Inference of S-system models of genetic networks using a genetic local search. - Shuhei Kimura; Mariko Hatakeyama; Akihiko Konagaya (IEEE Congress on Evolutionary Computation, 2003)

High dimensional function optimization using a new genetic local search suitable for parallel computers. - Shuhei Kimura; Akihiko Konagaya (SMC, 2003)

OBIYagns: a grid-based biochemical simulator with a parameter estimator. - Shuhei Kimura; Takuji Kawasaki; Mariko Hatakeyama; Takashi Naka; Fumikazu Konishi; Akihiko Konagaya (Bioinform., 2004)

Inference of genetic networks using neural network models. - Shuhei Kimura; Katsuki Sonoda; Soichiro Yamane; Koki Matsumura; Mariko Hatakeyama (Congress on Evolutionary Computation, 2005)

Genetic algorithms using low-discrepancy sequences. - Shuhei Kimura; Koki Matsumura (GECCO, 2005)

Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm. - Shuhei Kimura; Kaori Ide; Aiko Kashihara; Makoto Kano; Mariko Hatakeyama; Ryoji Masui; Noriko Nakagawa; Shigeyuki Yokoyama; Seiki Kuramitsu; Akihiko Konagaya (Bioinform., 2005)

Function Approximation Approach to the Inference of Normalized Gaussian Network Models of Genetic Networks. - Shuhei Kimura; Katsuki Sonoda; Soichiro Yamane; Koki Matsumura; Mariko Hatakeyama (IJCNN, 2006)

Inference of Genetic Networks using a Reduced NGnet Model. - Shuhei Kimura; Katsuki Sonoda; Soichiro Yamane; Kotaro Yoshida; Koki Matsumura; Mariko Hatakeyama (IJCNN, 2007)

Density estimation using crossover kernels and its application to a real-coded genetic algorithm. - Shuhei Kimura; Koki Matsumura (IEEE Congress on Evolutionary Computation, 2008)

Function approximation approach to the inference of reduced NGnet models of genetic networks. - Shuhei Kimura; Katsuki Sonoda; Soichiro Yamane; Hideki Maeda; Koki Matsumura; Mariko Hatakeyama (BMC Bioinform., 2008)

Inference of genetic networks using linear programming machines: Application of a priori knowledge. - Shuhei Kimura; Yuichi Shiraishi; Mariko Hatakeyama (IJCNN, 2009)

Genetic network inference as a series of discrimination tasks. - Shuhei Kimura; Satoshi Nakayama; Mariko Hatakeyama (Bioinform., 2009)

Effective parameter estimation for S-system models using LPMs and evolutionary algorithms. - Shuhei Kimura; Yusuke Amano; Koki Matsumura; Mariko Okada-Hatakeyama (IEEE Congress on Evolutionary Computation, 2010)

Bootstrap Analysis of Genetic Networks inferred by the Method Using LPMs. - Shuhei Kimura; Koki Matsumura; Mariko Okada-Hatakeyama (ICCSA Workshops, 2010)

Inferring cluster-based networks from differently stimulated multiple time-course gene expression data. - Yuichi Shiraishi; Shuhei Kimura; Mariko Okada (Bioinform., 2010)

Inference of Genetic Networks Using Lpms: Assessment of Confidence Values of Regulations. - Shuhei Kimura; Yuichi Shiraishi; Mariko Okada (J. Bioinform. Comput. Biol., 2010)

Constrained multimodal function optimization using a simple evolutionary algorithm. - Shuhei Kimura; Koki Matsumura (IEEE Congress on Evolutionary Computation, 2011)

Computation of restoration of ligand response in the random kinetics of a prostate cancer cell signaling pathway. - Saswati Dana; Takashi Nakakuki; Mariko Hatakeyama; Shuhei Kimura; Soumyendu Raha (Comput. Methods Programs Biomed., 2011)

Move code refactoring with dynamic analysis. - Shuhei Kimura; Yoshiki Higo; Hiroshi Igaki; Shinji Kusumoto (ICSM, 2012)

Inference of S-system models of genetic networks by solving linear programming problems and sets of linear algebraic equations. - Shuhei Kimura; Koki Matsumura; Mariko Okada-Hatakeyama (IJCNN, 2012)

Development of an efficient parameter estimation method for the inference of Vohradský's neural network models of genetic networks. - Shuhei Kimura; Masanao Sato; Mariko Okada-Hatakeyama (IJCNN, 2013)

Does return null matter? - Shuhei Kimura; Keisuke Hotta; Yoshiki Higo; Hiroshi Igaki; Shinji Kusumoto (CSMR-WCRE, 2014)

Improvement of reliabilities of regulations using a hierarchical structure in a genetic network. - Shuhei Kimura; Mariko Okada-Hatakeyama (IJCNN, 2015)

An Effective Method for the Inference of Reduced S-system Models of Genetic Networks. - Shuhei Kimura; Masanao Sato; Mariko Okada-Hatakeyama (Inf. Media Technol., 2015)

Recommending paragraphs of wikipedia pages as a travel guide. - Masato Tokuhisa; Yuuki Ishihara; Shuhei Kimura; Kenta Oku (IWCIA, 2016)

Simultaneous execution method of gene clustering and network inference. - Shuhei Kimura; Masato Tokuhisa; Mariko Okada-Hatakeyama (CIBCB, 2016)

Inference of genetic networks from time-series of gene expression levels using random forests. - Shuhei Kimura; Masato Tokuhisa; Mariko Okada-Hatakeyama (CIBCB, 2017)

Inference of Genetic Networks Using Random Forests: Use of Different Weights for Time-Series and Static Gene Expression Data. - Shuhei Kimura; Masato Tokuhisa; Mariko Okada-Hatakeyama (BIBE, 2018)

Feature Selection based on Random Forests and its Application to a Modeling of Sewage Treatment Plant. - Shuhei Kimura; Masato Tokuhisa; Akiyuki Uemura; Mariko Okada (TAAI, 2019)

Inference of genetic networks using random forests: Assigning different weights for gene expression data. - Shuhei Kimura; Masato Tokuhisa; Mariko Okada (J. Bioinform. Comput. Biol., 2019)

Detection of Weak Relevant Variables using Random Forests. - Shuhei Kimura; Masato Tokuhisa (SICE, 2020)

Admittance Control-based Bilateral Control System Considering Position Error. - Shuhei Kimura; Takahiro Nozaki; Toshiyuki Murakami (ICM, 2021)

Feature Selection using Modified Null Importance. - Shuhei Kimura; Daichi Oda; Masato Tokuhisa (SSCI, 2021)

Inference of Genetic Networks using Random Forests: A Quantitative Weighting Method for Gene Expression Data. - Shuhei Kimura; Kazuki Sota; Masato Tokuhisa (CIBCB, 2022)

Inference of Genetic Networks from Steady-State and Pseudo Time-Series of Single-Cell Gene Expression Data using Modified Random Forests. - Shuhei Kimura; Hirotaka Kitajima; Masato Tokuhisa; Mariko Okada (SSCI, 2023)

A Bias in Training Data Degrades the Quality of Variable Importance Scores of Random Forests. - Shuhei Kimura; Kenta Yuasa; Masato Tokuhisa (SCIS/ISIS, 2024)