Ozlem Uzuner

Yanjun Gao, Dmitriy Dligach, Timothy Miller et al. · harvard

Daily progress notes are common types in the electronic health record (EHR) where healthcare providers document the patient's daily progress and treatment plans. The EHR is designed to document all the care provided to patients, but it also enables note bloat with extraneous information that distracts from the diagnoses and treatment plans. Applications of natural language processing (NLP) in the EHR is a growing field with the majority of methods in information extraction. Few tasks use NLP methods for downstream diagnostic decision support. We introduced the 2022 National NLP Clinical Challenge (N2C2) Track 3: Progress Note Understanding - Assessment and Plan Reasoning as one step towards a new suite of tasks. The Assessment and Plan Reasoning task focuses on the most critical components of progress notes, Assessment and Plan subsections where health problems and diagnoses are contained. The goal of the task was to develop and evaluate NLP systems that automatically predict causal relations between the overall status of the patient contained in the Assessment section and its relation to each component of the Plan section which contains the diagnoses and treatment plans. The goal of the task was to identify and prioritize diagnoses as the first steps in diagnostic decision support to find the most relevant information in long documents like daily progress notes. We present the results of 2022 n2c2 Track 3 and provide a description of the data, evaluation, participation and system performance.

Maryam Heidari, James H Jr Jones, Ozlem Uzuner

Social media platforms can expose influential trends in many aspects of everyday life. However, the movements they represent can be contaminated by disinformation. Social bots are one of the significant sources of disinformation in social media. Social bots can pose serious cyber threats to society and public opinion. This research aims to develop machine learning models to detect bots based on the extracted user's profile from a Tweet's text. Online users' profile shows the user's personal information, such as age, gender, education, and personality. In this work, the user's profile is constructed based on the user's online posts. This work's main contribution is three-fold: First, we aim to improve bot detection through machine learning models based on the user's personal information generated by the user's online comments. When comparing two online posts, the similarity of personal information makes it difficult to differentiate a bot from a human user. However, this research turns personal information similarity among two online posts into an advantage for the new bot detection model. The new proposed model for bot detection creates user profiles based on personal information such as age, personality, gender, education from users' online posts and introduces a machine learning model to detect social bots with high prediction accuracy based on personal information. Second, create a new public data set that shows the user's profile for more than 6900 Twitter accounts in the Cresci 2017 data set.

Nicholas J Dobbins, Bin Han, Weipeng Zhou et al.

Objective: Identifying study-eligible patients within clinical databases is a critical step in clinical research. However, accurate query design typically requires extensive technical and biomedical expertise. We sought to create a system capable of generating data model-agnostic queries while also providing novel logical reasoning capabilities for complex clinical trial eligibility criteria. Materials and Methods: The task of query creation from eligibility criteria requires solving several text-processing problems, including named entity recognition and relation extraction, sequence-to-sequence transformation, normalization, and reasoning. We incorporated hybrid deep learning and rule-based modules for these, as well as a knowledge base of the Unified Medical Language System (UMLS) and linked ontologies. To enable data-model agnostic query creation, we introduce a novel method for tagging database schema elements using UMLS concepts. To evaluate our system, called LeafAI, we compared the capability of LeafAI to a human database programmer to identify patients who had been enrolled in 8 clinical trials conducted at our institution. We measured performance by the number of actual enrolled patients matched by generated queries. Results: LeafAI matched a mean 43% of enrolled patients with 27,225 eligible across 8 clinical trials, compared to 27% matched and 14,587 eligible in queries by a human database programmer. The human programmer spent 26 total hours crafting queries compared to several minutes by LeafAI. Conclusions: Our work contributes a state-of-the-art data model-agnostic query generation system capable of conditional reasoning using a knowledge base. We demonstrate that LeafAI can rival an experienced human programmer in finding patients eligible for clinical trials.

Nicholas J Dobbins, Tony Mullen, Ozlem Uzuner et al.

Identifying cohorts of patients based on eligibility criteria such as medical conditions, procedures, and medication use is critical to recruitment for clinical trials. Such criteria are often most naturally described in free-text, using language familiar to clinicians and researchers. In order to identify potential participants at scale, these criteria must first be translated into queries on clinical databases, which can be labor-intensive and error-prone. Natural language processing (NLP) methods offer a potential means of such conversion into database queries automatically. However they must first be trained and evaluated using corpora which capture clinical trials criteria in sufficient detail. In this paper, we introduce the Leaf Clinical Trials (LCT) corpus, a human-annotated corpus of over 1,000 clinical trial eligibility criteria descriptions using highly granular structured labels capturing a range of biomedical phenomena. We provide details of our schema, annotation process, corpus quality, and statistics. Additionally, we present baseline information extraction results on this corpus as benchmarks for future work.

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.

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.

A H M Rezaul Karim, Ozlem Uzuner

Conversational nurse-patient transcripts contain actionable observations, but converting these transcripts into structured representations at scale remains challenging. Documentation burden is substantial, with prior studies showing clinicians spend large portions of their workday on documentation and related desk work rather than direct patient care. MEDIQA-SYNUR focuses on observation extraction from conversational nurse-patient transcripts, requiring systems to normalize these narratives into a predefined schema with value-type constraints. We propose a modular retrieval-augmented generation (RAG) pipeline that uses the training set as an exemplar corpus, combines schema-constrained prompting (full schema vs. pruned candidate schema), deterministic schema-based postprocessing, and a second-pass audit, with two LLM backbones: Llama-4-Scout-17B-16E-Instruct and GPT-5.2 with corresponding embedding models for RAG. Our best configuration uses GPT-5.2 with full schema, RAG, and a second-pass auditing, achieving 80.36% F1 score. Overall, our results show that RAG consistently improves performance, while the optimal degree of schema constraint depends on the model, and second-pass auditing yields modest additional gains by correcting residual schema-adherence errors.

Fardin Ahsan Sakib, Ahnaf Atef Choudhury, Ozlem Uzuner

Depression is a mental health disorder that has a profound impact on people's lives. Recent research suggests that signs of depression can be detected in the way individuals communicate, both through spoken words and written texts. In particular, social media posts are a rich and convenient text source that we may examine for depressive symptoms. The Beck Depression Inventory (BDI) Questionnaire, which is frequently used to gauge the severity of depression, is one instrument that can aid in this study. We can narrow our study to only those symptoms since each BDI question is linked to a particular depressive symptom. It's important to remember that not everyone with depression exhibits all symptoms at once, but rather a combination of them. Therefore, it is extremely useful to be able to determine if a sentence or a piece of user-generated content is pertinent to a certain condition. With this in mind, the eRisk 2023 Task 1 was designed to do exactly that: assess the relevance of different sentences to the symptoms of depression as outlined in the BDI questionnaire. This report is all about how our team, Mason-NLP, participated in this subtask, which involved identifying sentences related to different depression symptoms. We used a deep learning approach that incorporated MentalBERT, RoBERTa, and LSTM. Despite our efforts, the evaluation results were lower than expected, underscoring the challenges inherent in ranking sentences from an extensive dataset about depression, which necessitates both appropriate methodological choices and significant computational resources. We anticipate that future iterations of this shared task will yield improved results as our understanding and techniques evolve.

Yujuan Fu, Ozlem Uzuner, Meliha Yetisgen et al.

Large language models (LLMs) have demonstrated great performance across various benchmarks, showing potential as general-purpose task solvers. However, as LLMs are typically trained on vast amounts of data, a significant concern in their evaluation is data contamination, where overlap between training data and evaluation datasets inflates performance assessments. Multiple approaches have been developed to identify data contamination. These approaches rely on specific assumptions that may not hold universally across different settings. To bridge this gap, we systematically review 50 papers on data contamination detection, categorize the underlying assumptions, and assess whether they have been rigorously validated. We identify and analyze eight categories of assumptions and test three of them as case studies. Our case studies focus on detecting direct, instance-level data contamination, which is also referred to as Membership Inference Attacks (MIA). Our analysis reveals that MIA approaches based on these three assumptions can have similar performance to random guessing, on datasets used in LLM pretraining, suggesting that current LLMs might learn data distributions rather than memorizing individual instances. Meanwhile, MIA can easily fail when there are data distribution shifts between the seen and unseen instances.

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.

Zhaoyi Sun, Wen-Wai Yim, Ozlem Uzuner et al.

Objective: This review aims to explore the potential and challenges of using Natural Language Processing (NLP) to detect, correct, and mitigate medically inaccurate information, including errors, misinformation, and hallucination. By unifying these concepts, the review emphasizes their shared methodological foundations and their distinct implications for healthcare. Our goal is to advance patient safety, improve public health communication, and support the development of more reliable and transparent NLP applications in healthcare. Methods: A scoping review was conducted following PRISMA guidelines, analyzing studies from 2020 to 2024 across five databases. Studies were selected based on their use of NLP to address medically inaccurate information and were categorized by topic, tasks, document types, datasets, models, and evaluation metrics. Results: NLP has shown potential in addressing medically inaccurate information on the following tasks: (1) error detection (2) error correction (3) misinformation detection (4) misinformation correction (5) hallucination detection (6) hallucination mitigation. However, challenges remain with data privacy, context dependency, and evaluation standards. Conclusion: This review highlights the advancements in applying NLP to tackle medically inaccurate information while underscoring the need to address persistent challenges. Future efforts should focus on developing real-world datasets, refining contextual methods, and improving hallucination management to ensure reliable and transparent healthcare applications.

A H M Rezaul Karim, Ozlem Uzuner

Medical order extraction is essential for structuring actionable clinical information, supporting decision-making, and enabling downstream applications such as documentation and workflow automation. Orders may be embedded in diverse sources, including electronic health records, discharge summaries, and multi-turn doctor-patient dialogues, and can span categories such as medications, laboratory tests, imaging studies, and follow-up actions. The MEDIQA-OE 2025 shared task focuses on extracting structured medical orders from extended conversational transcripts, requiring the identification of order type, description, reason, and provenance. We present the MasonNLP submission, which ranked 5th among 17 participating teams with 105 total submissions. Our approach uses a general-purpose, instruction-tuned LLaMA-4 17B model without domain-specific fine-tuning, guided by a single in-context example. This few-shot configuration achieved an average F1 score of 37.76, with notable improvements in reason and provenance accuracy. These results demonstrate that large, non-domain-specific LLMs, when paired with effective prompt engineering, can serve as strong, scalable baselines for specialized clinical NLP tasks.

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.

Sadiya Sayara Chowdhury Puspo, Md Nishat Raihan, Dhiman Goswami et al.

This paper presents the MasonTigers entry to the SemEval-2024 Task 8 - Multigenerator, Multidomain, and Multilingual Black-Box Machine-Generated Text Detection. The task encompasses Binary Human-Written vs. Machine-Generated Text Classification (Track A), Multi-Way Machine-Generated Text Classification (Track B), and Human-Machine Mixed Text Detection (Track C). Our best performing approaches utilize mainly the ensemble of discriminator transformer models along with sentence transformer and statistical machine learning approaches in specific cases. Moreover, zero-shot prompting and fine-tuning of FLAN-T5 are used for Track A and B.

Md Badsha Biswas, Ozlem Uzuner

The spread of misinformation across digital platforms can pose significant societal risks. Claim verification, a.k.a. fact-checking, systems can help identify potential misinformation. However, their efficacy is limited by the knowledge sources that they rely on. Most automated claim verification systems depend on a single knowledge source and utilize the supporting evidence from that source; they ignore the disagreement of their source with others. This limits their knowledge coverage and transparency. To address these limitations, we present a novel system for open-domain claim verification (ODCV) that leverages large language models (LLMs), multi-perspective evidence retrieval, and cross-source disagreement analysis. Our approach introduces a novel retrieval strategy that collects evidence for both the original and the negated forms of a claim, enabling the system to capture supporting and contradicting information from diverse sources: Wikipedia, PubMed, and Google. These evidence sets are filtered, deduplicated, and aggregated across sources to form a unified and enriched knowledge base that better reflects the complexity of real-world information. This aggregated evidence is then used for claim verification using LLMs. We further enhance interpretability by analyzing model confidence scores to quantify and visualize inter-source disagreement. Through extensive evaluation on four benchmark datasets with five LLMs, we show that knowledge aggregation not only improves claim verification but also reveals differences in source-specific reasoning. Our findings underscore the importance of embracing diversity, contradiction, and aggregation in evidence for building reliable and transparent claim verification systems

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.

A H M Rezaul Karim, Ozlem Uzuner

Medical Visual Question Answering (MedVQA) enables natural language queries over medical images to support clinical decision-making and patient care. The MEDIQA-WV 2025 shared task addressed wound-care VQA, requiring systems to generate free-text responses and structured wound attributes from images and patient queries. We present the MasonNLP system, which employs a general-domain, instruction-tuned large language model with a retrieval-augmented generation (RAG) framework that incorporates textual and visual examples from in-domain data. This approach grounds outputs in clinically relevant exemplars, improving reasoning, schema adherence, and response quality across dBLEU, ROUGE, BERTScore, and LLM-based metrics. Our best-performing system ranked 3rd among 19 teams and 51 submissions with an average score of 41.37%, demonstrating that lightweight RAG with general-purpose LLMs -- a minimal inference-time layer that adds a few relevant exemplars via simple indexing and fusion, with no extra training or complex re-ranking -- provides a simple and effective baseline for multimodal clinical NLP tasks.

Fardin Ahsan Sakib, Ziwei Zhu, Karen Trister Grace et al.

Social determinants of health (SDOH) extraction from clinical text is critical for downstream healthcare analytics. Although large language models (LLMs) have shown promise, they may rely on superficial cues leading to spurious predictions. Using the MIMIC portion of the SHAC (Social History Annotation Corpus) dataset and focusing on drug status extraction as a case study, we demonstrate that mentions of alcohol or smoking can falsely induce models to predict current/past drug use where none is present, while also uncovering concerning gender disparities in model performance. We further evaluate mitigation strategies - such as prompt engineering and chain-of-thought reasoning - to reduce these false positives, providing insights into enhancing LLM reliability in health domains.

Fatemah Husain, Ozlem Uzuner

The problem of online offensive language limits the health and security of online users. It is essential to apply the latest state-of-the-art techniques in developing a system to detect online offensive language and to ensure social justice to the online communities. Our study investigates the effects of fine-tuning across several Arabic offensive language datasets. We develop multiple classifiers that use four datasets individually and in combination in order to gain knowledge about online Arabic offensive content and classify users comments accordingly. Our results demonstrate the limited effects of transfer learning on the classifiers performance, particularly for highly dialectal comments.

Yanjun Gao, Dmitriy Dligach, Leslie Christensen et al.

Objective: to provide a scoping review of papers on clinical natural language processing (NLP) tasks that use publicly available electronic health record data from a cohort of patients. Materials and Methods: We searched six databases, including biomedical research and computer science literature database. A round of title/abstract screening and full-text screening were conducted by two reviewers. Our method followed the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. Results: A total of 35 papers with 47 clinical NLP tasks met inclusion criteria between 2007 and 2021. We categorized the tasks by the type of NLP problems, including name entity recognition, summarization, and other NLP tasks. Some tasks were introduced with a topic of clinical decision support applications, such as substance abuse, phenotyping, cohort selection for clinical trial. We summarized the tasks by publication and dataset information. Discussion: The breadth of clinical NLP tasks keeps growing as the field of NLP evolves with advancements in language systems. However, gaps exist in divergent interests between general domain NLP community and clinical informatics community, and in generalizability of the data sources. We also identified issues in data selection and preparation including the lack of time-sensitive data, and invalidity of problem size and evaluation. Conclusions: The existing clinical NLP tasks cover a wide range of topics and the field will continue to grow and attract more attention from both general domain NLP and clinical informatics community. We encourage future work to incorporate multi-disciplinary collaboration, reporting transparency, and standardization in data preparation.

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.

Kahyun Lee, Nicholas J. Dobbins, Bridget McInnes et al.

Objective: Neural network de-identification studies have focused on individual datasets. These studies assume the availability of a sufficient amount of human-annotated data to train models that can generalize to corresponding test data. In real-world situations, however, researchers often have limited or no in-house training data. Existing systems and external data can help jump-start de-identification on in-house data; however, the most efficient way of utilizing existing systems and external data is unclear. This article investigates the transferability of a state-of-the-art neural clinical de-identification system, NeuroNER, across a variety of datasets, when it is modified architecturally for domain generalization and when it is trained strategically for domain transfer. Methods and Materials: We conducted a comparative study of the transferability of NeuroNER using four clinical note corpora with multiple note types from two institutions. We modified NeuroNER architecturally to integrate two types of domain generalization approaches. We evaluated each architecture using three training strategies. We measured: transferability from external sources; transferability across note types; the contribution of external source data when in-domain training data are available; and transferability across institutions. Results and Conclusions: Transferability from a single external source gave inconsistent results. Using additional external sources consistently yielded an F1-score of approximately 80%. Fine-tuning emerged as a dominant transfer strategy, with or without domain generalization. We also found that external sources were useful even in cases where in-domain training data were available. Transferability across institutions differed by note type and annotation label but resulted in improved performance.

Paul Barry, Sam Henry, Meliha Yetisgen et al.

We hypothesize that explicit integration of contextual information into an Multi-task Learning framework would emphasize the significance of context for boosting performance in jointly learning Named Entity Recognition (NER) and Relation Extraction (RE). Our work proves this hypothesis by segmenting entities from their surrounding context and by building contextual representations using each independent segment. This relation representation allows for a joint NER/RE system that achieves near state-of-the-art (SOTA) performance on both NER and RE tasks while beating the SOTA RE system at end-to-end NER & RE with a 49.07 F1.

Fatemah Husain, Ozlem Uzuner

Developing a system to detect online offensive language is very important to the health and the security of online users. Studies have shown that cyberhate, online harassment and other misuses of technology are on the rise, particularly during the global Coronavirus pandemic in 2020. According to the latest report by the Anti-Defamation League (ADL), 35% of online users reported online harassment related to their identity-based characteristics, which is a 3% increase over 2019. Applying advanced techniques from the Natural Language Processing (NLP) field to support the development of an online hate-free community is a critical task for social justice. Transfer learning enhances the performance of the classifier by allowing the transfer of knowledge from one domain or one dataset to others that have not been seen before, thus, supporting the classifier to be more generalizable. In our study, we apply the principles of transfer learning cross multiple Arabic offensive language datasets to compare the effects on system performance. This study aims at investigating the effects of fine-tuning and training Bidirectional Encoder Representations from Transformers (BERT) model on multiple Arabic offensive language datasets individually and testing it using other datasets individually. Our experiment starts with a comparison among multiple BERT models to guide the selection of the main model that is used for our study. The study also investigates the effects of concatenating all datasets to be used for fine-tuning and training BERT model. Our results demonstrate the limited effects of transfer learning on the performance of the classifiers, particularly for highly dialectic comments.

Fatemah Husain, Ozlem Uzuner

This paper adding more insights towards resources and datasets used in Arabic offensive language research. The main goal of this paper is to guide researchers in Arabic offensive language in selecting appropriate datasets based on their content, and in creating new Arabic offensive language resources to support and complement the available ones.

Fatemah Husain, Jooyeon Lee, Samuel Henry et al.

This paper describes SalamNET, an Arabic offensive language detection system that has been submitted to SemEval 2020 shared task 12: Multilingual Offensive Language Identification in Social Media. Our approach focuses on applying multiple deep learning models and conducting in depth error analysis of results to provide system implications for future development considerations. To pursue our goal, a Recurrent Neural Network (RNN), a Gated Recurrent Unit (GRU), and Long-Short Term Memory (LSTM) models with different design architectures have been developed and evaluated. The SalamNET, a Bi-directional Gated Recurrent Unit (Bi-GRU) based model, reports a macro-F1 score of 0.83.

Wilson Lau, Thomas H Payne, Ozlem Uzuner et al.

Communication of follow-up recommendations when abnormalities are identified on imaging studies is prone to error. In this paper, we present a natural language processing approach based on deep learning to automatically identify clinically important recommendations in radiology reports. Our approach first identifies the recommendation sentences and then extracts reason, test, and time frame of the identified recommendations. To train our extraction models, we created a corpus of 567 radiology reports annotated for recommendation information. Our extraction models achieved 0.92 f-score for recommendation sentence, 0.65 f-score for reason, 0.73 f-score for test, and 0.84 f-score for time frame. We applied the extraction models to a set of over 3.3 million radiology reports and analyzed the adherence of follow-up recommendations.

Ji Young Lee, Franck Dernoncourt, Ozlem Uzuner et al.

Patient notes contain a wealth of information of potentially great interest to medical investigators. However, to protect patients' privacy, Protected Health Information (PHI) must be removed from the patient notes before they can be legally released, a process known as patient note de-identification. The main objective for a de-identification system is to have the highest possible recall. Recently, the first neural-network-based de-identification system has been proposed, yielding state-of-the-art results. Unlike other systems, it does not rely on human-engineered features, which allows it to be quickly deployed, but does not leverage knowledge from human experts or from electronic health records (EHRs). In this work, we explore a method to incorporate human-engineered features as well as features derived from EHRs to a neural-network-based de-identification system. Our results show that the addition of features, especially the EHR-derived features, further improves the state-of-the-art in patient note de-identification, including for some of the most sensitive PHI types such as patient names. Since in a real-life setting patient notes typically come with EHRs, we recommend developers of de-identification systems to leverage the information EHRs contain.

Franck Dernoncourt, Ji Young Lee, Ozlem Uzuner et al.

Objective: Patient notes in electronic health records (EHRs) may contain critical information for medical investigations. However, the vast majority of medical investigators can only access de-identified notes, in order to protect the confidentiality of patients. In the United States, the Health Insurance Portability and Accountability Act (HIPAA) defines 18 types of protected health information (PHI) that needs to be removed to de-identify patient notes. Manual de-identification is impractical given the size of EHR databases, the limited number of researchers with access to the non-de-identified notes, and the frequent mistakes of human annotators. A reliable automated de-identification system would consequently be of high value. Materials and Methods: We introduce the first de-identification system based on artificial neural networks (ANNs), which requires no handcrafted features or rules, unlike existing systems. We compare the performance of the system with state-of-the-art systems on two datasets: the i2b2 2014 de-identification challenge dataset, which is the largest publicly available de-identification dataset, and the MIMIC de-identification dataset, which we assembled and is twice as large as the i2b2 2014 dataset. Results: Our ANN model outperforms the state-of-the-art systems. It yields an F1-score of 97.85 on the i2b2 2014 dataset, with a recall 97.38 and a precision of 97.32, and an F1-score of 99.23 on the MIMIC de-identification dataset, with a recall 99.25 and a precision of 99.06. Conclusion: Our findings support the use of ANNs for de-identification of patient notes, as they show better performance than previously published systems while requiring no feature engineering.

Weiyi Sun, Anna Rumshisky, Ozlem Uzuner

We analyze the RI-TIMEXes in temporally annotated corpora and propose two hypotheses regarding the normalization of RI-TIMEXes in the clinical narrative domain: the anchor point hypothesis and the anchor relation hypothesis. We annotate the RI-TIMEXes in three corpora to study the characteristics of RI-TMEXes in different domains. This informed the design of our RI-TIMEX normalization system for the clinical domain, which consists of an anchor point classifier, an anchor relation classifier and a rule-based RI-TIMEX text span parser. We experiment with different feature sets and perform error analysis for each system component. The annotation confirmed the hypotheses that we can simplify the RI-TIMEXes normalization task using two multi-label classifiers. Our system achieves anchor point classification, anchor relation classification and rule-based parsing accuracy of 74.68%, 87.71% and 57.2% (82.09% under relaxed matching criteria) respectively on the held-out test set of the 2012 i2b2 temporal relation challenge. Experiments with feature sets reveals some interesting findings such as the verbal tense feature does not inform the anchor relation classification in clinical narratives as much as the tokens near the RI-TIMEX. Error analysis shows that underrepresented anchor point and anchor relation classes are difficult to detect. We formulate the RI-TIMEX normalization problem as a pair of multi-label classification problems. Considering only the RI-TIMEX extraction and normalization, the system achieves statistically significant improvement over the RI-TIMEX results of the best systems in the 2012 i2b2 challenge.