5717822
A family competition evolutionary algorithm for automated docking of flexible ligands to proteins
We study an evolutionary algorithm for flexible ligand docking. Based on family competition and adaptive rules, the proposed approach consists of global and local strategies by integrating decreasing mutations and self-adaptive mutations. To demonstrate the robustness of the proposed approach, we apply it to the problems of the first international contests on evolutionary optimization. Following the description of function optimization, our approach is applied to a dihydrofolate reductase enzyme with the anti-cancer drug methotrexate and with two analogs of the antibacterial drug trimethoprim. Our numerical results indicate that the proposed approach is robust. The docked lowest energy structures have rms derivations ranging from 0.72 A to 1.98 A with respect to the corresponding crystal structure.
32059093
A Genetic Algorithm for Physical Mapping Problems
In this paper, we study a genetic algorithm for solving physical mapping problem. First, the physical mapping problem is transferred to an optimization problem by incorporating biological knowledge and limitations into the objective function. Based on the idea of genetic algorithms, the proposed approach integrates Edge Assembly Crossover (EAX) and Inver-over genetic operators to get the optimal solution. We analyze essential components of the proposed approach as well as implementation details. Our approach is then applied to some widely used test sets and simulated data, real data of this problem. Experimental results indicate that the new approach performs efficiently and precisely to solve physical mapping problem.
5502812
A Continuous Genetic Algorithm for Global Optimization
40205984
A Robust Evolutionary Algorithm for Training Neural Networks
A new evolutionary algorithm is introduced for training both feedforward and recurrent neural networks. The proposed approach, called the Family Competition Evolutionary Algorithm (FCEA), automatically achieves the balance of the solution quality and convergence speed by integrating multiple mutations, family competition and adaptive rules. We experimentally analyse the proposed approach by showing that its components can cooperate with one another, and possess good local and global properties. Following the description of implementation details, our approach is then applied to several benchmark problems, including an artificial ant problem, parity problems and a two-spiral problem. Experimental results indicate that the new approach is able to stably solve these problems, and is very competitive with the comparative evolutionary algorithms.
7776820
Scalable continuous query processing by tracking hotspots
This paper considers the problem of scalably processing a large number of continuous queries. We propose a flexible framework with novel data structures and algorithms for group-processing and indexing continuous queries by exploiting potential overlaps in query predicates. Our approach partitions the collection of continuous queries into groups based on the clustering patterns of the query ranges, and then applies specialized processing strategies to those heavily-clustered groups (or hotspots). To maintain the partition dynamically, we present efficient algorithms that maintain a nearly optimal partition in nearly amortized logarithmic time. We show how to use the hotspots to scalably process large numbers of continuous select-join and band-join queries, which are much more challenging than simple range selection queries. Experiments demonstrate that this approach can improve the processing throughput by orders of magnitude. As another application of hotspots, we show how to use them to build a high-quality histogram for intervals in linear time.
3829528
Dynamically inferring temporal properties
Model checking requires a specification of the target system's desirable properties, some of which are temporal. Formulating a temporal property of the system based on either its abstract model or implementation requires a deep understanding of its behavior and sophisticated knowledge of the chosen formalism. This has been a major impediment to documenting and verifying temporal properties. We propose a dynamic approach to automatically infer a program's temporal properties based on a set of property pattern templates. We describe a preliminary implementation of this approach, and report on our experience using it to discover interesting temporal properties of a small program.
368438
Perracotta: mining temporal API rules from imperfect traces
Dynamic inference techniques have been demonstrated to provide useful support for various software engineering tasks including bug finding, test suite evaluation and improvement, and specification generation. To date, however, dynamic inference has only been used effectively on small programs under controlled conditions. In this paper, we identify reasons why scaling dynamic inference techniques has proven difficult, and introduce solutions that enable a dynamic inference technique to scale to large programs and work effectively with the imperfect traces typically available in industrial scenarios. We describe our approximate inference algorithm, present and evaluate heuristics for winnowing the large number of inferred properties to a manageable set of interesting properties, and report on experiments using inferred properties. We evaluate our techniques on JBoss and the Windows kernel. Our tool is able to infer many of the properties checked by the Static Driver Verifier and leads us to discover a previously unknown bug in Windows.
388734
A statistical signal processing approach to image fusion for concealed weapon detection
A statistical signal processing approach to multisensor image fusion is presented for concealed weapon detection (CWD). This approach is based on an image formation model in which the sensor images are described as the true scene corrupted by additive non-Gaussian distortion. The expectation-maximization (EM) algorithm is used to estimate the model parameters and the fused image. We demonstrate the efficiency of this approach by applying this method to fusion of visual and non-visual images with emphasis on CWD applications.
1498767
Clustering by pattern similarity in large data sets
Clustering is the process of grouping a set of objects into classes of similar objects. Although definitions of similarity vary from one clustering model to another, in most of these models the concept of similarity is based on distances, e.g., Euclidean distance or cosine distance. In other words, similar objects are required to have close values on at least a set of dimensions. In this paper, we explore a more general type of similarity. Under the pCluster model we proposed, two objects are similar if they exhibit a coherent pattern on a subset of dimensions. For instance, in DNA microarray analysis, the expression levels of two genes may rise and fall synchronously in response to a set of environmental stimuli. Although the magnitude of their expression levels may not be close, the patterns they exhibit can be very much alike. Discovery of such clusters of genes is essential in revealing significant connections in gene regulatory networks. E-commerce applications, such as collaborative filtering, can also benefit from the new model, which captures not only the closeness of values of certain leading indicators but also the closeness of (purchasing, browsing, etc.) patterns exhibited by the customers. Our paper introduces an effective algorithm to detect such clusters, and we perform tests on several real and synthetic data sets to show its effectiveness.