Protein homology detection using string alignment kernels. - Hiroto Saigo; Jean-Philippe Vert; Nobuhisa Ueda; Tatsuya Akutsu (Bioinform., 2004)

Graph kernels for chemical informatics. - Liva Ralaivola; Sanjay Joshua Swamidass; Hiroto Saigo; Pierre Baldi (Neural Networks, 2005)

Optimizing amino acid substitution matrices with a local alignment kernel. - Hiroto Saigo; Jean-Philippe Vert; Tatsuya Akutsu (BMC Bioinform., 2006)

Functional Census of Mutation Sequence Spaces: The Example of p53 Cancer Rescue Mutants. - Samuel A. Danziger; Sanjay Joshua Swamidass; Jue Zeng; Lawrence R. Dearth; Qiang Lu; Jonathan H. Chen; Jianlin Cheng; Vinh P. Hoang; Hiroto Saigo; Ray Luo 001; Pierre Baldi; Rainer K. Brachmann; et al. (IEEE ACM Trans. Comput. Biol. Bioinform., 2006)

Mining complex genotypic features for predicting HIV-1 drug resistance. - Hiroto Saigo; Takeaki Uno; Koji Tsuda (Bioinform., 2007)

Iterative Subgraph Mining for Principal Component Analysis. - Hiroto Saigo; Koji Tsuda (ICDM, 2008)

Regression with interval output values. - Hisashi Kashima; Kazutaka Yamasaki; Akihiro Inokuchi; Hiroto Saigo (ICPR, 2008)

Partial least squares regression for graph mining. - Hiroto Saigo; Nicole Krämer 002; Koji Tsuda (KDD, 2008)

A Bayesian Approach to Graphy Regression with Relevant Subgraph Selection. - Silvia Chiappa; Hiroto Saigo; Koji Tsuda (SDM, 2009)

gBoost: a mathematical programming approach to graph classification and regression. - Hiroto Saigo; Sebastian Nowozin; Tadashi Kadowaki; Taku Kudo; Koji Tsuda (Mach. Learn., 2009)

Reaction graph kernels predict EC numbers of unknown enzymatic reactions in plant secondary metabolism. - Hiroto Saigo; Masahiro Hattori; Hisashi Kashima; Koji Tsuda (BMC Bioinform., 2010)

Graph Classification. - Koji Tsuda; Hiroto Saigo (Managing and Mining Graph Data, 2010)

Matrix Decomposition-based Dimensionality Reduction on Graph Data. - Hiroto Saigo; Koji Tsuda (Graph Data Management, 2011)

Extracting Sets of Chemical Substructures and Protein Domains Governing Drug-Target Interactions. - Yoshihiro Yamanishi; Edouard Pauwels; Hiroto Saigo; Véronique Stoven (J. Chem. Inf. Model., 2011)

Protein Clustering on a Grassmann Manifold. - Chendra Hadi Suryanto; Hiroto Saigo; Kazuhiro Fukui (PRIB, 2012)

Fast Iterative Mining Using Sparsity-Inducing Loss Functions. - Hiroto Saigo; Hisashi Kashima; Koji Tsuda (IEICE Trans. Inf. Syst., 2013)

Mining Discriminative Patterns from Graph Data with Multiple Labels and Its Application to Quantitative Structure-Activity Relationship (QSAR) Models. - Zheng Shao; Yuya Hirayama; Yoshihiro Yamanishi; Hiroto Saigo (J. Chem. Inf. Model., 2015)

Scalable Partial Least Squares Regression on Grammar-Compressed Data Matrices. - Yasuo Tabei; Hiroto Saigo; Yoshihiro Yamanishi; Simon J. Puglisi (KDD, 2016)

KDSNP: A kernel-based approach to detecting high-order SNP interactions. - Kento Kodama; Hiroto Saigo (J. Bioinform. Comput. Biol., 2016)

CNN-BLPred: a Convolutional neural network based predictor for β-Lactamases (BL) and their classes. - Clarence White; Hamid D. Ismail; Hiroto Saigo; K. C. Dukka B. (BMC Bioinform., 2017)

Entire Regularization Path for Sparse Nonnegative Interaction Model. - Mirai Takayanagi; Yasuo Tabei; Hiroto Saigo (ICDM, 2018)

RF-NR: Random Forest Based Approach for Improved Classification of Nuclear Receptors. - Hamid D. Ismail; Hiroto Saigo; K. C. Dukka B. (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Structural Class Classification of 3D Protein Structure Based on Multi-View 2D Images. - Chendra Hadi Suryanto; Hiroto Saigo; Kazuhiro Fukui (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Automatically mining Relevant Variable Interactions Via Sparse Bayesian Learning. - Ryoichiro Yafune; Daisuke Sakuma; Mirai Takayanagi; Yasuo Tabei; Noritaka Saito; Hiroto Saigo (ICPR, 2020)

Context-Aware Latent Dirichlet Allocation for Topic Segmentation. - Wenbo Li 011; Tetsu Matsukawa; Hiroto Saigo; Einoshin Suzuki (PAKDD (1), 2020)

DeepSuccinylSite: a deep learning based approach for protein succinylation site prediction. - Niraj Thapa; Meenal Chaudhari; Sean McManus; Kaushik Roy 003; Robert H. Newman; Hiroto Saigo; Dukka B. KC (BMC Bioinform., 2020)

Sparse Nonnegative Interaction Models. - Mirai Takayanagi; Yasuo Tabei; Einoshin Suzuki; Hiroto Saigo (IEEE Access, 2021)

Topic modeling for sequential documents based on hybrid inter-document topic dependency. - Wenbo Li 011; Hiroto Saigo; Bin Tong; Einoshin Suzuki (J. Intell. Inf. Syst., 2021)

Correction: DeepSuccinylSite: a deep learning based approach for protein succinylation site prediction. - Niraj Thapa; Meenal Chaudhari; Sean McManus; Kaushik Roy 003; Robert H. Newman; Hiroto Saigo; K. C. Dukka B. (BMC Bioinform., 2022)

pLMSNOSite: an ensemble-based approach for predicting protein S-nitrosylation sites by integrating supervised word embedding and embedding from pre-trained protein language model. - Pawel Pratyush; Suresh Pokharel; Hiroto Saigo; Dukka B. KC (BMC Bioinform., 2023)

A Branch-and-Bound Approach to Efficient Classification and Retrieval of Documents. - Kotaro Ii; Hiroto Saigo; Yasuo Tabei (ICPRAM, 2024)

Benchmarking a Wide Range of Unsupervised Learning Methods for Detecting Anomaly in Blast Furnace. - Kendai Itakura; Dukka Bahadur; Hiroto Saigo (ICPRAM, 2024)

MedMimic: Physician-Inspired Multimodal Fusion for Early Diagnosis of Fever of Unknown Origin. - Minrui Chen; Yi Zhou; Huidong Jiang; Yuhan Zhu; Guanjie Zou; Minqi Chen; Rong Tian; Hiroto Saigo (CoRR, 2025)