These are Turkish translations, and interpretations on Islam. We worked on creating system prompts with care, ensuring they provide instructions that prevent harmful, offensive, or disrespectful responses. We also tested the MufassirQAS and ChatGPT with sensitive questions. We got better performance with our system. Study and enhancements are still in progress. Results and future works are given.

Keeping track of scientific challenges, advances and emerging directions is a fundamental part of research. However, researchers face a flood of papers that hinders discovery of important knowledge. In biomedicine, this directly impacts human lives. To address this problem, we present a novel task of extraction and search of scientific challenges and directions, to facilitate rapid knowledge discovery. We construct and release an expert-annotated corpus of texts sampled from full-length papers, labeled with novel semantic categories that generalize across many types of challenges and directions. We focus on a large corpus of interdisciplinary work relating to the COVID-19 pandemic, ranging from biomedicine to areas such as AI and economics. We apply a model trained on our data to identify challenges and directions across the corpus and build a dedicated search engine. In experiments with 19 researchers and clinicians using our system, we outperform a popular scientific search engine in assisting knowledge discovery. Finally, we show that models trained on our resource generalize to the wider biomedical domain and to AI papers, highlighting its broad utility. We make our data, model and search engine publicly available. https://challenges.apps.allenai.org/

We describe the setting and results of the ConvAI2 NeurIPS competition that aims to further the state-of-the-art in open-domain chatbots. Some key takeaways from the competition are: (i) pretrained Transformer variants are currently the best performing models on this task, (ii) but to improve performance on multi-turn conversations with humans, future systems must go beyond single word metrics like perplexity to measure the performance across sequences of utterances (conversations) -- in terms of repetition, consistency and balance of dialogue acts (e.g. how many questions asked vs. answered).

Objective: Data unavailability has been one of the biggest barriers in clinical natural language processing. This paper is aimed at providing a large-scale and publicly available patient note dataset, named PMC-Patients, with relevant articles and similar patients annotations. The ultimate goal of PMC-Patients is to facilitate the development of retrieval-based clinical decision support systems. Materials and Methods: To collect PMC-Patients, we extract patient notes from case reports in PubMed Central by recognizing certain section patterns. Patient-article relevance and patient-patient similarity are annotated by citation relationships in PubMed. In addition, we perform three tasks with PMC-Patients to demonstrate its utility in providing clinical decision support for a given patient, including (1) classifying whether another patient is similar, (2) retrieving similar patients in PMC-Patients, and (3) retrieving relevant articles in PubMed. Results: We collect and release PMC-Patients under the CC BY-NC-SA license, which becomes the largest publicly available patient note dataset so far. PMC-Patients contains 167k patient notes that are annotated with 3.1M relevant articles and 293k similar patients. Qualitative and quantitative analyses reveal the high quality and richness of our dataset. Experiments show that classifying the similarity of patient pairs is relatively easy, but it is hard to retrieve similar patients or relevant articles for a given patient from a large set of candidates. Conclusion: We present PMC-Patients, a large-scale dataset of patient notes with high quality, easy access, diverse conditions, and rich annotations. The proposed dataset can also serve as a hard benchmark for evaluating retrieval-based clinical decision support systems.

Decision-makers are often experts of their domain and take actions based on their domain knowledge. Doctors, for instance, may prescribe treatments by predicting the likely outcome of each available treatment. Actions of an expert thus naturally encode part of their domain knowledge, and can help make inferences within the same domain: Knowing doctors try to prescribe the best treatment for their patients, we can tell treatments prescribed more frequently are likely to be more effective. Yet in machine learning, the fact that most decision-makers are experts is often overlooked, and "expertise" is seldom leveraged as an inductive bias. This is especially true for the literature on treatment effect estimation, where often the only assumption made about actions is that of overlap. In this paper, we argue that expertise - particularly the type of expertise the decision-makers of a domain are likely to have - can be informative in designing and selecting methods for treatment effect estimation. We formally define two types of expertise, predictive and prognostic, and demonstrate empirically that: (i) the prominent type of expertise in a domain significantly influences the performance of different methods in treatment effect estimation, and (ii) it is possible to predict the type of expertise present in a dataset, which can provide a quantitative basis for model selection.

Widely deployed large language models (LLMs) can produce convincing yet incorrect outputs, potentially misleading users who may rely on them as if they were correct. To reduce such overreliance, there have been calls for LLMs to communicate their uncertainty to end users. However, there has been little empirical work examining how users perceive and act upon LLMs' expressions of uncertainty. We explore this question through a large-scale, pre-registered, human-subject experiment (N=404) in which participants answer medical questions with or without access to responses from a fictional LLM-infused search engine. Using both behavioral and self-reported measures, we examine how different natural language expressions of uncertainty impact participants' reliance, trust, and overall task performance. We find that first-person expressions (e.g., "I'm not sure, but...") decrease participants' confidence in the system and tendency to agree with the system's answers, while increasing participants' accuracy. An exploratory analysis suggests that this increase can be attributed to reduced (but not fully eliminated) overreliance on incorrect answers. While we observe similar effects for uncertainty expressed from a general perspective (e.g., "It's not clear, but..."), these effects are weaker and not statistically significant. Our findings suggest that using natural language expressions of uncertainty may be an effective approach for reducing overreliance on LLMs, but that the precise language used matters. This highlights the importance of user testing before deploying LLMs at scale.

Over the past decade, machine learning has revolutionized computers' ability to analyze text through flexible computational models. Due to their structural similarity to written language, transformer-based architectures have also shown promise as tools to make sense of a range of multi-variate sequences from protein-structures, music, electronic health records to weather-forecasts. We can also represent human lives in a way that shares this structural similarity to language. From one perspective, lives are simply sequences of events: People are born, visit the pediatrician, start school, move to a new location, get married, and so on. Here, we exploit this similarity to adapt innovations from natural language processing to examine the evolution and predictability of human lives based on detailed event sequences. We do this by drawing on arguably the most comprehensive registry data in existence, available for an entire nation of more than six million individuals across decades. Our data include information about life-events related to health, education, occupation, income, address, and working hours, recorded with day-to-day resolution. We create embeddings of life-events in a single vector space showing that this embedding space is robust and highly structured. Our models allow us to predict diverse outcomes ranging from early mortality to personality nuances, outperforming state-of-the-art models by a wide margin. Using methods for interpreting deep learning models, we probe the algorithm to understand the factors that enable our predictions. Our framework allows researchers to identify new potential mechanisms that impact life outcomes and associated possibilities for personalized interventions.

Large language models (LLMs) have demonstrated impressive capabilities in natural language understanding and generation, but the quality bar for medical and clinical applications is high. Today, attempts to assess models' clinical knowledge typically rely on automated evaluations on limited benchmarks. There is no standard to evaluate model predictions and reasoning across a breadth of tasks. To address this, we present MultiMedQA, a benchmark combining six existing open question answering datasets spanning professional medical exams, research, and consumer queries; and HealthSearchQA, a new free-response dataset of medical questions searched online. We propose a framework for human evaluation of model answers along multiple axes including factuality, precision, possible harm, and bias. In addition, we evaluate PaLM (a 540-billion parameter LLM) and its instruction-tuned variant, Flan-PaLM, on MultiMedQA. Using a combination of prompting strategies, Flan-PaLM achieves state-of-the-art accuracy on every MultiMedQA multiple-choice dataset (MedQA, MedMCQA, PubMedQA, MMLU clinical topics), including 67.6% accuracy on MedQA (US Medical License Exam questions), surpassing prior state-of-the-art by over 17%. However, human evaluation reveals key gaps in Flan-PaLM responses. To resolve this we introduce instruction prompt tuning, a parameter-efficient approach for aligning LLMs to new domains using a few exemplars. The resulting model, Med-PaLM, performs encouragingly, but remains inferior to clinicians. We show that comprehension, recall of knowledge, and medical reasoning improve with model scale and instruction prompt tuning, suggesting the potential utility of LLMs in medicine. Our human evaluations reveal important limitations of today's models, reinforcing the importance of both evaluation frameworks and method development in creating safe, helpful LLM models for clinical applications.

Like other fields of Traditional Medicines, Unani Medicines have been found as an effective medical practice for ages. It is still widely used in the subcontinent, particularly in Pakistan and India. However, Unani Medicines Practitioners are lacking modern IT applications in their everyday clinical practices. An Online Clinical Decision Support System may address this challenge to assist apprentice Unani Medicines practitioners in their diagnostic processes. The proposed system provides a web-based interface to enter the patient's symptoms, which are then automatically analyzed by our system to generate a list of probable diseases. The system allows practitioners to choose the most likely disease and inform patients about the associated treatment options remotely. The system consists of three modules: an Online Clinical Decision Support System, an Artificial Intelligence Inference Engine, and a comprehensive Unani Medicines Database. The system employs advanced AI techniques such as Decision Trees, Deep Learning, and Natural Language Processing. For system development, the project team used a technology stack that includes React, FastAPI, and MySQL. Data and functionality of the application is exposed using APIs for integration and extension with similar domain applications. The novelty of the project is that it addresses the challenge of diagnosing diseases accurately and efficiently in the context of Unani Medicines principles. By leveraging the power of technology, the proposed Clinical Decision Support System has the potential to ease access to healthcare services and information, reduce cost, boost practitioner and patient satisfaction, improve speed and accuracy of the diagnostic process, and provide effective treatments remotely. The application will be useful for Unani Medicines Practitioners, Patients, Government Drug Regulators, Software Developers, and Medical Researchers.

Motivation: The development of novel compounds targeting proteins of interest is one of the most important tasks in the pharmaceutical industry. Deep generative models have been applied to targeted molecular design and have shown promising results. Recently, target-specific molecule generation has been viewed as a translation between the protein language and the chemical language. However, such a model is limited by the availability of interacting protein-ligand pairs. On the other hand, large amounts of unlabeled protein sequences and chemical compounds are available and have been used to train language models that learn useful representations. In this study, we propose exploiting pretrained biochemical language models to initialize (i.e. warm start) targeted molecule generation models. We investigate two warm start strategies: (i) a one-stage strategy where the initialized model is trained on targeted molecule generation (ii) a two-stage strategy containing a pre-finetuning on molecular generation followed by target specific training. We also compare two decoding strategies to generate compounds: beam search and sampling. Results: The results show that the warm-started models perform better than a baseline model trained from scratch. The two proposed warm-start strategies achieve similar results to each other with respect to widely used metrics from benchmarks. However, docking evaluation of the generated compounds for a number of novel proteins suggests that the one-stage strategy generalizes better than the two-stage strategy. Additionally, we observe that beam search outperforms sampling in both docking evaluation and benchmark metrics for assessing compound quality. Availability and implementation: The source code is available at https://github.com/boun-tabi/biochemical-lms-for-drug-design and the materials are archived in Zenodo at https://doi.org/10.5281/zenodo.6832145

Engaging the public with science is critical for a well-informed population. A popular method of scientific communication is documentaries. Once released, it can be difficult to assess the impact of such works on a large scale, due to the overhead required for in-depth audience feedback studies. In what follows, we overview our complementary approach to qualitative studies through quantitative impact and sentiment analysis of Amazon reviews for several scientific documentaries. In addition to developing a novel impact category taxonomy for this analysis, we release a dataset containing 1296 human-annotated sentences from 1043 Amazon reviews for six movies created in whole or part by a team of visualization designers who focus on cinematic presentations of scientific data. Using this data, we train and evaluate several machine learning and large language models, discussing their effectiveness and possible generalizability for documentaries beyond those focused on for this work. Themes are also extracted from our annotated dataset which, along with our large language model analysis, demonstrate a measure of the ability of scientific documentaries to engage with the public.

We introduce KorMedMCQA, the first Korean multiple-choice question answering (MCQA) benchmark derived from Korean healthcare professional licensing examinations, covering from the year 2012 to year 2023. This dataset consists of a selection of questions from the license examinations for doctors, nurses, and pharmacists, featuring a diverse array of subjects. We conduct baseline experiments on various large language models, including proprietary/open-source, multilingual/Korean-additional pretrained, and clinical context pretrained models, highlighting the potential for further enhancements. We make our data publicly available on HuggingFace and provide a evaluation script via LM-Harness, inviting further exploration and advancement in Korean healthcare environments.

Tacrolimus is one of the cornerstone immunosuppressive drugs in most transplantation centers worldwide following solid organ transplantation. Therapeutic drug monitoring of tacrolimus is necessary in order to avoid rejection of the transplanted organ or severe side effects. However, finding the right dose for a given patient is challenging, even for experienced clinicians. Consequently, a tool that can accurately estimate the drug exposure for individual dose adaptions would be of high clinical value. In this work, we propose a new technique using machine learning to estimate the tacrolimus exposure in kidney transplant recipients. Our models achieve predictive errors that are at the same level as an established population pharmacokinetic model, but are faster to develop and require less knowledge about the pharmacokinetic properties of the drug.

The drug development pipeline for a new compound can last 10-20 years and cost over 10 billion. Drug repurposing offers a more time- and cost-effective alternative. Computational approaches based on biomedical knowledge graph representations have recently yielded new drug repurposing hypotheses. In this study, we present a novel, disease-specific hypergraph representation learning technique to derive contextual embeddings of biological pathways of various lengths but that all start at any given drug and all end at the disease of interest. Further, we extend this method to multi-disease hypergraphs. To determine the repurposing potential of each of the 1,522 drugs, we derive drug-specific distributions of cosine similarity values and ultimately consider the median for ranking. Cosine similarity values are computed between (1) all biological pathways starting at the considered drug and ending at the disease of interest and (2) all biological pathways starting at drugs currently prescribed against that disease and ending at the disease of interest. We illustrate our approach with Alzheimer's disease (AD) and two of its risk factors: hypertension (HTN) and type 2 diabetes (T2D). We compare each drug's rank across four hypergraph settings (single- or multi-disease): AD only, AD + HTN, AD + T2D, and AD + HTN + T2D. Notably, our framework led to the identification of two promising drugs whose repurposing potential was significantly higher in hypergraphs combining two diseases: dapagliflozin (antidiabetic; moved up, from top 32% to top 7%, across all considered drugs) and debrisoquine (antihypertensive; moved up, from top 76% to top 23%). Our approach serves as a hypothesis generation tool, to be paired with a validation pipeline relying on laboratory experiments and semi-automated parsing of the biomedical literature.

A key trait of daily conversations between individuals is the ability to express empathy towards others, and exploring ways to implement empathy is a crucial step towards human-like dialogue systems. Previous approaches on this topic mainly focus on detecting and utilizing the user's emotion for generating empathetic responses. However, since empathy includes both aspects of affection and cognition, we argue that in addition to identifying the user's emotion, cognitive understanding of the user's situation should also be considered. To this end, we propose a novel approach for empathetic response generation, which leverages commonsense to draw more information about the user's situation and uses this additional information to further enhance the empathy expression in generated responses. We evaluate our approach on EmpatheticDialogues, which is a widely-used benchmark dataset for empathetic response generation. Empirical results demonstrate that our approach outperforms the baseline models in both automatic and human evaluations and can generate more informative and empathetic responses.

Researchers and developers increasingly rely on toxicity scoring to moderate generative language model outputs, in settings such as customer service, information retrieval, and content generation. However, toxicity scoring may render pertinent information inaccessible, rigidify or "value-lock" cultural norms, and prevent language reclamation processes, particularly for marginalized people. In this work, we extend the concept of algorithmic recourse to generative language models: we provide users a novel mechanism to achieve their desired prediction by dynamically setting thresholds for toxicity filtering. Users thereby exercise increased agency relative to interactions with the baseline system. A pilot study (n = 30) supports the potential of our proposed recourse mechanism, indicating improvements in usability compared to fixed-threshold toxicity-filtering of model outputs. Future work should explore the intersection of toxicity scoring, model controllability, user agency, and language reclamation processes -- particularly with regard to the bias that many communities encounter when interacting with generative language models.

Virtual counselors powered by large language models (LLMs) aim to create interactive support systems that effectively assist clients struggling with mental health challenges. To replicate counselor-client conversations, researchers have built an online mental health platform that allows professional counselors to provide clients with text-based counseling services for about an hour per session. Notwithstanding its effectiveness, challenges exist as human annotation is time-consuming, cost-intensive, privacy-protected, and not scalable. To address this issue and investigate the applicability of LLMs in psychological counseling conversation simulation, we propose a framework that employs two LLMs via role-playing for simulating counselor-client interactions. Our framework involves two LLMs, one acting as a client equipped with a specific and real-life user profile and the other playing the role of an experienced counselor, generating professional responses using integrative therapy techniques. We implement both the counselor and the client by zero-shot prompting the GPT-4 model. In order to assess the effectiveness of LLMs in simulating counselor-client interactions and understand the disparities between LLM- and human-generated conversations, we evaluate the synthetic data from various perspectives. We begin by assessing the client's performance through automatic evaluations. Next, we analyze and compare the disparities between dialogues generated by the LLM and those generated by professional counselors. Furthermore, we conduct extensive experiments to thoroughly examine the performance of our LLM-based counselor trained with synthetic interactive dialogues by benchmarking against state-of-the-art models for mental health.

Mobile mental health applications are seen as a promising way to fulfill the growing need for mental health care. Although there are more than ten thousand mental health apps available on app marketplaces, such as Google Play and Apple App Store, many of them are not evidence-based, or have been minimally evaluated or regulated. The real-life experience and concerns of the app users are largely unknown. To address this knowledge gap, we analyzed 2159 user reviews from 117 Android apps and 2764 user reviews from 76 iOS apps. Our findings include the critiques around inconsistent moderation standards and lack of transparency. App-embedded social features and chatbots were criticized for providing little support during crises. We provide research and design implications for future mental health app developers, discuss the necessity of developing a comprehensive and centralized app development guideline, and the opportunities of incorporating existing AI technology in mental health chatbots.

We take a snapshot of current resources available for teaching and learning AI with a focus on the Galleries, Libraries, Archives and Museums (GLAM) community. The review was carried out in 2021 and 2022. The review provides an overview of material we identified as being relevant, offers a description of this material and makes recommendations for future work in this area.

A reply to Drake (2013) "Early warning signals of stochastic switching" http://dx.doi.org/10.1098/rspb.2013.0686

Explaining Artificial Intelligence (AI) decisions is a major challenge nowadays in AI, in particular when applied to sensitive scenarios like medicine and law. However, the need to explain the rationale behind decisions is a main issue also for human-based deliberation as it is important to justify why a certain decision has been taken. Resident medical doctors for instance are required not only to provide a (possibly correct) diagnosis, but also to explain how they reached a certain conclusion. Developing new tools to aid residents to train their explanation skills is therefore a central objective of AI in education. In this paper, we follow this direction, and we present, to the best of our knowledge, the first multilingual dataset for Medical Question Answering where correct and incorrect diagnoses for a clinical case are enriched with a natural language explanation written by doctors. These explanations have been manually annotated with argument components (i.e., premise, claim) and argument relations (i.e., attack, support), resulting in the Multilingual CasiMedicos-Arg dataset which consists of 558 clinical cases in four languages (English, Spanish, French, Italian) with explanations, where we annotated 5021 claims, 2313 premises, 2431 support relations, and 1106 attack relations. We conclude by showing how competitive baselines perform over this challenging dataset for the argument mining task.

A ChatGPT-like system for drug compounds could be a game-changer in pharmaceutical research, accelerating drug discovery, enhancing our understanding of structure-activity relationships, guiding lead optimization, aiding drug repurposing, reducing the failure rate, and streamlining clinical trials. In this work, we make an initial attempt towards enabling ChatGPT-like capabilities on drug molecule graphs, by developing a prototype system DrugChat. DrugChat works in a similar way as ChatGPT. Users upload a compound molecule graph and ask various questions about this compound. DrugChat will answer these questions in a multi-turn, interactive manner. The DrugChat system consists of a graph neural network (GNN), a large language model (LLM), and an adaptor. The GNN takes a compound molecule graph as input and learns a representation for this graph. The adaptor transforms the graph representation produced by the GNN into another representation that is acceptable to the LLM. The LLM takes the compound representation transformed by the adaptor and users' questions about this compound as inputs and generates answers. All these components are trained end-to-end. To train DrugChat, we collected instruction tuning datasets which contain 10,834 drug compounds and 143,517 question-answer pairs. The code and data is available at https://github.com/UCSD-AI4H/drugchat

Intelligent Tutoring Systems (ITS) enhance personalized learning by predicting student answers to provide immediate and customized instruction. However, recent research has primarily focused on the correctness of the answer rather than the student's performance on specific answer choices, limiting insights into students' thought processes and potential misconceptions. To address this gap, we present MCQStudentBert, an answer forecasting model that leverages the capabilities of Large Language Models (LLMs) to integrate contextual understanding of students' answering history along with the text of the questions and answers. By predicting the specific answer choices students are likely to make, practitioners can easily extend the model to new answer choices or remove answer choices for the same multiple-choice question (MCQ) without retraining the model. In particular, we compare MLP, LSTM, BERT, and Mistral 7B architectures to generate embeddings from students' past interactions, which are then incorporated into a finetuned BERT's answer-forecasting mechanism. We apply our pipeline to a dataset of language learning MCQ, gathered from an ITS with over 10,000 students to explore the predictive accuracy of MCQStudentBert, which incorporates student interaction patterns, in comparison to correct answer prediction and traditional mastery-learning feature-based approaches. This work opens the door to more personalized content, modularization, and granular support.