| 2006 | ISMB | ProfilePSTMM: capturing tree-structure motifs in carbohydrate sugar chains. | Kiyoko F. Aoki-Kinoshita, Nobuhisa Ueda, Hiroshi Mamitsuka, Minoru Kanehisa |
| 2006 | KDD | A new efficient probabilistic model for mining labeled ordered trees. | Kosuke Hashimoto, Kiyoko F. Aoki-Kinoshita, Nobuhisa Ueda, Minoru Kanehisa, Hiroshi Mamitsuka |
| 2004 | ICML | Extensions of marginalized graph kernels. | Pierre Mah, Nobuhisa Ueda, Tatsuya Akutsu, Jean-Luc Perret, Jean-Philippe Vert |
| 2004 | ISMB | Application of a new probabilistic model for recognizing complex patterns in glycans. | Kiyoko F. Aoki, Nobuhisa Ueda, Atsuko Yamaguchi, Minoru Kanehisa, Tatsuya Akutsu, Hiroshi Mamitsuka |
| 2004 | SDM | A General Probabilistic Framework for Mining Labeled Ordered Trees. | Nobuhisa Ueda, Kiyoko F. Aoki, Hiroshi Mamitsuka |
| 2003 | ECCB | Inferring strengths of protein-protein interactions from experimental data using linear programming. | Morihiro Hayashida, Nobuhisa Ueda, Tatsuya Akutsu |
| 2001 | DIS | Simplified Training Algorithms for Hierarchical Hidden Markov Models. | Nobuhisa Ueda, Taisuke Sato |
| 1999 | DIS | A Graphical Method for Parameter Learning of Symbolic-Statistical Models. | Yoshitaka Kameya, Nobuhisa Ueda, Taisuke Sato |