ArticleGenome biology2020
Enhanced Integrated Gradients: improving interpretability of deep learning models using splicing codes as a case study.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 87 citations in OpenAlex.
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- Comprehensive review and assessment of multi-species splicing variant prediction: task-specific deep learning models and genomic foundation models.Briefings in bioinformatics · 2026Review
- A comprehensive evaluation of self-attention for detecting regulatory feature interactions.NAR genomics and bioinformatics · 2026Article
- Explainable deep learning framework incorporating medical knowledge for insulin titration in diabetes.Communications medicine · 2026Article
- Bioinspired Deep Neural Networks for Predicting Income-Reporting Discontinuities in the Chilean Student Loan Program.Biomimetics (Basel, Switzerland) · 2026Article
- STRIVE: interpretable multimodal subtype discovery in Women's cancers using an attention-weighted joint variational autoencoder.Frontiers in bioinformatics · 2026Article
- ACmix-Swin Deep Learning of 4-Day-OldGenes · 2025Article
- G4mer: An RNA language model for transcriptome-wide identification of G-quadruplexes and disease variants from population-scale genetic data.Nature communications · 2025Article
- HNF1A and A1CF coordinate a beta cell transcription-splicing axis that is disrupted in type 2 diabetes.Cell metabolism · 2025Article
- Adversarial attack of sequence-free enhancer prediction identifies chromatin architecture.Bioinformatics (Oxford, England) · 2025Article
- Challenges in AI-driven Biomedical Multimodal Data Fusion and Analysis.Genomics, proteomics & bioinformatics · 2025Review
- From computational models of the splicing code to regulatory mechanisms and therapeutic implications.Nature reviews. Genetics · 2025Review
- Non-Invasive Diagnosis of Moyamoya Disease Using Serum Metabolic Fingerprints and Machine Learning.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Perspective on recent developments and challenges in regulatory and systems genomics.Bioinformatics advances · 2025Review
- Gauge fixing for sequence-function relationships.PLoS computational biology · 2025Article
- Interpreting cis-regulatory interactions from large-scale deep neural networks.Nature genetics · 2024Article
- Gauge fixing for sequence-function relationships.bioRxiv : the preprint server for biology · 2024Article
- CIRI-Deep Enables Single-Cell and Spatial Transcriptomic Analysis of Circular RNAs with Deep Learning.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- InterpretingbioRxiv : the preprint server for biology · 2024Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Despite the success and fast adaptation of deep learning models in biomedical domains, their lack of interpretability remains an issue. Here, we introduce Enhanced Integrated Gradients (EIG), a method to identify significant features associated with a specific prediction task. Using RNA splicing prediction as well as digit classification as case studies, we demonstrate that EIG improves upon the original Integrated Gradients method and produces sets of informative features. We then apply EIG to identify A1CF as a key regulator of liver-specific alternative splicing, supporting this finding with subsequent analysis of relevant A1CF functional (RNA-seq) and binding data (PAR-CLIP).
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.