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Register a new userY-Net: Joint Segmentation and Classification for Diagnosis of Breast Biopsy Images
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Sachin Mehta
Publication date
2018
fields
Informatics Engineering
and research's language is
English
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In this paper, we introduce a conceptually simple network for generating discriminative tissue-level segmentation masks for the purpose of breast cancer diagnosis. Our method efficiently segments different types of tissues in breast biopsy images while simultaneously predicting a discriminative map for identifying important areas in an image. Our network, Y-Net, extends and generalizes U-Net by adding a parallel branch for discriminative map generation and by supporting convolutional block modularity, which allows the user to adjust network efficiency without altering the network topology. Y-Net delivers state-of-the-art segmentation accuracy while learning 6.6x fewer parameters than its closest competitors. The addition of descriptive power from Y-Nets discriminative segmentation masks improve diagnostic classification accuracy by 7% over state-of-the-art methods for diagnostic classification. Source code is available at: https://sacmehta.github.io/YNet.
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In the last few years, deep learning classifiers have shown promising results in image-based medical diagnosis. However, interpreting the outputs of these models remains a challenge. In cancer diagnosis, interpretability can be achieved by localizing the region of the input image responsible for the output, i.e. the location of a lesion. Alternatively, segmentation or detection models can be trained with pixel-wise annotations indicating the locations of malignant lesions. Unfortunately, acquiring such labels is labor-intensive and requires medical expertise. To overcome this difficulty, weakly-supervised localization can be utilized. These methods allow neural network classifiers to output saliency maps highlighting the regions of the input most relevant to the classification task (e.g. malignant lesions in mammograms) using only image-level labels (e.g. whether the patient has cancer or not) during training. When applied to high-resolution images, existing methods produce low-resolution saliency maps. This is problematic in applications in which suspicious lesions are small in relation to the image size. In this work, we introduce a novel neural network architecture to perform weakly-supervised segmentation of high-resolution images. The proposed model selects regions of interest via coarse-level localization, and then performs fine-grained segmentation of those regions. We apply this model to breast cancer diagnosis with screening mammography, and validate it on a large clinically-realistic dataset. Measured by Dice similarity score, our approach outperforms existing methods by a large margin in terms of localization performance of benign and malignant lesions, relatively improving the performance by 39.6% and 20.0%, respectively. Code and the weights of some of the models are available at https://github.com/nyukat/GLAM
Training end-to-end networks for classifying gigapixel size histopathological images is computationally intractable. Most approaches are patch-based and first learn local representations (patch-wise) before combining these local representations to produce image-level decisions. However, dividing large tissue structures into patches limits the context available to these networks, which may reduce their ability to learn representations from clinically relevant structures. In this paper, we introduce a novel attention-based network, the Holistic ATtention Network (HATNet) to classify breast biopsy images. We streamline the histopathological image classification pipeline and show how to learn representations from gigapixel size images end-to-end. HATNet extends the bag-of-words approach and uses self-attention to encode global information, allowing it to learn representations from clinically relevant tissue structures without any explicit supervision. It outperforms the previous best network Y-Net, which uses supervision in the form of tissue-level segmentation masks, by 8%. Importantly, our analysis reveals that HATNet learns representations from clinically relevant structures, and it matches the classification accuracy of human pathologists for this challenging test set. Our source code is available at url{https://github.com/sacmehta/HATNet}
Convolutional neural networks have led to significant breakthroughs in the domain of medical image analysis. However, the task of breast cancer segmentation in whole-slide images (WSIs) is still underexplored. WSIs are large histopathological images with extremely high resolution. Constrained by the hardware and field of view, using high-magnification patches can slow down the inference process and using low-magnification patches can cause the loss of information. In this paper, we aim to achieve two seemingly conflicting goals for breast cancer segmentation: accurate and fast prediction. We propose a simple yet efficient framework Reinforced Auto-Zoom Net (RAZN) to tackle this task. Motivated by the zoom-in operation of a pathologist using a digital microscope, RAZN learns a policy network to decide whether zooming is required in a given region of interest. Because the zoom-in action is selective, RAZN is robust to unbalanced and noisy ground truth labels and can efficiently reduce overfitting. We evaluate our method on a public breast cancer dataset. RAZN outperforms both single-scale and multi-scale baseline approaches, achieving better accuracy at low inference cost.
Breast cancer is the malignant tumor that causes the highest number of cancer deaths in females. Digital mammograms (DM or 2D mammogram) and digital breast tomosynthesis (DBT or 3D mammogram) are the two types of mammography imagery that are used in clinical practice for breast cancer detection and diagnosis. Radiologists usually read both imaging modalities in combination; however, existing computer-aided diagnosis tools are designed using only one imaging modality. Inspired by clinical practice, we propose an innovative convolutional neural network (CNN) architecture for breast cancer classification, which uses both 2D and 3D mammograms, simultaneously. Our experiment shows that the proposed method significantly improves the performance of breast cancer classification. By assembling three CNN classifiers, the proposed model achieves 0.97 AUC, which is 34.72% higher than the methods using only one imaging modality.
Multi-instance multi-label (MIML) learning is a challenging problem in many aspects. Such learning approaches might be useful for many medical diagnosis applications including breast cancer detection and classification. In this study subset of digiPATH dataset (whole slide digital breast cancer histopathology images) are used for training and evaluation of six state-of-the-art MIML methods. At the end, performance comparison of these approaches are given by means of effective evaluation metrics. It is shown that MIML-kNN achieve the best performance that is %65.3 average precision, where most of other methods attain acceptable results as well.
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