Histopathological Image Classification with Cell Morphology Aware Deep Neural Networks

• URL: http://arxiv.org/abs/2407.08625v1
• Date: Thu, 11 Jul 2024 16:03:59 GMT
• Title: Histopathological Image Classification with Cell Morphology Aware Deep Neural Networks
• Authors: Andrey Ignatov, Josephine Yates, Valentina Boeva,
• Abstract summary: We propose a novel DeepCMorph model pre-trained to learn cell morphology and identify a large number of different cancer types. We pretrained this module on the Pan-Cancer TCGA dataset consisting of over 270K tissue patches extracted from 8736 diagnostic slides from 7175 patients. The proposed solution achieved a new state-of-the-art performance on the dataset under consideration, detecting 32 cancer types with over 82% accuracy and outperforming all previously proposed solutions by more than 4%.
• Score: 11.749248917866915
• License: http://creativecommons.org/licenses/by-nc-sa/4.0/
• Abstract: Histopathological images are widely used for the analysis of diseased (tumor) tissues and patient treatment selection. While the majority of microscopy image processing was previously done manually by pathologists, recent advances in computer vision allow for accurate recognition of lesion regions with deep learning-based solutions. Such models, however, usually require extensive annotated datasets for training, which is often not the case in the considered task, where the number of available patient data samples is very limited. To deal with this problem, we propose a novel DeepCMorph model pre-trained to learn cell morphology and identify a large number of different cancer types. The model consists of two modules: the first one performs cell nuclei segmentation and annotates each cell type, and is trained on a combination of 8 publicly available datasets to ensure its high generalizability and robustness. The second module combines the obtained segmentation map with the original microscopy image and is trained for the downstream task. We pre-trained this module on the Pan-Cancer TCGA dataset consisting of over 270K tissue patches extracted from 8736 diagnostic slides from 7175 patients. The proposed solution achieved a new state-of-the-art performance on the dataset under consideration, detecting 32 cancer types with over 82% accuracy and outperforming all previously proposed solutions by more than 4%. We demonstrate that the resulting pre-trained model can be easily fine-tuned on smaller microscopy datasets, yielding superior results compared to the current top solutions and models initialized with ImageNet weights. The codes and pre-trained models presented in this paper are available at: https://github.com/aiff22/DeepCMorph

Related papers

• LVM-Med: Learning Large-Scale Self-Supervised Vision Models for Medical Imaging via Second-order Graph Matching [59.01894976615714]
  We introduce LVM-Med, the first family of deep networks trained on large-scale medical datasets. We have collected approximately 1.3 million medical images from 55 publicly available datasets. LVM-Med empirically outperforms a number of state-of-the-art supervised, self-supervised, and foundation models.
  arXiv  Detail & Related papers  (2023-06-20T22:21:34Z)
• AMIGO: Sparse Multi-Modal Graph Transformer with Shared-Context Processing for Representation Learning of Giga-pixel Images [53.29794593104923]
  We present a novel concept of shared-context processing for whole slide histopathology images. AMIGO uses the celluar graph within the tissue to provide a single representation for a patient. We show that our model is strongly robust to missing information to an extent that it can achieve the same performance with as low as 20% of the data.
  arXiv  Detail & Related papers  (2023-03-01T23:37:45Z)
• Application of Transfer Learning and Ensemble Learning in Image-level Classification for Breast Histopathology [9.037868656840736]
  In Computer-Aided Diagnosis (CAD), traditional classification models mostly use a single network to extract features. This paper proposes a deep ensemble model based on image-level labels for the binary classification of benign and malignant lesions. Result: In the ensemble network model with accuracy as the weight, the image-level binary classification achieves an accuracy of $98.90%$.
  arXiv  Detail & Related papers  (2022-04-18T13:31:53Z)
• One Model is All You Need: Multi-Task Learning Enables Simultaneous Histology Image Segmentation and Classification [3.8725005247905386]
  We present a multi-task learning approach for segmentation and classification of tissue regions. We enable simultaneous prediction with a single network. As a result of feature sharing, we also show that the learned representation can be used to improve downstream tasks.
  arXiv  Detail & Related papers  (2022-02-28T20:22:39Z)
• Multi-Scale Input Strategies for Medulloblastoma Tumor Classification using Deep Transfer Learning [59.30734371401316]
  Medulloblastoma is the most common malignant brain cancer among children. CNN has shown promising results for MB subtype classification. We study the impact of tile size and input strategy.
  arXiv  Detail & Related papers  (2021-09-14T09:42:37Z)
• Medulloblastoma Tumor Classification using Deep Transfer Learning with Multi-Scale EfficientNets [63.62764375279861]
  We propose an end-to-end MB tumor classification and explore transfer learning with various input sizes and matching network dimensions. Using a data set with 161 cases, we demonstrate that pre-trained EfficientNets with larger input resolutions lead to significant performance improvements.
  arXiv  Detail & Related papers  (2021-09-10T13:07:11Z)
• Acute Lymphoblastic Leukemia Detection from Microscopic Images Using Weighted Ensemble of Convolutional Neural Networks [4.095759108304108]
  This article has automated the ALL detection task from microscopic cell images, employing deep Convolutional Neural Networks (CNNs) Various data augmentations and pre-processing are incorporated for achieving a better generalization of the network. Our proposed weighted ensemble model, using the kappa values of the ensemble candidates as their weights, has outputted a weighted F1-score of 88.6 %, a balanced accuracy of 86.2 %, and an AUC of 0.941 in the preliminary test set.
  arXiv  Detail & Related papers  (2021-05-09T18:58:48Z)
• Generative Adversarial U-Net for Domain-free Medical Image Augmentation [49.72048151146307]
  The shortage of annotated medical images is one of the biggest challenges in the field of medical image computing. In this paper, we develop a novel generative method named generative adversarial U-Net. Our newly designed model is domain-free and generalizable to various medical images.
  arXiv  Detail & Related papers  (2021-01-12T23:02:26Z)
• Deep learning for lithological classification of carbonate rock micro-CT images [52.77024349608834]
  This work intends to present an application of deep learning techniques to identify patterns in Brazilian pre-salt carbonate rock microtomographic images. Four convolutional neural network models were proposed. According to accuracy, Model 2 trained on resized images achieved the best results, reaching an average of 75.54% for the first evaluation approach and an average of 81.33% for the second.
  arXiv  Detail & Related papers  (2020-07-30T19:14:00Z)
• An interpretable classifier for high-resolution breast cancer screening images utilizing weakly supervised localization [45.00998416720726]
  We propose a framework to address the unique properties of medical images. This model first uses a low-capacity, yet memory-efficient, network on the whole image to identify the most informative regions. It then applies another higher-capacity network to collect details from chosen regions. Finally, it employs a fusion module that aggregates global and local information to make a final prediction.
  arXiv  Detail & Related papers  (2020-02-13T15:28:42Z)
• Segmentation of Cellular Patterns in Confocal Images of Melanocytic Lesions in vivo via a Multiscale Encoder-Decoder Network (MED-Net) [2.0487455621441377]
  "Multiscale-Decoder Network (MED-Net)" provides pixel-wise labeling into classes of patterns in a quantitative manner. We trained and tested our model on non-overlapping partitions of 117 reflectance confocal microscopy (RCM) mosaics of melanocytic lesions.
  arXiv  Detail & Related papers  (2020-01-03T22:34:52Z)

This list is automatically generated from the titles and abstracts of the papers in this site.

This site does not guarantee the quality of this site (including all information) and is not responsible for any consequences.