arXiv subjects

Lei Bai

Publications and source records attributed to Lei Bai.

At least 55 records · Page 3Linked to original sources

arXiv2026

SciForge: An AI-Native, Multimodal Workbench for Scientific Discovery

Scientific work increasingly spans heterogeneous artifacts -- papers, code, datasets, scientific file formats, model outputs, figures, manuscripts, and team decisions -- yet general-purpose AI assistants rarely preserve these objects as a coherent, auditable research state. We present SciForge, a multimodal research-native AI workbench that reserves the graphical interface for human judgment while search, parsing, model routing, workflow execution, plotting, writing, and presentation generation run as modular agent-accessible services. SciForge is built around five pillars: (i) \emph{goal-scoped scientific decision governance} for \textbf{goal-oriented} research, with review gates and shared review surfaces; (ii) \emph{translate-then-reason} for \textbf{multimodal} input, routing scientific objects through domain translators before the agent reasons; (iii) \emph{evidence governance} for \textbf{auditable} traceability, linking claims to provenance chains and audit findings; (iv) \emph{collaborative team science} for \textbf{collaborative} research, enabling multi-role decision governance, with shared team workspaces planned for future releases; and (v) \emph{real-world application scenarios} for \textbf{practical} impact, demonstrated through eight end-to-end user cases, with flagship demonstrations including multi-day agentic research sprints for gene discovery, AI-guided de novo protein design, molecular optimization, and genome-to-BGC discovery. The system combines a thin interaction layer, contextual research capability patterns, an Agent Runtime and Workflow Engine, an Evidence-DAG audit sidecar and a Scientific Model Router. SciForge currently runs as a desktop application, with mobile supervision support; future releases will deepen team collaboration. The system is open-source and available at https://github.com/AGI4Sci/SciForge

cs.AI↗

arXiv2026

TSSM: Triaxial State Space Model for Global Station Weather Forecasting with Temporal-Variable-Historical Modeling

Global Station Weather Forecasting (GSWF) is pivotal for localized and extreme weather prediction over key regions. Despite efforts to exploit look-back windows, existing methods show limited accuracy gains and struggle with extreme events and error accumulation. These limitations stem from overreliance on short-term patterns, which are insufficient to capture chaotic weather dynamics, especially under partial observations. To address this problem, we propose a novel Triaxial State Space Model (TSSM) with a history-enhanced Temporal-VariableHistorical paradigm, which incorporates period-aligned historical weather data to compensate for long-term, large-scale periodic, and full-window weather patterns beyond the temporal lookback window. Specifically, TSSM stacks historical samples into period-aligned batches, where forecasting is causally supported by historical and current observations. Temporal, variable, and historical scanning are designed to capture axial temporal dependencies, variable correlations, and historical evolution. This structure is hierarchically shared to model seasonal to extreme events while alleviating misalignment across historical patterns. TSSM achieves SOTA performance on Weather-5K, the largest station weather dataset to date, with 10% and 61% gains in accuracy and extreme event metrics, and obtains 95% best or second-best results on human-involved datasets. Its advantages are more pronounced in long-horizon and iterative forecasting, reaching a 37.5% gain at 240h and up to 103.5% under a 48h times 5 iterative setting. Moreover, TSSM retains > 90% performance under up to 80% missing observations, compared with < 43% for baselines, demonstrating robustness and practical potential for reliable GSWF in global in-situ observation networks.

cs.LG↗

arXiv2026

Scaling the Horizon, Not the Parameters: Reaching Trillion-Parameter Performance with a 35B Agent

We introduce Agents-A1, a 35B Mixture-of-Experts Agentic Model that reaches trillion-parameter-level performance by scaling the agent horizon. We investigate agent-horizon scaling from two perspectives: scaling long-horizon trajectories and scaling heterogeneous agent abilities. To support this goal, we build a long-horizon knowledge-action infrastructure that connects external knowledge, actions, observations, and verifier outcomes, producing agentic trajectories with an average length of 45K tokens. Based on this, we train Agents-A1 with a three-stage recipe. First, we perform full-domain supervised fine-tuning to align the base model with broad agentic behaviors. Second, we train domain-level teacher models to capture specialized expertise in each domain. Third, we propose a multi-teacher domain-routed on-policy distillation with salient vocabulary alignment to improve knowledge transfer efficiency across different domains, unifying six heterogeneous domains into one deployable student model. Agents-A1 achieves strong and broad performance for long-horizon agent benchmarks. Compared with 1T-parameter model such as Kimi-K2.6 and DeepSeek-V4-pro, Agents-A1 achieves leading results on SEAL-0 (56.4), IFBench (80.6), HiPhO (46.4), FrontierScience-Olympiad (79.0), and MolBench-Bind (56.8), and remains highly competitive on SciCode (44.3), HLE (47.6) and BrowseComp (75.5). We hope this work provides the community with a practical path for scaling the horizon using a 35B agent that can reach or match the performance of 1T models on long-horizon tasks.

cs.CL↗

arXiv2026

Active rejection enables reliable generalization of universal machine-learning interatomic potentials

Universal machine learning interatomic potentials (uMLIPs) bridge quantum-mechanical accuracy and large-scale molecular dynamics, but the cost of high-accuracy calculations such as r$^2$SCAN limits training to datasets that remain small relative to the open materials space. Strong average benchmark performance also does not guarantee reliable energy--force predictions for every structure. We propose Adaptive Multi-Teacher Routing (ATR), which reformulates high-fidelity data construction as a structure-wise decision problem under uncertainty. Using a small set of real r$^2$SCAN labels, ATR calibrates multiple pretrained uMLIP teachers and combines structural descriptors, teacher identity, and inter-teacher disagreement to estimate the reliability of each structure--teacher pair. It selects high-confidence predictions for pseudo-label generation and rejects structures for which no teacher is sufficiently reliable. With real r$^2$SCAN labels for only 0.2\% of candidate structures, ATR distils 2.89 million traceable r$^2$SCAN-level pseudo-labels for pretraining. On held-out r$^2$SCAN structures and the MP-r$^2$SCAN benchmark, a lightweight CHGNet trained on the ATR-generated dataset consistently outperforms the baseline and non-routed controls. Finite-temperature molecular dynamics further shows that ATR improves dynamical robustness across multiple material systems, maintaining stable trajectories where baseline simulations undergo catastrophic structural collapse. These results establish active rejection as an effective mechanism for converting multiple pretrained uMLIPs into a scalable and reliable data-construction system for high-fidelity uMLIPs.

cs.LG↗

arXiv2026

Accurate, Interdisciplinary and Transparent Structure-property Understanding with Deep Native Structural Reasoning

Structure-property relationships are foundational to biology, chemistry and materials science, where function, reactivity and physical response emerge from spatial, chemical and periodic organization. Mechanistically explaining these relationships requires interpreting structural evidence through scientific principles and physical constraints, from stereochemistry and bonding to symmetry, energetics and periodic order. However, applying artificial intelligence to this process presents a joint challenge of representation and reasoning: models must preserve domain-native structural information while showing how specific evidence supports predictions under these constraints. Here we introduce SciReasoner, a multimodal scientific foundation model for native structural reasoning across proteins, small molecules and inorganic crystals. SciReasoner discretizes coordinates, topologies and periodic connectivities into a unified structure-aware vocabulary, treating structural tokens as addressable evidence units during reasoning. In homology-controlled Gene Ontology prediction, SciReasoner improves Cellular Component annotation for low-homology and orphan-like proteins, increasing $F_{\max}$ from 0.42 to 0.55. In chemistry, it raises single-step retrosynthesis accuracy from 0.63 to 0.72 while generating fragment-level disconnection and precursor-verification traces. In materials science, its representations separate elemental and compound phases and resolve high- and low-band-gap regimes. Across 86 benchmarks, SciReasoner achieves state-of-the-art performance on 67 tasks. Double-blind expert evaluation rates its reasoning traces as preferred or at least comparable to those of a frontier large language model in 98% of cases. By making structure an inspectable substrate for reasoning under scientific constraints, SciReasoner connects accurate prediction with interpretable scientific inference.

cs.CL↗

arXiv2026

VASP Agent: An Agentic Framework for Autonomous First-principles Calculations

Large Language Models (LLMs) are increasingly embedded in agentic frameworks for scientific discovery. First-principles materials computation imposes a demanding standard for autonomy: successful execution depends on internally consistent inputs, supervision of long-running calculations, and verified outputs. Here we present VASP Agent, a coding-agent-centered system that combines reusable domain skills, deterministic tools, workspace-state inspection, runtime evidence, and scientific guardrails to execute multi-step VASP calculations. The system is evaluated across multiple tasks including structural relaxation, bandgap calculation, equilibrium lattice constant determination, and CO/Pt(111) adsorption. VASP Agent completes all evaluated cases, and its computed numerical results are compared with those obtained using pymatgen and other agentic tools. When large deviations occur, the calculation parameters produced by VASP Agent are more appropriate than those produced by LLM-based workflows. Failure analysis shows that errors that terminate fixed pipelines can be diagnosed and recovered under agentic control.

cs.AI↗

arXiv2026

ResearchClawBench: A Benchmark for End-to-End Autonomous Scientific Research

AI coding agents are increasingly used for scientific work, but their end-to-end autonomous research capability remains difficult to verify. We present ResearchClawBench, a benchmark for evaluating autonomous scientific research across 40 tasks from 10 scientific domains. Each task is grounded in a real published paper, provides related literature and raw data, and hides the target paper during evaluation. Expert-curated multimodal rubrics decompose the target scientific artifacts into weighted criteria, enabling evaluation of target-paper-level re-discovery while leaving room for new discovery. We evaluate seven autonomous research (auto-research) agents under a unified protocol and seventeen native LLMs through the lightweight ResearchHarness. Current systems remain far from reliable re-discovery: the strongest autonomous agent, Claude Code, averages 21.5, and the strongest ResearchHarness LLM, Claude-Opus-4.7, averages 20.7, with an LLM frontier mean of only 26.5. Error analysis shows that failures concentrate in experimental protocol mismatch, evidence mismatch, and missing scientific core. ResearchClawBench provides a reproducible evaluation frontier for measuring progress toward autonomous scientific research.

cs.LG↗

arXiv2026

A Self-Evolving Agentic System for Automated Generation and Execution of Biological Protocols

Autonomous wet-lab experimentation requires more than plausible protocol text: biological intent, quantitative procedures, device constraints and experimental feedback must remain aligned from protocol and SOP design to code and physical execution. We developed ProtoPilot, a self-evolving multi-agent system, together with an expert-grounded benchmark and evaluation framework for testing this conversion as an experimental automation problem. The framework spans 294 synthetic-biology and molecular-biology tasks derived from 98 gold-standard protocols, wet-lab expert rubrics, device-level validity gates and real experimental tests. ProtoPilot incorporates layer-wise verifiability, multi-agent orchestration and a runtime-updated skill library to generate protocols, expand SOPs, synthesize SDK-compliant code and revise workflows from wet-lab feedback. It achieved a Top@3 expert-preference rate of 90.2%, an overall protocol-to-code gate pass rate of 89.5% and an Opentrons pass rate of 88.24%, compared with 32.35% for OpenTrons-AI. Wet-lab validation produced interpretable readouts, Sanger-confirmed products and feedback-corrected PCA-assembled DNA targets, establishing a verifiable route to autonomous experimentation. Together, these results show that the evaluation framework captures execution-relevant requirements for autonomous wet-lab automation, and that ProtoPilot can meet them by converting protocol and code generation into validated execution and feedback-guided revision.

cs.AI↗

arXiv2026

Deep Research in Physical Sciences: A Multi-Agent Framework and Comprehensive Benchmark

Deep research agents are Large Language Model (LLM)-based systems designed for autonomous, multi-step scientific reasoning, and they hold immense potential for accelerating research in the physical sciences. However, comprehensive and in-depth evaluations of their capabilities within this domain remain lacking. To address this gap, we introduce PhySciBench, a benchmark highly relevant to physical science research, comprising 200 expert-curated questions, balanced between physics and chemistry, across six task categories that reflect real-world scientific workflows. Evaluations of state-of-the-art models and agent systems on PhySciBench reveal limited performance; even the strongest baseline, Gemini Deep Research, achieves an accuracy of only 33.5%. Analysis of failure cases identifies three recurrent deficiencies: fragility in extended reasoning chains, limited knowledge transfer across steps, and a lack of physics-grounded self-verification. Motivated by these findings, we develop DelveAgent, a modular multi-agent framework equipped with an adaptive planning loop, dual-granularity memory, and a hierarchical physics-grounded reflection mechanism. Across four scientific benchmarks, DelveAgent improves accuracy by up to 7.5 percentage points while reducing inference costs to approximately one-third of the strongest baseline. These results establish the significance of PhySciBench as a critical benchmark for evaluating AI systems in the physical sciences and demonstrate that architectural specialization can effectively enhance the reliability of autonomous scientific research. Our data and code are publicly available at https://github.com/yigengjiang/physci-deepresearch.

physics.comp-ph↗

arXiv2026

SCI-PRM: A Tool Aware Process Reward Model for Scientific Reasoning Verification

While Process Reward Models (PRMs) have achieved remarkable success in mathematical reasoning, their application in complex scientific domains-such as biology, chemistry, and physics remains largely unexplored. Scientific problems demand not only logical rigor but also factual consistency and the precise usage of domain-specific tools, areas where current models often suffer from hallucinations and lack of verification. In this paper, we first construct SCIPRM70K, a large-scale dataset featuring Chain-of-Tool trajectories that explicitly interleave reasoning with the execution of scientific tools. Building upon this, we train an efficient reward model called Sci-PRM to provide fine-grained supervision on tool selection, execution accuracy, and result interpretation at each step in one inference. Experiments demonstrate that Sci-PRM significantly enhances foundation models in two key aspects: (1) it enables effective test-time scaling via Best-of-N selection; and (2) when integrated into Reinforcement Learning, it serves as a dense reward signal that mitigates the critical issue of advantage disappearance, allowing the model to break through existing performance ceilings.

cs.AI↗

arXiv2026

Benchmarking Physics-Informed Time-Series Models for Operational Global Station Weather Forecasting

The development of Time-Series Forecasting (TSF) models is often constrained by the lack of comprehensive datasets, especially in Global Station Weather Forecasting (GSWF), where existing datasets are small, temporally short, and spatially sparse. To address this, we introduce WEATHER-5K, a large-scale observational weather dataset that better reflects real-world conditions, supporting improved model training and evaluation. While recent TSF methods perform well on benchmarks, they lag behind operational Numerical Weather Prediction systems in capturing complex weather dynamics and extreme events. We propose PhysicsFormer, a physics-informed forecasting model combining a dynamic core with a Transformer residual to predict future weather states. Physical consistency is enforced via pressure-wind alignment and energy-aware smoothness losses, ensuring plausible dynamics while capturing complex temporal patterns. We benchmark PhysicsFormer and other TSF models against operational systems across several weather variables, extreme event prediction, and model complexity, providing a comprehensive assessment of the gap between academic TSF models and operational forecasting. The dataset and benchmark implementation are available at: https://github.com/taohan10200/WEATHER-5K.

cs.LG↗

arXiv2026

LabVLA: Grounding Vision-Language-Action Models in Scientific Laboratories

Scientific laboratories increasingly rely on AI systems to reason about experiments, but the physical act of doing science remains largely outside their reach. AI can help read literature, generate hypotheses, and plan protocols, yet the execution of those protocols at the bench still requires a human operator. Vision-Language-Action (VLA) models provide one possible interface between written protocols and robot execution, but existing policies are trained mostly on household and tabletop demonstrations and rarely encounter the instruments, transparent liquids, or fixed protocol workflows found in scientific laboratories. Closing this gap requires both laboratory-specific supervision and a unified learning framework that can accommodate the diverse robot embodiments used to execute experimental protocols. We therefore identify data and embodiment as central bottlenecks alongside model design. To address the data side, we build RoboGenesis, a simulation-based workflow and data engine that composes configured laboratory workflows from atomic skills, validates and filters rollouts, and exports structured demonstrations across supported robot profiles. On the policy side, we present LabVLA, trained with a two-stage recipe: FAST action token pretraining first makes the Qwen3-VL-4B-Instruct backbone action aware before any continuous control is learned, and flow matching posttraining then attaches a DiT action expert under knowledge insulation. On the LabUtopia benchmark, LabVLA achieves the highest average success rate among all evaluated baselines under both in-distribution and out-of-distribution settings.

cs.CL↗

arXiv2026

MASLab: A Unified and Comprehensive Codebase for LLM-based Multi-Agent Systems

LLM-based multi-agent systems (MAS) have demonstrated significant potential in enhancing single LLMs to address complex and diverse tasks in practical applications. Despite considerable advancements, the field lacks a unified codebase that consolidates existing methods, resulting in redundant re-implementation efforts, unfair comparisons, and high entry barriers for researchers. To address these challenges, we introduce MASLab, a unified, comprehensive, and research-friendly codebase for LLM-based MAS. (1) MASLab integrates over 20 established methods across multiple domains, each rigorously validated by comparing step-by-step outputs with its official implementation. (2) MASLab provides a unified environment with various benchmarks for fair comparisons among methods, ensuring consistent inputs and standardized evaluation protocols. (3) MASLab implements methods within a shared streamlined structure, lowering the barriers for understanding and extension. Building on MASLab, we conduct extensive experiments covering 10+ benchmarks and 8 models, offering researchers a clear and comprehensive view of the current landscape of MAS methods. MASLab will continue to evolve, tracking the latest developments in the field, and invite contributions from the broader open-source community.

cs.CL↗

arXiv2026

AMix-1: A Pathway to Test-Time Scalable Protein Foundation Model

We introduce AMix-1, a powerful protein foundation model built on Bayesian Flow Networks and empowered by a systematic training methodology, encompassing pretraining scaling laws, emergent capability analysis, in-context learning mechanism, and test-time scaling algorithm. To guarantee robust scalability, we establish a predictive scaling law and reveal the progressive emergence of structural understanding via loss perspective, culminating in a strong 1.7-billion model. Building on this foundation, we devise a multiple sequence alignment (MSA)-based in-context learning strategy to unify protein design into a general framework, where AMix-1 recognizes deep evolutionary signals among MSAs and consistently generates structurally and functionally coherent proteins. This framework enables the successful design of a dramatically improved AmeR variant with an up to $50\times$ activity increase over its wild type. Pushing the boundaries of protein engineering, we further empower AMix-1 with an evolutionary test-time scaling algorithm for in silico directed evolution that delivers substantial, scalable performance gains as verification budgets are intensified, laying the groundwork for next-generation lab-in-the-loop protein design.

q-bio.BM↗

arXiv2026

Are Tools Always Beneficial? Learning to Invoke Tools Adaptively for Dual-Mode Multimodal LLM Reasoning

Tool-augmented reasoning has emerged as a promising direction for enhancing the reasoning capabilities of multimodal large language models (MLLMs). However, existing studies mainly focus on enabling models to perform tool invocation, while neglecting the necessity of invoking tools. We argue that tool usage is not always beneficial, as redundant or inappropriate invocations largely increase reasoning overhead and even mislead model predictions. To address this issue, we introduce AutoTool, a model that adaptively decides whether to invoke tools according to the characteristics of each query. Within a reinforcement learning framework, we design an explicit dual-mode reasoning strategy with mode-specific reward functions to guide the model toward producing accurate responses. Moreover, to prevent premature bias toward a single reasoning mode, AutoTool jointly explores and balances tool-assisted and text-centric reasoning throughout training, and promotes free exploration in later stages. Extensive experiments demonstrate that AutoTool exhibits outstanding performance and high efficiency, yielding a 21.8\% accuracy gain on V* benchmark compared to the base model, and a 44.9\% improvement in efficiency over existing tool-augmented methods on POPE benchmark. Code is available at https://github.com/MQinghe/AutoTool.

cs.CL↗

arXiv2026

Trans2Occ: Voxel Occupancy Estimation and Grasp for Transparent Objects from Simulation to Reality

Transparent objects remain challenging for robotic perception due to unreliable depth sensing caused by refraction and reflection. While prior approaches rely on multi-view reconstruction or depth completion, they are often difficult to scale or deploy in real-world robotic systems. In this paper, we present a practical framework for transparent object perception and manipulation based on single-view RGB input. Our approach predicts voxel-space occupancy directly from a single image, providing a geometry-aware representation that supports downstream robotic grasping. To enable large-scale training, we construct a simulation pipeline that generates paired RGB images and voxel occupancy annotations under diverse materials and lighting conditions. We demonstrate that the predicted occupancy representation is robust to domain shifts and transfers effectively from simulation to real-world robotic setups without fine-tuning. A simple rule-based grasping strategy built on top of the occupancy further achieves reliable grasp performance on transparent objects. Extensive experiments in both simulation and real-world environments show that our framework provides accurate 3D understanding and enables practical manipulation of transparent objects. These results suggest that single-view occupancy prediction offers a scalable and effective solution for transparent object perception in robotics.

cs.RO↗

arXiv2026

SciAgentGym: Benchmarking Multi-Step Scientific Tool-use in LLM Agents

Scientific reasoning inherently demands integrating sophisticated toolkits to navigate domain-specific knowledge. Yet, current benchmarks largely overlook agents' ability to orchestrate tools for such rigorous workflows. To bridge this gap, we introduce SciAgentGym, a scalable interactive environment featuring 1,780 domain-specific tools across four natural science disciplines, supported by a robust execution infrastructure. Complementing this, we present SciAgentBench, a tiered evaluation suite designed to stress-test agentic capabilities from elementary actions to long-horizon workflows. Our evaluation identifies a critical bottleneck: state-of-the-art models still struggle with complex scientific tool-use, and their performance degrades substantially as interaction horizons extend. To address this, we propose SciForge, a data synthesis method that models the tool action space as a dependency graph to generate logic-aware training trajectories. By fine-tuning on these trajectories, our SciAgent-8B outperforms the significantly larger Qwen3-VL-235B-Instruct while exhibiting positive cross-domain transfer of scientific tool-use capabilities. These results underscore the promising potential of next-generation autonomous scientific agents.

cs.CL↗

arXiv2026

OmniMatBench: A Human-Calibrated Multimodal Reasoning Benchmark Across 19 Materials Science Subfields

As multimodal language models play an increasingly important role in scientific research, materials science offers a critical testbed due to its interdisciplinary, multimodal, and application-driven nature. However, existing materials benchmarks mainly focus on property prediction, knowledge QA, or characterization understanding, leaving the broader reasoning process from materials knowledge to application underexplored. To fill this gap, we present OmniMatBench, a human-calibrated multimodal reasoning benchmark for materials science. OmniMatBench contains 3,171 expert-curated QA and calculation problems across 19 materials-science subfields, spanning fundamental materials knowledge, structural and engineering materials, materials processing and manufacturing, and functional and applied materials. We evaluate 13 open-source and closed-source MLLMs and find that the best model achieves only a 0.372 overall score, revealing a substantial gap in current materials-science reasoning. Further analysis shows strong variation across subfields, fixed reasoning heuristics, uneven materials knowledge, and limited high-level knowledge application under formula-, retrieval-, and code-assisted settings. OmniMatBench provides crucial insights into the capabilities and limitations of current MLLMs and establishes a foundation for reliable AI assistants in materials-science research.

cs.AI↗