Entity Linking

Public software repositories, like GitHub and Software Heritage Archive, store billions of files, yet extracting their implicit engineering knowledge ---i.e., the algorithms they implement, the paradigms they follow, the patterns they instantiate, and the application domains they serve--- remains challenging, as current tools are constrained to syntactic and token-level analysis. We present a pipeline for building an open-taxonomy semantic annotation of source code using a code-specialised Large Language Model. The extracted entities are grounded in Wikidata through a three-stage linking procedure: a deterministic SPARQL stage handles unambiguous entities, a Deep Research Agent resolves the residual long tail, and a hierarchy-rollup stage imports the parent-of closure of each resolved Wikidata identifier. The resulting annotations are materialised as a source-code-specific open-taxonomy knowledge graph. We further introduce a calibrated quality-assurance protocol that quantifies annotation precision by combining a small human gold set with an LLM-as-a-judge filter. We applied our pipeline to the 167 million files of the Stack-Edu corpus, creating the first known large-scale open-taxonomy knowledge graph for source code. Our graph, named CodeGraph, contains approximately 158 million nodes, which include around 145 million files, about 63,000 extracted concept entities (such as algorithms, paradigms, design patterns, and application domains), and roughly 19,800 grounded Wikidata entities. Furthermore, CodeGraph features approximately 1 billion typed edges that connect files to their respective concepts, link these concepts to their grounded Wikidata identifiers, and relate them to their parent categories, covering 14 programming languages.

Biomedical Entity Linking disambiguates mentions to entities in a knowledge base (KB), making it the cornerstone of information extraction pipelines. While embedding-based models are a popular approach for the task, they suffer from a key limitation. They compress mentions (and entities) into a single vector, forcing the model to average away crucial fine-grained differences. We present BELXTR, a novel embedding model based on the multi-vector (a.k.a. late interaction) architecture, which allows to leverage token-level matching information. BELXTR extends the original XTR model to biomedical entity linking by integrating an existing task-specific training objective and exploring active query expansion. Experiments across ten corpora and five KBs show that BELXTR improves upon current state-of-the-art in half of the corpora with an average improvement of 5pp recall@1. The largest gains are reported on the challenging cross-species gene disambiguation subtask, where BELXTR outperforms an LLM-powered retrieve-and-rerank pipeline and closely approaches a specialized rule-based system. Our results highlight multi-vector models as a practical alternative to hard-to-maintain rule-based systems or in scenarios where LLM-based reranking is too costly as in PubMed-scale mining. The code to reproduce our experiments can be found at: https://github.com/sg-wbi/belxtr.

Multimodal entity linking grounds entity mentions in text and images to knowledge-base entries. These systems degrade on rare entities, but prior work measures rarity primarily through popularity-based metrics such as pageviews. We broaden this view using knowledge-graph structural metrics that capture how well an entity is documented and connected. These metrics identify many rare entities that popularity metrics miss. Across the resulting rare-entity slices, state-of-the-art accuracy drops by 15.4-39.9%, showing that different rarity definitions expose different failure modes. To address these failures, we introduce a simple, training-free framework in which a reasoning-capable vision-language model iteratively searches and reasons over Wikipedia, gathering evidence dynamically. Controlled experiments show that reasoning and retrieval are complementary. Reasoning alone does not significantly improve accuracy on rare entities. Retrieval without reasoning improves rare-entity accuracy but can hurt overall accuracy. Their combination performs best. On MERLIN, a multilingual multimodal entity linking benchmark over five languages (Hindi, Indonesian, Japanese, Tamil, Vietnamese), our best system improves over the state of the art by 6.9% overall and by up to 23.3% on rare-entity slices. We release MERLIN-Rare, rare-entity test slices for targeted evaluation, with our framework.

The exponential growth of scientific publications calls for automatic Information Extraction (IE) systems to support knowledge discovery. In this context, the GutBrainIE benchmark evaluates Named Entity Recognition (NER), Named Entity Recognition and Disambiguation (NERD), and Relation Extraction (RE) systems in the gut-brain axis domain. We propose Two-stage Workflow for Information eXtraction (TWIX), an end-to-end IE pipeline featuring three interconnected modules, each leveraging a two-stage framework to solve all four GutBrainIE subtasks. Evaluation on the development and test sets shows that our method substantially outperforms the baseline by a wide margin, while also ranking first among all participant submissions across all subtasks. These results indicate that the proposed two-stage pipeline effectively improves both precision and recall in practical settings.

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.

Whether political elites organise into rent-seeking coalitions that capture public resources or civic networks that sustain governance is a central question in comparative politics. Yet observing these complex, informal, and adversarial ties at scale has historically required intensive manual coding, while automated text-as-data methods have largely been limited to simple co-occurrence. Recent large language model (LLM) approaches offer a path forward but often rely on proprietary APIs, lack cross-lingual capability, and struggle with scalable entity resolution. We present a modular, fully open-weight pipeline for multilingual joint entity-relation extraction that builds signed, temporal knowledge graphs from massive unstructured news corpora. It combines span-based named-entity recognition (NER) with a three-stage linking cascade mapping mentions to language-independent Wikidata identifiers; a high-throughput, ontology-constrained mixture-of-experts model then uses guided decoding to extract directed, signed relationships grounded in a domain ontology. A full-coverage spot-check against a 3491-relation gold standard shows high textual correctness (68.2% strict to 93.7% lenient). Two large-scale case studies validate the pipeline against the public record. In Austria, it reconstructs a political party's complete lifecycle, dating internal fractures and tracking personnel into successor factions and court convictions. In a Polish corpus, it uncovers the overlapping economic and governance networks of state-enterprise patronage, alongside the structurally balanced, signed conflict network of the polarized Civic Platform (Platforma Obywatelska, PO)--Law and Justice (Prawo i Sprawiedliwość, PiS) duopoly. By bridging raw multilingual text and structured relational data, our framework provides a robust, replicable foundation for cross-national empirical computational social science.

Dominant approaches to Knowledge Base Question Answering (KBQA) fall into two categories. First is the generation of a formal query that suffers from brittleness and limited explainability, and the second is direct answer retrieval through KB exploration that is computationally costly and prone to hallucination. To combine the strengths of both paradigms while mitigating their respective weaknesses, we introduce DeSQ (Decomposition-based SPARQL Query Generation), a KB-agnostic framework that operates in three stages. First, it decomposes complex questions into Atomic Constraints (ACs) that mirror the relational structure of the underlying KB. Second, it generates a two-part structured output: (a) Mapping of each AC to its corresponding SPARQL Fragment, using standardized variable and URIs placeholders, and (b) URIs Grounding block describing each placeholder. Third, it assembles these fragments into a complete SPARQL query. DeSQ surpasses state-of-the-art approaches on four out of five major benchmarks and demonstrates superior robustness to lexical variation. Beyond performance gains, our framework greatly simplifies evaluation by eliminating the need for a live KB endpoint, and its structured output enables fine-grained error analysis, allowing more targeted interventions for improvement.

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.

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.

Biomedical entity linking maps textual mentions to concepts in structured knowledge bases such as UMLS or SNOMED CT. Most existing systems link each mention independently, using only the mention or its surrounding sentence. This ignores dependencies between mentions in the same document and can lead to inconsistent predictions, especially when the same concept appears under different surface forms. We introduce LongBEL, a document-level generative framework that combines full-document context with a memory of previous predictions. To make this memory robust, LongBEL is trained with cross-validated predictions rather than gold labels, reducing the mismatch between training and inference and limiting cascading errors. Experiments on five biomedical benchmarks across English, French, and Spanish show that LongBEL improves over sentence-level generative baselines, with the largest gains on datasets where concepts frequently recur within documents. An ensemble of local, global, and memory-based variants achieves the best results across all benchmarks. Further analysis shows that the largest gains occur on recurring concepts, suggesting that LongBEL mainly improves document-level consistency rather than isolated mention disambiguation.

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.

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.

Associating user search queries with the correct brand entity is critical for e-commerce product retrieval, yet remains challenging due to the brevity of queries (three to four words on average), their lack of grammatical structure, and a catalog of hundreds of thousands of distinct brands. We formulate this as a brand entity linking task and develop two complementary solutions deployed at scale: (1) a cascaded pipeline that first detects brand mentions via sequence labeling and then disambiguates against a brand knowledge base, and (2) a single-stage approach that frames linking as extreme multiclass classification, directly mapping queries to brand identifiers. Through extensive multilingual evaluation (11 languages) and a controlled online experiment, we demonstrate that the proposed methods substantially improve brand recall while maintaining high precision, leading to measurable gains in customer engagement.

Large language models (LLMs) have recently shown promise for historical entity linking, but preference optimization for this task is often formulated with only one negative candidate per training instance. This discards information from the remaining candidates retrieved for the same mention. We introduce multi-negative direct preference optimisation (MDPO), a reference-based pairwise objective that compares the correct entity with all valid rejected candidates associated with each mention. MDPO preserves the Bradley-Terry formulation of DPO while exploiting the complete candidate set through masked, length-normalised sequence scores. We evaluate MDPO on hipe-2020 and newseye, covering French, German, English, Swedish, and Finnish historical newspaper text. Experiments show that MDPO improves over supervised fine-tuning and single-negative DPO, with particularly strong gains for NIL mentions, semantic ambiguity, OCR noise, and historically difficult names. Further analyses disentangle candidate-generation and selection errors, showing that candidate retrieval remains a key bottleneck for end-to-end entity linking. These results demonstrate that incorporating all within-instance negative candidates is a simple and effective improvement for LLM-based historical entity linking.