Ilseyar Alimova


2020

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Proceedings of the Fifth Social Media Mining for Health Applications Workshop & Shared Task
Graciela Gonzalez-Hernandez | Ari Z. Klein | Ivan Flores | Davy Weissenbacher | Arjun Magge | Karen O'Connor | Abeed Sarker | Anne-Lyse Minard | Elena Tutubalina | Zulfat Miftahutdinov | Ilseyar Alimova
Proceedings of the Fifth Social Media Mining for Health Applications Workshop & Shared Task

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Overview of the Fifth Social Media Mining for Health Applications (#SMM4H) Shared Tasks at COLING 2020
Ari Klein | Ilseyar Alimova | Ivan Flores | Arjun Magge | Zulfat Miftahutdinov | Anne-Lyse Minard | Karen O’Connor | Abeed Sarker | Elena Tutubalina | Davy Weissenbacher | Graciela Gonzalez-Hernandez
Proceedings of the Fifth Social Media Mining for Health Applications Workshop & Shared Task

The vast amount of data on social media presents significant opportunities and challenges for utilizing it as a resource for health informatics. The fifth iteration of the Social Media Mining for Health Applications (#SMM4H) shared tasks sought to advance the use of Twitter data (tweets) for pharmacovigilance, toxicovigilance, and epidemiology of birth defects. In addition to re-runs of three tasks, #SMM4H 2020 included new tasks for detecting adverse effects of medications in French and Russian tweets, characterizing chatter related to prescription medication abuse, and detecting self reports of birth defect pregnancy outcomes. The five tasks required methods for binary classification, multi-class classification, and named entity recognition (NER). With 29 teams and a total of 130 system submissions, participation in the #SMM4H shared tasks continues to grow.

2019

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Detecting Adverse Drug Reactions from Biomedical Texts with Neural Networks
Ilseyar Alimova | Elena Tutubalina
Proceedings of the 57th Annual Meeting of the Association for Computational Linguistics: Student Research Workshop

Detection of adverse drug reactions in postapproval periods is a crucial challenge for pharmacology. Social media and electronic clinical reports are becoming increasingly popular as a source for obtaining health related information. In this work, we focus on extraction information of adverse drug reactions from various sources of biomedical textbased information, including biomedical literature and social media. We formulate the problem as a binary classification task and compare the performance of four state-of-the-art attention-based neural networks in terms of the F-measure. We show the effectiveness of these methods on four different benchmarks.

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KFU NLP Team at SMM4H 2019 Tasks: Want to Extract Adverse Drugs Reactions from Tweets? BERT to The Rescue
Zulfat Miftahutdinov | Ilseyar Alimova | Elena Tutubalina
Proceedings of the Fourth Social Media Mining for Health Applications (#SMM4H) Workshop & Shared Task

This paper describes a system developed for the Social Media Mining for Health (SMM4H) 2019 shared tasks. Specifically, we participated in three tasks. The goals of the first two tasks are to classify whether a tweet contains mentions of adverse drug reactions (ADR) and extract these mentions, respectively. The objective of the third task is to build an end-to-end solution: first, detect ADR mentions and then map these entities to concepts in a controlled vocabulary. We investigate the use of a language representation model BERT trained to obtain semantic representations of social media texts. Our experiments on a dataset of user reviews showed that BERT is superior to state-of-the-art models based on recurrent neural networks. The BERT-based system for Task 1 obtained an F1 of 57.38%, with improvements up to +7.19% F1 over a score averaged across all 43 submissions. The ensemble of neural networks with a voting scheme for named entity recognition ranked first among 9 teams at the SMM4H 2019 Task 2 and obtained a relaxed F1 of 65.8%. The end-to-end model based on BERT for ADR normalization ranked first at the SMM4H 2019 Task 3 and obtained a relaxed F1 of 43.2%.

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Entity-level Classification of Adverse Drug Reactions: a Comparison of Neural Network Models
Ilseyar Alimova | Elena Tutubalina
Proceedings of the 2019 Workshop on Widening NLP

This paper presents our experimental work on exploring the potential of neural network models developed for aspect-based sentiment analysis for entity-level adverse drug reaction (ADR) classification. Our goal is to explore how to represent local context around ADR mentions and learn an entity representation, interacting with its context. We conducted extensive experiments on various sources of text-based information, including social media, electronic health records, and abstracts of scientific articles from PubMed. The results show that Interactive Attention Neural Network (IAN) outperformed other models on four corpora in terms of macro F-measure. This work is an abridged version of our recent paper accepted to Programming and Computer Software journal in 2019.