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| Presentation | 2023-06-30 14:20 Analogy Tasks in BioConceptVec using Biological Pathways Hiroaki Yamagiwa, Ryoma Hashimoto (Kyoto Univ.), Kiwamu Arakane, Ken Murakami (IPR), Momose Oyama, Hidetoshi Shimodaira (Kyoto Univ.), Mariko Okada (IPR)  NC2023-18 IBISML2023-18 |
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| Abstract | (in Japanese) | (See Japanese page) |
| (in English) | Natural language processing (NLP), often employing models like skip-gram, is widely utilized across numerous application domains to convert words in text into feature vectors known as word embeddings. The utility of this approach has recently been noted in the field of biology, with the introduction of BioConceptVec, a model trained on about 30 million PubMed abstracts using normalized concepts. In general, skip-gram can solve analogy tasks by manipulating word embeddings, such as predicting $emph{text{queen}}$ from $emph{text{king}} - emph{text{man}} + emph{text{woman}}$. In this study, we applied this principle to biological pathways, conducting analogy tasks for pairs of drugs and genes, treating pathway types as relationships. Our results demonstrated high accuracy in these tasks when defining a vector to represent the pathway relationship for pairs of drugs and genes that belong to the same pathway. | |
| Keyword | (in Japanese) | (See Japanese page) |
| (in English) | natural language processing / distributed representations / word embeddings / analogy / Biology / PubMed / / | |
| Reference Info. | IEICE Tech. Rep., vol. 123, no. 91, IBISML2023-18, pp. 113-120, June 2023. | |
| Paper # | IBISML2023-18 | |
| Date of Issue | 2023-06-22 (NC, IBISML) | |
| ISSN | Online edition: ISSN 2432-6380 | |
| Copyright and reproduction |
All rights are reserved and no part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopy, recording, or any information storage and retrieval system, without permission in writing from the publisher. Notwithstanding, instructors are permitted to photocopy isolated articles for noncommercial classroom use without fee. (License No.: 10GA0019/12GB0052/13GB0056/17GB0034/18GB0034) | |
| Download PDF | NC2023-18 IBISML2023-18 |
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| Conference Information | |
| Committee | NC IBISML IPSJ-BIO IPSJ-MPS |
| Conference Date | 2023-06-29 - 2023-07-01 |
| Place (in Japanese) | (See Japanese page) |
| Place (in English) | OIST Conference Center |
| Topics (in Japanese) | (See Japanese page) |
| Topics (in English) | |
| Paper Information | |
| Registration To | IBISML |
| Conference Code | 2023-06-NC-IBISML-BIO-MPS |
| Language | Japanese |
| Title (in Japanese) | (See Japanese page) |
| Sub Title (in Japanese) | (See Japanese page) |
| Title (in English) | Analogy Tasks in BioConceptVec using Biological Pathways |
| Sub Title (in English) | |
| Keyword(1) | natural language processing |
| Keyword(2) | distributed representations |
| Keyword(3) | word embeddings |
| Keyword(4) | analogy |
| Keyword(5) | Biology |
| Keyword(6) | PubMed |
| Keyword(7) | |
| Keyword(8) | |
| 1st Author's Name | Hiroaki Yamagiwa |
| 1st Author's Affiliation | Kyoto University (Kyoto Univ.) |
| 2nd Author's Name | Ryoma Hashimoto |
| 2nd Author's Affiliation | Kyoto University (Kyoto Univ.) |
| 3rd Author's Name | Kiwamu Arakane |
| 3rd Author's Affiliation | Institute for Protein Research, Osaka University (IPR) |
| 4th Author's Name | Ken Murakami |
| 4th Author's Affiliation | Institute for Protein Research, Osaka University (IPR) |
| 5th Author's Name | Momose Oyama |
| 5th Author's Affiliation | Kyoto University (Kyoto Univ.) |
| 6th Author's Name | Hidetoshi Shimodaira |
| 6th Author's Affiliation | Kyoto University (Kyoto Univ.) |
| 7th Author's Name | Mariko Okada |
| 7th Author's Affiliation | Institute for Protein Research, Osaka University (IPR) |
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| Speaker | Author-1 |
| Date Time | 2023-06-30 14:20:00 |
| Presentation Time | 25 minutes |
| Registration for | IBISML |
| Paper # | NC2023-18, IBISML2023-18 |
| Volume (vol) | vol.123 |
| Number (no) | no.90(NC), no.91(IBISML) |
| Page | pp.113-120 |
| #Pages | 8 |
| Date of Issue | 2023-06-22 (NC, IBISML) |
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