OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials

Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning potentials. Arbitrary PyTorch models can be added to a simulation and used to compute forces and energy. A higher-level interface allows users to easily model their molecules of interest with general purpose, pretrained potential functions. A collection of optimized CUDA kernels and custom PyTorch operations greatly improves the speed of simulations. We demonstrate these features on simulations of cyclin-dependent kinase 8 (CDK8) and the green fluorescent protein (GFP) chromophore in water. Taken together, these features make it practical to use machine learning to improve the accuracy of simulations at only a modest increase in cost.

Texture and Color-based Image Retrieval Using the Local Extrema Features and Riemannian Distance

A novel efficient method for content-based image retrieval (CBIR) is developed in this paper using both texture and color features. Our motivation is to represent and characterize an input image by a set of local descriptors extracted at characteristic points (i.e. keypoints) within the image. Then, dissimilarity measure between images is calculated based on the geometric distance between the topological feature spaces (i.e. manifolds) formed by the sets of local descriptors generated from these images. In this work, we propose to extract and use the local extrema pixels as our feature points. Then, the so-called local extrema-based descriptor (LED) is generated for each keypoint by integrating all color, spatial as well as gradient information captured by a set of its nearest local extrema. Hence, each image is encoded by a LED feature point cloud and riemannian distances between these point clouds enable us to tackle CBIR. Experiments performed on Vistex, Stex and colored Brodatz texture databases using the proposed approach provide very efficient and competitive results compared to the state-of-the-art methods.