Optimal clone identifier based on dynamic rules and process algebra

The rule creation to clone selection in different projects is a hard task to perform by using traditional implementations to control all the processes of the system. The use of an algebraic language is an alternative approach to manage all of system flow in a flexible way. In order to increase the power of versatility and consistency in defining the rules for optimal clone selection, this paper presents the software OCI 2 in which uses process algebra in the flow behavior of the system. OCI 2, controlled by an algebraic approach was applied in the rules elaboration for clone selection containing unique genes in the partial genome of the bacterium Bradyrhizobium elkanii Semia 587 and in the whole genome of the bacterium Xanthomonas axonopodis pv. citri. Copyright© (2009) by the International Society for Research in Science and Technology.

SKPDB: A structural database of shikimate pathway enzymes

Background: The functional and structural characterisation of enzymes that belong to microbial metabolic pathways is very important for structure-based drug design. The main interest in studying shikimate pathway enzymes involves the fact that they are essential for bacteria but do not occur in humans, making them selective targets for design of drugs that do not directly impact humans.Description: The ShiKimate Pathway DataBase (SKPDB) is a relational database applied to the study of shikimate pathway enzymes in microorganisms and plants. The current database is updated regularly with the addition of new data; there are currently 8902 enzymes of the shikimate pathway from different sources. The database contains extensive information on each enzyme, including detailed descriptions about sequence, references, and structural and functional studies. All files (primary sequence, atomic coordinates and quality scores) are available for downloading. The modeled structures can be viewed using the Jmol program.Conclusions: The SKPDB provides a large number of structural models to be used in docking simulations, virtual screening initiatives and drug design. It is freely accessible at http://lsbzix.rc.unesp.br/skpdb/. © 2010 Arcuri et al; licensee BioMed Central Ltd.

Fast automatic microstructural segmentation of ferrous alloy samples using optimum-path forest

In this work we propose a novel automatic cast iron segmentation approach based on the Optimum-Path Forest classifier (OPF). Microscopic images from nodular, gray and malleable cast irons are segmented using OPF, and Support Vector Machines (SVM) with Radial Basis Function and SVM without kernel mapping. Results show accurate and fast segmented images, in which OPF outperformed SVMs. Our work is the first into applying OPF for automatic cast iron segmentation. © 2010 Springer-Verlag.

Swarm control designs applied to a micro-electro-mechanical gyroscope system (MEMS)

This paper analyzes the non-linear dynamics of a MEMS Gyroscope system, modeled with a proof mass constrained to move in a plane with two resonant modes, which are nominally orthogonal. The two modes are ideally coupled only by the rotation of the gyro about the plane's normal vector. We demonstrated that this model has an unstable behavior. Control problems consist of attempts to stabilize a system to an equilibrium point, a periodic orbit, or more general, about a given reference trajectory. We also developed a particle swarm optimization technique for reducing the oscillatory movement of the nonlinear system to a periodic orbit. © 2010 Springer-Verlag.

Improving the accuracy of the optimum-path forest supervised classifier for large datasets

In this work, a new approach for supervised pattern recognition is presented which improves the learning algorithm of the Optimum-Path Forest classifier (OPF), centered on detection and elimination of outliers in the training set. Identification of outliers is based on a penalty computed for each sample in the training set from the corresponding number of imputable false positive and false negative classification of samples. This approach enhances the accuracy of OPF while still gaining in classification time, at the expense of a slight increase in training time. © 2010 Springer-Verlag.

Selecting candidate labels for hierarchical document clusters using association rules

One way to organize knowledge and make its search and retrieval easier is to create a structural representation divided by hierarchically related topics. Once this structure is built, it is necessary to find labels for each of the obtained clusters. In many cases the labels have to be built using only the terms in the documents of the collection. This paper presents the SeCLAR (Selecting Candidate Labels using Association Rules) method, which explores the use of association rules for the selection of good candidates for labels of hierarchical document clusters. The candidates are processed by a classical method to generate the labels. The idea of the proposed method is to process each parent-child relationship of the nodes as an antecedent-consequent relationship of association rules. The experimental results show that the proposed method can improve the precision and recall of labels obtained by classical methods. © 2010 Springer-Verlag.

Statistical model applied to NetFlow for network intrusion detection

The computers and network services became presence guaranteed in several places. These characteristics resulted in the growth of illicit events and therefore the computers and networks security has become an essential point in any computing environment. Many methodologies were created to identify these events; however, with increasing of users and services on the Internet, many difficulties are found in trying to monitor a large network environment. This paper proposes a methodology for events detection in large-scale networks. The proposal approaches the anomaly detection using the NetFlow protocol, statistical methods and monitoring the environment in a best time for the application. © 2010 Springer-Verlag Berlin Heidelberg.

The Poisson-exponential lifetime distribution

In this paper we proposed a new two-parameters lifetime distribution with increasing failure rate. The new distribution arises on a latent complementary risk problem base. The properties of the proposed distribution are discussed, including a formal proof of its probability density function and explicit algebraic formulae for its reliability and failure rate functions, quantiles and moments, including the mean and variance. A simple EM-type algorithm for iteratively computing maximum likelihood estimates is presented. The Fisher information matrix is derived analytically in order to obtaining the asymptotic covariance matrix. The methodology is illustrated on a real data set. © 2010 Elsevier B.V. All rights reserved.

Precipitates segmentation from scanning electron microscope images through machine learning techniques

The presence of precipitates in metallic materials affects its durability, resistance and mechanical properties. Hence, its automatic identification by image processing and machine learning techniques may lead to reliable and efficient assessments on the materials. In this paper, we introduce four widely used supervised pattern recognition techniques to accomplish metallic precipitates segmentation in scanning electron microscope images from dissimilar welding on a Hastelloy C-276 alloy: Support Vector Machines, Optimum-Path Forest, Self Organizing Maps and a Bayesian classifier. Experimental results demonstrated that all classifiers achieved similar recognition rates with good results validated by an expert in metallographic image analysis. © 2011 Springer-Verlag Berlin Heidelberg.

Improving accuracy and speed of optimum-path forest classifier using combination of disjoint training subsets

The Optimum-Path Forest (OPF) classifier is a recent and promising method for pattern recognition, with a fast training algorithm and good accuracy results. Therefore, the investigation of a combining method for this kind of classifier can be important for many applications. In this paper we report a fast method to combine OPF-based classifiers trained with disjoint training subsets. Given a fixed number of subsets, the algorithm chooses random samples, without replacement, from the original training set. Each subset accuracy is improved by a learning procedure. The final decision is given by majority vote. Experiments with simulated and real data sets showed that the proposed combining method is more efficient and effective than naive approach provided some conditions. It was also showed that OPF training step runs faster for a series of small subsets than for the whole training set. The combining scheme was also designed to support parallel or distributed processing, speeding up the procedure even more. © 2011 Springer-Verlag.

A graph-based framework for thermal faceprint characterization

Thermal faceprint has been paramount in the last years. Since we can handle with face recognition using images acquired in the infrared spectrum, an unique individual's signature can be obtained through the blood vessels network of the face. In this work, we propose a novel framework for thermal faceprint extraction using a collection of graph-based techniques, which were never used to this task up to date. A robust method of thermal face segmentation is also presented. The experiments, which were conducted over the UND Collection C dataset, have showed promising results. © 2011 Springer-Verlag.

Wavelets and decision trees for target detection over sea surface using cosmo-skymed SAR data

We are investigating the combination of wavelets and decision trees to detect ships and other maritime surveillance targets from medium resolution SAR images. Wavelets have inherent advantages to extract image descriptors while decision trees are able to handle different data sources. In addition, our work aims to consider oceanic features such as ship wakes and ocean spills. In this incipient work, Haar and Cohen-Daubechies-Feauveau 9/7 wavelets obtain detailed descriptors from targets and ocean features and are inserted with other statistical parameters and wavelets into an oblique decision tree. © 2011 Springer-Verlag.

LUTS: A lightweight user-level transaction scheduler

Software Transactional Memory (STM) systems have poor performance under high contention scenarios. Since many transactions compete for the same data, most of them are aborted, wasting processor runtime. Contention management policies are typically used to avoid that, but they are passive approaches as they wait for an abort to happen so they can take action. More proactive approaches have emerged, trying to predict when a transaction is likely to abort so its execution can be delayed. Such techniques are limited, as they do not replace the doomed transaction by another or, when they do, they rely on the operating system for that, having little or no control on which transaction should run. In this paper we propose LUTS, a Lightweight User-Level Transaction Scheduler, which is based on an execution context record mechanism. Unlike other techniques, LUTS provides the means for selecting another transaction to run in parallel, thus improving system throughput. Moreover, it avoids most of the issues caused by pseudo parallelism, as it only launches as many system-level threads as the number of available processor cores. We discuss LUTS design and present three conflict-avoidance heuristics built around LUTS scheduling capabilities. Experimental results, conducted with STMBench7 and STAMP benchmark suites, show LUTS efficiency when running high contention applications and how conflict-avoidance heuristics can improve STM performance even more. In fact, our transaction scheduling techniques are capable of improving program performance even in overloaded scenarios. © 2011 Springer-Verlag.

FTMOntology: An ontology to fill the semantic gap between music, mood, personality, and human physiology

This paper presents a domain ontology, the FeelingTheMusic Ontology - FTMOntology. FTMOntology is designed to represent the complex domain of music and how it relates to other domains like mood, personality and physiology. This includes representing the main concepts and relations of music domain with each of the above-mentioned domains. The concepts and relations between music, mood, personality and physiology. The main contribution of this work is to model and relate these different domains in a consistent ontology. © 2011 Springer-Verlag.

A study on automatic methods based on mathematical morphology for Martian dust devil tracks detection

This paper presents three methods for automatic detection of dust devils tracks in images of Mars. The methods are mainly based on Mathematical Morphology and results of their performance are analyzed and compared. A dataset of 21 images from the surface of Mars representative of the diversity of those track features were considered for developing, testing and evaluating our methods, confronting their outputs with ground truth images made manually. Methods 1 and 3, based on closing top-hat and path closing top-hat, respectively, showed similar mean accuracies around 90% but the time of processing was much greater for method 1 than for method 3. Method 2, based on radial closing, was the fastest but showed worse mean accuracy. Thus, this was the tiebreak factor. © 2011 Springer-Verlag.