A Hierarchical Entity Graph Convolutional Network for Relation Extraction across Documents

Analysis on topological features of deterministic hierarchical complex network

With the continuous improvement of the related relation extraction model, researchers focused on optimizations of the input of the sentence expression structures, such as dependency trees, and slight improvements and integrations of basic models applied to this task. This paper utilizes position-aware attention mechanisms to highlight critical information and makes good use of global information generated by the bidirectional LSTM, absorbing characteristics and advantages of those related models to propose a new Position-Aware Graph Convolutional Network (PA-GCN) model and describe it in three steps. Moreover, this paper trials the model on the RACRED dataset to evaluate its performance and suitability. The experiment results demonstrate that the PA-GCN model outperformed others listed in this paper, achieving an F_1 score of 66.6%, which verifies an improvement of the model and the effectiveness of adding an attention-aware mechanism.

Two evaluations on Ontology-style relation annotations

Relation Extraction (RE) is at the core of many Natural Language Understanding tasks, including knowledge-base population and Question Answering.However, any Natural Language Processing system is exposed to biases, and the analysis of these has not received much attention in RE.We propose a new method for inspecting bias in the RE pipeline, which is completely transparent in terms of interpretability.Specifically, in this work we analyze biases related to gender and place of birth.Our methodology includes (i) obtaining semantic triplets (subject, object, semantic relation) involving 'person' entities from RE resources, (ii) collecting meta-information ('gender' and 'place of birth') using Entity Linking technologies, and then (iii) analyze the distribution of triplets across different groups (e.g., men versus women).We investigate bias at two levels: In the training data of three commonly used RE datasets (SRED FM , CrossRE, NYT), and in the predictions of a state-of-the-art RE approach (ReLiK).To enable cross-dataset analysis, we introduce a taxonomy of relation types mapping the label sets of different RE datasets to a unified label space.Our findings reveal that bias is a compounded issue affecting underrepresented groups within data and predictions for RE.

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.

In the expanding landscape of biomedical literature, numerous latent associations outlined in scholarly papers await discovery and integration into biomedical databases. Biomedical Natural Language Processing (NLP) research focuses on automating knowledge extraction and mining from this literature, particularly emphasizing the essential task of Relation Extraction (RE). However, existing models have limitations, mainly in their applicability to partial datasets for RE tasks. Moreover, conventional models often treat RE as a binary classification challenge, which proves suboptimal given the diverse relationships, including intricate ones like similarity and hierarchy, present in the RE dataset. These limitations are exacerbated by the models’ inability to capture word-level positional nuances and sentence-level language features. In response to these challenges, we present a novel RE model called BicapBert. This model integrates neural networks and capsule networks, enhancing them with hybrid knowledge graph embeddings to extract relevant features. BicapBert utilizes PubMedBERT and capsule networks to extract word-level positional and sentence-level language features. It further captures knowledge features from a biomedical knowledge graph, integrating them with the aforementioned linguistic features. The amalgamated information is then input into a multi-layer perceptron, culminating in results derived through a softmax classifier. Experimental evaluations on three extensive RE task datasets showcase the state-of-the-art performance of our proposed model. Additionally, we validate the model’s efficacy on three randomly selected biomedical datasets for various tasks, further affirming its superiority.

In this paper, we present GraphRel, an end-to-end relation extraction model which uses graph convolutional networks (GCNs) to jointly learn named entities and relations. In contrast to previous baselines, we consider the interaction between named entities and relations via a 2nd-phase relation-weighted GCN to better extract relations. Linear and dependency structures are both used to extract both sequential and regional features of the text, and a complete word graph is further utilized to extract implicit features among all word pairs of the text. With the graph-based approach, the prediction for overlapping relations is substantially improved over previous sequential approaches. We evaluate GraphRel on two public datasets: NYT and WebNLG. Results show that GraphRel maintains high precision while increasing recall substantially. Also, GraphRel outperforms previous work by 3.2% and 5.8% (F1 score), achieving a new state-of-the-art for relation extraction.

Diverse classifiers with label dependencies for long-tail relation extraction in big data

Non-point source pollution from agricultural activities poses a significant threat to water quality by introducing excess nutrients like nitrogen into aquatic ecosystems, leading to issues such as eutrophication and groundwater contamination. In agricultural watersheds, nitrate transport involves intricate physical, chemical, and biological processes influenced by meteorological conditions, hydrological features, and spatial topologies, making accurate short-term predictions challenging. Traditional data-driven deep learning models often fail to incorporate physical constraints and complex spatiotemporal dynamics, limiting their interpretability and predictive accuracy. Here we show a hierarchical transformer and graph neural network model that accurately predicts watershed nitrate concentrations by integrating multi-source data and simulating pollutant migration. The model captures nonlinear multivariate temporal patterns through hierarchical transformers, fuses global meteorological and local hydrological features via neural networks, and models runoff topologies with physically constrained graph neural networks. For predicting the concentration changes of pollutants discharged from watersheds, it outperforms baselines like multi-layer perceptrons, recurrent neural networks, and long short-term memory networks, with state-of-the-art performance in root mean square error, mean absolute error, and R2. Ablation studies confirm the essential roles of multi-source data integration and watershed topological modeling in enhancing performance. This method of directly modeling physical processes by leveraging the characteristics of different neural network architectures opens up a new path for addressing the interpretability problem in neural earth system modeling, apart from the process-guided deep learning and differentiable modelling methods.

Governments are issuing regulations and laws demanding that companies protect collected and processed personal data. In Brazil, the federal government sanctioned the General Personal Data Protection law, which defines personal and sensitive data associated with Brazilian citizens. One existing barrier for companies to comply with the law is identifying where personal data is stored inside their infrastructure, mainly concerning personal data inserted into unstructured documents. Named Entity Recognition and Classification (NERC) can support companies in this task by implementing supervised learning models to identify personal data. In this study, we designed an experiment to evaluate machine learning-based NERC using BERT and LSTM approaches to recognize personal data related to Brazil’s context. We established a generic training corpus based on online documents and trained two models for each approach, one considering the original corpus and another after lowercasing it. The study also assessed relation extraction to differentiate personal entities from others. For NERC and relation extraction evaluations, we established a training corpus comprising documents from two organizations related to the education and health sectors. BERT fine-tuned with uncased corpus scored an F1 measure of 0.8 and achieved the best performance in recognizing entities, followed by LSTM based on the same corpus. After applying relation extraction, BERT models achieved better F1 scores than LSTM models. The uncased BERT model achieved an F1 score of 0.85, which was the best. Experiment results also indicated that relation extraction improves the performance of BERT models to discover personal entities.

Relation extraction is an important task for understanding relationships between entities, building knowledge graphs, and facilitating knowledge discovery. Pre-trained models can be fine-tuned for relation extraction if a substantial amount of labeled data is available. However, acquiring extensive labeled data is generally challenging. Semi-supervised techniques for low-resource relation extraction, such as self-training, offer a promising solution by leveraging both limited labeled data and vast unlabeled data to mitigate this challenge. Traditional self-training methods use a teacher-student framework, where a student is iteratively trained with pseudo-labels generated by the teacher. This may lead to noisy pseudo-labels and impact performance. To address this limitation, we introduce a new model called RE-AUM-LLM that generates high-quality pseudo-labels using self-training combined with Area Under the Margin (AUM) and Large Language Models (LLMs), such as Llama 3.1. Experimental results on two benchmark datasets show that the proposed approach achieves state-of-the-art results for low-resource relation extraction by comparison with several strong baselines. We will make the code publicly available to enable reproducibility and further research in this area.

Document-level relation extraction (RE) poses new challenges compared to its sentence-level counterpart. One document commonly contains multiple entity pairs, and one entity pair occurs multiple times in the document associated with multiple possible relations. In this paper, we propose two novel techniques, adaptive thresholding and localized context pooling, to solve the multi-label and multi-entity problems. The adaptive thresholding replaces the global threshold for multi-label classification in the prior work with a learnable entities-dependent threshold. The localized context pooling directly transfers attention from pre-trained language models to locate relevant context that is useful to decide the relation. We experiment on three document-level RE benchmark datasets: DocRED, a recently released large-scale RE dataset, and two datasets CDRand GDA in the biomedical domain. Our ATLOP (Adaptive Thresholding and Localized cOntext Pooling) model achieves an F1 score of 63.4, and also significantly outperforms existing models on both CDR and GDA. We have released our code at https://github.com/wzhouad/ATLOP.

The syntactic information of a dependency tree is an essential feature in relation extraction studies. Traditional dependency-based relation extraction methods can be categorized into hard pruning methods, which aim to remove unnecessary information, and soft pruning methods, which aim to utilize all lexical information. However, hard pruning has the potential to overlook important lexical information, while soft pruning can weaken the syntactic information between entities. As a result, recent studies in relation extraction have been shifting from dependency-based methods to pre-trained language model (LM) based methods. Nonetheless, LM-based methods increasingly demand larger language models and additional data. This trend leads to higher resource consumption, longer training times, and increased computational costs, yet often results in only marginal performance improvements. To address this problem, we propose a relation extraction model based on an entity-centric dependency tree: a dependency tree that is reconstructed by considering entities as root nodes. Using the entity-centric dependency tree, the proposed method can capture the syntactic information of an input sentence without losing lexical information. Additionally, we propose a novel model that utilizes entity-centric dependency trees in conjunction with language models, enabling efficient relation extraction without the need for additional data or larger models. In experiments with representative sentence-level relation extraction datasets such as TACRED, Re-TACRED, and SemEval 2010 Task 8, the proposed method achieves F1-scores of 74.9%, 91.2%, and 90.5%, respectively, which are state-of-the-art performances.

Organized relational knowledge in the form of “knowledge graphs” is important for many applications. However, the ability to populate knowledge bases with facts automatically extracted from documents has improved frustratingly slowly. This paper simultaneously addresses two issues that have held back prior work. We first propose an effective new model, which combines an LSTM sequence model with a form of entity position-aware attention that is better suited to relation extraction. Then we build TACRED, a large (119,474 examples) supervised relation extraction dataset obtained via crowdsourcing and targeted towards TAC KBP relations. The combination of better supervised data and a more appropriate high-capacity model enables much better relation extraction performance. When the model trained on this new dataset replaces the previous relation extraction component of the best TAC KBP 2015 slot filling system, its F1 score increases markedly from 22.2% to 26.7%.

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/.