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.

MedAgentGym: Training LLM Agents for Code-Based Medical Reasoning at Scale

We introduce MedAgentGYM, the first publicly available training environment designed to enhance coding-based medical reasoning capabilities in large language model (LLM) agents. MedAgentGYM comprises 72,413 task instances across 129 categories derived from authentic real-world biomedical scenarios. Tasks are encapsulated within executable coding environments, each featuring detailed task descriptions, interactive feedback mechanisms, verifiable ground-truth annotations, and scalable training trajectory generation. Extensive benchmarking of over 30 LLMs reveals a notable performance disparity between commercial API-based models and open-source counterparts. Leveraging MedAgentGYM, Med-Copilot-7B achieves substantial performance gains through supervised fine-tuning (+36.44%) and continued reinforcement learning (+42.47%), emerging as an affordable and privacy-preserving alternative competitive with gpt-4o. By offering both a comprehensive benchmark and accessible, expandable training resources within unified execution environments, MedAgentGYM delivers an integrated platform to develop LLM-based coding assistants for advanced biomedical research and practice.