Joey Chan

Joey Chan, Wonbin Kweon, Ashley Shin et al.

Large language models (LLMs) have shown promise for molecular property prediction, but their ability to reason over chemical structures remains limited, as molecular representations such as SMILES differ substantially from the natural language on which LLMs are primarily trained. To bridge this semantic and chemical knowledge gap, we propose MolE-RAG, a training-free, molecule-centric retrieval-augmented generation framework for LLM-based molecular property prediction. MolE-RAG augments each prediction with three complementary sources of inference-time context: retrieved chemistry literature, molecule-specific information including compound synonyms, identifiers, functional group annotations, and physicochemical descriptors, and structurally similar molecules retrieved from the training set. We evaluate MolE-RAG across nine molecular property prediction tasks using proprietary, chemistry-specialized, and open-source LLMs. Across general-purpose LLMs, MolE-RAG improves ROC-AUC by up to 28 percentage points on classification tasks and reduces regression RMSE by up to 67% relative to a SMILES-only baseline. We further find that the utility of each context source varies across models and tasks, with different models benefiting most from textual retrieval, molecular context, or structural retrieval. These results suggest that molecule-centric retrieval can improve LLM-based molecular property prediction without model fine-tuning while providing a flexible framework for integrating heterogeneous chemical knowledge at inference time.

Joey Chan, Zhen Chen, Ershun Pan

With the rapid proliferation of electric vehicles, the safety and reliability of lithium-ion batteries have become critical concerns. Effective anomaly detection is essential for ensuring safe battery operation. However, as battery systems and operating scenarios become increasingly complex, battery fault diagnosis and maintenance require stronger cross-domain adaptability and human-AI collaboration. Traditional fault detection and diagnosis methods are usually designed for specific scenarios and predefined workflows, making them less effective in complex real-world applications. To address the scarcity of open-source battery fault report corpora and the lack of unified maintenance knowledge representation, this study proposes a descriptive text modeling approach for battery signal reports. Monitoring signals, statistical features, anomaly records, and state assessment results are transformed into structured and readable natural language descriptions, forming a language corpus for battery health diagnosis and maintenance. Based on this corpus, we propose VBFDD-Agent, a vehicle battery fault detection and diagnosis agent for automotive-grade battery systems. VBFDD-Agent integrates descriptive battery-state texts, historical case retrieval, local maintenance manuals, and large language model reasoning to generate structured diagnostic results and maintenance recommendations. Experiments show that the proposed framework can accurately perform anomaly monitoring based on descriptive textual representations and provide flexible, efficient, and actionable maintenance suggestions. Expert evaluation further confirms the practical value of the generated recommendations. Overall, VBFDD-Agent extends traditional battery diagnosis from label prediction to interpretable and maintenance-oriented decision support.

Zhizheng Wang, Chih-Hsuan Wei, Joey Chan et al.

Trustworthiness and transparency are essential for the clinical adoption of artificial intelligence (AI) in healthcare and biomedical research. Recent deep research systems aim to accelerate evidence-grounded scientific discovery by integrating AI agents with multi-hop information retrieval, reasoning, and synthesis. However, most existing systems lack explicit and inspectable criteria for evidence appraisal, creating a risk of compounding errors and making it difficult for researchers and clinicians to assess the reliability of their outputs. In parallel, current benchmarking approaches rarely evaluate performance on complex, real-world medical questions. Here, we introduce DeepER-Med, a Deep Evidence-based Research framework for Medicine with an agentic AI system. DeepER-Med frames deep medical research as an explicit and inspectable workflow of evidence-based generation, consisting of three modules: research planning, agentic collaboration, and evidence synthesis. To support realistic evaluation, we also present DeepER-MedQA, an evidence-grounded dataset comprising 100 expert-level research questions derived from authentic medical research scenarios and curated by a multidisciplinary panel of 11 biomedical experts. Expert manual evaluation demonstrates that DeepER-Med consistently outperforms widely used production-grade platforms across multiple criteria, including the generation of novel scientific insights. We further demonstrate the practical utility of DeepER-Med through eight real-world clinical cases. Human clinician assessment indicates that DeepER-Med's conclusions align with clinical recommendations in seven cases, highlighting its potential for medical research and decision support.

Joey Chan, Huan Wang, Haoyu Pan et al.

Accurate forecasting of battery capacity fade is essential for the safety, reliability, and long-term efficiency of energy storage systems. However, the strong heterogeneity across cell chemistries, form factors, and operating conditions makes it difficult to build a single model that generalizes beyond its training domain. This work proposes a unified capacity forecasting framework that maintains robust performance across diverse chemistries and usage scenarios. We curate 20 public aging datasets into a large-scale corpus covering 1,704 cells and 3,961,195 charge-discharge cycle segments, spanning temperatures from $-5\,^{\circ}\mathrm{C}$ to $45\,^{\circ}\mathrm{C}$, multiple C-rates, and application-oriented profiles such as fast charging and partial cycling. On this corpus, we adopt a Time-Series Foundation Model (TSFM) backbone and apply parameter-efficient Low-Rank Adaptation (LoRA) together with physics-guided contrastive representation learning to capture shared degradation patterns. Experiments on both seen and deliberately held-out unseen datasets show that a single unified model achieves competitive or superior accuracy compared with strong per-dataset baselines, while retaining stable performance on chemistries, capacity scales, and operating conditions excluded from training. These results demonstrate the potential of TSFM-based architectures as a scalable and transferable solution for capacity degradation forecasting in real battery management systems.

Chih-Hsuan Wei, Chi-Ping Day, Zhizheng Wang et al.

Drug repurposing is often framed as a candidate identification task, but existing approaches provide limited guidance for distinguishing biologically plausible candidates from historically well-connected ones. Here we introduce DrugKLM, a hybrid framework that integrates biomedical knowledge graph structure with large language model-based mechanistic reasoning to enable mechanistically grounded therapeutic prioritization. Across benchmark datasets, DrugKLM outperforms knowledge graph-only and language model-only baselines, including TxGNN. Beyond improved recall, DrugKLM confidence scores exhibit functional alignment with molecular phenotypes: higher scores are associated with transcriptional signatures linked to improved survival across 12 TCGA cancers. The scoring framework preferentially captures biologically perturbational signals rather than historical indication patterns. Expert curation across five cancers further reveals systematic differences in prioritization behavior, with DrugKLM elevating candidates supported by coherent mechanistic rationale and disease-specific clinical context. Together, these results establish DrugKLM as an evidence-integrative framework that translates heterogeneous biomedical data into mechanistically interpretable and clinically grounded therapeutic hypotheses.

Yikun Han, Joey Chan, Jingyuan Chen et al.

Patient-clinician communication is an asymmetric-information problem: patients often do not disclose fears, misconceptions, or practical barriers unless clinicians elicit them skillfully. Effective medical dialogue therefore requires reasoning under partial observability: clinicians must elicit latent concerns, confirm them through interaction, and respond in ways that guide patients toward appropriate care. However, existing medical dialogue benchmarks largely sidestep this challenge by exposing hidden patient state, collapsing elicitation into extraction, or evaluating responses without modeling what remains hidden. We present MedConceal, a benchmark with an interactive patient simulator for evaluating hidden-concern reasoning in medical dialogue, comprising 300 curated cases and 600 clinician-LLM interactions. Built from clinician-answered online health discussions, each case pairing clinician-visible context with simulator-internal hidden concerns derived from prior literature and structured using an expert-developed taxonomy. The simulator withholds these concerns from the dialogue agent, tracks whether they have been revealed and addressed via theory-grounded turn-level communication signals, and is clinician-reviewed for clinical plausibility. This enables process-aware evaluation of both task success and the interaction process that leads to it. We study two abilities: confirmation, surfacing hidden concerns through multi-turn dialogue, and intervention, addressing the primary concern and guiding the patient toward a target plan. Results show that no single system dominates: frontier models lead on different confirmation metrics, while human clinicians (N=159) remain strongest on intervention success. Together, these results identify hidden-concern reasoning under partial observability as a key unresolved challenge for medical dialogue systems.

Rezarta Islamaj, Robert Leaman, Joey Chan et al.

Evaluating large language models (LLMs) in the biomedical domain requires benchmarks that can distinguish reasoning from pattern matching and remain discriminative as model capabilities improve. Existing biomedical question answering (QA) benchmarks are limited in this respect. Multiple-choice formats can allow models to succeed through answer elimination rather than inference, while widely circulated exam-style datasets are increasingly vulnerable to performance saturation and training data contamination. Multi-hop reasoning, defined as the ability to integrate information across multiple sources to derive an answer, is central to clinically meaningful tasks such as diagnostic support, literature-based discovery, and hypothesis generation, yet remains underrepresented in current biomedical QA benchmarks. MedHopQA is a disease-centered multi-hop reasoning benchmark consisting of 1,000 expert-curated question-answer pairs introduced as a shared task at BioCreative IX. Each question requires synthesis of information across two distinct Wikipedia articles, and answers are provided in an open-ended free-text format. Gold annotations are augmented with ontology-grounded synonym sets from MONDO, NCBI Gene, and NCBI Taxonomy to support both lexical and concept-level evaluation. MedHopQA was constructed through a structured process combining human annotation, triage, iterative verification, and LLM-as-a-judge validation. To reduce leaderboard gaming and contamination risk, the 1,000 scored questions are embedded within a publicly downloadable set of 10,000 questions, with answers withheld, on a CodaBench leaderboard. MedHopQA provides both a benchmark and a reusable framework for constructing future biomedical QA datasets that prioritize compositional reasoning, saturation resistance, and contamination resistance as core design constraints.

Rezarta Islamaj, Joey Chan, Robert Leaman et al.

Multi-hop question answering (QA) remains a significant challenge in the biomedical domain, requiring systems to integrate information across multiple sources to answer complex questions. To address this problem, the BioCreative IX MedHopQA shared task was designed to benchmark in multi-hop reasoning for large language models (LLMs). We developed a novel dataset of 1,000 challenging QA pairs spanning diseases, genes, and chemicals, with particular emphasis on rare diseases. Each question was constructed to require two-hop reasoning through the integration of information from two distinct Wikipedia pages. The challenge attracted 48 submissions from 13 teams. Systems were evaluated using both surface string comparison and conceptual accuracy (MedCPT score). The results showed a substantial performance gap between baseline LLMs and enhanced systems. The top-ranked submission achieved an 89.30% F1 score on the MedCPT metric and an 87.30% exact match (EM) score, compared with 67.40% and 60.20%, respectively, for the zero-shot baseline. A central finding of the challenge was that retrieval-augmented generation (RAG) and related retrieval-based strategies were critical for strong performance. In addition, concept-level evaluation improved answer assessment when correct responses differed in surface form. The MedHopQA dataset is publicly available to support continued progress in this important area. Challenge materials: https://www.ncbi.nlm.nih.gov/research/bionlp/medhopqa and benchmark https://www.codabench.org/competitions/7609/

Qiao Jin, Yin Fang, Lauren He et al.

Assessing whether an article supports an assertion is essential for hallucination detection and claim verification. While large language models (LLMs) have the potential to automate this task, achieving strong performance requires frontier models such as GPT-5 that are prohibitively expensive to deploy at scale. To efficiently perform biomedical evidence attribution, we present Med-V1, a family of small language models with only three billion parameters. Trained on high-quality synthetic data newly developed in this study, Med-V1 substantially outperforms (+27.0% to +71.3%) its base models on five biomedical benchmarks unified into a verification format. Despite its smaller size, Med-V1 performs comparably to frontier LLMs such as GPT-5, along with high-quality explanations for its predictions. We use Med-V1 to conduct a first-of-its-kind use case study that quantifies hallucinations in LLM-generated answers under different citation instructions. Results show that the format instruction strongly affects citation validity and hallucination, with GPT-5 generating more claims but exhibiting hallucination rates similar to GPT-4o. Additionally, we present a second use case showing that Med-V1 can automatically identify high-stakes evidence misattributions in clinical practice guidelines, revealing potentially negative public health impacts that are otherwise challenging to identify at scale. Overall, Med-V1 provides an efficient and accurate lightweight alternative to frontier LLMs for practical and real-world applications in biomedical evidence attribution and verification tasks. Med-V1 is available at https://github.com/ncbi-nlp/Med-V1.

Joey Chan, Yikun Han, Jingyuan Chen et al.

Plain Language Summaries (PLS) aim to make research accessible to lay readers, but they are typically written in a one-size-fits-all style that ignores differences in readers' information needs and comprehension. In health contexts, this limitation is particularly important because misunderstanding scientific information can affect real-world decisions. Large language models (LLMs) offer new opportunities for personalizing PLS, but it remains unclear whether personalization helps, which strategies are most effective, and how to balance personalization with safety. We introduce ReLay, a dataset of 300 participant--PLS pairs from 50 lay participants in both static (expert-written) and interactive (LLM-personalized) settings. ReLay includes user characteristics, health information needs, information-seeking behavior, comprehension outcomes, interaction logs, and quality ratings. We use ReLay to evaluate five LLMs across two personalization methods. Personalization improves comprehension and perceived quality, but it also raises the risk of reinforcing user biases and introducing hallucinations, revealing a trade-off between personalization and safety. These findings highlight the need for personalization methods that are both effective and trustworthy for diverse lay audiences.

Joey Chan, Zhen Chen, Ershun Pan

Accurate estimation of lithium-ion battery capacity degradation is critical for enhancing the reliability and safety of battery operations. Traditional expert models, tailored to specific scenarios, provide isolated estimations. With the rapid advancement of data-driven techniques, a series of general-purpose time-series foundation models have been developed. However, foundation models specifically designed for battery capacity degradation remain largely unexplored. To enable zero-shot generalization in battery degradation prediction using large model technology, this study proposes a degradation-aware fine-tuning strategy for time-series foundation models. We apply this strategy to fine-tune the Timer model on approximately 10 GB of open-source battery charge discharge data. Validation on our released CycleLife-SJTUIE dataset demonstrates that the fine-tuned Battery-Timer possesses strong zero-shot generalization capability in capacity degradation forecasting. To address the computational challenges of deploying large models, we further propose a knowledge distillation framework that transfers the knowledge of pre-trained foundation models into compact expert models. Distillation results across several state-of-the-art time-series expert models confirm that foundation model knowledge significantly improves the multi-condition generalization of expert models.

Nicholas Wan, Qiao Jin, Joey Chan et al.

Although large language models (LLMs) have been assessed for general medical knowledge using licensing exams, their ability to support clinical decision-making, such as selecting medical calculators, remains uncertain. We assessed nine LLMs, including open-source, proprietary, and domain-specific models, with 1,009 multiple-choice question-answer pairs across 35 clinical calculators and compared LLMs to humans on a subset of questions. While the highest-performing LLM, OpenAI o1, provided an answer accuracy of 66.0% (CI: 56.7-75.3%) on the subset of 100 questions, two human annotators nominally outperformed LLMs with an average answer accuracy of 79.5% (CI: 73.5-85.0%). Ultimately, we evaluated medical trainees and LLMs in recommending medical calculators across clinical scenarios like risk stratification and diagnosis. With error analysis showing that the highest-performing LLMs continue to make mistakes in comprehension (49.3% of errors) and calculator knowledge (7.1% of errors), our findings highlight that LLMs are not superior to humans in calculator recommendation.

Zifeng Wang, Lang Cao, Qiao Jin et al.

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.

Jash Rajesh Parekh, Wonbin Kweon, Joey Chan et al.

Current biomedical question answering (QA) systems often assume that medical knowledge applies uniformly, yet real-world clinical reasoning is inherently conditional: nearly every decision depends on patient-specific factors such as comorbidities and contraindications. Existing benchmarks do not evaluate such conditional reasoning, and retrieval-augmented or graph-based methods lack explicit mechanisms to ensure that retrieved knowledge is applicable to given context. To address this gap, we propose CondMedQA, the first benchmark for conditional biomedical QA, consisting of multi-hop questions whose answers vary with patient conditions. Furthermore, we propose Condition-Gated Reasoning (CGR), a novel framework that constructs condition-aware knowledge graphs and selectively activates or prunes reasoning paths based on query conditions. Our findings show that CGR more reliably selects condition-appropriate answers while matching or exceeding state-of-the-art performance on biomedical QA benchmarks, highlighting the importance of explicitly modeling conditionality for robust medical reasoning.

Joey Chan, Qiao Jin, Nicholas Wan et al.

Clinical trials are crucial for assessing new treatments; however, recruitment challenges - such as limited awareness, complex eligibility criteria, and referral barriers - hinder their success. With the growth of online platforms, patients increasingly turn to social media and health communities for support, research, and advocacy, expanding recruitment pools and established enrollment pathways. Recognizing this potential, we utilized TrialGPT, a framework that leverages a large language model (LLM) as its backbone, to match 50 online patient cases (collected from published case reports and a social media website) to clinical trials and evaluate performance against traditional keyword-based searches. Our results show that TrialGPT outperforms traditional methods by 46% in identifying eligible trials, with each patient, on average, being eligible for around 7 trials. Additionally, our outreach efforts to case authors and trial organizers regarding these patient-trial matches yielded highly positive feedback, which we present from both perspectives.