First-principles molecular structure search with a genetic algorithm

The identification of low-energy conformers for a given molecule is a fundamental problem in computational chemistry and cheminformatics. We assess here a conformer search that employs a genetic algorithm for sampling the low-energy segment of the conformation space of molecules. The algorithm is designed to work with first-principles methods, facilitated by the incorporation of local optimization and blacklisting conformers to prevent repeated evaluations of very similar solutions. The aim of the search is not only to find the global minimum, but to predict all conformers within an energy window above the global minimum. The performance of the search strategy is: (i) evaluated for a reference data set extracted from a database with amino acid dipeptide conformers obtained by an extensive combined force field and first-principles search and (ii) compared to the performance of a systematic search and a random conformer generator for the example of a drug-like ligand with 43 atoms, 8 rotatable bonds and 1 cis/trans bond

Improved decision support for engine-in-the-loop experimental design optimization

Experimental optimization with hardware in the loop is a common procedure in engineering and has been the subject of intense development, particularly when it is applied to relatively complex combinatorial systems that are not completely understood, or where accurate modelling is not possible owing to the dimensions of the search space. A common source of difficulty arises because of the level of noise associated with experimental measurements, a combination of limited instrument precision, and extraneous factors. When a series of experiments is conducted to search for a combination of input parameters that results in a minimum or maximum response, under the imposition of noise, the underlying shape of the function being optimized can become very difficult to discern or even lost. A common methodology to support experimental search for optimal or suboptimal values is to use one of the many gradient descent methods. However, even sophisticated and proven methodologies, such as simulated annealing, can be significantly challenged in the presence of noise, since approximating the gradient at any point becomes highly unreliable. Often, experiments are accepted as a result of random noise which should be rejected, and vice versa. This is also true for other sampling techniques, including tabu and evolutionary algorithms. After the general introduction, this paper is divided into two main sections (sections 2 and 3), which are followed by the conclusion. Section 2 introduces a decision support methodology based upon response surfaces, which supplements experimental management based on a variable neighbourhood search and is shown to be highly effective in directing experiments in the presence of a significant signal-to-noise ratio and complex combinatorial functions. The methodology is developed on a three-dimensional surface with multiple local minima, a large basin of attraction, and a high signal-to-noise ratio. In section 2, the methodology is applied to an automotive combinatorial search in the laboratory, on a real-time engine-in-the-loop application. In this application, it is desired to find the maximum power output of an experimental single-cylinder spark ignition engine operating under a quasi-constant-volume operating regime. Under this regime, the piston is slowed at top dead centre to achieve combustion in close to constant volume conditions. As part of the further development of the engine to incorporate a linear generator to investigate free-piston operation, it is necessary to perform a series of experiments with combinatorial parameters. The objective is to identify the maximum power point in the least number of experiments in order to minimize costs. This test programme provides peak power data in order to achieve optimal electrical machine design. The decision support methodology is combined with standard optimization and search methods – namely gradient descent and simulated annealing – in order to study the reductions possible in experimental iterations. It is shown that the decision support methodology significantly reduces the number of experiments necessary to find the maximum power solution and thus offers a potentially significant cost saving to hardware-in-the-loop experi- mentation

Online games: a novel approach to explore how partial information influences human random searches

Many natural processes rely on optimizing the success ratio of a search process. We use an experimental setup consisting of a simple online game in which players have to find a target hidden on a board, to investigate the how the rounds are influenced by the detection of cues. We focus on the search duration and the statistics of the trajectories traced on the board. The experimental data are explained by a family of random-walk-based models and probabilistic analytical approximations. If no initial information is given to the players, the search is optimized for cues that cover an intermediate spatial scale. In addition, initial information about the extension of the cues results, in general, in faster searches. Finally, strategies used by informed players turn into non-stationary processes in which the length of each displacement evolves to show a well-defined characteristic scale that is not found in non-informed searches.Comment: 17 pages, 10 figure

Convolutional neural networks: a magic bullet for gravitational-wave detection?

In the last few years, machine learning techniques, in particular convolutional neural networks, have been investigated as a method to replace or complement traditional matched filtering techniques that are used to detect the gravitational-wave signature of merging black holes. However, to date, these methods have not yet been successfully applied to the analysis of long stretches of data recorded by the Advanced LIGO and Virgo gravitational-wave observatories. In this work, we critically examine the use of convolutional neural networks as a tool to search for merging black holes. We identify the strengths and limitations of this approach, highlight some common pitfalls in translating between machine learning and gravitational-wave astronomy, and discuss the interdisciplinary challenges. In particular, we explain in detail why convolutional neural networks alone cannot be used to claim a statistically significant gravitational-wave detection. However, we demonstrate how they can still be used to rapidly flag the times of potential signals in the data for a more detailed follow-up. Our convolutional neural network architecture as well as the proposed performance metrics are better suited for this task than a standard binary classifications scheme. A detailed evaluation of our approach on Advanced LIGO data demonstrates the potential of such systems as trigger generators. Finally, we sound a note of caution by constructing adversarial examples, which showcase interesting "failure modes" of our model, where inputs with no visible resemblance to real gravitational-wave signals are identified as such by the network with high confidence.Comment: First two authors contributed equally; appeared at Phys. Rev.

Scaling Monte Carlo Tree Search on Intel Xeon Phi

Many algorithms have been parallelized successfully on the Intel Xeon Phi coprocessor, especially those with regular, balanced, and predictable data access patterns and instruction flows. Irregular and unbalanced algorithms are harder to parallelize efficiently. They are, for instance, present in artificial intelligence search algorithms such as Monte Carlo Tree Search (MCTS). In this paper we study the scaling behavior of MCTS, on a highly optimized real-world application, on real hardware. The Intel Xeon Phi allows shared memory scaling studies up to 61 cores and 244 hardware threads. We compare work-stealing (Cilk Plus and TBB) and work-sharing (FIFO scheduling) approaches. Interestingly, we find that a straightforward thread pool with a work-sharing FIFO queue shows the best performance. A crucial element for this high performance is the controlling of the grain size, an approach that we call Grain Size Controlled Parallel MCTS. Our subsequent comparing with the Xeon CPUs shows an even more comprehensible distinction in performance between different threading libraries. We achieve, to the best of our knowledge, the fastest implementation of a parallel MCTS on the 61 core Intel Xeon Phi using a real application (47 relative to a sequential run).Comment: 8 pages, 9 figure

Fast micro-differential evolution for topological active net optimization

This paper studies the optimization problem of topological active net (TAN), which is often seen in image segmentation and shape modeling. A TAN is a topological structure containing many nodes, whose positions must be optimized while a predefined topology needs to be maintained. TAN optimization is often time-consuming and even constructing a single solution is hard to do. Such a problem is usually approached by a ``best improvement local search'' (BILS) algorithm based on deterministic search (DS), which is inefficient because it spends too much efforts in nonpromising probing. In this paper, we propose the use of micro-differential evolution (DE) to replace DS in BILS for improved directional guidance. The resultant algorithm is termed deBILS. Its micro-population efficiently utilizes historical information for potentially promising search directions and hence improves efficiency in probing. Results show that deBILS can probe promising neighborhoods for each node of a TAN. Experimental tests verify that deBILS offers substantially higher search speed and solution quality not only than ordinary BILS, but also the genetic algorithm and scatter search algorithm