An attentive joint model with transformer-based weighted graph convolutional network for extracting adverse drug event relation.

Adverse drug event (ADE) relation extraction is a crucial task for drug safety surveillance which aims to discover potential relations between ADE mentions from unstructured medical texts. To date, the graph convolutional networks (GCN) have been the state-of-the-art solutions for improving the ability of relation extraction task. However, there are many challenging issues that should be addressed. Among these, the syntactic information is not fully exploited by GCN-based methods, especially the diversified dependency edges. Still, these methods fail to effectively extract complex relations that include nested, discontinuous and overlapping mentions. Besides, the task is primarily regarded as a classification problem where each candidate relation is treated independently which neglects the interaction between other relations. To deal with these issues, in this paper, we propose an attentive joint model with transformer-based weighted GCN for extracting ADE Relations, called ADERel. Firstly, the ADERel system formulates the ADE relation extraction task as an N-level sequence labelling so as to model the complex relations in different levels and capture greater interaction between relations. Then, it exploits our neural joint model to process the N-level sequences jointly. The joint model leverages the contextual and structural information by adopting a shared representation that combines a bidirectional encoder representation from transformers (BERT) and our proposed weighted GCN (WGCN). The latter assigns a score to each dependency edge within a sentence so as to capture rich syntactic features and determine the most influential edges for extracting ADE relations. Finally, the system employs a multi-head attention to exchange boundary knowledge across levels. We evaluate ADERel on two benchmark datasets from TAC 2017 and n2c2 2018 shared tasks. The experimental results show that ADERel is superior in performance compared with several state-of-the-art methods. The results also demonstrate that incorporating a transformer model with WGCN makes the proposed system more effective for extracting various types of ADE relations. The evaluations further highlight that ADERel takes advantage of joint learning, showing its effectiveness in recognizing complex relations.

SemBioNLQA: A semantic biomedical question answering system for retrieving exact and ideal answers to natural language questions.

BACKGROUND AND OBJECTIVE: Question answering (QA), the identification of short accurate answers to users questions written in natural language expressions, is a longstanding issue widely studied over the last decades in the open-domain. However, it still remains a real challenge in the biomedical domain as the most of the existing systems support a limited amount of question and answer types as well as still require further efforts in order to improve their performance in terms of precision for the supported questions. Here, we present a semantic biomedical QA system named SemBioNLQA which has the ability to handle the kinds of yes/no, factoid, list, and summary natural language questions. METHODS: This paper describes the system architecture and an evaluation of the developed end-to-end biomedical QA system named SemBioNLQA, which consists of question classification, document retrieval, passage retrieval and answer extraction modules. It takes natural language questions as input, and outputs both short precise answers and summaries as results. The SemBioNLQA system, dealing with four types of questions, is based on (1) handcrafted lexico-syntactic patterns and a machine learning algorithm for question classification, (2) PubMed search engine and UMLS similarity for document retrieval, (3) the BM25 model, stemmed words and UMLS concepts for passage retrieval, and (4) UMLS metathesaurus, BioPortal synonyms, sentiment analysis and term frequency metric for answer extraction. RESULTS AND CONCLUSION: Compared with the current state-of-the-art biomedical QA systems, SemBioNLQA, a fully automated system, has the potential to deal with a large amount of question and answer types. SemBioNLQA retrieves quickly users' information needs by returning exact answers (e.g., "yes", "no", a biomedical entity name, etc.) and ideal answers (i.e., paragraph-sized summaries of relevant information) for yes/no, factoid and list questions, whereas it provides only the ideal answers for summary questions. Moreover, experimental evaluations performed on biomedical questions and answers provided by the BioASQ challenge especially in 2015, 2016 and 2017 (as part of our participation), show that SemBioNLQA achieves good performances compared with the most current state-of-the-art systems and allows a practical and competitive alternative to help information seekers find exact and ideal answers to their biomedical questions. The SemBioNLQA source code is publicly available at https://github.com/sarrouti/sembionlqa.

An adverse drug effect mentions extraction method based on weighted online recurrent extreme learning machine.

BACKGROUND AND OBJECTIVE: Automatic extraction of adverse drug effect (ADE) mentions from biomedical texts is a challenging research problem that has attracted significant attention from the pharmacovigilance and biomedical text mining communities. Indeed, deep learning based methods have recently been employed to solve this issue with great success. However, they fail to effectively identify the boundary of mentions. In this paper, we propose a weighted online recurrent extreme learning machine (WOR-ELM) based method to overcome this drawback. METHODS: The proposed method for ADE mentions extraction from biomedical texts is divided into two stages: span detection and ADE mentions classification. At the first stage, we identify the boundary of the mentions irrespective of their types with a WOR-ELM in a given sentence. At the second stage, another WOR-ELM is used to classify the identified mentions to the appropriate type. Both stages use the concatenation of character-level and word-level embeddings as features. The character-level embedding is obtained using a modified online recurrent extreme learning machine, whereas the word-level embedding is obtained from a pre-trained model. RESULTS: Several experiments were carried out on a well-known ADE corpus to evaluate the effectiveness and demonstrate the usefulness of the proposed method. The obtained results show that our method achieves an F-score of 87.5%, which outperforms the current state-of-the-art methods. CONCLUSIONS: Our research results indicate that the proposed method for adverse drug effect mentions extraction from text can significantly improve performance over existing methods. Our experiments show the effectiveness of incorporating word-level and character level embeddings as features for WOR-ELM. They also illustrate the benefits of using IOU segment to represent ADE mentions.

A Machine Learning-based Method for Question Type Classification in Biomedical Question Answering.

BACKGROUND AND OBJECTIVE: Biomedical question type classification is one of the important components of an automatic biomedical question answering system. The performance of the latter depends directly on the performance of its biomedical question type classification system, which consists of assigning a category to each question in order to determine the appropriate answer extraction algorithm. This study aims to automatically classify biomedical questions into one of the four categories: (1) yes/no, (2) factoid, (3) list, and (4) summary. METHODS: In this paper, we propose a biomedical question type classification method based on machine learning approaches to automatically assign a category to a biomedical question. First, we extract features from biomedical questions using the proposed handcrafted lexico-syntactic patterns. Then, we feed these features for machine-learning algorithms. Finally, the class label is predicted using the trained classifiers. RESULTS: Experimental evaluations performed on large standard annotated datasets of biomedical questions, provided by the BioASQ challenge, demonstrated that our method exhibits significant improved performance when compared to four baseline systems. The proposed method achieves a roughly 10-point increase over the best baseline in terms of accuracy. Moreover, the obtained results show that using handcrafted lexico-syntactic patterns as features' provider of support vector machine (SVM) lead to the highest accuracy of 89.40 %. CONCLUSION: The proposed method can automatically classify BioASQ questions into one of the four categories: yes/no, factoid, list, and summary. Furthermore, the results demonstrated that our method produced the best classification performance compared to four baseline systems.

A passage retrieval method based on probabilistic information retrieval model and UMLS concepts in biomedical question answering.

BACKGROUND AND OBJECTIVE: Passage retrieval, the identification of top-ranked passages that may contain the answer for a given biomedical question, is a crucial component for any biomedical question answering (QA) system. Passage retrieval in open-domain QA is a longstanding challenge widely studied over the last decades. However, it still requires further efforts in biomedical QA. In this paper, we present a new biomedical passage retrieval method based on Stanford CoreNLP sentence/passage length, probabilistic information retrieval (IR) model and UMLS concepts. METHODS: In the proposed method, we first use our document retrieval system based on PubMed search engine and UMLS similarity to retrieve relevant documents to a given biomedical question. We then take the abstracts from the retrieved documents and use Stanford CoreNLP for sentence splitter to make a set of sentences, i.e., candidate passages. Using stemmed words and UMLS concepts as features for the BM25 model, we finally compute the similarity scores between the biomedical question and each of the candidate passages and keep the N top-ranked ones. RESULTS: Experimental evaluations performed on large standard datasets, provided by the BioASQ challenge, show that the proposed method achieves good performances compared with the current state-of-the-art methods. The proposed method significantly outperforms the current state-of-the-art methods by an average of 6.84% in terms of mean average precision (MAP). CONCLUSION: We have proposed an efficient passage retrieval method which can be used to retrieve relevant passages in biomedical QA systems with high mean average precision.