BrainPilot: Automating Brain Discovery with Agentic Research

Understanding the brain increasingly depends on integrating evidence across scales, modalities, and disciplines. Addressing a single research question therefore requires a coordinated sequence of operations, from surveying prior work to executing analyses and interpreting results in light of domain knowledge. AI agents promise to accelerate this process, but current agents lack domain expertise in brain science, may fabricate claims, drift during multi-step reasoning, and offer few defined points for expert intervention. These failures are especially costly in brain science, where conclusions feed into downstream scientific claims and depend on laboratory-specific expertise and careful human judgment. We present \textbf{BrainPilot} a \textbf{fully open-source} multi-agent system that accelerates brain science research with traceable logs and agent-verified results. A principal investigator (PI) agent coordinates specialist agents grounded in curated domain knowledge: a unified brain science knowledge base containing 7{,}233 indexed items and a skill library of 72 reusable methodology units across seven research domains. Every major step is recorded in the Graph of Trace, an auditable record that links subgoals, tool use, evidence, and claims and allows researchers to follow and inspect the workflow. An Auditor agent further integrates fabrication checking into the workflow. For evaluation, we run three brain science tasks from Agents' Last Exam, introduce our own benchmark, \textbf{BrainPilotBench-v0}, and present additional end-to-end case studies. Across these evaluations, BrainPilot with an open-source backbone model attains performance comparable to state-of-the-art agent framework with less costs.

Towards Understanding the Power and Limits of the Muon Optimizer: A River-Valley Perspective

Recently, Muon has gained substantial attention as an appealing alternative to Adam-like optimizers, with many works highlighting its advantages through spectral normalization and improved conditioning. Yet this positive theoretical narrative contrasts with its empirical performance in large language model (LLM) training, where Muon's gains over Adam/AdamW are often mixed, schedule-sensitive, and not uniformly superior. To address this gap, we develop a trajectory-level theory characterizing both the strengths and limitations of Muon. We introduce a mixed-spiked matrix sensing model whose sensing operator decomposes into signal, spike, and bulk components, capturing a mixture of anisotropic structure and long-tail information reminiscent of LLM training. On top of it, we adopted a river-valley perspective in which we view the landscape as composed of a river direction flowing to the desired solution and hill directions encoding nuisance or task-irrelevant information. In the momentum-free setting, we show that Muon moves faster along the information-bearing river direction during early optimization, but can converge much more slowly near the river bottom than gradient descent. We then extend the river-valley perspective to general nonconvex objectives with momentum by studying points on the spectral river. There, while Muon converges faster early on, its orthogonalized update removes residual scale information, making it prone to overshooting and oscillation near the target solution. Together, these results suggest that our characterizations extend beyond spiked matrix sensing and motivate switching to GD-like refinement optimizers in the final phase, rather than relying only on a fixed learning-rate schedule for Muon. We also provide preliminary evidence supporting this two-stage approach in language model training experiments.