arXiv subjects

Weinan E

Publications and source records attributed to Weinan E.

At least 19 recordsLinked to original sources

arXiv2026

A First-Principles Theory of Slow Thinking and Active Perception

As part of a series on first-principles modeling of cognitive functions, this paper attempts to provide a mathematical formulation of thinking and perception. It formally derives slow thinking or more generally, active perception, and encompasses the design, training and inference of slow thinking large language models. Our starting point is the lifting and projection of probability distributions on the observable and latent spaces, with the objective of representing complex data distributions by simple function families such as neural networks. A theory called "active lifting" is proposed, based on the sampling of latent sequences and an intrinsic drive to reduce uncertainty with maximum rate. It derives a large design space, containing the slow thinking models in a subspace that we call the static theory. These models are positioned on the representation hierarchy and sampler hierarchy induced by the static theory, and can be upgraded by climbing the two hierarchies. Active lifting further derives an inference process with an internal time axis, and a training objective that resembles minimum-length coding as well as the invention of languages. Thus, it characterizes the agency of perception, including the emergence of the slow thinking formats. Technical by-products of this theory include a three-stage pathway for improving slow thinking models, a unified approach to constructing encoders and generative models for all data modalities, a priori formation of human-like visual representations, and a possible solution to policy collapse.

cs.AI↗

arXiv2026

EvoMaster: A Foundational Evolving Agent Framework for Agentic Science at Scale

The convergence of large language models and agents is catalyzing a new era of scientific discovery: Agentic Science. However, common agent infrastructure is repeatedly rebuilt across scientific fields (loop fragmentation) and useful evidence and experience are lost in long-horizon research (loop discontinuity), bringing obstacles to Agentic Science at Scale. We introduce EvoMaster, a foundational evolving agent framework for Agentic Science at Scale. EvoMaster handles loop fragmentation and loop discontinuity by implementing Loop Research in which external evidence persists and improves later decisions. Through three nested loops, Execution, Exploration and Evolution (E$^3$), loop research connects research within runs, across experiments and across studies. Across ten benchmarks spanning scientific research, coding and reasoning, EvoMaster achieves the best score among four agents using GPT-5.4, reaching a mean score of 58.02%, and outperforms the strongest competing agent Codex(40.29%) while costing 35.6% less. These results show that a shared loop-research foundation can support diverse scientific agents at scale.

cs.AI↗

arXiv2026

PRL-Bench: A Comprehensive Benchmark Evaluating LLMs' Capabilities in Frontier Physics Research

The paradigm of agentic science requires AI systems to conduct robust reasoning and engage in long-horizon, autonomous exploration. However, current scientific benchmarks remain confined to domain knowledge comprehension and complex reasoning, failing to evaluate the exploratory nature and procedural complexity of real-world research. In this work, we present research-oriented evaluations in theoretical and computational physics, a natural testbed with comprehensive domain knowledge, complex reasoning, and verifiable end-to-end workflows without reliance on experiments. Here we introduce PRL-Bench (Physics Research by LLMs), a benchmark designed to systematically map the capability boundaries of LLMs in executing end-to-end physics research. Constructed from 100 curated papers from the latest issues of Physical Review Letters since August 2025 and validated by domain experts, PRL-Bench covers five major theory- and computation-intensive subfields of modern physics: astrophysics, condensed matter physics, high-energy physics, quantum information, and statistical physics. Each task in the benchmark is designed to replicate the core properties of authentic scientific research, including exploration-oriented formulation, long-horizon workflows, and objective verifiability, thereby reconstructing the essential reasoning processes and research workflows of real physics research. Evaluation across frontier models shows that performance remains limited, with the best overall score below 50, revealing a pronounced gap between current LLM capabilities and the demands of real scientific research. PRL-Bench serves a reliable testbed for accessing next generation AI scientists advancing AI systems toward autonomous scientific discovery.

cs.LG↗

arXiv2026

Solving the inverse problem of X-ray absorption spectroscopy via physics-informed deep learning

Resolving transient atomic configurations in non-crystalline or dynamic environments remains a fundamental bottleneck in the physical sciences. While X-ray absorption spectroscopy (XAS) is a premier probe of local structure, inverting spectra into structural descriptors is a notoriously ill-posed problem due to inherent many-to-one mapping. Here, we present the Spectral Pattern Translator (SPT), a physics-informed deep learning framework that establishes a robust bridge between large-scale theoretical datasets and experimental reality. Our strategy exploits the Fourier duality between spectral energy oscillations and spatial scattering paths to overcome the "simulation-to-experiment" gap. By decomposing spectra into frequency domains, SPT effectively isolates robust structural coordination signals from the destabilizing noise inherent in experimental data. Trained on a massive library of diverse atomic environments, this approach achieves state-of-the-art accuracy in resolving continuous phase transitions in battery cathodes and deciphering local order in amorphous materials. With millisecond-scale latency, SPT removes the primary computational barrier to autonomous materials discovery, establishing a robust, noise-resilient engine for closed-loop robotic chemistry.

cond-mat.mtrl-sci↗

arXiv2026

DataFlex: A Unified Framework for Data-Centric Dynamic Training of Large Language Models

Data-centric training has emerged as a promising direction for improving large language models (LLMs) by optimizing not only model parameters but also the selection, composition, and weighting of training data during optimization. However, existing approaches to data selection, data mixture optimization, and data reweighting are often developed in isolated codebases with inconsistent interfaces, hindering reproducibility, fair comparison, and practical integration. In this paper, we present DataFlex, a unified data-centric dynamic training framework built upon LLaMA-Factory. DataFlex supports three major paradigms of dynamic data optimization: sample selection, domain mixture adjustment, and sample reweighting, while remaining fully compatible with the original training workflow. It provides extensible trainer abstractions and modular components, enabling a drop-in replacement for standard LLM training, and unifies key model-dependent operations such as embedding extraction, inference, and gradient computation, with support for large-scale settings including DeepSpeed ZeRO-3. We conduct comprehensive experiments across multiple data-centric methods. Dynamic data selection consistently outperforms static full-data training on MMLU across both Mistral-7B and Llama-3.2-3B. For data mixture, DoReMi and ODM improve both MMLU accuracy and corpus-level perplexity over default proportions when pretraining Qwen2.5-1.5B on SlimPajama at 6B and 30B token scales. DataFlex also achieves consistent runtime improvements over original implementations. These results demonstrate that DataFlex provides an effective, efficient, and reproducible infrastructure for data-centric dynamic training of LLMs.

cs.LG↗

arXiv2026

Towards Next-Generation LLM Training: From the Data-Centric Perspective

Large language models (LLMs) have demonstrated remarkable performance across a wide range of tasks and domains, with data playing a central role in enabling these advances. Despite this success, the preparation and effective utilization of the massive datasets required for LLM training remain major bottlenecks. In current practice, LLM training data is often constructed using ad hoc scripts, and there is still a lack of mature, agent-based data preparation systems that can automatically construct robust and reusable data workflows, thereby freeing data scientists from repetitive and error-prone engineering efforts. Moreover, once collected, datasets are often consumed largely in their entirety during training, without systematic mechanisms for data selection, mixture optimization, or reweighting. To address these limitations, we advocate two complementary research directions. First, we propose building a robust, agent-based automatic data preparation system that supports automated workflow construction and scalable data management. Second, we argue for a unified data-model interaction training system in which data is dynamically selected, mixed, and reweighted throughout the training process, enabling more efficient, adaptive, and performance-aware data utilization. Finally, we discuss the remaining challenges and outline promising directions for future research and system development.

cs.CL↗

arXiv2026

Mixture of experts architectures for machine learning interatomic potentials

Machine Learning Interatomic Potentials (MLIPs) enable accurate large-scale atomistic simulations, yet improving their expressive capacity efficiently remains challenging. Here we systematically investigate Mixture-of-Experts (MoE) and Mixture-of-Linear-Experts (MoLE) architectures within the DPA3 framework for MLIPs and analyze the effects of routing strategies and expert designs. We show that sparse activation combined with shared experts yields substantial performance gains, and that nonlinear MoE formulations outperform MoLE when shared experts are present, underscoring the importance of nonlinear expert specialization. Furthermore, element-wise routing consistently surpasses configuration-level routing, while global MoE routing often leads to numerical instability. The resulting element-wise MoE model consistently outperforms all DPA3-based baselines across the OMol25, OMat24, and OC20M benchmarks. Analysis of routing patterns reveals chemically interpretable expert specialization aligned with periodic-table trends, indicating that the model effectively captures element-specific chemical characteristics for precise interatomic modeling.

physics.chem-ph↗

arXiv2026

Experimental Powder X-ray Diffraction Crystal Structure Determination with RealPXRD-Solver

Determining crystal structures from experimental powder X-ray diffraction data remains challenging because peak overlap, preferred orientation, and impurity phases obscure atomic arrangements. We present RealPXRD-Solver, a generative model trained on 6,250,238 theoretical structures with experiment-mimicking augmentations and a universal encoder of d-spacing--intensity fingerprints, enabling both lattice-conditioned and lattice-free inference. RealPXRD-Solver reaches a 98.3% Top-20 match rate on a 10,000-structure theoretical benchmark and achieves Top-1/Top-20 accuracies of 77.9%/91.9% on CNRS and 78.8%/92.9% on RRUFF experimental datasets, and it solved 39 previously unreported Powder Diffraction File entries.

cond-mat.mtrl-sci↗

arXiv2026

NMRPeak: a ready-to-use intelligent system for molecular structure elucidation enabled by synergistic cross-modal learning

One-dimensional nuclear magnetic resonance (NMR) spectroscopy is essential for molecular structure elucidation in organic synthesis, drug discovery, natural product characterization, and metabolomics, yet its interpretation remains heavily dependent on expert knowledge and difficult to scale. Although machine learning has been applied to NMR spectrum prediction, library retrieval, and structure generation, these tasks have evolved in isolation using simulated data and incompatible spectral representations, limiting their utility under real experimental scenarios. Here we present NMRPeak, a unified cross-modal learning system that integrates these three tasks through experimentally grounded design. We curate approximately 1.8 million experimental and simulated spectra to construct the largest benchmark for NMR-based structure elucidation and systematically quantify the distribution shift between these domains. We introduce a chemically-aware adaptive tokenizer that dynamically balances discretization granularity to preserve spectral semantics while controlling vocabulary size, and an assignment-free peak-aware similarity metric that enables direct comparison between predicted and experimental spectra. Through a unified molecule-to-spectrum paradigm and synergistic coupling of prediction, retrieval, and generation modules, NMRPeak achieves transformative performance on experimental benchmarks: it overcomes the longstanding simulation-to-experiment gap in spectrum prediction while delivering over 95% top-1 accuracy in molecular retrieval and approximately 75% top-1 accuracy in stereochemistry-aware de novo structure generation. These capabilities establish a foundation for automated, high-throughput molecular structure elucidation in organic synthesis, drug discovery, and chemical biology.

cond-mat.mtrl-sci↗

arXiv2026

DIA-CLIP: a universal representation learning framework for zero-shot DIA proteomics

Data-independent acquisition mass spectrometry (DIA-MS) has established itself as a cornerstone of proteomic profiling and large-scale systems biology, offering unparalleled depth and reproducibility. Current DIA analysis frameworks, however, require semi-supervised training within each run for peptide-spectrum match (PSM) re-scoring. This approach is prone to overfitting and lacks generalizability across diverse species and experimental conditions. Here, we present DIA-CLIP, a pre-trained model shifting the DIA analysis paradigm from semi-supervised training to universal cross-modal representation learning. By integrating dual-encoder contrastive learning framework with encoder-decoder architecture, DIA-CLIP establishes a unified cross-modal representation for peptides and corresponding spectral features, achieving high-precision, zero-shot PSM inference. Extensive evaluations across diverse benchmarks demonstrate that DIA-CLIP consistently outperforms state-of-the-art tools, yielding up to a 45% increase in protein identification while achieving a 12% reduction in entrapment identifications. Moreover, DIA-CLIP holds immense potential for diverse practical applications, such as single-cell and spatial proteomics, where its enhanced identification depth facilitates the discovery of novel biomarkers and the elucidates of intricate cellular mechanisms.

cs.LG↗

arXiv2026

Innovator-VL: A Multimodal Large Language Model for Scientific Discovery

We present Innovator-VL, a scientific multimodal large language model designed to advance understanding and reasoning across diverse scientific domains while maintaining excellent performance on general vision tasks. Contrary to the trend of relying on massive domain-specific pretraining and opaque pipelines, our work demonstrates that principled training design and transparent methodology can yield strong scientific intelligence with substantially reduced data requirements. (i) First, we provide a fully transparent, end-to-end reproducible training pipeline, covering data collection, cleaning, preprocessing, supervised fine-tuning, reinforcement learning, and evaluation, along with detailed optimization recipes. This facilitates systematic extension by the community. (ii) Second, Innovator-VL exhibits remarkable data efficiency, achieving competitive performance on various scientific tasks using fewer than five million curated samples without large-scale pretraining. These results highlight that effective reasoning can be achieved through principled data selection rather than indiscriminate scaling. (iii) Third, Innovator-VL demonstrates strong generalization, achieving competitive performance on general vision, multimodal reasoning, and scientific benchmarks. This indicates that scientific alignment can be integrated into a unified model without compromising general-purpose capabilities. Our practices suggest that efficient, reproducible, and high-performing scientific multimodal models can be built even without large-scale data, providing a practical foundation for future research.

cs.CV↗

arXiv2026

From Human Labels to Literature: Semi-Supervised Learning of NMR Chemical Shifts at Scale

Accurate prediction of nuclear magnetic resonance (NMR) chemical shifts is fundamental to spectral analysis and molecular structure elucidation, yet existing machine learning methods rely on limited, labor-intensive atom-assigned datasets. We propose a semi-supervised framework that learns NMR chemical shifts from millions of literature-extracted spectra without explicit atom-level assignments, integrating a small amount of labeled data with large-scale unassigned spectra. We formulate chemical shift prediction from literature spectra as a permutation-invariant set supervision problem, and show that under commonly satisfied conditions on the loss function, optimal bipartite matching reduces to a sorting-based loss, enabling stable large-scale semi-supervised training beyond traditional curated datasets. Our models achieve substantially improved accuracy and robustness over state-of-the-art methods and exhibit stronger generalization on significantly larger and more diverse molecular datasets. Moreover, by incorporating solvent information at scale, our approach captures systematic solvent effects across common NMR solvents for the first time. Overall, our results demonstrate that large-scale unlabeled spectra mined from the literature can serve as a practical and effective data source for training NMR shift models, suggesting a broader role of literature-derived, weakly structured data in data-centric AI for science.

cs.LG↗

arXiv2026

Toward Ultra-Long-Horizon Agentic Science: Cognitive Accumulation for Machine Learning Engineering

The advancement of artificial intelligence toward agentic science is currently bottlenecked by the challenge of ultra-long-horizon autonomy, the ability to sustain strategic coherence and iterative correction over experimental cycles spanning days or weeks. While Large Language Models (LLMs) have demonstrated prowess in short-horizon reasoning, they are easily overwhelmed by execution details in the high-dimensional, delayed-feedback environments of real-world research, failing to consolidate sparse feedback into coherent long-term guidance. Here, we present ML-Master 2.0, an autonomous agent that masters ultra-long-horizon machine learning engineering (MLE) which is a representative microcosm of scientific discovery. By reframing context management as a process of cognitive accumulation, our approach introduces Hierarchical Cognitive Caching (HCC), a multi-tiered architecture inspired by computer systems that enables the structural differentiation of experience over time. By dynamically distilling transient execution traces into stable knowledge and cross-task wisdom, HCC allows agents to decouple immediate execution from long-term experimental strategy, effectively overcoming the scaling limits of static context windows. In evaluations on OpenAI's MLE-Bench under 24-hour budgets, ML-Master 2.0 achieves a state-of-the-art medal rate of 56.44%. Our findings demonstrate that ultra-long-horizon autonomy provides a scalable blueprint for AI capable of autonomous exploration beyond human-precedent complexities.

cs.AI↗

arXiv2025

Bohrium + SciMaster: Building the Infrastructure and Ecosystem for Agentic Science at Scale

AI agents are emerging as a practical way to run multi-step scientific workflows that interleave reasoning with tool use and verification, pointing to a shift from isolated AI-assisted steps toward \emph{agentic science at scale}. This shift is increasingly feasible, as scientific tools and models can be invoked through stable interfaces and verified with recorded execution traces, and increasingly necessary, as AI accelerates scientific output and stresses the peer-review and publication pipeline, raising the bar for traceability and credible evaluation. However, scaling agentic science remains difficult: workflows are hard to observe and reproduce; many tools and laboratory systems are not agent-ready; execution is hard to trace and govern; and prototype AI Scientist systems are often bespoke, limiting reuse and systematic improvement from real workflow signals. We argue that scaling agentic science requires an infrastructure-and-ecosystem approach, instantiated in Bohrium+SciMaster. Bohrium acts as a managed, traceable hub for AI4S assets -- akin to a HuggingFace of AI for Science -- that turns diverse scientific data, software, compute, and laboratory systems into agent-ready capabilities. SciMaster orchestrates these capabilities into long-horizon scientific workflows, on which scientific agents can be composed and executed. Between infrastructure and orchestration, a \emph{scientific intelligence substrate} organizes reusable models, knowledge, and components into executable building blocks for workflow reasoning and action, enabling composition, auditability, and improvement through use. We demonstrate this stack with eleven representative master agents in real workflows, achieving orders-of-magnitude reductions in end-to-end scientific cycle time and generating execution-grounded signals from real workloads at multi-million scale.

cs.AI↗

arXiv2025

PhysMaster: Building an Autonomous AI Physicist for Theoretical and Computational Physics Research

Advances in LLM reasoning and tool use have enabled agentic science, yet frontier theoretical and computational physics remains challenging because research requires deep domain expertise, long-horizon reasoning, and reliable numerical computation. We introduce PRL-Bench, a research-reproduction benchmark adapted from 100 Physical Review Letters papers across major areas of modern physics. PRL-Bench distills realistic research workflows into traceable tasks with explicit intermediate artifacts and diverse evaluation rubrics; each task is estimated by domain experts to require more than six hours for a specialized PhD student to reproduce independently. Evaluations show that existing agents remain unreliable on extended research workflows. We therefore present PhysMaster, a scientific agent combining adaptive MCTS-based multi-trajectory exploration with hierarchical memory to improve long-horizon robustness and knowledge accumulation. PhysMaster achieves the highest overall PRL-Bench score of 51.08, outperforming Codex, OpenHands, OpenClaw, and ReAct, and yields relative improvements of 14.13 percent to 93.38 percent across backbone models. Error analysis shows that PhysMaster substantially reduces failures from incomplete long-horizon execution, while remaining bottlenecks lie in physics knowledge and analytical reasoning. Together, PRL-Bench and PhysMaster provide a rigorous benchmark and effective system for advancing autonomous AI research in frontier physics.

cs.AI↗

arXiv2025

DataFlow: An LLM-Driven Framework for Unified Data Preparation and Workflow Automation in the Era of Data-Centric AI

The rapidly growing demand for high-quality data in Large Language Models (LLMs) has intensified the need for scalable, reliable, and semantically rich data preparation pipelines. However, current practices remain dominated by ad-hoc scripts and loosely specified workflows, which lack principled abstractions, hinder reproducibility, and offer limited support for model-in-the-loop data generation. To address these challenges, we present DataFlow, a unified and extensible LLM-driven data preparation framework. DataFlow is designed with system-level abstractions that enable modular, reusable, and composable data transformations, and provides a PyTorch-style pipeline construction API for building debuggable and optimizable dataflows. The framework consists of nearly 200 reusable operators and six domain-general pipelines spanning text, mathematical reasoning, code, Text-to-SQL, agentic RAG, and large-scale knowledge extraction. To further improve usability, we introduce DataFlow-Agent, which automatically translates natural-language specifications into executable pipelines via operator synthesis, pipeline planning, and iterative verification. Across six representative use cases, DataFlow consistently improves downstream LLM performance. Our math, code, and text pipelines outperform curated human datasets and specialized synthetic baselines, achieving up to +3\% execution accuracy in Text-to-SQL over SynSQL, +7\% average improvements on code benchmarks, and 1--3 point gains on MATH, GSM8K, and AIME. Moreover, a unified 10K-sample dataset produced by DataFlow enables base models to surpass counterparts trained on 1M Infinity-Instruct data. These results demonstrate that DataFlow provides a practical and high-performance substrate for reliable, reproducible, and scalable LLM data preparation, and establishes a system-level foundation for future data-centric AI development.

cs.LG↗

arXiv2025

TeachMaster: Generative Teaching via Code

The scalability of high-quality online education is hindered by the high costs and slow cycles of manual content creation. Despite advancements in video generation, current approaches often fail to ensure pedagogical structure and precise control due to their pixel-level, black-box nature. In this paper, we propose Generative Teaching, a novel paradigm shifting educators from manual creators to high-level directors who focus on pedagogical intents while agents handle the execution. To realize this vision, we introduce TeachMaster, a multi-agent framework that leverages code as an intermediate semantic medium. Unlike traditional video generation methods, TeachMaster orchestrates a collaborative team of agents, spanning planning, design, and rendering, to automate the production of interpretable, editable, and curriculum-ready educational videos. Experiments validate that TeachMaster significantly boosts production efficiency without compromising structural coherence or visual fidelity, slashing production costs to only 0.3% of traditional online course videos and providing a robust solution for scalable education.

cs.CY↗

arXiv2025

Inverse Knowledge Search over Verifiable Reasoning: Synthesizing a Scientific Encyclopedia from a Long Chains-of-Thought Knowledge Base

Most scientific materials compress reasoning, presenting conclusions while omitting the derivational chains that justify them. This compression hinders verification by lacking explicit, step-wise justifications and inhibits cross-domain links by collapsing the very pathways that establish the logical and causal connections between concepts. We introduce a scalable framework that decompresses scientific reasoning, constructing a verifiable Long Chain-of-Thought (LCoT) knowledge base and projecting it into an emergent encyclopedia, SciencePedia. Our pipeline operationalizes an endpoint-driven, reductionist strategy: a Socratic agent, guided by a curriculum of around 200 courses, generates approximately 3 million first-principles questions. To ensure high fidelity, multiple independent solver models generate LCoTs, which are then rigorously filtered by prompt sanitization and cross-model answer consensus, retaining only those with verifiable endpoints. This verified corpus powers the Brainstorm Search Engine, which performs inverse knowledge search -- retrieving diverse, first-principles derivations that culminate in a target concept. This engine, in turn, feeds the Plato synthesizer, which narrates these verified chains into coherent articles. The initial SciencePedia comprises approximately 200,000 fine-grained entries spanning mathematics, physics, chemistry, biology, engineering, and computation. In evaluations across six disciplines, Plato-synthesized articles (conditioned on retrieved LCoTs) exhibit substantially higher knowledge-point density and significantly lower factual error rates than an equally-prompted baseline without retrieval (as judged by an external LLM). Built on this verifiable LCoT knowledge base, this reasoning-centric approach enables trustworthy, cross-domain scientific synthesis at scale and establishes the foundation for an ever-expanding encyclopedia.

cs.AI↗