A Frustratingly Easy Approach for Entity and Relation Extraction

Named entity recognition and relation extraction are two important core subtasks of information extraction, which aim to identify named entities and extract relations between them. In recent years, span representation methods have received a lot of attention and are widely used to extract entities and corresponding relations from plain texts. Most recent works focus on how to obtain better span representations from pre-trained encoders, but ignore the negative impact of a large number of span candidates on slowing down the model performance. In our work, we propose a joint entity and relation extraction model with an attention mechanism and position-attentive markers. The attention score of each candidate span is calculated, and most of the candidate spans with low attention scores are pruned before being fed into the span classifier, thus achieving the goal of removing the most irrelevant spans. At the same time, in order to explore whether the position information can improve the performance of the model, we add position-attentive markers to the model. The experimental results show that our model is effective. With the same pre-trained encoder, our model achieves the new state-of-the-art on standard benchmarks (ACE05, CoNLL04 and SciERC), obtaining a 4.7%-17.8% absolute improvement in relation F1.

Biomedical relation extraction from scientific publications is a key task in biomedical natural language processing (NLP) and can facilitate the creation of large knowledge bases, enable more efficient knowledge discovery, and accelerate evidence synthesis. In this paper, building upon our previous effort in the BioCreative VIII BioRED Track, we propose an enhanced end-to-end pipeline approach for biomedical relation extraction (RE) and novelty detection (ND) that effectively leverages existing datasets and integrates state-of-the-art deep learning methods. Our pipeline consists of four tasks performed sequentially: named entity recognition (NER), entity linking (EL), RE, and ND. We trained models using the BioRED benchmark corpus that was the basis of the shared task. We explored several methods for each task and combinations thereof: for NER, we compared a BERT-based sequence labeling model that uses the BIO scheme with a span classification model. For EL, we trained a convolutional neural network model for diseases and chemicals and used an existing tool, PubTator 3.0, for mapping other entity types. For RE and ND, we adapted the BERT-based, sentence-bound PURE model to bidirectional and document-level extraction. We also performed extensive hyperparameter tuning to improve model performance. We obtained our best performance using BERT-based models for NER, RE, and ND, and the hybrid approach for EL. Our enhanced and optimized pipeline showed substantial improvement compared to our shared task submission, NER: 93.53 (+3.09), EL: 83.87 (+9.73), RE: 46.18 (+15.67), and ND: 38.86 (+14.9). While the performances of the NER and EL models are reasonably high, RE and ND tasks remain challenging at the document level. Further enhancements to the dataset could enable more accurate and useful models for practical use. We provide our models and code at https://github.com/janinaj/e2eBioMedRE/. Database URL: https://github.com/janinaj/e2eBioMedRE/.

Understanding the biology underpinning the natural regeneration of plant species in order to make plans for effective reforestation is a complex task. This can be aided by providing access to databases that contain long-term and wide-scale geographical information on species distribution, habitat, and reproduction. Although there exists widely-used biodiversity databases that contain structured information on species and their occurrences, such as the Global Biodiversity Information Facility (GBIF) and the Atlas of Living Australia (ALA), the bulk of knowledge about biodiversity still remains embedded in textual documents. Unstructured information can be made more accessible and useful for large-scale studies if there are tools and services that automatically extract meaningful information from text and store it in structured formats, e.g., open biodiversity databases, ready to be consumed for analysis (Thessen et al. 2022). We aim to enrich biodiversity occurrence databases with information on species reproductive condition and habitat, derived from text. In previous work, we developed unsupervised approaches to extract related habitats and their locations, and related reproductive condition and temporal expressions (Gabud and Batista-Navarro 2018). We built a new unsupervised hybrid approach for relation extraction (RE), which is a combination of classical rule-based pattern-matching methods and transformer-based language models that framed our RE task as a natural language inference (NLI) task. Using our hybrid approach for RE, we were able to extract related biodiversity entities from text even without a large training dataset. In this work, we implement an information extraction (IE) pipeline comprised of a named entity recognition (NER) tool and our hybrid relation extraction (RE) tool. The NER tool is a transformer-based language model that was pretrained on scientific text and then fine-tuned using COPIOUS (Conserving Philippine Biodiversity by Understanding big data; Nguyen et al. 2019), a gold standard corpus containing named entities relevant to species occurrence. We applied the NER tool to automatically annotate geographical location, temporal expression and habitat information contained within sentences. A dictionary-based approach is then used to identify mentions of reproductive conditions in text (e.g., phrases such as "fruited heavily" and "mass flowering"). We then use our hybrid RE tool to extract reproductive condition - temporal expression and habitat - geographical location entity pairs. We test our IE pipeline on the forestry compendium available in the CABI Digital Library (Centre for Agricultural and Biosciences International), and show that our work enables the enrichment of descriptive information on reproductive and habitat conditions of species. This work is a step towards enhancing a biodiversity database with the inclusion of habitat and reproductive condition information extracted from text.

We present an end-to-end joint entity and relation extraction approach based on transformer-based language models. We apply the model to the task of linking mathematical symbols to their descriptions in LaTeX documents. In contrast to existing approaches, which perform entity and relation extraction in sequence, our system incorporates information from relation extraction into entity extraction. This means that the system can be trained even on data sets where only a subset of all valid entity spans is annotated.

Document-level relation extraction (DocRE) aims to extract relations among entities within a document, which is crucial for applications like knowledge graph construction. Existing methods usually assume that entities and their mentions are identified beforehand, which falls short of real-world applications. To overcome this limitation, we propose TaG, a novel table-to-graph generation model for joint extractionof entities and relations at document-level. To enhance the learning of task dependencies, TaG induces a latent graph among mentions, with different types of edges indicating different task information, which is further broadcast with a relational graph convolutional network. To alleviate the error propagation problem, we adapt the hierarchical agglomerative clustering algorithm to back-propagate task information at decoding stage. Experiments on the benchmark dataset, DocRED, demonstrate that TaG surpasses previous methods by a large margin and achieves state-of-the-art results.

A region-based hypergraph network for joint entity-relation extraction

Recent entity and relation extraction works focus on investigating how to obtain a better span representation from the pre-trained encoder. However, a major limitation of existing works is that they ignore the interrelation between spans (pairs). In this work, we propose a novel span representation approach, named Packed Levitated Markers (PL-Marker), to consider the interrelation between the spans (pairs) by strategically packing the markers in the encoder. In particular, we propose a neighborhood-oriented packing strategy, which considers the neighbor spans integrally to better model the entity boundary information. Furthermore, for those more complicated span pair classification tasks, we design a subject-oriented packing strategy, which packs each subject and all its objects to model the interrelation between the same-subject span pairs. The experimental results show that, with the enhanced marker feature, our model advances baselines on six NER benchmarks, and obtains a 4.1%-4.3% strict relation F1 improvement with higher speed over previous state-of-the-art models on ACE04 and ACE05.

This paper presents our algorithmic approach for information and relation extraction from unstructured texts (such as from eBook sections or webpages), performing other useful analytics on the text, and automatically generating a semantically meaningful structure (RDF schema). Our algorithmic formulation parses the unstructured text from eBooks and identifies key concepts described in the eBook along with relationship between the concepts. The extracted information is then used for four purposes: (a) for generating some computed metadata about the text source (such as readability of an eBook), (b) generate a concept profile for each distinct part of text, (c) identifying and plotting relationship between key concepts described in the text, and (d) to generate RDF representation for the text source. We have done our experiments on eBook texts from Computer Science domain; however, the approach can be applied to work on different forms of text in other domains as well. The results are not only useful for concept based tagging and navigation of unstructured text documents (such as eBook) but can also be used to design a comprehensive and sophisticated learning recommendation system.

The automatic extraction of relations from unstructured natural text is challenging but offers practical solutions for many problems like automatic text understanding and semantic retrieval. Relation extraction can be formulated as a classification problem using support vector machines and kernels for structured data that may include parse trees to account for syntactic structure. In this paper we present new tree kernels over dependency parse trees automatically generated from natural language text. Experiments on a public benchmark data set show that our kernels with richer structural features significantly outperform all published approaches for kernel-based relation extraction from dependency trees. In addition we optimize kernel computations to improve the actual runtime compared to previous solutions.KeywordsParse TreeRelation ExtractionRelation ArgumentFrequent Itemset MiningNatural Language TextThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Boundary assembling method for joint entity and relation extraction

State-of-the-art NLP models can adopt shallow heuristics that limit their generalization capability (McCoy et al., 2019). Such heuristics include lexical overlap with the training set in Named-Entity Recognition (Taillé et al., 2020) and Event or Type heuristics in Relation Extraction (Rosenman et al., 2020). In the more realistic end-to-end RE setting, we can expect yet another heuristic: the mere retention of training relation triples. In this work, we propose several experiments confirming that retention of known facts is a key factor of performance on standard benchmarks. Furthermore, our behavioral testing experiment suggests that a pipeline model able to use intermediate type representations is less prone to over-rely on retention.

To optimize in-context learning in biomedical natural language processing by improving example selection. We introduce a novel multi-mode retrieval-augmented generation (MMRAG) framework, which integrates 4 retrieval strategies: (1) Random Mode, selecting examples arbitrarily; (2) Top Mode, retrieving the most relevant examples based on similarity; (3) Diversity Mode, ensuring variation in selected examples; and (4) Class Mode, selecting category-representative examples. This study evaluates MMRAG on 3 core biomedical NLP tasks: Named Entity Recognition (NER), Relation Extraction (RE), and Text Classification (TC). The datasets used include BC2GM for gene and protein mention recognition (NER), DDI for drug-drug interaction extraction (RE), GIT for general biomedical information extraction (RE), and HealthAdvice for health-related text classification (TC). The framework is tested with 2 large language models (Llama-2-7B and Llama-3-8B) and 3 retrievers (Contriever, MedCPT, and BGE-Large) to assess performance across different retrieval strategies. The results from the Random Mode indicate that providing more examples in the prompt improves the model's generation performance. Meanwhile, Top Mode and Diversity Mode significantly outperform Random Mode on the RE (DDI) task, achieving an F1 score of 0.9669-a 26.4% improvement. Among the 3 retrievers tested, Contriever outperformed the other 2 in a greater number of experiments. Additionally, Llama 2 and Llama 3 demonstrated varying capabilities across different tasks, with Llama 3 showing a clear advantage in handling NER tasks. MMRAG effectively enhances biomedical in-context learning by refining example selection, mitigating data scarcity issues, and demonstrating superior adaptability for NLP-driven healthcare applications.

Two evaluations on Ontology-style relation annotations

The paper describes a methodology for bootstrapping relation extraction from unstructured text in the context of GATE, but also applied to the KIM semantic annotation platform. The focus is on identifying a set of relations between entities previously found by named entity recognizer. The methodology is developed and applied to three kinds of relations and evaluated both with the ANNIE system and the default information extraction module of KIM. The methodology covers the problem of identifying the task, the target domain, the development of training and testing corpora, and useful lexical resources, the choice of a particular relation extraction approach. The application of information extraction for the Semantic Web also brings a new interesting dimension of not merely recognizing the entity type, but going into instantiation of entity references and linking them to an entity instance in a semantic repository.KeywordsRelation Information ExtractionSemantic WebMethodology

Distant Supervision is a relation extraction approach that allows automatic labeling of a dataset. However, this labeling introduces noise in the labels (e.g., when two entities in a sentence are automatically labeled with an invalid relation). Noise in labels makes difficult the relation extraction task. This noise is precisely one of the main challenges of this task. Until now, the methods that incorporate a previous noise reduction step do not evaluate the performance of this step. This paper evaluates the noise reduction using a new representation obtained with autoencoders. In addition, it was incoporated more information to the input of the autoencoder proposed in the state-of-the-art to improve the representation over which the noise is reduced. Also, three methods were proposed to select the instances considered as real. As a result, it was obtained the highest values of the area under the ROC curves using the improved input combined with state-of-the-art anomaly detection methods. Moreover, the three proposed selection methods significantly improve the existing method in the literature.KeywordsNoise reductionDistant supervisionAdversarial autoencodersData representation