REET: robustness evaluation and enhancement toolbox for computational pathology

A Foote, A Asif, N Rajpoot, F Minhas - Bioinformatics, 2022 - academic.oup.com
Motivation Digitization of pathology laboratories through digital slide scanners and
advances in deep learning approaches for objective histological assessment have resulted …

Built to last? Reproducibility and reusability of deep learning algorithms in computational pathology

SJ Wagner, C Matek, SS Boushehri, M Boxberg… - Modern Pathology, 2024 - Elsevier
Recent progress in computational pathology has been driven by deep learning. While code
and data availability are essential to reproduce findings from preceding publications …

DeepMed: a unified, modular pipeline for end-to-end deep learning in computational pathology

M van Treeck, D Cifci, NG Laleh, OL Saldanha… - BioRxiv, 2021 - biorxiv.org
The interpretation of digitized histopathology images has been transformed thanks to
artificial intelligence (AI). End-to-end AI algorithms can infer high-level features directly from …

Equipping Computational Pathology Systems with Artifact Processing Pipelines: A Showcase for Computation and Performance Trade-offs

N Kanwal, F Khoraminia, U Kiraz… - medRxiv, 2024 - medrxiv.org
Background: Histopathology is a gold standard for cancer diagnosis. It involves extracting
tissue specimens from suspicious areas to prepare a glass slide for a microscopic …

Make deep learning algorithms in computational pathology more reproducible and reusable

SJ Wagner, C Matek, S Shetab Boushehri… - Nature Medicine, 2022 - nature.com
Make deep learning algorithms in computational pathology more reproducible and reusable |
Nature Medicine Skip to main content Thank you for visiting nature.com. You are using a browser …

Deep learning models for digital pathology

A BenTaieb, G Hamarneh - arXiv preprint arXiv:1910.12329, 2019 - arxiv.org
Histopathology images; microscopy images of stained tissue biopsies contain fundamental
prognostic information that forms the foundation of pathological analysis and diagnostic …

Regression-based Deep-Learning predicts molecular biomarkers from pathology slides

OSM El Nahhas, CML Loeffler, ZI Carrero… - nature …, 2024 - nature.com
Deep Learning (DL) can predict biomarkers from cancer histopathology. Several clinically
approved applications use this technology. Most approaches, however, predict categorical …

Low-resource finetuning of foundation models beats state-of-the-art in histopathology

B Roth, V Koch, SJ Wagner, JA Schnabel… - arXiv preprint arXiv …, 2024 - arxiv.org
To handle the large scale of whole slide images in computational pathology, most
approaches first tessellate the images into smaller patches, extract features from these …

Deep learning and its applications in computational pathology

R Hong, D Fenyö - BioMedInformatics, 2022 - mdpi.com
Deep learning techniques, such as convolutional neural networks (CNNs), generative
adversarial networks (GANs), and graph neural networks (GNNs) have, over the past …

How to learn with intentional mistakes: NoisyEnsembles to overcome poor tissue quality for deep learning in computational pathology

RS Mayer, S Gretser, LE Heckmann, PK Ziegler… - Frontiers in …, 2022 - frontiersin.org
There is a lot of recent interest in the field of computational pathology, as many algorithms
are introduced to detect, for example, cancer lesions or molecular features. However, there …