Bio-Knowledge Engineering Research Laboratory

Institute for Chemical Research, Kyoto University

Gokasho, Uji, Kyoto, 611-0011, Japan

Email: *$myaccoutname* @kuicr.kyoto-u.ac.jp

- D.A. Nguyen, C.H. Nguyen, H. Mamitsuka, "Central-Smoothing Hypergraph Neural Networks
for Predicting Drug-Drug Interactions",
*IEEE Transactions on Neural Networks and Learning Systems*, vol., no., pp. pdf - C.H. Nguyen, "Semi-Supervised Learning on Large Graphs: is Poisson Learning a Game-Changer?",
*arXiv:2202.13608v2 [stat.ML]* - D.A. Nguyen, C.H. Nguyen, P. Petschner, H. Mamitsuka, "SPARSE: a sparse hypergraph neural network for learning multiple types of latent combinations to accurately predict drug-drug interactions",
*Bioinformatics, (ISMB 2022)*, vol. 38, no. 1, pp. i333-i341 pdf - C.H. Nguyen, H. Mamitsuka, "On Convex Clustering Solutions",
*arXiv:2105.08348v1 [stat.ML]* - D.H. Nguyen, C.H. Nguyen, H. Mamitsuka, "Learning subtree pattern importance for Weisfeiler-Lehman based graph kernels".
*Machine Learning*, vol. 10, no. 7, pp. 1585-1607, 2021. pdf - D. A. Nguyen, K. A. Nguyen, C. H. Nguyen, K. Than, "Boosting prior knowledge in streaming variational Bayes",
*Neurocomputing*, vol. 424, pp. 143-159, 2021. pdf - M. Cai, C. H. Nguyen, H. Mamitsuka, L. Li, "XGSEA: CROSS-species Gene Set Enrichment Analysis via domain adaptation".
*Briefings in Bioinformatics*, vol. 22, no. 5, 2021. pdf - H. Kaneko et. al., "Eukaryotic virus composition can predict the efficiency of carbon export in the global ocean",
*iScience*, vol. 24, no. 1, 2021. html - D. A., Nguyen, C. H., Nguyen and H. Mamitsuka, "A Survey on Adverse Drug Reaction Studies: Data, Tasks, and Machine Learning Methods",
*Briefings in Bioinformatics*, vol. 22, no 1, pp. 164-177 , 2021. pdf - C. H. Nguyen, "Structured Learning in Biological Domain",
*Journal of Systems Science and Systems Engineering*, vol.29, no. 4, pp 440-453, 2020. html - C. H. Nguyen and H. Mamitsuka, "Learning on Hypergraphs with Sparsity",
*IEEE Transactions on Pattern Analysis and Machine Intelligence*, vol. 43, pp. 2710-2722, Aug. 2021. pdf - L. Sun, C.H. Nguyen, H. Mamitsuka, "Fast and Robust Multi-View Multi-Task Learning via Group Sparsity", in
*Proceedings of the 28th International Joint Conference on Artificial Intelligence (IJCAI 2019)*, pp. 3499-3505, 2019. pdf supplementary - L. Sun, C.H. Nguyen, H. Mamitsuka, "Multiplicative Sparse Feature Decomposition for Efficient Multi-View Multi-Task Learning", in
*Proceedings of the 28th International Joint Conference on Artificial Intelligence (IJCAI 2019)*, pp. 3506-3512, 2019. pdf supplementary - D.H. Nguyen, C.H. Nguyen, H. Mamitsuka, "ADAPTIVE: leArning DAta-dePendenT, concIse molecular VEctors for fast, accurate metabolite identification from tandem mass spectra".
*Bioinformatics 35, (Proceedings of the 26th International Conference on Intelligent Systems for Molecular Biology (ISMB 2019)*, vol. 23, no. 14, pp. i164-i172 pdf - H., Seki, C.H., Nguyen, V.-N., Huynh, M., Inuiguchi (Eds.)
*Integrated Uncertainty in Knowledge Modelling and Decision Making Proceedings of 7th International Symposium, IUKM 2019,*Springer LNCS 11471, 2019. html - N. Wicker, C.H. Nguyen, H. Mamitsuka, "A p-Laplacian random walk: application to video games".
*Austrian Journal of Statistics*, vol. 48, no. 5, pp. 11-16, 2019. pdf - D.H. Nguyen, C.H. Nguyen, H. Mamitsuka, "Recent advances and prospects of computational methods for metabolite identification: a review with emphasis on machine learning approaches",
*Briefings in Bioinformatics*, vol. 20, no. 6, pp. 2028-2043, 2019. pdf - D.H. Nguyen, C.H. Nguyen, H. Mamitsuka, "SIMPLE: Sparse Interaction Model over Peaks of MoLEcules for Fast, Interpretable Metabolite Identification from Tandem Mass Spectra".
*Bioinformatics, (Proceedings of the 26th International Conference on Intelligent Systems for Molecular Biology (ISMB 2018)*, pp. i323-i332, 2018. pdf - N. Wicker, C.H. Nguyen, H. Mamitsuka, "Some Properties of a Dissimilarity Measure for Labeled Graphs".
*Publications Mathematiques de Besancon*. pp. 85-94, 2016. pdf - A. Mohamed, C.H. Nguyen, H. Mamitsuka, "NMRPro: An integrated web component for interactive processing and visualization of NMR spectra."
*Bioinformatics*, vol. 32, no. 13, pp. 2067-2068, 2016. pdf - C.H. Nguyen, H. Mamitsuka, "New Resistance Distances with Global Information on Large Graphs".
*JMLR Workshop and Conference Proceedings. Volume 51: Proceedings of the 19th International Conference on Artificial Intelligence and Statistics*, pp. 639-647, May 2016. pdf supplementary - A. Mohamed, C.H. Nguyen, H. Mamitsuka, "Current status and prospects of computational resources for natural product dereplication: A review"
*Briefings in Bioinformatics*, vol. 17, no. 2, pp. 309-321, 2016. pdf - A. Mohamed, T. Hancock, C.H. Nguyen, H. Mamitsuka, "NetPathMiner: R/Bioconductor package for network path mining through gene expression",
*Bioinformatics*. vol. 30, no. 21, pp. 3139-3141, Nov 01, 2014. pdf - C. H. Nguyen, N. Wicker and H. Mamitsuka, "Selecting Graph Cut Solutions via Global Graph Similarity",
*IEEE Transactions on Neural Networks and Learning Systems.*vol. 25, no. 7, pp. 1407-1412, 2014. pdf - N. Wicker, C. H. Nguyen and H. Mamitsuka, "A new dissimilarity measure for comparing labeled graphs",
*Linear Algebra and its Applications.*vol. 438, no. 5, pp. 2331-2338. Mar 01, 2013. pdf - C. H. Nguyen and H. Mamitsuka, "Latent Feature Kernels for Link Prediction on Sparse Graphs"
*IEEE Transactions on Neural Networks and Learning Systems.*vo. 23, no. 11, pp. 1793-1804, 2012. pdf - C. H. Nguyen and H. Mamitsuka, "Kernels for link prediction with latent feature models,"
*The European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (2) (ECML/PKDD 2011),*pp. 517-532, 2011. pdf - C. H. Nguyen and H. Mamitsuka, "Discriminative graph embedding for label propagation,"
*IEEE Transactions on Neural Networks,*vol. 22, no. 9, pp. 1395-1405, 2011. pdf - C. H. Nguyen, T. B. Ho, and V. Kreinovich, "Estimating quality of support vector machines learning under probabilistic and interval uncertainty: Algorithms and computational complexity,"
*Interval / Probabilistic Uncertainty and Non-Classical Logics,*pp. 57-69, 2008. pdf - C. H. Nguyen and T. B. Ho, "An efficient kernel matrix evaluation measure,"
*Pattern Recognition,*vol. 41, no. 11, pp. 3366-3372, 2008. pdf - H. Tanabe, T. B. Ho, C. H. Nguyen, and S. Kawasaki, "Simple but effective methods for combining kernels in computational biology,"
*RIVF,*pp. 71-78, 2008. pdf - C. H. Nguyen and T. B. Ho, "Kernel matrix evaluation,"
*International Joint Conference on Artificial Intelligence (IJCAI2007),*pp. 987-992, 2007. pdf - T. B. Ho, C. H. Nguyen, S. Kawasaki, S. Q. Le, and K. Takabayashi, "Exploiting temporal relations in mining hepatitis data,"
*New Generation Computing,*vol. 25, no. 3, pp. 247-262, 2007. pdf - T. B. Ho, C. H. Nguyen, S. Kawasaki, and K. Takabayashi, "Temporal relations extraction in mining hepatitis data,"
*The Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD2007),*pp. 523-530, 2007. - C. H. Nguyen and T. B. Ho, "Sampling for imbalanced data learning,"
*The International Workshop on Data-Mining and Statistical Science (DMSS2006),*pp. 12-19, 2006. - C. H. Nguyen and T. B. Ho, "An imbalanced data rule learner,"
*The European Conference on Principles and Practice of Knowledge Discovery in Databases (PKDD2005),*pp. 617-624, 2005. pdf