| Presentation | 2023-06-30 Analogy Tasks in BioConceptVec using Biological Pathways Hiroaki Yamagiwa, Ryoma Hashimoto, Kiwamu Arakane, Ken Murakami, Momose Oyama, Hidetoshi Shimodaira, Mariko Okada, |
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| PDF Download Page |  PDF download Page Link |
| Abstract(in Japanese) | (See Japanese page) |
| Abstract(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) |
| Keyword(in English) | natural language processing / distributed representations / word embeddings / analogy / Biology / PubMed |
| Paper # | NC2023-18,IBISML2023-18 |
| Date of Issue | 2023-06-22 (NC, IBISML) |
| Conference Information | |
| Committee | NC / IBISML / IPSJ-BIO / IPSJ-MPS |
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| Conference Date | 2023/6/29(3days) |
| Place (in Japanese) | (See Japanese page) |
| Place (in English) | OIST Conference Center |
| Topics (in Japanese) | (See Japanese page) |
| Topics (in English) | |
| Chair | Hirokazu Tanaka(Tokyo City Univ.) / Masashi Sugiyama(Univ. of Tokyo) |
| Vice Chair | Jun Izawa(Univ. of Tsukub) / Toshihiro Kamishima(AIST) / Koji Tsuda(Univ. of Tokyo) |
| Secretary | Jun Izawa(NTT) / Toshihiro Kamishima(NAIST) / Koji Tsuda(NTT) / (Hokkaido Univ.) |
| Assistant | Yoshimasa Tawatsuji(Waseda Univ.) / Takato Horii(Osaka Univ.) / Yoshinobu Kawahara(Osaka Univ.) / Taiji Suzuki(Tokyo Inst. of Tech.) |
| Paper Information | |
| Registration To | Technical Committee on Neurocomputing / Technical Committee on Information-Based Induction Sciences and Machine Learning / Special Interest Group on Bioinformatics and Genomics / Special Interest Group on Mathematical Modeling and Problem Solving |
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| Language | JPN |
| 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 |
| 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) |
| Date | 2023-06-30 |
| Paper # | NC2023-18,IBISML2023-18 |
| Volume (vol) | vol.123 |
| Number (no) | NC-90,IBISML-91 |
| Page | pp.pp.113-120(NC), pp.113-120(IBISML), |
| #Pages | 8 |
| Date of Issue | 2023-06-22 (NC, IBISML) |