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Register a new userReinforced Auto-Zoom Net: Towards Accurate and Fast Breast Cancer Segmentation in Whole-slide Images
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Nanqing Dong
Publication date
2018
fields
Informatics Engineering
and research's language is
English
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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.
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Tumor proliferation is an important biomarker indicative of the prognosis of breast cancer patients. Assessment of tumor proliferation in a clinical setting is highly subjective and labor-intensive task. Previous efforts to automate tumor proliferation assessment by image analysis only focused on mitosis detection in predefined tumor regions. However, in a real-world scenario, automatic mitosis detection should be performed in whole-slide images (WSIs) and an automatic method should be able to produce a tumor proliferation score given a WSI as input. To address this, we organized the TUmor Proliferation Assessment Challenge 2016 (TUPAC16) on prediction of tumor proliferation scores from WSIs. The challenge dataset consisted of 500 training and 321 testing breast cancer histopathology WSIs. In order to ensure fair and independent evaluation, only the ground truth for the training dataset was provided to the challenge participants. The first task of the challenge was to predict mitotic scores, i.e., to reproduce the manual method of assessing tumor proliferation by a pathologist. The second task was to predict the gene expression based PAM50 proliferation scores from the WSI. The best performing automatic method for the first task achieved a quadratic-weighted Cohens kappa score of $kappa$ = 0.567, 95% CI [0.464, 0.671] between the predicted scores and the ground truth. For the second task, the predictions of the top method had a Spearmans correlation coefficient of r = 0.617, 95% CI [0.581 0.651] with the ground truth. This was the first study that investigated tumor proliferation assessment from WSIs. The achieved results are promising given the difficulty of the tasks and weakly-labelled nature of the ground truth. However, further research is needed to improve the practical utility of image analysis methods for this task.
The use of multi-modal data such as the combination of whole slide images (WSIs) and gene expression data for survival analysis can lead to more accurate survival predictions. Previous multi-modal survival models are not able to efficiently excavate the intrinsic information within each modality. Moreover, despite experimental results show that WSIs provide more effective information than gene expression data, previous methods regard the information from different modalities as similarly important so they cannot flexibly utilize the potential connection between the modalities. To address the above problems, we propose a new asymmetrical multi-modal method, termed as AMMASurv. Specifically, we design an asymmetrical multi-modal attention mechanism (AMMA) in Transformer encoder for multi-modal data to enable a more flexible multi-modal information fusion for survival prediction. Different from previous works, AMMASurv can effectively utilize the intrinsic information within every modality and flexibly adapts to the modalities of different importance. Extensive experiments are conducted to validate the effectiveness of the proposed model. Encouraging results demonstrate the superiority of our method over other state-of-the-art methods.
Prostate cancer (PCa) is the second deadliest form of cancer in males, and it can be clinically graded by examining the structural representations of Gleason tissues. This paper proposes RV{a new method} for segmenting the Gleason tissues RV{(patch-wise) in order to grade PCa from the whole slide images (WSI).} Also, the proposed approach encompasses two main contributions: 1) A synergy of hybrid dilation factors and hierarchical decomposition of latent space representation for effective Gleason tissues extraction, and 2) A three-tiered loss function which can penalize different semantic segmentation models for accurately extracting the highly correlated patterns. In addition to this, the proposed framework has been extensively evaluated on a large-scale PCa dataset containing 10,516 whole slide scans (with around 71.7M patches), where it outperforms state-of-the-art schemes by 3.22% (in terms of mean intersection-over-union) for extracting the Gleason tissues and 6.91% (in terms of F1 score) for grading the progression of PCa.
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.
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
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