iMIL4PATH: A Semi-Supervised Interpretable Approach for Colorectal Whole-Slide Images

Neto, Pedro C.; Oliveira, Sara P.; Montezuma, Diana; Fraga, Jorge Gerardo Pereira; Monteiro, Ana Raquel; Ribeiro, Liliana; Gonçalves, Sofia; Pinto, Isabel; Cardoso, Jaime S.

doi:10.3390/cancers14102489

Cited by 16 publications

(21 citation statements)

References 30 publications

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“…and had a high consensus with experts. Subsequent studies have also applied MIL for Gleason grading [ 80 , 81 ], grading dysplasia of various cancers (i.e., normal, low-grade, and high-grade) [ 82 , 83 ], and grading of colorectal cancer (i.e., low-grade and high-grade) [ 84 ].…”

Section: Related Workmentioning

confidence: 99%

Contrastive Multiple Instance Learning: An Unsupervised Framework for Learning Slide-Level Representations of Whole Slide Histopathology Images without Labels

Tavolara

Gürcan

Niazi

2022

Cancers

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Recent methods in computational pathology have trended towards semi- and weakly-supervised methods requiring only slide-level labels. Yet, even slide-level labels may be absent or irrelevant to the application of interest, such as in clinical trials. Hence, we present a fully unsupervised method to learn meaningful, compact representations of WSIs. Our method initially trains a tile-wise encoder using SimCLR, from which subsets of tile-wise embeddings are extracted and fused via an attention-based multiple-instance learning framework to yield slide-level representations. The resulting set of intra-slide-level and inter-slide-level embeddings are attracted and repelled via contrastive loss, respectively. This resulted in slide-level representations with self-supervision. We applied our method to two tasks— (1) non-small cell lung cancer subtyping (NSCLC) as a classification prototype and (2) breast cancer proliferation scoring (TUPAC16) as a regression prototype—and achieved an AUC of 0.8641 ± 0.0115 and correlation (R2) of 0.5740 ± 0.0970, respectively. Ablation experiments demonstrate that the resulting unsupervised slide-level feature space can be fine-tuned with small datasets for both tasks. Overall, our method approaches computational pathology in a novel manner, where meaningful features can be learned from whole-slide images without the need for annotations of slide-level labels. The proposed method stands to benefit computational pathology, as it theoretically enables researchers to benefit from completely unlabeled whole-slide images.

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Section: Related Workmentioning

confidence: 99%

Contrastive Multiple Instance Learning: An Unsupervised Framework for Learning Slide-Level Representations of Whole Slide Histopathology Images without Labels

Tavolara

Gürcan

Niazi

2022

Cancers

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“…On the other hand, it is easier to label the dataset at the slide level. The inclusion of detailed spatial annotations on approximately 10% of the dataset has been shown to positively impact the performance of deep learning algorithms [17,31]. To fully leverage the potential of spatial and slide labels, we propose a deep learning pipeline, based on previous approaches [17,31], using mixed supervision.…”

Section: Problem Definitionmentioning

confidence: 99%

“…The inclusion of detailed spatial annotations on approximately 10% of the dataset has been shown to positively impact the performance of deep learning algorithms [17,31]. To fully leverage the potential of spatial and slide labels, we propose a deep learning pipeline, based on previous approaches [17,31], using mixed supervision. Each slide, S is composed of a set of tiles T s,n , where s represents the index of the slide and n ∈ {1, • • • , n s } the tile number.…”

Section: Problem Definitionmentioning

confidence: 99%

“…The spectrum of large-scale CRC/CRS datasets is slowly increasing due to the contributions of several researchers. Two datasets that have been recently introduced in the literature are the CRS1K [17] and CRS4K [31] datasets. Since the latter is an extension of the former with roughly four times more slides, it will be the baseline dataset for the remaining of this document.…”

Section: Datasetsmentioning

confidence: 99%

“…After this analysis, the five most severe tiles are selected for training. The number of selected tiles was chosen in accordance with previous studies [31]. These five tiles per slide are used to train the proposed model for one more epoch.…”

Section: Weakly-supervised Learningmentioning

confidence: 99%

See 2 more Smart Citations

A CAD System for Colorectal Cancer from WSI: A Clinically Validated Interpretable ML-based Prototype

Neto¹,

Montezuma²,

Oliveira³

et al. 2023

Preprint

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The integration of Artificial Intelligence (AI) and Digital Pathology has been increasing over the past years. Nowadays, applications of deep learning (DL) methods to diagnose cancer from whole-slide images (WSI) are, more than ever, a reality within different research groups. Nonetheless, the development of these systems was limited by a myriad of constraints regarding the lack of training samples, the scaling difficulties, the opaqueness of DL methods, and, more importantly, the lack of clinical validation. As such, we propose a system designed specifically for the diagnosis of colorectal samples. The construction of such a system consisted of four stages: (1) a careful data collection and annotation process, which resulted in one of the largest WSI colorectal samples datasets; (2) the design of an interpretable

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HER2GAN: Overcome the Scarcity of HER2 Breast Cancer Dataset Based on Transfer Learning and GAN Model

Mirimoghaddam,

Majidpour,

Pashaei

et al. 2024

Clinical Breast Cancer

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iMIL4PATH: A Semi-Supervised Interpretable Approach for Colorectal Whole-Slide Images

Cited by 16 publications

References 30 publications

Contrastive Multiple Instance Learning: An Unsupervised Framework for Learning Slide-Level Representations of Whole Slide Histopathology Images without Labels

Contrastive Multiple Instance Learning: An Unsupervised Framework for Learning Slide-Level Representations of Whole Slide Histopathology Images without Labels

A CAD System for Colorectal Cancer from WSI: A Clinically Validated Interpretable ML-based Prototype

HER2GAN: Overcome the Scarcity of HER2 Breast Cancer Dataset Based on Transfer Learning and GAN Model

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