arXiv subjects

Dajun Zeng

Publications and source records attributed to Dajun Zeng.

4 recordsLinked to original sources

arXiv2026

MatMind: A Structure-Activity Knowledge-Driven Generative Foundation Model for Materials Science

Progress in AI-driven crystal materials science has so far been carried by narrow architectures purpose-built for individual tasks -- graph neural networks for property prediction, diffusion and flow-matching models for crystal generation -- each excelling within its niche yet unable to act as a shared backbone across the full spectrum of materials problems. Generative large language models offer a fundamentally different paradigm, in which structural representation, quantitative prediction, and structure-activity reasoning can be unified within one model, but the materials community has yet to see this paradigm realized at a level competitive with established narrow specialists. Here we present MatMind, a generative foundation model purpose-built for crystal materials science under this paradigm, developed through the coordinated activation of structure-activity knowledge and physics-informed feedback within a progressive training framework -- combining structure-activity knowledge injection, a dual-head architecture that jointly trains language reasoning and numerical regression in a shared representation space, and multi-objective physics-informed reinforcement learning over stability, novelty, and structural diversity. Across three task families, MatMind attains the lowest mean absolute error on energy above hull, bulk modulus, and band gap -- surpassing graph neural network predictors purpose-built for these tasks -- reaches an S.U.N. rate of 65.3% on unconditional crystal generation, and achieves a comparable multiplicative improvement on magnetization-density-conditioned generation, where only 21 positive samples exist within over 600000 training entries. By matching or surpassing narrow specialists on their own ground while operating within a single unified model, MatMind shows that the LLM-based paradigm can serve as a viable backbone for crystal materials science going forward.

cond-mat.mtrl-sci↗

arXiv2025

BIOME-Bench: A Benchmark for Biomolecular Interaction Inference and Multi-Omics Pathway Mechanism Elucidation from Scientific Literature

Multi-omics studies often rely on pathway enrichment to interpret heterogeneous molecular changes, but pathway enrichment (PE)-based workflows inherit structural limitations of pathway resources, including curation lag, functional redundancy, and limited sensitivity to molecular states and interventions. Although recent work has explored using large language models (LLMs) to improve PE-based interpretation, the lack of a standardized benchmark for end-to-end multi-omics pathway mechanism elucidation has largely confined evaluation to small, manually curated datasets or ad hoc case studies, hindering reproducible progress. To address this issue, we introduce BIOME-Bench, constructed via a rigorous four-stage workflow, to evaluate two core capabilities of LLMs in multi-omics analysis: Biomolecular Interaction Inference and end-to-end Multi-Omics Pathway Mechanism Elucidation. We develop evaluation protocols for both tasks and conduct comprehensive experiments across multiple strong contemporary models. Experimental results demonstrate that existing models still exhibit substantial deficiencies in multi-omics analysis, struggling to reliably distinguish fine-grained biomolecular relation types and to generate faithful, robust pathway-level mechanistic explanations.

cs.CL↗

arXiv2025

S1-MatAgent: A planner driven multi-agent system for material discovery

The discovery of high-performance materials is crucial for technological advancement. Inverse design using multi-agent systems (MAS) shows great potential for new material discovery. However, current MAS for materials research rely on predefined configurations and tools, limiting their adaptability and scalability. To address these limitations, we developed a planner driven multi-agent system (S1-MatAgent) which adopts a Planner-Executor architecture. Planner automatically decomposes complex materials design tasks, dynamically configures various tools to generate dedicated Executor agents for each subtask, significantly reducing reliance on manual workflow construction and specialized configuration. Applied to high-entropy alloy catalysts for hydrogen evolution reactions in alkaline conditions, S1-MatAgent completed full-cycle closed-loop design from literature analysis and composition recommendation to performance optimization and experimental validation. To tackle the deviations between designed materials and target, as well as high experimental verification costs, S1-MatAgent employs a novel composition optimization algorithm based on gradients of machine learning interatomic potential, achieving 27.7 % improvement in material performance. S1-MatAgent designed 13 high-performance catalysts from 20 million candidates, with Ni4Co4Cu1Mo3Ru4 exhibiting an overpotential of 18.6 mV at 10 mA cm-2 and maintaining 97.5 % activity after 500 hours at 500 mA cm-2. The universal MAS framework offers a universal and scalable solution for material discovery, significantly improving design efficiency and adaptability.

cond-mat.mtrl-sci↗

arXiv2023

YAYI 2: Multilingual Open-Source Large Language Models

As the latest advancements in natural language processing, large language models (LLMs) have achieved human-level language understanding and generation abilities in many real-world tasks, and even have been regarded as a potential path to the artificial general intelligence. To better facilitate research on LLMs, many open-source LLMs, such as Llama 2 and Falcon, have recently been proposed and gained comparable performances to proprietary models. However, these models are primarily designed for English scenarios and exhibit poor performances in Chinese contexts. In this technical report, we propose YAYI 2, including both base and chat models, with 30 billion parameters. YAYI 2 is pre-trained from scratch on a multilingual corpus which contains 2.65 trillion tokens filtered by our pre-training data processing pipeline. The base model is aligned with human values through supervised fine-tuning with millions of instructions and reinforcement learning from human feedback. Extensive experiments on multiple benchmarks, such as MMLU and CMMLU, consistently demonstrate that the proposed YAYI 2 outperforms other similar sized open-source models.

cs.CL↗