Disease Network Constructor: a Pathway Extraction and Visualization

Mohammad Golam Sohrab, Khoa Duong, Goran Topić, Masami Ikeda, Nozomi Nagano, Yayoi Natsume-Kitatani, Masakata Kuroda, Mari Itoh, Hiroya Takamura

Abstract
We present Disease Network Constructor (DNC), a system that extracts and visualizes a disease network, in which nodes are entities such as diseases, proteins, and genes, and edges represent regulation relation. We focused on the disease network derived through regulation events found in scientific articles on idiopathic pulmonary fibrosis (IPF). The front-end web-base user interface of DNC includes two-dimensional (2D) and 3D visualizations of the constructed disease network. The back-end system of DNC includes several natural language processing (NLP) techniques to process biomedical text including BERT-based tokenization on the basis of Bidirectional Encoder Representations from Transformers (BERT), flat and nested named entity recognition (NER), candidate generation and candidate ranking for entity linking (EL) or, relation extraction (RE), and event extraction (EE) tasks. We evaluated the end-to-end EL and end-to-end nested EE systems to determine the DNC’s back-endimplementation performance. To the best of our knowledge, this is the first attempt that addresses neural NER, EL, RE, and EE tasks in an end-to-end manner that constructs a path-way visualization from events, which we name Disease Network Constructor. The demonstration video can be accessed from https://youtu.be/rFhWwAgcXE8. We release an online system for end users and the source code is available at https://github.com/aistairc/PRISM-APIs/.
Anthology ID:
2023.acl-demo.53
Volume:
Proceedings of the 61st Annual Meeting of the Association for Computational Linguistics (Volume 3: System Demonstrations)
Month:
July
Year:
2023
Address:
Toronto, Canada
Venue:
ACL
SIG:
Publisher:
Association for Computational Linguistics
Note:
Pages:
549–557
Language:
URL:
https://aclanthology.org/2023.acl-demo.53
DOI:
10.18653/v1/2023.acl-demo.53
Bibkey:
Cite (ACL):
Mohammad Golam Sohrab, Khoa Duong, Goran Topić, Masami Ikeda, Nozomi Nagano, Yayoi Natsume-Kitatani, Masakata Kuroda, Mari Itoh, and Hiroya Takamura. 2023. Disease Network Constructor: a Pathway Extraction and Visualization. In Proceedings of the 61st Annual Meeting of the Association for Computational Linguistics (Volume 3: System Demonstrations), pages 549–557, Toronto, Canada. Association for Computational Linguistics.
Cite (Informal):
Disease Network Constructor: a Pathway Extraction and Visualization (Sohrab et al., ACL 2023)
Copy Citation:
PDF:
https://preview.aclanthology.org/remove-xml-comments/2023.acl-demo.53.pdf
PDF Search