Deep learning (DL) methods have gained considerable attention since 2014. In this chapter we briefly review the state of the art in DL and then give several examples of applications from diverse areas of application. We will focus on convolutional neural networks (CNNs), which have since the seminal work of Krizhevsky et al. (2012) revolutionized image classification and even started surpassing human performance on some benchmark data sets (Ciresan et al., 2012a, He et al., 2015a). While deep neural networks have become popular primarily for image classification tasks, they can also be successfully applied to other areas and problems with some local structure in the data. We will first present a classical application of CNNs on image-like data, in particular, phenotype classification of cells based on their morphology, and then extend the task to clustering voices based on their spectrograms. Next, we will describe DL applications to semantic segmentation of newspaper pages into their corresponding articles based on clues in the pixels, and outlier detection in a predictive maintenance setting. We conclude by giving advice on how to work with DL having limited resources (e.g., training data).

Deep convolutional neural networks show outstanding performance in image-based phenotype classification given that all existing phenotypes are presented during the training of the network. However, in real-world high-content screening (HCS) experiments, it is often impossible to know all phenotypes in advance. Moreover, novel phenotype discovery itself can be an HCS outcome of interest. This aspect of HCS is not yet covered by classical deep learning approaches. When presenting an image with a novel phenotype to a trained network, it fails to indicate a novelty discovery but assigns the image to a wrong phenotype. To tackle this problem and address the need for novelty detection, we use a recently developed Bayesian approach for deep neural networks called Monte Carlo (MC) dropout to define different uncertainty measures for each phenotype prediction. With real HCS data, we show that these uncertainty measures allow us to identify novel or unclear phenotypes. In addition, we also found that the MC dropout method results in a significant improvement of classification accuracy. The proposed procedure used in our HCS case study can be easily transferred to any existing network architecture and will be beneficial in terms of accuracy and novelty detection.

Deep Learning has boosted artificial intelligence over the past 5 years and is seen now as one of the major technological innovation areas, predicted to replace lots of repetitive, but complex tasks of human labor within the next decade. It is also expected to be 'game changing' for research activities in pharma and life sciences, where large sets of similar yet complex data samples are systematically analyzed. Deep learning is currently conquering formerly expert domains especially in areas requiring perception, previously not amenable to standard machine learning. A typical example is the automated analysis of images which are typically produced en-masse in many domains, e. g., in high-content screening or digital pathology. Deep learning enables to create competitive applications in so-far defined core domains of 'human intelligence'. Applications of artificial intelligence have been enabled in recent years by (i) the massive availability of data samples, collected in pharma driven drug programs (='big data') as well as (ii) deep learning algorithmic advancements and (iii) increase in compute power. Such applications are based on software frameworks with specific strengths and weaknesses. Here, we introduce typical applications and underlying frameworks for deep learning with a set of practical criteria for developing production ready solutions in life science and pharma research. Based on our own experience in successfully developing deep learning applications we provide suggestions and a baseline for selecting the most suited frameworks for a future-proof and cost-effective development.