Daily Papers

Social media platforms are vital resources for sharing self-reported health experiences, offering rich data on various health topics. Despite advancements in Natural Language Processing (NLP) enabling large-scale social media data analysis, a gap remains in applying keyphrase extraction to health-related content. Keyphrase extraction is used to identify salient concepts in social media discourse without being constrained by predefined entity classes. This paper introduces a theme-driven keyphrase extraction framework tailored for social media, a pioneering approach designed to capture clinically relevant keyphrases from user-generated health texts. Themes are defined as broad categories determined by the objectives of the extraction task. We formulate this novel task of theme-driven keyphrase extraction and demonstrate its potential for efficiently mining social media text for the use case of treatment for opioid use disorder. This paper leverages qualitative and quantitative analysis to demonstrate the feasibility of extracting actionable insights from social media data and efficiently extracting keyphrases using minimally supervised NLP models. Our contributions include the development of a novel data collection and curation framework for theme-driven keyphrase extraction and the creation of MOUD-Keyphrase, the first dataset of its kind comprising human-annotated keyphrases from a Reddit community. We also identify the scope of minimally supervised NLP models to extract keyphrases from social media data efficiently. Lastly, we found that a large language model (ChatGPT) outperforms unsupervised keyphrase extraction models, and we evaluate its efficacy 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

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

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

Since the COVID-19 pandemic, clinicians have seen a large and sustained influx in patient portal messages, significantly contributing to clinician burnout. To the best of our knowledge, there are no large-scale public patient portal messages corpora researchers can use to build tools to optimize clinician portal workflows. Informed by our ongoing work with a regional hospital, this study introduces an LLM-powered framework for configurable and realistic patient portal message generation. Our approach leverages few-shot grounded text generation, requiring only a small number of de-identified patient portal messages to help LLMs better match the true style and tone of real data. Clinical experts in our team deem this framework as HIPAA-friendly, unlike existing privacy-preserving approaches to synthetic text generation which cannot guarantee all sensitive attributes will be protected. Through extensive quantitative and human evaluation, we show that our framework produces data of higher quality than comparable generation methods as well as all related datasets. We believe this work provides a path forward for (i) the release of large-scale synthetic patient message datasets that are stylistically similar to ground-truth samples and (ii) HIPAA-friendly data generation which requires minimal human de-identification efforts.

Large Language Models (LLMs), with their flexible generation abilities, can be powerful data sources in domains with few or no available corpora. However, problems like hallucinations and biases limit such applications. In this case study, we pick nutrition counselling, a domain lacking any public resource, and show that high-quality datasets can be gathered by combining LLMs, crowd-workers and nutrition experts. We first crowd-source and cluster a novel dataset of diet-related issues, then work with experts to prompt ChatGPT into producing related supportive text. Finally, we let the experts evaluate the safety of the generated text. We release HAI-coaching, the first expert-annotated nutrition counselling dataset containing ~2.4K dietary struggles from crowd workers, and ~97K related supportive texts generated by ChatGPT. Extensive analysis shows that ChatGPT while producing highly fluent and human-like text, also manifests harmful behaviours, especially in sensitive topics like mental health, making it unsuitable for unsupervised use.

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

Generating synthetic text addresses the challenge of data availability in privacy-sensitive domains such as healthcare. This study explores the applicability of synthetic data in real-world medical settings. We introduce MedSyn, a novel medical text generation framework that integrates large language models with a Medical Knowledge Graph (MKG). We use MKG to sample prior medical information for the prompt and generate synthetic clinical notes with GPT-4 and fine-tuned LLaMA models. We assess the benefit of synthetic data through application in the ICD code prediction task. Our research indicates that synthetic data can increase the classification accuracy of vital and challenging codes by up to 17.8% compared to settings without synthetic data. Furthermore, to provide new data for further research in the healthcare domain, we present the largest open-source synthetic dataset of clinical notes for the Russian language, comprising over 41k samples covering 219 ICD-10 codes.

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

Mental health is a significant and growing public health concern. As language usage can be leveraged to obtain crucial insights into mental health conditions, there is a need for large-scale, labeled, mental health-related datasets of users who have been diagnosed with one or more of such conditions. In this paper, we investigate the creation of high-precision patterns to identify self-reported diagnoses of nine different mental health conditions, and obtain high-quality labeled data without the need for manual labelling. We introduce the SMHD (Self-reported Mental Health Diagnoses) dataset and make it available. SMHD is a novel large dataset of social media posts from users with one or multiple mental health conditions along with matched control users. We examine distinctions in users' language, as measured by linguistic and psychological variables. We further explore text classification methods to identify individuals with mental conditions through their language.

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

Millions of users share their experiences on social media sites, such as Twitter, which in turn generate valuable data for public health monitoring, digital epidemiology, and other analyses of population health at global scale. The first, critical, task for these applications is classifying whether a personal health event was mentioned, which we call the (PHM) problem. This task is challenging for many reasons, including typically short length of social media posts, inventive spelling and lexicons, and figurative language, including hyperbole using diseases like "heart attack" or "cancer" for emphasis, and not as a health self-report. This problem is even more challenging for rarely reported, or frequent but ambiguously expressed conditions, such as "stroke". To address this problem, we propose a general, robust method for detecting PHMs in social media, which we call WESPAD, that combines lexical, syntactic, word embedding-based, and context-based features. WESPAD is able to generalize from few examples by automatically distorting the word embedding space to most effectively detect the true health mentions. Unlike previously proposed state-of-the-art supervised and deep-learning techniques, WESPAD requires relatively little training data, which makes it possible to adapt, with minimal effort, to each new disease and condition. We evaluate WESPAD on both an established publicly available Flu detection benchmark, and on a new dataset that we have constructed with mentions of multiple health conditions. Our experiments show that WESPAD outperforms the baselines and state-of-the-art methods, especially in cases when the number and proportion of true health mentions in the training data is small.

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.

Clinical notes in Electronic Health Records (EHR) present rich documented information of patients to inference phenotype for disease diagnosis and study patient characteristics for cohort selection. Unsupervised user embedding aims to encode patients into fixed-length vectors without human supervisions. Medical concepts extracted from the clinical notes contain rich connections between patients and their clinical categories. However, existing unsupervised approaches of user embeddings from clinical notes do not explicitly incorporate medical concepts. In this study, we propose a concept-aware unsupervised user embedding that jointly leverages text documents and medical concepts from two clinical corpora, MIMIC-III and Diabetes. We evaluate user embeddings on both extrinsic and intrinsic tasks, including phenotype classification, in-hospital mortality prediction, patient retrieval, and patient relatedness. Experiments on the two clinical corpora show our approach exceeds unsupervised baselines, and incorporating medical concepts can significantly improve the baseline performance.

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

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.

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

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.

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

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

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

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

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

The limited availability of psychologists necessitates efficient identification of individuals requiring urgent mental healthcare. This study explores the use of Natural Language Processing (NLP) pipelines to analyze text data from online mental health forums used for consultations. By analyzing forum posts, these pipelines can flag users who may require immediate professional attention. A crucial challenge in this domain is data privacy and scarcity. To address this, we propose utilizing readily available curricular texts used in institutes specializing in mental health for pre-training the NLP pipelines. This helps us mimic the training process of a psychologist. Our work presents CASE-BERT that flags potential mental health disorders based on forum text. CASE-BERT demonstrates superior performance compared to existing methods, achieving an f1 score of 0.91 for Depression and 0.88 for Anxiety, two of the most commonly reported mental health disorders. Our code is publicly available.

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.

Social and behavioral determinants of health (SDOH) play a significant role in shaping health outcomes, and extracting these determinants from clinical notes is a first step to help healthcare providers systematically identify opportunities to provide appropriate care and address disparities. Progress on using NLP methods for this task has been hindered by the lack of high-quality publicly available labeled data, largely due to the privacy and regulatory constraints on the use of real patients' information. This paper introduces a new dataset, SDOH-NLI, that is based on publicly available notes and which we release publicly. We formulate SDOH extraction as a natural language inference (NLI) task, and provide binary textual entailment labels obtained from human raters for a cross product of a set of social history snippets as premises and SDOH factors as hypotheses. Our dataset differs from standard NLI benchmarks in that our premises and hypotheses are obtained independently. We evaluate both "off-the-shelf" entailment models as well as models fine-tuned on our data, and highlight the ways in which our dataset appears more challenging than commonly used NLI datasets.

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.

Previous studies reveal that Electronic Health Records (EHR), which have been widely adopted in the U.S. to allow patients to access their personal medical information, do not have high readability to patients due to the prevalence of medical jargon. Tailoring medical notes to individual comprehension by identifying jargon that is difficult for each person will enhance the utility of generative models. We present the first quantitative analysis to measure the impact of role-playing in LLM in medical term extraction. By comparing the results of Mechanical Turk workers over 20 sentences, our study demonstrates that LLM role-playing improves F1 scores in 95% of cases across 14 different socio-demographic backgrounds. Furthermore, applying role-playing with in-context learning outperformed the previous state-of-the-art models. Our research showed that ChatGPT can improve traditional medical term extraction systems by utilizing role-play to deliver personalized patient education, a potential that previous models had not achieved.

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

In this report, we introduce SciFive, a domain-specific T5 model that has been pre-trained on large biomedical corpora. Our model outperforms the current SOTA methods (i.e. BERT, BioBERT, Base T5) on tasks in named entity relation, relation extraction, natural language inference, and question-answering. We show that text-generation methods have significant potential in a broad array of biomedical NLP tasks, particularly those requiring longer, more complex outputs. Our results support the exploration of more difficult text generation tasks and the development of new methods in this area

In the era of modern healthcare, swiftly generating medical question summaries is crucial for informed and timely patient care. Despite the increasing complexity and volume of medical data, existing studies have focused solely on text-based summarization, neglecting the integration of visual information. Recognizing the untapped potential of combining textual queries with visual representations of medical conditions, we introduce the Multimodal Medical Question Summarization (MMQS) Dataset. This dataset, a major contribution to our work, pairs medical queries with visual aids, facilitating a richer and more nuanced understanding of patient needs. We also propose a framework, utilizing the power of Contrastive Language Image Pretraining(CLIP) and Large Language Models(LLMs), consisting of four modules that identify medical disorders, generate relevant context, filter medical concepts, and craft visually aware summaries. Our comprehensive framework harnesses the power of CLIP, a multimodal foundation model, and various general-purpose LLMs, comprising four main modules: the medical disorder identification module, the relevant context generation module, the context filtration module for distilling relevant medical concepts and knowledge, and finally, a general-purpose LLM to generate visually aware medical question summaries. Leveraging our MMQS dataset, we showcase how visual cues from images enhance the generation of medically nuanced summaries. This multimodal approach not only enhances the decision-making process in healthcare but also fosters a more nuanced understanding of patient queries, laying the groundwork for future research in personalized and responsive medical care

Text generation has become more accessible than ever, and the increasing interest in these systems, especially those using large language models, has spurred an increasing number of related publications. We provide a systematic literature review comprising 244 selected papers between 2017 and 2024. This review categorizes works in text generation into five main tasks: open-ended text generation, summarization, translation, paraphrasing, and question answering. For each task, we review their relevant characteristics, sub-tasks, and specific challenges (e.g., missing datasets for multi-document summarization, coherence in story generation, and complex reasoning for question answering). Additionally, we assess current approaches for evaluating text generation systems and ascertain problems with current metrics. Our investigation shows nine prominent challenges common to all tasks and sub-tasks in recent text generation publications: bias, reasoning, hallucinations, misuse, privacy, interpretability, transparency, datasets, and computing. We provide a detailed analysis of these challenges, their potential solutions, and which gaps still require further engagement from the community. This systematic literature review targets two main audiences: early career researchers in natural language processing looking for an overview of the field and promising research directions, as well as experienced researchers seeking a detailed view of tasks, evaluation methodologies, open challenges, and recent mitigation strategies.

With increasing usage of generative models for text generation and widespread use of machine generated texts in various domains, being able to distinguish between human written and machine generated texts is a significant challenge. While existing models and proprietary systems focus on identifying whether given text is entirely human written or entirely machine generated, only a few systems provide insights at sentence or paragraph level at likelihood of being machine generated at a non reliable accuracy level, working well only for a set of domains and generators. This paper introduces few reliable approaches for the novel task of identifying which part of a given text is machine generated at a word level while comparing results from different approaches and methods. We present a comparison with proprietary systems , performance of our model on unseen domains' and generators' texts. The findings reveal significant improvements in detection accuracy along with comparison on other aspects of detection capabilities. Finally we discuss potential avenues for improvement and implications of our work. The proposed model is also well suited for detecting which parts of a text are machine generated in outputs of Instruct variants of many LLMs.

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

Users of social platforms often perceive these sites as supportive spaces to post about their mental health issues. Those conversations contain important traces about individuals' health risks. Recently, researchers have exploited this online information to construct mental health detection models, which aim to identify users at risk on platforms like Twitter, Reddit or Facebook. Most of these models are centred on achieving good classification results, ignoring the explainability and interpretability of the decisions. Recent research has pointed out the importance of using clinical markers, such as the use of symptoms, to improve trust in the computational models by health professionals. In this paper, we propose using transformer-based architectures to detect and explain the appearance of depressive symptom markers in the users' writings. We present two approaches: i) train a model to classify, and another one to explain the classifier's decision separately and ii) unify the two tasks simultaneously using a single model. Additionally, for this latter manner, we also investigated the performance of recent conversational LLMs when using in-context learning. Our natural language explanations enable clinicians to interpret the models' decisions based on validated symptoms, enhancing trust in the automated process. We evaluate our approach using recent symptom-based datasets, employing both offline and expert-in-the-loop metrics to assess the quality of the explanations generated by our models. The experimental results show that it is possible to achieve good classification results while generating interpretable symptom-based explanations.

With the rapid development of large language models (LLMs), assessing their performance on health-related inquiries has become increasingly essential. It is critical that these models provide accurate and trustworthy health information, as their application in real-world contexts--where misinformation can have serious consequences for individuals seeking medical advice and support--depends on their reliability. In this work, we present CHBench, the first comprehensive Chinese Health-related Benchmark designed to evaluate LLMs' capabilities in understanding physical and mental health across diverse scenarios. CHBench includes 6,493 entries related to mental health and 2,999 entries focused on physical health, covering a broad spectrum of topics. This dataset serves as a foundation for evaluating Chinese LLMs' capacity to comprehend and generate accurate health-related information. Our extensive evaluations of four popular Chinese LLMs demonstrate that there remains considerable room for improvement in their understanding of health-related information. The code is available at https://github.com/TracyGuo2001/CHBench.

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

Knowledge of the medical decision process, which can be modeled as medical decision trees (MDTs), is critical to build clinical decision support systems. However, the current MDT construction methods rely heavily on time-consuming and laborious manual annotation. In this work, we propose a novel task, Text2MDT, to explore the automatic extraction of MDTs from medical texts such as medical guidelines and textbooks. We normalize the form of the MDT and create an annotated Text-to-MDT dataset in Chinese with the participation of medical experts. We investigate two different methods for the Text2MDT tasks: (a) an end-to-end framework which only relies on a GPT style large language models (LLM) instruction tuning to generate all the node information and tree structures. (b) The pipeline framework which decomposes the Text2MDT task to three subtasks. Experiments on our Text2MDT dataset demonstrate that: (a) the end-to-end method basd on LLMs (7B parameters or larger) show promising results, and successfully outperform the pipeline methods. (b) The chain-of-thought (COT) prompting method Wei2022ChainOT can improve the performance of the fine-tuned LLMs on the Text2MDT test set. (c) the lightweight pipelined method based on encoder-based pretrained models can perform comparably with LLMs with model complexity two magnititudes smaller. Our Text2MDT dataset is open-sourced at https://tianchi.aliyun.com/dataset/95414, and the source codes are open-sourced at https://github.com/michael-wzhu/text2dt.

Automatic medical text simplification can assist providers with patient-friendly communication and make medical texts more accessible, thereby improving health literacy. But curating a quality corpus for this task requires the supervision of medical experts. In this work, we present Med-EASi (textbf{Med}ical dataset for textbf{E}laborative and textbf{A}bstractive textbf{Si}mplification), a uniquely crowdsourced and finely annotated dataset for supervised simplification of short medical texts. Its expert-layman-AI collaborative annotations facilitate controllability over text simplification by marking four kinds of textual transformations: elaboration, replacement, deletion, and insertion. To learn medical text simplification, we fine-tune T5-large with four different styles of input-output combinations, leading to two control-free and two controllable versions of the model. We add two types of controllability into text simplification, by using a multi-angle training approach: position-aware, which uses in-place annotated inputs and outputs, and position-agnostic, where the model only knows the contents to be edited, but not their positions. Our results show that our fine-grained annotations improve learning compared to the unannotated baseline. Furthermore, position-aware control generates better simplification than the position-agnostic one. The data and code are available at https://github.com/Chandrayee/CTRL-SIMP.

Medical research generates a large number of publications with the PubMed database already containing >35 million research articles. Integration of the knowledge scattered across this large body of literature could provide key insights into physiological mechanisms and disease processes leading to novel medical interventions. However, it is a great challenge for researchers to utilize this information in full since the scale and complexity of the data greatly surpasses human processing abilities. This becomes especially problematic in cases of extreme urgency like the COVID-19 pandemic. Automated text mining can help extract and connect information from the large body of medical research articles. The first step in text mining is typically the identification of specific classes of keywords (e.g., all protein or disease names), so called Named Entity Recognition (NER). Here we present an end-to-end pipeline for NER of typical entities found in medical research articles, including diseases, cells, chemicals, genes/proteins, and species. The pipeline can access and process large medical research article collections (PubMed, CORD-19) or raw text and incorporates a series of deep learning models fine-tuned on the HUNER corpora collection. In addition, the pipeline can perform dictionary-based NER related to COVID-19 and other medical topics. Users can also load their own NER models and dictionaries to include additional entities. The output consists of publication-ready ranked lists and graphs of detected entities and files containing the annotated texts. An associated script allows rapid inspection of the results for specific entities of interest. As model use cases, the pipeline was deployed on two collections of autophagy-related abstracts from PubMed and on the CORD19 dataset, a collection of 764 398 research article abstracts related to COVID-19.

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.

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

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/

Background: Recent advancements in large language models (LLMs) offer potential benefits in healthcare, particularly in processing extensive patient records. However, existing benchmarks do not fully assess LLMs' capability in handling real-world, lengthy clinical data. Methods: We present the LongHealth benchmark, comprising 20 detailed fictional patient cases across various diseases, with each case containing 5,090 to 6,754 words. The benchmark challenges LLMs with 400 multiple-choice questions in three categories: information extraction, negation, and sorting, challenging LLMs to extract and interpret information from large clinical documents. Results: We evaluated nine open-source LLMs with a minimum of 16,000 tokens and also included OpenAI's proprietary and cost-efficient GPT-3.5 Turbo for comparison. The highest accuracy was observed for Mixtral-8x7B-Instruct-v0.1, particularly in tasks focused on information retrieval from single and multiple patient documents. However, all models struggled significantly in tasks requiring the identification of missing information, highlighting a critical area for improvement in clinical data interpretation. Conclusion: While LLMs show considerable potential for processing long clinical documents, their current accuracy levels are insufficient for reliable clinical use, especially in scenarios requiring the identification of missing information. The LongHealth benchmark provides a more realistic assessment of LLMs in a healthcare setting and highlights the need for further model refinement for safe and effective clinical application. We make the benchmark and evaluation code publicly available.

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

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.

Recent large language models (LLMs) offer the potential to support public health monitoring by facilitating health disclosure through open-ended conversations but rarely preserve the knowledge gained about individuals across repeated interactions. Augmenting LLMs with long-term memory (LTM) presents an opportunity to improve engagement and self-disclosure, but we lack an understanding of how LTM impacts people's interaction with LLM-driven chatbots in public health interventions. We examine the case of CareCall -- an LLM-driven voice chatbot with LTM -- through the analysis of 1,252 call logs and interviews with nine users. We found that LTM enhanced health disclosure and fostered positive perceptions of the chatbot by offering familiarity. However, we also observed challenges in promoting self-disclosure through LTM, particularly around addressing chronic health conditions and privacy concerns. We discuss considerations for LTM integration in LLM-driven chatbots for public health monitoring, including carefully deciding what topics need to be remembered in light of public health goals.

With the introduction of ChatGPT, Large Language Models (LLMs) have received enormous attention in healthcare. Despite their potential benefits, researchers have underscored various ethical implications. While individual instances have drawn much attention, the debate lacks a systematic overview of practical applications currently researched and ethical issues connected to them. Against this background, this work aims to map the ethical landscape surrounding the current stage of deployment of LLMs in medicine and healthcare. Electronic databases and preprint servers were queried using a comprehensive search strategy. Studies were screened and extracted following a modified rapid review approach. Methodological quality was assessed using a hybrid approach. For 53 records, a meta-aggregative synthesis was performed. Four fields of applications emerged and testify to a vivid exploration phase. Advantages of using LLMs are attributed to their capacity in data analysis, personalized information provisioning, support in decision-making, mitigating information loss and enhancing information accessibility. However, we also identifies recurrent ethical concerns connected to fairness, bias, non-maleficence, transparency, and privacy. A distinctive concern is the tendency to produce harmful misinformation or convincingly but inaccurate content. A recurrent plea for ethical guidance and human oversight is evident. Given the variety of use cases, it is suggested that the ethical guidance debate be reframed to focus on defining what constitutes acceptable human oversight across the spectrum of applications. This involves considering diverse settings, varying potentials for harm, and different acceptable thresholds for performance and certainty in healthcare. In addition, a critical inquiry is necessary to determine the extent to which the current experimental use of LLMs is necessary and justified.

Objective: The reading level of health educational materials significantly influences the understandability and accessibility of the information, particularly for minoritized populations. Many patient educational resources surpass the reading level and complexity of widely accepted standards. There is a critical need for high-performing text simplification models in health information to enhance dissemination and literacy. This need is particularly acute in cancer education, where effective prevention and screening education can substantially reduce morbidity and mortality. Methods: We introduce Simplified Digestive Cancer (SimpleDC), a parallel corpus of cancer education materials tailored for health text simplification research, comprising educational content from the American Cancer Society, Centers for Disease Control and Prevention, and National Cancer Institute. Utilizing SimpleDC alongside the existing Med-EASi corpus, we explore Large Language Model (LLM)-based simplification methods, including fine-tuning, reinforcement learning (RL), reinforcement learning with human feedback (RLHF), domain adaptation, and prompt-based approaches. Our experimentation encompasses Llama 2 and GPT-4. A novel RLHF reward function is introduced, featuring a lightweight model adept at distinguishing between original and simplified texts, thereby enhancing the model's effectiveness with unlabeled data. Results: Fine-tuned Llama 2 models demonstrated high performance across various metrics. Our innovative RLHF reward function surpassed existing RL text simplification reward functions in effectiveness. The results underscore that RL/RLHF can augment fine-tuning, facilitating model training on unlabeled text and improving performance.

In this work, we introduce Multiple Embedding Model for EHR (MEME), an approach that views Electronic Health Records (EHR) as multimodal data. This approach incorporates "pseudo-notes", textual representations of tabular EHR concepts such as diagnoses and medications, and allows us to effectively employ Large Language Models (LLMs) for EHR representation. This framework also adopts a multimodal approach, embedding each EHR modality separately. We demonstrate the effectiveness of MEME by applying it to several tasks within the Emergency Department across multiple hospital systems. Our findings show that MEME surpasses the performance of both single modality embedding methods and traditional machine learning approaches. However, we also observe notable limitations in generalizability across hospital institutions for all tested models.

There is enormous enthusiasm and concerns in using large language models (LLMs) in healthcare, yet current assumptions are all based on general-purpose LLMs such as ChatGPT. This study develops a clinical generative LLM, GatorTronGPT, using 277 billion words of mixed clinical and English text with a GPT-3 architecture of 20 billion parameters. GatorTronGPT improves biomedical natural language processing for medical research. Synthetic NLP models trained using GatorTronGPT generated text outperform NLP models trained using real-world clinical text. Physicians Turing test using 1 (worst) to 9 (best) scale shows that there is no significant difference in linguistic readability (p = 0.22; 6.57 of GatorTronGPT compared with 6.93 of human) and clinical relevance (p = 0.91; 7.0 of GatorTronGPT compared with 6.97 of human) and that physicians cannot differentiate them (p < 0.001). This study provides insights on the opportunities and challenges of LLMs for medical research and healthcare.

We present a new text-to-SQL dataset for electronic health records (EHRs). The utterances were collected from 222 hospital staff members, including physicians, nurses, and insurance review and health records teams. To construct the QA dataset on structured EHR data, we conducted a poll at a university hospital and used the responses to create seed questions. We then manually linked these questions to two open-source EHR databases, MIMIC-III and eICU, and included various time expressions and held-out unanswerable questions in the dataset, which were also collected from the poll. Our dataset poses a unique set of challenges: the model needs to 1) generate SQL queries that reflect a wide range of needs in the hospital, including simple retrieval and complex operations such as calculating survival rate, 2) understand various time expressions to answer time-sensitive questions in healthcare, and 3) distinguish whether a given question is answerable or unanswerable. We believe our dataset, EHRSQL, can serve as a practical benchmark for developing and assessing QA models on structured EHR data and take a step further towards bridging the gap between text-to-SQL research and its real-life deployment in healthcare. EHRSQL is available at https://github.com/glee4810/EHRSQL.

Personalized text generation is an emerging research area that has attracted much attention in recent years. Most studies in this direction focus on a particular domain by designing bespoke features or models. In this work, we propose a general approach for personalized text generation using large language models (LLMs). Inspired by the practice of writing education, we develop a multistage and multitask framework to teach LLMs for personalized generation. In writing instruction, the task of writing from sources is often decomposed into multiple steps that involve finding, evaluating, summarizing, synthesizing, and integrating information. Analogously, our approach to personalized text generation consists of multiple stages: retrieval, ranking, summarization, synthesis, and generation. In addition, we introduce a multitask setting that helps the model improve its generation ability further, which is inspired by the observation in education that a student's reading proficiency and writing ability are often correlated. We evaluate our approach on three public datasets, each of which covers a different and representative domain. Our results show significant improvements over a variety of baselines.

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

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

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

Seeking health-related advice on the internet has become a common practice in the digital era. Determining the trustworthiness of medical claims found online and finding appropriate evidence for this information is increasingly challenging. Fact-checking has emerged as an approach to assess the veracity of factual claims using evidence from credible knowledge sources. To help advance the automation of this task, in this paper, we introduce a novel dataset of 750 health-related claims, labeled for veracity by medical experts and backed with evidence from appropriate clinical studies. We provide an analysis of the dataset, highlighting its characteristics and challenges. The dataset can be used for Machine Learning tasks related to automated fact-checking such as evidence retrieval, veracity prediction, and explanation generation. For this purpose, we provide baseline models based on different approaches, examine their performance, and discuss the findings.

Clinical predictive models often rely on patients' electronic health records (EHR), but integrating medical knowledge to enhance predictions and decision-making is challenging. This is because personalized predictions require personalized knowledge graphs (KGs), which are difficult to generate from patient EHR data. To address this, we propose GraphCare, an open-world framework that uses external KGs to improve EHR-based predictions. Our method extracts knowledge from large language models (LLMs) and external biomedical KGs to build patient-specific KGs, which are then used to train our proposed Bi-attention AugmenTed (BAT) graph neural network (GNN) for healthcare predictions. On two public datasets, MIMIC-III and MIMIC-IV, GraphCare surpasses baselines in four vital healthcare prediction tasks: mortality, readmission, length of stay (LOS), and drug recommendation. On MIMIC-III, it boosts AUROC by 17.6\% and 6.6\% for mortality and readmission, and F1-score by 7.9\% and 10.8\% for LOS and drug recommendation, respectively. Notably, GraphCare demonstrates a substantial edge in scenarios with limited data availability. Our findings highlight the potential of using external KGs in healthcare prediction tasks and demonstrate the promise of GraphCare in generating personalized KGs for promoting personalized medicine.

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

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.

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.

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

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.

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.

This work delved into the realm of automatic text generation, exploring a variety of techniques ranging from traditional deterministic approaches to more modern stochastic methods. Through analysis of greedy search, beam search, top-k sampling, top-p sampling, contrastive searching, and locally typical searching, this work has provided valuable insights into the strengths, weaknesses, and potential applications of each method. Each text-generating method is evaluated using several standard metrics and a comparative study has been made on the performance of the approaches. Finally, some future directions of research in the field of automatic text generation are also identified.

Medical open-domain question answering demands substantial access to specialized knowledge. Recent efforts have sought to decouple knowledge from model parameters, counteracting architectural scaling and allowing for training on common low-resource hardware. The retrieve-then-read paradigm has become ubiquitous, with model predictions grounded on relevant knowledge pieces from external repositories such as PubMed, textbooks, and UMLS. An alternative path, still under-explored but made possible by the advent of domain-specific large language models, entails constructing artificial contexts through prompting. As a result, "to generate or to retrieve" is the modern equivalent of Hamlet's dilemma. This paper presents MedGENIE, the first generate-then-read framework for multiple-choice question answering in medicine. We conduct extensive experiments on MedQA-USMLE, MedMCQA, and MMLU, incorporating a practical perspective by assuming a maximum of 24GB VRAM. MedGENIE sets a new state-of-the-art (SOTA) in the open-book setting of each testbed, even allowing a small-scale reader to outcompete zero-shot closed-book 175B baselines while using up to 706times fewer parameters. Overall, our findings reveal that generated passages are more effective than retrieved counterparts in attaining higher accuracy.

Keyphrase generation is the task consisting in generating a set of words or phrases that highlight the main topics of a document. There are few datasets for keyphrase generation in the biomedical domain and they do not meet the expectations in terms of size for training generative models. In this paper, we introduce kp-biomed, the first large-scale biomedical keyphrase generation dataset with more than 5M documents collected from PubMed abstracts. We train and release several generative models and conduct a series of experiments showing that using large scale datasets improves significantly the performances for present and absent keyphrase generation. The dataset is available under CC-BY-NC v4.0 license at https://huggingface.co/ datasets/taln-ls2n/kpbiomed.

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

Large language models (LLMs) have received much attention and shown their potential in digital health, while their application in mental health is subject to ongoing debate. This systematic review aims to summarize and characterize the use of LLMs in mental health by investigating the strengths and limitations of the latest work in LLMs and discusses the challenges and opportunities for early screening, digital interventions, and other clinical applications in mental health. Following PRISMA guidelines, we examined English articles from PubMed, DBLP Computer Science Bibliography, and IEEE Xplore, published between 1 January 2017, and 1 September 2023, focusing on mental health and LLMs. The review analyzed 32 articles, including mental health analysis using social media datasets (n=13), mental health chatbots (n=10), and other mental health applications (n=9). Findings reveal LLMs' effectiveness in mental health issue detection and the enhancement of telepsychological services through personalised healthcare. Nonetheless, risks like text inconsistencies, hallucinatory content, and the lack of an ethical framework raise concerns about their clinical use. Despite these challenges, the advancement of LLMs underscores their potential as innovative clinical tools, necessitating further research and development. The review emphasizes that LLMs should complement, not replace, professional mental health services.

This paper introduces RiskCards, a framework for structured assessment and documentation of risks associated with an application of language models. As with all language, text generated by language models can be harmful, or used to bring about harm. Automating language generation adds both an element of scale and also more subtle or emergent undesirable tendencies to the generated text. Prior work establishes a wide variety of language model harms to many different actors: existing taxonomies identify categories of harms posed by language models; benchmarks establish automated tests of these harms; and documentation standards for models, tasks and datasets encourage transparent reporting. However, there is no risk-centric framework for documenting the complexity of a landscape in which some risks are shared across models and contexts, while others are specific, and where certain conditions may be required for risks to manifest as harms. RiskCards address this methodological gap by providing a generic framework for assessing the use of a given language model in a given scenario. Each RiskCard makes clear the routes for the risk to manifest harm, their placement in harm taxonomies, and example prompt-output pairs. While RiskCards are designed to be open-source, dynamic and participatory, we present a "starter set" of RiskCards taken from a broad literature survey, each of which details a concrete risk presentation. Language model RiskCards initiate a community knowledge base which permits the mapping of risks and harms to a specific model or its application scenario, ultimately contributing to a better, safer and shared understanding of the risk landscape.

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

Large language models (LLMs) have performed well in providing general and extensive health suggestions in single-turn conversations, exemplified by systems such as ChatGPT, ChatGLM, ChatDoctor, DoctorGLM, and etc. However, the limited information provided by users during single turn results in inadequate personalization and targeting of the generated suggestions, which requires users to independently select the useful part. It is mainly caused by the missing ability to engage in multi-turn questioning. In real-world medical consultations, doctors usually employ a series of iterative inquiries to comprehend the patient's condition thoroughly, enabling them to provide effective and personalized suggestions subsequently, which can be defined as chain of questioning (CoQ) for LLMs. To improve the CoQ of LLMs, we propose BianQue, a ChatGLM-based LLM finetuned with the self-constructed health conversation dataset BianQueCorpus that is consist of multiple turns of questioning and health suggestions polished by ChatGPT. Experimental results demonstrate that the proposed BianQue can simultaneously balance the capabilities of both questioning and health suggestions, which will help promote the research and application of LLMs in the field of proactive health.

Motivation: The gut microbiota has recently emerged as a key factor that underpins certain connections between diet and human health. A tremendous amount of knowledge has been amassed from experimental studies on diet, human metabolism and microbiome. However, this evidence remains mostly buried in scientific publications, and biomedical literature mining in this domain remains scarce. We developed DiMB-RE, a comprehensive corpus annotated with 15 entity types (e.g., Nutrient, Microorganism) and 13 relation types (e.g., increases, improves) capturing diet-microbiome associations. We also trained and evaluated state-of-the-art natural language processing (NLP) models for named entity, trigger, and relation extraction as well as factuality detection using DiMB-RE. Results: DiMB-RE consists of 14,450 entities and 4,206 relationships from 165 articles. While NLP models performed reasonably well for named entity recognition (0.760 F_{1}), end-to-end relation extraction performance was modest (0.356 F_{1}), partly due to missed entities and triggers as well as cross-sentence relations. Conclusions: To our knowledge, DiMB-RE is largest and most diverse dataset focusing on diet-microbiome interactions. It can serve as a benchmark corpus for biomedical literature mining. Availability: DiMB-RE and the NLP models are available at https://github.com/ScienceNLP-Lab/DiMB-RE.

The goal of text generation is to make machines express in human language. It is one of the most important yet challenging tasks in natural language processing (NLP). Since 2014, various neural encoder-decoder models pioneered by Seq2Seq have been proposed to achieve the goal by learning to map input text to output text. However, the input text alone often provides limited knowledge to generate the desired output, so the performance of text generation is still far from satisfaction in many real-world scenarios. To address this issue, researchers have considered incorporating various forms of knowledge beyond the input text into the generation models. This research direction is known as knowledge-enhanced text generation. In this survey, we present a comprehensive review of the research on knowledge enhanced text generation over the past five years. The main content includes two parts: (i) general methods and architectures for integrating knowledge into text generation; (ii) specific techniques and applications according to different forms of knowledge data. This survey can have broad audiences, researchers and practitioners, in academia and industry.

Automatically generating short summaries from users' online mental health posts could save counselors' reading time and reduce their fatigue so that they can provide timely responses to those seeking help for improving their mental state. Recent Transformers-based summarization models have presented a promising approach to abstractive summarization. They go beyond sentence selection and extractive strategies to deal with more complicated tasks such as novel word generation and sentence paraphrasing. Nonetheless, these models have a prominent shortcoming; their training strategy is not quite efficient, which restricts the model's performance. In this paper, we include a curriculum learning approach to reweigh the training samples, bringing about an efficient learning procedure. We apply our model on extreme summarization dataset of MentSum posts -- a dataset of mental health related posts from Reddit social media. Compared to the state-of-the-art model, our proposed method makes substantial gains in terms of Rouge and Bertscore evaluation metrics, yielding 3.5% (Rouge-1), 10.4% (Rouge-2), and 4.7% (Rouge-L), 1.5% (Bertscore) relative improvements.

Large Language Models (LLMs) have demonstrated remarkable capabilities in natural language processing, and yet, their factual inaccuracies and hallucinations limits their application, particularly in critical domains like healthcare. Context retrieval methods, by introducing relevant information as input, have emerged as a crucial approach for enhancing LLM factuality and reliability. This study explores the boundaries of context retrieval methods within the healthcare domain, optimizing their components and benchmarking their performance against open and closed alternatives. Our findings reveal how open LLMs, when augmented with an optimized retrieval system, can achieve performance comparable to the biggest private solutions on established healthcare benchmarks (multiple-choice question answering). Recognizing the lack of realism of including the possible answers within the question (a setup only found in medical exams), and after assessing a strong LLM performance degradation in the absence of those options, we extend the context retrieval system in that direction. In particular, we propose OpenMedPrompt a pipeline that improves the generation of more reliable open-ended answers, moving this technology closer to practical application.

Machine learning (ML) approaches have demonstrated promising results in a wide range of healthcare applications. Data plays a crucial role in developing ML-based healthcare systems that directly affect people's lives. Many of the ethical issues surrounding the use of ML in healthcare stem from structural inequalities underlying the way we collect, use, and handle data. Developing guidelines to improve documentation practices regarding the creation, use, and maintenance of ML healthcare datasets is therefore of critical importance. In this work, we introduce Healthsheet, a contextualized adaptation of the original datasheet questionnaire ~gebru2018datasheets for health-specific applications. Through a series of semi-structured interviews, we adapt the datasheets for healthcare data documentation. As part of the Healthsheet development process and to understand the obstacles researchers face in creating datasheets, we worked with three publicly-available healthcare datasets as our case studies, each with different types of structured data: Electronic health Records (EHR), clinical trial study data, and smartphone-based performance outcome measures. Our findings from the interviewee study and case studies show 1) that datasheets should be contextualized for healthcare, 2) that despite incentives to adopt accountability practices such as datasheets, there is a lack of consistency in the broader use of these practices 3) how the ML for health community views datasheets and particularly Healthsheets as diagnostic tool to surface the limitations and strength of datasets and 4) the relative importance of different fields in the datasheet to healthcare concerns.

We present ToTTo, an open-domain English table-to-text dataset with over 120,000 training examples that proposes a controlled generation task: given a Wikipedia table and a set of highlighted table cells, produce a one-sentence description. To obtain generated targets that are natural but also faithful to the source table, we introduce a dataset construction process where annotators directly revise existing candidate sentences from Wikipedia. We present systematic analyses of our dataset and annotation process as well as results achieved by several state-of-the-art baselines. While usually fluent, existing methods often hallucinate phrases that are not supported by the table, suggesting that this dataset can serve as a useful research benchmark for high-precision conditional text generation.

Table-to-text generation refers to generating a descriptive text from a key-value table. Traditional autoregressive methods, though can generate text with high fluency, suffer from low coverage and poor faithfulness problems. To mitigate these problems, we propose a novel Skeleton-based two-stage method that combines both Autoregressive and Non-Autoregressive generations (SANA). Our approach includes: (1) skeleton generation with an autoregressive pointer network to select key tokens from the source table; (2) edit-based non-autoregressive generation model to produce texts via iterative insertion and deletion operations. By integrating hard constraints from the skeleton, the non-autoregressive model improves the generation's coverage over the source table and thus enhances its faithfulness. We conduct automatic and human evaluations on both WikiPerson and WikiBio datasets. Experimental results demonstrate that our method outperforms the previous state-of-the-art methods in both automatic and human evaluation, especially on coverage and faithfulness. In particular, we achieve PARENT-T recall of 99.47 in WikiPerson, improving over the existing best results by more than 10 points.

Social and behavioral determinants of health (SBDH) play a crucial role in health outcomes and are frequently documented in clinical text. Automatically extracting SBDH information from clinical text relies on publicly available good-quality datasets. However, existing SBDH datasets exhibit substantial limitations in their availability and coverage. In this study, we introduce Synth-SBDH, a novel synthetic dataset with detailed SBDH annotations, encompassing status, temporal information, and rationale across 15 SBDH categories. We showcase the utility of Synth-SBDH on three tasks using real-world clinical datasets from two distinct hospital settings, highlighting its versatility, generalizability, and distillation capabilities. Models trained on Synth-SBDH consistently outperform counterparts with no Synth-SBDH training, achieving up to 62.5% macro-F improvements. Additionally, Synth-SBDH proves effective for rare SBDH categories and under-resource constraints. Human evaluation demonstrates a Human-LLM alignment of 71.06% and uncovers areas for future refinements.

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

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

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.

Long-text generation is seemingly ubiquitous in real-world applications of large language models such as generating an email or writing a review. Despite the fundamental importance and prevalence of long-text generation in many practical applications, existing work on personalized generation has focused on the generation of very short text. To overcome these limitations, we study the problem of personalized long-text generation, that is, generating long-text that is personalized for a specific user while being practically useful for the vast majority of real-world applications that naturally require the generation of longer text. In this work, we demonstrate the importance of user-specific personalization for long-text generation tasks and develop the Long-text Language Model Personalization (LongLaMP) Benchmark. LongLaMP provides a comprehensive and diverse evaluation framework for personalized long-text generation. Extensive experiments on LongLaMP for zero-shot and fine-tuned language tasks demonstrate the effectiveness of the proposed benchmark and its utility for developing and evaluating techniques for personalized long-text generation across a wide variety of long-text generation tasks. The results highlight the importance of personalization across a wide variety of long-text generation tasks. Finally, we release the benchmark for others to use for this important problem.

With the rapid development of artificial intelligence, large language models (LLMs) have shown promising capabilities in mimicking human-level language comprehension and reasoning. This has sparked significant interest in applying LLMs to enhance various aspects of healthcare, ranging from medical education to clinical decision support. However, medicine involves multifaceted data modalities and nuanced reasoning skills, presenting challenges for integrating LLMs. This paper provides a comprehensive review on the applications and implications of LLMs in medicine. It begins by examining the fundamental applications of general-purpose and specialized LLMs, demonstrating their utilities in knowledge retrieval, research support, clinical workflow automation, and diagnostic assistance. Recognizing the inherent multimodality of medicine, the review then focuses on multimodal LLMs, investigating their ability to process diverse data types like medical imaging and EHRs to augment diagnostic accuracy. To address LLMs' limitations regarding personalization and complex clinical reasoning, the paper explores the emerging development of LLM-powered autonomous agents for healthcare. Furthermore, it summarizes the evaluation methodologies for assessing LLMs' reliability and safety in medical contexts. Overall, this review offers an extensive analysis on the transformative potential of LLMs in modern medicine. It also highlights the pivotal need for continuous optimizations and ethical oversight before these models can be effectively integrated into clinical practice. Visit https://github.com/mingze-yuan/Awesome-LLM-Healthcare for an accompanying GitHub repository containing latest papers.

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

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

This article presents the Cogni-CISMeF project, which aims at improving medical information search in the CISMeF system (Catalog and Index of French-language health resources) by including a conversational agent to interact with the user in natural language. To study the cognitive processes involved during the information search, a bottom-up methodology was adopted. Experimentation has been set up to obtain human dialogs between a user (playing the role of patient) dealing with medical information search and a CISMeF expert refining the request. The analysis of these dialogs underlined the use of discursive evidence: vocabulary, reformulation, implicit or explicit expression of user intentions, conversational sequences, etc. A model of artificial agent is proposed. It leads the user in its information search by proposing to him examples, assistance and choices. This model was implemented and integrated in the CISMeF system. ---- Cet article d\'ecrit le projet Cogni-CISMeF qui propose un module de dialogue Homme-Machine \`a int\'egrer dans le syst\`eme d'indexation de connaissances m\'edicales CISMeF (Catalogue et Index des Sites M\'edicaux Francophones). Nous avons adopt\'e une d\'emarche de mod\'elisation cognitive en proc\'edant \`a un recueil de corpus de dialogues entre un utilisateur (jouant le r\^ole d'un patient) d\'esirant une information m\'edicale et un expert CISMeF af inant cette demande pour construire la requ\^ete. Nous avons analys\'e la structure des dialogues ainsi obtenus et avons \'etudi\'e un certain nombre d'indices discursifs : vocabulaire employ\'e, marques de reformulation, commentaires m\'eta et \'epilinguistiques, expression implicite ou explicite des intentions de l'utilisateur, encha\^inement conversationnel, etc. De cette analyse, nous avons construit un mod\`ele d'agent artificiel dot\'e de capacit\'es cognitives capables d'aider l'utilisateur dans sa t\^ache de recherche d'information. Ce mod\`ele a \'et\'e impl\'ement\'e et int\'egr\'e dans le syst\`eme CISMeF.

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.

Large language models (LLMs) represent a transformative class of AI tools capable of revolutionizing various aspects of healthcare by generating human-like responses across diverse contexts and adapting to novel tasks following human instructions. Their potential application spans a broad range of medical tasks, such as clinical documentation, matching patients to clinical trials, and answering medical questions. In this primer paper, we propose an actionable guideline to help healthcare professionals more efficiently utilize LLMs in their work, along with a set of best practices. This approach consists of several main phases, including formulating the task, choosing LLMs, prompt engineering, fine-tuning, and deployment. We start with the discussion of critical considerations in identifying healthcare tasks that align with the core capabilities of LLMs and selecting models based on the selected task and data, performance requirements, and model interface. We then review the strategies, such as prompt engineering and fine-tuning, to adapt standard LLMs to specialized medical tasks. Deployment considerations, including regulatory compliance, ethical guidelines, and continuous monitoring for fairness and bias, are also discussed. By providing a structured step-by-step methodology, this tutorial aims to equip healthcare professionals with the tools necessary to effectively integrate LLMs into clinical practice, ensuring that these powerful technologies are applied in a safe, reliable, and impactful manner.

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

Large Language Models (LLMs) are notorious for blending fact with fiction and generating non-factual content, known as hallucinations. To tackle this challenge, we propose an interactive system that helps users obtain insights into the reliability of the generated text. Our approach is based on the idea that the self-consistency of multiple samples generated by the same LLM relates to its confidence in individual claims in the generated texts. Using this idea, we design RELIC, an interactive system that enables users to investigate and verify semantic-level variations in multiple long-form responses. This allows users to recognize potentially inaccurate information in the generated text and make necessary corrections. From a user study with ten participants, we demonstrate that our approach helps users better verify the reliability of the generated text. We further summarize the design implications and lessons learned from this research for inspiring future studies on reliable human-LLM interactions.

The current state of adoption of well-structured electronic health records and integration of digital methods for storing medical patient data in structured formats can often considered as inferior compared to the use of traditional, unstructured text based patient data documentation. Data mining in the field of medical data analysis often needs to rely solely on processing of unstructured data to retrieve relevant data. In natural language processing (NLP), statistical models have been shown successful in various tasks like part-of-speech tagging, relation extraction (RE) and named entity recognition (NER). In this work, we present GERNERMED, the first open, neural NLP model for NER tasks dedicated to detect medical entity types in German text data. Here, we avoid the conflicting goals of protection of sensitive patient data from training data extraction and the publication of the statistical model weights by training our model on a custom dataset that was translated from publicly available datasets in foreign language by a pretrained neural machine translation model. The sample code and the statistical model is available at: https://github.com/frankkramer-lab/GERNERMED

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

A long-running goal of the clinical NLP community is the extraction of important variables trapped in clinical notes. However, roadblocks have included dataset shift from the general domain and a lack of public clinical corpora and annotations. In this work, we show that large language models, such as InstructGPT, perform well at zero- and few-shot information extraction from clinical text despite not being trained specifically for the clinical domain. Whereas text classification and generation performance have already been studied extensively in such models, here we additionally demonstrate how to leverage them to tackle a diverse set of NLP tasks which require more structured outputs, including span identification, token-level sequence classification, and relation extraction. Further, due to the dearth of available data to evaluate these systems, we introduce new datasets for benchmarking few-shot clinical information extraction based on a manual re-annotation of the CASI dataset for new tasks. On the clinical extraction tasks we studied, the GPT-3 systems significantly outperform existing zero- and few-shot baselines.

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

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

We present PhysioLLM, an interactive system that leverages large language models (LLMs) to provide personalized health understanding and exploration by integrating physiological data from wearables with contextual information. Unlike commercial health apps for wearables, our system offers a comprehensive statistical analysis component that discovers correlations and trends in user data, allowing users to ask questions in natural language and receive generated personalized insights, and guides them to develop actionable goals. As a case study, we focus on improving sleep quality, given its measurability through physiological data and its importance to general well-being. Through a user study with 24 Fitbit watch users, we demonstrate that PhysioLLM outperforms both the Fitbit App alone and a generic LLM chatbot in facilitating a deeper, personalized understanding of health data and supporting actionable steps toward personal health goals.

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.

In this paper, we aim to develop an open-source, multilingual language model for medicine, that the benefits a wider, linguistically diverse audience from different regions. In general, we present the contribution from the following aspects: first, for multilingual medical-specific adaptation, we construct a new multilingual medical corpus, that contains approximately 25.5B tokens encompassing 6 main languages, termed as MMedC, that enables auto-regressive training for existing general LLMs. second, to monitor the development of multilingual LLMs in medicine, we propose a new multilingual medical multi-choice question-answering benchmark with rationale, termed as MMedBench; third, we have assessed a number of popular, opensource large language models (LLMs) on our benchmark, along with those further auto-regressive trained on MMedC, as a result, our final model, termed as MMedLM 2, with only 7B parameters, achieves superior performance compared to all other open-source models, even rivaling GPT-4 on MMedBench. We will make the resources publicly available, including code, model weights, and datasets.

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

Depression is a global burden and one of the most challenging mental health conditions to control. Experts can detect its severity early using the Beck Depression Inventory (BDI) questionnaire, administer appropriate medication to patients, and impede its progression. Due to the fear of potential stigmatization, many patients turn to social media platforms like Reddit for advice and assistance at various stages of their journey. This research extracts text from Reddit to facilitate the diagnostic process. It employs a proposed labeling approach to categorize the text and subsequently fine-tunes the Longformer model. The model's performance is compared against baseline models, including Naive Bayes, Random Forest, Support Vector Machines, and Gradient Boosting. Our findings reveal that the Longformer model outperforms the baseline models in both English (48%) and Luganda (45%) languages on a custom-made dataset.

We survey clinical document corpora, with focus on German textual data. Due to rigid data privacy legislation in Germany these resources, with only few exceptions, are stored in safe clinical data spaces and locked against clinic-external researchers. This situation stands in stark contrast with established workflows in the field of natural language processing where easy accessibility and reuse of data collections are common practice. Hence, alternative corpus designs have been examined to escape from this data poverty. Besides machine translation of English clinical datasets and the generation of synthetic corpora with fictitious clinical contents, several other types of domain proxies have come up as substitutes for authentic clinical documents. Common instances of close proxies are medical journal publications, clinical therapy guidelines, drug labels, etc., more distant proxies include online encyclopedic medical articles or medical contents from social media channels. After PRISM-conformant screening of 359 hits from four bibliographic systems, 75 relevant documents were finally selected for this review and 59 distinct corpora were determined. We identified 24 real clinical corpora (from 40 publications) out of which only 5 are publicly distributable. 2 translations of real corpora and 3 synthetic ones complement the set of clinical corpora. 14 corpora were categorized as close domain proxies, 16 as distant ones. There is a clear divide between the large number of non-accessible authentic clinical German-language corpora and their publicly accessible substitutes: translated or synthetic, close or more distant proxies. So on first sight, the data bottleneck seems broken. Intuitively yet, differences in genre-specific writing style, wording and medical domain expertise in this typological space are also obvious. This raises the question how valid alternative corpus designs really are.

The primary goal of drug safety researchers and regulators is to promptly identify adverse drug reactions. Doing so may in turn prevent or reduce the harm to patients and ultimately improve public health. Evaluating and monitoring drug safety (i.e., pharmacovigilance) involves analyzing an ever growing collection of spontaneous reports from health professionals, physicians, and pharmacists, and information voluntarily submitted by patients. In this scenario, facilitating analysis of such reports via automation has the potential to rapidly identify safety signals. Unfortunately, public resources for developing natural language models for this task are scant. We present PHEE, a novel dataset for pharmacovigilance comprising over 5000 annotated events from medical case reports and biomedical literature, making it the largest such public dataset to date. We describe the hierarchical event schema designed to provide coarse and fine-grained information about patients' demographics, treatments and (side) effects. Along with the discussion of the dataset, we present a thorough experimental evaluation of current state-of-the-art approaches for biomedical event extraction, point out their limitations, and highlight open challenges to foster future research in this area.

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.

Following each patient visit, physicians draft long semi-structured clinical summaries called SOAP notes. While invaluable to clinicians and researchers, creating digital SOAP notes is burdensome, contributing to physician burnout. In this paper, we introduce the first complete pipelines to leverage deep summarization models to generate these notes based on transcripts of conversations between physicians and patients. After exploring a spectrum of methods across the extractive-abstractive spectrum, we propose Cluster2Sent, an algorithm that (i) extracts important utterances relevant to each summary section; (ii) clusters together related utterances; and then (iii) generates one summary sentence per cluster. Cluster2Sent outperforms its purely abstractive counterpart by 8 ROUGE-1 points, and produces significantly more factual and coherent sentences as assessed by expert human evaluators. For reproducibility, we demonstrate similar benefits on the publicly available AMI dataset. Our results speak to the benefits of structuring summaries into sections and annotating supporting evidence when constructing summarization corpora.

In response to the pressing need for advanced clinical problem-solving tools in healthcare, we introduce BooksMed, a novel framework based on a Large Language Model (LLM). BooksMed uniquely emulates human cognitive processes to deliver evidence-based and reliable responses, utilizing the GRADE (Grading of Recommendations, Assessment, Development, and Evaluations) framework to effectively quantify evidence strength. For clinical decision-making to be appropriately assessed, an evaluation metric that is clinically aligned and validated is required. As a solution, we present ExpertMedQA, a multispecialty clinical benchmark comprised of open-ended, expert-level clinical questions, and validated by a diverse group of medical professionals. By demanding an in-depth understanding and critical appraisal of up-to-date clinical literature, ExpertMedQA rigorously evaluates LLM performance. BooksMed outperforms existing state-of-the-art models Med-PaLM 2, Almanac, and ChatGPT in a variety of medical scenarios. Therefore, a framework that mimics human cognitive stages could be a useful tool for providing reliable and evidence-based responses to clinical inquiries.

Automatically summarizing patients' main problems from daily progress notes using natural language processing methods helps to battle against information and cognitive overload in hospital settings and potentially assists providers with computerized diagnostic decision support. Problem list summarization requires a model to understand, abstract, and generate clinical documentation. In this work, we propose a new NLP task that aims to generate a list of problems in a patient's daily care plan using input from the provider's progress notes during hospitalization. We investigate the performance of T5 and BART, two state-of-the-art seq2seq transformer architectures, in solving this problem. We provide a corpus built on top of progress notes from publicly available electronic health record progress notes in the Medical Information Mart for Intensive Care (MIMIC)-III. T5 and BART are trained on general domain text, and we experiment with a data augmentation method and a domain adaptation pre-training method to increase exposure to medical vocabulary and knowledge. Evaluation methods include ROUGE, BERTScore, cosine similarity on sentence embedding, and F-score on medical concepts. Results show that T5 with domain adaptive pre-training achieves significant performance gains compared to a rule-based system and general domain pre-trained language models, indicating a promising direction for tackling the problem summarization task.

In this study, we investigated the ability of the large language model (LLM) to enhance healthcare data interoperability. We leveraged the LLM to convert clinical texts into their corresponding FHIR resources. Our experiments, conducted on 3,671 snippets of clinical text, demonstrated that the LLM not only streamlines the multi-step natural language processing and human calibration processes but also achieves an exceptional accuracy rate of over 90% in exact matches when compared to human annotations.

People often utilise online media (e.g., Facebook, Reddit) as a platform to express their psychological distress and seek support. State-of-the-art NLP techniques demonstrate strong potential to automatically detect mental health issues from text. Research suggests that mental health issues are reflected in emotions (e.g., sadness) indicated in a person's choice of language. Therefore, we developed a novel emotion-annotated mental health corpus (EmoMent), consisting of 2802 Facebook posts (14845 sentences) extracted from two South Asian countries - Sri Lanka and India. Three clinical psychology postgraduates were involved in annotating these posts into eight categories, including 'mental illness' (e.g., depression) and emotions (e.g., 'sadness', 'anger'). EmoMent corpus achieved 'very good' inter-annotator agreement of 98.3% (i.e. % with two or more agreement) and Fleiss' Kappa of 0.82. Our RoBERTa based models achieved an F1 score of 0.76 and a macro-averaged F1 score of 0.77 for the first task (i.e. predicting a mental health condition from a post) and the second task (i.e. extent of association of relevant posts with the categories defined in our taxonomy), respectively.

Machine translation is indispensable in healthcare for enabling the global dissemination of medical knowledge across languages. However, complex medical terminology poses unique challenges to achieving adequate translation quality and accuracy. This study introduces a novel "LLMs-in-the-loop" approach to develop supervised neural machine translation models optimized specifically for medical texts. While large language models (LLMs) have demonstrated powerful capabilities, this research shows that small, specialized models trained on high-quality in-domain (mostly synthetic) data can outperform even vastly larger LLMs. Custom parallel corpora in six languages were compiled from scientific articles, synthetically generated clinical documents, and medical texts. Our LLMs-in-the-loop methodology employs synthetic data generation, rigorous evaluation, and agent orchestration to enhance performance. We developed small medical translation models using the MarianMT base model. We introduce a new medical translation test dataset to standardize evaluation in this domain. Assessed using BLEU, METEOR, ROUGE, and BERT scores on this test set, our MarianMT-based models outperform Google Translate, DeepL, and GPT-4-Turbo. Results demonstrate that our LLMs-in-the-loop approach, combined with fine-tuning high-quality, domain-specific data, enables specialized models to outperform general-purpose and some larger systems. This research, part of a broader series on expert small models, paves the way for future healthcare-related AI developments, including deidentification and bio-medical entity extraction models. Our study underscores the potential of tailored neural translation models and the LLMs-in-the-loop methodology to advance the field through improved data generation, evaluation, agent, and modeling techniques.

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

Advances in large language models (LLMs) have empowered a variety of applications. However, there is still a significant gap in research when it comes to understanding and enhancing the capabilities of LLMs in the field of mental health. In this work, we present the first comprehensive evaluation of multiple LLMs, including Alpaca, Alpaca-LoRA, FLAN-T5, GPT-3.5, and GPT-4, on various mental health prediction tasks via online text data. We conduct a broad range of experiments, covering zero-shot prompting, few-shot prompting, and instruction fine-tuning. The results indicate a promising yet limited performance of LLMs with zero-shot and few-shot prompt designs for the mental health tasks. More importantly, our experiments show that instruction finetuning can significantly boost the performance of LLMs for all tasks simultaneously. Our best-finetuned models, Mental-Alpaca and Mental-FLAN-T5, outperform the best prompt design of GPT-3.5 (25 and 15 times bigger) by 10.9% on balanced accuracy and the best of GPT-4 (250 and 150 times bigger) by 4.8%. They further perform on par with the state-of-the-art task-specific language model. We also conduct an exploratory case study on LLMs' capability on the mental health reasoning tasks, illustrating the promising capability of certain models such as GPT-4. We summarize our findings into a set of action guidelines for potential methods to enhance LLMs' capability for mental health tasks. Meanwhile, we also emphasize the important limitations before achieving deployability in real-world mental health settings, such as known racial and gender bias. We highlight the important ethical risks accompanying this line of research.

Social media is a great source of data for users reporting information and regarding their health and how various things have had an effect on them. This paper presents various approaches using Transformers and Large Language Models and their ensembles, their performance along with advantages and drawbacks for various tasks of SMM4H'24 - Classifying texts on impact of nature and outdoor spaces on the author's mental health (Task 3), Binary classification of tweets reporting their children's health disorders like Asthma, Autism, ADHD and Speech disorder (task 5), Binary classification of users self-reporting their age (task 6).

Background: Natural Language Processing (NLP) is widely used to extract clinical insights from Electronic Health Records (EHRs). However, the lack of annotated data, automated tools, and other challenges hinder the full utilisation of NLP for EHRs. Various Machine Learning (ML), Deep Learning (DL) and NLP techniques are studied and compared to understand the limitations and opportunities in this space comprehensively. Methodology: After screening 261 articles from 11 databases, we included 127 papers for full-text review covering seven categories of articles: 1) medical note classification, 2) clinical entity recognition, 3) text summarisation, 4) deep learning (DL) and transfer learning architecture, 5) information extraction, 6) Medical language translation and 7) other NLP applications. This study follows the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Result and Discussion: EHR was the most commonly used data type among the selected articles, and the datasets were primarily unstructured. Various ML and DL methods were used, with prediction or classification being the most common application of ML or DL. The most common use cases were: the International Classification of Diseases, Ninth Revision (ICD-9) classification, clinical note analysis, and named entity recognition (NER) for clinical descriptions and research on psychiatric disorders. Conclusion: We find that the adopted ML models were not adequately assessed. In addition, the data imbalance problem is quite important, yet we must find techniques to address this underlining problem. Future studies should address key limitations in studies, primarily identifying Lupus Nephritis, Suicide Attempts, perinatal self-harmed and ICD-9 classification.

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.

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

Large-scale language models (LLMs), such as ChatGPT, are capable of generating human-like responses for various downstream tasks, such as task-oriented dialogues and question answering. However, applying LLMs to medical domains remains challenging due to their inability to leverage domain-specific knowledge. In this study, we present the Large-scale Language Models Augmented with Medical Textbooks (LLM-AMT), which integrates authoritative medical textbooks as the cornerstone of its design, enhancing its proficiency in the specialized domain through plug-and-play modules, comprised of a Hybrid Textbook Retriever, supplemented by the Query Augmenter and the LLM Reader. Experimental evaluation on three open-domain medical question-answering tasks reveals a substantial enhancement in both the professionalism and accuracy of the LLM responses when utilizing LLM-AMT, exhibiting an improvement ranging from 11.4% to 13.2%. Despite being 100 times smaller, we found that medical textbooks as the retrieval corpus serves as a more valuable external knowledge source than Wikipedia in the medical domain. Our experiments show that textbook augmentation results in a performance improvement ranging from 9.7% to 12.2% over Wikipedia augmentation.

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.

Over the course of the COVID-19 pandemic, large volumes of biomedical information concerning this new disease have been published on social media. Some of this information can pose a real danger to people's health, particularly when false information is shared, for instance recommendations on how to treat diseases without professional medical advice. Therefore, automatic fact-checking resources and systems developed specifically for the medical domain are crucial. While existing fact-checking resources cover COVID-19-related information in news or quantify the amount of misinformation in tweets, there is no dataset providing fact-checked COVID-19-related Twitter posts with detailed annotations for biomedical entities, relations and relevant evidence. We contribute CoVERT, a fact-checked corpus of tweets with a focus on the domain of biomedicine and COVID-19-related (mis)information. The corpus consists of 300 tweets, each annotated with medical named entities and relations. We employ a novel crowdsourcing methodology to annotate all tweets with fact-checking labels and supporting evidence, which crowdworkers search for online. This methodology results in moderate inter-annotator agreement. Furthermore, we use the retrieved evidence extracts as part of a fact-checking pipeline, finding that the real-world evidence is more useful than the knowledge indirectly available in pretrained language models.

In this paper, we explore the use of large language models to assess human interpretations of real world events. To do so, we use a language model trained prior to 2020 to artificially generate news articles concerning COVID-19 given the headlines of actual articles written during the pandemic. We then compare stylistic qualities of our artificially generated corpus with a news corpus, in this case 5,082 articles produced by CBC News between January 23 and May 5, 2020. We find our artificially generated articles exhibits a considerably more negative attitude towards COVID and a significantly lower reliance on geopolitical framing. Our methods and results hold importance for researchers seeking to simulate large scale cultural processes via recent breakthroughs in text generation.

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

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

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.

Background: Large language models (LLMs) are trained to follow directions, but this introduces a vulnerability to blindly comply with user requests even if they generate wrong information. In medicine, this could accelerate the generation of misinformation that impacts human well-being. Objectives/Methods: We analyzed compliance to requests to generate misleading content about medications in settings where models know the request is illogical. We investigated whether in-context directions and instruction-tuning of LLMs to prioritize logical reasoning over compliance reduced misinformation risk. Results: While all frontier LLMs complied with misinformation requests, both prompt-based and parameter-based approaches can improve the detection of logic flaws in requests and prevent the dissemination of medical misinformation. Conclusion: Shifting LLMs to prioritize logic over compliance could reduce risks of exploitation for medical misinformation.

Large language models (LLMs) have recently become the leading source of answers for users' questions online. Despite their ability to offer eloquent answers, their accuracy and reliability can pose a significant challenge. This is especially true for sensitive domains such as biomedicine, where there is a higher need for factually correct answers. This paper introduces a biomedical retrieval-augmented generation (RAG) system designed to enhance the reliability of generated responses. The system is based on a fine-tuned LLM for the referenced question-answering, where retrieved relevant abstracts from PubMed are passed to LLM's context as input through a prompt. Its output is an answer based on PubMed abstracts, where each statement is referenced accordingly, allowing the users to verify the answer. Our retrieval system achieves an absolute improvement of 23% compared to the PubMed search engine. Based on the manual evaluation on a small sample, our fine-tuned LLM component achieves comparable results to GPT-4 Turbo in referencing relevant abstracts. We make the dataset used to fine-tune the models and the fine-tuned models based on Mistral-7B-instruct-v0.1 and v0.2 publicly available.

Recent breakthroughs in large language models (LLMs) offer unprecedented natural language understanding and generation capabilities. However, existing surveys on LLMs in biomedicine often focus on specific applications or model architectures, lacking a comprehensive analysis that integrates the latest advancements across various biomedical domains. This review, based on an analysis of 484 publications sourced from databases including PubMed, Web of Science, and arXiv, provides an in-depth examination of the current landscape, applications, challenges, and prospects of LLMs in biomedicine, distinguishing itself by focusing on the practical implications of these models in real-world biomedical contexts. Firstly, we explore the capabilities of LLMs in zero-shot learning across a broad spectrum of biomedical tasks, including diagnostic assistance, drug discovery, and personalized medicine, among others, with insights drawn from 137 key studies. Then, we discuss adaptation strategies of LLMs, including fine-tuning methods for both uni-modal and multi-modal LLMs to enhance their performance in specialized biomedical contexts where zero-shot fails to achieve, such as medical question answering and efficient processing of biomedical literature. Finally, we discuss the challenges that LLMs face in the biomedicine domain including data privacy concerns, limited model interpretability, issues with dataset quality, and ethics due to the sensitive nature of biomedical data, the need for highly reliable model outputs, and the ethical implications of deploying AI in healthcare. To address these challenges, we also identify future research directions of LLM in biomedicine including federated learning methods to preserve data privacy and integrating explainable AI methodologies to enhance the transparency of LLMs.

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

We introduce a novel graph-based Retrieval-Augmented Generation (RAG) framework specifically designed for the medical domain, called MedGraphRAG, aimed at enhancing Large Language Model (LLM) capabilities and generating evidence-based results, thereby improving safety and reliability when handling private medical data. Our comprehensive pipeline begins with a hybrid static-semantic approach to document chunking, significantly improving context capture over traditional methods. Extracted entities are used to create a three-tier hierarchical graph structure, linking entities to foundational medical knowledge sourced from medical papers and dictionaries. These entities are then interconnected to form meta-graphs, which are merged based on semantic similarities to develop a comprehensive global graph. This structure supports precise information retrieval and response generation. The retrieval process employs a U-retrieve method to balance global awareness and indexing efficiency of the LLM. Our approach is validated through a comprehensive ablation study comparing various methods for document chunking, graph construction, and information retrieval. The results not only demonstrate that our hierarchical graph construction method consistently outperforms state-of-the-art models on multiple medical Q\&A benchmarks, but also confirms that the responses generated include source documentation, significantly enhancing the reliability of medical LLMs in practical applications. Code will be at: https://github.com/MedicineToken/Medical-Graph-RAG/tree/main

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.

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

The recent success of Large Language Models (LLMs) has had a significant impact on the healthcare field, providing patients with medical advice, diagnostic information, and more. However, due to a lack of professional medical knowledge, patients are easily misled by generated erroneous information from LLMs, which may result in serious medical problems. To address this issue, we focus on tuning the LLMs to be medical assistants who collaborate with more experienced doctors. We first conduct a two-stage survey by inspiration-feedback to gain a broad understanding of the real needs of doctors for medical assistants. Based on this, we construct a Chinese medical dataset called DoctorFLAN to support the entire workflow of doctors, which includes 92K Q\&A samples from 22 tasks and 27 specialists. Moreover, we evaluate LLMs in doctor-oriented scenarios by constructing the DoctorFLAN-test containing 550 single-turn Q\&A and DotaBench containing 74 multi-turn conversations. The evaluation results indicate that being a medical assistant still poses challenges for existing open-source models, but DoctorFLAN can help them significantly. It demonstrates that the doctor-oriented dataset and benchmarks we construct can complement existing patient-oriented work and better promote medical LLMs research.

With the development of web technology, social media texts are becoming a rich source for automatic mental health analysis. As traditional discriminative methods bear the problem of low interpretability, the recent large language models have been explored for interpretable mental health analysis on social media, which aims to provide detailed explanations along with predictions. The results show that ChatGPT can generate approaching-human explanations for its correct classifications. However, LLMs still achieve unsatisfactory classification performance in a zero-shot/few-shot manner. Domain-specific finetuning is an effective solution, but faces 2 challenges: 1) lack of high-quality training data. 2) no open-source LLMs for interpretable mental health analysis were released to lower the finetuning cost. To alleviate these problems, we build the first multi-task and multi-source interpretable mental health instruction (IMHI) dataset on social media, with 105K data samples. The raw social media data are collected from 10 existing sources covering 8 mental health analysis tasks. We use expert-written few-shot prompts and collected labels to prompt ChatGPT and obtain explanations from its responses. To ensure the reliability of the explanations, we perform strict automatic and human evaluations on the correctness, consistency, and quality of generated data. Based on the IMHI dataset and LLaMA2 foundation models, we train MentalLLaMA, the first open-source LLM series for interpretable mental health analysis with instruction-following capability. We also evaluate the performance of MentalLLaMA on the IMHI evaluation benchmark with 10 test sets, where their correctness for making predictions and the quality of explanations are examined. The results show that MentalLLaMA approaches state-of-the-art discriminative methods in correctness and generates high-quality explanations.

Scientific news reports serve as a bridge, adeptly translating complex research articles into reports that resonate with the broader public. The automated generation of such narratives enhances the accessibility of scholarly insights. In this paper, we present a new corpus to facilitate this paradigm development. Our corpus comprises a parallel compilation of academic publications and their corresponding scientific news reports across nine disciplines. To demonstrate the utility and reliability of our dataset, we conduct an extensive analysis, highlighting the divergences in readability and brevity between scientific news narratives and academic manuscripts. We benchmark our dataset employing state-of-the-art text generation models. The evaluation process involves both automatic and human evaluation, which lays the groundwork for future explorations into the automated generation of scientific news reports. The dataset and code related to this work are available at https://dongqi.me/projects/SciNews.

People primarily consult tables to conduct data analysis or answer specific questions. Text generation systems that can provide accurate table summaries tailored to users' information needs can facilitate more efficient access to relevant data insights. However, existing table-to-text generation studies primarily focus on converting tabular data into coherent statements, rather than addressing information-seeking purposes. In this paper, we define a new query-focused table summarization task, where text generation models have to perform human-like reasoning and analysis over the given table to generate a tailored summary, and we introduce a new benchmark named QTSumm for this task. QTSumm consists of 5,625 human-annotated query-summary pairs over 2,437 tables on diverse topics. Moreover, we investigate state-of-the-art models (i.e., text generation, table-to-text generation, and large language models) on the QTSumm dataset. Experimental results and manual analysis reveal that our benchmark presents significant challenges in table-to-text generation for future research.

Pre-trained language models have attracted increasing attention in the biomedical domain, inspired by their great success in the general natural language domain. Among the two main branches of pre-trained language models in the general language domain, i.e., BERT (and its variants) and GPT (and its variants), the first one has been extensively studied in the biomedical domain, such as BioBERT and PubMedBERT. While they have achieved great success on a variety of discriminative downstream biomedical tasks, the lack of generation ability constrains their application scope. In this paper, we propose BioGPT, a domain-specific generative Transformer language model pre-trained on large scale biomedical literature. We evaluate BioGPT on six biomedical NLP tasks and demonstrate that our model outperforms previous models on most tasks. Especially, we get 44.98%, 38.42% and 40.76% F1 score on BC5CDR, KD-DTI and DDI end-to-end relation extraction tasks respectively, and 78.2% accuracy on PubMedQA, creating a new record. Our larger model BioGPT-Large achieves 81.0% on PubMedQA. Our case study on text generation further demonstrates the advantage of BioGPT on biomedical literature to generate fluent descriptions for biomedical terms. Code is available at https://github.com/microsoft/BioGPT.

The rise of large language models (LLMs) had a transformative impact on search, ushering in a new era of search engines that are capable of generating search results in natural language text, imbued with citations for supporting sources. Building generative information-seeking models demands openly accessible datasets, which currently remain lacking. In this paper, we introduce a new dataset, HAGRID (Human-in-the-loop Attributable Generative Retrieval for Information-seeking Dataset) for building end-to-end generative information-seeking models that are capable of retrieving candidate quotes and generating attributed explanations. Unlike recent efforts that focus on human evaluation of black-box proprietary search engines, we built our dataset atop the English subset of MIRACL, a publicly available information retrieval dataset. HAGRID is constructed based on human and LLM collaboration. We first automatically collect attributed explanations that follow an in-context citation style using an LLM, i.e. GPT-3.5. Next, we ask human annotators to evaluate the LLM explanations based on two criteria: informativeness and attributability. HAGRID serves as a catalyst for the development of information-seeking models with better attribution capabilities.

Objective To solve major clinical natural language processing (NLP) tasks using a unified text-to-text learning architecture based on a generative large language model (LLM) via prompt tuning. Methods We formulated 7 key clinical NLP tasks as text-to-text learning and solved them using one unified generative clinical LLM, GatorTronGPT, developed using GPT-3 architecture and trained with up to 20 billion parameters. We adopted soft prompts (i.e., trainable vectors) with frozen LLM, where the LLM parameters were not updated (i.e., frozen) and only the vectors of soft prompts were updated, known as prompt tuning. We added additional soft prompts as a prefix to the input layer, which were optimized during the prompt tuning. We evaluated the proposed method using 7 clinical NLP tasks and compared them with previous task-specific solutions based on Transformer models. Results and Conclusion The proposed approach achieved state-of-the-art performance for 5 out of 7 major clinical NLP tasks using one unified generative LLM. Our approach outperformed previous task-specific transformer models by ~3% for concept extraction and 7% for relation extraction applied to social determinants of health, 3.4% for clinical concept normalization, 3.4~10% for clinical abbreviation disambiguation, and 5.5~9% for natural language inference. Our approach also outperformed a previously developed prompt-based machine reading comprehension (MRC) model, GatorTron-MRC, for clinical concept and relation extraction. The proposed approach can deliver the ``one model for all`` promise from training to deployment using a unified generative LLM.

This work introduces BioLORD, a new pre-training strategy for producing meaningful representations for clinical sentences and biomedical concepts. State-of-the-art methodologies operate by maximizing the similarity in representation of names referring to the same concept, and preventing collapse through contrastive learning. However, because biomedical names are not always self-explanatory, it sometimes results in non-semantic representations. BioLORD overcomes this issue by grounding its concept representations using definitions, as well as short descriptions derived from a multi-relational knowledge graph consisting of biomedical ontologies. Thanks to this grounding, our model produces more semantic concept representations that match more closely the hierarchical structure of ontologies. BioLORD establishes a new state of the art for text similarity on both clinical sentences (MedSTS) and biomedical concepts (MayoSRS).

In recent years, Large Language Models (LLMs) have become integrated into our daily lives, serving as invaluable assistants in completing tasks. Widely embraced by users, the abuse of LLMs is inevitable, particularly in using them to generate text content for various purposes, leading to difficulties in distinguishing between text generated by LLMs and that written by humans. In this study, we present a dataset named ViDetect, comprising 6.800 samples of Vietnamese essay, with 3.400 samples authored by humans and the remainder generated by LLMs, serving the purpose of detecting text generated by AI. We conducted evaluations using state-of-the-art methods, including ViT5, BartPho, PhoBERT, mDeberta V3, and mBERT. These results contribute not only to the growing body of research on detecting text generated by AI but also demonstrate the adaptability and effectiveness of different methods in the Vietnamese language context. This research lays the foundation for future advancements in AI-generated text detection and provides valuable insights for researchers in the field of natural language processing.

Continuity of care is crucial to ensuring positive health outcomes for patients discharged from an inpatient hospital setting, and improved information sharing can help. To share information, caregivers write discharge notes containing action items to share with patients and their future caregivers, but these action items are easily lost due to the lengthiness of the documents. In this work, we describe our creation of a dataset of clinical action items annotated over MIMIC-III, the largest publicly available dataset of real clinical notes. This dataset, which we call CLIP, is annotated by physicians and covers 718 documents representing 100K sentences. We describe the task of extracting the action items from these documents as multi-aspect extractive summarization, with each aspect representing a type of action to be taken. We evaluate several machine learning models on this task, and show that the best models exploit in-domain language model pre-training on 59K unannotated documents, and incorporate context from neighboring sentences. We also propose an approach to pre-training data selection that allows us to explore the trade-off between size and domain-specificity of pre-training datasets for this task.

Recent advances in large language models have led to renewed interest in natural language processing in healthcare using the free text of clinical notes. One distinguishing characteristic of clinical notes is their long time span over multiple long documents. The unique structure of clinical notes creates a new design choice: when the context length for a language model predictor is limited, which part of clinical notes should we choose as the input? Existing studies either choose the inputs with domain knowledge or simply truncate them. We propose a framework to analyze the sections with high predictive power. Using MIMIC-III, we show that: 1) predictive power distribution is different between nursing notes and discharge notes and 2) combining different types of notes could improve performance when the context length is large. Our findings suggest that a carefully selected sampling function could enable more efficient information extraction from clinical notes.

The development of large language models tailored for handling patients' clinical notes is often hindered by the limited accessibility and usability of these notes due to strict privacy regulations. To address these challenges, we first create synthetic large-scale clinical notes using publicly available case reports extracted from biomedical literature. We then use these synthetic notes to train our specialized clinical large language model, Asclepius. While Asclepius is trained on synthetic data, we assess its potential performance in real-world applications by evaluating it using real clinical notes. We benchmark Asclepius against several other large language models, including GPT-3.5-turbo and other open-source alternatives. To further validate our approach using synthetic notes, we also compare Asclepius with its variants trained on real clinical notes. Our findings convincingly demonstrate that synthetic clinical notes can serve as viable substitutes for real ones when constructing high-performing clinical language models. This conclusion is supported by detailed evaluations conducted by both GPT-4 and medical professionals. All resources including weights, codes, and data used in the development of Asclepius are made publicly accessible for future research.

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

Brief hospital course (BHC) summaries are common clinical documents generated by summarizing clinical notes. While large language models (LLMs) depict remarkable capabilities in automating real-world tasks, their capabilities for healthcare applications such as BHC synthesis have not been shown. To enable the adaptation of LLMs for BHC synthesis, we introduce a novel benchmark consisting of a pre-processed dataset extracted from MIMIC-IV notes, encapsulating clinical note, and brief hospital course (BHC) pairs. We assess the performance of two general-purpose LLMs and three healthcare-adapted LLMs to improve BHC synthesis from clinical notes. Using clinical notes as input for generating BHCs, we apply prompting-based (using in-context learning) and fine-tuning-based adaptation strategies to three open-source LLMs (Clinical-T5-Large, Llama2-13B, FLAN-UL2) and two proprietary LLMs (GPT-3.5, GPT-4). We quantitatively evaluate the performance of these LLMs across varying context-length inputs using conventional natural language similarity metrics. We further perform a qualitative study where five diverse clinicians blindly compare clinician-written BHCs and two LLM-generated BHCs for 30 samples across metrics of comprehensiveness, conciseness, factual correctness, and fluency. Overall, we present a new benchmark and pre-processed dataset for using LLMs in BHC synthesis from clinical notes. We observe high-quality summarization performance for both in-context proprietary and fine-tuned open-source LLMs using both quantitative metrics and a qualitative clinical reader study. We propose our work as a benchmark to motivate future works to adapt and assess the performance of LLMs in BHC synthesis.

"An idea is nothing more nor less than a new combination of old elements" (Young, J.W.). The widespread adoption of Large Language Models (LLMs) and publicly available ChatGPT have marked a significant turning point in the integration of Artificial Intelligence (AI) into people's everyday lives. This study explores the capability of LLMs in generating novel research ideas based on information from research papers. We conduct a thorough examination of 4 LLMs in five domains (e.g., Chemistry, Computer, Economics, Medical, and Physics). We found that the future research ideas generated by Claude-2 and GPT-4 are more aligned with the author's perspective than GPT-3.5 and Gemini. We also found that Claude-2 generates more diverse future research ideas than GPT-4, GPT-3.5, and Gemini 1.0. We further performed a human evaluation of the novelty, relevancy, and feasibility of the generated future research ideas. This investigation offers insights into the evolving role of LLMs in idea generation, highlighting both its capability and limitations. Our work contributes to the ongoing efforts in evaluating and utilizing language models for generating future research ideas. We make our datasets and codes publicly available.

Medical information retrieval (MIR) is essential for retrieving relevant medical knowledge from diverse sources, including electronic health records, scientific literature, and medical databases. However, achieving effective zero-shot dense retrieval in the medical domain poses substantial challenges due to the lack of relevance-labeled data. In this paper, we introduce a novel approach called Self-Learning Hypothetical Document Embeddings (SL-HyDE) to tackle this issue. SL-HyDE leverages large language models (LLMs) as generators to generate hypothetical documents based on a given query. These generated documents encapsulate key medical context, guiding a dense retriever in identifying the most relevant documents. The self-learning framework progressively refines both pseudo-document generation and retrieval, utilizing unlabeled medical corpora without requiring any relevance-labeled data. Additionally, we present the Chinese Medical Information Retrieval Benchmark (CMIRB), a comprehensive evaluation framework grounded in real-world medical scenarios, encompassing five tasks and ten datasets. By benchmarking ten models on CMIRB, we establish a rigorous standard for evaluating medical information retrieval systems. Experimental results demonstrate that SL-HyDE significantly surpasses existing methods in retrieval accuracy while showcasing strong generalization and scalability across various LLM and retriever configurations. CMIRB data and evaluation code are publicly available at: https://github.com/CMIRB-benchmark/CMIRB.

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

Large language models (LLMs) have demonstrated remarkable capability to generate fluent responses to a wide variety of user queries, but this has also resulted in concerns regarding the potential misuse of such texts in journalism, educational, and academic context. In this work, we aim to develop automatic systems to identify machine-generated text and to detect potential misuse. We first introduce a large-scale benchmark M4, which is multi-generator, multi-domain, and multi-lingual corpus for machine-generated text detection. Using the dataset, we experiment with a number of methods and we show that it is challenging for detectors to generalize well on unseen examples if they are either from different domains or are generated by different large language models. In such cases, detectors tend to misclassify machine-generated text as human-written. These results show that the problem is far from solved and there is a lot of room for improvement. We believe that our dataset M4, which covers different generators, domains and languages, will enable future research towards more robust approaches for this pressing societal problem. The M4 dataset is available at https://github.com/mbzuai-nlp/M4.

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

Learning to represent free text is a core task in many clinical machine learning (ML) applications, as clinical text contains observations and plans not otherwise available for inference. State-of-the-art methods use large language models developed with immense computational resources and training data; however, applying these models is challenging because of the highly varying syntax and vocabulary in clinical free text. Structured information such as International Classification of Disease (ICD) codes often succinctly abstracts the most important facts of a clinical encounter and yields good performance, but is often not as available as clinical text in real-world scenarios. We propose a multi-view learning framework that jointly learns from codes and text to combine the availability and forward-looking nature of text and better performance of ICD codes. The learned text embeddings can be used as inputs to predictive algorithms independent of the ICD codes during inference. Our approach uses a Graph Neural Network (GNN) to process ICD codes, and Bi-LSTM to process text. We apply Deep Canonical Correlation Analysis (DCCA) to enforce the two views to learn a similar representation of each patient. In experiments using planned surgical procedure text, our model outperforms BERT models fine-tuned to clinical data, and in experiments using diverse text in MIMIC-III, our model is competitive to a fine-tuned BERT at a tiny fraction of its computational effort.

Personalization in Information Retrieval (IR) is a topic studied by the research community since a long time. However, there is still a lack of datasets to conduct large-scale evaluations of personalized IR; this is mainly due to the fact that collecting and curating high-quality user-related information requires significant costs and time investment. Furthermore, the creation of datasets for Personalized IR (PIR) tasks is affected by both privacy concerns and the need for accurate user-related data, which are often not publicly available. Recently, researchers have started to explore the use of Large Language Models (LLMs) to generate synthetic datasets, which is a possible solution to generate data for low-resource tasks. In this paper, we investigate the potential of Large Language Models (LLMs) for generating synthetic documents to train an IR system for a Personalized Community Question Answering task. To study the effectiveness of IR models fine-tuned on LLM-generated data, we introduce a new dataset, named Sy-SE-PQA. We build Sy-SE-PQA based on an existing dataset, SE-PQA, which consists of questions and answers posted on the popular StackExchange communities. Starting from questions in SE-PQA, we generate synthetic answers using different prompt techniques and LLMs. Our findings suggest that LLMs have high potential in generating data tailored to users' needs. The synthetic data can replace human-written training data, even if the generated data may contain incorrect information.

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.

Recently, there has been a rise in the development of powerful pre-trained natural language models, including GPT-2, Grover, and XLM. These models have shown state-of-the-art capabilities towards a variety of different NLP tasks, including question answering, content summarisation, and text generation. Alongside this, there have been many studies focused on online authorship attribution (AA). That is, the use of models to identify the authors of online texts. Given the power of natural language models in generating convincing texts, this paper examines the degree to which these language models can generate texts capable of deceiving online AA models. Experimenting with both blog and Twitter data, we utilise GPT-2 language models to generate texts using the existing posts of online users. We then examine whether these AI-based text generators are capable of mimicking authorial style to such a degree that they can deceive typical AA models. From this, we find that current AI-based text generators are able to successfully mimic authorship, showing capabilities towards this on both datasets. Our findings, in turn, highlight the current capacity of powerful natural language models to generate original online posts capable of mimicking authorial style sufficiently to deceive popular AA methods; a key finding given the proposed role of AA in real world applications such as spam-detection and forensic investigation.

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

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

There has been an increasing research interest in developing specialized dialogue systems that can offer mental health support. However, gathering large-scale and real-life multi-turn conversations for mental health support poses challenges due to the sensitivity of personal information, as well as the time and cost involved. To address these issues, we introduce the SMILE approach, an inclusive language expansion technique that employs ChatGPT to extend public single-turn dialogues into multi-turn ones. Our research first presents a preliminary exploratory study that validates the effectiveness of the SMILE approach. Furthermore, we conduct a comprehensive and systematic contrastive analysis of datasets generated with and without the SMILE approach, demonstrating that the SMILE method results in a large-scale, diverse, and close-to-real-life multi-turn mental health support conversation corpus, including dialog topics, lexical and semantic features. Finally, we use the collected corpus (SMILECHAT) to develop a more effective dialogue system that offers emotional support and constructive suggestions in multi-turn conversations for mental health support.

Summaries of medical text shall be faithful by being consistent and factual with source inputs, which is an important but understudied topic for safety and efficiency in healthcare. In this paper, we investigate and improve faithfulness in summarization on a broad range of medical summarization tasks. Our investigation reveals that current summarization models often produce unfaithful outputs for medical input text. We then introduce FaMeSumm, a framework to improve faithfulness by fine-tuning pre-trained language models based on medical knowledge. FaMeSumm performs contrastive learning on designed sets of faithful and unfaithful summaries, and it incorporates medical terms and their contexts to encourage faithful generation of medical terms. We conduct comprehensive experiments on three datasets in two languages: health question and radiology report summarization datasets in English, and a patient-doctor dialogue dataset in Chinese. Results demonstrate that FaMeSumm is flexible and effective by delivering consistent improvements over mainstream language models such as BART, T5, mT5, and PEGASUS, yielding state-of-the-art performances on metrics for faithfulness and general quality. Human evaluation by doctors also shows that FaMeSumm generates more faithful outputs. Our code is available at https://github.com/psunlpgroup/FaMeSumm .

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.

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

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.

Keyphrase generation is the task of predicting a set of lexical units that conveys the main content of a source text. Existing datasets for keyphrase generation are only readily available for the scholarly domain and include non-expert annotations. In this paper we present KPTimes, a large-scale dataset of news texts paired with editor-curated keyphrases. Exploring the dataset, we show how editors tag documents, and how their annotations differ from those found in existing datasets. We also train and evaluate state-of-the-art neural keyphrase generation models on KPTimes to gain insights on how well they perform on the news domain. The dataset is available online at https://github.com/ygorg/KPTimes .

The growing prominence of large language models, such as GPT-4 and ChatGPT, has led to increased concerns over academic integrity due to the potential for machine-generated content and paraphrasing. Although studies have explored the detection of human- and machine-paraphrased content, the comparison between these types of content remains underexplored. In this paper, we conduct a comprehensive analysis of various datasets commonly employed for paraphrase detection tasks and evaluate an array of detection methods. Our findings highlight the strengths and limitations of different detection methods in terms of performance on individual datasets, revealing a lack of suitable machine-generated datasets that can be aligned with human expectations. Our main finding is that human-authored paraphrases exceed machine-generated ones in terms of difficulty, diversity, and similarity implying that automatically generated texts are not yet on par with human-level performance. Transformers emerged as the most effective method across datasets with TF-IDF excelling on semantically diverse corpora. Additionally, we identify four datasets as the most diverse and challenging for paraphrase detection.

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.

Recently, retrieval-augmented text generation attracted increasing attention of the computational linguistics community. Compared with conventional generation models, retrieval-augmented text generation has remarkable advantages and particularly has achieved state-of-the-art performance in many NLP tasks. This paper aims to conduct a survey about retrieval-augmented text generation. It firstly highlights the generic paradigm of retrieval-augmented generation, and then it reviews notable approaches according to different tasks including dialogue response generation, machine translation, and other generation tasks. Finally, it points out some important directions on top of recent methods to facilitate future research.

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

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.

The introduction of ChatGPT has garnered widespread attention in both academic and industrial communities. ChatGPT is able to respond effectively to a wide range of human questions, providing fluent and comprehensive answers that significantly surpass previous public chatbots in terms of security and usefulness. On one hand, people are curious about how ChatGPT is able to achieve such strength and how far it is from human experts. On the other hand, people are starting to worry about the potential negative impacts that large language models (LLMs) like ChatGPT could have on society, such as fake news, plagiarism, and social security issues. In this work, we collected tens of thousands of comparison responses from both human experts and ChatGPT, with questions ranging from open-domain, financial, medical, legal, and psychological areas. We call the collected dataset the Human ChatGPT Comparison Corpus (HC3). Based on the HC3 dataset, we study the characteristics of ChatGPT's responses, the differences and gaps from human experts, and future directions for LLMs. We conducted comprehensive human evaluations and linguistic analyses of ChatGPT-generated content compared with that of humans, where many interesting results are revealed. After that, we conduct extensive experiments on how to effectively detect whether a certain text is generated by ChatGPT or humans. We build three different detection systems, explore several key factors that influence their effectiveness, and evaluate them in different scenarios. The dataset, code, and models are all publicly available at https://github.com/Hello-SimpleAI/chatgpt-comparison-detection.

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).

Medical vision-and-language models (MVLMs) have attracted substantial interest due to their capability to offer a natural language interface for interpreting complex medical data. Their applications are versatile and have the potential to improve diagnostic accuracy and decision-making for individual patients while also contributing to enhanced public health monitoring, disease surveillance, and policy-making through more efficient analysis of large data sets. MVLMS integrate natural language processing with medical images to enable a more comprehensive and contextual understanding of medical images alongside their corresponding textual information. Unlike general vision-and-language models trained on diverse, non-specialized datasets, MVLMs are purpose-built for the medical domain, automatically extracting and interpreting critical information from medical images and textual reports to support clinical decision-making. Popular clinical applications of MVLMs include automated medical report generation, medical visual question answering, medical multimodal segmentation, diagnosis and prognosis and medical image-text retrieval. Here, we provide a comprehensive overview of MVLMs and the various medical tasks to which they have been applied. We conduct a detailed analysis of various vision-and-language model architectures, focusing on their distinct strategies for cross-modal integration/exploitation of medical visual and textual features. We also examine the datasets used for these tasks and compare the performance of different models based on standardized evaluation metrics. Furthermore, we highlight potential challenges and summarize future research trends and directions. The full collection of papers and codes is available at: https://github.com/YtongXie/Medical-Vision-and-Language-Tasks-and-Methodologies-A-Survey.

Probabilistic text generators have been used to produce fake scientific papers for more than a decade. Such nonsensical papers are easily detected by both human and machine. Now more complex AI-powered generation techniques produce texts indistinguishable from that of humans and the generation of scientific texts from a few keywords has been documented. Our study introduces the concept of tortured phrases: unexpected weird phrases in lieu of established ones, such as 'counterfeit consciousness' instead of 'artificial intelligence.' We combed the literature for tortured phrases and study one reputable journal where these concentrated en masse. Hypothesising the use of advanced language models we ran a detector on the abstracts of recent articles of this journal and on several control sets. The pairwise comparisons reveal a concentration of abstracts flagged as 'synthetic' in the journal. We also highlight irregularities in its operation, such as abrupt changes in editorial timelines. We substantiate our call for investigation by analysing several individual dubious articles, stressing questionable features: tortured writing style, citation of non-existent literature, and unacknowledged image reuse. Surprisingly, some websites offer to rewrite texts for free, generating gobbledegook full of tortured phrases. We believe some authors used rewritten texts to pad their manuscripts. We wish to raise the awareness on publications containing such questionable AI-generated or rewritten texts that passed (poor) peer review. Deception with synthetic texts threatens the integrity of the scientific literature.