# Rethinking Multiple Instance Learning for Whole Slide Image Classification: A Good Instance Classifier is All You Need

arXiv: https://arxiv.org/abs/2307.02249 · HTML: https://mlsanity.com/paper/2307.02249/

## Key facts

- Cited by 22 papers in the map (data through 14 Oct 2026).
- Builds on 32 of its 58 references that are in the map.
- First posted on arXiv 5 Jul 2023.

## Builds on (most cited first, 30 of 32)

- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Momentum Contrast for Unsupervised Visual Representation Learning](https://mlsanity.com/paper/1911.05722/) (2019)
- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [Attention-based Deep Multiple Instance Learning](https://mlsanity.com/paper/1802.04712/) (2018)
- [Data Efficient and Weakly Supervised Computational Pathology on Whole Slide Images](https://mlsanity.com/paper/2004.09666/) (2020)
- [TransMIL: Transformer based Correlated Multiple Instance Learning for Whole Slide Image Classification](https://mlsanity.com/paper/2106.00908/) (2021)
- [Dual-stream Multiple Instance Learning Network for Whole Slide Image Classification with Self-supervised Contrastive Learning](https://mlsanity.com/paper/2011.08939/) (2020)
- [Scaling Vision Transformers to Gigapixel Images via Hierarchical Self-Supervised Learning](https://mlsanity.com/paper/2206.02647/) (2022)
- [DTFD-MIL: Double-Tier Feature Distillation Multiple Instance Learning for Histopathology Whole Slide Image Classification](https://mlsanity.com/paper/2203.12081/) (2022)
- [Not-so-supervised: a survey of semi-supervised, multi-instance, and transfer learning in medical image analysis](https://mlsanity.com/paper/1804.06353/) (2018)
- [Whole Slide Images based Cancer Survival Prediction using Attention Guided Deep Multiple Instance Learning Networks](https://mlsanity.com/paper/2009.11169/) (2020)
- [Pathomic Fusion: An Integrated Framework for Fusing Histopathology and Genomic Features for Cancer Diagnosis and Prognosis](https://mlsanity.com/paper/1912.08937/) (2019)
- [Deep neural network models for computational histopathology: A survey](https://mlsanity.com/paper/1912.12378/) (2019)
- [Revisiting Multiple Instance Neural Networks](https://mlsanity.com/paper/1610.02501/) (2016)
- [Deep Learning-based Computational Pathology Predicts Origins for Cancers of Unknown Primary](https://mlsanity.com/paper/2006.13932/) (2020)
- [A graph-transformer for whole slide image classification](https://mlsanity.com/paper/2205.09671/) (2022)
- [Multi-scale Domain-adversarial Multiple-instance CNN for Cancer Subtype Classification with Unannotated Histopathological Images](https://mlsanity.com/paper/2001.01599/) (2020)
- [Deep Adversarial Training for Multi-Organ Nuclei Segmentation in Histopathology Images](https://mlsanity.com/paper/1810.00236/) (2018)
- [Federated Learning for Computational Pathology on Gigapixel Whole Slide Images](https://mlsanity.com/paper/2009.10190/) (2020)
- [Self-Supervised Vision Transformers Learn Visual Concepts in Histopathology](https://mlsanity.com/paper/2203.00585/) (2022)
- [Bi-directional Weakly Supervised Knowledge Distillation for Whole Slide Image Classification](https://mlsanity.com/paper/2210.03664/) (2022)
- [The Rise of AI Language Pathologists: Exploring Two-level Prompt Learning for Few-shot Weakly-supervised Whole Slide Image Classification](https://mlsanity.com/paper/2305.17891/) (2023)
- [DGMIL: Distribution Guided Multiple Instance Learning for Whole Slide Image Classification](https://mlsanity.com/paper/2206.08861/) (2022)
- [Classifying and Segmenting Microscopy Images Using Convolutional Multiple Instance Learning](https://mlsanity.com/paper/1511.05286/) (2015)
- [Semi-Supervised Histology Classification using Deep Multiple Instance Learning and Contrastive Predictive Coding](https://mlsanity.com/paper/1910.10825/) (2019)
- [Accounting for Dependencies in Deep Learning Based Multiple Instance Learning for Whole Slide Imaging](https://mlsanity.com/paper/2111.01556/) (2021)
- [Towards Label-efficient Automatic Diagnosis and Analysis: A Comprehensive Survey of Advanced Deep Learning-based Weakly-supervised, Semi-supervised and Self-supervised Techniques in Histopathological Image Analysis](https://mlsanity.com/paper/2208.08789/) (2022)
- [Deep Weakly-Supervised Learning Methods for Classification and Localization in Histology Images: A Survey](https://mlsanity.com/paper/1909.03354/) (2019)
- [ProtoMIL: Multiple Instance Learning with Prototypical Parts for Whole-Slide Image Classification](https://mlsanity.com/paper/2108.10612/) (2021)
- [PiCO+: Contrastive Label Disambiguation for Robust Partial Label Learning](https://mlsanity.com/paper/2201.08984/) (2022)

## Built on by (most cited first, 22 of 22)

- [MSCPT: Few-shot Whole Slide Image Classification with Multi-scale and Context-focused Prompt Tuning](https://mlsanity.com/paper/2408.11505/) (2024)
- [From Correlation to Causation: Max-Pooling-Based Multi-Instance Learning Leads to More Robust Whole Slide Image Classification](https://mlsanity.com/paper/2408.09449/) (2024)
- [ASMIL: Attention-Stabilized Multiple Instance Learning for Whole Slide Imaging](https://mlsanity.com/paper/2603.06658/) (2026)
- [Hard Negative Sample Mining for Whole Slide Image Classification](https://mlsanity.com/paper/2410.02212/) (2024)
- [Enhancing Zero-Shot Brain Tumor Subtype Classification via Fine-Grained Patch-Text Alignment](https://mlsanity.com/paper/2508.01602/) (2025)
- [Rethinking Attention-Based Multiple Instance Learning for Whole-Slide Pathological Image Classification: An Instance Attribute Viewpoint](https://mlsanity.com/paper/2404.00351/) (2024)
- [ME-Mamba: Multi-Expert Mamba with Efficient Knowledge Capture and Fusion for Multimodal Survival Analysis](https://mlsanity.com/paper/2509.16900/) (2025)
- [Multi-Scale Heterogeneity-Aware Hypergraph Representation for Histopathology Whole Slide Images](https://mlsanity.com/paper/2404.19334/) (2024)
- [Advancing H&E-to-IHC Stain Translation in Breast Cancer: A Multi-Magnification and Attention-Based Approach](https://mlsanity.com/paper/2408.01929/) (2024)
- [Slide-Level Prompt Learning with Vision Language Models for Few-Shot Multiple Instance Learning in Histopathology](https://mlsanity.com/paper/2503.17238/) (2025)
- [Multiple Instance Learning Framework with Masked Hard Instance Mining for Gigapixel Histopathology Image Analysis](https://mlsanity.com/paper/2509.11526/) (2025)
- [MsaMIL-Net: An End-to-End Multi-Scale Aware Multiple Instance Learning Network for Efficient Whole Slide Image Classification](https://mlsanity.com/paper/2503.08581/) (2025)
- [Weakly Semi-supervised Whole Slide Image Classification by Two-level Cross Consistency Supervision](https://mlsanity.com/paper/2504.12132/) (2025)
- [Denoising Mutual Knowledge Distillation in Bi-Directional Multiple Instance Learning](https://mlsanity.com/paper/2505.12074/) (2025)
- [SemaMIL: Semantic-Aware Multiple Instance Learning with Retrieval-Guided State Space Modeling for Whole Slide Images](https://mlsanity.com/paper/2509.00442/) (2025)
- [Cluster-Level Sparse Multi-Instance Learning for Whole-Slide Images](https://mlsanity.com/paper/2509.11034/) (2025)
- [Fusing Pixels and Genes: Spatially-Aware Learning in Computational Pathology](https://mlsanity.com/paper/2602.13944/) (2026)
- [MB-DSMIL-CL-PL: Scalable Weakly Supervised Ovarian Cancer Subtype Classification and Localisation Using Contrastive and Prototype Learning with Frozen Patch Features](https://mlsanity.com/paper/2602.15138/) (2026)
- [Dictionary-based Pathology Mining with Hard-instance-assisted Classifier Debiasing for Genetic Biomarker Prediction from WSIs](https://mlsanity.com/paper/2603.26809/) (2026)
- [Spatial Blindness in Whole-Slide Multiple Instance Learning](https://mlsanity.com/paper/2605.17449/) (2026)
- [GCE-MIL: Faithful and Recoverable Evidence for Multiple Instance Learning in Whole-Slide Imaging](https://mlsanity.com/paper/2605.17456/) (2026)
- [ProtoPur: Prototype-Purity Pseudo-Labeling for Weakly Supervised Instance Learning in Pathology](https://mlsanity.com/paper/2610.15669/) (2026)

## Abstract (arXiv)

Weakly supervised whole slide image classification is usually formulated as a multiple instance learning (MIL) problem, where each slide is treated as a bag, and the patches cut out of it are treated as instances. Existing methods either train an instance classifier through pseudo-labeling or aggregate instance features into a bag feature through attention mechanisms and then train a bag classifier, where the attention scores can be used for instance-level classification. However, the pseudo instance labels constructed by the former usually contain a lot of noise, and the attention scores constructed by the latter are not accurate enough, both of which affect their performance. In this paper, we propose an instance-level MIL framework based on contrastive learning and prototype learning to effectively accomplish both instance classification and bag classification tasks. To this end, we propose an instance-level weakly supervised contrastive learning algorithm for the first time under the MIL setting to effectively learn instance feature representation. We also propose an accurate pseudo label generation method through prototype learning. We then develop a joint training strategy for weakly supervised contrastive learning, prototype learning, and instance classifier training. Extensive experiments and visualizations on four datasets demonstrate the powerful performance of our method. Codes are available at https://github.com/miccaiif/INS.