Preprint
Evaluation and optimization of sequence-based gene regulatory deep learning models
bioRxiv, 2023.
Research-oriented Books
Hierarchical Feature Selection for Knowledge Discovery: Application of Data Mining to the Biology of Ageing
Springer, 2019. ISBN: 978-3-319-97918-2. Publisher's webpage
Journals
Improving cell-type identification with Gaussian noise-augmented single-cell RNA-seq contrastive learning
Briefings in Functional Genomics, elad059, 2024.
DOI: 10.1093/bfgp/elad059. PubMed
(SJR quartile 1).
Protein function prediction is improved by creating synthetic feature samples with generative adversarial networks
Nature Machine Intelligence, 2:540-550, 2020.
DOI: 10.1038/s42256-020-0222-1. Reprint
(SJR quartile 1 – the 2nd top-ranked artificial intelligence journal).
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
Genome Biology, 20(1):244, 2019.
DOI:10.1186/s13059-019-1835-8. PubMed
(SJR quartile 1 – the 5th top-ranked genetics journal).
Using Deep Maxout Neural Networks to Improve the Accuracy of Function Prediction from Protein Interaction Networks
PLOS One, 14(7): e0209958, 2019.
DOI:10.1371/journal.pone.0209958. PubMed
(SJR quartile 1).
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, 2018.
DOI:10.1007/s10462-017-9541-y. Preprint (original research article, source code available onGitHub)
(SJR quartile 1).
Predicting Human Protein Function with Multi-task Deep Neural Networks
PLOS One, 13(6): e0198216, 2018.
DOI:10.1371/journal.pone.0198216. PubMed
(SJR quartile 1).
Analysis of temporal transcription expression profiles reveal links between protein function and developmental stages of Drosophila melanogaster
PLOS Computational Biology, 13(10): e1005791, 2017.
DOI:10.1371/journal.pcbi.1005791. PubMed (novel fly protein function predictions)
(SJR quartile 1 – the 8th top-ranked computational theory and mathematics journal).
Systematic analysis of the gerontome reveals links between aging and age-related diseases
Human Molecular Genetics, 25(21), 4804-4818, 2016.
DOI:10.1093/hmg/ddw307. PubMed
(SJR quartile 1 – the 8th top-ranked Genetics (clinical) journal).
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, 12(2):262-275, 2015.
DOI:10.1109/TCBB.2014.2355218. PubMed (Datasets Used in the Experiments)
(SJR quartile 2).
Conferences/Workshops (focusing on machine learning algorithmic novelty)
Predicting the effect of genes on longevity with novel hierarchical dependency-constrained tree augmented naive Bayes classifiers
In: Proceedings of the 2023 IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2023), Istanbul, Turkey, 2023.
Positive Feature Values Prioritized Hierarchical Dependency Constrained Averaged One-dependence Estimators for Gene Ontology Feature Spaces
In: Proceedings of the 2022 IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2022), Las Vegas, USA, pages: 826-829, 2022.
DOI:10.1109/BIBM55620.2022.9995482
Positive Feature Values Prioritized Hierarchical Redundancy Eliminated Tree Augmented Naive Bayes Classifier for Hierarchical Feature Spaces
In: Proceedings of the 2022 IEEE International Conference on Systems, Man, and Cybernetics (IEEE SMC 2022), Prague, Czech Republic, pages: 106-110, 2022.
DOI:10.1109/SMC53654.2022.9945578. Preprint
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), online (Aalborg, Denmark), PMLR, 138:557-568, 2020. Reprint
A New Hierarchical Redundancy Eliminated Tree Augmented Naive Bayes Classifier for Coping with Gene Ontology-based Features
In: Proceedings of the 33rd International Conference on Machine Learning (ICML 2016) Workshop on Computational Biology, New York, USA.
(paper, poster, selected for spotlight talk). Reprint
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, pages: 27-36, 2015.
DOI:10.1145/2808719.2808722. Reprint
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), Shanghai, China, pages: 373-380, 2013.
DOI:10.1109/BIBM.2013.6732521. PubMed
Newsletter & Others
Novel Hierarchical Feature Selection Algorithms for Predicting Genes' Aging-related Function
AI Matters, 2(3):23-24, 2016.
DOI:10.1145/2911172.2911180. Reprint
The application of a perceptron model to classify an individual's response to a proposed loading dose regimen of Warfarin
arXiv:1211.2945, 2012. Reprint
PhD Thesis
Novel Hierarchical Feature Selection Methods for Classification and Their Application to Datasets of Ageing-Related Genes
Doctor of Philosophy (PhD) thesis, University of Kent, 2015. Reprint