arXiv subjects

Weinan E

Publications and source records attributed to Weinan E.

At least 37 records · Page 2Linked to original sources

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

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↗

arXiv2025

Progressive Optimal Path Sampling for Closed-Loop Optimal Control Design with Deep Neural Networks

Closed-loop optimal control design for high-dimensional nonlinear systems has been a long-standing challenge. Traditional methods, such as solving the associated Hamilton-Jacobi-Bellman equation, suffer from the curse of dimensionality. Recent literature proposed a new promising approach based on supervised learning, by leveraging powerful open-loop optimal control solvers to generate training data and neural networks as efficient high-dimensional function approximators to fit the closed-loop optimal control. This approach successfully handles certain high-dimensional optimal control problems but still performs poorly on more challenging problems. One of the crucial reasons for the failure is the so-called distribution mismatch phenomenon brought by the controlled dynamics. In this paper, we investigate this phenomenon and propose the Progressive Optimal Path Sampling (POPS) method to mitigate this problem. We theoretically prove that this enhanced sampling strategy outperforms both the vanilla approach and the widely used Dataset Aggregation (DAgger) method on the classical linear-quadratic regulator by a factor proportional to the total time duration. We further numerically demonstrate that the proposed sampling strategy significantly improves the performance on tested control problems, including the optimal landing problem of a quadrotor and the optimal reaching problem of a 7 DoF manipulator.

math.OC↗

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

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

Ab Initio bulk free energy surface of proper ferroelectrics

We report a systematic and accurate approach for deriving the bulk free energy surface (FES), a function of temperature, polarization, and strain, from the first-principles density functional theory (DFT) of proper ferroelectrics. The core of our approach is the metadynamics algorithm that extracts the polarization dependence of the FES from all-atom molecular dynamics simulations without an a priori ansatz. The rest of the FES is derived from the metadynamics trajectories that span the relevant phase space. We demonstrate our approach in the case of lead titanate. The errors across the phase transition, due to DFT numerics, all-atom molecular dynamics, and free energy evaluation by enhanced sampling, can be systematically controlled and are of the order of 1meV/atom. The accuracy of the resulting ab initio FES is only limited by the adopted functional approximation of DFT.

cond-mat.mtrl-sci↗

arXiv2025

Unified Cross-Scale 3D Generation and Understanding via Autoregressive Modeling

3D structure modeling is essential across scales, enabling applications from fluid simulation and 3D reconstruction to protein folding and molecular docking. Yet, despite shared 3D spatial patterns, current approaches remain fragmented, with models narrowly specialized for specific domains and unable to generalize across tasks or scales. We propose Uni-3DAR, a unified autoregressive framework for cross-scale 3D generation and understanding. At its core is a coarse-to-fine tokenizer based on octree data structures, which compresses diverse 3D structures into compact 1D token sequences. We further propose a two-level subtree compression strategy, which reduces the octree token sequence by up to 8x. To address the challenge of dynamically varying token positions introduced by compression, we introduce a masked next-token prediction strategy that ensures accurate positional modeling, significantly boosting model performance. Extensive experiments across multiple 3D generation and understanding tasks, including small molecules, proteins, polymers, crystals, and macroscopic 3D objects, validate its effectiveness and versatility. Notably, Uni-3DAR surpasses previous state-of-the-art diffusion models by a substantial margin, achieving up to 256\% relative improvement while delivering inference speeds up to 21.8x faster.

cs.LG↗

arXiv2025

NMR-Solver: Automated Structure Elucidation via Large-Scale Spectral Matching and Physics-Guided Fragment Optimization

Nuclear Magnetic Resonance (NMR) spectroscopy is one of the most powerful and widely used tools for molecular structure elucidation in organic chemistry. However, the interpretation of NMR spectra to determine unknown molecular structures remains a labor-intensive and expertise-dependent process, particularly for complex or novel compounds. Although recent methods have been proposed for molecular structure elucidation, they often underperform in real-world applications due to inherent algorithmic limitations and limited high-quality data. Here, we present NMR-Solver, a practical and interpretable framework for the automated determination of small organic molecule structures from $^1$H and $^{13}$C NMR spectra. Our method introduces an automated framework for molecular structure elucidation, integrating large-scale spectral matching with physics-guided fragment-based optimization that exploits atomic-level structure-spectrum relationships in NMR. We evaluate NMR-Solver on simulated benchmarks, curated experimental data from the literature, and real-world experiments, demonstrating its strong generalization, robustness, and practical utility in challenging, real-life scenarios. NMR-Solver unifies computational NMR analysis, deep learning, and interpretable chemical reasoning into a coherent system. By incorporating the physical principles of NMR into molecular optimization, it enables scalable, automated, and chemically meaningful molecular identification, establishing a generalizable paradigm for solving inverse problems in molecular science.

physics.chem-ph↗

arXiv2025

LAMBench: A Benchmark for Large Atomistic Models

Large Atomistic Models (LAMs) have undergone remarkable progress recently, emerging as universal or fundamental representations of the potential energy surface defined by the first-principles calculations of atomistic systems. However, our understanding of the extent to which these models achieve true universality, as well as their comparative performance across different models, remains limited. This gap is largely due to the lack of comprehensive benchmarks capable of evaluating the effectiveness of LAMs as approximations to the universal potential energy surface. In this study, we introduce LAMBench, a benchmarking system designed to evaluate LAMs in terms of their generalizability, adaptability, and applicability. These attributes are crucial for deploying LAMs as ready-to-use tools across a diverse array of scientific discovery contexts. We benchmark ten state-of-the-art LAMs released prior to August 1, 2025, using LAMBench. Our findings reveal a significant gap between the current LAMs and the ideal universal potential energy surface. They also highlight the need for incorporating cross-domain training data, supporting multi-fidelity modeling, and ensuring the models' conservativeness and differentiability. As a dynamic and extensible platform, LAMBench is intended to continuously evolve, thereby facilitating the development of robust and generalizable LAMs capable of significantly advancing scientific research. The LAMBench code is open-sourced at https://github.com/deepmodeling/lambench, and an interactive leaderboard is available at https://www.aissquare.com/openlam?tab=Benchmark.

physics.comp-ph↗

arXiv2025

Solving multiscale dynamical systems by deep learning

Multiscale dynamical systems, modeled by high-dimensional stiff ordinary differential equations (ODEs) with wide-ranging characteristic timescales, arise across diverse fields of science and engineering, but their numerical solvers often encounter severe efficiency bottlenecks. This paper introduces a novel DeePODE method, which consists of an Evolutionary Monte Carlo Sampling method (EMCS) and an efficient end-to-end deep neural network (DNN) to predict multiscale dynamical systems. We validate this finding across dynamical systems from ecological systems to reactive flows, including a predator-prey model, a power system oscillation, a battery electrolyte thermal runaway, and turbulent reaction-diffusion systems with complex chemical kinetics. The method demonstrates robust generalization capabilities, allowing pre-trained DNN models to accurately predict the behavior in previously unseen scenarios, largely due to the delicately constructed dataset. While theoretical guarantees remain to be established, empirical evidence shows that DeePODE achieves the accuracy of implicit numerical schemes while maintaining the computational efficiency of explicit schemes. This work underscores the crucial relationship between training data distribution and neural network generalization performance. This work demonstrates the potential of deep learning approaches in modeling complex dynamical systems across scientific and engineering domains.

math.NA↗

arXiv2025

Uni-Mol3: A Multi-Molecular Foundation Model for Advancing Organic Reaction Modeling

Organic reaction, the foundation of modern chemical industry, is crucial for new material development and drug discovery. However, deciphering reaction mechanisms and modeling multi-molecular relationships remain formidable challenges due to the complexity of molecular dynamics. While several state-of-the-art models like Uni-Mol2 have revolutionized single-molecular representation learning, their extension to multi-molecular systems, where chemical reactions inherently occur, has been underexplored. This paper introduces Uni-Mol3, a novel deep learning framework that employs a hierarchical pipeline for multi-molecular reaction modeling. At its core, Uni-Mol3 adopts a multi-scale molecular tokenizer (Mol-Tokenizer) that encodes 3D structures of molecules and other features into discrete tokens, creating a 3D-aware molecular language. The framework innovatively combines two pre-training stages: molecular pre-training to learn the molecular grammars and reaction pre-training to capture fundamental reaction principles, forming a progressive learning paradigm from single- to multi-molecular systems. With prompt-aware downstream fine-tuning, Uni-Mol3 demonstrates exceptional performance in diverse organic reaction tasks and supports multi-task prediction with strong generalizability. Experimental results across 10 datasets spanning 4 downstream tasks show that Uni-Mol3 outperforms existing methods, validating its effectiveness in modeling complex organic reactions. This work not only ushers in an alternative paradigm for multi-molecular computational modeling but also charts a course for intelligent organic reaction by bridging molecular representation with reaction mechanism understanding.

physics.chem-ph↗

arXiv2025

Learning Free Terminal Time Optimal Closed-loop Control of Manipulators

This paper presents a novel approach to learning free terminal time closed-loop control for robotic manipulation tasks, enabling dynamic adjustment of task duration and control inputs to enhance performance. We extend the supervised learning approach, namely solving selected optimal open-loop problems and utilizing them as training data for a policy network, to the free terminal time scenario. Three main challenges are addressed in this extension. First, we introduce a marching scheme that enhances the solution quality and increases the success rate of the open-loop solver by gradually refining time discretization. Second, we extend the QRnet in Nakamura-Zimmerer et al. (2021b) to the free terminal time setting to address discontinuity and improve stability at the terminal state. Third, we present a more automated version of the initial value problem (IVP) enhanced sampling method from previous work (Zhang et al., 2022) to adaptively update the training dataset, significantly improving its quality. By integrating these techniques, we develop a closed-loop policy that operates effectively over a broad domain with varying optimal time durations, achieving near globally optimal total costs.

math.OC↗

arXiv2025

SynBridge: Bridging Reaction States via Discrete Flow for Bidirectional Reaction Prediction

The essence of a chemical reaction lies in the redistribution and reorganization of electrons, which is often manifested through electron transfer or the migration of electron pairs. These changes are inherently discrete and abrupt in the physical world, such as alterations in the charge states of atoms or the formation and breaking of chemical bonds. To model the transition of states, we propose SynBridge, a bidirectional flow-based generative model to achieve multi-task reaction prediction. By leveraging a graph-to-graph transformer network architecture and discrete flow bridges between any two discrete distributions, SynBridge captures bidirectional chemical transformations between graphs of reactants and products through the bonds' and atoms' discrete states. We further demonstrate the effectiveness of our method through extensive experiments on three benchmark datasets (USPTO-50K, USPTO-MIT, Pistachio), achieving state-of-the-art performance in both forward and retrosynthesis tasks. Our ablation studies and noise scheduling analysis reveal the benefits of structured diffusion over discrete spaces for reaction prediction.

cs.LG↗

arXiv2025

SciMaster: Towards General-Purpose Scientific AI Agents, Part I. X-Master as Foundation: Can We Lead on Humanity's Last Exam?

The rapid advancements of AI agents have ignited the long-held ambition of leveraging them to accelerate scientific discovery. Achieving this goal requires a deep understanding of the frontiers of human knowledge. As such, Humanity's Last Exam (HLE) provides an exceptionally challenging touchstone for evaluating scientific AI agents. In this work, we aim to construct the foundational architecture for general-purpose agents and validate the capabilities through leading performance on HLE. To achieve this, we introduce X-Master, a tool-augmented reasoning agent designed to emulate human researchers by interacting flexibly with external tools during its reasoning process. This agent, guided by the conceptualization of code as an interaction language, can flexibly leverage built-in Python libraries and our customized tools to augment the reasoning. We further scale its capabilities through X-Masters, a scattered-and-stacked agentic workflow that systematically enhances breadth and depth of reasoning. Our open-source solution, X-Masters, sets a new state-of-the-art record on HLE with a score of 32.1%, surpassing OpenAI's and Google's Deep Research (26.6% and 26.9%) and becoming the first to exceed the 30% threshold. This work allows us to gain a deeper understanding of complex task-solving and accumulates valuable experience that can inform future advancements, guiding subsequent model training.

cs.AI↗

arXiv2025

pUniFind: a unified large pre-trained deep learning model pushing the limit of mass spectra interpretation

Deep learning has advanced mass spectrometry data interpretation, yet most models remain feature extractors rather than unified scoring frameworks. We present pUniFind, the first large-scale multimodal pre-trained model in proteomics that integrates end-to-end peptide-spectrum scoring with open, zero-shot de novo sequencing. Trained on over 100 million open search-derived spectra, pUniFind aligns spectral and peptide modalities via cross modality prediction and outperforms traditional engines across diverse datasets, particularly achieving a 42.6 percent increase in the number of identified peptides in immunopeptidomics. Supporting over 1,300 modifications, pUniFind identifies 60 percent more PSMs than existing de novo methods despite a 300-fold larger search space. A deep learning based quality control module further recovers 38.5 percent additional peptides including 1,891 mapped to the genome but absent from reference proteomes while preserving full fragment ion coverage. These results establish a unified, scalable deep learning framework for proteomic analysis, offering improved sensitivity, modification coverage, and interpretability.

cs.LG↗

arXiv2025

ML-Master: Towards AI-for-AI via Integration of Exploration and Reasoning

As AI capabilities advance toward and potentially beyond human-level performance, a natural transition emerges where AI-driven development becomes more efficient than human-centric approaches. A promising pathway toward this transition lies in AI-for-AI (AI4AI), which leverages AI techniques to automate and optimize the design, training, and deployment of AI systems themselves. While LLM-based agents have shown the potential to realize AI4AI, they are often unable to fully leverage the experience accumulated by agents during the exploration of solutions in the reasoning process, leading to inefficiencies and suboptimal performance. To address this limitation, we propose ML-Master, a novel AI4AI agent that seamlessly integrates exploration and reasoning by employing a selectively scoped memory mechanism. This approach allows ML-Master to efficiently combine diverse insights from parallel solution trajectories with analytical reasoning, guiding further exploration without overwhelming the agent with excessive context. We evaluate ML-Master on the MLE-Bench, where it achieves a 29.3% average medal rate, significantly surpassing existing methods, particularly in medium-complexity tasks, while accomplishing this superior performance within a strict 12-hour time constraint-half the 24-hour limit used by previous baselines. These results demonstrate ML-Master's potential as a powerful tool for advancing AI4AI.

cs.AI↗

arXiv2025

The Sharpness Disparity Principle in Transformers for Accelerating Language Model Pre-Training

Transformers consist of diverse building blocks, such as embedding layers, normalization layers, self-attention mechanisms, and point-wise feedforward networks. Thus, understanding the differences and interactions among these blocks is important. In this paper, we uncover a clear Sharpness Disparity across these blocks, which emerges early in training and intriguingly persists throughout the training process. Motivated by this finding, we propose Blockwise Learning Rate (LR), a strategy that tailors the LR to each block's sharpness, accelerating large language model (LLM) pre-training. By integrating Blockwise LR into AdamW, we consistently achieve lower terminal loss and nearly $2\times$ speedup compared to vanilla AdamW. We demonstrate this acceleration across GPT-2 and LLaMA, with model sizes ranging from 0.12B to 2B and datasets of OpenWebText, MiniPile, and C4. Finally, we incorporate Blockwise LR into Adam-mini (Zhang et al., 2024), a recently proposed memory-efficient variant of Adam, achieving a combined $2\times$ speedup and $2\times$ memory saving. These results underscore the potential of exploiting the sharpness disparity to improve LLM training.

cs.LG↗