Nuclear Magnetic Resonance (NMR) Spectroscopy is a widely used technique to predict the native structure of proteins. However, NMR machines are only able to report approximate and partial distances between pair of atoms. To build the protein structure one has to solve the Euclidean distance geometry problem given the incomplete interval distance data produced by NMR machines. In this paper, we propose a new genetic algorithm for solving the Euclidean distance geometry problem for protein structure prediction given sparse NMR data. Our genetic algorithm uses a greedy mutation operator to intensify the search, a twin removal technique for diversification in the population and a random restart method to recover stagnation. On a standard set of benchmark dataset, our algorithm significantly outperforms standard genetic algorithms.
Among the general purpose methods, spatial branch and bound @cite_0 and variable neighborhood search (VNS) @cite_15 methods are not scalable @cite_3 . Smoothing based methods like DGSOL @cite_2 @cite_5 also fail for large instances of the problem. In @cite_1 , VNS was combined with DGSOL approaches which provided better results for larger instances but resulted into a slow algorithm. A combinatorial build up algorithm was proposed in @cite_11 . It is important to note that all these methods were tested on dense instances only. Among other methods applied to this problem graph decomposition methods @cite_14 and NLP formulations @cite_18 are notable.
@cite_18 @cite_14 @cite_1 @cite_3 @cite_0 @cite_2 @cite_5 @cite_15 @cite_11
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We consider the necessary redistribution of bicycles in public bicycle sharing systems in order to avoid rental stations to run empty or entirely full. For this purpose we propose a general Variable Neighborhood Search (VNS) with an embedded Variable Neighborhood Descent (VND) that exploits a series of neighborhood structures. While this metaheuristic generates candidate routes for vehicles to visit unbalanced rental stations, the numbers of bikes to be loaded or unloaded at each stop are efficiently derived by one of three alternative methods based on a greedy heuristic, a maximum flow calculation, and linear programming, respectively. Tests are performed on instances derived from real-world data and indicate that the VNS based on a greedy heuristic represents the best compromise for practice. In general the VNS yields good solutions and scales much better to larger instances than two mixed integer programming approaches. Given a textual description of an image, phrase grounding localizes objects in the image referred by query phrases in the description. State-of-the-art methods address the problem by ranking a set of proposals based on the relevance to each query, which are limited by the performance of independent proposal generation systems and ignore useful cues from context in the description. In this paper, we adopt a spatial regression method to break the performance limit, and introduce reinforcement learning techniques to further leverage semantic context information. We propose a novel Query-guided Regression network with Context policy (QRC Net) which jointly learns a Proposal Generation Network (PGN), a Query-guided Regression Network (QRN) and a Context Policy Network (CPN). Experiments show QRC Net provides a significant improvement in accuracy on two popular datasets: Flickr30K Entities and Referit Game, with 14.25 and 17.14 increase over the state-of-the-arts respectively. The nearestor near-neighbor query problems arise in a large variety of database applications, usually in the context of similarity searching. Of late, there has been increasing interest in building search index structures for performing similarity search over high-dimensional data, e.g., image databases, document collections, time-series databases, and genome databases. Unfortunately, all known techniques for solving this problem fall prey to the of dimensionality." That is, the data structures scale poorly with data dimensionality; in fact, if the number of dimensions exceeds 10 to 20, searching in k-d trees and related structures involves the inspection of a large fraction of the database, thereby doing no better than brute-force linear search. It has been suggested that since the selection of features and the choice of a distance metric in typical applications is rather heuristic, determining an approximate nearest neighbor should su ce for most practical purposes. In this paper, we examine a novel scheme for approximate similarity search based on hashing. The basic idea is to hash the points Supported by NAVY N00014-96-1-1221 grant and NSF Grant IIS-9811904. Supported by Stanford Graduate Fellowship and NSF NYI Award CCR-9357849. Supported by ARO MURI Grant DAAH04-96-1-0007, NSF Grant IIS-9811904, and NSF Young Investigator Award CCR9357849, with matching funds from IBM, Mitsubishi, Schlumberger Foundation, Shell Foundation, and Xerox Corporation. Permission to copy without fee all or part of this material is granted provided that the copies are not made or distributed for direct commercial advantage, the VLDB copyright notice and the title of the publication and its date appear, and notice is given that copying is by permission of the Very Large Data Base Endowment. To copy otherwise, or to republish, requires a fee and or special permission from the Endowment. Proceedings of the 25th VLDB Conference, Edinburgh, Scotland, 1999. from the database so as to ensure that the probability of collision is much higher for objects that are close to each other than for those that are far apart. We provide experimental evidence that our method gives signi cant improvement in running time over other methods for searching in highdimensional spaces based on hierarchical tree decomposition. Experimental results also indicate that our scheme scales well even for a relatively large number of dimensions (more than 50). Large CNNs have delivered impressive performance in various computer vision applications. But the storage and computation requirements make it problematic for deploying these models on mobile devices. Recently, tensor decompositions have been used for speeding up CNNs. In this paper, we further develop the tensor decomposition technique. We propose a new algorithm for computing the low-rank tensor decomposition for removing the redundancy in the convolution kernels. The algorithm finds the exact global optimizer of the decomposition and is more effective than iterative methods. Based on the decomposition, we further propose a new method for training low-rank constrained CNNs from scratch. Interestingly, while achieving a significant speedup, sometimes the low-rank constrained CNNs delivers significantly better performance than their non-constrained counterparts. On the CIFAR-10 dataset, the proposed low-rank NIN model achieves @math accuracy (without data augmentation), which also improves upon state-of-the-art result. We evaluated the proposed method on CIFAR-10 and ILSVRC12 datasets for a variety of modern CNNs, including AlexNet, NIN, VGG and GoogleNet with success. For example, the forward time of VGG-16 is reduced by half while the performance is still comparable. Empirical success suggests that low-rank tensor decompositions can be a very useful tool for speeding up large CNNs.