Semantic segmentation of robotic instruments is an important problem for the robot-assisted surgery. One of the main challenges is to correctly detect an instrument's position for the tracking and pose estimation in the vicinity of surgical scenes. Accurate pixel-wise instrument segmentation is needed to address this challenge. In this paper we describe our winning solution for MICCAI 2017 Endoscopic Vision SubChallenge: Robotic Instrument Segmentation. Our approach demonstrates an improvement over the state-of-the-art results using several novel deep neural network architectures. It addressed the binary segmentation problem, where every pixel in an image is labeled as an instrument or background from the surgery video feed. In addition, we solve a multi-class segmentation problem, where we distinguish different instruments or different parts of an instrument from the background. In this setting, our approach outperforms other methods in every task subcategory for automatic instrument segmentation thereby providing state-of-the-art solution for this problem. The source code for our solution is made publicly available at https://github.com/ternaus/robot-surgery-segmentation

* 9 pages, 3 figures. arXiv admin note: substantial text overlap with arXiv:1804.08024
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Accurate detection and localization for angiodysplasia lesions is an important problem in early stage diagnostics of gastrointestinal bleeding and anemia. Gold-standard for angiodysplasia detection and localization is performed using wireless capsule endoscopy. This pill-like device is able to produce thousand of high enough resolution images during one passage through gastrointestinal tract. In this paper we present our winning solution for MICCAI 2017 Endoscopic Vision SubChallenge: Angiodysplasia Detection and Localization its further improvements over the state-of-the-art results using several novel deep neural network architectures. It address the binary segmentation problem, where every pixel in an image is labeled as an angiodysplasia lesions or background. Then, we analyze connected component of each predicted mask. Based on the analysis we developed a classifier that predict angiodysplasia lesions (binary variable) and a detector for their localization (center of a component). In this setting, our approach outperforms other methods in every task subcategory for angiodysplasia detection and localization thereby providing state-of-the-art results for these problems. The source code for our solution is made publicly available at https://github.com/ternaus/angiodysplasia-segmentatio

* 12 pages, 6 figures
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Breast cancer is one of the main causes of cancer death worldwide. Early diagnostics significantly increases the chances of correct treatment and survival, but this process is tedious and often leads to a disagreement between pathologists. Computer-aided diagnosis systems showed potential for improving the diagnostic accuracy. In this work, we develop the computational approach based on deep convolution neural networks for breast cancer histology image classification. Hematoxylin and eosin stained breast histology microscopy image dataset is provided as a part of the ICIAR 2018 Grand Challenge on Breast Cancer Histology Images. Our approach utilizes several deep neural network architectures and gradient boosted trees classifier. For 4-class classification task, we report 87.2% accuracy. For 2-class classification task to detect carcinomas we report 93.8% accuracy, AUC 97.3%, and sensitivity/specificity 96.5/88.0% at the high-sensitivity operating point. To our knowledge, this approach outperforms other common methods in automated histopathological image classification. The source code for our approach is made publicly available at https://github.com/alexander-rakhlin/ICIAR2018

* 8 pages, 4 figures
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Data augmentation is a commonly used technique for increasing both the size and the diversity of labeled training sets by leveraging input transformations that preserve output labels. In computer vision domain, image augmentations have become a common implicit regularization technique to combat overfitting in deep convolutional neural networks and are ubiquitously used to improve performance. While most deep learning frameworks implement basic image transformations, the list is typically limited to some variations and combinations of flipping, rotating, scaling, and cropping. Moreover, the image processing speed varies in existing tools for image augmentation. We present Albumentations, a fast and flexible library for image augmentations with many various image transform operations available, that is also an easy-to-use wrapper around other augmentation libraries. We provide examples of image augmentations for different computer vision tasks and show that Albumentations is faster than other commonly used image augmentation tools on the most of commonly used image transformations. The source code for Albumentations is made publicly available online at https://github.com/albu/albumentations

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Neural network-based methods for image processing are becoming widely used in practical applications. Modern neural networks are computationally expensive and require specialized hardware, such as graphics processing units. Since such hardware is not always available in real life applications, there is a compelling need for the design of neural networks for mobile devices. Mobile neural networks typically have reduced number of parameters and require a relatively small number of arithmetic operations. However, they usually still are executed at the software level and use floating-point calculations. The use of mobile networks without further optimization may not provide sufficient performance when high processing speed is required, for example, in real-time video processing (30 frames per second). In this study, we suggest optimizations to speed up computations in order to efficiently use already trained neural networks on a mobile device. Specifically, we propose an approach for speeding up neural networks by moving computation from software to hardware and by using fixed-point calculations instead of floating-point. We propose a number of methods for neural network architecture design to improve the performance with fixed-point calculations. We also show an example of how existing datasets can be modified and adapted for the recognition task in hand. Finally, we present the design and the implementation of a floating-point gate array-based device to solve the practical problem of real-time handwritten digit classification from mobile camera video feed.

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This Perspective provides examples of current and future applications of deep learning in pharmacogenomics, including: (1) identification of novel regulatory variants located in noncoding domains and their function as applied to pharmacoepigenomics; (2) patient stratification from medical records; and (3) prediction of drugs, targets, and their interactions. Deep learning encapsulates a family of machine learning algorithms that over the last decade has transformed many important subfields of artificial intelligence (AI) and has demonstrated breakthrough performance improvements on a wide range of tasks in biomedicine. We anticipate that in the future deep learning will be widely used to predict personalized drug response and optimize medication selection and dosing, using knowledge extracted from large and complex molecular, epidemiological, clinical, and demographic datasets.

* Alexandr A. Kalinin and Gerald A. Higgins contributed equally to this work. Corresponding author: Brian D. Athey, <bleu@umich.edu>
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