2026)
- Yuji Okamoto, Transformers for Time-Series Forecasting: A Comprehensive Survey through 2024, NOLTA, E17-N(1), 2026/1, (In press)
2025)
- Ito S, Koyama T, Matsumoto S, Kojima R, Okamoto Y, Kuroda M, Kawashima H, Watanabe R, Yonezawa T, Sumiyoshi T, Ikeda K, Mizuguchi K, Iwata H, Okuno Y, Improving ADME Prediction with Multitask Graph Neural Networks and Assessing Explainability in Lead Optimization, J Chem Inf Model, 65(21):11796-11803, 2025/11/10, Epub 2025 Oct 22, doi:10.1021/acs.jcim.5c00758
- Takashi Nakaoku, Shigenari Nukaga, Kouya Shiraishi, Kenta Hamabe, Akifumi Mochizuki, Yu Hamaguchi, Emi Ogawa, Nguyen Le, Yoko Shimada, Hanako Ono, Hitomi Nishinakamura, Yoshihisa Kobayashi, Junko Hamamoto, Ayako Ui, Mitsugu Araki, Yukari Sagae, Keiko Ohgino, Kai Sugihara, Satoshi Endo, Jun Miyakoshi, Yuichi Shiraishi, Hiroyuki Yasuda, Yasushi Okuno, Tatsuya Yoshida, Yasushi Goto, Yuichiro Ohe, Shun-ichi Watanabe, Yasushi Yatabe, Hiroyoshi Nishikawa, Ryuji Hamamoto, and Takashi Kohno, Mutation of CMTR2 in Lung Adenocarcinoma Alters RNA Alternative Splicing and Reveals Therapeutic Vulnerabilities, Nature Communications, 2025, (In press)
- Takuto Koyama, Hiroaki Iwata, Ryosuke Kojima, Takao Otsuka, Aki Hasegawa, Hiroshi Ueda, Toshiharu Morimoto, Ryoko Sasaki, Nao Torimoto, Sei Murakami, Manabu Tojo, Teruki Honma, Shigeyuki Matsumoto, Yasushi Okuno, Empowering Federated Learning for Robust Compound-Protein Interaction Prediction across Heterogeneous Cross-Pharma Domains, ChemRxiv, 2025/9/24, https://chemrxiv.org/engage/chemrxiv/article-details/68cbfe759008f1a46762e3e810.1371/journal.pone.0331650
- Yamamoto T*, Sakuragi M*, Tuji Y, Okamoto Y, Uchino E, Yanagita M, Muto M, Kamada M, Okuno Y, Predicting mortality dynamics in cancer patients: A machine learning approach to pre-death events, PLoS One, 20(9):e0331650, 2025/9/9, doi:10.1371/journal.pone.0331650
- Minoru Sakuragi, Riko Asada, Mayumi Kamada, Yasushi Okuno, Multimodal Gene–Environment Modeling of Disease Onset Using a Context-Aware Genome Language Model, Proceedings of IIBMP 2025(Oral Presentation (Peer-reviewed)), 2025/9/4
- Sakuragi M, Suzuki H, Sumitomo R, Ishimura T, Hayashi A, Kakita H, Niwa A, Higashi Y, Huang C, Matsubara T, & Tsukamoto T, Identifying Multiple Pleuroperitoneal Communications by Computed Tomography Peritoneography, Kidney International, 108(2):332, 2025/8, doi:10.1016/j.kint.2025.03.024
- Shuntaro Chiba , Yasushi Okuno, In Silico Prediction and Selection of Exon-Skipping Antisense Oligonucleotide Sequences Using eSkip-Finder, Methods Mol Biol., 2025;2964:109-116, 2025/7/29, doi:10.1007/978-1-0716-4730-1_6
- Akada M, Tabuchi H, Okamoto Y, Tanabe M, Nishikawa R, Yamane S, Tsujikawa A, Okuno Y, Quantitative Assessment of Microsurgical Skill in Intrascleral Fixation Surgery Using Wearable Strain Sensors: A Pilot Study, Transl Vis Sci Technol., 14(7):7, 2025/7/1, doi:10.1167/tvst.14.7.7
- Sho Oshima*, Yuji Okamoto*, Taisei Tosaki, Ryosuke Kojima, Yasushi Okuno (*Equal Contribution), Supervised Graph Contrastive Learning for Gene Regulatory Network, arXiv:2505.17786v2 , 2025/6/5, https://arxiv.org/pdf/2505.17786
- Taisei Tosaki, Eiichiro Uchino, Ryosuke Kojima, Yohei Mineharu, Yuji Okamoto, Mikio Arita, Nobuyuki Miyai, Yoshinori Tamada, Tatsuya Mikami, Koichi Murashita, Shigeyuki Nakaji, Yasushi Okuno, Out-of-distribution reject option method for dataset shift problem in early disease onset prediction, Sci Rep, 15(1):19240, 2025/6/2, doi:10.1038/s41598-025-01811-8
- 戸﨑泰誠, 荒武奈々瑛, 岡本有司, 内野詠一郎, 小島諒介, 奥野恭史, 区分線形埋め込みを用いた Decoder 型 Tabualr Transformer モデルの検討, 2025年度人工知能学会全国大会論文集(第39回), pp. 2Win505-2Win505, 2025/5/27-5/30, https://doi.org/10.11517/pjsai.JSAI2025.0_2Win505
- 荒武奈々瑛, 戸﨑泰誠, 岡本有司, 内野詠一郎, 小島諒介, 奥野恭史, Tabular Transformer のラベル名と値に対して独立な新しい Masked Prediction 手法の提案と検討, 2025年度人工知能学会全国大会論文集(第39回), pp. 2Win506-2Win506, 2025/5/27-5/30, https://doi.org/10.11517/pjsai.JSAI2025.0_2Win506
- 大島将, 岡本有司, 戸﨑泰誠, 奥野恭史, ノックダウン細胞株の遺伝子制御ネットワークを用いたグラフニューラルネットワークの転移学習と薬剤応答推定, 2025年度人工知能学会全国大会論文集(第39回), pp. 3H5OS10c04-3H5OS10c04, 2025/5/27-5/30, https://doi.org/10.11517/pjsai.JSAI2025.0_3H5OS10c04
- Yusuke Sakemi, Yuji Okamoto, Takashi Morie, Sou Nobukawa, Takeo Hosomi, Kazuyuki Aihara, (2025). Harnessing Nonidealities in Analog In-Memory Computing Circuits: A Physical Modeling Approach for Neuromorphic Systems, arXiv:2412.09010, 2025/5/21(ver2), Advanced Intelligent Systems 2025. (In Production) , https://arxiv.org/abs/2412.09010
- Yuji Okamoto, Tomoya Takeuchi, Yusuke Sakemi, (2025). Learning the Simplest Neural ODE, arXiv:2505.02019, 2025/5/4, 2025 SICE Festival with Annual Conference (SICE FES). (accepted), https://arxiv.org/abs/2505.02019
- Shoma Ito, Takuto Koyama, Shigeyuki Matsumoto, Ryosuke Kojima, Yuji Okamoto, Masataka Kuroda, Hitoshi Kawashima, Reiko Watanabe, Tomoki Yonezawa, Takaaki Sumiyoshi, Kazuyoshi Ikeda, Kenji Mizuguchi, Hiroaki Iwata, Yasushi Okuno, (2025) Improving ADME Prediction with Multitask Graph Neural Networks and Assessing Explainability in Lead Optimization, ChemRxiv, 2025/4/25, https://chemrxiv.org/engage/chemrxiv/article-details/680aee7350018ac7c512f652
- Mineharu Y, Kamata T, Tomoto M, Sato N, Tamada Y, Funaki T, Oichi Y, Harada KH, Koizumi A, Kimura T, Inoue I, Okuno Y, Miyamoto S, Arakawa Y, Peripheral blood GATA2 expression impacts RNF213 mutation penetrance and clinical severity in moyamoya disease, Stroke Vasc Neurol, svn-2024-003970. Epub ahead of print, 2025/4/23, doi:10.1136/svn-2024-003970
- Imamura T, Makiyama T, Ozawa J, Sonoda K, Kato K, Aizawa T, Kashiwa A, Gao J, Huang H, Yamamoto Y, Kohjitani H, Aoki H, Watanabe S, Muraji S, Kojima T, Yoshinaga M, Ohno S, Suzuki H, Sumitomo N, Nakagawa Y, Ono K, Horie M, Kimura T, Sex-specific clinical course of young patients with Brugada syndrome, European heart journal, 46(13):1263-1266, 2025/4/1, doi:10.1093/eurheartj/ehae739
- Fujii T, Murata K, Kohjitani H, Onishi A, Murakami K, Tanaka M, Yamamoto W, Nagai K, Yoshikawa A, Etani Y, Okita Y, Yoshida N, Amuro H, Okano T, Ueda Y, Okano T, Hara R, Hashimoto M, Morinobu A, Matsuda S, Predicting rheumatoid arthritis progression from seronegative undifferentiated arthritis using machine learning: a deep learning model trained on the KURAMA cohort and externally validated with the ANSWER cohort, Arthritis research & therapy, 27(1):65, 2025/3/26, doi:10.1186/s13075-025-03541-8
- Matsumoto S, Isaka Y, Kanada R, Ma B, Araki M, Chiba S, Tokuhisa A, Iwata H, Ishida S, Akinaga Y, Terayama K, Kojima R, Harada Y, Takemura K, Honma T, Kitao A, Okuno Y, Precision spatiotemporal analysis of large-scale compound-protein interactions through molecular dynamics simulation, PNAS Nexus, 4(3):pgaf094, 2025/3/22, doi:10.1093/pnasnexus/pgaf094
- Cozac R, Hasic H, Choong JJ, Richard V, Beheshti L, Froehlich C, Koyama T, Matsumoto S, Kojima R, Iwata H, Hasegawa A, Otsuka T, Okuno Y, kMoL: an open-source machine and federated learning library for drug discovery, Journal of Cheminformatics, 17(1):22, 2025/2/25 , doi:10.1186/s13321-025-00967-9
- Fujita A, Goto K, Ueda A, Kuroda Y, Kawai T, Okuzu Y, Okuno Y, Matsuda S. Measurement of the Acetabular Cup Orientation After Total Hip Arthroplasty Based on 3-Dimensional Reconstruction From a Single X-Ray Image Using Generative Adversarial Networks, The Journal of Arthroplasty, 40(1):136-143.e1., 2025/1, doi:10.1016/j.arth.2024.06.059
