CT Texture Analysis Challenges: Influence of Acquisition and Reconstruction Parameters: A Comprehensive Review.

Texture analysis in medical imaging is a promising tool that is designed to improve the characterization of abnormal images from patients, to ultimately serve as a predictive or prognostic biomarker. However, the nature of image acquisition itself implies variability in each pixel/voxel value that could jeopardize the usefulness of texture analysis in the medical field. In this review, a search was performed to identify current published data for computed tomography (CT) texture reproducibility and variability. On the basis of this analysis, the critical steps were identified with a view of using texture analysis as a reliable tool in medical imaging. The need to specify the CT scanners used and the associated parameters in published studies is highlighted. Harmonizing acquisition parameters between studies is a crucial step for future texture analysis.

Protein model quality assessment using 3D oriented convolutional neural networks.

MOTIVATION: Protein model quality assessment (QA) is a crucial and yet open problem in structural bioinformatics. The current best methods for single-model QA typically combine results from different approaches, each based on different input features constructed by experts in the field. Then, the prediction model is trained using a machine-learning algorithm. Recently, with the development of convolutional neural networks (CNN), the training paradigm has changed. In computer vision, the expert-developed features have been significantly overpassed by automatically trained convolutional filters. This motivated us to apply a three-dimensional (3D) CNN to the problem of protein model QA. RESULTS: We developed Ornate (Oriented Routed Neural network with Automatic Typing)-a novel method for single-model QA. Ornate is a residue-wise scoring function that takes as input 3D density maps. It predicts the local (residue-wise) and the global model quality through a deep 3D CNN. Specifically, Ornate aligns the input density map, corresponding to each residue and its neighborhood, with the backbone topology of this residue. This circumvents the problem of ambiguous orientations of the initial models. Also, Ornate includes automatic identification of atom types and dynamic routing of the data in the network. Established benchmarks (CASP 11 and CASP 12) demonstrate the state-of-the-art performance of our approach among single-model QA methods. AVAILABILITY AND IMPLEMENTATION: The method is available at https://team.inria.fr/nano-d/software/Ornate/. It consists of a C++ executable that transforms molecular structures into volumetric density maps, and a Python code based on the TensorFlow framework for applying the Ornate model to these maps. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.