# CAR-MIL: Counterfactual Attention Regularization for Multiple Instance Learning

arXiv: https://arxiv.org/abs/2609.08419 · HTML: https://mlsanity.com/paper/2609.08419/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 27 of its 40 references that are in the map.
- First posted on arXiv 8 Sep 2026.

## Builds on (most cited first, 27 of 27)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [Learning Important Features Through Propagating Activation Differences](https://mlsanity.com/paper/1704.02685/) (2017)
- [Sanity Checks for Saliency Maps](https://mlsanity.com/paper/1810.03292/) (2018)
- [Attention-based Deep Multiple Instance Learning](https://mlsanity.com/paper/1802.04712/) (2018)
- [Counterfactual Explanations without Opening the Black Box: Automated Decisions and the GDPR](https://mlsanity.com/paper/1711.00399/) (2017)
- [Data Efficient and Weakly Supervised Computational Pathology on Whole Slide Images](https://mlsanity.com/paper/2004.09666/) (2020)
- [Towards Faithfully Interpretable NLP Systems: How should we define and evaluate faithfulness?](https://mlsanity.com/paper/2004.03685/) (2020)
- [Dual-stream Multiple Instance Learning Network for Whole Slide Image Classification with Self-supervised Contrastive Learning](https://mlsanity.com/paper/2011.08939/) (2020)
- [Nystr"omformer: A Nystr"om-Based Algorithm for Approximating Self-Attention](https://mlsanity.com/paper/2102.03902/) (2021)
- [The (Un)reliability of saliency methods](https://mlsanity.com/paper/1711.00867/) (2017)
- [DTFD-MIL: Double-Tier Feature Distillation Multiple Instance Learning for Histopathology Whole Slide Image Classification](https://mlsanity.com/paper/2203.12081/) (2022)
- [BRACS: A Dataset for BReAst Carcinoma Subtyping in H&E Histology Images](https://mlsanity.com/paper/2111.04740/) (2021)
- [Counterfactual Attention Learning for Fine-Grained Visual Categorization and Re-identification](https://mlsanity.com/paper/2108.08728/) (2021)
- [On the Tractability of SHAP Explanations](https://mlsanity.com/paper/2009.08634/) (2020)
- [Deep Learning-based Computational Pathology Predicts Origins for Cancers of Unknown Primary](https://mlsanity.com/paper/2006.13932/) (2020)
- [General Pitfalls of Model-Agnostic Interpretation Methods for Machine Learning Models](https://mlsanity.com/paper/2007.04131/) (2020)
- [Feature Re-Embedding: Towards Foundation Model-Level Performance in Computational Pathology](https://mlsanity.com/paper/2402.17228/) (2024)
- [Attention-Challenging Multiple Instance Learning for Whole Slide Image Classification](https://mlsanity.com/paper/2311.07125/) (2023)
- [Multiple Instance Learning Framework with Masked Hard Instance Mining for Whole Slide Image Classification](https://mlsanity.com/paper/2307.15254/) (2023)
- [iNNvestigate neural networks!](https://mlsanity.com/paper/1808.04260/) (2018)
- [Additive MIL: Intrinsically Interpretable Multiple Instance Learning for Pathology](https://mlsanity.com/paper/2206.01794/) (2022)
- [Bi-directional Weakly Supervised Knowledge Distillation for Whole Slide Image Classification](https://mlsanity.com/paper/2210.03664/) (2022)
- [Inherently Interpretable Time Series Classification via Multiple Instance Learning](https://mlsanity.com/paper/2311.10049/) (2023)
- [xMIL: Insightful Explanations for Multiple Instance Learning in Histopathology](https://mlsanity.com/paper/2406.04280/) (2024)
- [Model Agnostic Interpretability for Multiple Instance Learning](https://mlsanity.com/paper/2201.11701/) (2022)
- [Improving Interpretability for Computer-aided Diagnosis tools on Whole Slide Imaging with Multiple Instance Learning and Gradient-based Explanations](https://mlsanity.com/paper/2009.14001/) (2020)

## Abstract (arXiv)

Multiple Instance Learning (MIL) is widely used for weakly supervised learning, particularly in digital pathology, where fine-grained annotations are costly. Most MIL methods aggregate instance features via attention mechanisms. However, attention weights do not always faithfully reflect instance importance and may focus on spuriously correlated regions. In this work, we propose CAR-MIL, a framework that explicitly guides attention learning through a counterfactual attention regularization objective inspired by counterfactual explanations. Built on a standard attention-based MIL architecture, our approach introduces a lightweight counterfactual attention branch trained to produce an alternative prediction while remaining close to the factual attention distribution. This encourages prediction changes to arise from minimal, structured redistributions of attention, leading to more informative evidence allocation. The resulting factual and counterfactual attention maps capture complementary evidence: the former highlights regions supporting the prediction, while the latter reveals regions whose reweighting would challenge it. We evaluate our method on synthetic MIL benchmarks with instance-level ground truth enabling controlled analysis of attention behavior and on five digital pathology datasets across four tasks. CAR-MIL maintains competitive classification performance, with the largest gains observed on more challenging tasks, while improving attention reliability, demonstrating the benefits of integrating counterfactual explainability reasoning into attention learning. Code is available at: https://github.com/ImaneCR/CAR-MIL/.