Exploration of Reaction Pathways and Chemical Transformation Networks

For the investigation of chemical reaction networks, the identification of all relevant intermediates and elementary reactions is mandatory. Many algorithmic approaches exist that perform explorations efficiently and automatedly. These approaches differ in their application range, the level of completeness of the exploration, as well as the amount of heuristics and human intervention required. Here, we describe and compare the different approaches based on these criteria. Future directions leveraging the strengths of chemical heuristics, human interaction, and physical rigor are discussed.Comment: 48 pages, 4 figure

Multi-agent evolutionary systems for the generation of complex virtual worlds

Modern films, games and virtual reality applications are dependent on convincing computer graphics. Highly complex models are a requirement for the successful delivery of many scenes and environments. While workflows such as rendering, compositing and animation have been streamlined to accommodate increasing demands, modelling complex models is still a laborious task. This paper introduces the computational benefits of an Interactive Genetic Algorithm (IGA) to computer graphics modelling while compensating the effects of user fatigue, a common issue with Interactive Evolutionary Computation. An intelligent agent is used in conjunction with an IGA that offers the potential to reduce the effects of user fatigue by learning from the choices made by the human designer and directing the search accordingly. This workflow accelerates the layout and distribution of basic elements to form complex models. It captures the designer's intent through interaction, and encourages playful discovery

An Efficient Algorithm for Automatic Structure Optimization in X-ray Standing-Wave Experiments

X-ray standing-wave photoemission experiments involving multilayered samples are emerging as unique probes of the buried interfaces that are ubiquitous in current device and materials research. Such data require for their analysis a structure optimization process comparing experiment to theory that is not straightforward. In this work, we present a new computer program for optimizing the analysis of standing-wave data, called SWOPT, that automates this trial-and-error optimization process. The program includes an algorithm that has been developed for computationally expensive problems: so-called black-box simulation optimizations. It also includes a more efficient version of the Yang X-ray Optics Program (YXRO) [Yang, S.-H., Gray, A.X., Kaiser, A.M., Mun, B.S., Sell, B.C., Kortright, J.B., Fadley, C.S., J. Appl. Phys. 113, 1 (2013)] which is about an order of magnitude faster than the original version. Human interaction is not required during optimization. We tested our optimization algorithm on real and hypothetical problems and show that it finds better solutions significantly faster than a random search approach. The total optimization time ranges, depending on the sample structure, from minutes to a few hours on a modern laptop computer, and can be up to 100x faster than a corresponding manual optimization. These speeds make the SWOPT program a valuable tool for realtime analyses of data during synchrotron experiments

Multi-body Non-rigid Structure-from-Motion

Conventional structure-from-motion (SFM) research is primarily concerned with the 3D reconstruction of a single, rigidly moving object seen by a static camera, or a static and rigid scene observed by a moving camera --in both cases there are only one relative rigid motion involved. Recent progress have extended SFM to the areas of {multi-body SFM} (where there are {multiple rigid} relative motions in the scene), as well as {non-rigid SFM} (where there is a single non-rigid, deformable object or scene). Along this line of thinking, there is apparently a missing gap of "multi-body non-rigid SFM", in which the task would be to jointly reconstruct and segment multiple 3D structures of the multiple, non-rigid objects or deformable scenes from images. Such a multi-body non-rigid scenario is common in reality (e.g. two persons shaking hands, multi-person social event), and how to solve it represents a natural {next-step} in SFM research. By leveraging recent results of subspace clustering, this paper proposes, for the first time, an effective framework for multi-body NRSFM, which simultaneously reconstructs and segments each 3D trajectory into their respective low-dimensional subspace. Under our formulation, 3D trajectories for each non-rigid structure can be well approximated with a sparse affine combination of other 3D trajectories from the same structure (self-expressiveness). We solve the resultant optimization with the alternating direction method of multipliers (ADMM). We demonstrate the efficacy of the proposed framework through extensive experiments on both synthetic and real data sequences. Our method clearly outperforms other alternative methods, such as first clustering the 2D feature tracks to groups and then doing non-rigid reconstruction in each group or first conducting 3D reconstruction by using single subspace assumption and then clustering the 3D trajectories into groups.Comment: 21 pages, 16 figure