Sunjae Kwon

Jiatan Huang, Mingchen Li, Ziming Li et al.

Multi-agent LLM systems often treat agreement as evidence: when many agents in a panel give the same answer, that answer is assumed to be more reliable. We show that this assumption can fail after agents communicate. Communication can induce correlated failures and false consensus, so the same vote share may reflect reliable agreement in one topology but over-confidence in another. We propose CAGE-CAL, a counterfactual agent-graph calibration framework for multi-agent LLMs. For each query, CAGE-CAL compares an observed post-communication agent graph with a matched counterfactual no-communication graph, capturing both pairwise failure correlations and group-level dependencies. Rather than simply counting how many agents agree, CAGE-CAL estimates the counterfactual shift between observed and no-communication dependence, and calibrates confidence accordingly. Across five benchmarks, CAGE-CAL improves reliability discrimination with competitive ECE, and its calibrated confidence further improves topology selection over the best fixed-topology strategy.

Zhichao Yang, Sunjae Kwon, Zonghai Yao et al.

Automatic International Classification of Diseases (ICD) coding aims to assign multiple ICD codes to a medical note with an average of 3,000+ tokens. This task is challenging due to the high-dimensional space of multi-label assignment (155,000+ ICD code candidates) and the long-tail challenge - Many ICD codes are infrequently assigned yet infrequent ICD codes are important clinically. This study addresses the long-tail challenge by transforming this multi-label classification task into an autoregressive generation task. Specifically, we first introduce a novel pretraining objective to generate free text diagnoses and procedure using the SOAP structure, the medical logic physicians use for note documentation. Second, instead of directly predicting the high dimensional space of ICD codes, our model generates the lower dimension of text descriptions, which then infer ICD codes. Third, we designed a novel prompt template for multi-label classification. We evaluate our Generation with Prompt model with the benchmark of all code assignment (MIMIC-III-full) and few shot ICD code assignment evaluation benchmark (MIMIC-III-few). Experiments on MIMIC-III-few show that our model performs with a marco F1 30.2, which substantially outperforms the previous MIMIC-III-full SOTA model (marco F1 4.3) and the model specifically designed for few/zero shot setting (marco F1 18.7). Finally, we design a novel ensemble learner, a cross attention reranker with prompts, to integrate previous SOTA and our best few-shot coding predictions. Experiments on MIMIC-III-full show that our ensemble learner substantially improves both macro and micro F1, from 10.4 to 14.6 and from 58.2 to 59.1, respectively.

Sunjae Kwon, Zonghai Yao, Harmon S. Jordan et al.

This paper proposes a new natural language processing (NLP) application for identifying medical jargon terms potentially difficult for patients to comprehend from electronic health record (EHR) notes. We first present a novel and publicly available dataset with expert-annotated medical jargon terms from 18K+ EHR note sentences ($MedJ$). Then, we introduce a novel medical jargon extraction ($MedJEx$) model which has been shown to outperform existing state-of-the-art NLP models. First, MedJEx improved the overall performance when it was trained on an auxiliary Wikipedia hyperlink span dataset, where hyperlink spans provide additional Wikipedia articles to explain the spans (or terms), and then fine-tuned on the annotated MedJ data. Secondly, we found that a contextualized masked language model score was beneficial for detecting domain-specific unfamiliar jargon terms. Moreover, our results show that training on the auxiliary Wikipedia hyperlink span datasets improved six out of eight biomedical named entity recognition benchmark datasets. Both MedJ and MedJEx are publicly available.

Sunjae Kwon, Xun Wang, Weisong Liu et al.

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.

Sunjae Kwon, Cheongwoong Kang, Jiyeon Han et al.

Many contextualized word representations are now learned by intricate neural network models, such as masked neural language models (MNLMs) which are made up of huge neural network structures and trained to restore the masked text. Such representations demonstrate superhuman performance in some reading comprehension (RC) tasks which extract a proper answer in the context given a question. However, identifying the detailed knowledge trained in MNLMs is challenging owing to numerous and intermingled model parameters. This paper provides new insights and empirical analyses on commonsense knowledge included in pretrained MNLMs. First, we use a diagnostic test that evaluates whether commonsense knowledge is properly trained in MNLMs. We observe that a large proportion of commonsense knowledge is not appropriately trained in MNLMs and MNLMs do not often understand the semantic meaning of relations accurately. In addition, we find that the MNLM-based RC models are still vulnerable to semantic variations that require commonsense knowledge. Finally, we discover the fundamental reason why some knowledge is not trained. We further suggest that utilizing an external commonsense knowledge repository can be an effective solution. We exemplify the possibility to overcome the limitations of the MNLM-based RC models by enriching text with the required knowledge from an external commonsense knowledge repository in controlled experiments.

Jung Hoon Lim, Sunjae Kwon, Zonghai Yao et al.

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

Sunjae Kwon, Zhichao Yang, Hong Yu

In this paper, we introduce a comprehensive framework for developing a machine learning-based SOAP (Subjective, Objective, Assessment, and Plan) classification system without manually SOAP annotated training data or with less manually SOAP annotated training data. The system is composed of the following two parts: 1) Data construction, 2) A neural network-based SOAP classifier, and 3) Transfer learning framework. In data construction, since a manual construction of a large size training dataset is expensive, we propose a rule-based weak labeling method utilizing the structured information of an EHR note. Then, we present a SOAP classifier composed of a pre-trained language model and bi-directional long-short term memory with conditional random field (Bi-LSTM-CRF). Finally, we propose a transfer learning framework that re-uses the trained parameters of the SOAP classifier trained with the weakly labeled dataset for datasets collected from another hospital. The proposed weakly label-based learning model successfully performed SOAP classification (89.99 F1-score) on the notes collected from the target hospital. Otherwise, in the notes collected from other hospitals and departments, the performance dramatically decreased. Meanwhile, we verified that the transfer learning framework is advantageous for inter-hospital adaptation of the model increasing the models' performance in every cases. In particular, the transfer learning approach was more efficient when the manually annotated data size was smaller. We showed that SOAP classification models trained with our weakly labeling algorithm can perform SOAP classification without manually annotated data on the EHR notes from the same hospital. The transfer learning framework helps SOAP classification model's inter-hospital migration with a minimal size of the manually annotated dataset.

Zonghai Yao, Nandyala Siddharth Kantu, Guanghao Wei et al.

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

Won Seok Jang, Sharmin Sultana, Zonghai Yao et al.

OpenNotes enables patients to access EHR notes, but medical jargon can hinder comprehension. To improve understanding, we evaluated closed- and open-source LLMs for extracting and prioritizing key medical terms using prompting, fine-tuning, and data augmentation. We assessed LLMs on 106 expert-annotated EHR notes, experimenting with (i) general vs. structured prompts, (ii) zero-shot vs. few-shot prompting, (iii) fine-tuning, and (iv) data augmentation. To enhance open-source models in low-resource settings, we used ChatGPT for data augmentation and applied ranking techniques. We incrementally increased the augmented dataset size (10 to 10,000) and conducted 5-fold cross-validation, reporting F1 score and Mean Reciprocal Rank (MRR). Our result show that fine-tuning and data augmentation improved performance over other strategies. GPT-4 Turbo achieved the highest F1 (0.433), while Mistral7B with data augmentation had the highest MRR (0.746). Open-source models, when fine-tuned or augmented, outperformed closed-source models. Notably, the best F1 and MRR scores did not always align. Few-shot prompting outperformed zero-shot in vanilla models, and structured prompts yielded different preferences across models. Fine-tuning improved zero-shot performance but sometimes degraded few-shot performance. Data augmentation performed comparably or better than other methods. Our evaluation highlights the effectiveness of prompting, fine-tuning, and data augmentation in improving model performance for medical jargon extraction in low-resource scenarios.

Ye Eun Chun, Sunjae Kwon, Kyunghwan Sohn et al.

In this paper, we introduce CR-COPEC called Causal Rationale of Corporate Performance Changes from financial reports. This is a comprehensive large-scale domain-adaptation causal sentence dataset to detect financial performance changes of corporate. CR-COPEC contributes to two major achievements. First, it detects causal rationale from 10-K annual reports of the U.S. companies, which contain experts' causal analysis following accounting standards in a formal manner. This dataset can be widely used by both individual investors and analysts as material information resources for investing and decision making without tremendous effort to read through all the documents. Second, it carefully considers different characteristics which affect the financial performance of companies in twelve industries. As a result, CR-COPEC can distinguish causal sentences in various industries by taking unique narratives in each industry into consideration. We also provide an extensive analysis of how well CR-COPEC dataset is constructed and suited for classifying target sentences as causal ones with respect to industry characteristics. Our dataset and experimental codes are publicly available.

Zhichao Yang, Avijit Mitra, Sunjae Kwon et al.

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

Hochul Hwang, Sunjae Kwon, Yekyung Kim et al.

Safely navigating street intersections is a complex challenge for blind and low-vision individuals, as it requires a nuanced understanding of the surrounding context - a task heavily reliant on visual cues. Traditional methods for assisting in this decision-making process often fall short, lacking the ability to provide a comprehensive scene analysis and safety level. This paper introduces an innovative approach that leverages large multimodal models (LMMs) to interpret complex street crossing scenes, offering a potential advancement over conventional traffic signal recognition techniques. By generating a safety score and scene description in natural language, our method supports safe decision-making for the blind and low-vision individuals. We collected crosswalk intersection data that contains multiview egocentric images captured by a quadruped robot and annotated the images with corresponding safety scores based on our predefined safety score categorization. Grounded on the visual knowledge, extracted from images, and text prompt, we evaluate a large multimodal model for safety score prediction and scene description. Our findings highlight the reasoning and safety score prediction capabilities of a LMM, activated by various prompts, as a pathway to developing a trustworthy system, crucial for applications requiring reliable decision-making support.

Parth Vashisht, Abhilasha Lodha, Mukta Maddipatla et al.

This paper presents our team's participation in the MEDIQA-ClinicalNLP2024 shared task B. We present a novel approach to diagnosing clinical dermatology cases by integrating large multimodal models, specifically leveraging the capabilities of GPT-4V under a retriever and a re-ranker framework. Our investigation reveals that GPT-4V, when used as a retrieval agent, can accurately retrieve the correct skin condition 85% of the time using dermatological images and brief patient histories. Additionally, we empirically show that Naive Chain-of-Thought (CoT) works well for retrieval while Medical Guidelines Grounded CoT is required for accurate dermatological diagnosis. Further, we introduce a Multi-Agent Conversation (MAC) framework and show its superior performance and potential over the best CoT strategy. The experiments suggest that using naive CoT for retrieval and multi-agent conversation for critique-based diagnosis, GPT-4V can lead to an early and accurate diagnosis of dermatological conditions. The implications of this work extend to improving diagnostic workflows, supporting dermatological education, and enhancing patient care by providing a scalable, accessible, and accurate diagnostic tool.

Zonghai Yao, Michael Sun, Won Seok Jang et al.

Discharge communication is a critical yet underexplored component of patient care, where the goal shifts from diagnosis to education. While recent large language model (LLM) benchmarks emphasize in-visit diagnostic reasoning, they fail to evaluate models' ability to support patients after the visit. We introduce DischargeSim, a novel benchmark that evaluates LLMs on their ability to act as personalized discharge educators. DischargeSim simulates post-visit, multi-turn conversations between LLM-driven DoctorAgents and PatientAgents with diverse psychosocial profiles (e.g., health literacy, education, emotion). Interactions are structured across six clinically grounded discharge topics and assessed along three axes: (1) dialogue quality via automatic and LLM-as-judge evaluation, (2) personalized document generation including free-text summaries and structured AHRQ checklists, and (3) patient comprehension through a downstream multiple-choice exam. Experiments across 18 LLMs reveal significant gaps in discharge education capability, with performance varying widely across patient profiles. Notably, model size does not always yield better education outcomes, highlighting trade-offs in strategy use and content prioritization. DischargeSim offers a first step toward benchmarking LLMs in post-visit clinical education and promoting equitable, personalized patient support.

Sunjae Kwon, Rishabh Garodia, Minhwa Lee et al.

Visual Word Sense Disambiguation (VWSD) is a task to find the image that most accurately depicts the correct sense of the target word for the given context. Previously, image-text matching models often suffered from recognizing polysemous words. This paper introduces an unsupervised VWSD approach that uses gloss information of an external lexical knowledge-base, especially the sense definitions. Specifically, we suggest employing Bayesian inference to incorporate the sense definitions when sense information of the answer is not provided. In addition, to ameliorate the out-of-dictionary (OOD) issue, we propose a context-aware definition generation with GPT-3. Experimental results show that the VWSD performance significantly increased with our Bayesian inference-based approach. In addition, our context-aware definition generation achieved prominent performance improvement in OOD examples exhibiting better performance than the existing definition generation method.

Sunjae Kwon, Dongsuk Oh, Youngjoong Ko

In natural language processing, word-sense disambiguation (WSD) is an open problem concerned with identifying the correct sense of words in a particular context. To address this problem, we introduce a novel knowledge-based WSD system. We suggest the adoption of two methods in our system. First, we suggest a novel method to encode the word vector representation by considering the graphical semantic relationships from the lexical knowledge-base. Second, we propose a method for extracting the contextual words from the text for analyzing an ambiguous word based on the similarity of word vector representations. To validate the effectiveness of our WSD system, we conducted experiments on the five benchmark English WSD corpora (Senseval-02, Senseval-03, SemEval-07, SemEval-13, and SemEval-15). The obtained results demonstrated that the suggested methods significantly enhanced the WSD performance. Furthermore, our system outperformed the existing knowledge-based WSD systems and showed a performance comparable to that of the state-of-the-art supervised WSD systems.

Sunjae Kwon, Cheongwoong Kang, Jiyeon Han et al.

Currently, contextualized word representations are learned by intricate neural network models, such as masked neural language models (MNLMs). The new representations significantly enhanced the performance in automated question answering by reading paragraphs. However, identifying the detailed knowledge trained in the MNLMs is difficult owing to numerous and intermingled parameters. This paper provides empirical but insightful analyses on the pretrained MNLMs with respect to common sense knowledge. First, we propose a test that measures what types of common sense knowledge do pretrained MNLMs understand. From the test, we observed that MNLMs partially understand various types of common sense knowledge but do not accurately understand the semantic meaning of relations. In addition, based on the difficulty of the question-answering task problems, we observed that pretrained MLM-based models are still vulnerable to problems that require common sense knowledge. We also experimentally demonstrated that we can elevate existing MNLM-based models by combining knowledge from an external common sense repository.