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.
GNN-based Knowledge Graph Question Answering (KGQA) pipelines process queries through four discrete stages: entity linking, subgraph retrieval, GNN reasoning, and answer generation. Standard robustness evaluations conflate stage-level failures into a single end-to-end metric, obscuring both the source of brittleness and the appropriate mitigation target. We ask which stage fails, and why, when the pipeline is subjected to adversarial perturbations on the input question. We introduce a stage-isolation protocol with two answer-preserving adversarial perturbations verified against the knowledge graph: Compositional Restructuring (CR) and Relation Synonym Swap (RS) target distinct stages while leaving entity seeds intact. Evaluated across ComplexWebQuestions and WebQSP, the results run counter to prevailing assumptions: the GNN reasoning stage retains near-baseline accuracy when the subgraph is intact, while subgraph construction accounts for over 99\% of the end-to-end collapse under CR, occurring even when the gold answer is present in 74\% of retrieved subgraphs. This exposes a fundamental distinction between answer presence and answer reachability that end-to-end metrics cannot detect, and places the mitigation target firmly at the subgraph construction stage rather than the reasoning model. Perturbed datasets and evaluation infrastructure are released at https://anonymous.4open.science/r/atkgrag-E85C .
The FAIR Digital Object (FDO) framework mandates that metadata attribute values be expressed as persistent identifiers (PIDs) wherever possible, to produce a fully machine-actionable graph in which every reference is resolvable. The Europeana Data Model was designed long before the FDO specification, and it stores most metadata values as plain text. This serves human browsing well enough, but gives an automated agent nothing to follow across records or collections. We present a pipeline that transforms flat Europeana records into an FDO-compliant knowledge graph structured with CIDOC-CRM. Following the FDO specification, we model every heritage entity as a discrete FDO with its own PID, type, profile, and metadata layer. The core technical challenge is automating the FDO-prescribed distinction between values that must become PID references (resolvable entities) and those that may remain literals (terminal leaves such as notes, measurements, and dates). We address this with a large language model that classifies each metadata value, routes it to a controlled vocabulary (Getty AAT, Wikidata, VIAF, PeriodO), and links it to a shared entity FDO. We evaluate using 637 archaeological records from five Europeana providers, processing each with the LLM. The pipeline links 86% of metadata slots, resolving 58.5% of values Europeana had not already enriched. It also merges cross-lingual surface forms that byte-identical matching keeps apart, where 17 of 33 such merges are correct on manual review. Graph connectivity does not separate this from string matching; what distinguishes the FDO graph is that every node is typed and resolvable.
Biomedical entity linking grounds mentions in clinical and scientific text to entities in a curated knowledge base (KB) with ontological structure, which supports downstream applications such as literature-scale information extraction and patient-record normalization. The task has several challenges at once: the KB contains large numbers of entities, mentions are often ambiguous, and gold labels follow annotation conventions specific to each corpus. To address these challenges, we propose PILOT, a three-stage framework made up of neighborhood-aware retrieval, dual reranking, and score fusion. The retriever injects ontological structure from both the query and KB side, by reformulating mentions and pooling entity embeddings. The retrieved pool is then scored from two complementary views, one over surface forms and one over context, and fused together. PILOT achieves the state of the art on average across five widely-used benchmarks and remains efficient at inference.
Entity linking in tables matches short and ambiguous cell mentions to their corresponding knowledge-base entities. Existing approaches typically rely on data preprocessing pipelines that retain either compact or extensive table content as contextual evidence, and then formulate entity linking as a language generation task for instruction-tuned models; recent systems further incorporate explicit reasoning to disambiguate challenging mentions. However, their training supervision is usually static: fixed preference data cannot adapt to the residual errors of an evolving model, while variations in reasoning length can bias sequence-level preference learning. To address these limitations, we present TELLER: Table Entity Linking through Learning from Errors and Reasoning. We first retrieve and rank Wikidata candidates and retain reduced table evidence in the prompt. The direct-answer path applies iterative direct preference optimization and refreshes its preference data with residual errors from the updated model. The reasoning path uses filtered and compressed chain-of-thought rationales for supervised fine-tuning, followed by our iterative length-normalized regularized preference optimization. On the TableInstruct entity-linking subset, the direct-answer path improves accuracy from 94.35\% to 94.50\%; on the MammoTab V2 evaluation set, it improves accuracy from 87.59\% to 88.20\%. The reasoning path improves accuracy from 92.90\% to 92.95\% on TableInstruct and from 79.09\% to 81.85\% on MammoTab V2, while maintaining high rates of complete reasoning generation. These results show that iterative preference learning benefits both concise entity prediction and explicit reasoning.
Ting Cai, Rakesh R. Menon, Yiru Chen +8cs.CL cs.AI cs.DB
Generating accurate and informative column descriptions (e.g. "membership status of customers" for the column name "cust_mem") is essential for a wide range of downstream NLP tasks on tabular data, including NL2SQL, table question answering, and entity linking. This problem arises in enterprises, domain sciences, government data portals, and so on. Despite its importance, most real-world datasets suffer from missing or cryptic documentation, often due to abbreviated column names or domain-specific jargon. Existing approaches largely rely on single-prompt large language models (LLMs), which struggle with three key issues: (i) inconsistent or incorrect handling of abbreviations, (ii) hallucinated or incomplete descriptions, and (iii) redundancy or vagueness that hinders downstream performance. We present TACO, a task-aware framework for automatic column description generation using LLMs. TACO introduces a three-step pipeline: (1) abbreviation expansion, which standardizes column names; (2) description generation, which produces initial semantic descriptions enriched with synonyms and search-oriented keywords; and (3) description revision, which refines these outputs using simulated downstream tasks. In addition, we investigate human-in-the-loop extensions and release new evaluation datasets for entity linking and schema enrichment. Extensive experiments across public and proprietary datasets show that TACO consistently outperforms existing methods, improving downstream task performance by up to 32%.
Linking FDA-approved medical devices to their underlying United States Patent and Trademark Office (USPTO) patents enables critical applications such as recall root-cause analysis, M&A-driven IP discovery, and technology trajectory mapping. However, this cross-domain entity linking task remains unexplored due to severe *semantic gaps*: FDA documents focus on clinical outcomes, while patents describe technical mechanisms, yielding minimal lexical overlap. We formalize medical device-patent linking as a challenging cross-domain entity linking problem characterized by label scarcity and domain shifts. Using cardiovascular devices as a high-impact, representative domain featuring diverse technologies, high recall rates, and abundant disclosures, we construct a benchmark with 434 devices, 698K patents, and 585 high-fidelity expert-verified pairs. To address these challenges, we propose Bridge-MedDevKG, a coarse-to-fine framework that integrates (1) **MedDevOnto**, a domain-specific ontology that anchors device concepts via three-tier UMLS normalization; (2) **Multi-signal candidate generation** fusing company affiliation, semantic similarity, and ontology-weighted entity overlap; and (3) **Heterogeneous reranking** with multi-signal scoring and XGBoost classification on hard negatives. Our approach achieves a conservative lower-bound recall of 91.6% on the gold standard with 50.9% noise reduction, substantially outperforming LLM baselines under comparable evaluation. The resulting MedDevKG provides 6.8M high-confidence links, laying a scalable foundation for regulatory-IP integration across medical specialties.
Darya Shlyk, Stefano Montanelli, Lawrence Huntercs.CL cs.AI cs.IR
Despite recent progress, Biomedical Entity Linking (BEL) with large language models (LLMs) remains computationally inefficient and challenging to deploy in practical settings. In this work, we demonstrate that instruction-tuning of open-source generative models can offer an effective solution when applied at the re-ranking stage of the BEL pipeline. We propose a set-wise instruction-tuning formulation that enables fast and accurate candidate selection. Our method demonstrates strong performance on multiple BEL benchmarks, yielding significant improvements in linking accuracy (3%-24%) while reducing inference time compared to the state-of-the-art. We integrate our generative re-ranker into BeLink, a modular, end-to-end system designed for practical real-world BEL applications.
Albin Andersson, Salam Jonasson, Fredrik Wastring +1cs.CL
The digitization of old encyclopedias represents an important step to improve access to historically structured knowledge. Often, however, this process does not go beyond an optical character recognition, leaving all the underlying structure unexploited. In addition, many encyclopedias had multiple editions reflecting the evolution of knowledge. The lack of structure in the raw text makes it difficult to track changes across these editions. In this work, we built a pipeline to restore the text structure, where we extract the headwords and identify entries; categorize the entities; match entries across editions; and link entries to a Wikidata item. We applied this pipeline to the four major editions of \textit{Nordisk familjebok}, an authoritative Swedish encyclopedia published between 1876 and 1951. We could extract the headwords with an F1 score of 97.8\% and we obtained an F1 score of 93.4\% on the headword classification. On a small-scale evaluation, we reached a 93\% precision on the cross-edition matching, 85\% precision and 16.5\% recall on the Wikidata linking. This shows that an automated approach to digitized historical knowledge is possible. This should facilitate the preservation of general knowledge and the understanding of knowledge transmission. The datasets and programs are available online.