Gonzalez Hernandez, Ferran;
Smith, Victoria;
Nguyen, Quang;
Chotsiri, Palang;
Wattanakul, Thanaporn;
Antonio cordero, José;
Rosa Ballester, Maria;
... Kloprogge, Frank; + view all
(2024)
End-to-End Relation Extraction of Pharmacokinetic Estimates from the
Scientific Literature.
In: Demner-Fushman, Dina and Ananiadou, Sophia and Miwa, Makoto and Roberts, Kirk and Tsujii, Junichi, (eds.)
Proceedings of the 23rd Workshop on Biomedical Natural Language Processing.
(pp. pp. 144-154).
Association for Computational Linguistics: Bangkok, Thailand.
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Abstract
The lack of comprehensive and standardised databases containing Pharmacokinetic (PK) parameters presents a challenge in the drug development pipeline. Efficiently managing the increasing volume of published PK Parameters requires automated approaches that centralise information from diverse studies. In this work, we present the Pharmacokinetic Relation Extraction Dataset (PRED), a novel, manually curated corpus developed by pharmacometricians and NLP specialists, covering multiple types of PK parameters and numerical expressions reported in open-access scientific articles. PRED covers annotations for various entities and relations involved in PK parameter measurements from 3,600 sentences. We also introduce an end-to-end relation extraction model based on BioBERT, which is trained with joint named entity recognition (NER) and relation extraction objectives. The optimal pipeline achieved a micro-average F1-score of 94% for NER and over 85% F1-score across all relation types. This work represents the first resource for training and evaluating models for PK end-to-end extraction across multiple parameters and study types. We make our corpus and model openly available to accelerate the construction of large PK databases and to support similar endeavours in other scientific disciplines.
| Type: | Proceedings paper |
|---|---|
| Title: | End-to-End Relation Extraction of Pharmacokinetic Estimates from the Scientific Literature |
| Event: | The 62nd Annual Meeting of the Association for Computational Linguistics |
| Location: | Thailand |
| Dates: | 11 Aug 2024 - 16 Aug 2024 |
| ISBN-13: | 979-8-89176-130-8 |
| Open access status: | An open access version is available from UCL Discovery |
| Publisher version: | https://aclanthology.org/2024.bionlp-1.12/ |
| Language: | English |
| Additional information: | Creative Commons Attribution 4.0 International License, https://creativecommons.org/licenses/by/4.0/. |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences |
| URI: | https://discovery-pp.ucl.ac.uk/id/eprint/10197152 |
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