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Faizy Ahsan

Alumni

Publications

PhyloPGM: boosting regulatory function prediction accuracy using evolutionary information
Faizy Ahsan
Zichao Yan
Doina Precup
Mathieu Blanchette
Abstract Motivation The computational prediction of regulatory function associated with a genomic sequence is of utter importance in -omics … (see more)study, which facilitates our understanding of the underlying mechanisms underpinning the vast gene regulatory network. Prominent examples in this area include the binding prediction of transcription factors in DNA regulatory regions, and predicting RNA–protein interaction in the context of post-transcriptional gene expression. However, existing computational methods have suffered from high false-positive rates and have seldom used any evolutionary information, despite the vast amount of available orthologous data across multitudes of extant and ancestral genomes, which readily present an opportunity to improve the accuracy of existing computational methods. Results In this study, we present a novel probabilistic approach called PhyloPGM that leverages previously trained TFBS or RNA–RBP binding predictors by aggregating their predictions from various orthologous regions, in order to boost the overall prediction accuracy on human sequences. Throughout our experiments, PhyloPGM has shown significant improvement over baselines such as the sequence-based RNA–RBP binding predictor RNATracker and the sequence-based TFBS predictor that is known as FactorNet. PhyloPGM is simple in principle, easy to implement and yet, yields impressive results. Availability and implementation The PhyloPGM package is available at https://github.com/BlanchetteLab/PhyloPGM Supplementary information Supplementary data are available at Bioinformatics online.
2022-06-27
Bioinformatics (published)
doi.org
Phylogenetic Manifold Regularization: A semi-supervised approach to predict transcription factor binding sites
Faizy Ahsan
Alexandre Drouin
Franccois Laviolette
Doina Precup
Mathieu Blanchette
The computational prediction of transcription factor binding sites remains a challenging problems in bioinformatics, despite significant met… (see more)hodological developments from the field of machine learning. Such computational models are essential to help interpret the non-coding portion of human genomes, and to learn more about the regulatory mechanisms controlling gene expression. In parallel, massive genome sequencing efforts have produced assembled genomes for hundred of vertebrate species, but this data is underused. We present PhyloReg, a new semi-supervised learning approach that can be used for a wide variety of sequence-to-function prediction problems, and that takes advantage of hundreds of millions of years of evolution to regularize predictors and improve accuracy. We demonstrate that PhyloReg can be used to better train a previously proposed deep learning model of transcription factor binding. Simulation studies further help delineate the benefits of the a pproach. G ains in prediction accuracy are obtained over a broad set of transcription factors and cell types.
2020-12-16
2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (published)
doi.org