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Magnification Prior: A Self-Supervised Method for Learning Representations on Breast Cancer Histopathological Images
Luleå University of Technology, Department of Computer Science, Electrical and Space Engineering, Embedded Internet Systems Lab.ORCID iD: 0000-0002-6903-7552
Luleå University of Technology, Department of Computer Science, Electrical and Space Engineering, Embedded Internet Systems Lab.ORCID iD: 0000-0001-9604-7193
Luleå University of Technology, Department of Computer Science, Electrical and Space Engineering, Embedded Internet Systems Lab.ORCID iD: 0000-0003-0100-4030
Luleå University of Technology, Department of Computer Science, Electrical and Space Engineering, Embedded Internet Systems Lab.ORCID iD: 0000-0001-8532-0895
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2023 (English)In: Proceedings: 2023 IEEE/CVF Winter Conference on Applications of Computer Vision (WACV 2023), IEEE, 2023, p. 2716-2726Conference paper, Published paper (Refereed)
Abstract [en]

This work presents a novel self-supervised pre-training method to learn efficient representations without labels on histopathology medical images utilizing magnification factors. Other state-of-the-art works mainly focus on fully supervised learning approaches that rely heavily on human annotations. However, the scarcity of labeled and unlabeled data is a long-standing challenge in histopathology. Currently, representation learning without labels remains unexplored in the histopathology domain. The proposed method, Magnification Prior Contrastive Similarity (MPCS), enables self-supervised learning of representations without labels on small-scale breast cancer dataset BreakHis by exploiting magnification factor, inductive transfer, and reducing human prior. The proposed method matches fully supervised learning state-of-the-art performance in malignancy classification when only 20% of labels are used in fine-tuning and outperform previous works in fully supervised learning settings for three public breast cancer datasets, including BreakHis. Further, It provides initial support for a hypothesis that reducing human-prior leads to efficient representation learning in self-supervision, which will need further investigation. The implementation of this work is available online on GitHub

Place, publisher, year, edition, pages
IEEE, 2023. p. 2716-2726
Series
Proceedings IEEE Workshop on Applications of Computer Vision, ISSN 2472-6737, E-ISSN 2642-9381
Keywords [en]
self-supervised learning, contrastive learning, representation learning, breast cancer, histopathological images, transfer learning, medical images
National Category
Computer Sciences
Research subject
Machine Learning
Identifiers
URN: urn:nbn:se:ltu:diva-94845DOI: 10.1109/WACV56688.2023.00274ISI: 000971500202081Scopus ID: 2-s2.0-85149049398ISBN: 978-1-6654-9346-8 (electronic)OAI: oai:DiVA.org:ltu-94845DiVA, id: diva2:1719276
Conference
2023 IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), January 2-7, 2023, Waikoloa, Hawaii, USA
Available from: 2022-12-14 Created: 2022-12-14 Last updated: 2024-03-07Bibliographically approved
In thesis
1. Self-supervised Representation Learning for Visual Domains Beyond Natural Scenes
Open this publication in new window or tab >>Self-supervised Representation Learning for Visual Domains Beyond Natural Scenes
2023 (English)Licentiate thesis, comprehensive summary (Other academic)
Abstract [en]

This thesis investigates the possibility of efficiently adapting self-supervised representation learning on visual domains beyond natural scenes, e.g., medical imagining and non-RGB sensory images. The thesis contributes to i) formalizing the self-supervised representation learning paradigm in a unified conceptual framework and ii) proposing the hypothesis based on supervision signal from data, called data-prior. Method adaptations following the hypothesis demonstrate significant progress in downstream tasks performance on microscopic histopathology and 3-dimensional particle management (3DPM) mining material non-RGB image domains.

Supervised learning has proven to be obtaining higher performance than unsupervised learning on computer vision downstream tasks, e.g., image classification, object detection, etc. However, it imposes limitations due to human supervision. To reduce human supervision, end-to-end learning, i.e., transfer learning, remains proven for fine-tuning tasks but does not leverage unlabeled data. Representation learning in a self-supervised manner has successfully reduced the need for labelled data in the natural language processing and vision domain. Advances in learning effective visual representations without human supervision through a self-supervised learning approach are thought-provoking.

This thesis performs a detailed conceptual analysis, method formalization, and literature study on the recent paradigm of self-supervised representation learning. The study’s primary goal is to identify the common methodological limitations across the various approaches for adaptation to the visual domain beyond natural scenes. The study finds a common component in transformations that generate distorted views for invariant representation learning. A significant outcome of the study suggests this component is closely dependent on human knowledge of the real world around the natural scene, which fits well the visual domain of the natural scenes but remains sub-optimal for other visual domains that are conceptually different.

A hypothesis is proposed to use the supervision signal from data (data-prior) to replace the human-knowledge-driven transformations in self-supervised pretraining to overcome the stated challenge. Two separate visual domains beyond the natural scene are considered to explore the mentioned hypothesis, which is breast cancer microscopic histopathology and 3-dimensional particle management (3DPM) mining material non-RGB image.

The first research paper explores the breast cancer microscopic histopathology images by actualizing the data-prior hypothesis in terms of multiple magnification factors as supervision signal from data, which is available in the microscopic histopathology images public dataset BreakHis. It proposes a self-supervised representation learning method, Magnification Prior Contrastive Similarity, which adapts the contrastive learning approach by replacing the standard image view transformations (augmentations) by utilizing magnification factors. The contributions to the work are multi-folded. It achieves significant performance improvement in the downstream task of malignancy classification during label efficiency and fully supervised settings. Pretrained models show efficient knowledge transfer on two additional public datasets supported by qualitative analysis on representation learning. The second research paper investigates the 3DPM mining material non-RGB image domain where the material’s pixel-mapped reflectance image and height (depth map) are captured. It actualizes the data-prior hypothesis by using depth maps of mining material on the conveyor belt. The proposed method, Depth Contrast, also adapts the contrastive learning method while replacing standard augmentations with depth maps for mining materials. It outperforms material classification over ImageNet transfer learning performance in fully supervised learning settings in fine-tuning and linear evaluation. It also shows consistent improvement in performance during label efficiency.

In summary, the data-prior hypothesis shows one promising direction for optimal adaptations of contrastive learning methods in self-supervision for the visual domain beyond the natural scene. Although, a detailed study on the data-prior hypothesis is required to explore other non-contrastive approaches of recent self-supervised representation learning, including knowledge distillation and information maximization.

Place, publisher, year, edition, pages
Luleå: Luleå tekniska universitet, 2023
Series
Licentiate thesis / Luleå University of Technology, ISSN 1402-1757
Keywords
self-supervised learning, representation learning, computer vision, learning with few labels
National Category
Computer Sciences
Research subject
Machine Learning
Identifiers
urn:nbn:se:ltu:diva-95425 (URN)978-91-8048-258-5 (ISBN)978-91-8048-259-2 (ISBN)
Presentation
2023-03-17, A117, Luleå tekniska universitet, Luleå, 10:00 (English)
Opponent
Supervisors
Available from: 2023-01-30 Created: 2023-01-30 Last updated: 2023-09-05Bibliographically approved

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