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Register a new userMultimodal Graph-based Transformer Framework for Biomedical Relation Extraction
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Added by
Shweta Yadav
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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The recent advancement of pre-trained Transformer models has propelled the development of effective text mining models across various biomedical tasks. However, these models are primarily learned on the textual data and often lack the domain knowledge of the entities to capture the context beyond the sentence. In this study, we introduced a novel framework that enables the model to learn multi-omnics biological information about entities (proteins) with the help of additional multi-modal cues like molecular structure. Towards this, rather developing modality-specific architectures, we devise a generalized and optimized graph based multi-modal learning mechanism that utilizes the GraphBERT model to encode the textual and molecular structure information and exploit the underlying features of various modalities to enable end-to-end learning. We evaluated our proposed method on ProteinProtein Interaction task from the biomedical corpus, where our proposed generalized approach is observed to be benefited by the additional domain-specific modality.
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The newly emerged transformer technology has a tremendous impact on NLP research. In the general English domain, transformer-based models have achieved state-of-the-art performances on various NLP benchmarks. In the clinical domain, researchers also have investigated transformer models for clinical applications. The goal of this study is to systematically explore three widely used transformer-based models (i.e., BERT, RoBERTa, and XLNet) for clinical relation extraction and develop an open-source package with clinical pre-trained transformer-based models to facilitate information extraction in the clinical domain. We developed a series of clinical RE models based on three transformer architectures, namely BERT, RoBERTa, and XLNet. We evaluated these models using 2 publicly available datasets from 2018 MADE1.0 and 2018 n2c2 challenges. We compared two classification strategies (binary vs. multi-class classification) and investigated two approaches to generate candidate relations in different experimental settings. In this study, we compared three transformer-based (BERT, RoBERTa, and XLNet) models for relation extraction. We demonstrated that the RoBERTa-clinical RE model achieved the best performance on the 2018 MADE1.0 dataset with an F1-score of 0.8958. On the 2018 n2c2 dataset, the XLNet-clinical model achieved the best F1-score of 0.9610. Our results indicated that the binary classification strategy consistently outperformed the multi-class classification strategy for clinical relation extraction. Our methods and models are publicly available at https://github.com/uf-hobi-informatics-lab/ClinicalTransformerRelationExtraction. We believe this work will improve current practice on clinical relation extraction and other related NLP tasks in the biomedical domain.
To minimize the accelerating amount of time invested in the biomedical literature search, numerous approaches for automated knowledge extraction have been proposed. Relation extraction is one such task where semantic relations between the entities are identified from the free text. In the biomedical domain, extraction of regulatory pathways, metabolic processes, adverse drug reaction or disease models necessitates knowledge from the individual relations, for example, physical or regulatory interactions between genes, proteins, drugs, chemical, disease or phenotype. In this paper, we study the relation extraction task from three major biomedical and clinical tasks, namely drug-drug interaction, protein-protein interaction, and medical concept relation extraction. Towards this, we model the relation extraction problem in multi-task learning (MTL) framework and introduce for the first time the concept of structured self-attentive network complemented with the adversarial learning approach for the prediction of relationships from the biomedical and clinical text. The fundamental notion of MTL is to simultaneously learn multiple problems together by utilizing the concepts of the shared representation. Additionally, we also generate the highly efficient single task model which exploits the shortest dependency path embedding learned over the attentive gated recurrent unit to compare our proposed MTL models. The framework we propose significantly improves overall the baselines (deep learning techniques) and single-task models for predicting the relationships, without compromising on the performance of all the tasks.
Most modern Information Extraction (IE) systems are implemented as sequential taggers and only model local dependencies. Non-local and non-sequential context is, however, a valuable source of information to improve predictions. In this paper, we introduce GraphIE, a framework that operates over a graph representing a broad set of dependencies between textual units (i.e. words or sentences). The algorithm propagates information between connected nodes through graph convolutions, generating a richer representation that can be exploited to improve word-level predictions. Evaluation on three different tasks --- namely textual, social media and visual information extraction --- shows that GraphIE consistently outperforms the state-of-the-art sequence tagging model by a significant margin.
Relation extraction is an important task in knowledge acquisition and text understanding. Existing works mainly focus on improving relation extraction by extracting effective features or designing reasonable model structures. However, few works have focused on how to validate and correct the results generated by the existing relation extraction models. We argue that validation is an important and promising direction to further improve the performance of relation extraction. In this paper, we explore the possibility of using question answering as validation. Specifically, we propose a novel question-answering based framework to validate the results from relation extraction models. Our proposed framework can be easily applied to existing relation classifiers without any additional information. We conduct extensive experiments on the popular NYT dataset to evaluate the proposed framework, and observe consistent improvements over five strong baselines.
Document-level relation extraction aims to extract relations among entities within a document. Different from sentence-level relation extraction, it requires reasoning over multiple sentences across a document. In this paper, we propose Graph Aggregation-and-Inference Network (GAIN) featuring double graphs. GAIN first constructs a heterogeneous mention-level graph (hMG) to model complex interaction among different mentions across the document. It also constructs an entity-level graph (EG), based on which we propose a novel path reasoning mechanism to infer relations between entities. Experiments on the public dataset, DocRED, show GAIN achieves a significant performance improvement (2.85 on F1) over the previous state-of-the-art. Our code is available at https://github.com/DreamInvoker/GAIN .
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