Sharma, Ashika, Jayakumar, Jaikishan, Mitra, Partha P, Chakraborti, Sutanu, Kumar, P Sreenivasa (June 2021) Application of Supervised Machine Learning to Extract Brain Connectivity Information from Neuroscience Research Articles. Interdisciplinary Sciences: Computational Life Sciences. ISSN 1913-2751
Abstract
Understanding the complex connectivity structure of the brain is a major challenge in neuroscience. Vast and ever-expanding literature about neuronal connectivity between brain regions already exists in published research articles and databases. However, with the ever-expanding increase in published articles and repositories, it becomes difficult for a neuroscientist to engage with the breadth and depth of any given field within neuroscience. Natural Language Processing (NLP) techniques can be used to mine 'Brain Region Connectivity' information from published articles to build a centralized connectivity resource helping neuroscience researchers to gain quick access to research findings. Manually curating and continuously updating such a resource involves significant time and effort. This paper presents an application of supervised machine learning algorithms that perform shallow and deep linguistic analysis of text to automatically extract connectivity between brain region mentions. Our proposed algorithms are evaluated using benchmark datasets collated from PubMed and our own dataset of full text articles annotated by a domain expert. We also present a comparison with state-of-the-art methods including BioBERT. Proposed methods achieve best recall and [Formula: see text] scores negating the need for any domain-specific predefined linguistic patterns. Our paper presents a novel effort towards automatically generating interpretable patterns of connectivity for extracting connected brain region mentions from text and can be expanded to include any other domain-specific information.
| Item Type: | Paper |
|---|---|
| Subjects: | bioinformatics bioinformatics > computational biology > algorithms organs, tissues, organelles, cell types and functions > organs types and functions > brain bioinformatics > computational biology bioinformatics > computational biology > algorithms > machine learning neurobiology neurobiology > neuroscience organs, tissues, organelles, cell types and functions > organs types and functions organs, tissues, organelles, cell types and functions |
| CSHL Authors: | |
| Communities: | CSHL labs > Mitra lab |
| SWORD Depositor: | CSHL Elements |
| Depositing User: | CSHL Elements |
| Date: | 2 June 2021 |
| Date Deposited: | 21 Jun 2021 18:11 |
| Last Modified: | 25 Jan 2024 16:41 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/40221 |
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