Publications
(Since 2002, sorted reverse chronologically)
Refereed Publications
-
Learning Subtree Pattern Importance for Weisfeiler-Lehman based Graph Kernels.
- Nguyen, D. H., Nguyen, C. H. and Mamitsuka, H.
- To appear in Machine Learning, 2021. (Special Issue of the ECML/PKDD 2021 Journal Track)
- [DOI].
-
Learning on Hypergraphs with Sparsity.
- Nguyen, C. H. and Mamitsuka, H.
- To appear in IEEE Transactions on Pattern Analysis and Machine Intelligence, 2021.
- [DOI].
-
DeepGraphGO: Graph Neural Net for Large-scale, Multispecies Protein Function Prediction.
- You, R., Yao, S., Mamitsuka H. and Zhu, S.
-
To appear in Proceedings of the 29th International Conference
on Intelligent Systems for Molecular Biology (ISMB/ECCB 2021)
(Bioinformatics), Virtual Event, 2021,
Oxford University Press.
- [DOI].
-
DIVERSE: Bayesian Data IntegratiVE learning for precise drug ResponSE prediction.
- Güvenç, B. P., Kaski, S. and Mamitsuka, H.
- To appear in IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2021.
- [DOI].
-
HPOFiller: Identifying Missing Protein-phenotype Associations by Graph Convolutional Network.
- Liu, L, Mamitsuka, H. and Zhu, S.
-
To appear in Bioinformatics, 2021.
- [DOI].
-
XGSEA: CROSS-species Gene Set Enrichment Analysis via Domain Adaptation.
- Cai, M., Nguyen, C. H., Mamitsuka, H. and Li, L.
- To appear in Briefings in Bioinformatics, 2021.
- [DOI].
-
Improving Drug Response Prediction by Integrating Multiple Data Sources:
Matrix Factorization, Kernel and Network-based Approaches.
- Güvenç, B. P., Mamitsuka, H. and Kaski, S.
- Briefings in Bioinformatics, 22 (1), 346-359, 2021.
- [DOI].
-
A Survey on Adverse Drug Reaction Studies: Data, Tasks, and Machine Learning Methods.
- Nguyen, D. A., Nguyen, C. H. and Mamitsuka, H.
- Briefings in Bioinformatics, 22 (1), 164-177, 2021.
- [DOI].
-
Eukaryotic Virus Composition Can Predict the Efficiency of Carbon Export in the Global Ocean.
- Kaneko, H., Blanc-Mathieu, R., Endo, H., Chaffron, S., Delmont, T. O., Gaia, M., Henry, N., Hernandez-Velazquez, R., Nguyen, C.-H., Mamitsuka, H., Forterre, P., Jaillon, O., de Vargas, C., Sullivan, M. B., Suttle, C. A., Guidi, L. and Ogata, H.
- iScience, 24 (1), 102002, 2021.
- [DOI].
-
Reshaped Tensor Nuclear Norms for Higher Order Tensor Completion.
- Wimalawarne, K. and Mamitsuka, H.
- Machine Learning, 110 (3), 507-531, 2021.
- [DOI].
-
BERTMeSH: Deep Contextual Representation Learning for Large-scale High-performance MeSH Indexing with Full Text.
- Yui, R., Liu, Y., Mamitsuka, H. and Zhu, S.
-
Bioinformatics, 37 (5), 684-692, 2021.
- [DOI].
-
HPOLabeler: Improving Prediction of Human Protein-phenotype Associations by Learning to Rank.
- Liu, L., Huang, X., Mamitsuka, H. and Zhu, S.
-
Bioinformatics, 36 (14), 4180-4188, 2020.
- [DOI].
-
Scalable Probabilistic Matrix Factorization with Graph-Based Priors.
- Strahl, J., Peltonen, J., Mamitsuka, H. and Kaski, S.
-
Proceedings of the AAAI Conference on Artificial
Intelligence (AAAI 2020), 34, 5851-5858, New York, USA, 2020.
- [DOI].
-
Efficiently Enumerating Substrings with Statistically Significant
Frequencies of Locally Optimal Occurrences in Gigantic
String.
- Nakamura, A., Takigawa, I. and Mamitsuka, H.
-
Proceedings of the AAAI Conference on Artificial
Intelligence (AAAI 2020), 34, 5240-5247, New York, USA, 2020.
- [DOI].
-
FullMeSH: Improving Large-Scale MeSH Indexing with Full Text.
- Dai, S., You, R., Lu, Z., Huang, X., Mamitsuka, H. and Zhu, S.
-
Bioinformatics, 36 (5), 1533-1541, 2020.
- [DOI].
-
Scaled Coupled Norms and Coupled Higher Order Tensor Completion.
- Wimalawarne, K., Yamada, M. and Mamitsuka, H.
-
Neural Computation, 32 (2), 447-484, 2020.
- [DOI].
-
Recent Advances and Prospects of Computational Methods for Metabolite Identification: A Review with Emphasis on Machine Learning Approaches.
- Nguyen, D. H., Nguyen, C. H. and Mamitsuka, H.
- Briefings in Bioinformatics, 20 (6), 2028-2043, 2019.
- [DOI].
-
AttentionXML: Label Tree-based Attention-Aware Deep Model for High-Performance Extreme Multi-Label Text Classification.
- You, R., Dai, S., Zhang, Z., Mamitsuka, H. and Zhu, S.
-
Proceedings of the 33rd Annual Conference on Neural Information Processing Systems (NeurIPS 2019), 5820-5830, Vancouver, Canada, 2019.
- [NeurIPS paper site].
-
Multiplicative Sparse Feature Decomposition for Efficient Multi-View Multi-Task Learning.
- Sun, L., Nguyen, C. H. and Mamitsuka, H.
-
Proceedings of the 28th International Joint Conference on Artificial Intelligence (IJCAI 2019), 3605-3512, Macao, China, 2019.
- [DOI].
-
Fast and Robust Multi-View Multi-Task Learning via Group Sparsity.
- Sun, L., Nguyen, C. H. and Mamitsuka, H.
-
Proceedings of the 28th International Joint Conference on Artificial Intelligence (IJCAI 2019), 3499-3505, Macao, China, 2019.
- [DOI].
-
NetGO: Improving Large-scale Protein Function Prediction with Massive Network Information.
- You, R., Yao, S., Xiong, Y., Huang, X., Sun, F., Mamitsuka, H. and Zhu, S.
-
Nucleic Acids Research, 47, W379-W387, 2019.
- [DOI].
-
ADAPTIVE: leArning DAta-dePendenT, concIse molecular VEctors for fast, accurate metabolite identification from tandem mass spectra.
- Nguyen, D. H., Nguyen, C. H. and Mamitsuka, H.
-
Proceedings of the 27th International Conference
on Intelligent Systems for Molecular Biology (ISMB/ECCB 2019)
(Bioinformatics, 35 (14)), i64-i72, Basel, Switzerland, 2019,
Oxford University Press.
- [DOI].
-
Modelling GxE with Historical Weather Information Improves Genomic Prediction in New Environments.
- Gillberg, J., Marttinen, P., Mamitsuka, H. and Kaski, S.
- Bioinformatics, 35 (20), 4045-4052, 2019.
- [DOI].
-
A Metropolis-Hastings Sampling of Subtrees in Graphs.
- Eid, A., Mamitsuka, H. and Wicker, N.
- Austrian Journal of Statistics, 48 (5), 17-33, 2019.
- [DOI].
-
A p-Laplacian Random Walk: Application to Video Games.
- Wicker, N., Nguyen, C. H. and Mamitsuka, H.
- Austrian Journal of Statistics, 48 (5), 11-16, 2019.
- [DOI].
-
Efficient Convex Completion of Coupled Tensors using Coupled Nuclear Norms.
- Wimalawarme, K. and Mamitsuka, H.
-
Proceedings of the Thirty-Second Annual Conference on Neural Information Processing Systems (NeurIPS 2018), 6902-6910, Montral, Canada, 2018.
- [NeurIPS paper site].
-
AiProAnnotator: Low-rank Approximation with Network Side Information for High-performance, Large-scale Human Protein Abnormality Annotator.
- Gao, J., Shuwei, Y., Mamitsuka, H. and Zhu, S.
-
Proceedings of the 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2018), 13-20, Madrid, Spain, December, 2018.
- (Best student paper)
- [DOI].
-
Convex Coupled Matrix and Tensor Completion.
- Wimalawarme, K., Yamada, M. and Mamitsuka, H.
- Neural Computation, 30 (11), 3095-3127, 2018.
- [DOI].
-
SIMPLE: Sparse Interaction Model over Peaks of MoLEcules for Fast, Interpretable Metabolite Identification from Tandem Mass Spectra.
- Nguyen, D. H., Nguyen, C. H. and Mamitsuka, H.
-
Proceedings of the 26th International Conference
on Intelligent Systems for Molecular Biology (ISMB 2018)
(Bioinformatics, 34 (13), 2018), i323-i332, Chicago, IL, USA, 2018,
Oxford University Press.
- [DOI].
-
GOLabeler: Improving Sequence-based Large-scale Protein Function Prediction by Learning to Rank.
- You, R., Zhang, Z., Xiong, Y., Sun, F., Mamitsuka, H. and Zhu, S.
- Bioinformatics, 34 (14), 2465-2478, 2018.
- [DOI].
-
Ultra High-Dimensional Nonlinear Feature Selection for Big Biological Data.
- Yamada, M., Tang, J., Lugo-Martinez, J., Hodzic, E., Shrestha, R., Saha, A., Ouyang, H., Yin, D., Mamitsuka, H., Sahinalp, C., Radivojac, P., Menczer, F. and Chang, Y.
- IEEE Transactions on Knowledge and Data Engineering, 30 (7), 1352-1365, 2018.
- [DOI].
-
Factor Analysis on a Graph.
- Karasuyama, M. and Mamitsuka, H.
-
Proceedings of the Twenty-first International Conference on Artificial Intelligence and Statistics (AISTATS 2018) (JMLR Workshop and Conference Proceedings (PMLR),84), 1117-1126, Playa Blanca, Lanzarote, Canary Islands, April, 2018.
- [PMLR paper site].
-
Convex Factorization Machine for Toxicogenomics Prediction.
- Yamada, M., Lian, W., Goyal, A., Chen, J., Wimalawarne, K., Kahn, S., Kaski, S., Mamitsuka H. and Chang, Y.
- Proceedings of the Twenth-third ACM SIGKDD International
Conference on Knowledge Discovery and Data Mining (KDD
2017), 1215-1224, Halifax, Nova Scotia, Canada, August 2017, ACM
Press.
- [DOI].
-
Adaptive Edge Weighting for Graph-Based Learning Algorithms.
- Karasuyama, M. and Mamitsuka, H.
- Machine Learning, 106 (2), 307-335, 2017.
- [DOI].
-
Generalized Sparse Learning of Linear Models over the Complete Subgraph Feature Set.
- Takigawa, I. and Mamitsuka, H.
- IEEE Transactions on Pattern Analysis and Machine Intelligence, 39 (3), 617-624, 2017.
- [DOI].
-
A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines.
-
Gnen, M., Weir, B. A., Cowley, G. S., Vazquez, F., Guan, Y., Jaiswal, A., Karasuyama, M., Uzunangelov, V., Wang, T., Tsherniak, A., Howell, S., Marbach, D., Hoff, B., Norman, T. C., Airola, A., Bivol, A., Bunte, K., Carlin, D., Chopra, B., Deran, A., Ellrott, K., Gopalacharyulu, P., Graim, K., Kaski, S., Khan, S. A., Newton, Y., Ng, S., Pahikkala, T., Paull, E., Sokolov, A., Tang, H., Tang, J., Wennerberg, K., Xie, Y., Zhan, X., Zhu, F., Broad-DREAM Community, Aittokallio, T., Mamitsuka, H., Stuart, J. M., Boehm, J., Root, D., Xiao, G., Stolovitzky, G., Hahn, W. C. and Margolin, A. A.
- Cell Systems, 5 (5), 485-497, 2017.
- [DOI].
-
Exploring Phenotype Patterns of Breast Cancer within Somatic Mutations.
-
Yotsukura, S., Karasuyama, M., Takigawa, I. and Mamitsuka, H.
- Briefings in Bioinformatics, 18 (4), 619-633, 2017.
- [DOI].
-
Computational Recognition for Long Non-coding RNA (lncRNA): Software and
Databases.
- Yotsukura, S., duVerle, D., Hancock, T., Natsume-Kitatani, Y. and
Mamitsuka, H.
- Briefings in Bioinformatics, 18 (1), 9-27, 2017.
- [DOI].
-
A Robust Convex Formulations for Ensemble Clustering.
- Gao, J., Yamada, M., Kaski, S., Mamitsuka, H. and Zhu, S.
-
Proceedings of the 25th International Joint Conference on Artificial Intelligence (IJCAI 2016), 1476-1482, New York City, NY, USA, July, 2016.
- [IJCAI paper site].
-
New Resistance Distances with Global Information on Large Graphs.
- Nguyen, C. H. and Mamitsuka, H.
-
Proceedings of the Nineteenth International Conference on Artificial Intelligence and Statistics (AISTATS 2016) (JMLR Workshop and Conference Proceedings,51), 639-647, Cadiz, Spain, May, 2016.
- [PMLR paper site].
-
Some Properties of a Dissimilarity Measure for Labeled Graphs.
- Wicker, N., Nguyen, C. H. and Mamitsuka, H.
- Publications Mathématiques de Besançon:
Algèbre et Théorie des Nombres, 85-94, 2016.
- [PDF].
-
DrugE-Rank: Improving Drug-Target Interaction Prediction of New
Candidate Drugs or Targets by Ensemble Learning to Rank.
- Yuan, Q.-J., Gao, J., Wu, D., Zhang, S., Mamitsuka, H. and Zhu,
S.
-
Proceedings of the 24th International Conference
on Intelligent Systems for Molecular Biology (ISMB 2016)
(Bioinformatics, 32 (12), 2016), i18-i27, Orlando, FL, USA, 2016,
Oxford University Press.
- [DOI].
-
DeepMeSH: Deep Semantic Representation for Improving Large-scale MeSH Indexing.
- Peng, S., You, R., Wang, H., Zhai, C., Mamitsuka, H. and Zhu, S.
-
Proceedings of the 24th International Conference
on Intelligent Systems for Molecular Biology (ISMB 2016)
(Bioinformatics, 32 (12), 2016), i70-i79, Orlando, FL, USA, 2016,
Oxford University Press.
- [DOI].
-
NMRPro: An Integrated Web Component for Interactive Processing and Visualization of NMR Spectra.
- Mohamed, A., Nguyen, C. H. and Mamitsuka, H.
- Bioinformatics. 32 (13), 2067-2068, 2016.
- [DOI].
-
Gene-proximity Models for Genome-Wide Association Studies.
- Johnston, I., Hancock, T., Mamitsuka, H. and Carvalho, L.
- Annals of Applied Statistics, 10 (3), 1217-1244, 2016.
- [DOI].
-
Classification of Promoters based on the Combination of Core Promoter
Elements Exhibits Different Histone Modification Patterns.
- Natsume-Kitatani, Y. and Mamitsuka, H.
- PLoS One, 11 (3), e0151917, 2016.
- [DOI].
-
Predictions of Cleavability of Calpain Proteolysis by Quantitative
Structure-Activity Relationship Analysis Using Newly
Determined Cleavage Sites and Catalytic Efficiencies of an
Oligopeptide Array.
- Shinkai-Ouchi, F., Koyama, S., Ono, Y., Hata, S., Ojima, K., Shindo, M.,
duVerle, D., Kitamura, F., Doi, N., Takigawa, I., Mamitsuka,
H. and Sorimachi, H.
-
Molecular and Cellular Proteomics, 15, 1262-1280, 2016.
- [DOI].
-
Mining Approximate Patterns with Frequent Locally Optimal Occurrences.
- Nakamura, A., Takigawa, I., Tosaka, H., Kudo, M. and Mamitsuka, H.
- Discrete Applied Mathematics, 200, 123-152, 2016.
- [DOI].
-
A Bioinformatics Approach for Understanding Genotype-phenotype Correlation in Breast Cancer.
-
Yotsukura, S., Karasuyama, M., Takigawa, I. and Mamitsuka, H.
- Big Data Analytics in Genomics, Chapter 13, 397-428, 2016.
- [DOI].
-
Current Status and Prospects of Computational Resources for Natural
Product Dereplication: A Review.
- Mohamed, A., Nguyen, C. H., and Mamitsuka, H.
- Briefings in Bioinformatics, 17(2),
309-312, 2016.
- [DOI].
-
Instance-wise Weighted Nonnegative Matrix Factorization for Aggregating Partitions with Locally Reliable Clusters.
- Zheng, X., Zhu, S., Gao, J. and Mamitsuka, H.
-
Proceedings of the 24th International Joint Conference on Artificial Intelligence (IJCAI 2015), 4091-4097, Buenos Aires, Argentina, July, 2015.
- [PDF].
-
MeSHLabeler: Improving the Accuracy of Large-scale MeSH indexing by
Integrating Diverse Evidence.
- Liu, K., Peng, S., Wu, J., Zhai, C., Mamitsuka H. and Zhu S.
-
Proceedings of
the 23rd International Conference on Intelligent Systems for
Molecular Biology (ISMB/ECCB 2015),
(Bioinformatics, 31(12), 2015), i339-i347,
Dublin, Ireland, July, 2015, Oxford University Press.
- [DOI].
-
MeSHSim: An R/Bioconductor Package for Measuring Semantic
Similarity over MeSH Headings and MEDLINE Documents.
- Zhou, J., Shui, Y., Peng, S., Li, X., Mamitsuka, H., Zhu, S.
- Journal of Bioinformatics and Computational Biology,
13(6), 1542002, 2015.
- [DOI].
-
In Silico Predictions of Human Skin Permeability using Nonlinear
Quantitative Structure-Property Relationship Models.
- Baba, H., Takahara, J. and Mamitsuka, H.
- Pharmaceutical Research, 32(7), 2360-2371, 2015.
- [DOI].
-
Non-negative Matrix Factorization with Auxiliary Information on
Overlapping Groups.
- Shiga, M. and Mamitsuka, H.
- IEEE Transactions on Knowledge and Data Engineering, 27(6),
1615-1628, 2015.
- [DOI].
-
BMExpert: Mining MEDLINE for Finding Experts in Biomedical Domains Based
on Language Model.
- Wang, B., Chen, X., Mamitsuka, H. and Zhu, S.
- IEEE/ACM Transactions on Computational Biology and
Bioinformatics, 12(6), 1286-1294, 2015.
- [DOI].
-
Evaluation of Serum-based Cancer Biomarkers: A Brief Review from a
Clinical and Computational Viewpoint.
- Yotsukura, S. and Mamitsuka, H.
- Critical Reviews in Oncology/Hematology,
95(2), 103-115, 2015.
- [DOI].
-
NetPathMiner:R/Bioconductor Package for Network Path Mining through Gene Expression.
- Mohamed, A., Hancock, T., Nguyen, C. H. and Mamitsuka, H.
- Bioinformatics,
30(21), 3139-3141, 2014.
- [DOI].
-
Detecting Differentially Coexpressed Genes from Labeled Expression Data:A Brief Review.
- Kayano, M., Shiga, M. and Mamitsuka, H.
- IEEE/ACM Transactions on Computational Biology and Bioinformatics,
11(1), 154-167, 2014.
- [DOI].
-
Selecting Graph Cut Solutions via Global Graph Similarity.
- Nguyen, C. H., Wicker, N. and Mamitsuka, H.
- IEEE Transactions on Neural Networks and Learning Systems,
25(7), 1407-1412, 2014.
- [DOI].
-
Similarity-based Machine Learning Methods for Predicting Drug-target Interactions: A Brief Review.
- Ding, H., Takigawa, I., Mamitsuka, H. and Zhu, S.
- Briefings in Bioinformatics,
15(5), 737-747, 2014.
- [DOI].
-
Manifold-based Similarity Adaptation for Label Propagation.
- Karasuyama, M. and Mamitsuka, H.
- Proceedings of the Twenty-Seventh Annual Conference on Neural Information Processing Systems (NIPS 2013), 1547-1555, Lake Tahoe, NV, USA, December, 2013.
- [NIPS Paper site].
-
SiBIC: A Web Server for Generating Gene Set Networks Based on Biclusters Obtained by Maximal Frequent Itemset Mining.
- Takahashi, K., Takigawa, I. and Mamitsuka, H.
- PLoS One,
8(12), e82890, 2013.
- [DOI].
-
Multiple Graph Label Propagation by Sparse Integration.
- Karasuyama, M. and Mamitsuka, H.
- IEEE Transactions on Neural Networks and Learning Systems,
24(12), 1999-2012, 2013.
- [DOI].
-
Collaborative Matrix Factorization with Multiple Similarities for Predicting Drug-target Interactions.
- Zheng, X., Ding, H., Mamitsuka, H. and Zhu, S.
- Proceedings of the Nineteenth ACM SIGKDD International
Conference on Knowledge Discovery and Data Mining (KDD
2013), 1025-1033, Chicago, IL, USA, August 2013, ACM
Press.
- [DOI, PDF (Preprints)].
-
Variational Bayes Co-clustering with Auxiliary Information.
- Shiga, M. and Mamitsuka, H.
- Proceedings of the 4th MultiClust Workshop on Multiple Clusterings, Multi-view Data, and Multi-source Knowledge-driven Clustering (MultiClust 2013), Article No. 5, Chicago, IL, USA, August, 2013.
- [DOI].
-
Fast Algorithms for Finding a Minimum Repetition Representation of Strings and Trees.
- Nakamura, A., Saito, T., Takigawa, I., Kudo, M. and Mamitsuka, H.
- Discrete Applied Mathematics,
161(10-11), 1556-1575, 2013.
- [DOI].
-
Efficient Semi-supervised MEDLINE Document Clustering with MeSH Semantic and Global Content Constraints.
- Gu, J., Feng, W., Zeng, J., Mamitsuka, H. and Zhu, S.
- IEEE Transactions on Cybernetics,
43(4), 1265-1276, 2013.
- [DOI].
-
A New Dissimilarity Measure for Comparing Labeled Graphs.
- Wicker, N., Nguyen, C. H. and Mamitsuka, H.
- Linear Algebra and its Applications,
438(5), 2331-2338, 2013.
- [DOI].
-
Integrated View of the Human Chromosome X-centric Proteome Project
- Yamamoto, T., Nakayama, K., Hirano, H., Tomonaga, T., Ishihama, Y., Yamada, T., Kondo, T., Kodera, Y., Sato, Y., Araki, N., Mamitsuka, H. and Goshima, N.
- Journal of Proteome Research,
12(1), 58-61, 2013.
- [DOI].
-
Graph Mining: Procedure, Application to Drug Discovery and Recent Advance
- Takigawa, I. and Mamitsuka, H.
- Drug Discovery Today, 18 (1/2), 50-57, 2013.
- Invited Review Paper.
- [DOI].
-
Latent Feature Kernels for Link Prediction on Sparse Graphs.
- Nguyen, C. H. and Mamitsuka, H.
- IEEE Transactions on Neural Networks and Learning Systems,
23(11), 1793-1804, 2012.
- [DOI].
-
Boosted Network Classifiers for Local Feature Selection.
- Hancock, T. and Mamitsuka, H.
- IEEE Transactions on Neural Networks and Learning Systems,
23(11), 1767-1778, 2012.
- [DOI].
-
Understanding the Substrate Specificity of Conventional Calpains.
- Sorimachi, H., Mamitsuka, H. and Ono, Y.
- Biological Chemistry,
393(9), 853-871, 2012.
- Invited Review Paper.
- [DOI].
-
Mining from Protein-Protein Interactions.
- Mamitsuka, H.
- WIREs Data Mining and Knowledge Discovery,
2(5), 400-410, 2012.
- Invited Review Paper.
- [DOI].
-
Identifying Neighborhoods of Coordinated Gene Expression and Metabolite Profiles.
- Hancock, T, Wicker, N., Takigawa, I. and Mamitsuka, H.
- PLoS One,
7(2), e31345, 2012.
- [DOI].
-
A Variational Bayesian Framework for Clustering with Multiple Graphs.
- Shiga, M. and Mamitsuka, H.
- IEEE Transactions on Knowledge and Data Engineering,
24(4), 577-590, 2012.
- [DOI].
-
TEPITOPEpan: Extending TEPITOPE for Peptide Binding Prediction Covering over 700 HLA-DR Molecules.
- Zhang, L, Chen, Y., Wong, H.-S., Zhou, S., Mamitsuka, H. and Zhu, S.
- PLoS One,
7(2), e30483, 2012.
- [DOI].
-
Toward More Accurate Pan-Specific MHC-Peptide Binding Prediction: A Review of Current Methods and Tools.
- Zhang, L, Udaka, K, Mamitsuka, H. and Zhu, S.
- Briefings in Bioinformatics,
13(3), 350-364, 2012.
- [DOI].
-
A Review of Statistical Methods for Prediction of Proteolytic Cleavage.
- duVerle, D. and Mamitsuka, H.
- Briefings in Bioinformatics,
13(3), 337-349, 2012.
- [DOI].
-
Machine Learning Sequence Classification Techniques: Application to Cysteine Protease Cleavage Prediction.
- duVerle, D. and Mamitsuka, H.
- Current Bioinformatics,
7(4), 415-523, 2012.
- Invited Review Paper.
-
Efficient Semi-Supervised Learning on Locally Informative Multiple Graphs.
- Shiga, M. and Mamitsuka, H.
- Pattern Recognition,
45(3), 1035-1049, 2012.
- [DOI].
-
Genome-wide Integration on Transcription Factors, Histone Acetylation and Gene Expression Reveals Genes Co-regulated by Histone Modification Patterns.
- Natsume-Kitatani, Y., Shiga, M. and Mamitsuka, H.
- PLoS One,
6(7), e22281, 2011.
- [DOI].
-
Discriminative Graph Embedding for Label Propagation.
- Nguyen, C. H. and Mamitsuka, H.
- IEEE Transactions on Neural Networks,
22(9), 1395-1495, 2011.
- [DOI].
-
Clustering Genes with Expression and Beyond.
- Shiga, M. and Mamitsuka, H.
- WIREs Data Mining and Knowledge Discovery,
1(6), 496-511, 2011.
- Invited Review Paper.
- [DOI].
-
Kernels for Link Prediction with Latent Feature Models.
- Nguyen, C. H. and Mamitsuka, H.
- Proceedings of the European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML PKDD 2011), Part II (Lecture Notes in Artificial Intelligence, 6912), 517-532,
Athens, Greece, September, 2011, Springer.
- [DOI].
-
Calpain Cleavage Prediction Using Multiple Kernel Learning.
- duVerle, D., Ono, Y., Sorimachi, H. and Mamitsuka, H.
- PLoS One,
6(5), e19035, 2011.
- [DOI].
-
ROS-DET: Robust Detector of Switching Mechanisms in Gene Expression.
- Kayano, M., Takigawa, I., Shiga, M., Tsuda, K. and Mamitsuka, H.
- Nucleic Acids Research,
39 (11), e74, 2011.
- [DOI].
-
Ensemble Approaches for Improving HLA Class I-peptide Binding Prediction.
- Hu, X., Mamitsuka, H. and Zhu, S.
- Journal of Immunological Methods,
374(1/2), 47-52, 2011.
- [DOI].
-
Mining Significant Substructure Pairs for Interpreting Polypharmacology
in Drug-Target Network.
- Takigawa, I., Tsuda, K. and Mamitsuka, H.
- PLoS One,
6(2), e16999, 2011.
- [DOI].
-
Efficiently Mining δ-Tolerance Closed Frequent Subgraphs.
- Takigawa, I. and Mamitsuka, H.
- Machine Learning,
82(2), 95-121, 2011.
- [DOI].
-
A Spectral Approach to Clustering Numerical Vectors as Nodes in a Network.
- Shiga, M., Takigawa, I. and Mamitsuka, H.
- Pattern Recognition,
44(2), 236-251, 2011.
- [DOI].
-
Mining Metabolic Pathways through Gene Expression.
- Hancock, T., Takigawa, I. and Mamitsuka, H.
- Bioinformatics,
26(17), 2128-2135, 2010.
- [DOI].
-
MetaMHC: A Meta Approach to Predict Peptides Binding to MHC Molecules.
- Hu, X., Zhou, W., Udaka, K., Mamitsuka, H. and Zhu, S.
- Nucleic Acids Research,
38, W474-W479, 2010.
- [DOI].
-
Boosted Optimization for Network Classification.
- Hancock, T. and Mamitsuka, H.,
- Proceedings of the Thirteenth International Conference on Artificial Intelligence and Statistics (AISTATS 2010) (JMLR: Workshop and Conference Proceedings, Vol. 9) , 305-312, Sardinia, Italy, May 2010, MIT Press.
- [PMLR paper site].
-
A Markov Classification Model for Metabolic Pathways.
- Hancock, T. and Mamitsuka, H.
- Algorithms for Molecular Biology,
5 (1), 10, 2010.
- Special Issue: Selected papers from WABI 2009
- [DOI].
-
Algorithms for Finding a Minimum Repetition Representation of a String
- Nakamura, A., Saito, T., Takigawa, I., Mamitsuka, H. and Kudo, M.
- Proceedings of the Seventeenth Symposium on String Processing and Information Retrieval (SPIRE 2010, Lecture Notes in Computer Science, 6393), 185-190,
Los Cabos, Mexico, October, 2010.
- [DOI].
-
Variational Bayes Learning over Multiple Graphs.
- Shiga, M. and Mamitsuka, H.
- Proceedings of the IEEE International Workshop on Machine Learning for Signal Processing (MLSP 2010), 166-171,
Kitilla, Finland, September, 2010.
- [DOI].
-
On Network-based Kernel Methods for Protein-Protein Interactions with Applications in Protein Functions.
- Li, L., Ching, W-K., Chan, Y-M. and Mamitsuka, H.
- Journal of Systems Science and Complexity
23(5), 917-930, 2010
- [DOI].
-
TAP Hunter: A SVM-based System for Predicting TAP Ligands using Local Description of Amino Acid Sequence.
- Lam, T. H., Mamitsuka, H., Ren, E. C., and Tong, J. C.
- Immunome Research,
6 (Suppl. 1), S6, 2010.
- [DOI].
-
Efficiently Finding Genome-wide Three-way Gene Interactions from Transcript- and Genotype-Data.
- Kayano, M., Takigawa, I., Shiga, M., Tsuda, K. and Mamitsuka, H.
- Bioinformatics,
25 (21), 2735-2743, 2009.
- [DOI].
-
Enhancing MEDLINE Document
Clustering by Incorporating MeSH Semantic Similarity.
- Zhu, S., Zeng, J. and Mamitsuka, H.
- Bioinformatics,
25 (15), 1944-1951, 2009.
- [DOI].
-
Field Independent Probabilistic Model for Clustering Multi-Field Documents.
- Zhu, S., Takigawa, I., Zeng, J. and Mamitsuka, H.
- Information Processing and Management,
45 (5), 555-570, 2009.
- [DOI, PDF (Advance access)].
-
HAMSTER: Visualizing Microarray Experiments as a Set of Minimum Spanning Trees.
- Wan, R., Kiseleva, L., Harada, H., Mamitsuka, H. and Horton, P.
- Source Code for Biology and Medicine,
4, 8, 2009.
- [DOI].
-
A Markov Classification Model for Metabolic Pathways.
- Hancock, T. and Mamitsuka, H.
- Proceedings of the Ninth Workshop on Algorithms in Bioinformatics (WABI 2009), (Lecture Notes in Bioinformatics, 5724), 121-132 , Philadelphia, PA, USA, September, 2009, Springer-Verlag.
- [DOI].
-
Efficient Probabilistic Latent Semantic Analysis through Parallelization.
- Wan, R., Vo, N. A. and Mamitsuka, H.
- Proceedings of the Fifth Asia Information Retrieval
Symposium (AIRS2009, Lecture Notes in Computer Science,
5839), 432-443,
Sapporo, Japan, October, 2009, Springer-Verlag.
- [DOI].
-
A Study of Network-based Kernel Methods on
Protein-Protein Interaction for Protein
Functions Prediction.
- Ching, W-K., Li, L., Chan, Y-M. and Mamitsuka, H.
- Proceedings of the Third International Symposium on Optimization
and Systems Biology (OSB 2009, Lecture Notes in Operations Research,
11), 25-32,
Zhangjiajie, China, September, 2009, APORC Press
- [PDF (APORC)].
-
Discovering Network Motifs in Protein Interaction Networks.
- Wan, R. and Mamitsuka, H.
- Biological Data Mining in Protein Interaction Networks, Chapter 8, 117-143, 2009, IGI Global.
- [Bibtex].
-
Mining Significant Tree Patterns in Carbohydrate Sugar Chains.
- Hashimoto, K., Takigawa, I., Shiga, M., Kanehisa, M. and Mamitsuka, H.
- Proceedings of the Seventh
European Conference on Computational Biology (ECCB 2008),
(Bioinformatics, 24 (16), 2008),
i167-i173, Cagliari, Sardinia-Italy, September, 2008, Oxford University Press.
- [DOI].
-
A New Efficient Probabilistic Model for Mining Labeled
Ordered Trees Applied to Glycobiology.
- Hashimoto, K., Aoki-Kinoshita, K. F., Ueda, N., Kanehisa, M. and
Mamitsuka, H.
- ACM Transactions on
Knowledge Discovery from Data, 2 (1), Article No. 6, 2008.
- [DOI].
-
Probabilistic Path Ranking Based on Adjacent Pairwise
Coexpression for Metabolic Transcripts Analysis.
- Takigawa, I. and Mamitsuka, H.
- Bioinformatics, 24 (2), 250-257, 2008.
- [DOI].
-
Informatic Innovations in Glycobiology: Relevance to Drug
Discovery.
- Mamitsuka, H.
- Drug Discovery Today, 13 (3/4), 118-123, 2008.
- Invited Review Paper.
- [DOI].
-
A Spectral Clustering Approach to Optimally Combining
Numerical Vectors with a Modular Network.
- Shiga, M., Takigawa, I. and Mamitsuka, H.,
- Proceedings of the Thirteenth ACM SIGKDD International
Conference on Knowledge Discovery and Data Mining (KDD
2007), 647-656, San Jose, CA, USA, August 2007, ACM
Press.
- [DOI, PDF (Preprints)].
-
Annotating Gene Function by Combining Expression Data
with a Modular Gene Network.
- Shiga, M., Takigawa, I. and Mamitsuka, H.
- Proceedings of the Fifteenth
International Conference on Intelligent Systems for
Molecular Biology (ISMB/ECCB 2007),
(Bioinformatics, 23 (13), 2007), i468-i478, Vienna,
Austria, July, 2007, Oxford University Press.
- [DOI].
-
A Hidden Markov Model-based Approach for Identifying
Timing Differences in Gene Expression under Different
Experimental Factors.
- Yoneya, T. and Mamitsuka, H.
- Bioinformatics, 23 (7), 842-849, 2007.
- [DOI].
-
A Probabilistic Model for Clustering Text Documents with
Multiple Fields.
- Zhu, S., Takigawa, I., Zhang, S. and Mamitsuka, H.
- Proceedings of the 29th European Conference on
Information Retrieval (ECIR 2007, Lecture Notes in Computer
Science, 4425), 331-342,
Roma, Italy, April, 2007, Springer-Verlag.
- [DOI].
-
Identification of Endocrine Disruptor Biodegradation by
Integration of Structure-activity Relationship with
Pathway Analysis.
- Kadowaki, T., Wheelock, C. E., Adachi, T., Kudo, T., Okamoto, S.,
Tanaka, N., Tonomura, K., Tsujimoto, G., Mamitsuka, H., Goto,
S. and Kanehisa, M.
- Environmental Science & Technology, 41 (23), 7997-8003, 2007.
- [DOI].
-
Selecting Features in Microarray Classification Using ROC Curves
- Mamitsuka, H.
- Pattern Recognition, 39 (12), 2393-2404, 2006.
- [DOI].
-
Applying Gaussian Distribution-dependent Criteria to Decision Trees for High-Dimensional Microarray Data
- Wan, R., Takigawa, I. and Mamitsuka, H.
- Proceedings of 2006 VLDB Workshop on Data Mining in Bioinformatics (Lecture Notes in Bioinformatics, 4316), 40-49 , Seoul, Korea, September, 2006, Springer-Verlag.
- [DOI].
-
A New Efficient Probabilistic Model for Mining Labeled Ordered Trees.
- Hashimoto, K., Aoki-Kinoshita, K. F., Ueda, N., Kanehisa, M. and
Mamitsuka, H.,
- Proceedings of the Twelfth ACM SIGKDD International
Conference on Knowledge Discovery and Data Mining (KDD
2006), 177-186, Philadelphia, PA, USA, August 2006, ACM
Press.
- [DOI, PDF (Preprints)].
-
ProfilePSTMM: Capturing Tree-structure Motifs in
Carbohydrate Sugar Chains.
- Aoki, K. F., Ueda, N., Mamitsuka, H. and Kanehisa, M.
- Proceedings of the Fourteenth
International Conference on Intelligent Systems for
Molecular Biology (ISMB 2006),
(Bioinformatics, 22 (14), e25-e34),
Fortaleza, Brazil, August, 2006, Oxford University Press.
- [DOI].
-
Application of a New Probabilistic Model for Mining
Implicit Associated Cancer Genes from OMIM and Medline.
- Zhu, S., Okuno, Y., Tsujimoto, G. and Mamitsuka, H.
- Cancer Informatics, 2, 361-371, 2006.
- [Cancer Informatics, Bibtex].
-
Improving MHC Binding Peptide Prediction by
Incorporating Binding Data of Auxiliary MHC Molecules.
- Zhu, S., Udaka, K., Sidney, J., Sette, A., Aoki-Kinoshita, K. F. and
Mamitsuka, H.
- Bioinformatics, 22 (13), 1648-1655, 2006.
- [DOI].
-
Query-Learning-Based Iterative Feature-Subset Selection for Learning from High-Dimensional Data Sets.
- Mamitsuka, H.
- Knowledge and Information Systems,
9 (1), 91-108, 2006.
- [DOI].
-
A Probabilistic Model for Mining Implicit ``Chemical Compound - Gene'' Relations from Literature.
- Zhu, S., Okuno, Y., Tsujimoto, G. and Mamitsuka, H.
- Proceedings of the Fourth
European Conference on Computational Biology (ECCB/JBI 2005),
(Bioinformatics, 21, Supplement 2, ii245-ii251),
Madrid, Spain, September, 2005, Oxford University Press.
- [DOI].
-
Finding the Biologically Optimal Alignment of Multiple Sequences
- Mamitsuka, H.
- Artificial Intelligence in Medicine, 35 (1), 9-18, 2005.
- [DOI].
-
Probabilistic Model for Mining Labeled Ordered Trees: Capturing
Patterns in Carbohydrate Sugar Chains.
- Ueda, N., Aoki-Kinoshita, K. F., Yamaguchi, A., Akutsu, T. and Mamitsuka, H.
- IEEE Transactions on Knowledge and Data Engineering, 17 (8),
1051-1064, 2005.
- [DOI].
-
Mining New Protein-Protein Interactions - Using a Hierarchical Latent-variable Model to Determine the Function of a Functionally Unknown Protein.
- Mamitsuka, H.
- IEEE Engineering in Medicine and Biology Magazine, 24 (3), 103-108, 2005.
- [DOI].
-
Essential Latent Knowledge for Protein-Protein
Interactions: Analysis by an Unsupervised Learning Approach.
- Mamitsuka, H.
- IEEE/ACM Transactions on Computational Biology
and Bioinformatics, 2 (2),
119-130, 2005.
- [DOI].
-
Efficient Unsupervised Mining from Noisy Co-occurrence Data.
- Mamitsuka, H.
- New Mathematics and Natural Computation, 1 (1),
173-193, 2005.
- [DOI].
-
A Score Matrix to Reveal the Hidden Links in Glycans.
- Aoki, K. F., Mamitsuka, H., Akutsu, T. and Kanehisa, M.
- Bioinformatics, 21 (8),
1457-1463, 2005.
- [DOI].
-
Cleaning Microarray Expression Data Using Markov Random Fields based on
Profile Similarity.
- Wan, R., Mamitsuka, H. and Aoki, K. F.
- Proceedings of the Twentieth ACM Symposium on Applied
Computing (SAC 2005), 206-207, Santa Fe, NM, USA, March, 2005, ACM Press.
- [DOI].
-
The Evolutionary Repertoires of the Eukaryotic-type ABC Transporters in
terms of the Phylogeny of ATP-binding Domains in Eukaryotes and
Prokaryotes.
- Igarashi, Y., Aoki, K. F., Mamitsuka, H., Kuma, K. and Kanehisa, M.
- Molecular Biology and Evolution, 21 (11),
2149-2160, 2004.
- [DOI].
-
Finding the Maximum Common Subgraph of a Partial
k-Tree and a Graph with a Polynomially Bounded Number of
Spanning Trees.
- Yamaguchi, A., Aoki, K. F. and Mamitsuka, H.
- Information Processing Letters, 92 (2),
57-63, 2004.
- [DOI].
-
A Hierarchical Mixture of Markov Models for Finding Biologically Active
Metabolic Paths using Gene Expression and Protein
Classes.
- Mamitsuka, H. and Okuno, Y.
- Proceedings of the IEEE Computational Systems
Bioinformatics Conference (CSB 2004), 341-352, Stanford, CA, USA, August, 2004, IEEE Computer Society Press.
- [DOI, PDF, Bibtex].
-
Application of a New Probabilistic Model for Recognizing
Complex Patterns in Glycans.
- Aoki, K. F., Ueda, N., Yamaguchi, A., Kanehisa, M.,
Akutsu, T. and Mamitsuka, H.
- Proceedings of the Twelfth
International Conference on Intelligent Systems for
Molecular Biology (ISMB/ECCB 2004),
(Bioinformatics, 20, Supplement 1, i6-i14),
Glasgow, UK, August, 2004, Oxford University Press.
- [DOI].
-
KCaM (KEGG Carbohydrate Matcher): A Software Tool for
Analyzing the Structures of Carbohydrate Sugar Chains.
- Aoki, K. F., Yamaguchi, A., Ueda, N., Akutsu, T., Mamitsuka, H., Goto, S. and Kanehisa, M.
- Nucleic Acids Research, 32, W267-W272, 2004.
- [DOI].
-
Managing and Analyzing Carbohydrate Data.
- Aoki, K. F., Ueda, N., Yamaguchi, A., Akutsu, T., Kanehisa, M. and Mamitsuka, H.
- ACM SIGMOD Record, 33 (2), 33-38, 2004.
- [DOI, PDF].
-
A General Probabilistic Framework for Mining Labeled Ordered Trees.
- Ueda, N., Aoki, K. F. and Mamitsuka, H.
- Proceedings of the Fourth SIAM
International Conference on Data Mining (SDM 2004), 357-368,
Orlando, FL, USA, April, 2004, SIAM.
- [PDF].
-
Mining Biologically Active Patterns in Metabolic Pathways
using Microarray Expression Profiles.
- Mamitsuka, H., Okuno, Y. and Yamaguchi, A.
- ACM SIGKDD Explorations, 5 (2):113-121, 2003.
- [DOI, PDF].
-
Finding the Maximum Common Subgraph of a Partial k-Tree
and a Graph with a Polynomially Bounded Number of
Spanning Trees.
- Yamaguchi, A. and Mamitsuka, H.
- Proceedings of the Fourteenth International Symposium
on Algorithm and Computation (ISAAC 2003, Lecture Notes in
Computer Science, 2906), 58-67, Kyoto, Japan, December,
2003, Springer-Verlag.
- [DOI].
-
Efficient Tree-Matching Methods for Accurate Carbohydrate Database Queries.
- Aoki, K. F., Yamaguchi, A., Okuno, Y., Akutsu, T., Ueda, N., Kanehisa, M. and Mamitsuka, H.
- Proceedings of the Fourteenth International Conference
on Genome Informatics (GIW 2003, Genome Informatics, 14), 134-143, Yokohama, Japan, December, 2003, Universal Academy Press.
- [PubMed].
-
Efficient Mining from Heterogeneous Data Sets for
Predicting Protein-Protein Interactions.
- Mamitsuka, H.
- Proceedings of the Fourteenth International Workshop
on Database and Expert Systems,
32-36, Prague, Czech Republic,
September, 2003, IEEE Computer Society Press.
- [DOI].
-
Selective Sampling with a Hierarchical Latent Variable Model.
- Mamitsuka, H.
- Proceedings of the Fifth International Symposium on
Intelligent Data Analysis (IDA 2003, Lecture Notes in Computer
Science, 2810), 352-363, Berlin, Germany,
August, 2003, Springer-Verlag.
- [DOI].
-
Hierarchical Latent Knowledge Analysis for Co-occurrence Data.
- Mamitsuka, H.
- Proceedings of the Twentieth International Conference
on Machine Learning (ICML 2003),
504-511, Washington DC, USA, August, 2003, AAAI Press.
- [Abstract (ICML2003)].
-
Efficient Unsupervised Mining from Noisy Data Sets:
Application to Clustering Co-occurrence Data.
- Mamitsuka, H.
- Proceedings of the Third SIAM International Conference on Data Mining (SDM 2003),
239-243, San Francisco, CA, USA, May, 2003, SIAM.
- [PDF].
-
Detecting Experimental Noise in Protein-Protein
Interactions with Iterative Sampling and Model-based Clustering.
- Mamitsuka, H.
- Proceedings of the Third IEEE International
Symposium on Bioinformatics and Bioengineering (BIBE 2003),
385-392, Bethesda, MD, USA,
March, 2003, IEEE Computer Society Press.
- [DOI].
-
Empirical Evaluation of Ensemble Feature Subset Selection
Methods for Learning from a High-Dimensional Database in
Drug Design.
- Mamitsuka, H.
- Proceedings of the Third IEEE International
Symposium on Bioinformatics and Bioengineering (BIBE 2003),
253-257, Bethesda, MD, USA,
March, 2003, IEEE Computer Society Press.
- [DOI].
-
Empirical Evaluation of a Dynamic Experiment Design
Method for Prediction of MHC Class I-binding Peptides.
- Udaka, K., Mamitsuka, H., Nakaseko, Y. and Abe, N.
- Journal of Immunology, 169 (10):5744-5753, 2002.
- [DOI]
-
Iteratively Selecting Feature Subsets for Mining from
High-Dimensional Databases.
- Mamitsuka, H.
- Proceedings of the Sixth European Conference on
Principles and Practice of Knowledge Discovery in
Databases (PKDD 2002, Lecture Notes in Artificial
Intelligence, 2431), 361-372,
Helsinki, Finland, August, 2002, Springer-Verlag.
- [DOI].
-
Active Ensemble Learning - Applications to Data Mining
and Bioinformatics - .
(in Japanese)
- Mamitsuka, H. and Abe, N.
- IEICE Transactions, J85-DII (5):717-724, 2002.
- Invited paper.
- [Abstract (IEICE), Bibtex].
-
Prediction of MHC Class I binding Peptides by a Query
Learning Algorithm based on Hidden Markov Models.
- Udaka, K., Mamitsuka, H., Nakaseko, Y. and Abe, N.
- Journal of Biological Physics., 28 (2):183-194, 2002.
- [DOI].
-
Efficient Data Mining by Active Learning.
- Mamitsuka, H. and Abe, N.
- Progress in Discovery Science, Lecture Notes in
Artificial Intelligence, 2281:258-267, 2002, Springer-Verlag.
- [DOI].
Unrefereed Publications
-
Machine Learning for Marketing.
- Mamitsuka, H.
- Global Data Science Publishing, 2019.
- Authored Book.
- [Supporting page].
-
CalCleaveMKL: a Tool for Calpain Cleavage Prediction.
- duVerle, D. and Mamitsuka, H.
- Calpain: Methods and Protocols Methods in Molecular Biology, 1915, 121-147, 2019.
- Book Chapter.
- [DOI].
-
Textbook of Machine Learning and Data Mining (with Bioinformatics Applications).
- Mamitsuka, H.
- Global Data Science Publishing, 2018.
- Authored Book.
- [Supporting page].
-
Data Mining for Systems Biology: Methods and Protocols (2nd Edition).
- Mamitsuka, H.
- Methods in Molecular Biology,
1807, 2018.
- Edited Book.
- [DOI].
-
SiBIC: a Tool for Generating a Network of Biclusters Captured by Maximal Frequent Itemset Mining.
- Takahashi, K., duVerle, D. A., Yotsukura, S., Takigawa, I. and Mamitsuka, H.
- Data Mining for Systems Biology: Methods and Protocols. (2nd Edition) Methods in Molecular Biology, 1807, 95-111, 2018.
- Book Chapter.
- [DOI].
-
DrugE-Rank: Predicting Drug-target Interactions by Learning to Rank.
- Deng, J., Yuan, Q., Mamitsuka, H. and Zhu, S.
- Data Mining for Systems Biology: Methods and Protocols. (2nd Edition) Methods in Molecular Biology, 1807, 195-202, 2018.
- Book Chapter.
- [DOI].
-
MeSHLabeler and DeepMeSH: Recent Progress in Large-scale MeSH Indexing.
- Peng, S., Mamitsuka, H. and Zhu, S.
- Data Mining for Systems Biology: Methods and Protocols. (2nd Edition) Methods in Molecular Biology, 1807, 203-209, 2018.
- Book Chapter.
- [DOI].
-
MetaMHCpan, A Meta Apporach for Pan-specific MHC Peptide Binding Prediction.
- Xu, Y., Luo, C., Mamitsuka, H. and Zhu, S.
- Vaccine Design: Methods and Protocols, Volume 2: Vaccines for Veterinary Diseases Methods in Molecular Biology, 1404, 753-760, 2016.
- Book Chapter.
- [DOI].
-
An In Silico Model for Interpreting Polypharmacology in Drug-Target Networks.
- Takigawa, I., Tsuda, K. and Mamitsuka, H.
- In Siilico Models for Drug Discovery Methods in Molecular Biology, 993, 67-80, 2013.
- Book Chapter.
- [DOI].
-
Identifying Pathways of Co-ordinated Gene Expression.
- Hancock, T., Takigawa, I. and Mamitsuka, H.
- Data Mining for Systems Biology: Methods and Protocols
Methods in Molecular Biology, 939, 69-85, 2013.
- Book Chapter.
- [DOI].
-
Data Mining for Systems Biology: Methods and Protocols.
- Mamitsuka, H., DeLisi, C. and Kanehisa, M.
- Methods in Molecular Biology,
939, 2013.
- Edited Book.
- [DOI].
-
Glycoinformatics: Data Mining-based Approaches.
- Mamitsuka, H.
- Chimia,
65(1/2), 10-13, 2011.
- Invited Review Paper.
- [DOI].
-
Mining Patterns from Glycan Structures.
- Takigawa, I., Hashimoto, K., Shiga, M., Kanehisa, M. and Mamitsuka, H.
- Proceedings of the International Beilstein Symposium on Glyco-Bioinformatics, 13-24,
2010.
- [Beilstein Institute, Bibtex].
-
On the Performance of Methods for Finding a Switching Mechanism in Gene Expression.
- Kayano, M., Takigawa, I., Shiga, M., Tsuda, K. and Mamitsuka, H.
- Proceedings of the Tenth Annual International Workshop on
Bioinformatics and Systems Biology (IBSB 2010, Genome
Informatics, 24), 69-83,
Kyoto, Japan, July, 2010, Imperial College Press.
- [DOI].
-
Active Pathway Identification and Classification with Probabilistic
Ensembles.
- Hancock, T. and Mamitsuka, H.
- Proceedings of the Ninth Annual International Workshop on
Bioinformatics and Systems Biology (IBSB 2009, Genome
Informatics, 22), 30-40,
Boston, USA, July, 2009, Imperial College Press.
- [DOI].
-
Annotating Gene Functions with Integrative Spectral Clustering on
Microarray Expressions and Sequences.
- Li, L., Shiga, M., Ching, W.-K. and Mamitsuka, H.
- Proceedings of the Ninth Annual International Workshop on
Bioinformatics and Systems Biology (IBSB 2009, Genome
Informatics, 22), 95-120,
Boston, USA, July, 2009, Imperial College Press.
- [DOI].
-
CaMPDB: a Resource for Calpain and Modulatory Proteolysis.
- duVerle, D., Takigawa, I., Ono, Y., Sorimachi, H. and Mamitsuka, H.
- Proceedings of the Ninth Annual International Workshop on
Bioinformatics and Systems Biology (IBSB 2009, Genome
Informatics, 22), 202-214,
Boston, USA, July, 2009, Imperial College Press.
- [DOI].
-
Semi-Supervised Graph Partitioning with Decision Trees.
- Hancock, T. and Mamitsuka, H.
- Proceedings of the Eighth Annual International Workshop on
Bioinformatics and Systems Biology (IBSB 2008, Genome
Informatics, 20), 102-111,
Berlin, Germany, June, 2008, Imperial College Press.
- [DOI].
-
A Framework for Determining Outlying Microarray Experiments.
- Wan, R., Wheelock, A. and Mamitsuka, H.
- Proceedings of the Eighth Annual International Workshop on
Bioinformatics and Systems Biology (IBSB 2008, Genome
Informatics, 20), 64-76,
Berlin, Germany, June, 2008, Imperial College Press.
- [DOI].
-
Clustering Analysis for Combining Multiple Genomic Data.
- Shiga, M., Takigawa, I. and Mamitsuka, H.
- Seibutsu-butsuri (Biophysics), 48 (3), 190-194, 2008.
- [DOI].
-
PURE: A PubMed Article Recommendation System Based on
Content-based Filtering.
- Yoneya, T. and Mamitsuka, H.
- Proceedings of the Seventh International Workshop on
Bioinformatics and Systems Biology (IBSB 2007, Genome
Informatics, 18), 267-276,
Tokyo, Japan, July, 2007, Imperial College Press.
- [DOI].
-
Computational Intelligence in Solving Bioinformatics Problems
- Cios, K. J., Mamitsuka, H., Nagashima, T. and Tadeusiewicz, R.
- Artificial Intelligence in Medicine, 35 (1), 1-8, 2005.
- [DOI].