# Challenges in explaining deep learning models for data with biological variation

arXiv: https://arxiv.org/abs/2406.09981 · HTML: https://mlsanity.com/paper/2406.09981/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 21 of its 48 references that are in the map.
- First posted on arXiv 14 Jun 2024.

## Builds on (most cited first, 21 of 21)

- [Batch Normalization: Accelerating Deep Network Training by Reducing Internal Covariate Shift](https://mlsanity.com/paper/1502.03167/) (2015)
- [Grad-CAM: Visual Explanations from Deep Networks via Gradient-based Localization](https://mlsanity.com/paper/1610.02391/) (2016)
- [A Unified Approach to Interpreting Model Predictions](https://mlsanity.com/paper/1705.07874/) (2017)
- ["Why Should I Trust You?": Explaining the Predictions of Any Classifier](https://mlsanity.com/paper/1602.04938/) (2016)
- [Axiomatic Attribution for Deep Networks](https://mlsanity.com/paper/1703.01365/) (2017)
- [Deep Inside Convolutional Networks: Visualising Image Classification Models and Saliency Maps](https://mlsanity.com/paper/1312.6034/) (2013)
- [Visualizing and Understanding Convolutional Networks](https://mlsanity.com/paper/1311.2901/) (2013)
- [Learning Important Features Through Propagating Activation Differences](https://mlsanity.com/paper/1704.02685/) (2017)
- [Interpretability Beyond Feature Attribution: Quantitative Testing with Concept Activation Vectors (TCAV)](https://mlsanity.com/paper/1711.11279/) (2017)
- [Striving for Simplicity: The All Convolutional Net](https://mlsanity.com/paper/1412.6806/) (2014)
- [ChestX-ray8: Hospital-scale Chest X-ray Database and Benchmarks on Weakly-Supervised Classification and Localization of Common Thorax Diseases](https://mlsanity.com/paper/1705.02315/) (2017)
- [Skin Lesion Analysis Toward Melanoma Detection: A Challenge at the 2017 International Symposium on Biomedical Imaging (ISBI), Hosted by the International Skin Imaging Collaboration (ISIC)](https://mlsanity.com/paper/1710.05006/) (2017)
- [Captum: A unified and generic model interpretability library for PyTorch](https://mlsanity.com/paper/2009.07896/) (2020)
- [On the (In)fidelity and Sensitivity for Explanations](https://mlsanity.com/paper/1901.09392/) (2019)
- [Evaluating and Aggregating Feature-based Model Explanations](https://mlsanity.com/paper/2005.00631/) (2020)
- [Quantus: An Explainable AI Toolkit for Responsible Evaluation of Neural Network Explanations and Beyond](https://mlsanity.com/paper/2202.06861/) (2022)
- [Recent advances and clinical applications of deep learning in medical image analysis](https://mlsanity.com/paper/2105.13381/) (2021)
- [Towards Best Practice in Explaining Neural Network Decisions with LRP](https://mlsanity.com/paper/1910.09840/) (2019)
- [Software for Dataset-wide XAI: From Local Explanations to Global Insights with Zennit, CoRelAy, and ViRelAy](https://mlsanity.com/paper/2106.13200/) (2021)
- [IROF: a low resource evaluation metric for explanation methods](https://mlsanity.com/paper/2003.08747/) (2020)
- [Robustness of Visual Explanations to Common Data Augmentation](https://mlsanity.com/paper/2304.08984/) (2023)

## Abstract (arXiv)

Much machine learning research progress is based on developing models and evaluating them on a benchmark dataset (e.g., ImageNet for images). However, applying such benchmark-successful methods to real-world data often does not work as expected. This is particularly the case for biological data where we expect variability at multiple time and spatial scales. In this work, we are using grain data and the goal is to detect diseases and damages. Pink fusarium, skinned grains, and other diseases and damages are key factors in setting the price of grains or excluding dangerous grains from food production. Apart from challenges stemming from differences of the data from the standard toy datasets, we also present challenges that need to be overcome when explaining deep learning models. For example, explainability methods have many hyperparameters that can give different results, and the ones published in the papers do not work on dissimilar images. Other challenges are more general: problems with visualization of the explanations and their comparison since the magnitudes of their values differ from method to method. An open fundamental question also is: How to evaluate explanations? It is a non-trivial task because the "ground truth" is usually missing or ill-defined. Also, human annotators may create what they think is an explanation of the task at hand, yet the machine learning model might solve it in a different and perhaps counter-intuitive way. We discuss several of these challenges and evaluate various post-hoc explainability methods on grain data. We focus on robustness, quality of explanations, and similarity to particular "ground truth" annotations made by experts. The goal is to find the methods that overall perform well and could be used in this challenging task. We hope the proposed pipeline will be used as a framework for evaluating explainability methods in specific use cases.