Qiaoyu Tan
2025
CrystalICL: Enabling In-Context Learning for Crystal Generation
Ruobing Wang
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Qiaoyu Tan
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Yili Wang
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Ying Wang
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Xin Wang
Proceedings of the 2025 Conference on Empirical Methods in Natural Language Processing
Designing crystal materials with desired physicochemical properties remains a fundamental challenge in materials science. While large language models (LLMs) have demonstrated strong in-context learning (ICL) capabilities, existing LLM-based crystal generation approaches are limited to zero-shot scenarios and are unable to benefit from few-shot scenarios. In contrast, human experts typically design new materials by modifying relevant known structures which aligns closely with the few-shot ICL paradigm. Motivated by this, we propose CrystalICL, a novel model designed for few-shot crystal generation. Specifically, we introduce a space-group based crystal tokenization method, which effectively reduces the complexity of modeling crystal symmetry in LLMs. We further introduce a condition-structure aware hybrid instruction tuning framework and a multi-task instruction tuning strategy, enabling the model to better exploit ICL by capturing structure-property relationships from limited data. Extensive experiments on four crystal generation benchmarks demonstrate the superiority of CrystalICL over the leading baseline methods on conditional and unconditional generation tasks.
GraphICL: Unlocking Graph Learning Potential in LLMs through Structured Prompt Design
Yuanfu Sun
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Zhengnan Ma
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Yi Fang
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Jing Ma
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Qiaoyu Tan
Findings of the Association for Computational Linguistics: NAACL 2025
The growing importance of textual and relational systems has driven interest in enhancing large language models (LLMs) for graph-structured data, particularly Text-Attributed Graphs (TAGs), where samples are represented by textual descriptions interconnected by edges. While research has largely focused on developing specialized graph LLMs through task-specific instruction tuning, a comprehensive benchmark for evaluating LLMs solely through prompt design remains surprisingly absent. Without such a carefully crafted evaluation benchmark, most if not all, tailored graph LLMs are compared against general LLMs using simplistic queries (e.g., zero-shot reasoning with LLaMA), which can potentially camouflage many advantages as well as unexpected predicaments of them. To achieve more general evaluations and unveil the true potential of LLMs for graph tasks, we introduce Graph In-context Learning (GraphICL) Benchmark, a comprehensive benchmark comprising novel prompt templates designed to capture graph structure and handle limited label knowledge. Our systematic evaluation shows that general-purpose LLMs equipped with our GraphICL outperform state-of-the-art specialized graph LLMs and graph neural network models in resource-constrained settings and out-of-domain tasks. These findings highlight the significant potential of prompt engineering to enhance LLM performance on graph learning tasks without training and offer a strong baseline for advancing research in graph LLMs.
2024
Reasoning Like a Doctor: Improving Medical Dialogue Systems via Diagnostic Reasoning Process Alignment
Kaishuai Xu
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Yi Cheng
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Wenjun Hou
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Qiaoyu Tan
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Wenjie Li
Findings of the Association for Computational Linguistics: ACL 2024
Medical dialogue systems have attracted significant attention for their potential to act as medical assistants. Enabling these medical systems to emulate clinicians’ diagnostic reasoning process has been the long-standing research focus. Previous studies rudimentarily realized the simulation of clinicians’ diagnostic process by fine-tuning language models on high-quality dialogue datasets. Nonetheless, they overly focus on the outcomes of the clinician’s reasoning process while ignoring their internal thought processes and alignment with clinician preferences. Our work aims to build a medical dialogue system that aligns with clinicians’ diagnostic reasoning processes. We propose a novel framework, Emulation, designed to generate an appropriate response that relies on abductive and deductive diagnostic reasoning analyses and aligns with clinician preferences through thought process modeling. Experimental results on two datasets confirm the efficacy of Emulation. Crucially, our framework furnishes clear explanations for the generated responses, enhancing its transparency in medical consultations.