arXiv subjects

Jimeng Sun

Publications and source records attributed to Jimeng Sun.

At least 73 records · Page 4Linked to original sources

arXiv2025

Beyond Label Attention: Transparency in Language Models for Automated Medical Coding via Dictionary Learning

Medical coding, the translation of unstructured clinical text into standardized medical codes, is a crucial but time-consuming healthcare practice. Though large language models (LLM) could automate the coding process and improve the efficiency of such tasks, interpretability remains paramount for maintaining patient trust. Current efforts in interpretability of medical coding applications rely heavily on label attention mechanisms, which often leads to the highlighting of extraneous tokens irrelevant to the ICD code. To facilitate accurate interpretability in medical language models, this paper leverages dictionary learning that can efficiently extract sparsely activated representations from dense language model embeddings in superposition. Compared with common label attention mechanisms, our model goes beyond token-level representations by building an interpretable dictionary which enhances the mechanistic-based explanations for each ICD code prediction, even when the highlighted tokens are medically irrelevant. We show that dictionary features can steer model behavior, elucidate the hidden meanings of upwards of 90% of medically irrelevant tokens, and are human interpretable.

cs.CL↗

arXiv2025

Automatically Labeling Clinical Trial Outcomes: A Large-Scale Benchmark for Drug Development

Background The cost of drug discovery and development is substantial, with clinical trial outcomes playing a critical role in regulatory approval and patient care. However, access to large-scale, high-quality clinical trial outcome data remains limited, hindering advancements in predictive modeling and evidence-based decision-making. Methods We present the Clinical Trial Outcome (CTO) benchmark, a fully reproducible, large-scale repository encompassing approximately 125,000 drug and biologics trials. CTO integrates large language model (LLM) interpretations of publications, trial phase progression tracking, sentiment analysis from news sources, stock price movements of trial sponsors, and additional trial-related metrics. Furthermore, we manually annotated a dataset of clinical trials conducted between 2020 and 2024 to enhance the quality and reliability of outcome labels. Results The trial outcome labels in the CTO benchmark agree strongly with expert annotations, achieving an F1 score of 94 for Phase 3 trials and 91 across all phases. Additionally, benchmarking standard machine learning models on our manually annotated dataset revealed distribution shifts in recent trials, underscoring the necessity of continuously updated labeling approaches. Conclusions By analyzing CTO's performance on recent clinical trials, we demonstrate the ongoing need for high-quality, up-to-date trial outcome labels. We publicly release the CTO knowledge base and annotated labels at https://chufangao.github.io/CTOD, with regular updates to support research on clinical trial outcomes and inform data-driven improvements in drug development.

cs.AI↗

arXiv2025

AnyECG: Foundational Models for Multitask Cardiac Analysis in Real-World Settings

Electrocardiogram (ECG), a non-invasive and affordable tool for cardiac monitoring, is highly sensitive in detecting acute heart attacks. However, due to the lengthy nature of ECG recordings, numerous machine learning methods have been developed for automated heart disease detection to reduce human workload. Despite these efforts, performance remains suboptimal. A key obstacle is the inherent complexity of ECG data, which includes heterogeneity (e.g., varying sampling rates), high levels of noise, demographic-related pattern shifts, and intricate rhythm-event associations. To overcome these challenges, this paper introduces AnyECG, a foundational model designed to extract robust representations from any real-world ECG data. Specifically, a tailored ECG Tokenizer encodes each fixed-duration ECG fragment into a token and, guided by proxy tasks, converts noisy, continuous ECG features into discrete, compact, and clinically meaningful local rhythm codes. These codes encapsulate basic morphological, frequency, and demographic information (e.g., sex), effectively mitigating signal noise. We further pre-train the AnyECG to learn rhythmic pattern associations across ECG tokens, enabling the capture of cardiac event semantics. By being jointly pre-trained on diverse ECG data sources, AnyECG is capable of generalizing across a wide range of downstream tasks where ECG signals are recorded from various devices and scenarios. The experimental results show that AnyECG achieves an average performance improvement of 6% across four critical tasks-anomaly detection, arrhythmia classification, corrupted lead generation, and ultra-long ECG recognition. AnyECG learns common ECG rhythm from data and significantly outperforms state-of-the-art methods in each of these tasks.

eess.SP↗

arXiv2025

Long-Term EEG Partitioning for Seizure Onset Detection

Deep learning models have recently shown great success in classifying epileptic patients using EEG recordings. Unfortunately, classification-based methods lack a sound mechanism to detect the onset of seizure events. In this work, we propose a two-stage framework, SODor, that explicitly models seizure onset through a novel task formulation of subsequence clustering. Given an EEG sequence, the framework first learns a set of second-level embeddings with label supervision. It then employs model-based clustering to explicitly capture long-term temporal dependencies in EEG sequences and identify meaningful subsequences. Epochs within a subsequence share a common cluster assignment (normal or seizure), with cluster or state transitions representing successful onset detections. Extensive experiments on three datasets demonstrate that our method can correct misclassifications, achieving 5\%-11\% classification improvements over other baselines and accurately detecting seizure onsets.

cs.LG↗

arXiv2025

Small Models are LLM Knowledge Triggers on Medical Tabular Prediction

Recent development in large language models (LLMs) has demonstrated impressive domain proficiency on unstructured textual or multi-modal tasks. However, despite with intrinsic world knowledge, their application on structured tabular data prediction still lags behind, primarily due to the numerical insensitivity and modality discrepancy that brings a gap between LLM reasoning and statistical tabular learning. Unlike textual or vision data (e.g., electronic clinical notes or medical imaging data), tabular data is often presented in heterogeneous numerical values (e.g., CBC reports). This ubiquitous data format requires intensive expert annotation, and its numerical nature limits LLMs' capability to effectively transfer untapped domain expertise. In this paper, we propose SERSAL, a general self-prompting method by synergy learning with small models to enhance LLM tabular prediction in an unsupervised manner. Specifically, SERSAL utilizes the LLM's prior outcomes as original soft noisy annotations, which are dynamically leveraged to teach a better small student model. Reversely, the outcomes from the trained small model are used to teach the LLM to further refine its real capability. This process can be repeatedly applied to gradually distill refined knowledge for continuous progress. Comprehensive experiments on widely used medical domain tabular datasets show that, without access to gold labels, applying SERSAL to OpenAI GPT reasoning process attains substantial improvement compared to linguistic prompting methods, which serves as an orthogonal direction for tabular LLM, and increasing prompting bonus is observed as more powerful LLMs appear.

cs.CL↗

arXiv2025

GeSubNet: Gene Interaction Inference for Disease Subtype Network Generation

Retrieving gene functional networks from knowledge databases presents a challenge due to the mismatch between disease networks and subtype-specific variations. Current solutions, including statistical and deep learning methods, often fail to effectively integrate gene interaction knowledge from databases or explicitly learn subtype-specific interactions. To address this mismatch, we propose GeSubNet, which learns a unified representation capable of predicting gene interactions while distinguishing between different disease subtypes. Graphs generated by such representations can be considered subtype-specific networks. GeSubNet is a multi-step representation learning framework with three modules: First, a deep generative model learns distinct disease subtypes from patient gene expression profiles. Second, a graph neural network captures representations of prior gene networks from knowledge databases, ensuring accurate physical gene interactions. Finally, we integrate these two representations using an inference loss that leverages graph generation capabilities, conditioned on the patient separation loss, to refine subtype-specific information in the learned representation. GeSubNet consistently outperforms traditional methods, with average improvements of 30.6%, 21.0%, 20.1%, and 56.6% across four graph evaluation metrics, averaged over four cancer datasets. Particularly, we conduct a biological simulation experiment to assess how the behavior of selected genes from over 11,000 candidates affects subtypes or patient distributions. The results show that the generated network has the potential to identify subtype-specific genes with an 83% likelihood of impacting patient distribution shifts.

cs.LG↗

arXiv2025

SynRL: Aligning Synthetic Clinical Trial Data with Human-preferred Clinical Endpoints Using Reinforcement Learning

Each year, hundreds of clinical trials are conducted to evaluate new medical interventions, but sharing patient records from these trials with other institutions can be challenging due to privacy concerns and federal regulations. To help mitigate privacy concerns, researchers have proposed methods for generating synthetic patient data. However, existing approaches for generating synthetic clinical trial data disregard the usage requirements of these data, including maintaining specific properties of clinical outcomes, and only use post hoc assessments that are not coupled with the data generation process. In this paper, we propose SynRL which leverages reinforcement learning to improve the performance of patient data generators by customizing the generated data to meet the user-specified requirements for synthetic data outcomes and endpoints. Our method includes a data value critic function to evaluate the quality of the generated data and uses reinforcement learning to align the data generator with the users' needs based on the critic's feedback. We performed experiments on four clinical trial datasets and demonstrated the advantages of SynRL in improving the quality of the generated synthetic data while keeping the privacy risks low. We also show that SynRL can be utilized as a general framework that can customize data generation of multiple types of synthetic data generators. Our code is available at https://anonymous.4open.science/r/SynRL-DB0F/.

cs.LG↗

arXiv2025

Bi-level Contrastive Learning for Knowledge-Enhanced Molecule Representations

Molecular representation learning is vital for various downstream applications, including the analysis and prediction of molecular properties and side effects. While Graph Neural Networks (GNNs) have been a popular framework for modeling molecular data, they often struggle to capture the full complexity of molecular representations. In this paper, we introduce a novel method called GODE, which accounts for the dual-level structure inherent in molecules. Molecules possess an intrinsic graph structure and simultaneously function as nodes within a broader molecular knowledge graph. GODE integrates individual molecular graph representations with multi-domain biochemical data from knowledge graphs. By pre-training two GNNs on different graph structures and employing contrastive learning, GODE effectively fuses molecular structures with their corresponding knowledge graph substructures. This fusion yields a more robust and informative representation, enhancing molecular property predictions by leveraging both chemical and biological information. When fine-tuned across 11 chemical property tasks, our model significantly outperforms existing benchmarks, achieving an average ROC-AUC improvement of 12.7% for classification tasks and an average RMSE/MAE improvement of 34.4% for regression tasks. Notably, GODE surpasses the current leading model in property prediction, with advancements of 2.2% in classification and 7.2% in regression tasks.

cs.LG↗

arXiv2025

GT2Vec: Large Language Models as Multi-Modal Encoders for Text and Graph-Structured Data

Graph-structured information offers rich contextual information that can enhance language models by providing structured relationships and hierarchies, leading to more expressive embeddings for various applications such as retrieval, question answering, and classification. However, existing methods for integrating graph and text embeddings, often based on Multi-layer Perceptrons (MLPs) or shallow transformers, are limited in their ability to fully exploit the heterogeneous nature of these modalities. To overcome this, we propose GT2Vec, a simple yet effective framework that leverages Large Language Models (LLMs) to jointly encode text and graph data. Specifically, GT2Vec employs an MLP adapter to project graph embeddings into the same space as text embeddings, allowing the LLM to process both modalities jointly. Unlike prior work, we also introduce contrastive learning to align the graph and text spaces more effectively, thereby improving the quality of learned joint embeddings. Empirical results across six datasets spanning three tasks, knowledge graph-contextualized question answering, graph-text pair classification, and retrieval, demonstrate that GT2Vec consistently outperforms existing baselines, achieving significant improvements across multiple datasets. These results highlight GT2Vec's effectiveness in integrating graph and text data. Ablation studies further validate the effectiveness of our method.

cs.CL↗

arXiv2025

Towards Physiologically Sensible Predictions via the Rule-based Reinforcement Learning Layer

This paper adds to the growing literature of reinforcement learning (RL) for healthcare by proposing a novel paradigm: augmenting any predictor with Rule-based RL Layer (RRLL) that corrects the model's physiologically impossible predictions. Specifically, RRLL takes as input states predicted labels and outputs corrected labels as actions. The reward of the state-action pair is evaluated by a set of general rules. RRLL is efficient, general and lightweight: it does not require heavy expert knowledge like prior work but only a set of impossible transitions. This set is much smaller than all possible transitions; yet it can effectively reduce physiologically impossible mistakes made by the state-of-the-art predictor models. We verify the utility of RRLL on a variety of important healthcare classification problems and observe significant improvements using the same setup, with only the domain-specific set of impossibility changed. In-depth analysis shows that RRLL indeed improves accuracy by effectively reducing the presence of physiologically impossible predictions.

cs.LG↗

arXiv2025

A foundation model for human-AI collaboration in medical literature mining

Systematic literature review is essential for evidence-based medicine, requiring comprehensive analysis of clinical trial publications. However, the application of artificial intelligence (AI) models for medical literature mining has been limited by insufficient training and evaluation across broad therapeutic areas and diverse tasks. Here, we present LEADS, an AI foundation model for study search, screening, and data extraction from medical literature. The model is trained on 633,759 instruction data points in LEADSInstruct, curated from 21,335 systematic reviews, 453,625 clinical trial publications, and 27,015 clinical trial registries. We showed that LEADS demonstrates consistent improvements over four cutting-edge generic large language models (LLMs) on six tasks. Furthermore, LEADS enhances expert workflows by providing supportive references following expert requests, streamlining processes while maintaining high-quality results. A study with 16 clinicians and medical researchers from 14 different institutions revealed that experts collaborating with LEADS achieved a recall of 0.81 compared to 0.77 experts working alone in study selection, with a time savings of 22.6%. In data extraction tasks, experts using LEADS achieved an accuracy of 0.85 versus 0.80 without using LEADS, alongside a 26.9% time savings. These findings highlight the potential of specialized medical literature foundation models to outperform generic models, delivering significant quality and efficiency benefits when integrated into expert workflows for medical literature mining.

cs.CL↗

arXiv2024

TrialSynth: Generation of Synthetic Sequential Clinical Trial Data

Analyzing data from past clinical trials is part of the ongoing effort to optimize the design, implementation, and execution of new clinical trials and more efficiently bring life-saving interventions to market. While there have been recent advances in the generation of static context synthetic clinical trial data, due to both limited patient availability and constraints imposed by patient privacy needs, the generation of fine-grained synthetic time-sequential clinical trial data has been challenging. Given that patient trajectories over an entire clinical trial are of high importance for optimizing trial design and efforts to prevent harmful adverse events, there is a significant need for the generation of high-fidelity time-sequence clinical trial data. Here we introduce TrialSynth, a Variational Autoencoder (VAE) designed to address the specific challenges of generating synthetic time-sequence clinical trial data. Distinct from related clinical data VAE methods, the core of our method leverages Hawkes Processes (HP), which are particularly well-suited for modeling event-type and time gap prediction needed to capture the structure of sequential clinical trial data. Our experiments demonstrate that TrialSynth surpasses the performance of other comparable methods that can generate sequential clinical trial data at varying levels of fidelity / privacy tradeoff, enabling the generation of highly accurate event sequences across multiple real-world sequential event datasets with small patient source populations. Notably, our empirical findings highlight that TrialSynth not only outperforms existing clinical sequence-generating methods but also produces data with superior utility while empirically preserving patient privacy.

cs.LG↗

arXiv2024

Compositional Representation of Polymorphic Crystalline Materials

Machine learning (ML) has seen promising developments in materials science, yet its efficacy largely depends on detailed crystal structural data, which are often complex and hard to obtain, limiting their applicability in real-world material synthesis processes. An alternative, using compositional descriptors, offers a simpler approach by indicating the elemental ratios of compounds without detailed structural insights. However, accurately representing materials solely with compositional descriptors presents challenges due to polymorphism, where a single composition can correspond to various structural arrangements, creating ambiguities in its representation. To this end, we introduce PCRL, a novel approach that employs probabilistic modeling of composition to capture the diverse polymorphs from available structural information. Extensive evaluations on sixteen datasets demonstrate the effectiveness of PCRL in learning compositional representation, and our analysis highlights its potential applicability of PCRL in material discovery. The source code for PCRL is available at https://github.com/Namkyeong/PCRL.

cond-mat.mtrl-sci↗

arXiv2024

A Perspective for Adapting Generalist AI to Specialized Medical AI Applications and Their Challenges

The integration of Large Language Models (LLMs) into medical applications has sparked widespread interest across the healthcare industry, from drug discovery and development to clinical decision support, assisting telemedicine, medical devices, and healthcare insurance applications. This perspective paper aims to discuss the inner workings of building LLM-powered medical AI applications and introduces a comprehensive framework for their development. We review existing literature and outline the unique challenges of applying LLMs in specialized medical contexts. Additionally, we introduce a three-step framework to organize medical LLM research activities: 1) Modeling: breaking down complex medical workflows into manageable steps for developing medical-specific models; 2) Optimization: optimizing the model performance with crafted prompts and integrating external knowledge and tools, and 3) System engineering: decomposing complex tasks into subtasks and leveraging human expertise for building medical AI applications. Furthermore, we offer a detailed use case playbook that describes various LLM-powered medical AI applications, such as optimizing clinical trial design, enhancing clinical decision support, and advancing medical imaging analysis. Finally, we discuss various challenges and considerations for building medical AI applications with LLMs, such as handling hallucination issues, data ownership and compliance, privacy, intellectual property considerations, compute cost, sustainability issues, and responsible AI requirements.

cs.CL↗

arXiv2024

Medical Video Generation for Disease Progression Simulation

Modeling disease progression is crucial for improving the quality and efficacy of clinical diagnosis and prognosis, but it is often hindered by a lack of longitudinal medical image monitoring for individual patients. To address this challenge, we propose the first Medical Video Generation (MVG) framework that enables controlled manipulation of disease-related image and video features, allowing precise, realistic, and personalized simulations of disease progression. Our approach begins by leveraging large language models (LLMs) to recaption prompt for disease trajectory. Next, a controllable multi-round diffusion model simulates the disease progression state for each patient, creating realistic intermediate disease state sequence. Finally, a diffusion-based video transition generation model interpolates disease progression between these states. We validate our framework across three medical imaging domains: chest X-ray, fundus photography, and skin image. Our results demonstrate that MVG significantly outperforms baseline models in generating coherent and clinically plausible disease trajectories. Two user studies by veteran physicians, provide further validation and insights into the clinical utility of the generated sequences. MVG has the potential to assist healthcare providers in modeling disease trajectories, interpolating missing medical image data, and enhancing medical education through realistic, dynamic visualizations of disease progression.

cs.CV↗

arXiv2024

Matching Patients to Clinical Trials with Large Language Models

Patient recruitment is challenging for clinical trials. We introduce TrialGPT, an end-to-end framework for zero-shot patient-to-trial matching with large language models. TrialGPT comprises three modules: it first performs large-scale filtering to retrieve candidate trials (TrialGPT-Retrieval); then predicts criterion-level patient eligibility (TrialGPT-Matching); and finally generates trial-level scores (TrialGPT-Ranking). We evaluate TrialGPT on three cohorts of 183 synthetic patients with over 75,000 trial annotations. TrialGPT-Retrieval can recall over 90% of relevant trials using less than 6% of the initial collection. Manual evaluations on 1,015 patient-criterion pairs show that TrialGPT-Matching achieves an accuracy of 87.3% with faithful explanations, close to the expert performance. The TrialGPT-Ranking scores are highly correlated with human judgments and outperform the best-competing models by 43.8% in ranking and excluding trials. Furthermore, our user study reveals that TrialGPT can reduce the screening time by 42.6% in patient recruitment. Overall, these results have demonstrated promising opportunities for patient-to-trial matching with TrialGPT.

cs.CL↗

arXiv2024

CARES: A Comprehensive Benchmark of Trustworthiness in Medical Vision Language Models

Artificial intelligence has significantly impacted medical applications, particularly with the advent of Medical Large Vision Language Models (Med-LVLMs), sparking optimism for the future of automated and personalized healthcare. However, the trustworthiness of Med-LVLMs remains unverified, posing significant risks for future model deployment. In this paper, we introduce CARES and aim to comprehensively evaluate the Trustworthiness of Med-LVLMs across the medical domain. We assess the trustworthiness of Med-LVLMs across five dimensions, including trustfulness, fairness, safety, privacy, and robustness. CARES comprises about 41K question-answer pairs in both closed and open-ended formats, covering 16 medical image modalities and 27 anatomical regions. Our analysis reveals that the models consistently exhibit concerns regarding trustworthiness, often displaying factual inaccuracies and failing to maintain fairness across different demographic groups. Furthermore, they are vulnerable to attacks and demonstrate a lack of privacy awareness. We publicly release our benchmark and code in https://cares-ai.github.io/.

cs.LG↗

arXiv2024

Accelerating Clinical Evidence Synthesis with Large Language Models

Synthesizing clinical evidence largely relies on systematic reviews of clinical trials and retrospective analyses from medical literature. However, the rapid expansion of publications presents challenges in efficiently identifying, summarizing, and updating clinical evidence. Here, we introduce TrialMind, a generative artificial intelligence (AI) pipeline for facilitating human-AI collaboration in three crucial tasks for evidence synthesis: study search, screening, and data extraction. To assess its performance, we chose published systematic reviews to build the benchmark dataset, named TrialReviewBench, which contains 100 systematic reviews and the associated 2,220 clinical studies. Our results show that TrialMind excels across all three tasks. In study search, it generates diverse and comprehensive search queries to achieve high recall rates (Ours 0.711-0.834 v.s. Human baseline 0.138-0.232). For study screening, TrialMind surpasses traditional embedding-based methods by 30% to 160%. In data extraction, it outperforms a GPT-4 baseline by 29.6% to 61.5%. We further conducted user studies to confirm its practical utility. Compared to manual efforts, human-AI collaboration using TrialMind yielded a 71.4% recall lift and 44.2% time savings in study screening and a 23.5% accuracy lift and 63.4% time savings in data extraction. Additionally, when comparing synthesized clinical evidence presented in forest plots, medical experts favored TrialMind's outputs over GPT-4's outputs in 62.5% to 100% of cases. These findings show the promise of LLM-based approaches like TrialMind to accelerate clinical evidence synthesis via streamlining study search, screening, and data extraction from medical literature, with exceptional performance improvement when working with human experts.

cs.CL↗