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PubMed1983

Using SEEK for multichannel pattern recognition.

The author's work on computerized analysis of the 2-channel, 24-hr electrocardiogram has previously resulted in the development of multichannel signal processing systems that learn by observation. A new tool for implementing such algorithms is described: the pattern recognition language SEEK. Programs written in SEEK build a knowledge base containing treelike data structures, each of which stores acquired information about a particular multichannel waveform. Input data are interpreted by performing an efficient parallel evaluation of the structures in the knowledge base. The work is applicable to a wide variety of pattern recognition problems that arise in medical signal processing. The approach is illustrated with examples drawn from ECG analysis.

Computers↗
PubMed2002

Protein therapeutics: promises and challenges for the 21st century.

Recent advances in massively parallel experimental and computational technologies are leading to radically new approaches to the early phases of the drug production pipeline. The revolution in DNA microarray technologies and the imminent emergence of its analogue for proteins, along with machine learning algorithms, promise rapid acceleration in the identification of potential drug targets, and in high-throughput screens for subpopulation-specific toxicity. Similarly, advances in structural genomics in conjunction with in vitro and in silico evolutionary methods will rapidly accelerate the number of lead drug candidates and substantially augment their target specificity. Taken collectively, these advances will usher in an era of predictive medicine, which will move medical practice from reactive therapy after disease onset, to proactive prevention.

Animals↗
PubMedDate not supplied

Symplectic molecular dynamics simulations on specially designed parallel computers.

We have developed a computer program for molecular dynamics (MD) simulation that implements the Split Integration Symplectic Method (SISM) and is designed to run on specialized parallel computers. The MD integration is performed by the SISM, which analytically treats high-frequency vibrational motion and thus enables the use of longer simulation time steps. The low-frequency motion is treated numerically on specially designed parallel computers, which decreases the computational time of each simulation time step. The combination of these approaches means that less time is required and fewer steps are needed and so enables fast MD simulations. We study the computational performance of MD simulation of molecular systems on specialized computers and provide a comparison to standard personal computers. The combination of the SISM with two specialized parallel computers is an effective way to increase the speed of MD simulations up to 16-fold over a single PC processor.

Algorithms↗
PubMed2006

Transport of single molecules along the periodic parallel lattices with coupling.

General discrete one-dimensional stochastic models to describe the transport of single molecules along coupled parallel lattices with period N are developed. Theoretical analysis that allows to calculate explicitly the steady-state dynamic properties of single molecules, such as mean velocity V and dispersion D, is presented for N=1 and N=2 models. For the systems with N>2 exact analytic expressions for the large-time dynamic properties are obtained in the limit of strong coupling between the lattices that leads to dynamic equilibrium between two parallel kinetic pathways. It is shown that for all systems dispersion is maximal when the coupling between channels is weak.

Algorithms↗
PubMed2006

Real-time myoprocessors for a neural controlled powered exoskeleton arm.

Exoskeleton robots are promising assistive/rehabilitative devices that can help people with force deficits or allow the recovery of patients who have suffered from pathologies such as stroke. The key component that allows the user to control the exoskeleton is the human machine interface (HMI). Setting the HMI at the neuro-muscular level may lead to seamless integration and intuitive control of the exoskeleton arm as a natural extension of the human body. At the core of the exoskeleton HMI there is a model of the human muscle, the "myoprocessor," running in real-time and in parallel to the physiological muscle, that predicts joint torques as a function of the joint kinematics and neural activation levels. This paper presents the development of myoprocessors for the upper limb based on the Hill phenomenological muscle model. Genetic algorithms are used to optimize the internal parameters of the myoprocessors utilizing an experimental database that provides inputs to the model and allows for performance assessment. The results indicate high correlation between joint moment predictions of the model and the measured data. Consequently, the myoprocessor seems an adequate model, sufficiently robust for further integration into the exoskeleton control system.

Arm↗
PubMed2006

Tomographic reconstruction using an adaptive tetrahedral mesh defined by a point cloud.

Medical images in nuclear medicine are commonly represented in three dimensions as a stack of two-dimensional images that are reconstructed from tomographic projections. Although natural and straightforward, this may not be an optimal visual representation for performing various diagnostic tasks. A method for three-dimensional (3-D) tomographic reconstruction is developed using a point cloud image representation. A point cloud is a set of points (nodes) in space, where each node of the point cloud is characterized by its position and intensity. The density of the nodes determines the local resolution allowing for the modeling of different parts of the image with different resolution. The reconstructed volume, which in general could be of any resolution, size, shape, and topology, is represented by a set of nonoverlapping tetrahedra defined by the nodes. The intensity at any point within the volume is defined by linearly interpolating inside a tetrahedron from the values at the four nodes that define the tetrahedron. This approach creates a continuous piecewise linear intensity over the reconstruction domain. The reconstruction provides a distinct multiresolution representation, which is designed to accurately and efficiently represent the 3-D image. The method is applicable to the acquisition of any tomographic geometry, such as parallel-, fan-, and cone-beam; and the reconstruction procedure can also model the physics of the image detection process. An efficient method for evaluating the system projection matrix is presented. The system matrix is used in an iterative algorithm to reconstruct both the intensity and location of the distribution of points in the point cloud. Examples of the reconstruction of projection data generated by computer simulations and projection data experimentally acquired using a Jaszczak cardiac torso phantom are presented. This work creates a framework for voxel-less multiresolution representation of images in nuclear medicine.

Algorithms↗
PubMed2005

Cellular automata with object-oriented features for parallel molecular network modeling.

Cellular automata are an important modeling paradigm for studying the dynamics of large, parallel systems composed of multiple, interacting components. However, to model biological systems, cellular automata need to be extended beyond the large-scale parallelism and intensive communication in order to capture two fundamental properties characteristic of complex biological systems: hierarchy and heterogeneity. This paper proposes extensions to a cellular automata language, Cellang, to meet this purpose. The extended language, with object-oriented features, can be used to describe the structure and activity of parallel molecular networks within cells. Capabilities of this new programming language include object structure to define molecular programs within a cell, floating-point data type and mathematical functions to perform quantitative computation, message passing capability to describe molecular interactions, as well as new operators, statements, and built-in functions. We discuss relevant programming issues of these features, including the object-oriented description of molecular interactions with molecule encapsulation, message passing, and the description of heterogeneity and anisotropy at the cell and molecule levels. By enabling the integration of modeling at the molecular level with system behavior at cell, tissue, organ, or even organism levels, the program will help improve our understanding of how complex and dynamic biological activities are generated and controlled by parallel functioning of molecular networks. Index Terms-Cellular automata, modeling, molecular network, object-oriented.

Algorithms↗
PubMed2006

Dynamic calibration of pan-tilt-zoom cameras for traffic monitoring.

Pan-tilt-zoom (PTZ) cameras have been widely used in recent years for monitoring and surveillance applications. These cameras provide flexible view selection as well as a wider observation range. This makes them suitable for vision-based traffic monitoring and enforcement systems. To employ PTZ cameras for image measurement applications, one first needs to calibrate the camera to obtain meaningful results. For instance, the accuracy of estimating vehicle speed depends on the accuracy of camera calibration and that of vehicle tracking results. This paper presents a novel calibration method for a PTZ camera overlooking a traffic scene. The proposed approach requires no manual operation to select the positions of special features. It automatically uses a set of parallel lane markings and the lane width to compute the camera parameters, namely, focal length, tilt angle, and pan angle. Image processing procedures have been developed for automatically finding parallel lane markings. Interesting experimental results are presented to validate the robustness and accuracy of the proposed method.

Algorithms↗
PubMed1981

Time-constant histograms from the forced expired volume signal.

The forced expired volume signal was analyzed using a parallel compartment model in which each compartment emptied exponentially. With this model the forced expired volume signal was represented by a histogram showing the fraction of the vital capacity as a functional of compartmental time constants. We developed an algorithm to compute this histogram from the volume signal. The algorithm used the least-squares criterion function with both smoothness and nonnegativity constraints. In a stimulation study reasonable histograms were obtained even in the presence of realistic random error. Three dependent forced expired volume signals from 16 subjects were analyzed, and the histograms were reproducible. Most histograms were bimodal with fast time constants of 0.12-0.55 s and slow time constants of 1.3-2.7 s. In all normal subjects and patients with restrictive disease more than 75% of the vital capacity was in the fast time-constant mode. Subjects with obstructive disease had more than 40% of the vital capacity in the slow time-constant mode.

Adult↗
PubMed1999

Discontinuities in recurrent neural networks.

This article studies the computational power of various discontinuous real computational models that are based on the classical analog recurrent neural network (ARNN). This ARNN consists of finite number of neurons; each neuron computes a polynomial net function and a sigmoid-like continuous activation function. We introduce arithmetic networks as ARNN augmented with a few simple discontinuous (e.g., threshold or zero test) neurons. We argue that even with weights restricted to polynomial time computable reals, arithmetic networks are able to compute arbitrarily complex recursive functions. We identify many types of neural networks that are at least as powerful as arithmetic nets, some of which are not in fact discontinuous, but they boost other arithmetic operations in the net function (e.g., neurons that can use divisions and polynomial net functions inside sigmoid-like continuous activation functions). These arithmetic networks are equivalent to the Blum-Shub-Smale model, when the latter is restricted to a bounded number of registers. With respect to implementation on digital computers, we show that arithmetic networks with rational weights can be simulated with exponential precision, but even with polynomial-time computable real weights, arithmetic networks are not subject to any fixed precision bounds. This is in contrast with the ARNN that are known to demand precision that is linear in the computation time. When nontrivial periodic functions (e.g., fractional part, sine, tangent) are added to arithmetic networks, the resulting networks are computationally equivalent to a massively parallel machine. Thus, these highly discontinuous networks can solve the presumably intractable class of PSPACE-complete problems in polynomial time.

Algorithms↗
PubMed2003

The treat-to-target trial: randomized addition of glargine or human NPH insulin to oral therapy of type 2 diabetic patients.

OBJECTIVE: To compare the abilities and associated hypoglycemia risks of insulin glargine and human NPH insulin added to oral therapy of type 2 diabetes to achieve 7% HbA(1c). RESEARCH DESIGN AND METHODS: In a randomized, open-label, parallel, 24-week multicenter trial, 756 overweight men and women with inadequate glycemic control (HbA(1c) >7.5%) on one or two oral agents continued prestudy oral agents and received bedtime glargine or NPH once daily, titrated using a simple algorithm seeking a target fasting plasma glucose (FPG) <or=100 mg/dl (5.5 mmol/l). Outcome measures were FPG, HbA(1c), hypoglycemia, and percentage of patients reaching HbA(1c) <or=7% without documented nocturnal hypoglycemia. RESULTS: Mean FPG at end point was similar with glargine and NPH (117 vs. 120 mg/dl [6.5 vs. 6.7 mmol/l]), as was HbA(1c) (6.96 vs. 6.97%). A majority of patients ( approximately 60%) attained HbA(1c) <or=7% with each insulin type. However, nearly 25% more patients attained this without documented nocturnal hypoglycemia (<or=72 mg/dl [4.0 mmol/l]) with glargine (33.2 vs. 26.7%, P < 0.05). Moreover, rates of other categories of symptomatic hypoglycemia were 21-48% lower with glargine. CONCLUSIONS: Systematically titrating bedtime basal insulin added to oral therapy can safely achieve 7% HbA(1c) in a majority of overweight patients with type 2 diabetes with HbA(1c) between 7.5 and 10.0% on oral agents alone. In doing this, glargine causes significantly less nocturnal hypoglycemia than NPH, thus reducing a leading barrier to initiating insulin. This simple regimen may facilitate earlier and effective insulin use in routine medical practice, improving achievement of recommended standards of diabetes care.

Administration, Oral↗
PubMed2005

Molecular basis of peptide recognition by the TCR: affinity differences calculated using large scale computing.

Free energy calculations of the wild-type and the variant human T cell lymphotropic virus type 1 Tax peptide presented by the MHC to the TCR have been performed using large scale massively parallel molecular dynamics simulations. The computed free energy difference (-1.86 +/- 0.44 kcal/mol) using alchemical mutation-based thermodynamic integration agrees well with experimental data (-2.9 +/- 0.2 kcal/mol). Our simulations exploit state-of-the-art hardware and codes whose algorithms have been optimized for supercomputing platforms. This enables us to simulate larger, more realistic biological systems for longer durations without the imposition of artificial constraints.

Binding Sites↗
PubMed1994

Genetic map construction with constraints.

A pilot program, CME, is described for generating a physical genetic map from hybridization fingerprinting data. CME is implemented in the parallel constraint logic programming language ElipSys. The features of constraint logic programming are used to enable the integration of pre-existing mapping information (partial probe orders from cytogenetic maps and local physical maps) into the global map generation process, while parallelism enables the search space to be traversed more efficiently. CME was tested using data from chromosome 2 of Schizosaccharomyces pombe and was found able to generate maps as well as (and sometimes better than) a more traditional method. This paper illustrates the practical benefits of using a symbolic logic programming language and shows that the features of constraint handling and parallel execution bring the development of practical systems based on AI programming technologies nearer to being a reality.

Algorithms↗
PubMed2006

Partial least-squares with residual bilinearization for the spectrofluorimetric determination of pesticides. A solution of the problems of inner-filter effects and matrix interferents.

This paper demonstrates for the first time the power of a chemometric second-order algorithm for predicting, in a simple way and using spectrofluorimetric data, the concentration of analytes in the presence of both the inner-filter effect and unsuspected species. The simultaneous determination of the systemic fungicides carbendazim and thiabendazole was achieved and employed for the discussion of the scopes of the applied second-order chemometric tools: parallel factor analysis (PARAFAC) and partial least-squares with residual bilinearization (PLS/RBL). The chemometric study was performed using fluorescence excitation-emission matrices obtained after the extraction of the analytes over a C18-membrane surface. The ability of PLS/RBL to recognize and overcome the significant changes produced by thiabendazole in both the excitation and emission spectra of carbendazim is demonstrated. The high performance of the selected PLS/RBL method was established with the determination of both pesticides in artificial and real samples.

Algorithms↗
PubMed2005

Data-partitioning using the Hilbert space filling curves: effect on the speed of convergence of Fuzzy ARTMAP for large database problems.

The Fuzzy ARTMAP algorithm has been proven to be one of the premier neural network architectures for classification problems. One of the properties of Fuzzy ARTMAP, which can be both an asset and a liability, is its capacity to produce new nodes (templates) on demand to represent classification categories. This property allows Fuzzy ARTMAP to automatically adapt to the database without having to a priori specify its network size. On the other hand, it has the undesirable side effect that large databases might produce a large network size (node proliferation) that can dramatically slow down the training speed of the algorithm. To address the slow convergence speed of Fuzzy ARTMAP for large database problems, we propose the use of space-filling curves, specifically the Hilbert space-filling curves (HSFC). Hilbert space-filling curves allow us to divide the problem into smaller sub-problems, each focusing on a smaller than the original dataset. For learning each partition of data, a different Fuzzy ARTMAP network is used. Through this divide-and-conquer approach we are avoiding the node proliferation problem, and consequently we speedup Fuzzy ARTMAP's training. Results have been produced for a two-class, 16-dimensional Gaussian data, and on the Forest database, available at the UCI repository. Our results indicate that the Hilbert space-filling curve approach reduces the time that it takes to train Fuzzy ARTMAP without affecting the generalization performance attained by Fuzzy ARTMAP trained on the original large dataset. Given that the resulting smaller datasets that the HSFC approach produces can independently be learned by different Fuzzy ARTMAP networks, we have also implemented and tested a parallel implementation of this approach on a Beowulf cluster of workstations that further speeds up Fuzzy ARTMAP's convergence to a solution for large database problems.

Algorithms↗
PubMed1987

Accuracy in clinical electron beam dose planning using pencil beam algorithms.

The accuracy of two different pencil beam models for electron beam dose planning is shown by comparisons with measured dose distributions. The investigation is restricted to two-dimensional geometries. In one model the multiple scattering of the electrons is considered by the small angle Gaussian approximation of Fermi and Eyges. In the other, the generalized Gaussian model, the large angle single scattering events are also considered. The parallel slab approximation is used in both models. The comparisons have been made for two different anatomical phantoms. One phantom was constructed to simulate a transversal cross-section through the chest wall and lung in radiotherapy of breast cancer. The other phantom was made to simulate the head at the level of the nose. The measurements in these phantoms were made with thermoluminescence dosimetry, LiF rods. The accuracy of the oblique incidence case was investigated in a homogenous water phantom. The results show that for oblique incidence and geometries where the semi-infinite slab approximation is reasonably good, the generalized Gaussian model is more accurate. Within and behind low density cavities, in the phantom, the Gaussian model often gives a better agreement to experimental data. This is shown to be due to mutually balancing errors from the semi-infinite slab approximation and the Gaussian approximation.

Algorithms↗
PubMed2002

Probabilistic sampling of protein conformations: new hope for brute force?

Protein structure prediction from sequence alone by "brute force" random methods is a computationally expensive problem. Estimates have suggested that it could take all the computers in the world longer than the age of the universe to compute the structure of a single 200-residue protein. Here we investigate the use of a faster version of our FOLDTRAJ probabilistic all-atom protein-structure-sampling algorithm. We have improved the method so that it is now over twenty times faster than originally reported, and capable of rapidly sampling conformational space without lattices. It uses geometrical constraints and a Leonard-Jones type potential for self-avoidance. We have also implemented a novel method to add secondary structure-prediction information to make protein-like amounts of secondary structure in sampled structures. In a set of 100,000 probabilistic conformers of 1VII, 1ENH, and 1PMC generated, the structures with smallest Calpha RMSD from native are 3.95, 5.12, and 5.95A, respectively. Expanding this test to a set of 17 distinct protein folds, we find that all-helical structures are "hit" by brute force more frequently than beta or mixed structures. For small helical proteins or very small non-helical ones, this approach should have a "hit" close enough to detect with a good scoring function in a pool of several million conformers. By fitting the distribution of RMSDs from the native state of each of the 17 sets of conformers to the extreme value distribution, we are able to estimate the size of conformational space for each. With a 0.5A RMSD cutoff, the number of conformers is roughly 2N where N is the number of residues in the protein. This is smaller than previous estimates, indicating an average of only two possible conformations per residue when sterics are accounted for. Our method reduces the effective number of conformations available at each residue by probabilistic bias, without requiring any particular discretization of residue conformational space, and is the fastest method of its kind. With computer speeds doubling every 18 months and parallel and distributed computing becoming more practical, the brute force approach to protein structure prediction may yet have some hope in the near future.

Algorithms↗
PubMed2000

Characterization of airborne transducers by optical tomography

This paper describes the application of an acousto-optic method to the measurement of airborne ultrasound. The method consists of a heterodyne interferometric probing of the pressure emitted by the transducer combined with a tomographic algorithm. The heterodyne interferometer measures the optical phase shift of the probe laser beam, proportional to the acoustic pressure integrated along the light path. A number of projections of the sound field, e.g. a set of ray integrals obtained along parallel paths, are made in moving the transducer to be tested. The main advantage of the method is its very high sensitivity in air (2 x 10(-4) Pa Hz-1/2), combined with a large bandwidth. Using the same principle as X-ray tomography the ultrasonic pressure in a plane perpendicular to the transducer axis can be reconstructed. Several ultrasonic fields emitted by wide-band home made electrostatic transducers, with operating frequencies between 200 and 700 kHz, have been measured. The sensitivities compared favorably with those of commercial airborne transducers.

Journal Article↗