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Register a new userAttention-Gated Graph Convolutions for Extracting Drug Interaction Information from Drug Labels
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Tung Tran
Publication date
2019
fields
Informatics Engineering
and research's language is
English
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Preventable adverse events as a result of medical errors present a growing concern in the healthcare system. As drug-drug interactions (DDIs) may lead to preventable adverse events, being able to extract DDIs from drug labels into a machine-processable form is an important step toward effective dissemination of drug safety information. In this study, we tackle the problem of jointly extracting drugs and their interactions, including interaction outcome, from drug labels. Our deep learning approach entails composing various intermediate representations including sequence and graph based context, where the latter is derived using graph convolutions (GC) with a novel attention-based gating mechanism (holistically called GCA). These representations are then composed in meaningful ways to handle all subtasks jointly. To overcome scarcity in training data, we additionally propose transfer learning by pre-training on related DDI data. Our model is trained and evaluated on the 2018 TAC DDI corpus. Our GCA model in conjunction with transfer learning performs at 39.20% F1 and 26.09% F1 on entity recognition (ER) and relation extraction (RE) respectively on the first official test set and at 45.30% F1 and 27.87% F1 on ER and RE respectively on the second official test set corresponding to an improvement over our prior best results by up to 6 absolute F1 points. After controlling for available training data, our model exhibits state-of-the-art performance by improving over the next comparable best outcome by roughly three F1 points in ER and 1.5 F1 points in RE evaluation across two official test sets.
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Traditional biomedical version of embeddings obtained from pre-trained language models have recently shown state-of-the-art results for relation extraction (RE) tasks in the medical domain. In this paper, we explore how to incorporate domain knowledge, available in the form of molecular structure of drugs, for predicting Drug-Drug Interaction from textual corpus. We propose a method, BERTChem-DDI, to efficiently combine drug embeddings obtained from the rich chemical structure of drugs along with off-the-shelf domain-specific BioBERT embedding-based RE architecture. Experiments conducted on the DDIExtraction 2013 corpus clearly indicate that this strategy improves other strong baselines architectures by 3.4% macro F1-score.
Preventable adverse drug reactions as a result of medical errors present a growing concern in modern medicine. As drug-drug interactions (DDIs) may cause adverse reactions, being able to extracting DDIs from drug labels into machine-readable form is an important effort in effectively deploying drug safety information. The DDI track of TAC 2018 introduces two large hand-annotated test sets for the task of extracting DDIs from structured product labels with linkage to standard terminologies. Herein, we describe our approach to tackling tasks one and two of the DDI track, which corresponds to named entity recognition (NER) and sentence-level relation extraction respectively. Namely, our approach resembles a multi-task learning framework designed to jointly model various sub-tasks including NER and interaction type and outcome prediction. On NER, our system ranked second (among eight teams) at 33.00% and 38.25% F1 on Test Sets 1 and 2 respectively. On relation extraction, our system ranked second (among four teams) at 21.59% and 23.55% on Test Sets 1 and 2 respectively.
Off-the-shelf biomedical embeddings obtained from the recently released various pre-trained language models (such as BERT, XLNET) have demonstrated state-of-the-art results (in terms of accuracy) for the various natural language understanding tasks (NLU) in the biomedical domain. Relation Classification (RC) falls into one of the most critical tasks. In this paper, we explore how to incorporate domain knowledge of the biomedical entities (such as drug, disease, genes), obtained from Knowledge Graph (KG) Embeddings, for predicting Drug-Drug Interaction from textual corpus. We propose a new method, BERTKG-DDI, to combine drug embeddings obtained from its interaction with other biomedical entities along with domain-specific BioBERT embedding-based RC architecture. Experiments conducted on the DDIExtraction 2013 corpus clearly indicate that this strategy improves other baselines architectures by 4.1% macro F1-score.
Motivation: Predicting Drug-Target Interaction (DTI) is a well-studied topic in bioinformatics due to its relevance in the fields of proteomics and pharmaceutical research. Although many machine learning methods have been successfully applied in this task, few of them aim at leveraging the inherent heterogeneous graph structure in the DTI network to address the challenge. For better learning and interpreting the DTI topological structure and the similarity, it is desirable to have methods specifically for predicting interactions from the graph structure. Results: We present an end-to-end framework, DTI-GAT (Drug-Target Interaction prediction with Graph Attention networks) for DTI predictions. DTI-GAT incorporates a deep neural network architecture that operates on graph-structured data with the attention mechanism, which leverages both the interaction patterns and the features of drug and protein sequences. DTI-GAT facilitates the interpretation of the DTI topological structure by assigning different attention weights to each node with the self-attention mechanism. Experimental evaluations show that DTI-GAT outperforms various state-of-the-art systems on the binary DTI prediction problem. Moreover, the independent study results further demonstrate that our model can be generalized better than other conventional methods. Availability: The source code and all datasets are available at https://github.com/Haiyang-W/DTI-GRAPH
When patients need to take medicine, particularly taking more than one kind of drug simultaneously, they should be alarmed that there possibly exists drug-drug interaction. Interaction between drugs may have a negative impact on patients or even cause death. Generally, drugs that conflict with a specific drug (or label drug) are usually described in its drug label or package insert. Since more and more new drug products come into the market, it is difficult to collect such information by manual. We take part in the Drug-Drug Interaction (DDI) Extraction from Drug Labels challenge of Text Analysis Conference (TAC) 2018, choosing task1 and task2 to automatically extract DDI related mentions and DDI relations respectively. Instead of regarding task1 as named entity recognition (NER) task and regarding task2 as relation extraction (RE) task then solving it in a pipeline, we propose a two step joint model to detect DDI and its related mentions jointly. A sequence tagging system (CNN-GRU encoder-decoder) finds precipitants first and search its fine-grained Trigger and determine the DDI for each precipitant in the second step. Moreover, a rule based model is built to determine the sub-type for pharmacokinetic interation. Our system achieved best result in both task1 and task2. F-measure reaches 0.46 in task1 and 0.40 in task2.
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