Basic Information

Affiliated programs (koza)

• Graduate School of Pharmaceutical Sciences, 医薬創成情報科学専攻 医薬創成情報科学講座, 講師

Academic Degree

• 修士（知識科学）(北陸先端科学技術大学院大学)
• 博士（知識科学）(北陸先端科学技術大学院大学)

Language of Instruction

• Japanese
• English
• Vietnamese

ID,URL

• ORCID ID

  0000-0002-0274-5693

• J-Global ID

  201401017286977497

• External link

  http://www.bic.kyoto-u.ac.jp/pathway/canhhao/index.html

Website(s) (URL(s))

• http://www.bic.kyoto-u.ac.jp/pathway/canhhao/index.html

researchmap URL

• https://researchmap.jp/7000009445

Research

Research Topics, Overview of the research

• Research Topics

  Machine Learning, Graph, Bioinformatics

Research Areas

• Informatics, Intelligent informatics

Papers

• PanKA: Leveraging population pangenome to predict antibiotic resistance.

  Van Hoan Do; Van Sang Nguyen; Son Hoang Nguyen; Duc Quang Le; Tam Thi Nguyen; Canh Hao Nguyen; Tho Huu Ho; Nam S Vo; Trang Nguyen; Hoang Anh Nguyen; Minh Duc Cao

  iScience, 20 Sep. 2024, Peer-reviewed

  
• Efficient inference of large prokaryotic pangenomes with PanTA.

  Duc Quang Le; Tien Anh Nguyen; Son Hoang Nguyen; Tam Thi Nguyen; Canh Hao Nguyen; Huong Thanh Phung; Tho Huu Ho; Nam S Vo; Trang Nguyen; Hoang Anh Nguyen; Minh Duc Cao

  Genome biology, 06 Aug. 2024, Peer-reviewed

  
• AMRomics: a scalable workflow to analyze large microbial genome collections.

  Duc Quang Le; Tam Thi Nguyen; Canh Hao Nguyen; Tho Huu Ho; Nam S Vo; Trang Nguyen; Hoang Anh Nguyen; Le Sy Vinh; Thanh Hai Dang; Minh Duc Cao; Son Hoang Nguyen

  BMC genomics, 22 Jul. 2024, Peer-reviewed

  
• Learning Low-Rank Tensor Cores with Probabilistic ℓ0-Regularized Rank Selection for Model Compression

  Tianxiao Cao; Lu Sun; Canh Hao Nguyen; Hiroshi Mamitsuka

  Proceedings of the Thirty-ThirdInternational Joint Conference on Artificial Intelligence, Aug. 2024, Peer-reviewed

  
• AMRViz enables seamless genomics analysis and visualization of antimicrobial resistance

  Duc Quang Le; Son Hoang Nguyen; Tam Thi Nguyen; Canh Hao Nguyen; Tho Huu Ho; Nam S. Vo; Trang Nguyen; Hoang Anh Nguyen; Minh Duc Cao

  BMC Bioinformatics, 16 May 2024, Peer-reviewed

  
• Pasa: leveraging population pangenome graph to scaffold prokaryote genome assemblies

  Van Hoan Do; Son Hoang Nguyen; Duc Quang Le; Tam Thi Nguyen; Canh Hao Nguyen; Tho Huu Ho; Nam S Vo; Trang Nguyen; Hoang Anh Nguyen; Minh Duc Cao

  Nucleic Acids Research, 12 Dec. 2023, Peer-reviewed

  
• Multiplicative Sparse Tensor Factorization for Multi-View Multi-Task Learning

  Xinyi Wang; Lu Sun; Canh Hao Nguyen; Hiroshi Mamitsuka

  Proceedings of the 26th European Conference on Artificial Intelligence (ECAI 2023), 28 Sep. 2023, Peer-reviewed

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• Central-Smoothing Hypergraph Neural Networks for Predicting Drug–Drug Interactions

  Duc Anh Nguyen; Canh Hao Nguyen; Hiroshi Mamitsuka

  IEEE Transactions on Neural Networks and Learning Systems, 2023, Peer-reviewed

  
• Machine Learning for Metabolic Identification

  Dai Hai Nguyen; Canh Hao Nguyen; Hiroshi Mamitsuka

  Creative Complex Systems, 2021, Peer-reviewed

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• SPARSE: a sparse hypergraph neural network for learning multiple types of latent combinations to accurately predict drug–drug interactions

  Duc Anh Nguyen; Canh Hao Nguyen; Peter Petschner; Hiroshi Mamitsuka

  Bioinformatics, 24 Jun. 2022, Peer-reviewed

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• Learning subtree pattern importance for Weisfeiler-Lehman based graph kernels

  Nguyen, D.H.; Nguyen, C.H.; Mamitsuka, H.

  Machine Learning, 13 Jun. 2021, Peer-reviewed

  
• Boosting prior knowledge in streaming variational Bayes

  Nguyen, D.A.; Ngo, V.L.; Nguyen, K.A.; Nguyen, C.H.; Than, K.

  Neurocomputing, Feb. 2021, Peer-reviewed

  
• XGSEA: CROSS-species gene set enrichment analysis via domain adaptation

  Cai, M.; Hao Nguyen, C.; Mamitsuka, H.; Li, L.

  Briefings in Bioinformatics, 30 Jan. 2021, Peer-reviewed

  
• Viruses of the eukaryotic plankton are predicted to increase carbon export efficiency in the global sunlit ocean

  Romain Blanc-Mathieu; Hiroto Kaneko; Hisashi Endo; Samuel Chaffron; Rodrigo Hernandez-Velazquez; Canh Hao Nguyen; Hiroshi Mamitsuka; Nicolas Henry; Colomban de Vargas; Matthew B. Sullivan; Curtis A. Suttle; Lionel Guidi; Hiroyuki Ogata

  iScience, 22 Jan. 2021, Peer-reviewed

  
• Eukaryotic virus composition can predict the efficiency of carbon export in the global ocean

  Hiroto Kaneko; Romain Blanc-Mathieu; Hisashi Endo; Samuel Chaffron; Tom O. Delmont; Morgan Gaia; Nicolas Henry; Rodrigo Hernández-Velázquez; Canh Hao Nguyen; Hiroshi Mamitsuka; Patrick Forterre; Olivier Jaillon; Colomban de Vargas; Matthew B. Sullivan; Curtis A. Suttle; Lionel Guidi; Hiroyuki Ogata

  iScience, Jan. 2021

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• Structured Learning in Biological Domain

  Nguyen, C.H.

  Journal of Systems Science and Systems Engineering, Aug. 2020, Peer-reviewed, Invited, Lead author, Corresponding author

  
• Learning on Hypergraphs with Sparsity

  Nguyen, C.H.; Mamitsuka, H.

  IEEE Transactions on Pattern Analysis and Machine Intelligence, 2021, Peer-reviewed

  
• A survey on adverse drug reaction studies: data, tasks and machine learning methods.

  Duc Anh Nguyen; Canh Hao Nguyen; Hiroshi Mamitsuka

  Briefings in bioinformatics, 15 Dec. 2019, Peer-reviewed

  
• Multiplicative Sparse Feature Decomposition for Efficient Multi-View Multi-Task Learning

  Lu Sun; Canh Hao Nguyen; Hiroshi Mamitsuka

  Proceedings of the Twenty-Eighth International Joint Conference on Artificial Intelligence, Aug. 2019, Peer-reviewed

  
• Fast and Robust Multi-View Multi-Task Learning via Group Sparsity

  Lu Sun; Canh Hao Nguyen; Hiroshi Mamitsuka

  Proceedings of the 28th International Joint Conference on Artificial Intelligence (IJCAI 2019), 2019, Peer-reviewed

  
• ADAPTIVE: LeArning DAta-dePendenT, concIse molecular VEctors for fast, accurate metabolite identification from tandem mass spectra

  Nguyen, D.H.; Nguyen, C.H.; Mamitsuka, H.

  Bioinformatics, 2019, Peer-reviewed

  
• Integrated Uncertainty in Knowledge Modelling and Decision Making

  Hirosato Seki; Canh Hao Nguyen; Van-Nam Huynh; Masahiro Inuiguchi

  Lecture Notes in Computer Science, 2019, Peer-reviewed

  
• A p-laplacian random walk: Application to video games

  Wicker, N.; Nguyen, C.H.; Mamitsuka, H.

  Austrian Journal of Statistics, 2019, Peer-reviewed

  
• SIMPLE: Sparse Interaction Model over Peaks of moLEcules for fast, interpretable metabolite identification from tandem mass spectra

  Nguyen, D.H.; Nguyen, C.H.; Mamitsuka, H.

  Bioinformatics, Jul. 2018, Peer-reviewed

  
• Recent advances and prospects of computational methods for metabolite identification: A review with emphasis on machine learning approaches

  Nguyen, D.H.; Nguyen, C.H.; Mamitsuka, H.

  Briefings in Bioinformatics, 2019, Peer-reviewed

  
• NMRPro: an integrated web component for interactive processing and visualization of NMR spectra

  Ahmed Mohamed; Canh Hao Nguyen; Hiroshi Mamitsuka

  BIOINFORMATICS, Jul. 2016, Peer-reviewed

  
• New Resistance Distances with Global Information on Large Graphs

  Canh Hao Nguyen; Hiroshi Mamitsuka

  JMLR Workshop and Conference Proceedings. Volume 51: Proceedings of the 19th International Conference on Artificial Intelligence and Statistics, May 2016, Peer-reviewed

  
• Current status and prospects of computational resources for natural product dereplication: a review

  Ahmed Mohamed; Canh Hao Nguyen; Hiroshi Mamitsuka

  BRIEFINGS IN BIOINFORMATICS, Mar. 2016, Peer-reviewed

  
• Some Properties of a Dissimilarity Measure for Labeled Graphs

  Nicolas Wicker; Canh Hao Nguyen; Hiroshi Mamitsuka

  Publications Mathematiques de Besancon, 2016, Peer-reviewed

  
• NetPathMiner: R/Bioconductor package for network path mining through gene expression

  Ahmed Mohamed; Timothy Hancock; Canh Hao Nguyen; Hiroshi Mamitsuka

  BIOINFORMATICS, Nov. 2014, Peer-reviewed

  
• Selecting Graph Cut Solutions via Global Graph Similarity

  Canh Hao Nguyen; Nicolas Wicker; Hiroshi Mamitsuka

  IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS, Jul. 2014, Peer-reviewed

  
• A new dissimilarity measure for comparing labeled graphs

  Nicolas Wicker; Canh Hao Nguyen; Hiroshi Mamitsuka

  LINEAR ALGEBRA AND ITS APPLICATIONS, Mar. 2013, Peer-reviewed

  
• Latent Feature Kernels for Link Prediction on Sparse Graphs

  Canh Hao Nguyen; Hiroshi Mamitsuka

  IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS, Nov. 2012, Peer-reviewed

  
• Discriminative Graph Embedding for Label Propagation

  Canh Hao Nguyen; Hiroshi Mamitsuka

  IEEE TRANSACTIONS ON NEURAL NETWORKS, Sep. 2011, Peer-reviewed

  
• Kernels for Link Prediction with Latent Feature Models

  Canh Hao Nguyen; Hiroshi Mamitsuka

  MACHINE LEARNING AND KNOWLEDGE DISCOVERY IN DATABASES, PT II, 2011, Peer-reviewed

  
• An efficient kernel matrix evaluation measure

  Canh Hao Nguyen; Tu Bao Ho

  PATTERN RECOGNITION, Nov. 2008, Peer-reviewed

  
• Simple but effective methods for combining kernels in computational biology

  Hiroaki Tanabe; Tu Bao Ho; Canh Hao Nguyen; Saori Kawasaki

  RIVF 2008 - 2008 IEEE International Conference on Research, Innovation and Vision for the Future in Computing and Communication Technologies, 2008, Peer-reviewed

  
• Estimating quality of support vector machines learning under probabilistic and interval uncertainty: Algorithms and computational complexity

  Canh Hao Nguyen; Mi Bao Ho; Vladik Kreinovich

  INTERVAL / PROBABILISTIC UNCERTAINTY AND NON-CLASSICAL LOGICS, 2008, Peer-reviewed

  
• Integration of learning methods, medical literature and expert inspection in medical data mining

  Tu Bao Ho; Saori Kawasaki; Katsuhiko Takabayashi; Canh Hao Nguyen

  IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS, Oct. 2007, Peer-reviewed

  
• Exploiting temporal relations in mining hepatitis data

  Tu-Bao Ho; Canh-Hao Nguyen; Saori Kawasaki; Si-Quang Le; Katsuhiko Takabayashi

  NEW GENERATION COMPUTING, 2007, Peer-reviewed

  
• Kernel matrix evaluation

  C.H. Nguyen; T.B. Ho

  IJCAI International Joint Conference on Artificial Intelligence, 2007, Peer-reviewed

  
• Temporal relations extraction in mining hepatitis data

  Tu Bao Ho; Canh Hao Nguyen; Saori Kawasaki; Katsuhiko Takabayashi

  ADVANCES IN KNOWLEDGE DISCOVERY AND DATA MINING, PROCEEDINGS, 2007, Peer-reviewed

  
• An imbalanced data rule learner

  CH Nguyen; TB Ho

  KNOWLEDGE DISCOVERY IN DATABASES: PKDD 2005, 2005, Peer-reviewed

  

External funds: Kakenhi

• Machine Learning on Large Graphs

  Grant-in-Aid for Scientific Research (C)

  Basic Section 61030:Intelligent informatics-related

  Kyoto University

  Canh Hao Nguyen

  From 01 Apr. 2018, To 31 Mar. 2023, Project Closed

  machine learning;Graph analysis;bioinformatics;large graph;graph neural networks;Convex clustering;graph Laplacian;hypergraph;sparsistency;Learning on graphs;distances on graphs;semi-supervised learning;graph embedding

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-18K11434/
• Estimating data structure embedded in semi-structured data

  Grant-in-Aid for Scientific Research (B)

  Kyoto University

  Hiroshi Mamitsuka

  From 01 Apr. 2012, To 31 Mar. 2016, Project Closed

  知識発見とデータマイニング;グラフマイニング;機械学習;生体生命情報学;人工知能;ゲノム;プロテオーム

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-24300054/
• Machine Learning for Structure-Rich Data-Scarce Domains

  Grant-in-Aid for Scientific Research (C)

  Basic Section 61030:Intelligent informatics-related

  Kyoto University

  NGUYEN Canh・Hao

  From 01 Apr. 2022, To 31 Mar. 2025, Granted

  Graph neural networks;Convex Clustering;machine learning;Machine learning;Structured data;Deep learning;Sparse learning

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-22K12150/

Education

Teaching subject(s)

• From 01 Apr. 2025, To 31 Mar. 2026

  Medicinal Frontier Science Research A

  8406, Year-long, Graduate School of Pharmaceutical Sciences, 4
• From 01 Apr. 2025, To 31 Mar. 2026

  Medicinal Frontier Science Research C

  8408, Year-long, Graduate School of Pharmaceutical Sciences, 4
• From 01 Apr. 2025, To 31 Mar. 2026

  Medicinal Frontier Science Research B

  8407, Year-long, Graduate School of Pharmaceutical Sciences, 4
• From 01 Apr. 2025, To 31 Mar. 2026

  Introduction to Bioinformatics for Drug Discovery

  8104, Spring, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2025, To 31 Mar. 2026

  Seminar on Critical Reading of Scientific Papers A

  8404, Year-long, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2025, To 31 Mar. 2026

  Seminar on Critical Reading of Scientific Papers B

  8405, Year-long, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2024, To 31 Mar. 2025

  Medicinal Frontier Science Research C

  8408, Year-long, Graduate School of Pharmaceutical Sciences, 4
• From 01 Apr. 2024, To 31 Mar. 2025

  Seminar on Critical Reading of Scientific Papers A

  8404, Year-long, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2024, To 31 Mar. 2025

  Introduction to Bioinformatics for Drug Discovery

  8104, Spring, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2024, To 31 Mar. 2025

  Introduction to Bioinformatics for Drug Discovery

  1114, Spring, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2024, To 31 Mar. 2025

  Seminar on Critical Reading of Scientific Papers B

  8405, Year-long, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2023, To 31 Mar. 2024

  Research Proposal Writing Practice B

  8403, Year-long, Graduate School of Pharmaceutical Sciences, 1
• From 01 Apr. 2023, To 31 Mar. 2024

  Research Proposal Writing Practice A

  8402, Year-long, Graduate School of Pharmaceutical Sciences, 1
• From 01 Apr. 2023, To 31 Mar. 2024

  Pharmaceutical Laboratory Coaching Practice A

  8301, Year-long, Graduate School of Pharmaceutical Sciences, 1
• From 01 Apr. 2023, To 31 Mar. 2024

  Medicinal Frontier Science Research B

  8407, Year-long, Graduate School of Pharmaceutical Sciences, 4
• From 01 Apr. 2023, To 31 Mar. 2024

  Medicinal Frontier Science Research A

  8406, Year-long, Graduate School of Pharmaceutical Sciences, 4
• From 01 Apr. 2023, To 31 Mar. 2024

  Skill Development for Chemoinformatics

  5002, Year-long, Graduate School of Pharmaceutical Sciences, 4
• From 01 Apr. 2023, To 31 Mar. 2024

  Seminar on Critical Reading of Scientific Papers B

  8405, Year-long, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2023, To 31 Mar. 2024

  Seminar on Critical Reading of Scientific Papers A

  8404, Year-long, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2023, To 31 Mar. 2024

  Introduction to Bioinformatics for Drug Discovery

  8104, Spring, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2023, To 31 Mar. 2024

  Introduction to Bioinformatics for Drug Discovery

  1114, Spring, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2022, To 31 Mar. 2023

  Pharmaceutical Laboratory Coaching Practice A

  8301, Year-long, Graduate School of Pharmaceutical Sciences, 1
• From 01 Apr. 2022, To 31 Mar. 2023

  Skill Development for Chemoinformatics

  5002, Year-long, Graduate School of Pharmaceutical Sciences, 4
• From 01 Apr. 2022, To 31 Mar. 2023

  Seminar on Critical Reading of Scientific Papers A

  8404, Year-long, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2022, To 31 Mar. 2023

  Introduction to Bioinformatics for Drug Discovery

  1114, Spring, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2022, To 31 Mar. 2023

  Research Proposal Writing Practice A

  8402, Year-long, Graduate School of Pharmaceutical Sciences, 1
• From 01 Apr. 2022, To 31 Mar. 2023

  Introduction to Bioinformatics for Drug Discovery

  8104, Spring, Graduate School of Pharmaceutical Sciences, 2
• From 01 Apr. 2022, To 31 Mar. 2023

  Medical Frontier Science Research A

  8406, Year-long, Graduate School of Pharmaceutical Sciences, 4
• From Apr. 2014, To Mar. 2015

  Introduction to Bioinformatics

  Spring, 薬学研究科
• From Apr. 2014, To Mar. 2015

  Skill Development for Chemoinformatics

  Year-long, 薬学研究科
• From Apr. 2015, To Mar. 2016

  Skill Development for Chemoinformatics

  Year-long, 薬学研究科
• From Apr. 2015, To Mar. 2016

  Introduction to Bioinformatics

  Spring, 薬学研究科
• From Apr. 2016, To Mar. 2017

  Skill Development for Chemoinformatics

  Year-long, 薬学研究科
• From Apr. 2016, To Mar. 2017

  Introduction to Bioinformatics

  Spring, 薬学研究科
• From Apr. 2017, To Mar. 2018

  Introduction to Bioinformatics for Drug Discovery

  Spring, 薬学研究科
• From Apr. 2017, To Mar. 2018

  Skill Development for Chemoinformatics

  Year-long, 薬学研究科
• From Apr. 2018, To Mar. 2019

  Introduction to Bioinformatics for Drug Discovery

  Spring, 薬学研究科
• From Apr. 2018, To Mar. 2019

  Skill Development for Chemoinformatics

  Year-long, 薬学研究科
• From Apr. 2019, To Mar. 2020

  Introduction to Bioinformatics for Drug Discovery

  Spring, 薬学研究科
• From Apr. 2019, To Mar. 2020

  Skill Development for Chemoinformatics

  Year-long, 薬学研究科
• From Apr. 2020, To Mar. 2021

  Introduction to Bioinformatics for Drug Discovery

  Spring, 薬学研究科
• From Apr. 2020, To Mar. 2021

  Skill Development for Chemoinformatics

  Year-long, 薬学研究科
• From Apr. 2021, To Mar. 2022

  Introduction to Bioinformatics for Drug Discovery

  Spring, 薬学研究科
• From Apr. 2021, To Mar. 2022

  Skill Development for Chemoinformatics

  Year-long, 薬学研究科

Administration

Faculty management (title, position)

• From 01 Apr. 2015, To 31 Mar. 2016

  化学研究所情報システム技術委員会 委員
• From 01 Apr. 2016, To 31 Mar. 2017

  化学研究所情報システム技術委員会 委員
• From 01 Apr. 2017, To 31 Mar. 2018

  化学研究所情報システム技術委員会 委員
• From 01 Apr. 2018, To 31 Mar. 2019

  化学研究所情報システム技術委員会 委員
• From 01 Apr. 2019, To 31 Mar. 2020

  化学研究所情報システム技術委員会 委員
• From 01 Apr. 2020, To 31 Mar. 2021

  化学研究所情報システム技術委員会委員
• From 01 Apr. 2021, To 31 Mar. 2022

  化学研究所情報システム技術委員会委員