With the rise of knowledge graph based retrieval-augmented generation (RAG) techniques such as GraphRAG and Pike-RAG, the role of knowledge graphs in enhancing the reasoning capabilities of large language models (LLMs) has become increasingly prominent. However, traditional Knowledge Graph Construction (KGC) methods face challenges like complex entity disambiguation, rigid schema definition, and insufficient cross-document knowledge integration. This paper focuses on the task of automatic document-level knowledge graph construction. It proposes the Document-level Retrieval Augmented Knowledge Graph Construction (RAKG) framework. RAKG extracts pre-entities from text chunks and utilizes these pre-entities as queries for RAG, effectively addressing the issue of long-context forgetting in LLMs and reducing the complexity of Coreference Resolution. In contrast to conventional KGC methods, RAKG more effectively captures global information and the interconnections among disparate nodes, thereby enhancing the overall performance of the model. Additionally, we transfer the RAG evaluation framework to the KGC field and filter and evaluate the generated knowledge graphs, thereby avoiding incorrectly generated entities and relationships caused by hallucinations in LLMs. We further developed the MINE dataset by constructing standard knowledge graphs for each article and experimentally validated the performance of RAKG. The results show that RAKG achieves an accuracy of 95.91 % on the MINE dataset, a 6.2 % point improvement over the current best baseline, GraphRAG (89.71 %). The code is available at https://github.com/LMMApplication/RAKG.
We introduce FewTopNER, a novel framework that integrates few-shot named entity recognition (NER) with topic-aware contextual modeling to address the challenges of cross-lingual and low-resource scenarios. FewTopNER leverages a shared multilingual encoder based on XLM-RoBERTa, augmented with language-specific calibration mechanisms, to generate robust contextual embeddings. The architecture comprises a prototype-based entity recognition branch, employing BiLSTM and Conditional Random Fields for sequence labeling, and a topic modeling branch that extracts document-level semantic features through hybrid probabilistic and neural methods. A cross-task bridge facilitates dynamic bidirectional attention and feature fusion between entity and topic representations, thereby enhancing entity disambiguation by incorporating global semantic context. Empirical evaluations on multilingual benchmarks across English, French, Spanish, German, and Italian demonstrate that FewTopNER significantly outperforms existing state-of-the-art few-shot NER models. In particular, the framework achieves improvements of 2.5-4.0 percentage points in F1 score and exhibits enhanced topic coherence, as measured by normalized pointwise mutual information. Ablation studies further confirm the critical contributions of the shared encoder and cross-task integration mechanisms to the overall performance. These results underscore the efficacy of incorporating topic-aware context into few-shot NER and highlight the potential of FewTopNER for robust cross-lingual applications in low-resource settings.
Questions within surveys, called survey items, are used in the social sciences to study latent concepts, such as the factors influencing life satisfaction. Instead of using explicit citations, researchers paraphrase the content of the survey items they use in-text. However, this makes it challenging to find survey items of interest when comparing related work. Automatically parsing and linking these implicit mentions to survey items in a knowledge base can provide more fine-grained references. We model this task, called Survey Item Linking (SIL), in two stages: mention detection and entity disambiguation. Due to an imprecise definition of the task, existing datasets used for evaluating the performance for SIL are too small and of low-quality. We argue that latent concepts and survey item mentions should be differentiated. To this end, we create a high-quality and richly annotated dataset consisting of 20,454 English and German sentences. By benchmarking deep learning systems for each of the two stages independently and sequentially, we demonstrate that the task is feasible, but observe that errors propagate from the first stage, leading to a lower overall task performance. Moreover, mentions that require the context of multiple sentences are more challenging to identify for models in the first stage. Modeling the entire context of a document and combining the two stages into an end-to-end system could mitigate these problems in future work, and errors could additionally be reduced by collecting more diverse data and by improving the quality of the knowledge base. The data and code are available at https://github.com/e-tornike/SIL .
In the ever-evolving landscape of natural language processing and information retrieval, the need for robust and domain-specific entity linking algorithms has become increasingly apparent. It is crucial in a considerable number of fields such as humanities, technical writing and biomedical sciences to enrich texts with semantics and discover more knowledge. The use of Named Entity Disambiguation (NED) in such domains requires handling noisy texts, low resource settings and domain-specific KBs. Existing approaches are mostly inappropriate for such scenarios, as they either depend on training data or are not flexible enough to work with domain-specific KBs. Thus in this work, we present an unsupervised approach leveraging the concept of Group Steiner Trees (GST), which can identify the most relevant candidates for entity disambiguation using the contextual similarities across candidate entities for all the mentions present in a document. We outperform the state-of-the-art unsupervised methods by more than 40\% (in avg.) in terms of Precision@1 across various domain-specific datasets.
In the U.S. historically, local newspapers drew their content largely from newswires like the Associated Press. Historians argue that newswires played a pivotal role in creating a national identity and shared understanding of the world, but there is no comprehensive archive of the content sent over newswires. We reconstruct such an archive by applying a customized deep learning pipeline to hundreds of terabytes of raw image scans from thousands of local newspapers. The resulting dataset contains 2.7 million unique public domain U.S. newswire articles, written between 1878 and 1977. Locations in these articles are georeferenced, topics are tagged using customized neural topic classification, named entities are recognized, and individuals are disambiguated to Wikipedia using a novel entity disambiguation model. To construct the Newswire dataset, we first recognize newspaper layouts and transcribe around 138 millions structured article texts from raw image scans. We then use a customized neural bi-encoder model to de-duplicate reproduced articles, in the presence of considerable abridgement and noise, quantifying how widely each article was reproduced. A text classifier is used to ensure that we only include newswire articles, which historically are in the public domain. The structured data that accompany the texts provide rich information about the who (disambiguated individuals), what (topics), and where (georeferencing) of the news that millions of Americans read over the course of a century. We also include Library of Congress metadata information about the newspapers that ran the articles on their front pages. The Newswire dataset is useful both for large language modeling - expanding training data beyond what is available from modern web texts - and for studying a diversity of questions in computational linguistics, social science, and the digital humanities.
Extracting structured information from unstructured text is critical for many downstream NLP applications and is traditionally achieved by closed information extraction (cIE). However, existing approaches for cIE suffer from two limitations: (i) they are often pipelines which makes them prone to error propagation, and/or (ii) they are restricted to sentence level which prevents them from capturing long-range dependencies and results in expensive inference time. We address these limitations by proposing REXEL, a highly efficient and accurate model for the joint task of document level cIE (DocIE). REXEL performs mention detection, entity typing, entity disambiguation, coreference resolution and document-level relation classification in a single forward pass to yield facts fully linked to a reference knowledge graph. It is on average 11 times faster than competitive existing approaches in a similar setting and performs competitively both when optimised for any of the individual subtasks and a variety of combinations of different joint tasks, surpassing the baselines by an average of more than 6 F1 points. The combination of speed and accuracy makes REXEL an accurate cost-efficient system for extracting structured information at web-scale. We also release an extension of the DocRED dataset to enable benchmarking of future work on DocIE, which is available at https://github.com/amazon-science/e2e-docie.
Entity Linking in natural language processing seeks to match text entities to their corresponding entries in a dictionary or knowledge base. Traditional approaches rely on contextual models, which can be complex, hard to train, and have limited transferability across different domains. Generative large language models like GPT offer a promising alternative but often underperform with naive prompts. In this study, we introduce EntGPT, employing advanced prompt engineering to enhance EL tasks. Our three-step hard-prompting method (EntGPT-P) significantly boosts the micro-F_1 score by up to 36% over vanilla prompts, achieving competitive performance across 10 datasets without supervised fine-tuning. Additionally, our instruction tuning method (EntGPT-I) improves micro-F_1 scores by 2.1% on average in supervised EL tasks and outperforms several baseline models in six Question Answering tasks. Our methods are compatible with both open-source and proprietary LLMs. All data and code are available on GitHub at https://github.com/yifding/In_Context_EL.
A variety of knowledge graph embedding approaches have been developed. Most of them obtain embeddings by learning the structure of the knowledge graph within a link prediction setting. As a result, the embeddings reflect only the structure of a single knowledge graph, and embeddings for different knowledge graphs are not aligned, e.g., they cannot be used to find similar entities across knowledge graphs via nearest neighbor search. However, knowledge graph embedding applications such as entity disambiguation require a more global representation, i.e., a representation that is valid across multiple sources. We propose to learn universal knowledge graph embeddings from large-scale interlinked knowledge sources. To this end, we fuse large knowledge graphs based on the owl:sameAs relation such that every entity is represented by a unique identity. We instantiate our idea by computing universal embeddings based on DBpedia and Wikidata yielding embeddings for about 180 million entities, 15 thousand relations, and 1.2 billion triples. We believe our computed embeddings will support the emerging field of graph foundation models. Moreover, we develop a convenient API to provide embeddings as a service. Experiments on link prediction suggest that universal knowledge graph embeddings encode better semantics compared to embeddings computed on a single knowledge graph. For reproducibility purposes, we provide our source code and datasets open access.
Zero-shot entity linking (EL) aims at aligning entity mentions to unseen entities to challenge the generalization ability. Previous methods largely focus on the candidate retrieval stage and ignore the essential candidate ranking stage, which disambiguates among entities and makes the final linking prediction. In this paper, we propose a read-and-select (ReS) framework by modeling the main components of entity disambiguation, i.e., mention-entity matching and cross-entity comparison. First, for each candidate, the reading module leverages mention context to output mention-aware entity representations, enabling mention-entity matching. Then, in the selecting module, we frame the choice of candidates as a sequence labeling problem, and all candidate representations are fused together to enable cross-entity comparison. Our method achieves the state-of-the-art performance on the established zero-shot EL dataset ZESHEL with a 2.55% micro-average accuracy gain, with no need for laborious multi-phase pre-training used in most of the previous work, showing the effectiveness of both mention-entity and cross-entity interaction.
Despite their impressive performance, large language models (LMs) still struggle with reliably generating complex output structures when not finetuned to follow the required output format exactly. To address this issue, grammar-constrained decoding (GCD) can be used to control the generation of LMs, guaranteeing that the output follows a given structure. Most existing GCD methods are, however, limited to specific tasks, such as parsing or code generation. In this work, we demonstrate that formal grammars can describe the output space for a much wider range of tasks and argue that GCD can serve as a unified framework for structured NLP tasks in general. For increased flexibility, we introduce input-dependent grammars, which allow the grammar to depend on the input and thus enable the generation of different output structures for different inputs. We then empirically demonstrate the power and flexibility of GCD-enhanced LMs on (1) information extraction, (2) entity disambiguation, and (3) constituency parsing. Our results indicate that grammar-constrained LMs substantially outperform unconstrained LMs or even beat task-specific finetuned models. Grammar constraints thus hold great promise for harnessing off-the-shelf LMs for a wide range of structured NLP tasks, especially where training data is scarce or finetuning is expensive. Code and data: https://github.com/epfl-dlab/GCD.
Biomedical entity linking (EL) consists of named entity recognition (NER) and named entity disambiguation (NED). EL models are trained on corpora labeled by a predefined KB. However, it is a common scenario that only entities within a subset of the KB are precious to stakeholders. We name this scenario partial knowledge base inference: training an EL model with one KB and inferring on the part of it without further training. In this work, we give a detailed definition and evaluation procedures for this practically valuable but significantly understudied scenario and evaluate methods from three representative EL paradigms. We construct partial KB inference benchmarks and witness a catastrophic degradation in EL performance due to dramatically precision drop. Our findings reveal these EL paradigms can not correctly handle unlinkable mentions (NIL), so they are not robust to partial KB inference. We also propose two simple-and-effective redemption methods to combat the NIL issue with little computational overhead. Codes are released at https://github.com/Yuanhy1997/PartialKB-EL.
Name Entity Disambiguation is the Natural Language Processing task of identifying textual records corresponding to the same Named Entity, i.e. real-world entities represented as a list of attributes (names, places, organisations, etc.). In this work, we face the task of disambiguating companies on the basis of their written names. We propose a Siamese LSTM Network approach to extract -- via supervised learning -- an embedding of company name strings in a (relatively) low dimensional vector space and use this representation to identify pairs of company names that actually represent the same company (i.e. the same Entity). Given that the manual labelling of string pairs is a rather onerous task, we analyse how an Active Learning approach to prioritise the samples to be labelled leads to a more efficient overall learning pipeline. With empirical investigations, we show that our proposed Siamese Network outperforms several benchmark approaches based on standard string matching algorithms when enough labelled data are available. Moreover, we show that Active Learning prioritisation is indeed helpful when labelling resources are limited, and let the learning models reach the out-of-sample performance saturation with less labelled data with respect to standard (random) data labelling approaches.
Large pre-trained language models (PLMs) have been shown to retain implicit knowledge within their parameters. To enhance this implicit knowledge, we propose Knowledge Injection into Language Models (KILM), a novel approach that injects entity-related knowledge into encoder-decoder PLMs, via a generative knowledge infilling objective through continued pre-training. This is done without architectural modifications to the PLMs or adding additional parameters. Experimental results over a suite of knowledge-intensive tasks spanning numerous datasets show that KILM enables models to retain more knowledge and hallucinate less, while preserving their original performance on general NLU and NLG tasks. KILM also demonstrates improved zero-shot performances on tasks such as entity disambiguation, outperforming state-of-the-art models having 30x more parameters.
In our continuously evolving world, entities change over time and new, previously non-existing or unknown, entities appear. We study how this evolutionary scenario impacts the performance on a well established entity linking (EL) task. For that study, we introduce TempEL, an entity linking dataset that consists of time-stratified English Wikipedia snapshots from 2013 to 2022, from which we collect both anchor mentions of entities, and these target entities' descriptions. By capturing such temporal aspects, our newly introduced TempEL resource contrasts with currently existing entity linking datasets, which are composed of fixed mentions linked to a single static version of a target Knowledge Base (e.g., Wikipedia 2010 for CoNLL-AIDA). Indeed, for each of our collected temporal snapshots, TempEL contains links to entities that are continual, i.e., occur in all of the years, as well as completely new entities that appear for the first time at some point. Thus, we enable to quantify the performance of current state-of-the-art EL models for: (i) entities that are subject to changes over time in their Knowledge Base descriptions as well as their mentions' contexts, and (ii) newly created entities that were previously non-existing (e.g., at the time the EL model was trained). Our experimental results show that in terms of temporal performance degradation, (i) continual entities suffer a decrease of up to 3.1% EL accuracy, while (ii) for new entities this accuracy drop is up to 17.9%. This highlights the challenge of the introduced TempEL dataset and opens new research prospects in the area of time-evolving entity disambiguation.
Local models have recently attained astounding performances in Entity Disambiguation (ED), with generative and extractive formulations being the most promising research directions. However, previous works limited their studies to using, as the textual representation of each candidate, only its Wikipedia title. Although certainly effective, this strategy presents a few critical issues, especially when titles are not sufficiently informative or distinguishable from one another. In this paper, we address this limitation and investigate to what extent more expressive textual representations can mitigate it. We thoroughly evaluate our approach against standard benchmarks in ED and find extractive formulations to be particularly well-suited to these representations: we report a new state of the art on 2 out of 6 benchmarks we consider and strongly improve the generalization capability over unseen patterns. We release our code, data and model checkpoints at https://github.com/SapienzaNLP/extend.
We introduce ReFinED, an efficient end-to-end entity linking model which uses fine-grained entity types and entity descriptions to perform linking. The model performs mention detection, fine-grained entity typing, and entity disambiguation for all mentions within a document in a single forward pass, making it more than 60 times faster than competitive existing approaches. ReFinED also surpasses state-of-the-art performance on standard entity linking datasets by an average of 3.7 F1. The model is capable of generalising to large-scale knowledge bases such as Wikidata (which has 15 times more entities than Wikipedia) and of zero-shot entity linking. The combination of speed, accuracy and scale makes ReFinED an effective and cost-efficient system for extracting entities from web-scale datasets, for which the model has been successfully deployed. Our code and pre-trained models are available at https://github.com/alexa/ReFinED
The medical conversational system can relieve the burden of doctors and improve the efficiency of healthcare, especially during the pandemic. This paper presents a medical conversational question answering (CQA) system based on the multi-modal knowledge graph, namely "LingYi", which is designed as a pipeline framework to maintain high flexibility. Our system utilizes automated medical procedures including medical triage, consultation, image-text drug recommendation and record. To conduct knowledge-grounded dialogues with patients, we first construct a Chinese Medical Multi-Modal Knowledge Graph (CM3KG) and collect a large-scale Chinese Medical CQA (CMCQA) dataset. Compared with the other existing medical question-answering systems, our system adopts several state-of-the-art technologies including medical entity disambiguation and medical dialogue generation, which is more friendly to provide medical services to patients. In addition, we have open-sourced our codes which contain back-end models and front-end web pages at https://github.com/WENGSYX/LingYi. The datasets including CM3KG at https://github.com/WENGSYX/CM3KG and CMCQA at https://github.com/WENGSYX/CMCQA are also released to further promote future research.
Named entity disambiguation (NED), which involves mapping textual mentions to structured entities, is particularly challenging in the medical domain due to the presence of rare entities. Existing approaches are limited by the presence of coarse-grained structural resources in biomedical knowledge bases as well as the use of training datasets that provide low coverage over uncommon resources. In this work, we address these issues by proposing a cross-domain data integration method that transfers structural knowledge from a general text knowledge base to the medical domain. We utilize our integration scheme to augment structural resources and generate a large biomedical NED dataset for pretraining. Our pretrained model with injected structural knowledge achieves state-of-the-art performance on two benchmark medical NED datasets: MedMentions and BC5CDR. Furthermore, we improve disambiguation of rare entities by up to 57 accuracy points.
Generative approaches have been recently shown to be effective for both Entity Disambiguation and Entity Linking (i.e., joint mention detection and disambiguation). However, the previously proposed autoregressive formulation for EL suffers from i) high computational cost due to a complex (deep) decoder, ii) non-parallelizable decoding that scales with the source sequence length, and iii) the need for training on a large amount of data. In this work, we propose a very efficient approach that parallelizes autoregressive linking across all potential mentions and relies on a shallow and efficient decoder. Moreover, we augment the generative objective with an extra discriminative component, i.e., a correction term which lets us directly optimize the generator's ranking. When taken together, these techniques tackle all the above issues: our model is >70 times faster and more accurate than the previous generative method, outperforming state-of-the-art approaches on the standard English dataset AIDA-CoNLL. Source code available at https://github.com/nicola-decao/efficient-autoregressive-EL
Knowledge about software used in scientific investigations is important for several reasons, for instance, to enable an understanding of provenance and methods involved in data handling. However, software is usually not formally cited, but rather mentioned informally within the scholarly description of the investigation, raising the need for automatic information extraction and disambiguation. Given the lack of reliable ground truth data, we present SoMeSci (Software Mentions in Science) a gold standard knowledge graph of software mentions in scientific articles. It contains high quality annotations (IRR: $\kappa{=}.82$) of 3756 software mentions in 1367 PubMed Central articles. Besides the plain mention of the software, we also provide relation labels for additional information, such as the version, the developer, a URL or citations. Moreover, we distinguish between different types, such as application, plugin or programming environment, as well as different types of mentions, such as usage or creation. To the best of our knowledge, SoMeSci is the most comprehensive corpus about software mentions in scientific articles, providing training samples for Named Entity Recognition, Relation Extraction, Entity Disambiguation, and Entity Linking. Finally, we sketch potential use cases and provide baseline results.