MOTIVATION: Accurately predicting protein secondary structure and relative solvent accessibility is important for the study of protein evolution, structure and an early-stage component of typical protein 3D structure prediction pipelines. RESULTS: We present a new improved version of the SSpro/ACCpro suite of predictors for the prediction of protein secondary structure (in three and eight classes) and relative solvent accessibility. The changes include improved, TensorFlow-trained, deep learning predictors, a richer set of profile features (232 features per residue position) and sequence-only features (71 features per position), a more recent Protein Data Bank (PDB) snapshot for training, better hyperparameter tuning and improvements made to the HOMOLpro module, which leverages structural information from protein segment homologs in the PDB. The new SSpro 6 outperforms the previous version (SSpro 5) by 3-4% in Q3 accuracy and, when used with HOMOLPRO, reaches accuracy in the 95-100% range. AVAILABILITY AND IMPLEMENTATION: The predictors' software, data and web servers are available through the SCRATCH suite of protein structure predictors at http://scratch.proteomics.ics.uci.edu. To maximize comptatibility and ease of use, the deep learning predictors are re-implemented as pure Python/numpy code without TensorFlow dependency. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Likely drug candidates which are identified in traditional pre-clinical drug screens often fail in patient trials, increasing the societal burden of drug discovery. A major contributing factor to this phenomenon is the failure of traditional in vitro models of drug response to accurately mimic many of the more complex properties of human biology. We have recently introduced a new microphysiological system for growing vascularized, perfused microtissues that more accurately models human physiology and is suitable for large drug screens. In this work, we develop a machine learning model that can quickly and accurately flag compounds which effectively disrupt vascular networks from images taken before and after drug application in vitro. The system is based on a convolutional neural network and achieves near perfect accuracy while committing potentially no expensive false negatives.

Deep neural networks have achieved great successes on various machine learning tasks, however, there are many open fundamental questions to be answered. In this paper, we tackle the problem of quantifying the quality of learned wights of different networks with possibly different architectures, going beyond considering the final classification error as the only metric. We introduce \emphExtended Data Jacobian Matrix to help analyze properties of networks of various structures, finding that, the spectrum of the extended data jacobian matrix is a strong discriminating factor for networks of different structures and performance. Based on such observation, we propose a novel regularization method, which manages to improve the network performance comparably to dropout, which in turn verifies the observation.