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Updated: May 30, 2025

Analyzing and Building Nucleic Acid Structures with 3DNA
Published on: April 26, 2013
Recipes and ingredients for deep learning models of 3D genome folding
Paulina N Smaruj1, Yao Xiao1, Geoffrey Fudenberg1
1Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
Abstract:
Three-dimensional genome folding plays roles in gene regulation and disease. In this review, we compare and contrast recent deep learning models for predicting genome contact maps. We survey preprocessing, architecture, training, evaluation, and interpretation methods, highlighting the capabilities and limitations of different models. In each area, we highlight challenges, opportunities, and potential future directions for genome-folding models.
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