Deep Learning in Genomics


Date Topic Slides
Thurs, 1/21 Welcome to CSCI 1850: Deep Learning in Genomics Slides
Section I: Predicting from DNA Sequences
Tues, 1/26 The Central Dogma, TF Binding Prediction Slides
Thurs, 1/28 TF Binding Prediciton Using Deep Learning Methods Slides
Tues, 2/2 DeepBind, Evaluation Metrics Slides
Thurs, 2/4 Evaluation Metrics cont., Chromatin Accesibility Prediction Slides
Tues, 2/9 DeepSEA, DanQ Slides
Thurs, 2/11 Basenji, Section I Summary Slides
Section II: Predicting from Other Genomic Signals
Thurs, 2/18 Gene expression: task, biology, previous work Slides
Tues, 2/23 3D conformation capture through HiC, HiCPlus Slides
Thurs, 2/25 HiCNN, GANs, HiCGAN Slides
Section III: Imputation
Tues, 3/2 HiCGAN cont., Imputation of genomic signals Slides
Tues, 3/9 PREDICTD, Avocado, DeepCpG Slides
Thurs, 3/11 Autoencoders, DCA Slides
Section IV: Interpretation of Deep Learning Models
Tues, 3/23 Perturbation, saliency maps Slides
Thurs, 3/25 Class based optimization, Attention-based methods Slides
Tues, 3/30 Other gradient based methods Slides
Thurs, 4/1 Integrated gradients, DeepLIFT Slides
Section V: Other Interesting Applications
Tues, 4/6 Modeling polypharmacy side effects (Decagon) Slides
Thurs, 4/8 Manifold alignments in single cells (MAGAN) Slides