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 corresponding output labels. In computer vision, image augmentations have become a common implicit regularization technique to combat overfitting in deep learning models and are ubiquitously used to improve performance. While most deep learning frameworks implement basic image transformations, the list is typically limited to some variations of flipping, rotating, scaling, and cropping. Moreover, image processing speed varies in existing image augmentation libraries. We present Albumentations, a fast and flexible open source library for image augmentation with many various image transform operations available that is also an easy-to-use wrapper around other augmentation libraries. We discuss the design principles that drove the implementation of Albumentations and give an overview of the key features and distinct capabilities. Finally, we provide examples of image augmentations for different computer vision tasks and demonstrate that Albumentations is faster than other commonly used image augmentation tools on most image transform operations.

Deep learning describes a class of machine learning algorithms that are capable of combining raw inputs into layers of intermediate features. These algorithms have recently shown impressive results across a variety of domains. Biology and medicine are data-rich disciplines, but the data are complex and often ill-understood. Hence, deep learning techniques may be particularly well suited to solve problems of these fields. We examine applications of deep learning to a variety of biomedical problems—patient classification, fundamental biological processes and treatment of patients—and discuss whether deep learning will be able to transform these tasks or if the biomedical sphere poses unique challenges. Following from an extensive literature review, we find that deep learning has yet to revolutionize biomedicine or definitively resolve any of the most pressing challenges in the field, but promising advances have been made on the prior state of the art. Even though improvements over previous baselines have been modest in general, the recent progress indicates that deep learning methods will provide valuable means for speeding up or aiding human investigation. Though progress has been made linking a specific neural network's prediction to input features, understanding how users should interpret these models to make testable hypotheses about the system under study remains an open challenge. Furthermore, the limited amount of labelled data for training presents problems in some domains, as do legal and privacy constraints on work with sensitive health records. Nonetheless, we foresee deep learning enabling changes at both bench and bedside with the potential to transform several areas of biology and medicine.

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 deep learning-based approach for robotic instrument segmentation. Our approach demonstrates an improvement over the state-of-the-art results using several 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 address a multi-class segmentation problem, in which we distinguish between different instruments or different parts of an instrument from the background. In this setting, our approach outperforms other methods for automatic instrument segmentation 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/robot-surgery-segmentation.

The identification of genetic and chemical perturbations with similar impacts on cell morphology can elucidate compounds’ mechanisms of action or novel regulators of genetic pathways. Research on methods for identifying such similarities has lagged due to a lack of carefully designed and well-annotated image sets of cells treated with chemical and genetic perturbations. Here we create such a Resource dataset, CPJUMP1, in which each perturbed gene’s product is a known target of at least two chemical compounds in the dataset. We systematically explore the directionality of correlations among perturbations that target the same protein encoded by a given gene, and we find that identifying matches between chemical and genetic perturbations is a challenging task. Our dataset and baseline analyses provide a benchmark for evaluating methods that measure perturbation similarities and impact, and more generally, learn effective representations of cellular state from microscopy images. Such advancements would accelerate the applications of image-based profiling of cellular states, such as uncovering drug mode of action or probing functional genomics.

This Perspective provides examples of current and future applications of deep learning in pharmacogenomics, including: identification of novel regulatory variants located in noncoding domains of the genome and their function as applied to pharmacoepigenomics; patient stratification from medical records; and the mechanistic prediction of drug response, targets and their interactions. Deep learning encapsulates a family of machine learning algorithms that has transformed many important subfields of artificial intelligence over the last decade, 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.