# A Knowledge-based Learning Framework for Self-supervised Pre-training Towards Enhanced Recognition of Biomedical Microscopy Images

arXiv: https://arxiv.org/abs/2211.14715 · HTML: https://mlsanity.com/paper/2211.14715/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 44 of its 69 references that are in the map.
- First posted on arXiv 27 Nov 2022.

## Builds on (most cited first, 30 of 44)

- [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)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Representation Learning with Contrastive Predictive Coding](https://mlsanity.com/paper/1807.03748/) (2018)
- [Momentum Contrast for Unsupervised Visual Representation Learning](https://mlsanity.com/paper/1911.05722/) (2019)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [Bootstrap your own latent: A new approach to self-supervised Learning](https://mlsanity.com/paper/2006.07733/) (2020)
- [Dropout as a Bayesian Approximation: Representing Model Uncertainty in Deep Learning](https://mlsanity.com/paper/1506.02142/) (2015)
- [Unsupervised Learning of Visual Features by Contrasting Cluster Assignments](https://mlsanity.com/paper/2006.09882/) (2020)
- [Improved Baselines with Momentum Contrastive Learning](https://mlsanity.com/paper/2003.04297/) (2020)
- [Unsupervised Feature Learning via Non-Parametric Instance-level Discrimination](https://mlsanity.com/paper/1805.01978/) (2018)
- [Barlow Twins: Self-Supervised Learning via Redundancy Reduction](https://mlsanity.com/paper/2103.03230/) (2021)
- [CheXpert: A Large Chest Radiograph Dataset with Uncertainty Labels and Expert Comparison](https://mlsanity.com/paper/1901.07031/) (2019)
- [Big Self-Supervised Models are Strong Semi-Supervised Learners](https://mlsanity.com/paper/2006.10029/) (2020)
- [Contrastive Multiview Coding](https://mlsanity.com/paper/1906.05849/) (2019)
- [Learning deep representations by mutual information estimation and maximization](https://mlsanity.com/paper/1808.06670/) (2018)
- [Attention-based Deep Multiple Instance Learning](https://mlsanity.com/paper/1802.04712/) (2018)
- [Deep Clustering for Unsupervised Learning of Visual Features](https://mlsanity.com/paper/1807.05520/) (2018)
- [What Makes for Good Views for Contrastive Learning?](https://mlsanity.com/paper/2005.10243/) (2020)
- [A Review of Uncertainty Quantification in Deep Learning: Techniques, Applications and Challenges](https://mlsanity.com/paper/2011.06225/) (2020)
- [Self-Supervised Learning of Pretext-Invariant Representations](https://mlsanity.com/paper/1912.01991/) (2019)
- [Self-supervised Learning: Generative or Contrastive](https://mlsanity.com/paper/2006.08218/) (2020)
- [MedMNIST v2 -- A large-scale lightweight benchmark for 2D and 3D biomedical image classification](https://mlsanity.com/paper/2110.14795/) (2021)
- [Skin Lesion Analysis Toward Melanoma Detection 2018: A Challenge Hosted by the International Skin Imaging Collaboration (ISIC)](https://mlsanity.com/paper/1902.03368/) (2019)
- [Self-supervised Visual Feature Learning with Deep Neural Networks: A Survey](https://mlsanity.com/paper/1902.06162/) (2019)
- [Prototypical Contrastive Learning of Unsupervised Representations](https://mlsanity.com/paper/2005.04966/) (2020)
- [Self-labelling via simultaneous clustering and representation learning](https://mlsanity.com/paper/1911.05371/) (2019)
- [The Liver Tumor Segmentation Benchmark (LiTS)](https://mlsanity.com/paper/1901.04056/) (2019)

## Built on by (most cited first, 1 of 1)

- [Investigating the Quality of DermaMNIST and Fitzpatrick17k Dermatological Image Datasets](https://mlsanity.com/paper/2401.14497/) (2024)

## Abstract (arXiv)

Self-supervised pre-training has become the priory choice to establish reliable neural networks for automated recognition of massive biomedical microscopy images, which are routinely annotation-free, without semantics, and without guarantee of quality. Note that this paradigm is still at its infancy and limited by closely related open issues: 1) how to learn robust representations in an unsupervised manner from unlabelled biomedical microscopy images of low diversity in samples? and 2) how to obtain the most significant representations demanded by a high-quality segmentation? Aiming at these issues, this study proposes a knowledge-based learning framework (TOWER) towards enhanced recognition of biomedical microscopy images, which works in three phases by synergizing contrastive learning and generative learning methods: 1) Sample Space Diversification: Reconstructive proxy tasks have been enabled to embed a priori knowledge with context highlighted to diversify the expanded sample space; 2) Enhanced Representation Learning: Informative noise-contrastive estimation loss regularizes the encoder to enhance representation learning of annotation-free images; 3) Correlated Optimization: Optimization operations in pre-training the encoder and the decoder have been correlated via image restoration from proxy tasks, targeting the need for semantic segmentation. Experiments have been conducted on public datasets of biomedical microscopy images against the state-of-the-art counterparts (e.g., SimCLR and BYOL), and results demonstrate that: TOWER statistically excels in all self-supervised methods, achieving a Dice improvement of 1.38 percentage points over SimCLR. TOWER also has potential in multi-modality medical image analysis and enables label-efficient semi-supervised learning, e.g., reducing the annotation cost by up to 99% in pathological classification.