arXiv subjects

Lei Bai

Publications and source records attributed to Lei Bai.

At least 73 records · Page 4Linked to original sources

arXiv2026

AMix-2: Establishing Protein as a Native Modality in Large Language Models

We present AMix-2, a protein-text foundation model that establishes protein as a native modality in large language models (LLMs), unifying protein understanding and sequence design within a single foundation model. AMix-2 is built upon two key ideas: (1) a unified protein-text formulation that embeds natural language and protein sequence in a shared token space, enabling one model to perform biological reasoning and conditional design instead of separate downstream task-specialized models; and (2) a block-wise diffusion language modeling backbone that combines causal generation across blocks with bidirectional context and iterative refinement within blocks. This scheme better matches the intrinsic nature of proteins than a strict left-to-right factorization. To evaluate protein foundation models under realistic generalization settings, we further introduce ProteinArena, a comprehensive benchmark with time-aware and homology-aware protocols across various understanding and design tasks, and with baselines covering classical bioinformatics tools, protein-specialized models and LLMs. On ProteinArena, AMix-2 outperforms frontier LLMs and demonstrates competitive performance to task-specific protein models. Controlled experiments further show that the diffusion-based paradigm generally surpasses its autoregressive counterpart, highlighting the advantage of flexible generation order for protein sequences. We release both AMix-2 and ProteinArena to facilitate open research in protein foundation models.

q-bio.BM↗

arXiv2026

LabBuilder: Protocol-Grounded 3D Layout Generation for Interactable and Safe Laboratory

Automated laboratories hold the promise of accelerating scientific discovery, yet their deployment is bottlenecked by the difficulty of designing safe and executable environments. While simulator-based design offers scalability, existing 3D scene generation methods are primarily tailored for household settings, optimizing for visual plausibility while neglecting the protocol grounding and layout-level safety constraints essential for scientific experimentation. We present LabBuilder, an end-to-end system that generates and verifies 3D laboratory layouts from concise textual specifications. It operates through three tightly coupled components: LabForge first curates a meta-dataset of annotated assets and chemical knowledge, translating natural language specifications into structured protocols; building on these protocols, LabGen synthesizes laboratory layouts via an iterative, constraint-aware optimization strategy; finally, LabTouchstone evaluates the resulting layouts as a unified benchmark. Extensive experiments demonstrate that LabBuilder significantly outperforms existing state-of-the-art methods, producing laboratory environments that are realistic and valid under modeled geometric, chemical-safety, and navigation constraints.

cs.CV↗

arXiv2026

RealBench: Benchmarking Data-Driven Numerical Weather Forecasting Under Operational Conditions and Extreme Event Challenges

Accurate evaluation of weather forecasting models is critical for their reliable deployment in real-world applications. However, existing benchmarks predominantly rely on reanalysis products such as ERA5, which are generated through delayed data assimilation and do not reflect the constraints of real-time operational forecasting, thereby resulting in a systematic mismatch between benchmark performance and real-world forecasting. In this work, we introduce RealBench, a next-generation benchmark for AI weather forecasting that emphasizes realistic evaluation under operational conditions. RealBench features a strictly out-of-distribution test set spanning 2025 to eliminate data leakage and capture recent atmospheric regimes. It integrates multiple data sources, including low-latency operational analysis and a large-scale global in-situ observation dataset comprising over 10,000 stations, enabling direct evaluation against real atmospheric measurements. Beyond standard global metrics, RealBench provides a comprehensive evaluation framework for high-impact extreme events, including heatwaves, cold surges, and tropical cyclones, using event-specific metrics that better reflect real-world forecasting priorities. The evaluation results reveal substantial discrepancies between reanalysis-based metrics and real-world performance, particularly concerning extreme events. By highlighting the limitations of existing benchmarks, this work establishes a more faithful and operationally relevant evaluation paradigm, providing a rigorous foundation for advancing next-generation AI weather forecasting systems. The benchmark implementation is available at: https://github.com/lixruize-del/NWP-Benchmark.

cs.LG↗

arXiv2026

MolClaw: An Autonomous Agent with Hierarchical Skills for Drug Molecule Evaluation, Screening, and Optimization

Computational drug discovery, particularly the complex workflows of drug molecule screening and optimization, requires orchestrating dozens of specialized tools in multi-step workflows, yet current AI agents struggle to maintain robust performance and consistently underperform in these high-complexity scenarios. Here we present MolClaw, an autonomous agent that leads drug molecule evaluation, screening, and optimization. It unifies over 30 specialized domain resources through a three-tier hierarchical skill architecture (70 skills in total) that facilitates agent long-term interaction at runtime: tool-level skills standardize atomic operations, workflow-level skills compose them into validated pipelines with quality check and reflection, and a discipline-level skill supplies scientific principles governing planning and verification across all scenarios in the field. Additionally, we introduce MolBench, a benchmark comprising molecular screening, optimization, and end-to-end discovery challenges spanning 8 to 50+ sequential tool calls. MolClaw achieves state-of-the-art performance across all metrics, and ablation studies confirm that gains concentrate on tasks that demand structured workflows while vanishing on those solvable with ad hoc scripting, establishing workflow orchestration competence as the primary capability bottleneck for AI-driven drug discovery.

cs.AI↗

arXiv2026

Learning more physically realistic dynamics in machine-learning based weather forecasting with latent-space constraints

Data-driven machine learning (ML) models are reshaping weather forecasting and have shown the potential to accelerate and surpass traditional physics-based approaches, leading to a second revolution in the field after data assimilation. However, most ML forecast models are trained with weighted variable-wise losses on rollout forecasts that neglect cross-variable and spatial error covariance induced by physical coupling, often yielding overly smooth and physically unrealistic long-range forecasts. To address this, we reformulate model training as a four-dimensional variational data assimilation (4DVar) problem that treats reanalysis data as imperfect observations. This enables the loss function to incorporate cross-variable error covariance structures that capture multivariate dependencies and their associated errors. In practice, we approximate this objective by computing the loss in an autoencoder-learned latent space of global atmospheric states. By encoding complex nonlinear couplings among atmospheric variables, this representation allows the high-dimensional, complex error covariance matrix in model space to be approximated as nearly diagonal in latent space, substantially simplifying implementation. We show that rollout training with latent-space constraints improves long-term forecast skill, while better preserving fine-scale structures and physical realism than the widely used model-space loss. Finally, we extend this framework to accommodate heterogeneous data sources, enabling the forecast model to be trained jointly on reanalysis and multi-source observations within a unified theoretical formulation.

cs.LG↗

arXiv2026

A Scalable Multi-LLM Collaboration System with Retrieval-based Selection and Exploration-Exploitation-Driven Enhancement

Existing multi-LLM collaboration systems often encounter scalability challenges when integrating new LLMs and tasks, leading to suboptimal performance. To address this, we propose SMCS, a Scalable Multi-LLM Collaboration System designed to effectively coordinate multiple open-source LLMs. The system consists of two core components: a Retrieval-based Prior Selection (RPS) module, which dynamically selects the most suitable LLMs for each input, and an Exploration-Exploitation-Driven Posterior Enhancement (EPE) module, which fosters response diversity and selects high-quality outputs through a hybrid scoring mechanism. Experiments on eight mainstream benchmarks validate the effectiveness of our system: by integrating fifteen open-source LLMs, SMCS outperforms prevailing closed-source LLMs, e.g., GPT-4.1(+5.36%) and GPT-o3-mini(+5.28%) across multiple tasks. Remarkably, it even exceeds the average of best results on different datasets with open-source LLMs (+2.86%), significantly advancing the empirical performance frontier of open-source collaboration. The code is released at https://github.com/magent4aci/SMCS.

cs.CL↗

arXiv2026

GGBound: A Genome-Grounded Agent for Microbial Life-Boundary Prediction

Characterizing the physiological life boundaries of microbial strains, including viable temperature, pH, salinity, substrate utilization, and morphology, is central to biotechnology and ecology, yet traditionally requires exhaustive in vitro screening. Existing computational approaches either treat physiological traits as isolated supervised targets or repurpose biological foundation models as static encoders, leaving the genotype-to-physiology gap largely unbridged. We formulate microbial life-boundary prediction as a unified genome-to-physiology task and address it with a genome-conditioned, tool-augmented LLM agent. To support this task, we curate a strain-centric benchmark from IJSEM, NCBI, and BacDive covering 1,525 strains and 6,448 instances across viability intervals, environmental optima, substrate utilization, categorical traits, and morphology. Architecturally, the agent injects frozen LucaOne genome embeddings into a Qwen backbone via lightweight token fusion, and reasons over a similarity-based RAG module and a Genome-scale Metabolic Model (GEM) perturbation tool. We optimize the agent through a three-stage pipeline of gene-text alignment, agentic SFT on distilled trajectories, and GRPO with a novel counterfactual gene-grounding reward that reinforces the policy only when the authentic genome embedding causally improves correct-token generation relative to a zero-gene ablation. The resulting 4B-parameter agent matches or surpasses substantially larger frontier LLMs, with ablations confirming that genome-token fusion, dynamic tool use, and the counterfactual reward each yield distinct, significant gains.

cs.CY↗

arXiv2026

ReCrit: Transition-Aware Reinforcement Learning for Scientific Critic Reasoning

Large language models can fail in critic interaction not only by answering incorrectly, but also by abandoning an initially correct scientific solution after user criticism. This is especially risky in scientific reasoning, where user criticism can turn a valid answer into an incorrect one. We frame critic interaction as an inter-turn correctness-transition problem rather than a final-answer accuracy problem, and identify three challenges: transition awareness, decoupling useful correction from harmful sycophancy, and scalable rollout. We propose ReCrit, a transition-aware reinforcement learning framework that decomposes Initial-to-Critic behavior into four quadrants: Correction, Sycophancy, Robustness, and Boundary. ReCrit rewards correction and robustness, penalizes sycophancy, and treats persistent errors as weak boundary signals. To make interaction training practical, ReCrit further uses dynamic asynchronous rollout with tail-adaptive completion to reduce rollout waiting. On three scientific reasoning benchmarks, ChemBench, TRQA, and EarthSE, ReCrit improves average Critic accuracy from 38.15 to 51.49 on Qwen3.5-4B and from 45.40 to 55.59 on Qwen3.5-9B. Ablations show that final-answer rewards provide little interaction-level gain, while transition-aware rewards and quadrant weighting produce more distinguishable training signals and larger net Critic-stage improvement. The code is available at https://github.com/black-yt/ReCrit .

cs.LG↗

arXiv2026

EMFormer: Efficient Multi-Scale Transformer for Accumulative Context Weather Forecasting

Long-term weather forecasting is critical for socioeconomic planning and disaster preparedness. While recent approaches employ finetuning to extend prediction horizons, they remain constrained by the issues of catastrophic forgetting, error accumulation, and high training overhead. To address these limitations, we present a novel pipeline across pretraining, finetuning and forecasting to enhance long-context modeling while reducing computational overhead. First, we introduce an Efficient Multi-scale Transformer (EMFormer) to extract multi-scale features through a single convolution in both training and inference. Based on the new architecture, we further employ an accumulative context finetuning to improve temporal consistency without degrading short-term accuracy. Additionally, we propose a composite loss that dynamically balances different terms via a sinusoidal weighting, thereby adaptively guiding the optimization trajectory throughout pretraining and finetuning. Experiments show that our approach achieves strong performance in weather forecasting and extreme event prediction, substantially improving long-term forecast accuracy. Moreover, EMFormer demonstrates strong generalization on vision benchmarks (ImageNet-1K and ADE20K) while delivering a 5.69x speedup over conventional multi-scale modules. Code: https://github.com/chenhao-zju/emformer

cs.CV↗

arXiv2026

Earth-o1: A Grid-free Observation-native Atmospheric World Model

Despite the unprecedented volume of multimodal data provided by modern Earth observation systems, our ability to model atmospheric dynamics remains constrained. Traditional modeling frameworks force heterogeneous measurements into predefined spatial grids, inherently limiting the full exploitation of raw sensor data and creating severe computational bottlenecks. Here we present Earth-o1, an observation-native atmospheric world model that overcomes these structural limitations. Rather than relying on conventional atmospheric dynamical modeling systems or traditional data assimilation, Earth-o1 directly learns the continuous, three-dimensional physical evolution of the Earth system from ungridded observational data. By integrating diverse sensor inputs into a unified, grid-free dynamical field, the model autonomously advances the atmospheric state in space and time. We show that this fundamentally distinct paradigm enables direct, real-time forecasting and cross-sensor inference without the overhead of explicit numerical solvers. In hindcast evaluations, Earth-o1 achieves surface forecast skill comparable to the operational Integrated Forecasting System (IFS). These results establish that continuous, observation-driven world models -- a new class of fully observation-native geophysical simulators -- can match the fidelity of established physical frameworks, providing a scalable data-driven foundation for a digital twin of the Earth.

cs.CV↗

arXiv2026

MSEarth: A Multimodal Benchmark for Earth Science Phenomenon Discovery with MLLMs

The rapid advancement of multimodal large language models (MLLMs) offers new opportunities for complex scientific challenges, yet their application in earth science-especially at the graduate level-remains underexplored due to a lack of benchmarks reflecting the depth and complexity of geoscientific reasoning. Existing datasets often rely on synthetic data or simple figure-caption pairs, failing to capture the nuanced reasoning required for real-world applications. To address this, we introduce MSEarth, a multimodal scientific dataset and benchmark curated from high-quality, open-access publications. Covering the five major spheres of Earth science-atmosphere, cryosphere, hydrosphere, lithosphere, and biosphere-MSEarth features over 289K figures with refined captions enriched by contextual discussions and reasoning from the original papers. The benchmark supports tasks such as scientific figure captioning, multiple choice questions, and open-ended reasoning, providing a scalable, high-fidelity resource for developing and evaluating MLLMs in scientific reasoning.

cs.AI↗

arXiv2026

ML-Agent: Reinforcing LLM Agents for Autonomous Machine Learning Engineering

The emergence of large language model (LLM)-based agents has significantly advanced the development of autonomous machine learning (ML) engineering. However, the dominant prompt-based paradigm exhibits limitations: smaller models lack the capacity to learn from execution trajectories for generalization, while large proprietary models incur high computational overhead, restricting accessibility and scalability. Focusing on this, for the first time, we explore the paradigm of learning-based agentic ML, where an LLM agent learns through interactive experimentation on ML tasks using online reinforcement learning (RL). To realize this, we propose a novel agentic ML training framework with three key components: (1) exploration-enriched fine-tuning, which enables LLM agents to generate diverse actions for enhanced RL exploration; (2) step-wise RL, which enables training on a single action step, accelerating experience collection and improving training efficiency; (3) an agentic ML-specific reward module, which unifies varied ML feedback signals into consistent rewards for RL optimization. Leveraging this framework, we train ML-Agent, driven by a 7B-sized Qwen-2.5 LLM for autonomous ML. Despite training on only 9 ML tasks, our 7B-sized ML-Agent achieves comparable performance to agents using much larger proprietary LLMs (e.g., GPT-5) but at significantly lower computational cost, demonstrating strong performance and cross-task generalization.

cs.CL↗

arXiv2026

Benchmarking virtual cell models for in-the-wild perturbation response

Virtual cell (VC) models aim to predict cellular responses to any perturbations in silico and have emerged as a promising approach for drug discovery and precision medicine. Yet, a clear gap still remains: while models routinely reported impressive results on standard benchmarks, it is unclear whether their predictions are truly meaningful in practice. This is mainly due to limitations in current evaluation setups, which are often overly simplified or inconsistent, and do not reflect the complexity and variability of real biological systems. Here, we introduce a standardized and modular benchmarking framework for virtual cell prediction. Our framework evaluates diverse models under in-the-wild challenging scenarios, including unseen cell contexts, unseen perturbations, and cross-dataset generalization, which better reflect practical applications. Our analysis shows that model performance is highly context-dependent and shaped by task design and evaluation criteria. In commonly used setups, performance is often overestimated, and naive dataset aggregation can even reduce performance. When evaluated under more strict conditions, model performance drops markedly, indicating limited robustness to shifts across cellular contexts. In unseen perturbation settings, models including simple linear approaches capture global transcriptional trends but fail to recover fine-grained perturbation-specific effects. In addition, different evaluation metrics focus on different biological properties, leading to substantially different model rankings. Together, our framework provides a more reliable and biologically grounded evaluation, offering clearer guidance for applying virtual cell models in real scenarios.

q-bio.CB↗

arXiv2026

MTRouter: Cost-Aware Multi-Turn LLM Routing with History-Model Joint Embeddings

Multi-turn, long-horizon tasks are increasingly common for large language models (LLMs), but solving them typically requires many sequential model invocations, accumulating substantial inference costs. Here, we study cost-aware multi-turn LLM routing: selecting which model to invoke at each turn from a model pool, given a fixed cost budget. We propose MTRouter, which encodes the interaction history and candidate models into joint history-model embeddings, and learns an outcome estimator from logged trajectories to predict turn-level model utility. Experiments show that MTRouter improves the performance-cost trade-off: on ScienceWorld, it surpasses GPT-5 while reducing total cost by 58.7%; on Humanity's Last Exam (HLE), it achieves competitive accuracy while reducing total cost by 43.4% relative to GPT-5, and these gains even carry over to held-out tasks. Further analyses reveal several mechanisms underlying its effectiveness: relative to prior multi-turn routers, MTRouter makes fewer model switches, is more tolerant to transient errors, and exhibits emergent specialization across models. Code: https://github.com/ZhangYiqun018/MTRouter

cs.CL↗

arXiv2026

STCast: Adaptive Boundary Alignment for Global and Regional Weather Forecasting

To gain finer regional forecasts, many works have explored the regional integration from the global atmosphere, e.g., by solving boundary equations in physics-based methods or cropping regions from global forecasts in data-driven methods. However, the effectiveness of these methods is often constrained by static and imprecise regional boundaries, resulting in poor generalization ability. To address this issue, we propose Spatial-Temporal Weather Forecasting (STCast), a novel AI-driven framework for adaptive regional boundary optimization and dynamic monthly forecast allocation. Specifically, our approach employs a Spatial-Aligned Attention (SAA) mechanism, which aligns global and regional spatial distributions to initialize boundaries and adaptively refines them based on attention-derived alignment patterns. Furthermore, we design a Temporal Mixture-of-Experts (TMoE) module, where atmospheric variables from distinct months are dynamically routed to specialized experts using a discrete Gaussian distribution, enhancing the model's ability to capture temporal patterns. Beyond global and regional forecasting, we evaluate our STCast on extreme event prediction and ensemble forecasting. Experimental results demonstrate consistent superiority over state-of-the-art methods across all four tasks. Code: https://github.com/chenhao-zju/STCast

cs.LG↗

arXiv2026

A Survey of Reinforcement Learning for Large Language Models under Data Scarcity: Challenges and Solutions

Reinforcement learning (RL) has emerged as a powerful post-training paradigm for enhancing the reasoning capabilities of large language models (LLMs). However, reinforcement learning for LLMs faces substantial data scarcity challenges, including the limited availability of high-quality external supervision and the constrained volume of model-generated experience. These limitations make data-efficient reinforcement learning a critical research direction. In this survey, we present the first systematic review of reinforcement learning for LLMs under data scarcity. We propose a bottom-up hierarchical framework built around three complementary perspectives: the data-centric perspective, the training-centric perspective, and the framework-centric perspective. We develop a taxonomy of existing methods, summarize representative approaches in each category, and analyze their strengths and limitations. Our taxonomy aims to provide a clear conceptual foundation for understanding the design space of data-efficient RL for LLMs and to guide researchers working in this emerging area. We hope this survey offers a comprehensive roadmap for future research and inspires new directions toward more efficient and scalable reinforcement learning post-training for LLMs.

cs.LG↗

arXiv2026

Easy Samples Are All You Need: Self-Evolving LLMs via Data-Efficient Reinforcement Learning

Previous LLMs-based RL studies typically follow either supervised learning with high annotation costs, or unsupervised paradigms using voting or entropy-based rewards. However, their performance remains far from satisfactory due to the substantial annotation cost and issues such as model collapse or reward hacking. To address these issues, we introduce a new perspective inspired by cognitive learning theory and propose a novel approach called EasyRL. The core of EasyRL is to simulate the human cognitive acquisition curve by integrating reliable knowledge transfer from easy labeled data with a progressive divide-and-conquer strategy that tackles increasingly difficult unlabeled data. Specifically, we initialize a warm-up model using supervised RL with few-shot labeled data. This is followed by a divide-and-conquer pseudo-labeling strategy on difficult unlabeled data, combining consistency-based selection for low-uncertainty cases and reflection-based resolution for medium-uncertainty cases. Finally, difficulty-progressive self-training with iterative pseudo-labeling and RL further strengthens the model's reasoning capability. EasyRL provides a unified self-evolving framework that facilitates data-efficient post-training of LLMs. Experimental results on mathematical and scientific benchmarks demonstrate that EasyRL, using only 10% of easy labeled data, consistently outperforms state-of-the-art baselines.

cs.LG↗

arXiv2026

Small Model as Master Orchestrator: Learning Unified Agent-Tool Orchestration with Parallel Subtask Decomposition

Multi-agent systems (MAS) demonstrate clear advantages in tackling complex problems by coordinating diverse agents and external tools. However, most existing orchestration methods rely on static workflows or serial agent scheduling, and are further constrained by heterogeneous interface protocols between tools and agents. This leads to high system complexity and poor extensibility. To mitigate these issues, we propose Agent-as-Tool, a unified parallel orchestration paradigm that abstracts both agents and tools into a standardized, learnable action space with protocol normalization and explicit state feedback. Building on this paradigm, we train a lightweight orchestrator, ParaManager, which decouples planning decisions from subtask solving, enabling state-aware parallel subtask decomposition, delegation, and asynchronous execution. For training, we adopt a two-stage ParaManager training pipeline. It improves robustness by incorporating supervised fine-tuning (SFT) trajectories equipped with recovery mechanisms, and further applies reinforcement learning (RL) to achieve an optimal balance among task success, protocol compliance, diversity, and reasoning efficiency. Experiments show that ParaManager achieves strong performance across multiple benchmarks and exhibits robust generalization under unseen model pools.

cs.AI↗