Eva Prakash

Towards More Realistic Simulated Datasets for Benchmarking Deep Learning Models in Regulatory Genomics

This paper benchmarks deep learning interpretation methods on more realistic simulated regulatory genomic data, finding that some methods perform poorly on complex datasets.

Gkmexplain: Fast and Accurate Interpretation of Nonlinear Gapped k-mer Support Vector Machines Using Integrated Gradients

gkmexplain provides a fast and accurate method to interpret gkm-SVM models of regulatory DNA sequences, outperforming existing methods in identifying predictive patterns and mutation impact scores.