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Register a new userTowards Incorporating Entity-specific Knowledge Graph Information in Predicting Drug-Drug Interactions
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Ishani Mondal
Publication date
2020
fields
Informatics Engineering
and research's language is
English
Authors
Ishani Mondal
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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.
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Gaining more comprehensive knowledge about drug-drug interactions (DDIs) is one of the most important tasks in drug development and medical practice. Recently graph neural networks have achieved great success in this task by modeling drugs as nodes and drug-drug interactions as links and casting DDI predictions as link prediction problems. However, correlations between link labels (e.g., DDI types) were rarely considered in existing works. We propose the graph energy neural network (GENN) to explicitly model link type correlations. We formulate the DDI prediction task as a structure prediction problem and introduce a new energy-based model where the energy function is defined by graph neural networks. Experiments on two real-world DDI datasets demonstrated that GENN is superior to many baselines without consideration of link type correlations and achieved $13.77%$ and $5.01%$ PR-AUC improvement on the two datasets, respectively. We also present a case study in which mname can better capture meaningful DDI correlations compared with baseline models.
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.
To combat COVID-19, both clinicians and scientists need to digest vast amounts of relevant biomedical knowledge in scientific literature to understand the disease mechanism and related biological functions. We have developed a novel and comprehensive knowledge discovery framework, COVID-KG to extract fine-grained multimedia knowledge elements (entities and their visual chemical structures, relations, and events) from scientific literature. We then exploit the constructed multimedia knowledge graphs (KGs) for question answering and report generation, using drug repurposing as a case study. Our framework also provides detailed contextual sentences, subfigures, and knowledge subgraphs as evidence.
The rapid growth in literature accumulates diverse and yet comprehensive biomedical knowledge hidden to be mined such as drug interactions. However, it is difficult to extract the heterogeneous knowledge to retrieve or even discover the latest and novel knowledge in an efficient manner. To address such a problem, we propose EGFI for extracting and consolidating drug interactions from large-scale medical literature text data. Specifically, EGFI consists of two parts: classification and generation. In the classification part, EGFI encompasses the language model BioBERT which has been comprehensively pre-trained on biomedical corpus. In particular, we propose the multi-head attention mechanism and pack BiGRU to fuse multiple semantic information for rigorous context modeling. In the generation part, EGFI utilizes another pre-trained language model BioGPT-2 where the generation sentences are selected based on filtering rules. We evaluated the classification part on DDIs 2013 dataset and DTIs dataset, achieving the FI score of 0.842 and 0.720 respectively. Moreover, we applied the classification part to distinguish high-quality generated sentences and verified with the exiting growth truth to confirm the filtered sentences. The generated sentences that are not recorded in DrugBank and DDIs 2013 dataset also demonstrate the potential of EGFI to identify novel drug relationships.
Interference between pharmacological substances can cause serious medical injuries. Correctly predicting so-called drug-drug interactions (DDI) does not only reduce these cases but can also result in a reduction of drug development cost. Presently, most drug-related knowledge is the result of clinical evaluations and post-marketing surveillance; resulting in a limited amount of information. Existing data-driven prediction approaches for DDIs typically rely on a single source of information, while using information from multiple sources would help improve predictions. Machine learning (ML) techniques are used, but the techniques are often unable to deal with skewness in the data. Hence, we propose a new ML approach for predicting DDIs based on multiple data sources. For this task, we use 12,000 drug features from DrugBank, PharmGKB, and KEGG drugs, which are integrated using Knowledge Graphs (KGs). To train our prediction model, we first embed the nodes in the graph using various embedding approaches. We found that the best performing combination was a ComplEx embedding method creating using PyTorch-BigGraph (PBG) with a Convolutional-LSTM network and classic machine learning-based prediction models. The model averaging ensemble method of three best classifiers yields up to 0.94, 0.92, 0.80 for AUPR, F1-score, and MCC, respectively during 5-fold cross-validation tests.
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