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Ruoqi Liu

Ruoqi Liu contributes to research discovery and scholarly infrastructure.

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Published work

3 published item(s)

preprint2026arXiv

PhysicianBench: Evaluating LLM Agents in Real-World EHR Environments

We introduce PhysicianBench, a benchmark for evaluating LLM agents on physician tasks grounded in real clinical setting within electronic health record (EHR) environments. Existing medical agent benchmarks primarily focus on static knowledge recall, single-step atomic actions, or action intent without verifiable execution against the environment. As a result, they fail to capture the long-horizon, composite workflows that characterize real clinical systems. PhysicianBench comprises 100 long-horizon tasks adapted from real consultation cases between primary care and subspecialty physicians, with each task independently reviewed by a separate panel of physicians. Tasks are instantiated in an EHR environment with real patient records and accessed through the same standard APIs used by commercial EHR vendors. Tasks span 21 specialties (e.g., cardiology, endocrinology, oncology, psychiatry) and diverse workflow types (e.g., diagnosis interpretation, medication prescribing, treatment planning), requiring an average of 27 tool calls per task. Solving each task requires retrieving data across encounters, reasoning over heterogeneous clinical information, executing consequential clinical actions, and producing clinical documentation. Each task is decomposed into structured checkpoints (670 in total across the benchmark) capturing distinct stages of completion graded by task-specific scripts with execution-grounded verification. Across 13 proprietary and open-source LLM agents, the best-performing model achieves only 46% success rate (pass@1), while open-source models reach at most 19%, revealing a substantial gap between current agent capabilities and the demands of real-world clinical workflows. PhysicianBench provides a realistic and execution-grounded benchmark for measuring progress toward autonomous clinical agents.

preprint2022arXiv

Deconfounding Actor-Critic Network with Policy Adaptation for Dynamic Treatment Regimes

Despite intense efforts in basic and clinical research, an individualized ventilation strategy for critically ill patients remains a major challenge. Recently, dynamic treatment regime (DTR) with reinforcement learning (RL) on electronic health records (EHR) has attracted interest from both the healthcare industry and machine learning research community. However, most learned DTR policies might be biased due to the existence of confounders. Although some treatment actions non-survivors received may be helpful, if confounders cause the mortality, the training of RL models guided by long-term outcomes (e.g., 90-day mortality) would punish those treatment actions causing the learned DTR policies to be suboptimal. In this study, we develop a new deconfounding actor-critic network (DAC) to learn optimal DTR policies for patients. To alleviate confounding issues, we incorporate a patient resampling module and a confounding balance module into our actor-critic framework. To avoid punishing the effective treatment actions non-survivors received, we design a short-term reward to capture patients' immediate health state changes. Combining short-term with long-term rewards could further improve the model performance. Moreover, we introduce a policy adaptation method to successfully transfer the learned model to new-source small-scale datasets. The experimental results on one semi-synthetic and two different real-world datasets show the proposed model outperforms the state-of-the-art models. The proposed model provides individualized treatment decisions for mechanical ventilation that could improve patient outcomes.

preprint2020arXiv

Clinical connectivity map for drug repurposing: using laboratory tests to bridge drugs and diseases

Drug repurposing has attracted increasing attention from both the pharmaceutical industry and the research community. Many existing computational drug repurposing methods rely on preclinical data (e.g., chemical structures, drug targets), resulting in translational problems for clinical trials. In this study, we propose a clinical connectivity map framework for drug repurposing by leveraging laboratory tests to analyze complementarity between drugs and diseases. We establish clinical drug effect vectors (i.e., drug-laboratory test associations) by applying a continuous self-controlled case series model on a longitudinal electronic health record data. We establish clinical disease sign vectors (i.e., disease-laboratory test associations) by applying a Wilcoxon rank sum test on a large-scale national survey data. Finally, we compute a repurposing possibility score for each drug-disease pair by applying a dot product-based scoring function on clinical disease sign vectors and clinical drug effect vectors. We comprehensively evaluate 392 drugs for 6 important chronic diseases (e.g., asthma, coronary heart disease, type 2 diabetes, etc.). We discover not only known associations between diseases and drugs but also many hidden drug-disease associations. Moreover, we are able to explain the predicted drug-disease associations via the corresponding complementarity between laboratory tests of drug effect vectors and disease sign vectors. The proposed clinical connectivity map framework uses laboratory tests from electronic clinical information to bridge drugs and diseases, which is explainable and has better translational power than existing computational methods. Experimental results demonstrate the effectiveness of the proposed framework and suggest that our method could help identify drug repurposing opportunities, which will benefit patients by offering more effective and safer treatments.