Patch-based Convolutional Neural Network for Whole Slide Tissue Image Classification

Convolutional Neural Networks (CNN) are state-of-the-art models for many image classification tasks. However, to recognize cancer subtypes automatically, training a CNN on gigapixel resolution Whole Slide Tissue Images (WSI) is currently computationally impossible. The differentiation of cancer subtypes is based on cellular-level visual features observed on image patch scale. Therefore, we argue that in this situation, training a patch-level classifier on image patches will perform better than or similar to an image-level classifier. The challenge becomes how to intelligently combine patch-level classification results and model the fact that not all patches will be discriminative. We propose to train a decision fusion model to aggregate patch-level predictions given by patch-level CNNs, which to the best of our knowledge has not been shown before. Furthermore, we formulate a novel Expectation-Maximization (EM) based method that automatically locates discriminative patches robustly by utilizing the spatial relationships of patches. We apply our method to the classification of glioma and non-small-cell lung carcinoma cases into subtypes. The classification accuracy of our method is similar to the inter-observer agreement between pathologists. Although it is impossible to train CNNs on WSIs, we experimentally demonstrate using a comparable non-cancer dataset of smaller images that a patch-based CNN can outperform an image-based CNN

Learning to Segment Breast Biopsy Whole Slide Images

We trained and applied an encoder-decoder model to semantically segment breast biopsy images into biologically meaningful tissue labels. Since conventional encoder-decoder networks cannot be applied directly on large biopsy images and the different sized structures in biopsies present novel challenges, we propose four modifications: (1) an input-aware encoding block to compensate for information loss, (2) a new dense connection pattern between encoder and decoder, (3) dense and sparse decoders to combine multi-level features, (4) a multi-resolution network that fuses the results of encoder-decoders run on different resolutions. Our model outperforms a feature-based approach and conventional encoder-decoders from the literature. We use semantic segmentations produced with our model in an automated diagnosis task and obtain higher accuracies than a baseline approach that employs an SVM for feature-based segmentation, both using the same segmentation-based diagnostic features.Comment: Added more WSI images in appendi

Fusing image representations for classification using support vector machines

In order to improve classification accuracy different image representations are usually combined. This can be done by using two different fusing schemes. In feature level fusion schemes, image representations are combined before the classification process. In classifier fusion, the decisions taken separately based on individual representations are fused to make a decision. In this paper the main methods derived for both strategies are evaluated. Our experimental results show that classifier fusion performs better. Specifically Bayes belief integration is the best performing strategy for image classification task.Comment: Image and Vision Computing New Zealand, 2009. IVCNZ '09. 24th International Conference, Wellington : Nouvelle-Z\'elande (2009

Exploiting Image-trained CNN Architectures for Unconstrained Video Classification

We conduct an in-depth exploration of different strategies for doing event detection in videos using convolutional neural networks (CNNs) trained for image classification. We study different ways of performing spatial and temporal pooling, feature normalization, choice of CNN layers as well as choice of classifiers. Making judicious choices along these dimensions led to a very significant increase in performance over more naive approaches that have been used till now. We evaluate our approach on the challenging TRECVID MED'14 dataset with two popular CNN architectures pretrained on ImageNet. On this MED'14 dataset, our methods, based entirely on image-trained CNN features, can outperform several state-of-the-art non-CNN models. Our proposed late fusion of CNN- and motion-based features can further increase the mean average precision (mAP) on MED'14 from 34.95% to 38.74%. The fusion approach achieves the state-of-the-art classification performance on the challenging UCF-101 dataset