# Prototype-Based Multiple Instance Learning for Gigapixel Whole Slide Image Classification

arXiv: https://arxiv.org/abs/2503.08384 · HTML: https://mlsanity.com/paper/2503.08384/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 16 of its 23 references that are in the map.
- First posted on arXiv 11 Mar 2025.

## Builds on (most cited first, 16 of 16)

- [Shortcut Learning in Deep Neural Networks](https://mlsanity.com/paper/2004.07780/) (2020)
- [Sparse Autoencoders Find Highly Interpretable Features in Language Models](https://mlsanity.com/paper/2309.08600/) (2023)
- [Attention-based Deep Multiple Instance Learning](https://mlsanity.com/paper/1802.04712/) (2018)
- [Concept Bottleneck Models](https://mlsanity.com/paper/2007.04612/) (2020)
- [Data Efficient and Weakly Supervised Computational Pathology on Whole Slide Images](https://mlsanity.com/paper/2004.09666/) (2020)
- [Discover-then-Name: Task-Agnostic Concept Bottlenecks via Automated Concept Discovery](https://mlsanity.com/paper/2407.14499/) (2024)
- [A Closer Look at the Intervention Procedure of Concept Bottleneck Models](https://mlsanity.com/paper/2302.14260/) (2023)
- [Post hoc Explanations may be Ineffective for Detecting Unknown Spurious Correlation](https://mlsanity.com/paper/2212.04629/) (2022)
- [Additive MIL: Intrinsically Interpretable Multiple Instance Learning for Pathology](https://mlsanity.com/paper/2206.01794/) (2022)
- [Learning to Intervene on Concept Bottlenecks](https://mlsanity.com/paper/2308.13453/) (2023)
- [SI-MIL: Taming Deep MIL for Self-Interpretability in Gigapixel Histopathology](https://mlsanity.com/paper/2312.15010/) (2023)
- [Right for the Wrong Reason: Can Interpretable ML Techniques Detect Spurious Correlations?](https://mlsanity.com/paper/2307.12344/) (2023)
- [Learning biologically relevant features in a pathology foundation model using sparse autoencoders](https://mlsanity.com/paper/2407.10785/) (2024)
- [Label-free Concept Based Multiple Instance Learning for Gigapixel Histopathology](https://mlsanity.com/paper/2501.02922/) (2025)
- [Mixing Histopathology Prototypes into Robust Slide-Level Representations for Cancer Subtyping](https://mlsanity.com/paper/2310.12769/) (2023)
- [Attri-Net: A Globally and Locally Inherently Interpretable Model for Multi-Label Classification Using Class-Specific Counterfactuals](https://mlsanity.com/paper/2406.05477/) (2024)

## Built on by (most cited first, 2 of 2)

- [CAPRMIL: Context-Aware Patch Representations for Multiple Instance Learning](https://mlsanity.com/paper/2512.14540/) (2025)
- [EXPOSE: Explainable and Domain-Robust Embeddings from Pathology Vision Foundation Models using Sparse Autoencoders](https://mlsanity.com/paper/2608.28191/) (2026)

## Abstract (arXiv)

Multiple Instance Learning (MIL) methods have succeeded remarkably in histopathology whole slide image (WSI) analysis. However, most MIL models only offer attention-based explanations that do not faithfully capture the model's decision mechanism and do not allow human-model interaction. To address these limitations, we introduce ProtoMIL, an inherently interpretable MIL model for WSI analysis that offers user-friendly explanations and supports human intervention. Our approach employs a sparse autoencoder to discover human-interpretable concepts from the image feature space, which are then used to train ProtoMIL. The model represents predictions as linear combinations of concepts, making the decision process transparent. Furthermore, ProtoMIL allows users to perform model interventions by altering the input concepts. Experiments on two widely used pathology datasets demonstrate that ProtoMIL achieves a classification performance comparable to state-of-the-art MIL models while offering intuitively understandable explanations. Moreover, we demonstrate that our method can eliminate reliance on diagnostically irrelevant information via human intervention, guiding the model toward being right for the right reason. Code will be publicly available at https://github.com/ss-sun/ProtoMIL.