| 2020 | ICISSP | Improving Accuracy and Speed of Network-based Intrusion Detection using Gradient Boosting Trees. | Ryosuke Terado, Morihiro Hayashida |
| 2018 | BIBE | Convolutional Neural Network Approach to Lung Cancer Classification Integrating Protein Interaction Network and Gene Expression Profiles. | Teppei Matsubara, Tomoshiro Ochiai, Morihiro Hayashida, Tatsuya Akutsu, Jose C. Nacher |
| 2016 | BIBE | Host-Pathogen Protein Interaction Prediction Based on Local Topology Structures of a Protein Interaction Network. | Jira Jindalertudomdee, Morihiro Hayashida, Jiangning Song, Tatsuya Akutsu |
| 2008 | APBC | Image Compression-based Approach to Measuring the Similarity of Protein Structures. | Morihiro Hayashida, Tatsuya Akutsu |
| 2007 | APBC | A Novel Clustering Method for Analysis of Biological Networks using Maximal Components of Graphs. | Morihiro Hayashida, Tatsuya Akutsu, Hiroshi Nagamochi |
| 2006 | APBC | On the Complexity of Finding Control Strategies for Boolean Networks. | Tatsuya Akutsu, Morihiro Hayashida, Wai-Ki Ching, Michael K. Ng |
| 2004 | BIBE | Protein Threading with Profiles and Constraints. | Tatsuya Akutsu, Morihiro Hayashida, Etsuji Tomita, Jun'ichi Suzuki, Katsuhisa Horimoto |
| 2003 | ECCB | Inferring strengths of protein-protein interactions from experimental data using linear programming. | Morihiro Hayashida, Nobuhisa Ueda, Tatsuya Akutsu |