Y-Net: Joint Segmentation and Classification for Diagnosis of Breast Biopsy Images

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-Net's 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.

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.