Pathway2Text: Dataset and Method for Biomedical Pathway Description Generation Article Swipe
Junwei Yang
,
Zequn Liu
,
Ming Zhang
,
Sheng Wang
·
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.18653/v1/2022.findings-naacl.108
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.18653/v1/2022.findings-naacl.108
Biomedical pathways have been extensively used to characterize the mechanism of complex diseases. One essential step in biomedical pathway analysis is to curate the description of a pathway based on its graph structure and node features. Neural text generation could be a plausible technique to circumvent the tedious manual curation. In this paper, we propose a new dataset Pathway2Text, which contains 2,367 pairs of biomedical pathways and textual descriptions. All pathway graphs are experimentally derived or manually curated. All textual descriptions are written by domain experts. We form this problem as a Graph2Text task and propose a novel graph-based text generation approach kNN-Graph2Text, which explicitly exploited descriptions of similar graphs to generate new descriptions. We observed substantial improvement of our method on both Graph2Text and the reverse task of Text2Graph. We further illustrated how our dataset can be used as a novel benchmark for biomedical named entity recognition. Collectively, we envision our method will become an important benchmark for evaluating Graph2Text methods and advance biomedical research for complex diseases.
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- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.18653/v1/2022.findings-naacl.108
- https://aclanthology.org/2022.findings-naacl.108.pdf
- OA Status
- hybrid
- Cited By
- 2
- References
- 70
- Related Works
- 10
- OpenAlex ID
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Raw OpenAlex JSON
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https://openalex.org/W4287855041Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.18653/v1/2022.findings-naacl.108Digital Object Identifier
- Title
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Pathway2Text: Dataset and Method for Biomedical Pathway Description GenerationWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2022Year of publication
- Publication date
-
2022-01-01Full publication date if available
- Authors
-
Junwei Yang, Zequn Liu, Ming Zhang, Sheng WangList of authors in order
- Landing page
-
https://doi.org/10.18653/v1/2022.findings-naacl.108Publisher landing page
- PDF URL
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https://aclanthology.org/2022.findings-naacl.108.pdfDirect link to full text PDF
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YesWhether a free full text is available
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hybridOpen access status per OpenAlex
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https://aclanthology.org/2022.findings-naacl.108.pdfDirect OA link when available
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Computer science, Benchmark (surveying), Artificial intelligence, Task (project management), Graph, Domain (mathematical analysis), Machine learning, Information retrieval, Natural language processing, Theoretical computer science, Economics, Mathematics, Geodesy, Mathematical analysis, Geography, ManagementTop concepts (fields/topics) attached by OpenAlex
- Cited by
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2Total citation count in OpenAlex
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2022: 2Per-year citation counts (last 5 years)
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70Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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| countries_distinct_count | 2 |
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