C. Wan (2019) Hierarchical Feature Selection for Knowledge Discovery: Application of Data Mining to the Biology of Ageing. Springer. FlyerÂ
Journal Articles
C. Wan, D.T. Jones (2020) Protein function prediction is improved by creating synthetic feature samples with generative adversarial networks, Nature Machine Intelligence, DOI: 10.1038/s42256-020-0222-1. Reprint.
N. Zhou, Y. Jiang, ..., C. Wan, ..., I. Friedberg (2019) The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens, Genome Biology, 20(244), DOI:10.1186/s13059-019-1835-8. PubMed
C. Wan, D. Cozzetto, R. Fa, D.T. Jones (2019) Using Deep Maxout Neural Networks to Improve the Accuracy of Function Prediction from Protein Interaction Networks, PLOS One, 14(7): e0209958, DOI:10.1371/journal.pone.0209958. PubMed
C. Wan, A.A. Freitas (2018) An Empirical Evaluation of Hierarchical Feature Selection Methods for Classification in Bioinformatics Datasets with Gene Ontology-based Features, Artificial Intelligence Review, 50(2), 201-240, DOI:10.1007/s10462-017-9541-y. pdf (original research article, source code available on GitHub)
R. Fa, D. Cozzetto, C. Wan, D.T. Jones (2018) Predicting Human Protein Function with Multi-task Deep Neural Networks, PLOS One, 13(6): e0198216, DOI:10.1371/journal.pone.0198216. PubMed
C. Wan, J.G. Lees, F. Minneci, C.A. Orengo, D.T. Jones (2017) Analysis of temporal transcription expression profiles reveal links between protein function and developmental stages of Drosophila melanogaster, PLOS Computational Biology, 13(10): e1005791, DOI:10.1371/journal.pcbi.1005791. PubMed (novel fly protein function predictions)
M. Fernandes, C. Wan, R. Tacutu, D. Barardo, A. Rajput, J. Wang, H. Thoppil, C. Yang, A.A. Freitas, J.P. de Magalhães (2016) Systematic analysis of the gerontome reveals links between aging and age-related diseases, Human Molecular Genetics, 25(21), 4804-4818, DOI:10.1093/hmg/ddw307. PubMed
C. Wan, A.A. Freitas, J.P. de Magalhaes (2015) Predicting the pro-longevity or anti-longevity effect of model organism genes with new hierarchical feature selection methods. IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 12, no. 2, pp. 262-275, DOI:10.1109/TCBB.2014.2355218. PubMed (Datasets Used in the Experiments)
Conference/Workshop Proceedings
(peer-reviewed regular research articles focusing on machine learning algorithmic novelty)
C. Wan, A.A. Freitas (2020) Hierarchical Dependency Constrained Averaged One-Dependence Estimators Classifiers for Hierarchical Feature Spaces, In: Proceedings of the 10th International Conference on Probabilistic Graphical Models (PGM 2020), PMLR, online. pdf
C. Wan, A.A. Freitas (2016) A New Hierarchical Redundancy Eliminated Tree Augmented Naive Bayes Classifier for Coping with Gene Ontology-based Features, the 33rd International Conference on Machine Learning (ICML 2016) Workshop on Computational Biology, New York, USA. (paper, poster, selected for spotlight talk). pdf
C. Wan, A.A. Freitas (2015) Two Methods for Constructing a Gene Ontology-based Feature Selection Network for a Bayesian Network Classifier and Applications to Datasets of Aging-related Genes. In: Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB 2015), Atlanta, USA, DOI:10.1145/2808719.2808722. (Acceptance rate: 34.0%, 48/141). pdf
C. Wan, A.A. Freitas (2013) Prediction of the pro-longevity or anti-longevity effect of Caenorhabditis Elegans genes based on Bayesian classification methods. In: Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine (IEEE-BIBM 2013), pp. 373-380. Shanghai, China, DOI:10.1109/BIBM.2013.6732521. (Acceptance rate: 19.6%, 60/306). pdf
Newsletter & Preprint
C. Wan (2016) Novel Hierarchical Feature Selection Algorithms for Predicting Genes’ Aging-related Function,  AI Matters, vol. 2, no. 3, pp. 23-24, Spring 2016, DOI:10.1145/2911172.2911180. pdf
C. Wan, I.V. Biktasheva, S. Lane (2012) The application of a perceptron model to classify an individual's response to a proposed loading dose regimen of Warfarin. arXiv:1211.2945. pdf
