Machine learning methods for histopathological image analysis

Abundant accumulation of digital histopathological images has led to the increased demand for their analysis, such as computer-aided diagnosis using machine learning techniques. However, digital pathological images and related tasks have some issues to be considered. In this mini-review, we introduce the application of digital pathological image analysis using machine learning algorithms, address some problems specific to such analysis, and propose possible solutions.Comment: 23 pages, 4 figure

Context-based Normalization of Histological Stains using Deep Convolutional Features

While human observers are able to cope with variations in color and appearance of histological stains, digital pathology algorithms commonly require a well-normalized setting to achieve peak performance, especially when a limited amount of labeled data is available. This work provides a fully automated, end-to-end learning-based setup for normalizing histological stains, which considers the texture context of the tissue. We introduce Feature Aware Normalization, which extends the framework of batch normalization in combination with gating elements from Long Short-Term Memory units for normalization among different spatial regions of interest. By incorporating a pretrained deep neural network as a feature extractor steering a pixelwise processing pipeline, we achieve excellent normalization results and ensure a consistent representation of color and texture. The evaluation comprises a comparison of color histogram deviations, structural similarity and measures the color volume obtained by the different methods.Comment: In: 3rd Workshop on Deep Learning in Medical Image Analysis (DLMIA 2017

Interpreting Deep Visual Representations via Network Dissection

The success of recent deep convolutional neural networks (CNNs) depends on learning hidden representations that can summarize the important factors of variation behind the data. However, CNNs often criticized as being black boxes that lack interpretability, since they have millions of unexplained model parameters. In this work, we describe Network Dissection, a method that interprets networks by providing labels for the units of their deep visual representations. The proposed method quantifies the interpretability of CNN representations by evaluating the alignment between individual hidden units and a set of visual semantic concepts. By identifying the best alignments, units are given human interpretable labels across a range of objects, parts, scenes, textures, materials, and colors. The method reveals that deep representations are more transparent and interpretable than expected: we find that representations are significantly more interpretable than they would be under a random equivalently powerful basis. We apply the method to interpret and compare the latent representations of various network architectures trained to solve different supervised and self-supervised training tasks. We then examine factors affecting the network interpretability such as the number of the training iterations, regularizations, different initializations, and the network depth and width. Finally we show that the interpreted units can be used to provide explicit explanations of a prediction given by a CNN for an image. Our results highlight that interpretability is an important property of deep neural networks that provides new insights into their hierarchical structure.Comment: *B. Zhou and D. Bau contributed equally to this work. 15 pages, 27 figure

Multilayer Complex Network Descriptors for Color-Texture Characterization

A new method based on complex networks is proposed for color-texture analysis. The proposal consists on modeling the image as a multilayer complex network where each color channel is a layer, and each pixel (in each color channel) is represented as a network vertex. The network dynamic evolution is accessed using a set of modeling parameters (radii and thresholds), and new characterization techniques are introduced to capt information regarding within and between color channel spatial interaction. An automatic and adaptive approach for threshold selection is also proposed. We conduct classification experiments on 5 well-known datasets: Vistex, Usptex, Outex13, CURet and MBT. Results among various literature methods are compared, including deep convolutional neural networks with pre-trained architectures. The proposed method presented the highest overall performance over the 5 datasets, with 97.7 of mean accuracy against 97.0 achieved by the ResNet convolutional neural network with 50 layers.Comment: 20 pages, 7 figures and 4 table