arXiv subjects

Lei Bai

Publications and source records attributed to Lei Bai.

At least 37 records · Page 2Linked to original sources

arXiv2026

UniGIO: Unified Generative Global In-situ Weather Modeling from Spatiotemporal Incomplete Observations

Global In-situ Observation (GIO) provides fine-scale, direct records of the global weather system from sparse point stations, making it an indispensable source for capturing localized and transient dynamics beyond the reach of satellite gridded data, and playing a critical role in key fields such as numerical weather prediction, disaster prevention, and agriculture. However, GIO exhibits strong spatiotemporal incompleteness, severely impairing accurate and real-time in-situ weather modeling. Unlike existing methods waiting for completed AI-ready data with extra introduced errors, in this work, we explore UniGIO, a novel generative framework for directly modeling global in-situ weather dynamics from native incomplete GIO. By generating missing data from observed ones annotated by masks, it unifies the coexisting forecasting, imputation, and generation under arbitrary missing ratios. Between the missing and observed, UniGIO captures station and region level complementarity through the Observation Mixer and Event Aligner, which diffuse discrete observations into continuous spaces where weather processes naturally span multiple stations. We further establish temporal dependencies with pattern shifts using the Adaptive Temporal Mixer, and track extreme events in chaotic local weather systems through a Mixture-ofExperts structure. Steady and extreme events are adapted in decoder by a Local Refiner. Extensive experiments on the up-todate largest global station weather dataset Weather-5K validate its SOTA performance with 11%, 12%, and 5% advantages on accuracy, fidelity, and extreme event capture, delivering a novel holistic solution for weather modeling in GIO networks.

cs.LG↗

arXiv2026

EasyBCI Agent: Towards Universal Neural Data Preprocessing for Brain-Computer Interfaces

Brain-computer interfaces translate neural activity into device commands, yet their performance hinges on preprocessing that remains manual, expert-dependent and poorly reproducible. Large language model agents can automate scientific coding, but existing systems lack the modality coverage, raw-data isolation, experience accumulation and domain oversight that neural preprocessing requires. We introduce EasyBCI, a two-phase LLM agent that plans and executes preprocessing pipelines for six signal types. A Plan Agent profiles each recording into a text-only Data Fingerprint that never exposes raw data to the model and selects a literature-grounded operator sequence. An Execution Agent generates, runs and self-corrects code until quality criteria are met, while a quality-gated experience system retains validated strategies as reusable skills. A domain expert intervenes at two decision gates, retaining human judgement where undetected error can invalidate downstream analyses. Evaluation on EEG with a fixed linear classifier shows that all five EasyBCI backbones preserve more task-relevant separability than the manual pipeline. Under same-backbone comparison, EasyBCI outperforms general-purpose coding agents on both label schemes for four of five configurations. EasyBCI extends to five additional modalities spanning nearly three orders of magnitude in sampling rate, producing complete reproducible pipelines with recorded decision provenance. These results indicate that domain-specific orchestration can bring auditable preprocessing within reach of laboratories lacking dedicated expertise, illustrating design principles applicable to AI agents in other scientific domains.

q-bio.QM↗

arXiv2026

Harness-of-Harness: Multi-Day Autonomous Software Development with Continual Improvement

This paper studies autonomous software development, in which LLM-based coding agents transform high-level requirements into complete, functional, and usable software systems without human intervention. We introduce Harness-of-Harness (HoH), a framework that enables coding agents to continually improve software during autonomous development. HoH operates on existing coding-agent harnesses, and organizes their executions into iterative planning-coding-testing loops. To sustain improvement across loops, HoH balances repair with capability growth, scopes development into small and verifiable increments, separates implementation-time testing from independent evaluation, and constrains verifiable outputs rather than prescribing agent workflows. It progressively exposes deliverables, role-specific tools, and skills, encourages reuse rather than recreation, and maintains versioned project histories. On GameCraft-Bench, FrontierSWE, and ProgramBench, three harness-model pairs (Codex with GPT-5.5, OpenCode with DeepSeek-V4-Pro, and Pi with MiniMax-M3), HoH consistently outperforms the corresponding standalone harnesses, achieving an average relative gain of 52.25 percent and a maximum gain of 82.86 percent after three iterations. In a multi-day deployment with more than 70 iterations, HoH autonomously develops a first-person-shooter game, featuring a coherent storyline, fully implemented core mechanics, human-playable experience, polished visuals and integrated audio. Github: https://github.com/Flesymeb/HarnessOfHarness Project Page: https://flesymeb.github.io/HarnessOfHarness/

cs.AI↗

arXiv2026

SCALE:Scalable Conditional Atlas-Level Endpoint transport for virtual cell perturbation prediction

Virtual-cell models aim to predict how cell populations respond to perturbations, but control and treated cells are measured as unpaired populations, complicating the learning of perturbation-specific effects. We present SCALE, a conditional transport model that represents cells as unordered sets and predicts treated populations without cell-level matching. A shared set-aware encoder and conditional DiT backbone learn latent transport, making endpoint supervision directly delta-aligned without an auxiliary delta objective. Across genetic, chemical, developmental and immune perturbations, SCALE recovered gene-expression changes, response directions and population structure. In CRISPR data with dominant cell-line effects, SCALE outperformed competing methods across seven metrics and maintained separation among gene-target representations rather than collapsing them into a shared region. SCALE further prioritized cytokines predicted to produce distinct immune activation and inflammatory responses. Experiments using matched PBMC samples from three donors confirmed these predicted differences. Together, SCALE enables perturbation-specific prediction from unpaired populations and supports experimental prioritization.

cs.LG↗

arXiv2026

PAPO: Stabilizing Rubric Integration Training via Decoupled Advantage Normalization

We propose Process-Aware Policy Optimization (PAPO), a method that integrates process-level evaluation into Group Relative Policy Optimization (GRPO) through decoupled advantage normalization, to address two limitations of existing reward designs. Outcome reward models (ORM) evaluate only final-answer correctness, treating all correct responses identically regardless of reasoning quality, and gradually lose the advantage signal as groups become uniformly correct. Process reward models (PRM) offer richer supervision, but directly using PRM scores causes reward hacking, where models exploit verbosity to inflate scores while accuracy collapses. PAPO resolves both by composing the advantage from an outcome component Aout, derived from ORM and normalized over all responses, and a process component Aproc, derived from a rubric-based PRM and normalized exclusively among correct responses. This decoupled design ensures that Aout anchors training on correctness while Aproc differentiates reasoning quality without distorting the outcome signal. Experiments across multiple model scales and six benchmarks demonstrate that PAPO consistently outperforms ORM, reaching 51.3% vs.\ 46.3% on OlympiadBench while continuing to improve as ORM plateaus and declines.

cs.AI↗

arXiv2026

SciOrch: Learning to Orchestrate Expert LLMs for Solving Frontier Multimodal Scientific Reasoning Tasks

Frontier scientific reasoning remains a major challenge for large language models (LLMs), where even the strongest commercial systems fall short of expert-level performance. A closer look at model behavior reveals substantial complementarity that single-model evaluation hides: different frontier models excel on different question types, and no single model captures the full picture. We present SciOrch, a framework that trains a lightweight 8B model to orchestrate frontier LLMs for scientific reasoning. The orchestrator decomposes each question, delegates sub-problems to selected commercial models through API calls, and synthesizes a final answer. Training such an orchestrator is fundamentally harder than conventional agentic RL: each action triggers an API call that is expensive in both dollar cost and latency, making standard online rollouts infeasible. We address this with MCTS-based approach, producing diverse orchestration trajectories, extracting per-node single-turn samples, and optimizing the orchestrator with GRPO-style training. On a 240-question test set spanning SGI-Reasoning and Scientists' First Exam, SciOrch reaches 56.66% average accuracy, outperforming the strongest single commercial model by 3.74% and the strongest multi-agent baseline by 3.33%. It also attains the best accuracy on both SGI and SFE with less than half the API cost of typical multi-agent methods.

cs.CL↗

arXiv2026

Learning from Hard Prompts: Difficulty-aware Advantage Amplification in Dynamic Sampling

Decoupled Clip and Dynamic Sampling Policy Optimization (DAPO) is a prominent variant of Group Relative Policy Optimization (GRPO). DAPO introduces several improvements over GRPO. Among these, Dynamic Sampling contributes the most to DAPO's accuracy gains relative to GRPO. To improve accuracy, Dynamic Sampling enhances training stability by eliminating zero policy gradients from zero advantages. Specifically, it avoids such zero gradients by filtering out prompts where sampled responses are either entirely correct or incorrect. However, our theoretical analysis shows that Dynamic Sampling decrease training efficiency as it cannot effectively utilize hard-to-sample correct responses on hard prompts. Formally, it asymmetrically amplifies the advantages of distinct responses to the same prompts. On hard prompts, incorrect responses undergo greater amplification than correct ones. This leads the model to avoid generating the observed incorrect responses rather than capitalizing on the hard-to-sample correct ones on hard prompts, resulting in low training efficiency. To improve training efficiency, we propose Direct Advantage Amplification (DAA), which amplifies the advantages of hard-to-sample correct responses on hard prompts, as obtained by Dynamic Sampling. This ensures that, when Dynamic Sampling is used, these hard-to-sample responses can be effectively capitalized on, implying higher training efficiency. By integrating DAA into DAPO, we obtain Difficulty-aware Advantage Amplification Policy Optimization (DA3PO), which is implemented with fewer than 30 lines of code from DAPO. Experiments show that DA3PO significantly outperforms GRPO and other classical GRPO variants.

cs.AI↗

arXiv2026

MolEmb: Multimodal Large Language Models Can Be Strong Molecular Embedding Models

Molecular embedding models can serve as foundational infrastructure for computational chemistry and drug discovery, where reusable vector representations support property prediction, virtual screening, and retrieval. Most molecular encoders are specialist models built around a single molecular view, producing unconditional vectors with no language interface for varying the representation. We ask whether multimodal large language models (MLLMs), which natively process images, text, and symbolic inputs, can instead serve as \emph{general molecular embedding models} that produce embeddings conditioned on both a molecular profile and a natural-language semantic context. We introduce \textbf{MolEmb}, a lightweight framework that adapts MLLMs by aligning molecular profiles with textual descriptions in a shared embedding space using a bidirectional contrastive objective. The resulting embedding model is competitive on molecular property prediction and supports cross-modal molecule--text retrieval in the same space. We further introduce \textbf{MolCAR}, a diagnostic benchmark for context-aware retrieval, and find that context-aware molecular embedding is primarily a data property of the supervision. These results suggest that MLLMs are not merely chemistry assistants or generators, but a viable and extensible route to general molecular embedding models.

cs.AI↗

arXiv2026

Self-Harness: Harnesses That Improve Themselves

The performance of LLM-based agents is jointly shaped by their base models and the harnesses that mediate their interaction with the environment. Because different models exhibit distinct behaviors, effective harness design is inherently model-specific. Yet agent harnesses are still largely engineered by human experts, a paradigm that scales poorly as modern LLMs become increasingly diverse and rapidly evolving. In this paper, we introduce Self-Harness, a new paradigm in which an LLM-based agent improves its own operating harness, without relying on human engineers or stronger external agents. We operationalize Self-Harness as an iterative loop with three stages: Weakness Mining, which identifies model-specific failure patterns from execution traces; Harness Proposal, which generates diverse yet minimal harness modifications tied to these failures; and Proposal Validation, which accepts candidate edits only after regression testing. We instantiate Self-Harness across Terminal-Bench-2.0, SWE-bench Verified, and AppWorld using a minimal initial harness and three base models from diverse families: MiniMax M2.5, Qwen3.5-35B-A3B, and GLM-5. Across all nine model--benchmark combinations, every final harness improves both held-in and held-out pass rates, with overall relative gains of up to 132%. Qualitative analyses further show that the retained mechanisms address benchmark-specific bottlenecks in artifact handling and runtime control, software-patch verification, and application-state retrieval. These results suggest a path toward LLM-based agents that are not merely shaped by their harnesses, but can also participate in reshaping them.

cs.CL↗

arXiv2026

SimpleOPD: Simple Tokenizer-Agnostic On-Policy Distillation for Long-Context Reasoning

On-policy distillation (OPD) offers a promising way to transfer reasoning capabilities from stronger teacher models, but applying it to long-context reasoning teachers and short-context students introduces practical challenges, including tokenizer mismatch, teacher-student distribution mismatch, response length explosion, and training instability. In this work, we study this setting by transferring proof-reasoning capabilities from the long-context reasoning model SU-01 to short-context student models. To handle tokenizer differences, we perform OPD in a shared text space and align only tokens that occupy identical text spans under the student and teacher tokenizers. To mitigate the problem of excessive generation length and frequent truncation, we introduce a student reference KL loss and mask the advantages of special termination tokens such as and <|im_end|>. This strategy constrains the student from drifting excessively from its initial policy, thereby mitigating the teacher-student distribution mismatch problem and fostering steady length growth. Experiments on both same-family and different-family student models, including Qwen3, Qwen3.5, Intern-S2, GLM-4.7, Gemma-4, show consistent gains in mathematical reasoning, especially natural-language math proving. Notably, Intern-S2-Preview improves by 21.2 points on ProofBench, reaching 55.2 and surpassing Gemini-2.5-Pro. It also improves on science benchmarks such as HLE and HiPhO, suggesting that OPD transfers reasoning capabilities that generalize beyond the mathematical training domain.

cs.CL↗

arXiv2026

Intern-S2-Preview: Scientific Agentic Foundation Model

Scientific discovery increasingly requires AI systems that can reason over scientific evidence of heterogeneous modalities, interact with scientific tools and environments, and sustain progress across long task horizons. We present Intern-S2-Preview, a series of scientific agentic foundation models designed to support multimodal scientific understanding, reasoning, generation, and long-horizon tasks. The training pipeline begins with scientific multimodal pre-training over rendered scientific documents, interleaved image-text data, and diverse scientific corpora. Starting from the pretrained checkpoint, we apply a unified post-training pipeline consisting of supervised fine-tuning, scalable multi-task reinforcement learning (RL), black- and white-box agentic RL, and on-policy distillation. This pipeline is supported by practical techniques that improve rollout and training stability and efficiency, including partial rollout with off-policy correction, adaptive length regularization, online speculative decoding, robust multi-task optimization, and trace-aware experience assembly for agentic tasks. At the architecture level, Intern-S2-Preview-397B extends time series modelling from efficient long-sequence understanding to numerical forecasting, while Memory Decoder is studied as a separate memory-augmented path for rapid scientific specialization without modifying the frozen 397B backbone. Evaluations across scientific, multimodal, agentic, and general-purpose benchmarks show that Intern-S2-Preview-397B achieves competitive or leading results in multiple settings. The time series modules improve scientific signal understanding and forecasting on SciTS, while the separate Intern-MemDec-4B extension improves the Biology-Instructions average score from 56.92 to 60.32 without modifying the frozen 397B backbone.

cs.LG↗

arXiv2026

Order Matters in Retrosynthesis: Structure-aware Generation via Reaction-Center-Guided Discrete Flow Matching

Template-free retrosynthesis methods treat the task as black-box sequence generation, limiting learning efficiency, while semi-template approaches rely on rigid reaction libraries that constrain generalization. We address this gap with a key insight: atom ordering in neural representations matters. Building on this insight, we propose a structure-aware template-free framework that encodes the two-stage nature of chemical reactions as a positional inductive bias. By placing reaction center atoms at the sequence head, our method transforms implicit chemical knowledge into explicit positional patterns that the model can readily capture. The proposed RetroDiT backbone, a graph transformer with rotary position embeddings, exploits this ordering to prioritize chemically critical regions. Combined with discrete flow matching, our approach decouples training from sampling and enables generation in 20--50 steps versus 500 for prior diffusion methods. Our method achieves state-of-the-art performance on both USPTO-50k (61.2% top-1) and the large-scale USPTO-Full (51.3% top-1) with predicted reaction centers. With oracle centers, performance reaches 71.1% and 63.4% respectively, surpassing foundation models trained on 10 billion reactions while using orders of magnitude less data. Ablation studies further reveal that structural priors outperform brute-force scaling: a 280K-parameter model with proper ordering matches a 65M-parameter model without it.

cs.LG↗

arXiv2026

A-SR: Self-Evolving Agentic LLMs for Symbolic Regression via Hierarchical Coordination

Symbolic regression aims to discover closed-form equations from data, but existing LLM-guided methods often rely on a unified proposal loop that compresses heterogeneous search failures into a scalar score and a single prompt. We propose A-SR, a self-evolving agentic framework that shifts the control unit from expression edits to role-conditioned evidence views. A-SR coordinates formula discovery through routing among coordination protocols, an online evaluator-reward role policy, and state-routed process memory. During search, evaluator feedback characterizes reliability and productivity, updates role-level utilities, and routes elite motifs, failure traces, and validity diagnostics to different agents. The framework self-evolves at two timescales: within a run, it adapts the search process without updating LLM parameters; across runs, recorded trajectories can be distilled into open-source LLMs as role-conditioned proposal priors. Averaged over the four LSR-Synth scientific domains in LLM-SRBench, A-SR improves Acc@0.01 over baselines from 25.79% to 48.30% with Llama3.1-8B, while A-SR-LoRA improves the corresponding Qwen3-4B result from 24.58% to 38.29%. On four real-world scientific discovery tasks, A-SR obtains the best in-distribution or out-of-distribution normalized mean squared error on 7 of 8 reported metrics.

cs.CL↗

arXiv2026

AgentPanel: Toward a New Paradigm for Human--AI Collaboration in Exploring Scientific Questions

Identifying promising scientific ideas remains an important challenge in research practice. Researchers commonly rely on small-group discussions or one-to-one interactions with a single large language model, yet these approaches often expose them to only a limited range of perspectives and directions. We present AgentPanel, a multi-agent forum for human--AI collaboration in scientific exploration. Heterogeneous agents asynchronously discuss scientific questions in a forum-style environment, while researchers can submit questions, browse and organize candidate ideas, engage agents in follow-up interactions, and optionally generate post-hoc summary reports. We evaluate AgentPanel in terms of idea quality, exploration breadth, interaction effectiveness, candidate-selection efficiency, and practical utility. Offline experiments show that AgentPanel outperforms a centralized multi-agent debate baseline. A human study with 20 participants further shows that users value AgentPanel for perspective diversity and exploration support. In experience-based comparisons with commonly used LLM tools, 65\% of participants favored AgentPanel for both breadth of research directions and overall suitability for early-stage exploration. The platform is publicly available at https://agentpanel.cc/.

cs.AI↗

arXiv2026

SeekBrain: An Autonomous Multi-Agent System for Accelerating Neuroscience Discovery

Modern neuroscience relies on integrating multi-scale, multimodal datasets to uncover the neural principles underlying intelligence. However, analytical challenges posed by highly heterogeneous data and fragmented workflows increasingly constrain discoveries. Here we introduce SeekBrain, an autonomous multi-agent framework designed to accelerate neuroscience discovery through domain-grounded hierarchical planning and cross-modal data analysis. SeekBrain dynamically constructs a repertoire of analysis recipes extracted from code-paper pairs. By coupling this codified expertise with agentic planning and execution engines, the framework scalably generates hypotheses and analytical pipelines on demand. Systematic evaluation on the expert-annotated BrainArena benchmark demonstrates that SeekBrain substantially outperforms state-of-the-art agent baselines across various analysis tasks. Crucially, when deployed in real-world research, SeekBrain integrated behavioral, neural, and anatomical data to reveal structured, distributed neural representations of larval zebrafish behavior and a shared axis of regional decoding strength across the brain in a mouse decision-making task. These results establish SeekBrain as a scalable and practical tool for accelerating data-driven discoveries in neuroscience.

cs.MA↗

arXiv2026

AutoSupervision: Closing the Feedback Loop in Scientific Workflows with Grounded Revision Verification

Recent advances in large language models (LLMs) have enabled AI systems to assist scientific research and peer review. However, an essential capability for reliable AI-assisted scientific workflows remains underexplored: verifying whether reviewer feedback leads to meaningful and evidence-supported manuscript improvements. We introduce AutoSupervision, which evaluates whether scientific manuscript revisions genuinely address reviewer concerns through grounded evidence. AutoSupervision leverages transparent peer-review records as a natural source of supervision, where reviewer comments specify scientific concerns, author responses describe claimed resolutions, and revised manuscripts provide evidence of changes. Given reviewer comments, author responses, and revised manuscripts, models must characterize reviewer concerns, determine whether concerns have been addressed, and identify supporting manuscript evidence. We construct AutoSupervision from 56,000 Nature Communications articles and corresponding review records. Then we conducted experiments on LLMs, the ablation study, and the case study. Our results show that while LLMs perform well in characterizing reviewer concerns, with GPT-5.5 achieving a score of 0.754, evidence-based verification remains the primary bottleneck, with the best-performing model reaching only 0.501.

cs.CL↗

arXiv2026

MoE$^2$-LoRA: When MoE Models Meet MoE-style Low-Rank Adaptation

Mixture-of-Experts (MoE) architectures have been widely adopted in large language models, yet parameter-efficient fine-tuning (PEFT) for MoE models remains underexplored. Existing PEFT methods for MoE either ignore router priors with uniform adapters, reducing efficiency and risking forgetting, or rely on static expert selection, limiting per-token capacity and cross-expert feature learning. In this paper, we make the first attempt to fine-tune MoE models with MoE-style low-rank adaptation: our method, entitled MoE$^2$-LoRA, deeply couples the pretrained expert specialization with task-specific adaptivity via a dual-channel Routing-Conditioned Projection (RCP) module, which reuses base router activations to inform LoRA routing. We further introduce a single global LoRA expert pool shared across all layers, enabling model-wide adaptation with emergent layer-wise affinities and balanced expert utilization. MoE$^2$-LoRA simultaneously benefits from the advantages of prior reuse, dynamic adapter routing, and model-wide knowledge sharing. Evaluated on multiple MoE backbones with varying scales and expert granularities, MoE$^2$-LoRA consistently achieves state-of-the-art downstream accuracy while retaining stronger general capabilities.

cs.CL↗

arXiv2026

Agents-K1: Towards Agent-native Knowledge Orchestration

Current LLM-based research agents have advanced through agent orchestration, yet largely overlook scientific knowledge orchestration. Existing works often reduce papers to abstracts, surface mentions, and flat \texttt{cites} edges, omitting key entities, claims, evidence, mechanisms, and method lineages essential for scientific reasoning. To this end, we introduce \textbf{Agents-K1}, an end-to-end knowledge orchestration pipeline that converts raw documents into agent-native scientific knowledge graphs. Agents-K1 integrates three components under a unifying theoretical foundation: a multimodal parser whose five-module schema captures entities, multimodal evidence, citations, and typed inter-entity relations across the full paper rather than abstracts alone; a 4B information-extraction backbone trained with GRPO under a rule-based reward; and a graphanything CLI, a tri-source agent interface that unifies web search, multimodal graph retrieval, and cross-document traversal. On top of this, we process 2.46 million scientific papers across six subjects to produce \textbf{Scholar-KG}, of which we release a one-million-paper subset, and the full Scholar-KG is accessible via the SCP link below. The same pipeline can be extended to general-domain corpora and to schema-conformant data synthesis. Extensive experiments demonstrate that Agents-K1 achieves superior performance in scientific information extraction, knowledge graph construction, and multi-hop scientific reasoning.

cs.AI↗