arXiv subjects

Jingru Gan

Publications and source records attributed to Jingru Gan.

8 recordsLinked to original sources

arXiv2026

RetroAgent: Harnessing LLMs to Search Over Structured Memory for Agentic Retrosynthesis Planning

Multi-step retrosynthesis planning seeks to decompose a target molecule into commercially available building blocks through a sequence of feasible reactions. The vast combinatorial search space makes this task challenging even for expert chemists. Traditional methods combine tree search with offline-trained value networks that score candidates in isolation, without reasoning about complete multi-step routes. Recent work leverages Large Language Models (LLMs) for this task, but relies on simple interfaces that limit exploration of the full search space. We introduce RetroAgent, an LLM agent that bridges symbolic search and neural reasoning through a harness with structured memory. Through memory and chemistry tools, the agent observes the full search state, including explored routes, available alternatives, and properties of intermediates, enabling informed decisions grounded in both global progress and domain knowledge. Experiments on in-distribution and out-of-distribution benchmarks demonstrate that RetroAgent delivers strong performance and generalization.

cs.AI↗

arXiv2025

Evaluating Large Language Models in Scientific Discovery

Large language models (LLMs) are increasingly applied to scientific research, yet prevailing science benchmarks probe decontextualized knowledge and overlook the iterative reasoning, hypothesis generation, and observation interpretation that drive scientific discovery. We introduce a scenario-grounded benchmark that evaluates LLMs across biology, chemistry, materials, and physics, where domain experts define research projects of genuine interest and decompose them into modular research scenarios from which vetted questions are sampled. The framework assesses models at two levels: (i) question-level accuracy on scenario-tied items and (ii) project-level performance, where models must propose testable hypotheses, design simulations or experiments, and interpret results. Applying this two-phase scientific discovery evaluation (SDE) framework to state-of-the-art LLMs reveals a consistent performance gap relative to general science benchmarks, diminishing return of scaling up model sizes and reasoning, and systematic weaknesses shared across top-tier models from different providers. Large performance variation in research scenarios leads to changing choices of the best performing model on scientific discovery projects evaluated, suggesting all current LLMs are distant to general scientific "superintelligence". Nevertheless, LLMs already demonstrate promise in a great variety of scientific discovery projects, including cases where constituent scenario scores are low, highlighting the role of guided exploration and serendipity in discovery. This SDE framework offers a reproducible benchmark for discovery-relevant evaluation of LLMs and charts practical paths to advance their development toward scientific discovery.

cs.AI↗

arXiv2025

MatSciBench: Benchmarking the Reasoning Ability of Large Language Models in Materials Science

Large Language Models have shown strong scientific reasoning ability, but their performance on materials science problems remains less studied. To fill this gap, we introduce MatSciBench, a comprehensive college-level benchmark comprising 1340 problems that span the essential subdisciplines of materials science. MatSciBench features a structured and fine-grained taxonomy that categorizes materials science questions into 6 primary fields and 31 subfields, together with a three-tier difficulty classification based on the reasoning length needed to solve each problem. MatSciBench includes detailed reference solutions for 946 questions, supports process-level error analysis, and contains 315 questions with images for evaluating multimodal reasoning. We evaluate leading thinking and non-thinking LLMs on MatSciBench, and further test three reasoning methods for non-thinking models: basic chain-of-thought prompting, tool augmentation, and self-correction. The results show that current models still face clear limits in college-level materials science reasoning. DeepSeek-R1 achieves the highest score on text-only questions at 75.22% accuracy, and GPT-5 performs the best on questions with images at 53.02%. Our analysis shows that tool augmentation improves many non-thinking models in a token-efficient way, while self-correction often fails to provide reliable gains and can revise correct answers into incorrect ones. We further analyze performance across difficulty levels, reasoning efficiency, multimodal reasoning, and failure patterns, and find that current models are mainly limited by domain knowledge gaps, calculation errors, problem comprehension failures, and difficulty in extracting precise information from scientific figures. Overall, MatSciBench provides a clear testbed for measuring current LLM limitations and guiding future work on scientific reasoning in materials science.

cs.AI↗

arXiv2025

Multimodal LLM With Hierarchical Mixture-of-Experts for VQA on 3D Brain MRI

Multiparametric 3D brain MRI (mpMRI) is central to neuroradiology, but producing tumor location, appearance, size, and involvement of critical structures for neurosurgical planning remains challenging. We introduce mpLLM, a multimodal LLM for visual question answering (VQA) on mpMRI that produces clinically interpretable tumor descriptors (e.g., volume, morphology, extent, and coarse localization) as an adjunct to clinical expertise for referring neurosurgeons. mpLLM uses a prompt-conditioned hierarchical mixture-of-experts (MoE) to fuse multiple 3D sequences via routing over modality- and token-level projection experts, enabling data-efficient end-to-end training without large-scale image-report pretraining. To address limited paired image-text supervision, we propose a synthetic VQA protocol that derives clinically grounded questions and answers from expert segmentation annotations and is validated with radiologist collaboration. Across multiple mpMRI datasets, mpLLM improves over strong medical VLM baselines by +5.5 points on average (+9.1% relative) and increases radiologist-rated clinical acceptability by +15.9 points (+46.6% relative). Our study features three main contributions: (1) the first VQA dataset for 3D brain mpMRI, (2) a hierarchical MoE architecture for joint reasoning over interrelated 3D sequences, and (3) expert-supported evidence of clinical utility. Source code is available at https://github.com/arvindmvepa/mpllm, and we will release the dataset upon publication.

cs.CV↗

arXiv2025

MetamatBench: Integrating Heterogeneous Data, Computational Tools, and Visual Interface for Metamaterial Discovery

Metamaterials, engineered materials with architected structures across multiple length scales, offer unprecedented and tunable mechanical properties that surpass those of conventional materials. However, leveraging advanced machine learning (ML) for metamaterial discovery is hindered by three fundamental challenges: (C1) Data Heterogeneity Challenge arises from heterogeneous data sources, heterogeneous composition scales, and heterogeneous structure categories; (C2) Model Complexity Challenge stems from the intricate geometric constraints of ML models, which complicate their adaptation to metamaterial structures; and (C3) Human-AI Collaboration Challenge comes from the "dual black-box'' nature of sophisticated ML models and the need for intuitive user interfaces. To tackle these challenges, we introduce a unified framework, named MetamatBench, that operates on three levels. (1) At the data level, we integrate and standardize 5 heterogeneous, multi-modal metamaterial datasets. (2) The ML level provides a comprehensive toolkit that adapts 17 state-of-the-art ML methods for metamaterial discovery. It also includes a comprehensive evaluation suite with 12 novel performance metrics with finite element-based assessments to ensure accurate and reliable model validation. (3) The user level features a visual-interactive interface that bridges the gap between complex ML techniques and non-ML researchers, advancing property prediction and inverse design of metamaterials for research and applications. MetamatBench offers a unified platform deployed at http://zhoulab-1.cs.vt.edu:5550 that enables machine learning researchers and practitioners to develop and evaluate new methodologies in metamaterial discovery. For accessibility and reproducibility, we open-source our benchmark and the codebase at https://github.com/cjpcool/Metamaterial-Benchmark.

physics.optics↗

arXiv2025

MatLLMSearch: Crystal Structure Discovery with Evolution-Guided Large Language Models

Crystal structure generation is fundamental to materials science, enabling the discovery of novel materials with desired properties. While existing approaches leverage Large Language Models (LLMs) through extensive fine-tuning on materials databases, we show that pre-trained LLMs can inherently generate novel and stable crystal structures without additional fine-tuning. Our framework employs LLMs as intelligent proposal agents within an evolutionary pipeline that guides them to perform implicit crossover and mutation operations while maintaining chemical validity. We demonstrate that MatLLMSearch achieves a 78.38% metastable rate validated by machine learning interatomic potentials and 31.7% DFT-verified stability, outperforming specialized models such as CrystalTextLLM. Beyond crystal structure generation, we further demonstrate that our framework adapts to diverse materials design tasks, including crystal structure prediction and multi-objective optimization of properties such as deformation energy and bulk modulus, all without fine-tuning. These results establish our framework as a versatile and effective framework for consistent high-quality materials discovery, offering training-free generation of novel stable structures with reduced overhead and broader accessibility.

cond-mat.mtrl-sci↗

arXiv2024

MetaScientist: A Human-AI Synergistic Framework for Automated Mechanical Metamaterial Design

The discovery of novel mechanical metamaterials, whose properties are dominated by their engineered structures rather than chemical composition, is a knowledge-intensive and resource-demanding process. To accelerate the design of novel metamaterials, we present MetaScientist, a human-in-the-loop system that integrates advanced AI capabilities with expert oversight with two primary phases: (1) hypothesis generation, where the system performs complex reasoning to generate novel and scientifically sound hypotheses, supported with domain-specific foundation models and inductive biases retrieved from existing literature; (2) 3D structure synthesis, where a 3D structure is synthesized with a novel 3D diffusion model based on the textual hypothesis and refined it with a LLM-based refinement model to achieve better structure properties. At each phase, domain experts iteratively validate the system outputs, and provide feedback and supplementary materials to ensure the alignment of the outputs with scientific principles and human preferences. Through extensive evaluation from human scientists, MetaScientist is able to deliver novel and valid mechanical metamaterial designs that have the potential to be highly impactful in the metamaterial field.

cs.AI↗

arXiv2023

Open-Set Knowledge-Based Visual Question Answering with Inference Paths

Given an image and an associated textual question, the purpose of Knowledge-Based Visual Question Answering (KB-VQA) is to provide a correct answer to the question with the aid of external knowledge bases. Prior KB-VQA models are usually formulated as a retriever-classifier framework, where a pre-trained retriever extracts textual or visual information from knowledge graphs and then makes a prediction among the candidates. Despite promising progress, there are two drawbacks with existing models. Firstly, modeling question-answering as multi-class classification limits the answer space to a preset corpus and lacks the ability of flexible reasoning. Secondly, the classifier merely consider "what is the answer" without "how to get the answer", which cannot ground the answer to explicit reasoning paths. In this paper, we confront the challenge of \emph{explainable open-set} KB-VQA, where the system is required to answer questions with entities at wild and retain an explainable reasoning path. To resolve the aforementioned issues, we propose a new retriever-ranker paradigm of KB-VQA, Graph pATH rankER (GATHER for brevity). Specifically, it contains graph constructing, pruning, and path-level ranking, which not only retrieves accurate answers but also provides inference paths that explain the reasoning process. To comprehensively evaluate our model, we reformulate the benchmark dataset OK-VQA with manually corrected entity-level annotations and release it as ConceptVQA. Extensive experiments on real-world questions demonstrate that our framework is not only able to perform open-set question answering across the whole knowledge base but provide explicit reasoning path.

cs.LG↗