Runze Shi

Haoxuan Li, Tianci Gao, Jianhe Li et al.

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.

Tianci Gao, Haoxuan Li, Jianhe Li et al.

Scientific AI agents can autonomously carry out complex research workflows, yet these unfolded workflows often remain difficult for humans to inspect and review, limiting interpretable, controllable and effective human-AI collaboration. To address this challenge, we present a monitoring and visualization framework that records fine-grained execution events and organizes them into a directed graph that makes agent workflows explicit as they proceed. The system records intermediate steps (e.g. tool calls and code executions), and renders them as real-time updated visual traces that expose workflow structure. This allows users to examine how results are produced, identify where failures emerge, and better understand agent behavior across different stages of the research process. We conduct an evaluation on complex research tasks with domain experts of interdisciplinary backgrounds in AI, neuroscience, and biology. Experts report that structured traces visualization improves understanding of agent workflows, perceived interpretability, and usability for analysis and further interaction.

Tianqi Shen, Jinji Yang, Runze Shi et al.

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.

Runze Shi, Shengyu Yan, Yuecheng Cai et al.

Automated alpha discovery is difficult because the search space of formulaic factors is combinatorial, the signal-to-noise ratio in daily equity data is low, and unconstrained program generation is operationally unsafe. We present Hubble, an agentic factor mining framework that combines large language models (LLMs) with a domain-specific operator language, an abstract syntax tree (AST) execution sandbox, a dual-channel retrieval-augmented generation (RAG) module, and a family-aware selection mechanism. Instead of treating the LLM as an unconstrained code generator, Hubble restricts generation to interpretable operator trees, evaluates every candidate through a deterministic cross-sectional pipeline, and feeds back both top formulas and structured family-level diagnostics to subsequent rounds. The current system additionally introduces positive/negative RAG, formula-similarity penalties, standardized multi-metric scoring, dual reporting of RankIC and Pearson IC, and persistent diagnostics artifacts for post-hoc research analysis. On a U.S. equity universe of roughly 500 stocks, our main run evaluates 104 valid candidates across three rounds with zero runtime crashes and discovers a top set dominated by range, volatility, and trend families rather than crowded volume-only motifs. We then fix the resulting top-5 factors and validate them on a held-out period from 2025-06-01 to 2026-03-13. In this out-of-sample window, the two range factors and two volatility factors remain positive and several achieve HAC-significant Pearson IC and long-short evidence, whereas the weakest in-sample trend factor decays materially. These results suggest that safe LLM-guided search can be upgraded from a syntax-compliant generator into a reproducible alpha-research workflow that jointly optimizes validity, diversity, interpretability, and family-level generalization.