MLCB 2020 Proceedings

The 15th Machine Learning in Computational Biology (MLCB) meeting was held virtually. For more information and recordings of the talks please see here

• Surag Nair, Avanti Shrikumar, Anshul Kundaje. fastISM: Performant in-silico saturation mutagenesis for convolutional neural networks. [pdf] [supplement]
• Maja Trebacz, Zohreh Shams, Mateja Jamnik, Paul Scherer, Nikola Simidjievski, Helena Andres Terre, Pietro Liò. Using ontology embeddings for structural inductive bias in gene expression data analysis. [pdf]
• Dimitrios Vitsios, Ryan S. Dhindsa, Ayal B. Gussow, Slavé Petrovski. Prioritization of non-coding variants based on human intolerance to variation and primary sequence context using deep learning. [pdf]
• Hannah Zhou, Avanti Shrikumar, Anshul Kundaje. Benchmarking Reverse-Complement Strategies for Deep Learning Models in Genomics. [pdf]
• Paul Scherer, Maja Trebacz, Nikola Simidjievski, Zohreh Shams, Helena Andres Terre, Pietro Liò, Mateja Jamnik. Incorporating network based protein complex discovery into automated model construction. [pdf]
• Jacob Schreiber, Yang Young Lu, William Stafford Noble . Ledidi: Designing genomic edits that induce functional activity. [pdf]
• Rui Yang, Alizera Karbalayghareh, Christina Leslie. HiC2Self: Self-supervised Hi-C contact map denoising. [pdf]
• Nicholas Nuechterlein, Beibin Li, Mehmet Saygin Seyfioglu, Sachin Mehta, Patrick J Cimino, Linda Shapiro. Leveraging Unlabeled Data for Glioma Molecular Subtype and Survival Prediction. [pdf] [supplement]
• Lotfi Slim, Clement Chatelain, Chloe-Agathe Azencott. Nonlinear post-selection inference for genome-wide association studies. [pdf]
• Joao Belo Pereira, Diogo Bastos, Erik Stroes, Evgeni Levin. Covered Information Disentanglement: Correcting Permutation Feature Importance in the Presence of Covariates. [pdf] [supplement]
• Hussein Mohsen, Jonathan Warrell, Martin Renqiang Min, Sahand Negahban, Mark Gerstein. Weight-based Neural Network Interpretability using Activation Tuning and Personalized Products. [pdf]
• Mukund Sudarshan, Susan E. Liao, Oded Regev. Novel Insights into RNA Splicing from Interpretable Machine Learning. [pdf]
• Nancy-Sarah Yacovzada, Iris Kalka, Eran Segal, Eran Hornstein. A Method for Pedigree-based Propagated Risk Phenotyping on Clalit Data. [pdf]
• Faezeh Bayat, Maxwell Libbrecht. VSS: Variance-stabilized signals for sequencing-based genomic signals. [pdf]
• Morteza M. Saber, Maxwell Libbrecht, Leonid Chindelevitch, Jesse Shapiro. Do machine learning predictors of microbial phenotype from genotype identify causal variants?. [pdf]
• Ahmad Pesaranghader, Justin Pelletier, Jean-Christophe Grenier, Raphaël Poujol, Julie Hussin. ImputeCoVNet: 2D ResNet Autoencoder for Imputation of SARS-CoV-2 Sequences. [pdf]
• Johannes Linder, Alyssa La Fleur, Sreeram Kannan, Zibo Chen, Ajasja Ljubetic, David Baker, Georg Seelig. Efficient inference of nonlinear feature attributions with Scrambling Neural Networks. [pdf]
• Yun Feng, Christopher Yau. RLevolution: Unravelling the history of genomic instability through deep reinforcement learning. [pdf]
• Sergei Rybakov, Mohammad Lotfollahi, Fabian J. Theis, F. Alexander Wolf. Learning interpretable latent autoencoder representations with annotations of feature sets. [pdf]
• Andrew J. Jung, Leo J. Lee, Alice J. Gao, Brendan J. Frey. Machine Learning Approaches for RNA Editing Prediction. [pdf]
• Amy X. Lu, Alex X. Lu, Alan Moses. Evolution Is All You Need: Phylogenetic Augmentation for Contrastive Learning. [pdf]
• Amy X. Lu, Haoran Zhang, Marzyeh Ghassemi, Alan Moses . Self-Supervised Contrastive Learning of Protein Representations By Mutual Information Maximization. [pdf]
• Alireza Karbalaygharch, Christina Leslie. Modeling Gene Regulation by Integrating 1D and 3D Epigenomic Data with Graph Attention Networks. [pdf]
• Dinesh Singh, Héctor Climente-González, Mathis Petrovich, Eiryo Kawakami, Makoto Yamada. FsNet: Feature Selection Network on High-dimensional Biological Data. [pdf]
• Zijun Zhang, Evan M. Cofer, Olga G. Troyanskaya. AMBIENT: Accelerated Convolutional Neural Network Architecture Search for Regulatory Genomics. [pdf]
• Mohit Goyal, Guillermo Serrano, Ilan Shomorony, Mikel Hernaez, Idoia Ocha. JIND: Joint Integration and Neural Discrimination for automated single-cell annotation. [pdf] [supplement]
• Amr M. Alexandari, Connor Horton, Avanti Shrikumar, Polly Fordyce, Anshul Kundaje. Neural networks can extract thermodynamic DNA sequence affinities from in vivo binding profiles of transcription factor binding. [pdf]
• Aishwarya Mandyam, Yuhao Wan, Luis Ceze, Jeff Nivala, Kevin Jamieson. Molecular Matchmaker: selecting binding peptide-aptamer pairs using machine learning. [pdf] [supplement]
• Amir Shanehsazzadeh, David Belanger, David Dohan. Fixed-Length Protein Embeddings using Contextual Lenses. [pdf]
• Einar Gabbasov, Miguel Moreno-Molina, I ̃naki Comas, Maxwell Libbrecht, Leonid Chin-delevitch. SplitStrains, a tool to identify and separate mixed Mycobacterium tuberculosis infections from WGS data. [pdf]
• Neda Shokranch, Maxwell W Libbrecht. Graph embedding for inferring genome domains from genome 3D structure. [pdf]
• Sanjit Singh Batra, Jeffrey Spence, Yun S. Song. Learning putatively causal gene regulatory programs using permutation-equivariant neural networks. [pdf]
• Pinar Demetci, Rebecca Santorella, Bjorn Sandstede, William Stafford Noble,Ritambhara Singh. Gromov–Wasserstein based optimal transport to align single-cell multi-omics data. [pdf]
• Antonio Moretti, Liyi Zhang, Itsik Pe’er. Variational Combinatorial Sequential Monte Carlo For Bayesian Phylogenetic Inference. [pdf]
• Andres F. Duque, Guy Wolf, Kevin R. Moon. Visualizing High Dimensional and High Frequency Electrical Biosignals. [pdf]
• Anushri Arora, Tetsuhiro Harimoto, Tal Danino, Itsik Pe’er. Spatial Microbial Dynamics. [pdf] [supplement]
• Manu Saraswat, Gherman Novakovsky. Etienne Meunier, Oriol Fomes, Sara Mostafavi, Wyeth W Wasserman. Convolutional Additive Models: a fully interpretable approach to Deep Learning in Genomics. [pdf]
• Omer Ronen, Or Zuk. Deep Homology-Based Protein Contact-Map Prediction. [pdf]
• Habib Daneshpajouh, Bowen Chen, Neda Shokranch, Shohre Masoumi, Kay C Wiese, Maxwell W Libbrecht. Continuous chromatin state feature annotation of the human epigenome. [pdf]