Scientific domain entity linking (EL) differs from general domain EL because mentions and entity names often lack lexical overlap. Another challenge is that specialized terminology is used in the scientific domain, which is rarely encountered in models pretrained on general domains. Therefore, models trained on general domains transfer poorly to scientific domains. To address this, in-domain fine-tuning is the natural remedy. However, many scientific domains lack expert-annotated data, motivating the need for a zero-human-annotation approach. Existing zero-shot methods heavily rely on LLMs to generate aliases across entire mention corpora, which incurs substantial computational cost, and those methods provide no mechanism to filter out noise from LLMs. To address these challenges, we propose Sci-ZSEL, a framework that selectively generates entity aliases with an LLM to control computational cost, and applies an ontology-aware filter to remove aliases that semantically drift toward ontology neighbors. Then, filtered aliases are used to construct pseudo-labeled mention-entity pairs for fine-tuning. To enable evaluation of EL under low lexical overlap, we also release a new animal science EL benchmark linked to three livestock trait ontologies, where mentions and entities exhibit substantially lower lexical overlap than in existing benchmarks. Across five benchmarks, Sci-ZSEL outperforms the non-fine-tuned baseline, is most useful on nonoverlapping mentions, and combining it with curated synonyms gives the best performance in most settings.
Entity linking is a key component of many downstream NLP systems, yet existing approaches are often tied to the specific target knowledge bases and domains, limiting their real world application. In this paper, we extend LELA, a modular and domain-agnostic LLM-based entity disambiguation method, into a practical Python library that integrates zero-shot Named Entity Recognition (NER) -thereby providing a complete end-toend pipeline for entity-linking in real-world usage. We provide experimental results validating LELA's performance and robustness across diverse entity linking settings. In our demo, users can play with the system on their own input texts.
Samy Haffoudhi, Nikola Dobričić, Fabian Suchanek +1
Cross-lingual biomedical entity linking (BEL) maps mentions in any language to unique identifiers in a biomedical knowledge base, supporting clinical and biomedical NLP applications. We identify two issues affecting current systems. First, the UMLS (Bodenreider,2004) aliases used to train cross-lingual BEL retrievers are heavily skewed toward English, so retrievers generalize poorly to non-English mentions. Second, although context is often necessary for disambiguation, naively injecting context into retrievers trained only to align aliases severely degrades retrieval. We propose BioELX, a retrieve-rerank framework that addresses both issues. For retrieval, we continue training SapBERT_multi (Liu et al., 2021b) using Wikidata-derived cross-lingual alias supervision, forming shared concept neighborhoods across languages. For reranking, we adapt pretrained LLM rerankers to entity linking through mention-anchored prompting, which marks the target mention so that rerankers score candidates with respect to the intended mention rather than other salient tokens in the context. Experiments show that BioELX achieves new state-of-the-art results on four cross-lingual BEL benchmarks, improving Recall@1 by 4.8 to 18.2 percentage points over prior best results, without any task-specific BEL annotations. Our code and resources are available at https://github.com/AI4MedCode/BioELX.
Scientific named entity recognition (SciNER) plays a crucial role in information extraction and knowledge discovery from scientific texts. Recently, large language models (LLMs) have demonstrated the capacity to achieve competitive SciNER performance with minimal human effort. Existing research highlights the importance of incorporating candidate entity type information for accurate entity recognition and classification by LLMs. However, when too many candidate entity types are provided in the prompt, LLMs struggle to accurately recognize and label entities in scientific texts, where entity types are more complex than in general domains. To address this challenge, we propose TdSciNER, a type-driven approach that effectively leverages entity type information to enhance SciNER performance. In TdSciNER, we first design an entity type filter model to identify the most likely entity types present in a given sentence. Subsequently, we introduce an auxiliary multi-class entity typing task within a multi-task learning framework alongside SciNER to obtain richer contextual representations. Then, we develop a novel demonstration selection strategy based on sentence similarity and entity type diversity to activate the in-context learning capabilities of LLMs, thereby improving entity recognition accuracy across diverse scientific domains. Experiments on three datasets demonstrate that our method achieves performance comparable to fully supervised models. Further analysis validates that each entity type-driven component in TdSciNER contributes to the improvement of SciNER performance. This work provides valuable insights for future advancements in SciNER and broader information extraction tasks in scientific text mining.