Hiroshi Mamitsuka

158 papers A* 17A 10B 5C 5Misc 1Journal 103Unranked 17

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Accelerated Multiple Wasserstein Gradient Flows for Multi-objective Distributional Optimization. CoRR Dai Hai Nguyen, Duc Dung Nguyen, Atsuyoshi Nakamura, Hiroshi Mamitsuka
2026	J	`jnl`	On Convex Clustering: Convexity, Bounding Balls and Characteristics. Mach. Learn. Canh Hao Nguyen, Hiroshi Mamitsuka
2025	J	`jnl`	Beyond rigid docking: deep learning approaches for fully flexible protein-ligand interactions. Briefings Bioinform. John Lee, Canh Hao Nguyen, Hiroshi Mamitsuka
2025	A	`conf`	Multiple Wasserstein Gradient Descent Algorithm for Multi-Objective Distributional Optimization. UAI Dai Hai Nguyen, Hiroshi Mamitsuka, Atsuyoshi Nakamura
2025	J	`jnl`	Multiple Wasserstein Gradient Descent Algorithm for Multi-Objective Distributional Optimization. CoRR Dai Hai Nguyen, Hiroshi Mamitsuka, Atsuyoshi Nakamura
2025	A	`conf`	Wasserstein Gradient Flow over Variational Parameter Space for Variational Inference. AISTATS Dai Hai Nguyen, Tetsuya Sakurai, Hiroshi Mamitsuka
2024	J	`jnl`	Central-Smoothing Hypergraph Neural Networks for Predicting Drug-Drug Interactions. IEEE Trans. Neural Networks Learn. Syst. Duc Anh Nguyen, Canh Hao Nguyen, Hiroshi Mamitsuka
2024	J	`jnl`	GORetriever: reranking protein-description-based GO candidates by literature-driven deep information retrieval for protein function annotation. Bioinform. Huiying Yan, Shaojun Wang, Hancheng Liu, Hiroshi Mamitsuka, Shanfeng Zhu
2024	A*	`conf`	Learning Low-Rank Tensor Cores with Probabilistic ℓ0-Regularized Rank Selection for Model Compression. IJCAI Tianxiao Cao, Lu Sun, Canh Hao Nguyen, Hiroshi Mamitsuka
2023	J	`jnl`	DeepMHCI: an anchor position-aware deep interaction model for accurate MHC-I peptide binding affinity prediction. Bioinform. Wei Qu, Ronghui You, Hiroshi Mamitsuka, Shanfeng Zhu
2023	A	`conf`	Multiplicative Sparse Tensor Factorization for Multi-View Multi-Task Learning. ECAI Xinyi Wang, Lu Sun, Canh Hao Nguyen, Hiroshi Mamitsuka
2023	J	`jnl`	Sc2Mol: a scaffold-based two-step molecule generator with variational autoencoder and transformer. Bioinform. Zhirui Liao, Lei Xie, Hiroshi Mamitsuka, Shanfeng Zhu
2023	J	`jnl`	Wasserstein Gradient Flow over Variational Parameter Space for Variational Inference. CoRR Dai Hai Nguyen, Tetsuya Sakurai, Hiroshi Mamitsuka
2022	J	`jnl`	DIVERSE: Bayesian Data IntegratiVE Learning for Precise Drug ResponSE Prediction. IEEE ACM Trans. Comput. Biol. Bioinform. Betül Güvenç Paltun, Samuel Kaski, Hiroshi Mamitsuka
2022	J	`jnl`	DeepMHCII: a novel binding core-aware deep interaction model for accurate MHC-II peptide binding affinity prediction. Bioinform. Ronghui You, Wei Qu, Hiroshi Mamitsuka, Shanfeng Zhu
2022	J	`jnl`	HPODNets: deep graph convolutional networks for predicting human protein-phenotype associations. Bioinform. Lizhi Liu, Hiroshi Mamitsuka, Shanfeng Zhu
2022	J	`jnl`	SPARSE: a sparse hypergraph neural network for learning multiple types of latent combinations to accurately predict drug-drug interactions. Bioinform. Duc Anh Nguyen, Canh Hao Nguyen, Peter Petschner, Hiroshi Mamitsuka
2021	J	`jnl`	A survey on adverse drug reaction studies: data, tasks and machine learning methods. Briefings Bioinform. Duc Anh Nguyen, Canh Hao Nguyen, Hiroshi Mamitsuka
2021	J	`jnl`	BERTMeSH: deep contextual representation learning for large-scale high-performance MeSH indexing with full text. Bioinform. Ronghui You, Yuxuan Liu, Hiroshi Mamitsuka, Shanfeng Zhu
2021	J	`jnl`	CentSmoothie: Central-Smoothing Hypergraph Neural Networks for Predicting Drug-Drug Interactions. CoRR Duc Anh Nguyen, Canh Hao Nguyen, Hiroshi Mamitsuka
2021	J	`jnl`	DIVERSE: bayesian Data IntegratiVE learning for precise drug ResponSE prediction. CoRR Betül Güvenç Paltun, Samuel Kaski, Hiroshi Mamitsuka
2021	J	`jnl`	DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction. Bioinform. Ronghui You, Shuwei Yao, Hiroshi Mamitsuka, Shanfeng Zhu
2021	—	`conf`	Drug3D-DTI: Improved Drug-target Interaction Prediction by Incorporating Spatial Information of Small Molecules. BIBM Zhirui Liao, Xiaodi Huang, Hiroshi Mamitsuka, Shanfeng Zhu
2021	J	`jnl`	HPOFiller: identifying missing protein-phenotype associations by graph convolutional network. Bioinform. Lizhi Liu, Hiroshi Mamitsuka, Shanfeng Zhu
2021	J	`jnl`	Improving drug response prediction by integrating multiple data sources: matrix factorization, kernel and network-based approaches. Briefings Bioinform. Betül Güvenç Paltun, Hiroshi Mamitsuka, Samuel Kaski
2021	J	`jnl`	Learning on Hypergraphs With Sparsity. IEEE Trans. Pattern Anal. Mach. Intell. Canh Hao Nguyen, Hiroshi Mamitsuka
2021	J	`jnl`	Learning subtree pattern importance for Weisfeiler-Lehman based graph kernels. Mach. Learn. Dai Hai Nguyen, Canh Hao Nguyen, Hiroshi Mamitsuka
2021	J	`jnl`	Learning subtree pattern importance for Weisfeiler-Lehmanbased graph kernels. CoRR Dai Hai Nguyen, Canh Hao Nguyen, Hiroshi Mamitsuka
2021	J	`jnl`	Machine learning approaches for drug combination therapies. Briefings Bioinform. Betül Güvenç Paltun, Samuel Kaski, Hiroshi Mamitsuka
2021	J	`jnl`	On Convex Clustering Solutions. CoRR Canh Hao Nguyen, Hiroshi Mamitsuka
2021	J	`jnl`	Reshaped tensor nuclear norms for higher order tensor completion. Mach. Learn. Kishan Wimalawarne, Hiroshi Mamitsuka
2021	J	`jnl`	XGSEA: CROSS-species gene set enrichment analysis via domain adaptation. Briefings Bioinform. Menglan Cai, Canh Hao Nguyen, Hiroshi Mamitsuka, Limin Li
2020	A*	`conf`	Efficiently Enumerating Substrings with Statistically Significant Frequencies of Locally Optimal Occurrences in Gigantic String. AAAI Atsuyoshi Nakamura, Ichigaku Takigawa, Hiroshi Mamitsuka
2020	J	`jnl`	FullMeSH: improving large-scale MeSH indexing with full text. Bioinform. Suyang Dai, Ronghui You, Zhiyong Lu, Xiaodi Huang, Hiroshi Mamitsuka, Shanfeng Zhu
2020	J	`jnl`	HPOLabeler: improving prediction of human protein-phenotype associations by learning to rank. Bioinform. Lizhi Liu, Xiaodi Huang, Hiroshi Mamitsuka, Shanfeng Zhu
2020	A*	`conf`	Scalable Probabilistic Matrix Factorization with Graph-Based Priors. AAAI Jonathan Strahl, Jaakko Peltonen, Hiroshi Mamitsuka, Samuel Kaski
2020	J	`jnl`	Scaled Coupled Norms and Coupled Higher-Order Tensor Completion. Neural Comput. Kishan Wimalawarne, Makoto Yamada, Hiroshi Mamitsuka
2019	J	`jnl`	ADAPTIVE: leArning DAta-dePendenT, concIse molecular VEctors for fast, accurate metabolite identification from tandem mass spectra. Bioinform. Dai Hai Nguyen, Canh Hao Nguyen, Hiroshi Mamitsuka
2019	A*	`conf`	AttentionXML: Label Tree-based Attention-Aware Deep Model for High-Performance Extreme Multi-Label Text Classification. NeurIPS Ronghui You, Zihan Zhang, Ziye Wang, Suyang Dai, Hiroshi Mamitsuka, Shanfeng Zhu
2019	J	`jnl`	Editorial. IEEE ACM Trans. Comput. Biol. Bioinform. Shuigeng Zhou, Yi-Ping Phoebe Chen, Hiroshi Mamitsuka
2019	A*	`conf`	Fast and Robust Multi-View Multi-Task Learning via Group Sparsity. IJCAI Lu Sun, Canh Hao Nguyen, Hiroshi Mamitsuka
2019	J	`jnl`	Modelling G×E with historical weather information improves genomic prediction in new environments. Bioinform. Jussi Gillberg, Pekka Marttinen, Hiroshi Mamitsuka, Samuel Kaski
2019	A*	`conf`	Multiplicative Sparse Feature Decomposition for Efficient Multi-View Multi-Task Learning. IJCAI Lu Sun, Canh Hao Nguyen, Hiroshi Mamitsuka
2019	J	`jnl`	NetGO: improving large-scale protein function prediction with massive network information. Nucleic Acids Res. Ronghui You, Shuwei Yao, Yi Xiong, Xiaodi Huang, Fengzhu Sun, Hiroshi Mamitsuka, Shanfeng Zhu
2019	J	`jnl`	Recent advances and prospects of computational methods for metabolite identification: a review with emphasis on machine learning approaches. Briefings Bioinform. Dai Hai Nguyen, Canh Hao Nguyen, Hiroshi Mamitsuka
2019	J	`jnl`	Scalable Probabilistic Matrix Factorization with Graph-Based Priors. CoRR Jonathan Strahl, Jaakko Peltonen, Hiroshi Mamitsuka, Samuel Kaski
2018	—	`conf`	AiProAnnotator: Low-rank Approximation with network side information for high-performance, large-scale human Protein abnormality Annotator. BIBM Junning Gao, Shuwei Yao, Hiroshi Mamitsuka, Shanfeng Zhu
2018	J	`jnl`	AttentionXML: Extreme Multi-Label Text Classification with Multi-Label Attention Based Recurrent Neural Networks. CoRR Ronghui You, Suyang Dai, Zihan Zhang, Hiroshi Mamitsuka, Shanfeng Zhu
2018	J	`jnl`	Convex Coupled Matrix and Tensor Completion. Neural Comput. Kishan Wimalawarne, Makoto Yamada, Hiroshi Mamitsuka
2018	A*	`conf`	Efficient Convex Completion of Coupled Tensors using Coupled Nuclear Norms. NeurIPS Kishan Wimalawarne, Hiroshi Mamitsuka
2018	A	`conf`	Factor Analysis on a Graph. AISTATS Masayuki Karasuyama, Hiroshi Mamitsuka
2018	J	`jnl`	GOLabeler: improving sequence-based large-scale protein function prediction by learning to rank. Bioinform. Ronghui You, Zihan Zhang, Yi Xiong, Fengzhu Sun, Hiroshi Mamitsuka, Shanfeng Zhu
2018	J	`jnl`	Learning on Hypergraphs with Sparsity. CoRR Canh Hao Nguyen, Hiroshi Mamitsuka
2018	J	`jnl`	SIMPLE: Sparse Interaction Model over Peaks of moLEcules for fast, interpretable metabolite identification from tandem mass spectra. Bioinform. Dai Hai Nguyen, Canh Hao Nguyen, Hiroshi Mamitsuka
2018	J	`jnl`	Ultra High-Dimensional Nonlinear Feature Selection for Big Biological Data. IEEE Trans. Knowl. Data Eng. Makoto Yamada, Jiliang Tang, Jose Lugo-Martinez, Ermin Hodzic, Raunak Shrestha, Avishek Saha, Hua Ouyang, Dawei Yin, Hiroshi Mamitsuka, Süleyman Cenk Sahinalp, Predrag Radivojac, Filippo Menczer, Yi Chang
2017	J	`jnl`	Adaptive edge weighting for graph-based learning algorithms. Mach. Learn. Masayuki Karasuyama, Hiroshi Mamitsuka
2017	J	`jnl`	Computational recognition for long non-coding RNA (lncRNA): Software and databases. Briefings Bioinform. Sohiya Yotsukura, David duVerle, Timothy Hancock, Yayoi Natsume-Kitatani, Hiroshi Mamitsuka
2017	A*	`conf`	Convex Factorization Machine for Toxicogenomics Prediction. KDD Makoto Yamada, Wenzhao Lian, Amit Goyal, Jianhui Chen, Kishan Wimalawarne, Suleiman A. Khan, Samuel Kaski, Hiroshi Mamitsuka, Yi Chang
2017	J	`jnl`	Exploring phenotype patterns of breast cancer within somatic mutations: a modicum in the intrinsic code. Briefings Bioinform. Sohiya Yotsukura, Masayuki Karasuyama, Ichigaku Takigawa, Hiroshi Mamitsuka
2017	J	`jnl`	Generalized Sparse Learning of Linear Models Over the Complete Subgraph Feature Set. IEEE Trans. Pattern Anal. Mach. Intell. Ichigaku Takigawa, Hiroshi Mamitsuka
2016	A*	`conf`	A Robust Convex Formulation for Ensemble Clustering. IJCAI Junning Gao, Makoto Yamada, Samuel Kaski, Hiroshi Mamitsuka, Shanfeng Zhu
2016	J	`jnl`	Current status and prospects of computational resources for natural product dereplication: a review. Briefings Bioinform. Ahmed Mohamed, Canh Hao Nguyen, Hiroshi Mamitsuka
2016	J	`jnl`	DeepMeSH: deep semantic representation for improving large-scale MeSH indexing. Bioinform. Shengwen Peng, Ronghui You, Hongning Wang, ChengXiang Zhai, Hiroshi Mamitsuka, Shanfeng Zhu
2016	J	`jnl`	DrugE-Rank: improving drug-target interaction prediction of new candidate drugs or targets by ensemble learning to rank. Bioinform. Qingjun Yuan, Junning Gao, Dongliang Wu, Shihua Zhang, Hiroshi Mamitsuka, Shanfeng Zhu
2016	J	`jnl`	Introduction to the special issue on GIW 2016. J. Bioinform. Comput. Biol. Shuigeng Zhou, Yi-Ping Phoebe Chen, Hiroshi Mamitsuka
2016	J	`jnl`	Mining approximate patterns with frequent locally optimal occurrences. Discret. Appl. Math. Atsuyoshi Nakamura, Ichigaku Takigawa, Hisashi Tosaka, Mineichi Kudo, Hiroshi Mamitsuka
2016	J	`jnl`	NMRPro: an integrated web component for interactive processing and visualization of NMR spectra. Bioinform. Ahmed Mohamed, Canh Hao Nguyen, Hiroshi Mamitsuka
2016	A	`conf`	New Resistance Distances with Global Information on Large Graphs. AISTATS Canh Hao Nguyen, Hiroshi Mamitsuka
2015	J	`jnl`	BMExpert: Mining MEDLINE for Finding Experts in Biomedical Domains Based on Language Model. IEEE ACM Trans. Comput. Biol. Bioinform. Beichen Wang, Xiaodong Chen, Hiroshi Mamitsuka, Shanfeng Zhu
2015	A*	`conf`	Instance-Wise Weighted Nonnegative Matrix Factorization for Aggregating Partitions with Locally Reliable Clusters. IJCAI Xiaodong Zheng, Shanfeng Zhu, Junning Gao, Hiroshi Mamitsuka
2015	J	`jnl`	MeSHLabeler: improving the accuracy of large-scale MeSH indexing by integrating diverse evidence. Bioinform. Ke Liu, Shengwen Peng, Junqiu Wu, ChengXiang Zhai, Hiroshi Mamitsuka, Shanfeng Zhu
2015	J	`jnl`	MeSHSim: An R/Bioconductor package for measuring semantic similarity over MeSH headings and MEDLINE documents. J. Bioinform. Comput. Biol. Jing Zhou, Yuxuan Shui, Shengwen Peng, Xuhui Li, Hiroshi Mamitsuka, Shanfeng Zhu
2015	J	`jnl`	Non-Negative Matrix Factorization with Auxiliary Information on Overlapping Groups. IEEE Trans. Knowl. Data Eng. Motoki Shiga, Hiroshi Mamitsuka
2014	J	`jnl`	Detecting Differentially Coexpressed Genesfrom Labeled Expression Data: A Brief Review. IEEE ACM Trans. Comput. Biol. Bioinform. Mitsunori Kayano, Motoki Shiga, Hiroshi Mamitsuka
2014	J	`jnl`	NetPathMiner: R/Bioconductor package for network path mining through gene expression. Bioinform. Ahmed Mohamed, Timothy Hancock, Canh Hao Nguyen, Hiroshi Mamitsuka
2014	J	`jnl`	Selecting Graph Cut Solutions via Global Graph Similarity. IEEE Trans. Neural Networks Learn. Syst. Canh Hao Nguyen, Nicolas Wicker, Hiroshi Mamitsuka
2014	J	`jnl`	Similarity-based machine learning methods for predicting drug-target interactions: a brief review. Briefings Bioinform. Hao Ding, Ichigaku Takigawa, Hiroshi Mamitsuka, Shanfeng Zhu
2013	A*	`conf`	Collaborative matrix factorization with multiple similarities for predicting drug-target interactions. KDD Xiaodong Zheng, Hao Ding, Hiroshi Mamitsuka, Shanfeng Zhu
2013	J	`jnl`	Efficient Semisupervised MEDLINE Document Clustering With MeSH-Semantic and Global-Content Constraints. IEEE Trans. Cybern. Jun Gu, Wei Feng, Jia Zeng, Hiroshi Mamitsuka, Shanfeng Zhu
2013	J	`jnl`	Fast algorithms for finding a minimum repetition representation of strings and trees. Discret. Appl. Math. Atsuyoshi Nakamura, Tomoya Saito, Ichigaku Takigawa, Mineichi Kudo, Hiroshi Mamitsuka
2013	—	`conf`	Manifold-based Similarity Adaptation for Label Propagation. NIPS Masayuki Karasuyama, Hiroshi Mamitsuka
2013	J	`jnl`	Multiple Graph Label Propagation by Sparse Integration. IEEE Trans. Neural Networks Learn. Syst. Masayuki Karasuyama, Hiroshi Mamitsuka
2013	—	`conf`	Variational Bayes co-clustering with auxiliary information. MultiClust@KDD Motoki Shiga, Hiroshi Mamitsuka
2012	J	`jnl`	A Variational Bayesian Framework for Clustering with Multiple Graphs. IEEE Trans. Knowl. Data Eng. Motoki Shiga, Hiroshi Mamitsuka
2012	J	`jnl`	A review of statistical methods for prediction of proteolytic cleavage. Briefings Bioinform. David duVerle, Hiroshi Mamitsuka
2012	J	`jnl`	Boosted Network Classifiers for Local Feature Selection. IEEE Trans. Neural Networks Learn. Syst. Timothy Hancock, Hiroshi Mamitsuka
2012	J	`jnl`	Efficient semi-supervised learning on locally informative multiple graphs. Pattern Recognit. Motoki Shiga, Hiroshi Mamitsuka
2012	J	`jnl`	Latent Feature Kernels for Link Prediction on Sparse Graphs. IEEE Trans. Neural Networks Learn. Syst. Canh Hao Nguyen, Hiroshi Mamitsuka
2012	J	`jnl`	Mining from protein-protein interactions. WIREs Data Mining Knowl. Discov. Hiroshi Mamitsuka
2012	J	`jnl`	Toward more accurate pan-specific MHC-peptide binding prediction: a review of current methods and tools. Briefings Bioinform. Lianming Zhang, Keiko Udaka, Hiroshi Mamitsuka, Shanfeng Zhu
2011	J	`jnl`	A spectral approach to clustering numerical vectors as nodes in a network. Pattern Recognit. Motoki Shiga, Ichigaku Takigawa, Hiroshi Mamitsuka
2011	J	`jnl`	Clustering genes with expression and beyond. WIREs Data Mining Knowl. Discov. Motoki Shiga, Hiroshi Mamitsuka
2011	J	`jnl`	Discriminative Graph Embedding for Label Propagation. IEEE Trans. Neural Networks Canh Hao Nguyen, Hiroshi Mamitsuka
2011	J	`jnl`	Efficiently mining Mach. Learn. Ichigaku Takigawa, Hiroshi Mamitsuka
2011	—	`conf`	Kernels for Link Prediction with Latent Feature Models. ECML/PKDD (2) Canh Hao Nguyen, Hiroshi Mamitsuka
2010	J	`jnl`	A markov classification model for metabolic pathways. Algorithms Mol. Biol. Timothy Hancock, Hiroshi Mamitsuka
2010	C	`conf`	Algorithms for Finding a Minimum Repetition Representation of a String. SPIRE Atsuyoshi Nakamura, Tomoya Saito, Ichigaku Takigawa, Hiroshi Mamitsuka, Mineichi Kudo
2010	A	`conf`	Boosted Optimization for Network Classification. AISTATS Timothy Hancock, Hiroshi Mamitsuka
2010	J	`jnl`	MetaMHC: a meta approach to predict peptides binding to MHC molecules. Nucleic Acids Res. Xihao Hu, Wenjian Zhou, Keiko Udaka, Hiroshi Mamitsuka, Shanfeng Zhu
2010	J	`jnl`	Mining metabolic pathways through gene expression. Bioinform. Timothy Hancock, Ichigaku Takigawa, Hiroshi Mamitsuka
2010	J	`jnl`	On network-based kernel methods for protein-protein interactions with applications in protein functions prediction. J. Syst. Sci. Complex. Limin Li, Wai-Ki Ching, Yatming Chan, Hiroshi Mamitsuka
2009	C	`conf`	A Markov Classification Model for Metabolic Pathways. WABI Timothy Hancock, Hiroshi Mamitsuka
2009	—	`conf`	Efficient Probabilistic Latent Semantic Analysis through Parallelization. AIRS Raymond Wan, Vo Ngoc Anh, Hiroshi Mamitsuka
2009	J	`jnl`	Efficiently finding genome-wide three-way gene interactions from transcript- and genotype-data. Bioinform. Mitsunori Kayano, Ichigaku Takigawa, Motoki Shiga, Koji Tsuda, Hiroshi Mamitsuka
2009	J	`jnl`	Enhancing MEDLINE document clustering by incorporating MeSH semantic similarity. Bioinform. Shanfeng Zhu, Jia Zeng, Hiroshi Mamitsuka
2009	J	`jnl`	Field independent probabilistic model for clustering multi-field documents. Inf. Process. Manag. Shanfeng Zhu, Ichigaku Takigawa, Jia Zeng, Hiroshi Mamitsuka
2009	J	`jnl`	HAMSTER: visualizing microarray experiments as a set of minimum spanning trees. Source Code Biol. Medicine Raymond Wan, Larisa Kiseleva, Hajime Harada, Hiroshi Mamitsuka, Paul Horton
2008	J	`jnl`	A new efficient probabilistic model for mining labeled ordered trees applied to glycobiology. ACM Trans. Knowl. Discov. Data Kosuke Hashimoto, Kiyoko F. Aoki-Kinoshita, Nobuhisa Ueda, Minoru Kanehisa, Hiroshi Mamitsuka
2008	C	`conf`	Mining significant tree patterns in carbohydrate sugar chains. ECCB Kosuke Hashimoto, Ichigaku Takigawa, Motoki Shiga, Minoru Kanehisa, Hiroshi Mamitsuka
2008	J	`jnl`	Probabilistic path ranking based on adjacent pairwise coexpression for metabolic transcripts analysis. Bioinform. Ichigaku Takigawa, Hiroshi Mamitsuka
2007	A	`conf`	A Probabilistic Model for Clustering Text Documents with Multiple Fields. ECIR Shanfeng Zhu, Ichigaku Takigawa, Shuqin Zhang, Hiroshi Mamitsuka
2007	J	`jnl`	A hidden Markov model-based approach for identifying timing differences in gene expression under different experimental factors. Bioinform. Takashi Yoneya, Hiroshi Mamitsuka
2007	A*	`conf`	A spectral clustering approach to optimally combining numericalvectors with a modular network. KDD Motoki Shiga, Ichigaku Takigawa, Hiroshi Mamitsuka
2007	J	`jnl`	Active ensemble learning: Application to data mining and bioinformatics. Syst. Comput. Jpn. Hiroshi Mamitsuka, Naoki Abe
2007	—	`conf`	Annotating gene function by combining expression data with a modular gene network. ISMB/ECCB (Supplement of Bioinformatics) Motoki Shiga, Ichigaku Takigawa, Hiroshi Mamitsuka
2007	—	`conf`	Passage Retrieval with Vector Space and Query-Level Aspect Models. TREC Raymond Wan, Vo Ngoc Anh, Hiroshi Mamitsuka
2007	J	`jnl`	Predicting implicit associated cancer genes from OMIM and MEDLINE by a new probabilistic model. BMC Syst. Biol. Shanfeng Zhu, Yasushi Okuno, Gozoh Tsujimoto, Hiroshi Mamitsuka
2006	A*	`conf`	A new efficient probabilistic model for mining labeled ordered trees. KDD Kosuke Hashimoto, Kiyoko F. Aoki-Kinoshita, Nobuhisa Ueda, Minoru Kanehisa, Hiroshi Mamitsuka
2006	—	`conf`	Applying Gaussian Distribution-Dependent Criteria to Decision Trees for High-Dimensional Microarray Data. VDMB Raymond Wan, Ichigaku Takigawa, Hiroshi Mamitsuka
2006	—	`conf`	Combining Vector-Space and Word-Based Aspect Models for Passage Retrieval. TREC Raymond Wan, Ichigaku Takigawa, Hiroshi Mamitsuka, Vo Ngoc Anh
2006	J	`jnl`	Improving MHC binding peptide prediction by incorporating binding data of auxiliary MHC molecules. Bioinform. Shanfeng Zhu, Keiko Udaka, John Sidney, Alessandro Sette, Kiyoko F. Aoki-Kinoshita, Hiroshi Mamitsuka
2006	—	`conf`	ProfilePSTMM: capturing tree-structure motifs in carbohydrate sugar chains. ISMB (Supplement of Bioinformatics) Kiyoko F. Aoki-Kinoshita, Nobuhisa Ueda, Hiroshi Mamitsuka, Minoru Kanehisa
2006	J	`jnl`	Query-learning-based iterative feature-subset selection for learning from high-dimensional data sets. Knowl. Inf. Syst. Hiroshi Mamitsuka
2006	J	`jnl`	Selecting features in microarray classification using ROC curves. Pattern Recognit. Hiroshi Mamitsuka
2005	J	`jnl`	A Probabilistic Model for Mining Labeled Ordered Trees: Capturing Patterns in Carbohydrate Sugar Chains. IEEE Trans. Knowl. Data Eng. Nobuhisa Ueda, Kiyoko F. Aoki-Kinoshita, Atsuko Yamaguchi, Tatsuya Akutsu, Hiroshi Mamitsuka
2005	—	`conf`	A probabilistic model for mining implicit 'chemical compound-gene' relations from literature. ECCB/JBI Shanfeng Zhu, Yasushi Okuno, Gozoh Tsujimoto, Hiroshi Mamitsuka
2005	J	`jnl`	A score matrix to reveal the hidden links in glycans. Bioinform. Kiyoko F. Aoki, Hiroshi Mamitsuka, Tatsuya Akutsu, Minoru Kanehisa
2005	Misc	`conf`	Cleaning microarray expression data using Markov random fields based on profile similarity. SAC Raymond Wan, Hiroshi Mamitsuka, Kiyoko F. Aoki
2005	J	`jnl`	Computational intelligence in solving bioinformatics problems. Artif. Intell. Medicine Krzysztof J. Cios, Hiroshi Mamitsuka, Tomomasa Nagashima, Ryszard Tadeusiewicz
2005	J	`jnl`	Essential Latent Knowledge for Protein-Protein Interactions: Analysis by an Unsupervised Learning Approach. IEEE ACM Trans. Comput. Biol. Bioinform. Hiroshi Mamitsuka
2005	J	`jnl`	Finding the biologically optimal alignment of multiple sequences. Artif. Intell. Medicine Hiroshi Mamitsuka
2004	A	`conf`	A General Probabilistic Framework for Mining Labeled Ordered Trees. SDM Nobuhisa Ueda, Kiyoko F. Aoki, Hiroshi Mamitsuka
2004	—	`conf`	A Hierarchical Mixture of Markov Models for Finding Biologically Active Metabolic Paths Using Gene Expression and Protein Classes. CSB Hiroshi Mamitsuka, Yasushi Okuno
2004	—	`conf`	Application of a new probabilistic model for recognizing complex patterns in glycans. ISMB/ECCB (Supplement of Bioinformatics) Kiyoko F. Aoki, Nobuhisa Ueda, Atsuko Yamaguchi, Minoru Kanehisa, Tatsuya Akutsu, Hiroshi Mamitsuka
2004	J	`jnl`	Finding the maximum common subgraph of a partial Inf. Process. Lett. Atsuko Yamaguchi, Kiyoko F. Aoki, Hiroshi Mamitsuka
2004	J	`jnl`	KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains. Nucleic Acids Res. Kiyoko F. Aoki, Atsuko Yamaguchi, Nobuhisa Ueda, Tatsuya Akutsu, Hiroshi Mamitsuka, Susumu Goto, Minoru Kanehisa
2004	J	`jnl`	Managing and Analyzing Carbohydrate Data. SIGMOD Rec. Kiyoko F. Aoki, Nobuhisa Ueda, Atsuko Yamaguchi, Tatsuya Akutsu, Minoru Kanehisa, Hiroshi Mamitsuka
2003	C	`conf`	Detecting Experimental Noises in Protein-Protein Interactions with Iterative Sampling and Model-Based Clustering. BIBE Hiroshi Mamitsuka
2003	—	`conf`	Efficient Mining from Heterogeneous Data Sets for Predicting Protein-Protein Interactions. DEXA Workshops Hiroshi Mamitsuka
2003	A	`conf`	Efficient Unsupervised Mining from Noisy Data Sets: Application to Clustering Co-occurrence Data. SDM Hiroshi Mamitsuka
2003	C	`conf`	Empirical Evaluation of Ensemble Feature Subset Selection Methods for Learning from a High-Dimensional Database in Drug Desig. BIBE Hiroshi Mamitsuka
2003	B	`conf`	Finding the Maximum Common Subgraph of a Partial k-Tree and a Graph with a Polynomially Bounded Number of Spanning Trees. ISAAC Atsuko Yamaguchi, Hiroshi Mamitsuka
2003	A*	`conf`	Hierarchical Latent Knowledge Analysis for Co-occurrence Data. ICML Hiroshi Mamitsuka
2003	J	`jnl`	Mining biologically active patterns in metabolic pathways using microarray expression profiles. SIGKDD Explor. Hiroshi Mamitsuka, Yasushi Okuno, Atsuko Yamaguchi
2003	B	`conf`	Selective Sampling with a Hierarchical Latent Variable Model. IDA Hiroshi Mamitsuka
2002	—	`conf`	Efficient Data Mining by Active Learning. Progress in Discovery Science Hiroshi Mamitsuka, Naoki Abe
2002	—	`conf`	Iteratively Selecting Feature Subsets for Mining from High-Dimensional Databases. PKDD Hiroshi Mamitsuka
2000	A*	`conf`	Efficient Mining from Large Databases by Query Learning. ICML Hiroshi Mamitsuka, Naoki Abe
1998	B	`conf`	Empirical Comparison of Competing Query Learning Methods. Discovery Science Naoki Abe, Hiroshi Mamitsuka, Atsuyoshi Nakamura
1998	A*	`conf`	Query Learning Strategies Using Boosting and Bagging. ICML Naoki Abe, Hiroshi Mamitsuka
1997	J	`jnl`	Predicting Protein Secondary Structure Using Stochastic Tree Grammars. Mach. Learn. Naoki Abe, Hiroshi Mamitsuka
1997	B	`conf`	Supervised learning of hidden Markov models for sequence discrimination. RECOMB Hiroshi Mamitsuka
1996	J	`jnl`	A Learning Method of Hidden Markov Models for Sequence Discrimination. J. Comput. Biol. Hiroshi Mamitsuka
1995	J	`jnl`	Representing inter-residue dependencies in protein sequences with probabilistic networks. Comput. Appl. Biosci. Hiroshi Mamitsuka
1995	J	`jnl`	alpha-Helix region prediction with stochastic rule learning. Comput. Appl. Biosci. Hiroshi Mamitsuka, Kenji Yamanishi
1994	A*	`conf`	A New Method for Predicting Protein Secondary Structures Based on Stochastic Tree Grammars. ICML Naoki Abe, Hiroshi Mamitsuka
1994	A	`conf`	Predicting Location and Structure Of beta-Sheet Regions Using Stochastic Tree Grammars. ISMB Hiroshi Mamitsuka, Naoki Abe
1992	B	`conf`	Protein Secondary Structure Prediction Based on Stochastic-Rule Learning. ALT Hiroshi Mamitsuka, Kenji Yamanishi