arXiv subjects

Fanyang Yu

Publications and source records attributed to Fanyang Yu.

3 recordsLinked to original sources

arXiv2026

TrialAtlas: Multi-Agent Research Organization for Clinical Trial Design and Optimization

Nearly 90% of drugs entering clinical development ultimately fail, despite billions of dollars in investment. Pharmaceutical companies therefore rely on clinical development planning (CDP) and probability of technical and regulatory success assessment to anticipate development risks, yet these decisions remain labor-intensive and subjective, requiring experts across clinical science, statistics, regulatory affairs, and competitive intelligence to jointly acquire, synthesize, and reason over heterogeneous evidence. Here, we introduce TrialAtlas, a memory-augmented multi-agent research organization for CDP that mirrors this collaborative process by coordinating specialized agents for literature synthesis, competitive trial intelligence, regulatory precedent analysis, and integrated reasoning over trial design and development risk. TrialAtlas further learns from historical clinical trials and regulatory outcomes, including prior New Drug Applications (NDAs), to ground its decisions in accumulated development experience. To evaluate these capabilities in an authentic regulatory setting, we introduce TrialAtlasBench, constructed from 291 FDA Complete Response Letters and spanning three practical tasks: detecting trial design deficiencies, recommending actionable design improvements, and predicting technical and regulatory success. TrialAtlas achieves an F1 score of 50.0% for deficiency detection, outperforming the strongest baseline by 6.1 points, and reaches 85.3% balanced accuracy and 84.7% F1 for prediction of technical and regulatory success, improving over the best baselines by 6.7 points in balanced accuracy and 12.0 points in Cohen's kappa. In expert evaluation, 86.4% of TrialAtlas-generated concerns were judged valid, compared with 83.1% for OpenAI DeepResearch and 59.3% for Gemini DeepResearch.

cs.CL↗

arXiv2024

Generative models of MRI-derived neuroimaging features and associated dataset of 18,000 samples

Availability of large and diverse medical datasets is often challenged by privacy and data sharing restrictions. For successful application of machine learning techniques for disease diagnosis, prognosis, and precision medicine, large amounts of data are necessary for model building and optimization. To help overcome such limitations in the context of brain MRI, we present GenMIND: a collection of generative models of normative regional volumetric features derived from structural brain imaging. GenMIND models are trained on real brain imaging regional volumetric measures from the iSTAGING consortium, which encompasses over 40,000 MRI scans across 13 studies, incorporating covariates such as age, sex, and race. Leveraging GenMIND, we produce and offer 18,000 synthetic samples spanning the adult lifespan (ages 22-90 years), alongside the model's capability to generate unlimited data. Experimental results indicate that samples generated from GenMIND agree with the distributions obtained from real data. Most importantly, the generated normative data significantly enhance the accuracy of downstream machine learning models on tasks such as disease classification. Data and models are available at: https://huggingface.co/spaces/rongguangw/GenMIND.

q-bio.QM↗

arXiv2023

Applications of Generative Adversarial Networks in Neuroimaging and Clinical Neuroscience

Generative adversarial networks (GANs) are one powerful type of deep learning models that have been successfully utilized in numerous fields. They belong to a broader family called generative methods, which generate new data with a probabilistic model by learning sample distribution from real examples. In the clinical context, GANs have shown enhanced capabilities in capturing spatially complex, nonlinear, and potentially subtle disease effects compared to traditional generative methods. This review appraises the existing literature on the applications of GANs in imaging studies of various neurological conditions, including Alzheimer's disease, brain tumors, brain aging, and multiple sclerosis. We provide an intuitive explanation of various GAN methods for each application and further discuss the main challenges, open questions, and promising future directions of leveraging GANs in neuroimaging. We aim to bridge the gap between advanced deep learning methods and neurology research by highlighting how GANs can be leveraged to support clinical decision making and contribute to a better understanding of the structural and functional patterns of brain diseases.

cs.LG↗