mlsanityData to 7 Oct 2026

Explainable AI in Genomics: Transcription Factor Binding Site Prediction with Mixture of Experts

arXiv 2507.09754 ↗First posted 13 Jul 2025cs.LG q-bio.GNcited by 0

On the map: Mixture-of-experts → Medical and biomedical MoE

Abstract (arXiv)

Transcription Factor Binding Site (TFBS) prediction is crucial for understanding gene regulation and various biological processes. This study introduces a novel Mixture of Experts (MoE) approach for TFBS prediction, integrating multiple pre-trained Convolutional Neural Network (CNN) models, each specializing in different TFBS patterns. We evaluate the performance of our MoE model against individual expert models on both in-distribution and out-of-distribution (OOD) datasets, using six randomly selected transcription factors (TFs) for OOD testing. Our results demonstrate that the MoE model achieves competitive or superior performance across diverse TF binding sites, particularly excelling in OOD scenarios. The Analysis of Variance (ANOVA) statistical test confirms the significance of these performance differences. Additionally, we introduce ShiftSmooth, a novel attribution mapping technique that provides more robust model interpretability by considering small shifts in input sequences. Through comprehensive explainability analysis, we show that ShiftSmooth offers superior attribution for motif discovery and localization compared to traditional Vanilla Gradient methods. Our work presents an efficient, generalizable, and interpretable solution for TFBS prediction, potentially enabling new discoveries in genome biology and advancing our understanding of transcriptional regulation.

Key facts. No citing papers in the map yet (data through 7 Oct 2026). Placed in Medical and biomedical MoE, one of 12 directions in Mixture-of-experts. Builds on 21 of its 70 references that are in the map. First posted on arXiv 13 Jul 2025.

Builds on

21 of 70 references.

References · 21

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9 more
  1. 2022From Anecdotal Evidence to Quantitative Evaluation Methods: A Systematic Review on Evaluating Explainable AIcited by 299
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