LiSA: an assisted literature search pipeline for detecting serious adverse drug events with deep learning
Abstract Introduction Detecting safety signals attributed to a drug in scientific literature is a fundamental issue in pharmacovigilance. The constant increase in the volume of publications requires the automation of this tedious task, in order to find and extract relevant articles from the pack. Th...
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| Format: | Article |
| Language: | English |
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BMC
2022-12-01
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| Series: | BMC Medical Informatics and Decision Making |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12911-022-02085-0 |
| _version_ | 1797977440846348288 |
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| author | Vincent Martenot Valentin Masdeu Jean Cupe Faustine Gehin Margot Blanchon Julien Dauriat Alexander Horst Michael Renaudin Philippe Girard Jean-Daniel Zucker |
| author_facet | Vincent Martenot Valentin Masdeu Jean Cupe Faustine Gehin Margot Blanchon Julien Dauriat Alexander Horst Michael Renaudin Philippe Girard Jean-Daniel Zucker |
| author_sort | Vincent Martenot |
| collection | DOAJ |
| description | Abstract Introduction Detecting safety signals attributed to a drug in scientific literature is a fundamental issue in pharmacovigilance. The constant increase in the volume of publications requires the automation of this tedious task, in order to find and extract relevant articles from the pack. This task is critical, as serious Adverse Drug Reactions (ADRs) still account for a large number of hospital admissions each year. Objectives The aim of this study is to develop an augmented intelligence methodology for automatically identifying relevant publications mentioning an established link between a Drug and a Serious Adverse Event, according to the European Medicines Agency (EMA) definition of seriousness. Methods The proposed pipeline, called LiSA (for Literature Search Application), is based on three independent deep learning models supporting a precise detection of safety signals in the biomedical literature. By combining a Bidirectional Encoder Representations from Transformers (BERT) algorithms and a modular architecture, the pipeline achieves a precision of 0.81 and a recall of 0.89 at sentences level in articles extracted from PubMed (either abstract or full-text). We also measured that by using LiSA, a medical reviewer increases by a factor of 2.5 the number of relevant documents it can collect and evaluate compared to a simple keyword search. In the interest of re-usability, emphasis was placed on building a modular pipeline allowing the insertion of other NLP modules to enrich the results provided by the system, and extend it to other use cases. In addition, a lightweight visualization tool was developed to analyze and monitor safety signal results. Conclusions Overall, the generic pipeline and the visualization tool proposed in this article allows for efficient and accurate monitoring of serious adverse drug reactions from the literature and can easily be adapted to similar pharmacovigilance use cases. To facilitate reproducibility and benefit other research studies, we also shared a first benchmark dataset for Serious Adverse Drug Events detection. |
| first_indexed | 2024-04-11T05:06:57Z |
| format | Article |
| id | doaj.art-e77bc466270f4498a9df7b2c803ce673 |
| institution | Directory Open Access Journal |
| issn | 1472-6947 |
| language | English |
| last_indexed | 2024-04-11T05:06:57Z |
| publishDate | 2022-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Medical Informatics and Decision Making |
| spelling | doaj.art-e77bc466270f4498a9df7b2c803ce6732022-12-25T12:18:45ZengBMCBMC Medical Informatics and Decision Making1472-69472022-12-0122111610.1186/s12911-022-02085-0LiSA: an assisted literature search pipeline for detecting serious adverse drug events with deep learningVincent Martenot0Valentin Masdeu1Jean Cupe2Faustine Gehin3Margot Blanchon4Julien Dauriat5Alexander Horst6Michael Renaudin7Philippe Girard8Jean-Daniel Zucker9QuintenQuintenQuintenQuintenQuintenQuintenSwiss Agency for Therapeutic Products, SwissmedicSwiss Agency for Therapeutic Products, SwissmedicSwiss Agency for Therapeutic Products, SwissmedicUMMISCO, Sorbonne University, IRDAbstract Introduction Detecting safety signals attributed to a drug in scientific literature is a fundamental issue in pharmacovigilance. The constant increase in the volume of publications requires the automation of this tedious task, in order to find and extract relevant articles from the pack. This task is critical, as serious Adverse Drug Reactions (ADRs) still account for a large number of hospital admissions each year. Objectives The aim of this study is to develop an augmented intelligence methodology for automatically identifying relevant publications mentioning an established link between a Drug and a Serious Adverse Event, according to the European Medicines Agency (EMA) definition of seriousness. Methods The proposed pipeline, called LiSA (for Literature Search Application), is based on three independent deep learning models supporting a precise detection of safety signals in the biomedical literature. By combining a Bidirectional Encoder Representations from Transformers (BERT) algorithms and a modular architecture, the pipeline achieves a precision of 0.81 and a recall of 0.89 at sentences level in articles extracted from PubMed (either abstract or full-text). We also measured that by using LiSA, a medical reviewer increases by a factor of 2.5 the number of relevant documents it can collect and evaluate compared to a simple keyword search. In the interest of re-usability, emphasis was placed on building a modular pipeline allowing the insertion of other NLP modules to enrich the results provided by the system, and extend it to other use cases. In addition, a lightweight visualization tool was developed to analyze and monitor safety signal results. Conclusions Overall, the generic pipeline and the visualization tool proposed in this article allows for efficient and accurate monitoring of serious adverse drug reactions from the literature and can easily be adapted to similar pharmacovigilance use cases. To facilitate reproducibility and benefit other research studies, we also shared a first benchmark dataset for Serious Adverse Drug Events detection.https://doi.org/10.1186/s12911-022-02085-0Adverse drug eventsAssisted literature reviewDeep LearningNLP |
| spellingShingle | Vincent Martenot Valentin Masdeu Jean Cupe Faustine Gehin Margot Blanchon Julien Dauriat Alexander Horst Michael Renaudin Philippe Girard Jean-Daniel Zucker LiSA: an assisted literature search pipeline for detecting serious adverse drug events with deep learning BMC Medical Informatics and Decision Making Adverse drug events Assisted literature review Deep Learning NLP |
| title | LiSA: an assisted literature search pipeline for detecting serious adverse drug events with deep learning |
| title_full | LiSA: an assisted literature search pipeline for detecting serious adverse drug events with deep learning |
| title_fullStr | LiSA: an assisted literature search pipeline for detecting serious adverse drug events with deep learning |
| title_full_unstemmed | LiSA: an assisted literature search pipeline for detecting serious adverse drug events with deep learning |
| title_short | LiSA: an assisted literature search pipeline for detecting serious adverse drug events with deep learning |
| title_sort | lisa an assisted literature search pipeline for detecting serious adverse drug events with deep learning |
| topic | Adverse drug events Assisted literature review Deep Learning NLP |
| url | https://doi.org/10.1186/s12911-022-02085-0 |
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