| 2025 | IJCAI | InstGAN: Instant Actor-Critic-Driven GAN for De Novo Molecule Generation and Property Optimization. | Huidong Tang, Chen Li, Sayaka Kamei, Yoshihiro Yamanishi, Yasuhiko Morimoto |
| 2024 | AAAI | GxVAEs: Two Joint VAEs Generate Hit Molecules from Gene Expression Profiles. | Chen Li, Yoshihiro Yamanishi |
| 2024 | AISTATS | TenGAN: Pure Transformer Encoders Make an Efficient Discrete GAN for De Novo Molecular Generation. | Chen Li, Yoshihiro Yamanishi |
| 2023 | APWEB | MacGAN: A Moment-Actor-Critic Reinforcement Learning-Based Generative Adversarial Network for Molecular Generation. | Huidong Tang, Chen Li, Shuai Jiang, Huachong Yu, Sayaka Kamei, Yoshihiro Yamanishi, Yasuhiko Morimoto |
| 2022 | IJCAI | Transformer-based Objective-reinforced Generative Adversarial Network to Generate Desired Molecules. | Chen Li, Chikashige Yamanaka, Kazuma Kaitoh, Yoshihiro Yamanishi |
| 2019 | ICDM | Space-Efficient Feature Maps for String Alignment Kernels. | Yasuo Tabei, Yoshihiro Yamanishi, Rasmus Pagh |
| 2016 | KDD | Scalable Partial Least Squares Regression on Grammar-Compressed Data Matrices. | Yasuo Tabei, Hiroto Saigo, Yoshihiro Yamanishi, Simon J. Puglisi |
| 2013 | KDD | Succinct interval-splitting tree for scalable similarity search of compound-protein pairs with property constraints. | Yasuo Tabei, Akihiro Kishimoto, Masaaki Kotera, Yoshihiro Yamanishi |
| 2009 | PAKDD | On Pairwise Kernels: An Efficient Alternative and Generalization Analysis. | Hisashi Kashima, Satoshi Oyama, Yoshihiro Yamanishi, Koji Tsuda |
| 2009 | SDM | Link Propagation: A Fast Semi-supervised Learning Algorithm for Link Prediction. | Hisashi Kashima, Tsuyoshi Kato, Yoshihiro Yamanishi, Masashi Sugiyama, Koji Tsuda |
| 2008 | ISMB | Prediction of drug-target interaction networks from the integration of chemical and genomic spaces. | Yoshihiro Yamanishi, Michihiro Araki, Alex Gutteridge, Wataru Honda, Minoru Kanehisa |
| 2005 | ISMB | Supervised enzyme network inference from the integration of genomic data and chemical information. | Yoshihiro Yamanishi, Jean-Philippe Vert, Minoru Kanehisa |
| 2004 | ISMB | Protein network inference from multiple genomic data: a supervised approach. | Yoshihiro Yamanishi, Jean-Philippe Vert, Minoru Kanehisa |
| 2003 | ISMB | Extraction of correlated gene clusters from multiple genomic data by generalized kernel canonical correlation analysis. | Yoshihiro Yamanishi, Jean-Philippe Vert, Akihiro Nakaya, Minoru Kanehisa |