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  4. Benchmarking table recognition performance on biomedical literature on neurological disorders
 
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2022
Journal Article
Title

Benchmarking table recognition performance on biomedical literature on neurological disorders

Abstract
Table recognition systems are widely used to extract and structure quantitative information from the vast amount of documents that are increasingly available from different open sources. While many systems already perform well on tables with a simple layout, tables in the biomedical domain are often much more complex. Benchmark and training data for such tables are however very limited. To address this issue, we present a novel, highly curated benchmark dataset based on a hand-curated literature corpus on neurological disorders, which can be used to tune and evaluate table extraction applications for this challenging domain. We evaluate several state-of-the-art table extraction systems based on our proposed benchmark and discuss challenges that emerged during the benchmark creation as well as factors that can impact the performance of recognition methods. For the evaluation procedure, we propose a new metric as well as several improvements that result in a better performance evaluation. The resulting benchmark dataset (https://zenodo.org/record/5549977) as well as the source code to our novel evaluation approach can be openly accessed. Supplementary data are available at Bioinformatics online.
Author(s)
Adams, Tim  
Fraunhofer-Institut für Algorithmen und Wissenschaftliches Rechnen SCAI  
Namysl, Marcin  
Fraunhofer-Institut für Intelligente Analyse- und Informationssysteme IAIS  
Kodamullil, Alpha Tom
Fraunhofer-Institut für Algorithmen und Wissenschaftliches Rechnen SCAI  
Behnke, Sven  
Fraunhofer-Institut für Intelligente Analyse- und Informationssysteme IAIS  
Jacobs, Marc  
Fraunhofer-Institut für Algorithmen und Wissenschaftliches Rechnen SCAI  
Journal
Bioinformatics  
Project(s)
MAVO
Funder
Fraunhofer-Gesellschaft FhG
DOI
10.1093/bioinformatics/btab843
Language
English
Fraunhofer-Institut für Intelligente Analyse- und Informationssysteme IAIS  
Fraunhofer-Institut für Algorithmen und Wissenschaftliches Rechnen SCAI  
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