Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Computing Methodologies”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 451 records · Page 25Linked to original sources

Discriminative components of data.

A simple probabilistic model is introduced to generalize classical linear discriminant analysis (LDA) in finding components that are informative of or relevant for data classes. The components maximize the predictability of the class distribution which is asymptotically equivalent to 1) maximizing mutual information with the classes, and 2) finding principal components in the so-called learning or Fisher metrics. The Fisher metric measures only distances that are relevant to the classes, that is, distances that cause changes in the class distribution. The components have applications in data exploration, visualization, and dimensionality reduction. In empirical experiments, the method outperformed, in addition to more classical methods, a Renyi entropy-based alternative while having essentially equivalent computational cost.

Algorithms↗

Coordinated decentralized adaptive output feedback control of interconnected systems.

A decentralized adaptive output feedback control design is proposed for large-scale interconnected systems. It is assumed that all the controllers share prior information about the system reference models. Based on that information, a linearly parameterized neural network is introduced for each subsystem to partially cancel the effect of the interconnections on tracking performance. Boundedness of error signals is shown through Lyapunov's direct method.

Algorithms↗

Observer-based direct adaptive fuzzy-neural control for nonaffine nonlinear systems.

In this paper, an observer-based direct adaptive fuzzy-neural control scheme is presented for nonaffine nonlinear systems in the presence of unknown structure of nonlinearities. A direct adaptive fuzzy-neural controller and a class of generalized nonlinear systems, which are called nonaffine nonlinear systems, are instead of the indirect one and affine nonlinear systems given by Leu et al. By using implicit function theorem and Taylor series expansion, the observer-based control law and the weight update law of the fuzzy-neural controller are derived for the nonaffine nonlinear systems. Based on strictly-positive-real (SPR) Lyapunov theory, the stability of the closed-loop system can be verified. Moreover, the overall adaptive scheme guarantees that all signals involved are bounded and the output of the closed-loop system will asymptotically track the desired output trajectory. To demonstrate the effectiveness of the proposed method, simulation results are illustrated in this paper.

Algorithms↗

Hardware implementation of fuzzy Petri net as a controller.

The paper presents a new approach to fuzzy Petri net (FPN) and its hardware implementation. The authors' motivation is as follows. Complex industrial processes can be often decomposed into many parallelly working subprocesses, which can, in turn, be modeled using Petri nets. If all the process variables (or events) are assumed to be two-valued signals, then it is possible to obtain a hardware or software control device, which works according to the algorithm described by conventional Petri net. However, the values of real signals are contained in some bounded interval and can be interpreted as events which are not only true or false, but rather true in some degree from the interval [0, 1]. Such a natural interpretation from multivalued logic (fuzzy logic) point of view, concerns sensor outputs, control signals, time expiration, etc. It leads to the idea of FPN as a controller, which one can rather simply obtain, and which would be able to process both analog, and binary signals. In the paper both graphical, and algebraic representations of the proposed FPN are given. The conditions under which transitions can be fired are described. The algebraic description of the net and a theorem which enables computation of new marking in the net, based on current marking, are formulated. Hardware implementation of the FPN, which uses fuzzy JK flip-flops and fuzzy gates, are proposed. An example illustrating usefulness of the proposed FPN for control algorithm description and its synthesis as a controller device for the concrete production process are presented.

Algorithms↗

Integrating computation and visualization for biomolecular analysis: an example using python and AVS.

One of the challenges in biocomputing is to enable the efficient use of a wide variety of fast-evolving computational methods to simulate, analyze, and understand the complex properties and interactions of molecular systems. Our laboratory investigates several areas including molecular visualization, protein-ligand docking, protein-protein docking, molecular surfaces, and the derivation of phenomenological potentials. In this paper we present an approach based on the Python programming language to achieve a high level of integration between these different computational methods and our primary visualization system AVS. This approach removes many limitations of AVS while increasing dramatically the inter-operability of our computational tools. Several examples are shown to illustrate how this approach enables a high level of integration and inter-operability between different tools, while retaining modularity and avoiding the creation of a large monolithic package that is difficult to extend and maintain.

Capsid↗

Partitioning a vocabulary's IS-A hierarchy into trees.

Controlled medical vocabularies are useful in application areas such as medical information-systems and decision-support. However, such vocabularies are large and complex, and working with them can be daunting. It is important to provide a means for orienting users to the vocabulary's contents. This paper introduces a methodology for partitioning a vocabulary into small, meaningful pieces. The partitioning is done with respect to the vocabulary's IS-A hierarchy. The methodology, based on a set of rules for refining the IS-A hierarchy, is a process carried out by a user in conjunction with the computer. The methodology is demonstrated on a complex portion of a vocabulary.

Classification↗

QU-GENE: a simulation platform for quantitative analysis of genetic models.

MOTIVATION: Classical quantitative genetics theory makes a number of simplifying assumptions in order to develop mathematical expressions that describe the mean and variation (genetic and phenotypic) within and among populations, and to predict how these are expected to change under the influence of external forces. These assumptions are often necessary to render the development of many aspects of the theory mathematically tractable. The availability of high-speed computers today provides opportunity for the use of computer simulation methodology to investigate the implications of relaxing many of the assumptions that are commonly made. RESULTS: QU-GENE (QUantitative-GENEtics) was developed as a flexible computer simulation platform for the quantitative analysis of genetic models. Three features of the QU-GENE software that contribute to its flexibility are (i) the core E(N:K) genetic model, where E is the number of types of environment, N is the number of genes, K indicates the level of epistasis and the parentheses indicate that different N:K genetic models can be nested within types of environments, (ii) the use of a two-stage architecture that separates the definition of the genetic model and genotype-environment system from the detail of the individual simulation experiments and (iii) the use of a series of interactive graphical windows that monitor the progress of the simulation experiments. The E(N:K) framework enables the generation of families of genetic models that incorporate the effects of genotype-by-environment (G x E) interactions and epistasis. By the design of appropriate application modules, many different simulation experiments can be conducted for any genotype-environment system. The structure of the QU-GENE simulation software is explained and demonstrated by way of two examples. The first concentrates on some aspects of the influence of G x E interactions on response to selection in plant breeding, and the second considers the influence of multiple-peak epistasis on the evolution of a four-gene epistatic network. AVAILABILITY: QU-GENE is available over the Internet at (http://pig.ag.uq.edu.au/qu-gene/) CONTACT: m.cooper@mailbox.uq.edu. au

Computer Simulation↗

DNA computation model to solve 0-1 programming problem.

0-1 programming problem is an important problem in opsearch with very widespread applications. In this paper, a new DNA computation model utilizing solution-based and surface-based methods is presented to solve the 0-1 programming problem. This model contains the major benefits of both solution-based and surface-based methods; including vast parallelism, extraordinary information density and ease of operation. The result, verified by biological experimentation, revealed the potential of DNA computation in solving complex programming problem.

Algorithms↗

A parallel graph decomposition algorithm for DNA sequencing with nanopores.

MOTIVATION: With the potential availability of nanopore devices that can sense the bases of translocating single-stranded DNA (ssDNA), it is likely that 'reads' of length approximately 10(5) will be available in large numbers and at high speed. We address the problem of complete DNA sequencing using such reads. We assume that approximately 10(2) copies of a DNA sequence are split into single strands that break into randomly sized pieces as they translocate the nanopore in arbitrary orientations. The nanopore senses and reports each individual base that passes through, but all information about orientation and complementarity of the ssDNA subsequences is lost. Random errors (both biological and transduction) in the reads create further complications. RESULTS: We have developed an algorithm that addresses these issues. It can be considered an extreme variation of the well-known Eulerian path approach. It searches over a space of de Bruijn graphs until it finds one in which (a) the impact of errors is eliminated and (b) both possible orientations of the two ssDNA sequences can be identified separately and unambiguously. Our algorithm is able to correctly reconstruct real DNA sequences of the order of 10(6) bases (e.g. the bacterium Mycoplasma pneumoniae) from simulated erroneous reads on a modest workstation in about 1 h. We describe, and give measured timings of, a parallel implementation of this algorithm on the Cray Multithreaded Architecture (MTA-2) supercomputer, whose architecture is ideally suited to this 'unstructured' problem. Our parallel implementation is crucial to the problem of rapidly sequencing long DNA sequences and also to the situation where multiple nanopores are used to obtain a high-bandwidth stream of reads.

Algorithms↗

The role of soft computing in intelligent machines.

An intelligent machine relies on computational intelligence in generating its intelligent behaviour. This requires a knowledge system in which representation and processing of knowledge are central functions. Approximation is a 'soft' concept, and the capability to approximate for the purposes of comparison, pattern recognition, reasoning, and decision making is a manifestation of intelligence. This paper examines the use of soft computing in intelligent machines. Soft computing is an important branch of computational intelligence, where fuzzy logic, probability theory, neural networks, and genetic algorithms are synergistically used to mimic the reasoning and decision making of a human. This paper explores several important characteristics and capabilities of machines that exhibit intelligent behaviour. Approaches that are useful in the development of an intelligent machine are introduced. The paper presents a general structure for an intelligent machine, giving particular emphasis to its primary components, such as sensors, actuators, controllers, and the communication backbone, and their interaction. The role of soft computing within the overall system is discussed. Common techniques and approaches that will be useful in the development of an intelligent machine are introduced, and the main steps in the development of an intelligent machine for practical use are given. An industrial machine, which employs the concepts of soft computing in its operation, is presented, and one aspect of intelligent tuning, which is incorporated into the machine, is illustrated.

Algorithms↗

A framework for three-dimensional simulation of morphogenesis.

We present COMPUCELL3D, a software framework for three-dimensional simulation of morphogenesis in different organisms. COMPUCELL3D employs biologically relevant models for cell clustering, growth, and interaction with chemical fields. COMPUCELL3D uses design patterns for speed, efficient memory management, extensibility, and flexibility to allow an almost unlimited variety of simulations. We have verified COMPUCELL3D by building a model of growth and skeletal pattern formation in the avian (chicken) limb bud. Binaries and source code are available, along with documentation and input files for sample simulations, at http:// compucell.sourceforge.net.

Animals↗

Stock trading using RSPOP: a novel rough set-based neuro-fuzzy approach.

This paper investigates the method of forecasting stock price difference on artificially generated price series data using neuro-fuzzy systems and neural networks. As trading profits is more important to an investor than statistical performance, this paper proposes a novel rough set-based neuro-fuzzy stock trading decision model called stock trading using rough set-based pseudo outer-product (RSPOP) which synergizes the price difference forecast method with a forecast bottleneck free trading decision model. The proposed stock trading with forecast model uses the pseudo outer-product based fuzzy neural network using the compositional rule of inference [POPFNN-CRI(S)] with fuzzy rules identified using the RSPOP algorithm as the underlying predictor model and simple moving average trading rules in the stock trading decision model. Experimental results using the proposed stock trading with RSPOP forecast model on real world stock market data are presented. Trading profits in terms of portfolio end values obtained are benchmarked against stock trading with dynamic evolving neural-fuzzy inference system (DENFIS) forecast model, the stock trading without forecast model and the stock trading with ideal forecast model. Experimental results showed that the proposed model identified rules with greater interpretability and yielded significantly higher profits than the stock trading with DENFIS forecast model and the stock trading without forecast model.

Algorithms↗

Distributed shared memory for roaming large volumes.

We present a cluster-based volume rendering system for roaming very large volumes. This system allows to move a gigabyte-sized probe inside a total volume of several tens or hundreds of gigabytes in real-time. While the size of the probe is limited by the total amount of texture memory on the cluster, the size of the total data set has no theoretical limit. The cluster is used as a distributed graphics processing unit that both aggregates graphics power and graphics memory. A hardware-accelerated volume renderer runs in parallel on the cluster nodes and the final image compositing is implemented using a pipelined sort-last rendering algorithm. Meanwhile, volume bricking and volume paging allow efficient data caching. On each rendering node, a distributed hierarchical cache system implements a global software-based distributed shared memory on the cluster. In case of a cache miss, this system first checks page residency on the other cluster nodes instead of directly accessing local disks. Using two Gigabit Ethernet network interfaces per node, we accelerate data fetching by a factor of 4 compared to directly accessing local disks. The system also implements asynchronous disk access and texture loading, which makes it possible to overlap data loading, volume slicing and rendering for optimal volume roaming.

Computer Graphics↗

Implementation of the DPM Monte Carlo code on a parallel architecture for treatment planning applications.

We have parallelized the Dose Planning Method (DPM), a Monte Carlo code optimized for radiotherapy class problems, on distributed-memory processor architectures using the Message Passing Interface (MPI). Parallelization has been investigated on a variety of parallel computing architectures at the University of Michigan-Center for Advanced Computing, with respect to efficiency and speedup as a function of the number of processors. We have integrated the parallel pseudo random number generator from the Scalable Parallel Pseudo-Random Number Generator (SPRNG) library to run with the parallel DPM. The Intel cluster consisting of 800 MHz Intel Pentium III processor shows an almost linear speedup up to 32 processors for simulating 1 x 10(8) or more particles. The speedup results are nearly linear on an Athlon cluster (up to 24 processors based on availability) which consists of 1.8 GHz+ Advanced Micro Devices (AMD) Athlon processors on increasing the problem size up to 8 x 10(8) histories. For a smaller number of histories (1 x 10(8)) the reduction of efficiency with the Athlon cluster (down to 83.9% with 24 processors) occurs because the processing time required to simulate 1 x 10(8) histories is less than the time associated with interprocessor communication. A similar trend was seen with the Opteron Cluster (consisting of 1400 MHz, 64-bit AMD Opteron processors) on increasing the problem size. Because of the 64-bit architecture Opteron processors are capable of storing and processing instructions at a faster rate and hence are faster as compared to the 32-bit Athlon processors. We have validated our implementation with an in-phantom dose calculation study using a parallel pencil monoenergetic electron beam of 20 MeV energy. The phantom consists of layers of water, lung, bone, aluminum, and titanium. The agreement in the central axis depth dose curves and profiles at different depths shows that the serial and parallel codes are equivalent in accuracy.

Algorithms↗

Contextual weighting for Support Vector Machines in literature mining: an application to gene versus protein name disambiguation.

BACKGROUND: The ability to distinguish between genes and proteins is essential for understanding biological text. Support Vector Machines (SVMs) have been proven to be very efficient in general data mining tasks. We explore their capability for the gene versus protein name disambiguation task. RESULTS: We incorporated into the conventional SVM a weighting scheme based on distances of context words from the word to be disambiguated. This weighting scheme increased the performance of SVMs by five percentage points giving performance better than 85% as measured by the area under ROC curve and outperformed the Weighted Additive Classifier, which also incorporates the weighting, and the Naive Bayes classifier. CONCLUSION: We show that the performance of SVMs can be improved by the proposed weighting scheme. Furthermore, our results suggest that in this study the increase of the classification performance due to the weighting is greater than that obtained by selecting the underlying classifier or the kernel part of the SVM.

Algorithms↗

Data mining in medical time series.

This article proposes a modular, computer-based methodology to describe and compare medical problems using data mining methods. The methodology focuses on a mathematical formulation of typical classification problems, systematic extraction of interpretable features from time series, and an evaluation adapted to problem-specific preferences and limitations (computational power, interpretability, etc.). The approach is applied to instrumented gait analysis and to the individual design of myoelectric controllers for hand prostheses.

Algorithms↗

Multiple model regression estimation.

This paper presents a new learning formulation for multiple model estimation (MME). Under this formulation, training data samples are generated by several (unknown) statistical models. Hence, most existing learning methods (for classification or regression) based on a single model formulation are no longer applicable. We describe a general framework for MME. Then we introduce a constructive support vector machine (SVM)-based methodology for multiple regression estimation. Several empirical comparisons using synthetic and real-life data sets are presented to illustrate the proposed approach for multiple model regression formulation.

Algorithms↗