# Fine-tuning a Multiple Instance Learning Feature Extractor with Masked Context Modelling and Knowledge Distillation

arXiv: https://arxiv.org/abs/2403.05325 · HTML: https://mlsanity.com/paper/2403.05325/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Placed in Distillation for medical imaging, one of 12 directions in Knowledge distillation.
- Builds on 31 of its 51 references that are in the map.
- First posted on arXiv 8 Mar 2024.

## Placed in

- Knowledge distillation / [Distillation for medical imaging](https://mlsanity.com/distill/distillation-for-medical-imaging/)

## Builds on (most cited first, 30 of 31)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Distilling the Knowledge in a Neural Network](https://mlsanity.com/paper/1503.02531/) (2015)
- [ImageNet Large Scale Visual Recognition Challenge](https://mlsanity.com/paper/1409.0575/) (2014)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [Deep Unsupervised Learning using Nonequilibrium Thermodynamics](https://mlsanity.com/paper/1503.03585/) (2015)
- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [EfficientNet: Rethinking Model Scaling for Convolutional Neural Networks](https://mlsanity.com/paper/1905.11946/) (2019)
- [Generative Adversarial Networks](https://mlsanity.com/paper/2203.00667/) (2022)
- [Bootstrap your own latent: A new approach to self-supervised Learning](https://mlsanity.com/paper/2006.07733/) (2020)
- [Training data-efficient image transformers & distillation through attention](https://mlsanity.com/paper/2012.12877/) (2020)
- [Gaussian Error Linear Units (GELUs)](https://mlsanity.com/paper/1606.08415/) (2016)
- [Exploring Simple Siamese Representation Learning](https://mlsanity.com/paper/2011.10566/) (2020)
- [An Empirical Study of Training Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.02057/) (2021)
- [Context Encoders: Feature Learning by Inpainting](https://mlsanity.com/paper/1604.07379/) (2016)
- [SimMIM: A Simple Framework for Masked Image Modeling](https://mlsanity.com/paper/2111.09886/) (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)
- [Domain Adaptation for Medical Image Analysis: A Survey](https://mlsanity.com/paper/2102.09508/) (2021)
- [Big Self-Supervised Models Advance Medical Image Classification](https://mlsanity.com/paper/2101.05224/) (2021)
- [Solo-learn: A Library of Self-supervised Methods for Visual Representation Learning](https://mlsanity.com/paper/2108.01775/) (2021)
- [ReSSL: Relational Self-Supervised Learning with Weak Augmentation](https://mlsanity.com/paper/2107.09282/) (2021)
- [Adversarial Masking for Self-Supervised Learning](https://mlsanity.com/paper/2201.13100/) (2022)
- [Fast Human Pose Estimation](https://mlsanity.com/paper/1811.05419/) (2018)
- [Multiple Instance Learning Framework with Masked Hard Instance Mining for Whole Slide Image Classification](https://mlsanity.com/paper/2307.15254/) (2023)

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

- [Histo-Miner: Deep learning based tissue features extraction pipeline from H&E whole slide images of cutaneous squamous cell carcinoma](https://mlsanity.com/paper/2505.04672/) (2025)
- [EFCM: Efficient Fine-tuning on Compressed Models for deployment of large models in medical image analysis](https://mlsanity.com/paper/2409.11817/) (2024)

## Abstract (arXiv)

The first step in Multiple Instance Learning (MIL) algorithms for Whole Slide Image (WSI) classification consists of tiling the input image into smaller patches and computing their feature vectors produced by a pre-trained feature extractor model. Feature extractor models that were pre-trained with supervision on ImageNet have proven to transfer well to this domain, however, this pre-training task does not take into account that visual information in neighboring patches is highly correlated. Based on this observation, we propose to increase downstream MIL classification by fine-tuning the feature extractor model using textitMasked Context Modelling with Knowledge Distillation. In this task, the feature extractor model is fine-tuned by predicting masked patches in a bigger context window. Since reconstructing the input image would require a powerful image generation model, and our goal is not to generate realistically looking image patches, we predict instead the feature vectors produced by a larger teacher network. A single epoch of the proposed task suffices to increase the downstream performance of the feature-extractor model when used in a MIL scenario, even capable of outperforming the downstream performance of the teacher model, while being considerably smaller and requiring a fraction of its compute.