Kevin Lybarger

Kevin Lybarger, Meliha Yetisgen, Özlem Uzuner

Objective: The n2c2/UW SDOH Challenge explores the extraction of social determinant of health (SDOH) information from clinical notes. The objectives include the advancement of natural language processing (NLP) information extraction techniques for SDOH and clinical information more broadly. This paper presents the shared task, data, participating teams, performance results, and considerations for future work. Materials and Methods: The task used the Social History Annotated Corpus (SHAC), which consists of clinical text with detailed event-based annotations for SDOH events such as alcohol, drug, tobacco, employment, and living situation. Each SDOH event is characterized through attributes related to status, extent, and temporality. The task includes three subtasks related to information extraction (Subtask A), generalizability (Subtask B), and learning transfer (Subtask C). In addressing this task, participants utilized a range of techniques, including rules, knowledge bases, n-grams, word embeddings, and pretrained language models (LM). Results: A total of 15 teams participated, and the top teams utilized pretrained deep learning LM. The top team across all subtasks used a sequence-to-sequence approach achieving 0.901 F1 for Subtask A, 0.774 F1 Subtask B, and 0.889 F1 for Subtask C. Conclusions: Similar to many NLP tasks and domains, pretrained LM yielded the best performance, including generalizability and learning transfer. An error analysis indicates extraction performance varies by SDOH, with lower performance achieved for conditions, like substance use and homelessness, that increase health risks (risk factors) and higher performance achieved for conditions, like substance abstinence and living with family, that reduce health risks (protective factors).

Giridhar Kaushik Ramachandran, Yujuan Fu, Bin Han et al. · uw

Social determinants of health (SDOH) documented in the electronic health record through unstructured text are increasingly being studied to understand how SDOH impacts patient health outcomes. In this work, we utilize the Social History Annotation Corpus (SHAC), a multi-institutional corpus of de-identified social history sections annotated for SDOH, including substance use, employment, and living status information. We explore the automatic extraction of SDOH information with SHAC in both standoff and inline annotation formats using GPT-4 in a one-shot prompting setting. We compare GPT-4 extraction performance with a high-performing supervised approach and perform thorough error analyses. Our prompt-based GPT-4 method achieved an overall 0.652 F1 on the SHAC test set, similar to the 7th best-performing system among all teams in the n2c2 challenge with SHAC.

Giridhar Kaushik Ramachandran, Kevin Lybarger, Yaya Liu et al.

An accurate and detailed account of patient medications, including medication changes within the patient timeline, is essential for healthcare providers to provide appropriate patient care. Healthcare providers or the patients themselves may initiate changes to patient medication. Medication changes take many forms, including prescribed medication and associated dosage modification. These changes provide information about the overall health of the patient and the rationale that led to the current care. Future care can then build on the resulting state of the patient. This work explores the automatic extraction of medication change information from free-text clinical notes. The Contextual Medication Event Dataset (CMED) is a corpus of clinical notes with annotations that characterize medication changes through multiple change-related attributes, including the type of change (start, stop, increase, etc.), initiator of the change, temporality, change likelihood, and negation. Using CMED, we identify medication mentions in clinical text and propose three novel high-performing BERT-based systems that resolve the annotated medication change characteristics. We demonstrate that our proposed systems improve medication change classification performance over the initial work exploring CMED.

Kevin Lybarger, Nicholas J Dobbins, Ritche Long et al.

Objective: Social determinants of health (SDOH) impact health outcomes and are documented in the electronic health record (EHR) through structured data and unstructured clinical notes. However, clinical notes often contain more comprehensive SDOH information, detailing aspects such as status, severity, and temporality. This work has two primary objectives: i) develop a natural language processing (NLP) information extraction model to capture detailed SDOH information and ii) evaluate the information gain achieved by applying the SDOH extractor to clinical narratives and combining the extracted representations with existing structured data. Materials and Methods: We developed a novel SDOH extractor using a deep learning entity and relation extraction architecture to characterize SDOH across various dimensions. In an EHR case study, we applied the SDOH extractor to a large clinical data set with 225,089 patients and 430,406 notes with social history sections and compared the extracted SDOH information with existing structured data. Results: The SDOH extractor achieved 0.86 F1 on a withheld test set. In the EHR case study, we found extracted SDOH information complements existing structured data with 32% of homeless patients, 19% of current tobacco users, and 10% of drug users only having these health risk factors documented in the clinical narrative. Conclusions: Utilizing EHR data to identify SDOH health risk factors and social needs may improve patient care and outcomes. Semantic representations of text-encoded SDOH information can augment existing structured data, and this more comprehensive SDOH representation can assist health systems in identifying and addressing these social needs.

Sitong Zhou, Kevin Lybarger, Meliha Yetisgen et al.

Symptom information is primarily documented in free-text clinical notes and is not directly accessible for downstream applications. To address this challenge, information extraction approaches that can handle clinical language variation across different institutions and specialties are needed. In this paper, we present domain generalization for symptom extraction using pretraining and fine-tuning data that differs from the target domain in terms of institution and/or specialty and patient population. We extract symptom events using a transformer-based joint entity and relation extraction method. To reduce reliance on domain-specific features, we propose a domain generalization method that dynamically masks frequent symptoms words in the source domain. Additionally, we pretrain the transformer language model (LM) on task-related unlabeled texts for better representation. Our experiments indicate that masking and adaptive pretraining methods can significantly improve performance when the source domain is more distant from the target domain.

Namu Park, Giridhar Kaushik Ramachandran, Kevin Lybarger et al.

Large language models (LLMs) have shown considerable promise in clinical natural language processing, yet few domain-specific datasets exist to rigorously evaluate their performance on radiology tasks. In this work, we introduce an annotated corpus of 6,393 radiology reports from 586 patients, each labeled for follow-up imaging status, to support the development and benchmarking of follow-up adherence detection systems. Using this corpus, we systematically compared traditional machine-learning classifiers, including logistic regression (LR), support vector machines (SVM), Longformer, and a fully fine-tuned Llama3-8B-Instruct, with recent generative LLMs. To evaluate generative LLMs, we tested GPT-4o and the open-source GPT-OSS-20B under two configurations: a baseline (Base) and a task-optimized (Advanced) setting that focused inputs on metadata, recommendation sentences, and their surrounding context. A refined prompt for GPT-OSS-20B further improved reasoning accuracy. Performance was assessed using precision, recall, and F1 scores with 95% confidence intervals estimated via non-parametric bootstrapping. Inter-annotator agreement was high (F1 = 0.846). GPT-4o (Advanced) achieved the best performance (F1 = 0.832), followed closely by GPT-OSS-20B (Advanced; F1 = 0.828). LR and SVM also performed strongly (F1 = 0.776 and 0.775), underscoring that while LLMs approach human-level agreement through prompt optimization, interpretable and resource-efficient models remain valuable baselines.

Yujuan Fu, Giridhar Kaushik Ramachandran, Ahmad Halwani et al.

Clinical notes contain unstructured representations of patient histories, including the relationships between medical problems and prescription drugs. To investigate the relationship between cancer drugs and their associated symptom burden, we extract structured, semantic representations of medical problem and drug information from the clinical narratives of oncology notes. We present Clinical Concept Annotations for Cancer Events and Relations (CACER), a novel corpus with fine-grained annotations for over 48,000 medical problems and drug events and 10,000 drug-problem and problem-problem relations. Leveraging CACER, we develop and evaluate transformer-based information extraction (IE) models such as BERT, Flan-T5, Llama3, and GPT-4 using fine-tuning and in-context learning (ICL). In event extraction, the fine-tuned BERT and Llama3 models achieved the highest performance at 88.2-88.0 F1, which is comparable to the inter-annotator agreement (IAA) of 88.4 F1. In relation extraction, the fine-tuned BERT, Flan-T5, and Llama3 achieved the highest performance at 61.8-65.3 F1. GPT-4 with ICL achieved the worst performance across both tasks. The fine-tuned models significantly outperformed GPT-4 in ICL, highlighting the importance of annotated training data and model optimization. Furthermore, the BERT models performed similarly to Llama3. For our task, LLMs offer no performance advantage over the smaller BERT models. The results emphasize the need for annotated training data to optimize models. Multiple fine-tuned transformer models achieved performance comparable to IAA for several extraction tasks.

Giridhar Kaushik Ramachandran, Haritha Gangavarapu, Kevin Lybarger et al.

In online forums like Reddit, users share their experiences with medical conditions and treatments, including making claims, asking questions, and discussing the effects of treatments on their health. Building systems to understand this information can effectively monitor the spread of misinformation and verify user claims. The Task-8 of the 2023 International Workshop on Semantic Evaluation focused on medical applications, specifically extracting patient experience- and medical condition-related entities from user posts on social media. The Reddit Health Online Talk (RedHot) corpus contains posts from medical condition-related subreddits with annotations characterizing the patient experience and medical conditions. In Subtask-1, patient experience is characterized by personal experience, questions, and claims. In Subtask-2, medical conditions are characterized by population, intervention, and outcome. For the automatic extraction of patient experiences and medical condition information, as a part of the challenge, we proposed language-model-based extraction systems that ranked $3^{rd}$ on both subtasks' leaderboards. In this work, we describe our approach and, in addition, explore the automatic extraction of this information using domain-specific language models and the inclusion of external knowledge.

Yujuan Velvin Fu, Giridhar Kaushik Ramachandran, Namu Park et al.

Large language models (LLMs) such as ChatGPT are fine-tuned on large and diverse instruction-following corpora, and can generalize to new tasks. However, those instruction-tuned LLMs often perform poorly in specialized medical natural language understanding (NLU) tasks that require domain knowledge, granular text comprehension, and structured data extraction. To bridge the gap, we: (1) propose a unified prompting format for 7 important NLU tasks, (2) curate an instruction-tuning dataset, MNLU-Instruct, utilizing diverse existing open-source medical NLU corpora, and (3) develop BioMistral-NLU, a generalizable medical NLU model, through fine-tuning BioMistral on MNLU-Instruct. We evaluate BioMistral-NLU in a zero-shot setting, across 6 important NLU tasks, from two widely adopted medical NLU benchmarks: BLUE and BLURB. Our experiments show that our BioMistral-NLU outperforms the original BioMistral, as well as the proprietary LLMs - ChatGPT and GPT-4. Our dataset-agnostic prompting strategy and instruction tuning step over diverse NLU tasks enhance LLMs' generalizability across diverse medical NLU tasks. Our ablation experiments show that instruction-tuning on a wider variety of tasks, even when the total number of training instances remains constant, enhances downstream zero-shot generalization.

Haritha Gangavarapu, Giridhar Kaushik Ramachandran, Kevin Lybarger et al.

A vast amount of medical knowledge is available for public use through online health forums, and question-answering platforms on social media. The majority of the population in the United States doesn't have the right amount of health literacy to make the best use of that information. Health literacy means the ability to obtain and comprehend the basic health information to make appropriate health decisions. To build the bridge between this gap, organizations advocate adapting this medical knowledge into plain language. Building robust systems to automate the adaptations helps both medical and non-medical professionals best leverage the available information online. The goal of the Plain Language Adaptation of Biomedical Abstracts (PLABA) track is to adapt the biomedical abstracts in English language extracted from PubMed based on the questions asked in MedlinePlus for the general public using plain language at the sentence level. As part of this track, we leveraged the best open-source Large Language Models suitable and fine-tuned for dialog use cases. We compare and present the results for all of our systems and our ranking among the other participants' submissions. Our top performing GPT-4 based model ranked first in the avg. simplicity measure and 3rd on the avg. accuracy measure.

Saadat Hasan Khan, Spencer Hong, Jingyu Wu et al.

Retrieval-augmented generation (RAG) is a common technique for grounding language model outputs in domain-specific information. However, RAG is often challenged by reasoning-intensive question-answering (QA), since common retrieval methods like cosine similarity maximize relevance at the cost of introducing redundant content, which can reduce information recall. To address this, we introduce Diversity-Focused Retrieval-Augmented Generation (DF-RAG), which systematically incorporates diversity into the retrieval step to improve performance on complex, reasoning-intensive QA benchmarks. DF-RAG builds upon the Maximal Marginal Relevance framework to select information chunks that are both relevant to the query and maximally dissimilar from each other. A key innovation of DF-RAG is its ability to optimize the level of diversity for each query dynamically at test time without requiring any additional fine-tuning or prior information. We show that DF-RAG improves F1 performance on reasoning-intensive QA benchmarks by 4-10 percent over vanilla RAG using cosine similarity and also outperforms other established baselines. Furthermore, we estimate an Oracle ceiling of up to 18 percent absolute F1 gains over vanilla RAG, of which DF-RAG captures up to 91.3 percent.

Yujuan Fu, Giridhar Kaushik Ramachandran, Nicholas J Dobbins et al.

Social determinants of health (SDoH) play a critical role in shaping health outcomes, particularly in pediatric populations where interventions can have long-term implications. SDoH are frequently studied in the Electronic Health Record (EHR), which provides a rich repository for diverse patient data. In this work, we present a novel annotated corpus, the Pediatric Social History Annotation Corpus (PedSHAC), and evaluate the automatic extraction of detailed SDoH representations using fine-tuned and in-context learning methods with Large Language Models (LLMs). PedSHAC comprises annotated social history sections from 1,260 clinical notes obtained from pediatric patients within the University of Washington (UW) hospital system. Employing an event-based annotation scheme, PedSHAC captures ten distinct health determinants to encompass living and economic stability, prior trauma, education access, substance use history, and mental health with an overall annotator agreement of 81.9 F1. Our proposed fine-tuning LLM-based extractors achieve high performance at 78.4 F1 for event arguments. In-context learning approaches with GPT-4 demonstrate promise for reliable SDoH extraction with limited annotated examples, with extraction performance at 82.3 F1 for event triggers.

Alphaeus Dmonte, Marcos Zampieri, Kevin Lybarger et al.

Politics is one of the most prevalent topics discussed on social media platforms, particularly during major election cycles, where users engage in conversations about candidates and electoral processes. Malicious actors may use this opportunity to disseminate misinformation to undermine trust in the electoral process. The emergence of Large Language Models (LLMs) exacerbates this issue by enabling malicious actors to generate misinformation at an unprecedented scale. Artificial intelligence (AI)-generated content is often indistinguishable from authentic user content, raising concerns about the integrity of information on social networks. In this paper, we present a novel taxonomy for characterizing election-related claims. This taxonomy provides an instrument for analyzing election-related claims, with granular categories related to jurisdiction, equipment, processes, and the nature of claims. We introduce ElectAI, a novel benchmark dataset that consists of 9,900 tweets, each labeled as human- or AI-generated. For AI-generated tweets, the specific LLM variant that produced them is specified. We annotated a subset of 1,550 tweets using the proposed taxonomy to capture the characteristics of election-related claims. We explored the capabilities of LLMs in extracting the taxonomy attributes and trained various machine learning models using ElectAI to distinguish between human- and AI-generated posts and identify the specific LLM variant.

Peter Beidler, Mark Nguyen, Kevin Lybarger et al.

PURPOSE: Incident reports are an important tool for safety and quality improvement in healthcare, but manual review is time-consuming and requires subject matter expertise. Here we present a natural language processing (NLP) screening tool to detect high-severity incident reports in radiation oncology across two institutions. METHODS AND MATERIALS: We used two text datasets to train and evaluate our NLP models: 7,094 reports from our institution (Inst.), and 571 from IAEA SAFRON (SF), all of which had severity scores labeled by clinical content experts. We trained and evaluated two types of models: baseline support vector machines (SVM) and BlueBERT which is a large language model pretrained on PubMed abstracts and hospitalized patient data. We assessed for generalizability of our model in two ways. First, we evaluated models trained using Inst.-train on SF-test. Second, we trained a BlueBERT_TRANSFER model that was first fine-tuned on Inst.-train then on SF-train before testing on SF-test set. To further analyze model performance, we also examined a subset of 59 reports from our Inst. dataset, which were manually edited for clarity. RESULTS Classification performance on the Inst. test achieved AUROC 0.82 using SVM and 0.81 using BlueBERT. Without cross-institution transfer learning, performance on the SF test was limited to an AUROC of 0.42 using SVM and 0.56 using BlueBERT. BlueBERT_TRANSFER, which was fine-tuned on both datasets, improved the performance on SF test to AUROC 0.78. Performance of SVM, and BlueBERT_TRANSFER models on the manually curated Inst. reports (AUROC 0.85 and 0.74) was similar to human performance (AUROC 0.81). CONCLUSION: In summary, we successfully developed cross-institution NLP models on incident report text from radiation oncology centers. These models were able to detect high-severity reports similarly to humans on a curated dataset.

Massimiliano Albanese, Xinming Ou, Kevin Lybarger et al.

Security Operations Centers (SOCs) face growing challenges in managing cybersecurity threats due to an overwhelming volume of alerts, a shortage of skilled analysts, and poorly integrated tools. Human-AI collaboration offers a promising path to augment the capabilities of SOC analysts while reducing their cognitive overload. To this end, we introduce an AI-driven human-machine co-teaming paradigm that leverages large language models (LLMs) to enhance threat intelligence, alert triage, and incident response workflows. We present a vision in which LLM-based AI agents learn from human analysts the tacit knowledge embedded in SOC operations, enabling the AI agents to improve their performance on SOC tasks through this co-teaming. We invite SOCs to collaborate with us to further develop this process and uncover replicable patterns where human-AI co-teaming yields measurable improvements in SOC productivity.

Namu Park, Kevin Lybarger, Giridhar Kaushik Ramachandran et al.

Medical imaging is critical to the diagnosis, surveillance, and treatment of many health conditions, including oncological, neurological, cardiovascular, and musculoskeletal disorders, among others. Radiologists interpret these complex, unstructured images and articulate their assessments through narrative reports that remain largely unstructured. This unstructured narrative must be converted into a structured semantic representation to facilitate secondary applications such as retrospective analyses or clinical decision support. Here, we introduce the Corpus of Annotated Medical Imaging Reports (CAMIR), which includes 609 annotated radiology reports from three imaging modality types: Computed Tomography, Magnetic Resonance Imaging, and Positron Emission Tomography-Computed Tomography. Reports were annotated using an event-based schema that captures clinical indications, lesions, and medical problems. Each event consists of a trigger and multiple arguments, and a majority of the argument types, including anatomy, normalize the spans to pre-defined concepts to facilitate secondary use. CAMIR uniquely combines a granular event structure and concept normalization. To extract CAMIR events, we explored two BERT (Bi-directional Encoder Representation from Transformers)-based architectures, including an existing architecture (mSpERT) that jointly extracts all event information and a multi-step approach (PL-Marker++) that we augmented for the CAMIR schema.

Md Tanvir Rouf Shawon, Mohammad Sabik Irbaz, Hadeel R. A. Elyazori et al.

Objective: This paper introduces a patient simulator designed to enable scalable, automated evaluation of healthcare conversational agents. The simulator generates realistic, controllable patient interactions that systematically vary across medical, linguistic, and behavioral dimensions, allowing annotators and an independent AI judge to assess agent performance, identify hallucinations and inaccuracies, and characterize risk patterns across diverse patient populations. Methods: The simulator is grounded in the NIST AI Risk Management Framework and integrates three profile components reflecting different dimensions of patient variation: (1) medical profiles constructed from electronic health records in the All of Us Research Program; (2) linguistic profiles modeling variation in health literacy and condition-specific communication patterns; and (3) behavioral profiles representing empirically observed interaction patterns, including cooperation, distraction, and adversarial engagement. We evaluated the simulator's effectiveness in identifying errors in an AI decision aid for antidepressant selection. Results: We generated 500 conversations between the patient simulator and the AI decision aid across systematic combinations of five linguistic and three behavioral profiles. Human annotators assessed 1,787 medical concepts across 100 conversations, achieving high agreement (F1=0.94, \k{appa}=0.73), and the LLM judge achieved comparable agreement with human annotators (F1=0.94, \k{appa}=0.78; paired bootstrap p=0.21). The simulator revealed a monotonic degradation in AI decision aid performance across the health literacy spectrum: rank-one concept retrieval accuracy increased from 47.9% for limited health literacy to 69.1% for functional and 81.6% for proficient.

Namu Park, Farzad Ahmed, Zhaoyi Sun et al.

Objective: To evaluate large language models (LLMs) against supervised baselines for fine-grained, lesion-level detection of incidentalomas requiring follow-up, addressing the limitations of current document-level classification systems. Methods: We utilized a dataset of 400 annotated radiology reports containing 1,623 verified lesion findings. We compared three supervised transformer-based encoders (BioClinicalModernBERT, ModernBERT, Clinical Longformer) against four generative LLM configurations (Llama 3.1-8B, GPT-4o, GPT-OSS-20b). We introduced a novel inference strategy using lesion-tagged inputs and anatomy-aware prompting to ground model reasoning. Performance was evaluated using class-specific F1-scores. Results: The anatomy-informed GPT-OSS-20b model achieved the highest performance, yielding an incidentaloma-positive macro-F1 of 0.79. This surpassed all supervised baselines (maximum macro-F1: 0.70) and closely matched the inter-annotator agreement of 0.76. Explicit anatomical grounding yielded statistically significant performance gains across GPT-based models (p < 0.05), while a majority-vote ensemble of the top systems further improved the macro-F1 to 0.90. Error analysis revealed that anatomy-aware LLMs demonstrated superior contextual reasoning in distinguishing actionable findings from benign lesions. Conclusion: Generative LLMs, when enhanced with structured lesion tagging and anatomical context, significantly outperform traditional supervised encoders and achieve performance comparable to human experts. This approach offers a reliable, interpretable pathway for automated incidental finding surveillance in radiology workflows.

Md Mushfiqur Rahman, Mohammad Sabik Irbaz, Kai North et al.

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.

Wilson Lau, Kevin Lybarger, Martin L. Gunn et al.

Radiology reports contain a diverse and rich set of clinical abnormalities documented by radiologists during their interpretation of the images. Comprehensive semantic representations of radiological findings would enable a wide range of secondary use applications to support diagnosis, triage, outcomes prediction, and clinical research. In this paper, we present a new corpus of radiology reports annotated with clinical findings. Our annotation schema captures detailed representations of pathologic findings that are observable on imaging ("lesions") and other types of clinical problems ("medical problems"). The schema used an event-based representation to capture fine-grained details, including assertion, anatomy, characteristics, size, count, etc. Our gold standard corpus contained a total of 500 annotated computed tomography (CT) reports. We extracted triggers and argument entities using two state-of-the-art deep learning architectures, including BERT. We then predicted the linkages between trigger and argument entities (referred to as argument roles) using a BERT-based relation extraction model. We achieved the best extraction performance using a BERT model pre-trained on 3 million radiology reports from our institution: 90.9%-93.4% F1 for finding triggers 72.0%-85.6% F1 for arguments roles. To assess model generalizability, we used an external validation set randomly sampled from the MIMIC Chest X-ray (MIMIC-CXR) database. The extraction performance on this validation set was 95.6% for finding triggers and 79.1%-89.7% for argument roles, demonstrating that the model generalized well to the cross-institutional data with a different imaging modality. We extracted the finding events from all the radiology reports in the MIMIC-CXR database and provided the extractions to the research community.

Kevin Lybarger, Aashka Damani, Martin Gunn et al.

Medical imaging is critical to the diagnosis and treatment of numerous medical problems, including many forms of cancer. Medical imaging reports distill the findings and observations of radiologists, creating an unstructured textual representation of unstructured medical images. Large-scale use of this text-encoded information requires converting the unstructured text to a structured, semantic representation. We explore the extraction and normalization of anatomical information in radiology reports that is associated with radiological findings. We investigate this extraction and normalization task using a span-based relation extraction model that jointly extracts entities and relations using BERT. This work examines the factors that influence extraction and normalization performance, including the body part/organ system, frequency of occurrence, span length, and span diversity. It discusses approaches for improving performance and creating high-quality semantic representations of radiological phenomena.

Kevin Lybarger, Linzee Mabrey, Matthew Thau et al.

Acute respiratory distress syndrome (ARDS) is a life-threatening condition that is often undiagnosed or diagnosed late. ARDS is especially prominent in those infected with COVID-19. We explore the automatic identification of ARDS indicators and confounding factors in free-text chest radiograph reports. We present a new annotated corpus of chest radiograph reports and introduce the Hierarchical Attention Network with Sentence Objectives (HANSO) text classification framework. HANSO utilizes fine-grained annotations to improve document classification performance. HANSO can extract ARDS-related information with high performance by leveraging relation annotations, even if the annotated spans are noisy. Using annotated chest radiograph images as a gold standard, HANSO identifies bilateral infiltrates, an indicator of ARDS, in chest radiograph reports with performance (0.87 F1) comparable to human annotations (0.84 F1). This algorithm could facilitate more efficient and expeditious identification of ARDS by clinicians and researchers and contribute to the development of new therapies to improve patient care.

Kevin Lybarger, Mari Ostendorf, Matthew Thompson et al.

Coronavirus disease 2019 (COVID-19) is a global pandemic. Although much has been learned about the novel coronavirus since its emergence, there are many open questions related to tracking its spread, describing symptomology, predicting the severity of infection, and forecasting healthcare utilization. Free-text clinical notes contain critical information for resolving these questions. Data-driven, automatic information extraction models are needed to use this text-encoded information in large-scale studies. This work presents a new clinical corpus, referred to as the COVID-19 Annotated Clinical Text (CACT) Corpus, which comprises 1,472 notes with detailed annotations characterizing COVID-19 diagnoses, testing, and clinical presentation. We introduce a span-based event extraction model that jointly extracts all annotated phenomena, achieving high performance in identifying COVID-19 and symptom events with associated assertion values (0.83-0.97 F1 for events and 0.73-0.79 F1 for assertions). In a secondary use application, we explored the prediction of COVID-19 test results using structured patient data (e.g. vital signs and laboratory results) and automatically extracted symptom information. The automatically extracted symptoms improve prediction performance, beyond structured data alone.

Kevin Lybarger, Mari Ostendorf, Meliha Yetisgen

Social determinants of health (SDOH) affect health outcomes, and knowledge of SDOH can inform clinical decision-making. Automatically extracting SDOH information from clinical text requires data-driven information extraction models trained on annotated corpora that are heterogeneous and frequently include critical SDOH. This work presents a new corpus with SDOH annotations, a novel active learning framework, and the first extraction results on the new corpus. The Social History Annotation Corpus (SHAC) includes 4,480 social history sections with detailed annotation for 12 SDOH characterizing the status, extent, and temporal information of 18K distinct events. We introduce a novel active learning framework that selects samples for annotation using a surrogate text classification task as a proxy for a more complex event extraction task. The active learning framework successfully increases the frequency of health risk factors and improves automatic extraction of these events over undirected annotation. An event extraction model trained on SHAC achieves high extraction performance for substance use status (0.82-0.93 F1), employment status (0.81-0.86 F1), and living status type (0.81-0.93 F1) on data from three institutions.