REET: Joint Relation Extraction and Entity Typing via Multi-task Learning

BackgroundSocial media platforms constitute a rich data source for natural language processing tasks such as named entity recognition, relation extraction, and sentiment analysis. In particular, social media platforms about health provide a different insight into patient’s experiences with diseases and treatment than those found in the scientific literature.ObjectiveThis paper aimed to report a study of entities related to chronic diseases and their relation in user-generated text posts. The major focus of our research is the study of biomedical entities found in health social media platforms and their relations and the way people suffering from chronic diseases express themselves.MethodsWe collected a corpus of 17,624 text posts from disease-specific subreddits of the social news and discussion website Reddit. For entity and relation extraction from this corpus, we employed the PKDE4J tool developed by Song et al (2015). PKDE4J is a text mining system that integrates dictionary-based entity extraction and rule-based relation extraction in a highly flexible and extensible framework.ResultsUsing PKDE4J, we extracted 2 types of entities and relations: biomedical entities and relations and subject-predicate-object entity relations. In total, 82,138 entities and 30,341 relation pairs were extracted from the Reddit dataset. The most highly mentioned entities were those related to oncological disease (2884 occurrences of cancer) and asthma (2180 occurrences). The relation pair anatomy-disease was the most frequent (5550 occurrences), the highest frequent entities in this pair being cancer and lymph. The manual validation of the extracted entities showed a very good performance of the system at the entity extraction task (3682/5151, 71.48% extracted entities were correctly labeled).ConclusionsThis study showed that people are eager to share their personal experience with chronic diseases on social media platforms despite possible privacy and security issues. The results reported in this paper are promising and demonstrate the need for more in-depth studies on the way patients with chronic diseases express themselves on social media platforms.

Relation extraction is a research hot-spot in the field of natural language processing, and aims at structured knowledge acquirement. However, existing methods still grapple with the issue of entity overlapping, where they treat relation types as inconsequential labels, overlooking the fact that relation type has a great influence on entity type hindering the performance of these models from further improving. Furthermore, current models are inadequate in handling the fine-grained aspect of entity positioning, which leads to ambiguity in entity boundary localization and uncertainty in relation inference, directly. In response to this challenge, a relation extraction model is proposed, which is guided by relational semantic cues and focused on entity boundary localization. The model uses an attention mechanism to align relation semantics with sentence information, so as to obtain the most relevant semantic expression to the target relation instance. It then incorporates an entity locator to harness additional positional features, thereby, enhancing the capability of the model to pinpoint entity start and end tags. Consequently, this approach effectively alleviates the problem of entity overlapping. Extensive experiments are conducted on the widely used datasets NYT and WebNLG. The experimental results show that the proposed model outperforms the baseline ones in F1 scores of the two datasets, and the improvement margin is up to 5.50% and 2.80%, respectively.

Current research on knowledge graph construction is focused chiefly on general-purpose fields, whereas constructing knowledge graphs in vertically segmented professional fields faces numerous difficulties. To solve the problems of complex relation types of domain entities, the lack of a large amount of annotated corpus, and the difficulty of extraction, this study proposed a method for constructing domain-annotated datasets based on publicly available texts on the web, which integrates remote supervision and semi-supervision. For the relational triad extraction of a given core entity (an entity lexicon defined semi-automatically by experts), an inflated gate attention network structure for increasing the perceptual field of the model is proposed. In addition, a relational extraction model, Ro-DGANet, was designed based on this structure, incorporating the idea of a probability graph. The Ro-DGANet model was experimentally evaluated on the publicly available Chinese datasets LIC2019 and CHIP2020 and compared with the mainstream relation extraction models, achieving the best results with F1 values of 82.99% and 66.39%, respectively. Finally, the Ro-DGANet model was applied to the relation extraction task of equipment components in industrial scenarios and to the relation extraction task of core knowledge points of programming languages. The analysis results show that the proposed method is applicable to open relation extraction among core entities in different domains with reliable performance and portability.

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

Relations extraction is a widely researched topic in nature language processing. However, most of the work in the literature concentrate on the methods that are dealing with single relation between two named entities. In the task of multiple relations extraction, traditional statistic-based methods have difficulties in selecting features and improving the performance of extraction model. In this paper, we presented formal definitions of multiple entities and multiple relations and put forward three labeling methods which were used to label entity categories, relation categories and relation conditions. We also proposed a novel relation extraction model which is based on dynamic long short-term memory network. To train our model, entity feature, entity position feature and part of speech feature are used together. These features are used to describe complex relations and improve the performance of relation extraction model. In the experiments, we classified the corpus into three sets which are composed of 0–20 words, 20–35 words and 35+ words sentences. On conll04.corp, the final precision, recall rate and F-measure reached 72.9, 70.8 and 67.9% respectively.

Boundary assembling method for joint entity and relation extraction

Entity and relation extraction (ERE) is a major task in information extraction and knowledge mapping. Existing methods usually consider two tasks, named entity recognition (NER) and relation extraction (RE), separately using a pipeline approach, which loses a lot of interaction information between tasks and contextual information of text sequences. In order to settle this problem, this paper proposes an end-to-end entity relation joint extraction method based on the head-entity attention mechanism and fusing contextual semantic features. The overall structure of this method adopts BERT-CRF to decode the header entity and its type, and then uses the header entity information as the Query in the attention mechanism, while fusing entity type label embedding and entity relative position to achieve feature enhancement, which enhances the information interaction between entity model and relational model. In the experiments of the commonly used English dataset NYT and Chinese dataset DuIE, this method has achieved high extraction accuracy and F1 score. It is shown that the model is applicable in both English and Chinese contexts.

Stepping from sentence-level to document-level, the research on relation extraction (RE) confronts increasing text length and more complicated entity interactions. Consequently, it is more challenging to encode the key information sources—relevant contexts and entity types. However, existing methods only implicitly learn to model these critical information sources while being trained for RE. As a result, they suffer the problems of ineffective supervision and uninterpretable model predictions. In contrast, we propose to explicitly teach the model to capture relevant contexts and entity types by supervising and augmenting intermediate steps (SAIS) for RE. Based on a broad spectrum of carefully designed tasks, our proposed SAIS method not only extracts relations of better quality due to more effective supervision, but also retrieves the corresponding supporting evidence more accurately so as to enhance interpretability. By assessing model uncertainty, SAIS further boosts the performance via evidence-based data augmentation and ensemble inference while reducing the computational cost. Eventually, SAIS delivers state-of-the-art RE results on three benchmarks (DocRED, CDR, and GDA) and outperforms the runner-up by 5.04% relatively in F1 score in evidence retrieval on DocRED.

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/.

In recent years, the plentiful information contained in Chinese legal documents has attracted a great deal of attention because of the large-scale release of the judgment documents on China Judgments Online. It is in great need of enabling machines to understand the semantic information stored in the documents which are transcribed in the form of natural language. The technique of information extraction provides a way of mining the valuable information implied in the unstructured judgment documents. We propose a Legal Triplet Extraction System for drug-related criminal judgment documents. The system extracts the entities and the semantic relations jointly and benefits from the proposed entity feature and multi-task learning framework. Furthermore, we manually annotate a dataset for Named Entity Recognition and Relation Extraction in Chinese legal domain, which contributes to training supervised triplet extraction models and evaluating the model performance. Our experimental results show that the entity feature introduction and multi-task learning framework are feasible and effective for the Legal Triplet Extraction System.

BackgroundDiabetic retinopathy (DR) is a leading cause of blindness in American adults. If detected, DR can be treated to prevent further damage causing blindness. There is an increasing interest in developing artificial intelligence (AI) technologies to help detect DR using electronic health records. The lesion-related information documented in fundus image reports is a valuable resource that could help diagnoses of DR in clinical decision support systems. However, most studies for AI-based DR diagnoses are mainly based on medical images; there is limited studies to explore the lesion-related information captured in the free text image reports.MethodsIn this study, we examined two state-of-the-art transformer-based natural language processing (NLP) models, including BERT and RoBERTa, compared them with a recurrent neural network implemented using Long short-term memory (LSTM) to extract DR-related concepts from clinical narratives. We identified four different categories of DR-related clinical concepts including lesions, eye parts, laterality, and severity, developed annotation guidelines, annotated a DR-corpus of 536 image reports, and developed transformer-based NLP models for clinical concept extraction and relation extraction. We also examined the relation extraction under two settings including ‘gold-standard’ setting—where gold-standard concepts were used–and end-to-end setting.ResultsFor concept extraction, the BERT model pretrained with the MIMIC III dataset achieve the best performance (0.9503 and 0.9645 for strict/lenient evaluation). For relation extraction, BERT model pretrained using general English text achieved the best strict/lenient F1-score of 0.9316. The end-to-end system, BERT_general_e2e, achieved the best strict/lenient F1-score of 0.8578 and 0.8881, respectively. Another end-to-end system based on the RoBERTa architecture, RoBERTa_general_e2e, also achieved the same performance as BERT_general_e2e in strict scores.ConclusionsThis study demonstrated the efficiency of transformer-based NLP models for clinical concept extraction and relation extraction. Our results show that it’s necessary to pretrain transformer models using clinical text to optimize the performance for clinical concept extraction. Whereas, for relation extraction, transformers pretrained using general English text perform better.

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.

Entity relation extraction (RE) is an very important research domain in information extraction, we can regard RE as a classification problem in this paper, RE is still original study field in Chinese language now, maximum entropy (ME)-based machine learning is the first time to be used to extract entity relations between named entities from Chinese texts, Thirteen features have been designed for entity relation extraction, which includes morphology, grammar and semantic feature. The system architecture for RE has been constructed. Experiment shows that the performance is promising. So it is useful for ME-based machine learning to solve RE problem

The task of entity relation extraction discovers new relation facts and enables broader applications of knowledge graph. Distant supervision is widely adopted for relation extraction, which requires large amounts of texts containing entity pairs as training data. However, in some specific domains such as medical-related applications, entity pairs that have certain relations might not appear together, thus it is difficult to meet the requirement for distantly supervised relation extraction. In the light of this challenge, we propose a novel path-based model to discover new entity relation facts. Instead of finding texts for relation extraction, the proposed method extracts path-only information for entity pairs from the current knowledge graph. For each pair of entities, multiple paths can be extracted, and some of them are more useful for relation extraction than others. In order to capture this observation, we employ attention mechanism to assign different weights for different paths, which highlights the useful paths for entity relation extraction. To demonstrate the effectiveness of the proposed method, we conduct various experiments on a large-scale medical knowledge graph. Compared with the state-of-the-art relation extraction methods using the structure of knowledge graph, the proposed method significantly improves the accuracy of extracted relation facts and achieves the best performance.

Ontology learning from unstructured text has become a critical task for knowledge-driven applications in Big Data and Artificial Intelligence. While significant advances have been made in the automatic extraction of concepts and relations using neural and Transformer-based models, the generation of formal Description Logic axioms required for constructing logically consistent and computationally tractable ontologies remains largely underexplored. This paper puts forward a novel pipeline for automated axiom generation through schema mapping. Our paper introduces three key innovations: a deterministic mapping framework that guarantees logical consistency (unlike stochastic Large Language Models); guaranteed formal consistency verified by OWL reasoners (unaddressed by prior statistical methods); and a transparent, scalable bridge from neural extractions to symbolic logic, eliminating manual post-processing. Technically, the pipeline builds upon the outputs of a Transformer-based fusion model for joint concept and relation extraction. We then map lexical relational phrases to formal ontological properties through a lemmatization-based schema alignment step. Entity typing and hierarchical induction are then employed to infer class structures, as well as domain and range constraints. Using RDFLib and structured data processing, we transform the extracted triples into both assertional (ABox) and terminological (TBox) axioms expressed in Description Logic. Experimental evaluation on benchmark datasets (Conll04 and NYT) demonstrates the efficacy of the approach, with expert validation showing high acceptance rates (>95%) and reasoners confirming zero inconsistencies. The pipeline thus establishes a reliable, scalable foundation for automated ontology learning, advancing the field from extraction to formally verifiable knowledge base construction.