Proteins play critical roles in biological systems, yet 99.7% of over 227 million known protein sequences remain uncharacterized due to the limitations of experimental methods. To assist experimentalists in narrowing down hypotheses and accelerating protein characterization, we present Protein2Text, a multimodal large language model that interprets protein sequences and generates informative text to address open-ended questions about protein functions and attributes. By integrating a resampling mechanism within an adapted LLaVA framework, our model effectively maps protein sequences into a language-compatible space, enhancing its capability to handle diverse and complex queries. Trained on a newly curated dataset derived from PubMed articles and rigorously evaluated using four comprehensive benchmarks-including in-domain and cross-domain evaluations-Protein2Text outperforms several existing models in open-ended question-answering tasks. Our work also highlights the limitations of current evaluation metrics applied to template-based approaches, which may lead to misleading results, emphasizing the need for unbiased assessment methods. Our model weights, evaluation datasets, and evaluation scripts are publicly available at https://github.com/alaaj27/Protein2Text.git.
While NLP models often seek to capture cognitive states via language, the validity of predicted states is determined by comparing them to annotations created without access the cognitive states of the authors. In behavioral sciences, cognitive states are instead measured via experiments. Here, we introduce an experiment-based framework for evaluating language-based cognitive style models against human behavior. We explore the phenomenon of decision making, and its relationship to the linguistic style of an individual talking about a recent decision they made. The participants then follow a classical decision-making experiment that captures their cognitive style, determined by how preferences change during a decision exercise. We find that language features, intended to capture cognitive style, can predict participants' decision style with moderate-to-high accuracy (AUC 0.8), demonstrating that cognitive style can be partly captured and revealed by discourse patterns.
Automatic question generation (QG) is essential for AI and NLP, particularly in intelligent tutoring, dialogue systems, and fact verification. Generating multiple-choice questions (MCQG) for professional exams, like the United States Medical Licensing Examination (USMLE), is particularly challenging, requiring domain expertise and complex multi-hop reasoning for high-quality questions. However, current large language models (LLMs) like GPT-4 struggle with professional MCQG due to outdated knowledge, hallucination issues, and prompt sensitivity, resulting in unsatisfactory quality and difficulty. To address these challenges, we propose MCQG-SRefine, an LLM self-refine-based (Critique and Correction) framework for converting medical cases into high-quality USMLE-style questions. By integrating expert-driven prompt engineering with iterative self-critique and self-correction feedback, MCQG-SRefine significantly enhances human expert satisfaction regarding both the quality and difficulty of the questions. Furthermore, we introduce an LLM-as-Judge-based automatic metric to replace the complex and costly expert evaluation process, ensuring reliable and expert-aligned assessments.
The cloze training objective of Masked Language Models makes them a natural choice for generating plausible distractors for human cloze questions. However, distractors must also be both distinct and incorrect, neither of which is directly addressed by existing neural methods. Evaluation of recent models has also relied largely on automated metrics, which cannot demonstrate the reliability or validity of human comprehension tests. In this work, we first formulate the pedagogically motivated objectives of plausibility, incorrectness, and distinctiveness in terms of conditional distributions from language models. Second, we present an unsupervised, interpretable method that uses these objectives to jointly optimize sets of distractors. Third, we test the reliability and validity of the resulting cloze tests compared to other methods with human participants. We find our method has stronger correlation with teacher-created comprehension tests than the state-of-the-art neural method and is more internally consistent. Our implementation is freely available and can quickly create a multiple choice cloze test from any given passage.
Pre-trained language models (PLMs) have attracted enormous attention over the past few years with their unparalleled performances. Meanwhile, the soaring cost to train PLMs as well as their amazing generalizability have jointly contributed to few-shot fine-tuning and prompting as the most popular training paradigms for natural language processing (NLP) models. Nevertheless, existing studies have shown that these NLP models can be backdoored such that model behavior is manipulated when trigger tokens are presented. In this paper, we propose PromptFix, a novel backdoor mitigation strategy for NLP models via adversarial prompt-tuning in few-shot settings. Unlike existing NLP backdoor removal methods, which rely on accurate trigger inversion and subsequent model fine-tuning, PromptFix keeps the model parameters intact and only utilizes two extra sets of soft tokens which approximate the trigger and counteract it respectively. The use of soft tokens and adversarial optimization eliminates the need to enumerate possible backdoor configurations and enables an adaptive balance between trigger finding and preservation of performance. Experiments with various backdoor attacks validate the effectiveness of the proposed method and the performances when domain shift is present further shows PromptFix's applicability to models pretrained on unknown data source which is the common case in prompt tuning scenarios.
Mental health issues differ widely among individuals, with varied signs and symptoms. Recently, language-based assessments have shown promise in capturing this diversity, but they require a substantial sample of words per person for accuracy. This work introduces the task of Adaptive Language-Based Assessment (ALBA), which involves adaptively ordering questions while also scoring an individual's latent psychological trait using limited language responses to previous questions. To this end, we develop adaptive testing methods under two psychometric measurement theories: Classical Test Theory and Item Response Theory. We empirically evaluate ordering and scoring strategies, organizing into two new methods: a semi-supervised item response theory-based method (ALIRT) and a supervised Actor-Critic model. While we found both methods to improve over non-adaptive baselines, We found ALIRT to be the most accurate and scalable, achieving the highest accuracy with fewer questions (e.g., Pearson r ≈ 0.93 after only 3 questions as compared to typically needing at least 7 questions). In general, adaptive language-based assessments of depression and anxiety were able to utilize a smaller sample of language without compromising validity or large computational costs.
Many diagnostic errors occur because clinicians cannot easily access relevant information in patient Electronic Health Records (EHRs). In this work we propose a method to use LLMs to identify pieces of evidence in patient EHR data that indicate increased or decreased risk of specific diagnoses; our ultimate aim is to increase access to evidence and reduce diagnostic errors. In particular, we propose a Neural Additive Model to make predictions backed by evidence with individualized risk estimates at time-points where clinicians are still uncertain, aiming to specifically mitigate delays in diagnosis and errors stemming from an incomplete differential. To train such a model, it is necessary to infer temporally fine-grained retrospective labels of eventual "true" diagnoses. We do so with LLMs, to ensure that the input text is from before a confident diagnosis can be made. We use an LLM to retrieve an initial pool of evidence, but then refine this set of evidence according to correlations learned by the model. We conduct an in-depth evaluation of the usefulness of our approach by simulating how it might be used by a clinician to decide between a pre-defined list of differential diagnoses.
Scientific jargon can impede researchers when they read materials from other domains. Current methods of jargon identification mainly use corpus-level familiarity indicators (e.g., Simple Wikipedia represents plain language). However, researchers' familiarity of a term can vary greatly based on their own background. We collect a dataset of over 10K term familiarity annotations from 11 computer science researchers for terms drawn from 100 paper abstracts. Analysis of this data reveals that jargon familiarity and information needs vary widely across annotators, even within the same sub-domain (e.g., NLP). We investigate features representing individual, sub-domain, and domain knowledge to predict individual jargon familiarity. We compare supervised and prompt-based approaches, finding that prompt-based methods including personal publications yields the highest accuracy, though zero-shot prompting provides a strong baseline. This research offers insight into features and methods to integrate personal data into scientific jargon identification.
Opioid related aberrant behaviors (ORABs) present novel risk factors for opioid overdose. This paper introduces a novel biomedical natural language processing benchmark dataset named ODD, for ORAB Detection Dataset. ODD is an expert-annotated dataset designed to identify ORABs from patients' EHR notes and classify them into nine categories; 1) Confirmed Aberrant Behavior, 2) Suggested Aberrant Behavior, 3) Opioids, 4) Indication, 5) Diagnosed opioid dependency, 6) Benzodiazepines, 7) Medication Changes, 8) Central Nervous System-related, and 9) Social Determinants of Health. We explored two state-of-the-art natural language processing models (fine-tuning and prompt-tuning approaches) to identify ORAB. Experimental results show that the prompt-tuning models outperformed the fine-tuning models in most categories and the gains were especially higher among uncommon categories (Suggested Aberrant Behavior, Confirmed Aberrant Behaviors, Diagnosed Opioid Dependence, and Medication Change). Although the best model achieved the highest 88.17% on macro average area under precision recall curve, uncommon classes still have a large room for performance improvement. ODD is publicly available.
Suicide is an important public health concern and one of the leading causes of death worldwide. Suicidal behaviors, including suicide attempts (SA) and suicide ideations (SI), are leading risk factors for death by suicide. Information related to patients' previous and current SA and SI are frequently documented in the electronic health record (EHR) notes. Accurate detection of such documentation may help improve surveillance and predictions of patients' suicidal behaviors and alert medical professionals for suicide prevention efforts. In this study, we first built Suicide Attempt and Ideation Events (ScAN) dataset, a subset of the publicly available MIMIC III dataset spanning over 12k+ EHR notes with 19k+ annotated SA and SI events information. The annotations also contain attributes such as method of suicide attempt. We also provide a strong baseline model ScANER (Suicide Attempt and Ideation Events Retriever), a multi-task RoBERTa-based model with a retrieval module to extract all the relevant suicidal behavioral evidences from EHR notes of an hospital-stay and, and a prediction module to identify the type of suicidal behavior (SA and SI) concluded during the patient's stay at the hospital. ScANER achieved a macro-weighted F1-score of 0.83 for identifying suicidal behavioral evidences and a macro F1-score of 0.78 and 0.60 for classification of SA and SI for the patient's hospital-stay, respectively. ScAN and ScANER are publicly available.
Summarization of clinical narratives is a long-standing research problem. Here, we introduce the task of hospital-course summarization. Given the documentation authored throughout a patient's hospitalization, generate a paragraph that tells the story of the patient admission. We construct an English, text-to-text dataset of 109,000 hospitalizations (2M source notes) and their corresponding summary proxy: the clinician-authored "Brief Hospital Course" paragraph written as part of a discharge note. Exploratory analyses reveal that the BHC paragraphs are highly abstractive with some long extracted fragments; are concise yet comprehensive; differ in style and content organization from the source notes; exhibit minimal lexical cohesion; and represent silver-standard references. Our analysis identifies multiple implications for modeling this complex, multi-document summarization task.
Analysis of client and therapist behavior in counseling sessions can provide helpful insights for assessing the quality of the session and consequently, the client's behavioral outcome. In this paper, we study the automatic classification of standardized behavior codes (i.e. annotations) used for assessment of psychotherapy sessions in Motivational Interviewing (MI). We develop models and examine the classification of client behaviors throughout MI sessions, comparing the performance by models trained on large pretrained embeddings (RoBERTa) versus interpretable and expert-selected features (LIWC). Our best performing model using the pretrained RoBERTa embeddings beats the baseline model, achieving an F1 score of 0.66 in the subject-independent 3-class classification. Through statistical analysis on the classification results, we identify prominent LIWC features that may not have been captured by the model using pretrained embeddings. Although classification using LIWC features underperforms RoBERTa, our findings motivate the future direction of incorporating auxiliary tasks in the classification of MI codes.
Embeddings of words and concepts capture syntactic and semantic regularities of language; however, they have seen limited use as tools to study characteristics of different corpora and how they relate to one another. We introduce TextEssence, an interactive system designed to enable comparative analysis of corpora using embeddings. TextEssence includes visual, neighbor-based, and similarity-based modes of embedding analysis in a lightweight, web-based interface. We further propose a new measure of embedding confidence based on nearest neighborhood overlap, to assist in identifying high-quality embeddings for corpus analysis. A case study on COVID-19 scientific literature illustrates the utility of the system. TextEssence can be found at https://textessence.github.io.
To keep pace with the increased generation and digitization of documents, automated methods that can improve search, discovery and mining of the vast body of literature are essential. Keyphrases provide a concise representation by identifying salient concepts in a document. Various supervised approaches model keyphrase extraction using local context to predict the label for each token and perform much better than the unsupervised counterparts. Unfortunately, this method fails for short documents where the context is unclear. Moreover, keyphrases, which are usually the gist of a document, need to be the central theme. We propose a new extraction model that introduces a centrality constraint to enrich the word representation of a Bidirectional long short-term memory. Performance evaluation on two publicly available datasets demonstrate our model outperforms existing state-of-the art approaches. Our model is publicly available at https://github.com/ZHgero/keyphrases_centrality.git.
In human-level NLP tasks, such as predicting mental health, personality, or demographics, the number of observations is often smaller than the standard 768+ hidden state sizes of each layer within modern transformer-based language models, limiting the ability to effectively leverage transformers. Here, we provide a systematic study on the role of dimension reduction methods (principal components analysis, factorization techniques, or multi-layer auto-encoders) as well as the dimensionality of embedding vectors and sample sizes as a function of predictive performance. We first find that fine-tuning large models with a limited amount of data pose a significant difficulty which can be overcome with a pre-trained dimension reduction regime. RoBERTa consistently achieves top performance in human-level tasks, with PCA giving benefit over other reduction methods in better handling users that write longer texts. Finally, we observe that a majority of the tasks achieve results comparable to the best performance with just 1/12 of the embedding dimensions.
Utilizing clinical texts in survival analysis is difficult because they are largely unstructured. Current automatic extraction models fail to capture textual information comprehensively since their labels are limited in scope. Furthermore, they typically require a large amount of data and high-quality expert annotations for training. In this work, we present a novel method of using BERT-based hidden layer representations of clinical texts as covariates for proportional hazards models to predict patient survival outcomes. We show that hidden layers yield notably more accurate predictions than predefined features, outperforming the previous baseline model by 5.7% on average across C-index and time-dependent AUC. We make our work publicly available at https://github.com/bionlplab/heart_failure_mortality.
Natural language processing (NLP) research combines the study of universal principles, through basic science, with applied science targeting specific use cases and settings. However, the process of exchange between basic NLP and applications is often assumed to emerge naturally, resulting in many innovations going unapplied and many important questions left unstudied. We describe a new paradigm of Translational NLP, which aims to structure and facilitate the processes by which basic and applied NLP research inform one another. Translational NLP thus presents a third research paradigm, focused on understanding the challenges posed by application needs and how these challenges can drive innovation in basic science and technology design. We show that many significant advances in NLP research have emerged from the intersection of basic principles with application needs, and present a conceptual framework outlining the stakeholders and key questions in translational research. Our framework provides a roadmap for developing Translational NLP as a dedicated research area, and identifies general translational principles to facilitate exchange between basic and applied research.
We consider the problem of learning to simplify medical texts. This is important because most reliable, up-to-date information in biomedicine is dense with jargon and thus practically inaccessible to the lay audience. Furthermore, manual simplification does not scale to the rapidly growing body of biomedical literature, motivating the need for automated approaches. Unfortunately, there are no large-scale resources available for this task. In this work we introduce a new corpus of parallel texts in English comprising technical and lay summaries of all published evidence pertaining to different clinical topics. We then propose a new metric based on likelihood scores from a masked language model pretrained on scientific texts. We show that this automated measure better differentiates between technical and lay summaries than existing heuristics. We introduce and evaluate baseline encoder-decoder Transformer models for simplification and propose a novel augmentation to these in which we explicitly penalize the decoder for producing "jargon" terms; we find that this yields improvements over baselines in terms of readability.
We introduce Trialstreamer, a living database of clinical trial reports. Here we mainly describe the evidence extraction component; this extracts from biomedical abstracts key pieces of information that clinicians need when appraising the literature, and also the relations between these. Specifically, the system extracts descriptions of trial participants, the treatments compared in each arm (the interventions), and which outcomes were measured. The system then attempts to infer which interventions were reported to work best by determining their relationship with identified trial outcome measures. In addition to summarizing individual trials, these extracted data elements allow automatic synthesis of results across many trials on the same topic. We apply the system at scale to all reports of randomized controlled trials indexed in MEDLINE, powering the automatic generation of evidence maps, which provide a global view of the efficacy of different interventions combining data from all relevant clinical trials on a topic. We make all code and models freely available alongside a demonstration of the web interface.
Unsupervised domain adaptation (UDA) is the task of modifying a statistical model trained on labeled data from a source domain to achieve better performance on data from a target domain, with access to only unlabeled data in the target domain. Existing state-of-the-art UDA approaches use neural networks to learn representations that can predict the values of subset of important features called "pivot features." In this work, we show that it is possible to improve on these methods by jointly training the representation learner with the task learner, and examine the importance of existing pivot selection methods.
