# Explainable AI Methods for Multi-Omics Analysis: A Survey

arXiv: https://arxiv.org/abs/2410.11910 · HTML: https://mlsanity.com/paper/2410.11910/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 11 of its 60 references that are in the map.
- First posted on arXiv 15 Oct 2024.

## Builds on (most cited first, 11 of 11)

- [Axiomatic Attribution for Deep Networks](https://mlsanity.com/paper/1703.01365/) (2017)
- [Learning Deep Features for Discriminative Localization](https://mlsanity.com/paper/1512.04150/) (2015)
- [Deep Inside Convolutional Networks: Visualising Image Classification Models and Saliency Maps](https://mlsanity.com/paper/1312.6034/) (2013)
- [Explainable Artificial Intelligence (XAI): Concepts, Taxonomies, Opportunities and Challenges toward Responsible AI](https://mlsanity.com/paper/1910.10045/) (2019)
- [Learning Important Features Through Propagating Activation Differences](https://mlsanity.com/paper/1704.02685/) (2017)
- [A Survey on Explainable Artificial Intelligence (XAI): Towards Medical XAI](https://mlsanity.com/paper/1907.07374/) (2019)
- [Visualizing the Effects of Predictor Variables in Black Box Supervised Learning Models](https://mlsanity.com/paper/1612.08468/) (2016)
- [Unbox the Black-box for the Medical Explainable AI via Multi-modal and Multi-centre Data Fusion: A Mini-Review, Two Showcases and Beyond](https://mlsanity.com/paper/2102.01998/) (2021)
- [Why model why? Assessing the strengths and limitations of LIME](https://mlsanity.com/paper/2012.00093/) (2020)
- [Explaining Explainability: Recommendations for Effective Use of Concept Activation Vectors](https://mlsanity.com/paper/2404.03713/) (2024)
- [Explainable Artificial Intelligence: Precepts, Methods, and Opportunities for Research in Construction](https://mlsanity.com/paper/2211.06579/) (2022)

## Abstract (arXiv)

Advancements in high-throughput technologies have led to a shift from traditional hypothesis-driven methodologies to data-driven approaches. Multi-omics refers to the integrative analysis of data derived from multiple 'omes', such as genomics, proteomics, transcriptomics, metabolomics, and microbiomics. This approach enables a comprehensive understanding of biological systems by capturing different layers of biological information. Deep learning methods are increasingly utilized to integrate multi-omics data, offering insights into molecular interactions and enhancing research into complex diseases. However, these models, with their numerous interconnected layers and nonlinear relationships, often function as black boxes, lacking transparency in decision-making processes. To overcome this challenge, explainable artificial intelligence (xAI) methods are crucial for creating transparent models that allow clinicians to interpret and work with complex data more effectively. This review explores how xAI can improve the interpretability of deep learning models in multi-omics research, highlighting its potential to provide clinicians with clear insights, thereby facilitating the effective application of such models in clinical settings.