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| Main Authors: | , , |
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| Format: | Preprint |
| Published: |
2023
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| Subjects: | |
| Online Access: | https://arxiv.org/abs/2301.10451 |
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| _version_ | 1866914801140105216 |
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| author | Ji, Shaoxiong Gao, Ya Marttinen, Pekka |
| author_facet | Ji, Shaoxiong Gao, Ya Marttinen, Pekka |
| contents | Adverse drug events (ADEs) are an important aspect of drug safety. Various texts such as biomedical literature, drug reviews, and user posts on social media and medical forums contain a wealth of information about ADEs. Recent studies have applied word embedding and deep learning -based natural language processing to automate ADE detection from text. However, they did not explore incorporating explicit medical knowledge about drugs and adverse reactions or the corresponding feature learning. This paper adopts the heterogenous text graph which describes relationships between documents, words and concepts, augments it with medical knowledge from the Unified Medical Language System, and proposes a concept-aware attention mechanism which learns features differently for the different types of nodes in the graph. We further utilize contextualized embeddings from pretrained language models and convolutional graph neural networks for effective feature representation and relational learning. Experiments on four public datasets show that our model achieves performance competitive to the recent advances and the concept-aware attention consistently outperforms other attention mechanisms. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2301_10451 |
| institution | arXiv |
| publishDate | 2023 |
| record_format | arxiv |
| spellingShingle | Knowledge-augmented Graph Neural Networks with Concept-aware Attention for Adverse Drug Event Detection Ji, Shaoxiong Gao, Ya Marttinen, Pekka Computation and Language Adverse drug events (ADEs) are an important aspect of drug safety. Various texts such as biomedical literature, drug reviews, and user posts on social media and medical forums contain a wealth of information about ADEs. Recent studies have applied word embedding and deep learning -based natural language processing to automate ADE detection from text. However, they did not explore incorporating explicit medical knowledge about drugs and adverse reactions or the corresponding feature learning. This paper adopts the heterogenous text graph which describes relationships between documents, words and concepts, augments it with medical knowledge from the Unified Medical Language System, and proposes a concept-aware attention mechanism which learns features differently for the different types of nodes in the graph. We further utilize contextualized embeddings from pretrained language models and convolutional graph neural networks for effective feature representation and relational learning. Experiments on four public datasets show that our model achieves performance competitive to the recent advances and the concept-aware attention consistently outperforms other attention mechanisms. |
| title | Knowledge-augmented Graph Neural Networks with Concept-aware Attention for Adverse Drug Event Detection |
| topic | Computation and Language |
| url | https://arxiv.org/abs/2301.10451 |