High-content analysis has revolutionized cancer drug discovery by identifying substances that alter the phenotype of a cell, which prevents tumor growth and metastasis. The high-resolution biofluorescence images from assays allow precise quantitative measures enabling the distinction of small molecules of a host cell from a tumor. In this work, we are particularly interested in the application of deep neural networks (DNNs), a cutting-edge machine learning method, to the classification of compounds in chemical mechanisms of action (MOAs). Compound classification has been performed using image-based profiling methods sometimes combined with feature reduction methods such as principal component analysis or factor analysis. In this article, we map the input features of each cell to a particular MOA class without using any treatment-level profiles or feature reduction methods. To the best of our knowledge, this is the first application of DNN in this domain, leveraging single-cell information. Furthermore, we use deep transfer learning (DTL) to alleviate the intensive and computational demanding effort of searching the huge parameter's space of a DNN. Results show that using this approach, we obtain a 30% speedup and a 2% accuracy improvement.

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Abstract. Transfer Learning is a paradigm in machine learning to solve a target problem by reusing the learning with minor modifications from a different but related source problem. In this paper we propose a novel feature transference approach, especially when the source and the target problems are drawn from different distributions. We use deep neural networks to transfer either low or middle or higher-layer features for a machine trained in either unsupervised or supervised way. Applying this feature transference approach on Convolutional Neural Network and Stacked Denoising Autoencoder on four different datasets, we achieve lower classification error rate with significant reduction in computation time with lower-layer features trained in supervised way and higher-layer features trained in unsupervised way for classifying images of uppercase and lowercase letters dataset.