ymoslem/acl-abstracts huggingface dataset:
Archetypes and Entropy: Theory-Driven Extraction of Evidence for Suicide Risk (2024)

Research on psychological risk factors for suicide has developed for decades. However, combining explainable theory with modern data-driven language model approaches is non-trivial. In this study, we propose and evaluate methods for identifying language patterns aligned with theories of suicide risk by combining theory-driven suicidal archetypes with language model-based and relative entropy-based approaches. Archetypes are based on prototypical statements that evince risk of suicidality while relative entropy considers the ratio of how unusual both a risk-familiar and unfamiliar model find the statements. While both approaches independently performed similarly, we find that combining the two significantly improved the performance in the shared task evaluations, yielding our combined system submission with a BERTScore Recall of 0.906. Consistent with the literature, we find that titles are highly informative as suicide risk evidence, despite the brevity. We conclude that a combination of theory- and data-driven methods are needed in the mental health space and can outperform more modern prompt-based methods.
Exploring Robustness in Doctor-Patient Conversation Summarization: An Analysis of Out-of-Domain SOAP Notes (2024)

Summarizing medical conversations poses unique challenges due to the specialized domain and the difficulty of collecting in-domain training data. In this study, we investigate the performance of state-of-the-art doctor-patient conversation generative summarization models on the out-of-domain data. We divide the summarization model of doctor-patient conversation into two configurations: (1) a general model, without specifying subjective (S), objective (O), and assessment (A) and plan (P) notes; (2) a SOAP-oriented model that generates a summary with SOAP sections. We analyzed the limitations and strengths of the fine-tuning language model-based methods and GPTs on both configurations. We also conducted a Linguistic Inquiry and Word Count analysis to compare the SOAP notes from different datasets. The results exhibit a strong correlation for reference notes across different datasets, indicating that format mismatch (i.e., discrepancies in word distribution) is not the main cause of performance decline on out-of-domain data. Lastly, a detailed analysis of SOAP notes is included to provide insights into missing information and hallucinations introduced by the models.
Efficient Medical Question Answering with Knowledge-Augmented Question Generation (2024)

In the expanding field of language model applications, medical knowledge representation remains a significant challenge due to the specialized nature of the domain. Large language models, such as GPT-4, obtain reasonable scores on medical question-answering tasks, but smaller models are far behind.In this work, we introduce a method to improve the proficiency of a small language model in the medical domain by employing a two-fold approach. We first fine-tune the model on a corpus of medical textbooks. Then, we use GPT-4 to generate questions similar to the downstream task, prompted with textbook knowledge, and use them to fine-tune the model. Additionally, we introduce ECN-QA, a novel Medical QA dataset containing {\textquotedblleft}progressive questions{\textquotedblright} composed of related sequential questions. We show the benefits of our training strategy on this dataset.The study`s findings highlight the potential of small language models in the medical domain when appropriately fine-tuned.
Gemini Goes to Med School: Exploring the Capabilities of Multimodal Large Language Models on Medical Challenge Problems \& Hallucinations (2024)

Large language models have the potential to be valuable in the healthcare industry, but it`s crucial to verify their safety and effectiveness through rigorous evaluation. In our study, we evaluated LLMs, including Google`s Gemini, across various medical tasks. Despite Gemini`s capabilities, it underperformed compared to leading models like MedPaLM 2 and GPT-4, particularly in medical visual question answering (VQA), with a notable accuracy gap (Gemini at 61.45{\%} vs. GPT-4V at 88{\%}). Our analysis revealed that Gemini is highly susceptible to hallucinations, overconfidence, and knowledge gaps, which indicate risks if deployed uncritically. We also performed a detailed analysis by medical subject and test type, providing actionable feedback for developers and clinicians. To mitigate risks, we implemented effective prompting strategies, improving performance, and contributed to the field by releasing a Python module for medical LLM evaluation and establishing a leaderboard on Hugging Face for ongoing research and development. Python module can be found at https://github.com/promptslab/RosettaEval
Retrieval augmented text-to-SQL generation for epidemiological question answering using electronic health records (2024)

Electronic health records (EHR) and claims data are rich sources of real-world data that reflect patient health status and healthcare utilization. Querying these databases to answer epidemiological questions is challenging due to the intricacy of medical terminology and the need for complex SQL queries. Here, we introduce an end-to-end methodology that combines text-to-SQL generation with retrieval augmented generation (RAG) to answer epidemiological questions using EHR and claims data. We show that our approach, which integrates a medical coding step into the text-to-SQL process, significantly improves the performance over simple prompting. Our findings indicate that although current language models are not yet sufficiently accurate for unsupervised use, RAG offers a promising direction for improving their capabilities, as shown in a realistic industry setting.
ClinicalMamba: A Generative Clinical Language Model on Longitudinal Clinical Notes (2024)

The advancement of natural language processing (NLP) systems in healthcare hinges on language models' ability to interpret the intricate information contained within clinical notes. This process often requires integrating information from various time points in a patient`s medical history. However, most earlier clinical language models were pretrained with a context length limited to roughly one clinical document. In this study, We introduce ClinicalMamba, a specialized version of the Mamba language model, pretrained on a vast corpus of longitudinal clinical notes to address the unique linguistic characteristics and information processing needs of the medical domain. ClinicalMamba models, with 130 million and 2.8 billion parameters, demonstrate superior performance in modeling clinical language across extended text lengths compared to Mamba and other clinical models based on longformer and Llama. With few-shot learning, ClinicalMamba achieves notable benchmarks in speed and performance, outperforming existing clinical language models and large language models like GPT-4 in longitudinal clinical tasks.
Working Alliance Transformer for Psychotherapy Dialogue Classification (2024)

As a predictive measure of the treatment outcome in psychotherapy, the working alliance measures the agreement of the patient and the therapist in terms of their bond, task and goal. Long been a clinical quantity estimated by the patients' and therapists' self-evaluative reports, we believe that the working alliance can be better characterized using natural language processing technique directly in the dialogue transcribed in each therapy session. In this work, we propose the Working Alliance Transformer (WAT), a Transformer-based classification model that has a psychological state encoder which infers the working alliance scores by projecting the embedding of the dialogues turns onto the embedding space of the clinical inventory for working alliance. We evaluate our method in a real-world dataset with over 950 therapy sessions with anxiety, depression, schizophrenia and suicidal patients and demonstrate an empirical advantage of using information about therapeutic states in the sequence classification task of psychotherapy dialogues.
Building A German Clinical Named Entity Recognition System without In-domain Training Data (2024)

Clinical Named Entity Recognition (NER) is essential for extracting important medical insights from clinical narratives. Given the challenges in obtaining expert training datasets for real-world clinical applications related to data protection regulations and the lack of standardised entity types, this work represents a collaborative initiative aimed at building a German clinical NER system with a focus on addressing these obstacles effectively. In response to the challenge of training data scarcity, we propose a Conditional Relevance Learning (CRL) approach in low-resource transfer learning scenarios. CRL effectively leverages a pre-trained language model and domain-specific open resources, enabling the acquisition of a robust base model tailored for clinical NER tasks, particularly in the face of changing label sets. This flexibility empowers the implementation of a Multilayered Semantic Annotation (MSA) schema in our NER system, capable of organizing a diverse array of entity types, thus significantly boosting the NER system`s adaptability and utility across various clinical domains. In the case study, we demonstrate how our NER system can be applied to overcome resource constraints and comply with data privacy regulations. Lacking prior training on in-domain data, feedback from expert users in respective domains is essential in identifying areas for system refinement. Future work will focus on the integration of expert feedback to improve system performance in specific clinical contexts.
DAIC-WOZ: On the Validity of Using the Therapist`s prompts in Automatic Depression Detection from Clinical Interviews (2024)

Automatic depression detection from conversational data has gained significant interest in recent years.The DAIC-WOZ dataset, interviews conducted by a human-controlled virtual agent, has been widely used for this task.Recent studies have reported enhanced performance when incorporating interviewer`s prompts into the model.In this work, we hypothesize that this improvement might be mainly due to a bias present in these prompts, rather than the proposed architectures and methods.Through ablation experiments and qualitative analysis, we discover that models using interviewer`s prompts learn to focus on a specific region of the interviews, where questions about past experiences with mental health issues are asked, and use them as discriminative shortcuts to detect depressed participants. In contrast, models using participant responses gather evidence from across the entire interview.Finally, to highlight the magnitude of this bias, we achieve a 0.90 F1 score by intentionally exploiting it, the highest result reported to date on this dataset using only textual information.Our findings underline the need for caution when incorporating interviewers' prompts into models, as they may inadvertently learn to exploit targeted prompts, rather than learning to characterize the language and behavior that are genuinely indicative of the patient`s mental health condition.
Parameter-Efficient Fine-Tuning of LLaMA for the Clinical Domain (2024)

Adapting pretrained language models to novel domains, such as clinical applications, traditionally involves retraining their entire set of parameters. Parameter-Efficient Fine-Tuning (PEFT) techniques for fine-tuning language models significantly reduce computational requirements by selectively fine-tuning small subsets of parameters. In this study, we propose a two-step PEFT framework and evaluate it in the clinical domain. Our approach combines a specialised PEFT adapter layer designed for clinical domain adaptation with another adapter specialised for downstream tasks. We evaluate the framework on multiple clinical outcome prediction datasets, comparing it to clinically trained language models. Our framework achieves a better AUROC score averaged across all clinical downstream tasks compared to clinical language models. In particular, we observe large improvements of 4-5{\%} AUROC in large-scale multilabel classification tasks, such as diagnoses and procedures classification. To our knowledge, this study is the first to provide an extensive empirical analysis of the interplay between PEFT techniques and domain adaptation in an important real-world domain of clinical applications.
A Multilevel Analysis of PubMed-only BERT-based Biomedical Models (2024)

Biomedical NLP models play a big role in the automatic extraction of information from biomedical documents, such as COVID research papers. Three landmark models have led the way in this area: BioBERT, MSR BiomedBERT, and BioLinkBERT. However, their shallow evaluation {--}a single mean score{--} forbid us to better understand how the contributions proposed in each model advance the Biomedical NLP field. We show through a Multilevel Analysis how we can assess these contributions. Our analyses across 5000 fine-tuned models show that, actually, BiomedBERT`s true effect is bigger than BioLinkBERT`s effect, and the success of BioLinkBERT does not seem to be due to its contribution {--}the Link function{--} but due to an unknown factor.
A Privacy-Preserving Corpus for Occupational Health in Spanish: Evaluation for NER and Classification Tasks (2024)

Annotated corpora are essential to reliable natural language processing. While they are expensive to create, they are essential for building and evaluating systems. This study introduces a new corpus of 2,869 medical and admission reports collected by an occupational insurance and health provider. The corpus has been carefully annotated for personally identifiable information (PII) and is shared, masking this information. Two annotators adhered to annotation guidelines during the annotation process, and a referee later resolved annotation conflicts in a consolidation process to build a gold standard subcorpus. The inter-annotator agreement values, measured in F1, range between 0.86 and 0.93 depending on the selected subcorpus. The value of the corpus is demonstrated by evaluating its use for NER of PII and a classification task. The evaluations find that fine-tuned models and GPT-3.5 reach F1 of 0.911 and 0.720 in NER of PII, respectively. In the case of the insurance coverage classification task, using the original or de-identified corpus results in similar performance. The annotated data are released in de-identified form.
DERA: Enhancing Large Language Model Completions with Dialog-Enabled Resolving Agents (2024)

Large language models (LLMs) have emerged as valuable tools for many natural language understanding tasks. In safety-critical applications such as healthcare, the utility of these models is governed by their ability to generate factually accurate and complete outputs. In this work, we present dialog-enabled resolving agents (DERA). DERA is a paradigm made possible by the increased conversational abilities of LLMs. It provides a simple, interpretable forum for models to communicate feedback and iteratively improve output. We frame our dialog as a discussion between two agent types {--} a Researcher, who processes information and identifies crucial problem components, and a Decider, who has the autonomy to integrate the Researcher`s information and makes judgments on the final output.We test DERA against three clinically-focused tasks, with GPT-4 serving as our LLM. DERA shows significant improvement over the base GPT-4 performance in both human expert preference evaluations and quantitative metrics for medical conversation summarization and care plan generation. In a new finding, we also show that GPT-4`s performance (70{\%}) on an open-ended version of the MedQA question-answering (QA) dataset (Jin 2021; USMLE) is well above the passing level (60{\%}), with DERA showing similar performance. We will release the open-ended MedQA dataset.
LlamaMTS: Optimizing Metastasis Detection with Llama Instruction Tuning and BERT-Based Ensemble in Italian Clinical Reports (2024)

Information extraction from Electronic Health Records (EHRs) is a crucial task in healthcare, and the lack of resources and language specificity pose significant challenges. This study addresses the limited availability of Italian Natural Language Processing (NLP) tools for clinical applications and the computational demand of large language models (LLMs) for training. We present LlamaMTS, an instruction-tuned Llama for the Italian language, leveraging the LoRA technique. It is ensembled with a BERT-based model to classify EHRs based on the presence or absence of metastasis in patients affected by Breast cancer. Through our evaluation analysis, we discovered that LlamaMTS exhibits superior performance compared to both zero-shot LLMs and other Italian BERT-based models specifically fine-tuned on the same metastatic task. LlamaMTS demonstrates promising results in resource-constrained environments, offering a practical solution for information extraction from Italian EHRs in oncology, potentially improving patient care and outcomes.
Using Structured Health Information for Controlled Generation of Clinical Cases in French (2024)

Text generation opens up new prospects for overcoming the lack of open corpora in fields such as healthcare, where data sharing is bound by confidentiality. In this study, we compare the performance of encoder-decoder and decoder-only language models for the controlled generation of clinical cases in French. To do so, we fine-tuned several pre-trained models on French clinical cases for each architecture and generate clinical cases conditioned by patient demographic information (gender and age) and clinical features.Our results suggest that encoder-decoder models are easier to control than decoder-only models, but more costly to train.
Large Language Models Provide Human-Level Medical Text Snippet Labeling (2024)

This study evaluates the proficiency of Large Language Models (LLMs) in accurately labeling clinical document excerpts. Our focus is on the assignment of potential or confirmed diagnoses and medical procedures to snippets of medical text sourced from unstructured clinical patient records. We explore how the performance of LLMs compare against human annotators in classifying these excerpts. Employing a few-shot, chain-of-thought prompting approach with the MIMIC-III dataset, Med-PaLM 2 showcases annotation accuracy comparable to human annotators, achieving a notable precision rate of approximately 92{\%} relative to the gold standard labels established by human experts.
Conversational Topic Recommendation in Counseling and Psychotherapy with Decision Transformer and Large Language Models (2024)

Given the increasing demand for mental health assistance, artificial intelligence (AI), particularly large language models (LLMs), may be valuable for integration into automated clinical support systems. In this work, we leverage a decision transformer architecture for topic recommendation in counseling conversations between patients and mental health professionals. The architecture is utilized for offline reinforcement learning, and we extract states (dialogue turn embeddings), actions (conversation topics), and rewards (scores measuring the alignment between patient and therapist) from previous turns within a conversation to train a decision transformer model. We demonstrate an improvement over baseline reinforcement learning methods, and propose a novel system of utilizing our model`s output as synthetic labels for fine-tuning a large language model for the same task. Although our implementation based on LLaMA-2 7B has mixed results, future work can undoubtedly build on the design.
Leveraging Wikidata for Biomedical Entity Linking in a Low-Resource Setting: A Case Study for German (2024)

Biomedical Entity Linking (BEL) is a challenging task for low-resource languages, due to the lack of appropriate resources: datasets, knowledge bases (KBs), and pre-trained models. In this paper, we propose an approach to create a biomedical knowledge base for German BEL using UMLS information from Wikidata, that provides good coverage and can be easily extended to further languages. As a further contribution, we adapt several existing approaches for use in the German BEL setup, and report on their results. The chosen methods include a sparse model using character n-grams, a multilingual biomedical entity linker, and two general-purpose text retrieval models. Our results show that a language-specific KB that provides good coverage leads to most improvement in entity linking performance, irrespective of the used model. The finetuned German BEL model, newly created UMLS$_{Wikidata}$ KB as well as the code to reproduce our results are publicly available.
Revisiting Clinical Outcome Prediction for MIMIC-IV (2024)

Clinical Decision Support Systems assist medical professionals in providing optimal care for patients.A prominent data source used for creating tasks for such systems is the Medical Information Mart for Intensive Care (MIMIC).MIMIC contains electronic health records (EHR) gathered in a tertiary hospital in the United States.The majority of past work is based on the third version of MIMIC, although the fourth is the most recent version.This new version, not only introduces more data into MIMIC, but also increases the variety of patients.While MIMIC-III is limited to intensive care units, MIMIC-IV also offers EHRs from the emergency department.In this work, we investigate how to adapt previous work to update clinical outcome prediction for MIMIC-IV.We revisit several established tasks, including prediction of diagnoses, procedures, length-of-stay, and also introduce a novel task: patient routing prediction.Furthermore, we quantitatively and qualitatively evaluate all tasks on several bio-medical transformer encoder models.Finally, we provide narratives for future research directions in the clinical outcome prediction domain. We make our source code publicly available to reproduce our experiments, data, and tasks.
Can LLMs Correct Physicians, Yet? Investigating Effective Interaction Methods in the Medical Domain (2024)

We explore the potential of Large Language Models (LLMs) to assist and potentially correct physicians in medical decision-making tasks. We evaluate several LLMs, including Meditron, Llama2, and Mistral, to analyze the ability of these models to interact effectively with physicians across different scenarios. We consider questions from PubMedQA and several tasks, ranging from binary (yes/no) responses to long answer generation, where the answer of the model is produced after an interaction with a physician. Our findings suggest that prompt design significantly influences the downstream accuracy of LLMs and that LLMs can provide valuable feedback to physicians, challenging incorrect diagnoses and contributing to more accurate decision-making. For example, when the physician is accurate 38{\%} of the time, Mistral can produce the correct answer, improving accuracy up to 74{\%} depending on the prompt being used, while Llama2 and Meditron models exhibit greater sensitivity to prompt choice. Our analysis also uncovers the challenges of ensuring that LLM-generated suggestions are pertinent and useful, emphasizing the need for further research in this area.