arXiv subjects

May Dongmei Wang

Publications and source records attributed to May Dongmei Wang.

3 recordsLinked to original sources

arXiv2026

Beyond Random Splits: Evaluating Drug-Target Affinity Models Under Chemically and Biologically Motivated Distribution Shifts Copy

Drug-target affinity (DTA) prediction is widely used to prioritize candidate compounds before costly experimental screening. DTA models are often compared under a single data split, even though deployment may require extrapolation to new chemical series, new protein targets, or both. We ask whether the distribution shift used for evaluation changes which architecture appears best. We curate 718,800 unique drug-protein pairs from the ChEMBL and BindingDB datasets. We compare a Morgan-fingerprint + protein-CNN baseline with 12 controlled architectures that combine four drug representations with three ESM-2 interaction modes. Mean validation RMSE increases from 0.950 and 0.945 under scaffold and fingerprint-cluster OOD to 1.299 and 1.321 under protein-cluster and dual OOD. Model rankings are similar across the two chemical shifts (tau = 0.79), but agreement with scaffold OOD falls under protein OOD (tau = 0.39) and reverses under dual OOD (tau = -0.55). Held-out evaluation, repeated seeds, group-aware bootstrap analysis, and a size-matched control support the same conclusion: architecture selection depends on the form of extrapolation, not only on average error or training-set size. DTA benchmarks should therefore match the chemical and target shifts expected at deployment.

cs.LG↗

arXiv2026

ClinEnv: An Interactive Multi-Stage Long Horizon EHR Environment for Agents

Clinical practice is not the selection of an answer from enumerated options: a physician gathers heterogeneous information incrementally and commits to sequential, irreversible decisions under uncertainty. Static benchmarks cannot probe and existing interactive medical benchmarks each compromise on at least one of them. We present ClinEnv, an interactive benchmark that evaluates LLMs as attending physicians over real inpatient admissions under a paradigm we term Longitudinal Inpatient Simulation. Each case is automatically constructed into an ordered sequence of decision stages; at every stage the model must actively query four specialized agents before committing to medications, procedures, and diagnoses. ClinEnv scores both what the model decides, through deterministic ontology-grounded matching, and how it gathers information. Across seven models, the strongest reaches only 0.31 decision F1, and outcome quality is sharply decoupled from process quality. Difficulty concentrates in management decisions and later stages, where models recover discharge diagnoses far more reliably than management actions (0.51 vs. 0.17 F1) and continue to issue redundant queries as cases progress. ClinEnv makes this information-acquisition gap, invisible to outcome-only evaluation, directly measurable.

cs.AI↗

arXiv2025

MENDR: Manifold Explainable Neural Data Representations

Foundation models for electroencephalography (EEG) signals have recently demonstrated success in learning generalized representations of EEGs, outperforming specialized models in various downstream tasks. However, many of these models lack transparency in their pretraining dynamics and offer limited insight into how well EEG information is preserved within their embeddings. For successful clinical integration, EEG foundation models must ensure transparency in pretraining, downstream fine-tuning, and the interpretability of learned representations. Current approaches primarily operate in the temporal domain, overlooking advancements in digital signal processing that enable the extraction of deterministic and traceable features, such as wavelet-based representations. We propose MENDR (Manifold Explainable Neural Data Representations), a filter bank-based EEG foundation model built on a novel Riemannian Manifold Transformer architecture to resolve these issues. MENDR learns symmetric positive definite matrix embeddings of EEG signals and is pretrained on a large corpus comprising over 4,000 hours of EEG data, decomposed via discrete wavelet packet transforms into multi-resolution coefficients. MENDR significantly enhances interpretability by visualizing symmetric positive definite embeddings as geometric ellipsoids and supports accurate reconstruction of EEG signals from learned embeddings. Evaluations across multiple clinical EEG tasks demonstrate that MENDR achieves near state-of-the-art performance with substantially fewer parameters, underscoring its potential for efficient, interpretable, and clinically applicable EEG analysis.

cs.LG↗