arXiv:2508.01643cs.IRcs.CL2025-08被引 3

专为化学文献检索优化的嵌入模型,显著提升搜索准确性。

ChEmbed: Enhancing Chemical Literature Search Through Domain-Specific Text Embeddings

  • 用化学语料微调,融合合成查询对与专用分词器。
  • 在新基准上将nDCG@10从0.82提升至0.91,增益9个百分点。
  • 适合需要高精度化学文献检索的研究者与RAG系统开发者。

化学领域的检索增强生成(RAG)系统高度依赖准确的文献检索,但通用文本嵌入模型难以有效表示复杂的化学术语,导致检索质量不佳。目前尚无专门针对化学文献检索的嵌入模型,性能差距明显。为此,我们提出ChEmbed,一个基于PubChem、Semantic Scholar和ChemRxiv语料库中化学文本微调的领域适配嵌入模型家族。通过大语言模型合成生成约170万条高质量查询-段落对构建训练数据,并在分词器中新增900个化学专用标记,显著减少如IUPAC命名等化学实体的碎片化。ChEmbed保持8192令牌上下文长度,相比多数开源模型(通常为512或2048),更高效支持长段落检索。在新提出的ChemRxiv Retrieval基准测试中,ChEmbed超越现有最优通用嵌入模型,nDCG@10从0.82提升至0.91(+9个百分点)。ChEmbed是一种实用、轻量且可复现的嵌入解决方案,有效提升了化学文献检索性能。

原文摘要 · Abstract (English)

Retrieval-Augmented Generation (RAG) systems in chemistry heavily depend on accurate and relevant retrieval of chemical literature. However, general-purpose text embedding models frequently fail to adequately represent complex chemical terminologies, resulting in suboptimal retrieval quality. Specialized embedding models tailored to chemical literature retrieval have not yet been developed, leaving a substantial performance gap. To address this challenge, we introduce ChEmbed, a domain-adapted family of text embedding models fine-tuned on a dataset comprising chemistry-specific text from the PubChem, Semantic Scholar, and ChemRxiv corpora. To create effective training data, we employ large language models to synthetically generate queries, resulting in approximately 1.7 million high-quality query-passage pairs. Additionally, we augment the tokenizer by adding 900 chemically specialized tokens to previously unused slots, which significantly reduces the fragmentation of chemical entities, such as IUPAC names. ChEmbed also maintains a 8192-token context length, enabling the efficient retrieval of longer passages compared to many other open-source embedding models, which typically have a context length of 512 or 2048 tokens. Evaluated on our newly introduced ChemRxiv Retrieval benchmark, ChEmbed outperforms state-of-the-art general embedding models, raising nDCG@10 from 0.82 to 0.91 (+9 pp). ChEmbed represents a practical, lightweight, and reproducible embedding solution that effectively improves retrieval for chemical literature search.

化学信息学文本嵌入文献检索RAG

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