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Self-selected modular recurrent neural networks with postural and inertial subnetworks applied to complex movements.

It has been shown that dynamic recurrent neural networks are successful in identifying the complex mapping relationship between full-wave-rectified electromyographic (EMG) signals and limb trajectories during complex movements. These connectionist models include two types of adaptive parameters: the interconnection weights between the units and the time constants associated to each neuron-like unit; they are governed by continuous-time equations. Due to their internal structure, these models are particularly appropriate to solve dynamical tasks (with time-varying input and output signals). We show in this paper that the introduction of a modular organization dedicated to different aspects of the dynamical mapping including privileged communication channels can refine the architecture of these recurrent networks. We first divide the initial individual network into two communicating subnetworks. These two modules receive the same EMG signals as input but are involved in different identification tasks related to position and acceleration. We then show that the introduction of an artificial distance in the model (using a Gaussian modulation factor of weights) induces a reduced modular architecture based on a self-elimination of null synaptic weights. Moreover, this self-selected reduced model based on two subnetworks performs the identification task better than the original single network while using fewer free parameters (better learning curve and better identification quality). We also show that this modular network exhibits several features that can be considered as biologically plausible after the learning process: self-selection of a specific inhibitory communicating path between both subnetworks after the learning process, appearance of tonic and phasic neurons, and coherent distribution of the values of the time constants within each subnetwork.

Adult↗

Parameter extraction from population codes: a critical assessment.

In perceptual systems, a stimulus parameter can be extracted by determining the center-of-gravity of the response profile of a population of neural sensors. Likewise at the motor end of a neural system, center-of-gravity decoding, also known as vector decoding, generates a movement direction from the neural activation profile. We evaluate these schemes from a statistical perspective, by comparing their statistical variance with the minimum variance possible for an unbiased parameter extraction from the noisy neuronal ensemble activation profile. Center-of-gravity decoding can be statistically optimal. This is the case for regular arrays of sensors with gaussian tuning profiles that have an output described by Poisson statistics, and for arrays of sensors with a sinusoidal tuning profile for the (angular) parameter estimated. However, there are also many cases in which center-of-gravity decoding is highly inefficient. This includes the important case where sensor positions are very irregular. Finally, we study the robustness of center-of-gravity decoding against response nonlinearities at different stages of an information processing hierarchy. We conclude that, in neural systems, instead of representing a parameter explicitly, it is safer to leave the parameter coded implicitly in a neuronal ensemble activation profile.

Algorithms↗

Comparison of performance of spherical and realistic head models in dipole localization from noisy EEG.

The performance of a three-shell spherical head model versus the performance of a realistic head model is investigated when solving the inverse problem with a single dipole, in the presence of noise. This is evaluated by calculating the average dipole location error for 1000 noisy scalp potential sets, originating from the same test dipole and having the same noise level. The average location errors are obtained utilizing a local linearization, which is validated with a Monte-Carlo simulation. When the difference between the average location error utilizing a spherical and a realistic head model, represented by deltaR, is large for a large number of test dipoles, then it is worth using the more computationally demanding realistic head model. However, if deltaR is small for a large number of test dipoles, then it does not matter which model is used. For 27 electrodes, an electroencephalogram (EEG) epoch of one time sample and spatially white Gaussian noise, we found that the importance of the realistic head model over the spherical head model reduces by increasing the noise level. We further found that increasing the number of scalp electrodes from 27 to 44 has limited impact on the importance of the realistic head model over the spherical head model in EEG dipole source analysis. By increasing the number of time samples to six, the performance of the realistic head model in the inverse calculation gains importance compared with the three-shell spherical head model. Finally, we used spatially and temporally correlated background EEG instead of Gaussian noise. The advantage of the realistic head model over the spherical head model is reduced when applying correlated noise compared to Gaussian noise.

Algorithms↗

An optimal rotator for iterative reconstruction.

For implementations of iterative reconstruction algorithms that rotate the image matrix, the characteristics of the rotator may affect the reconstruction quality. Desirable qualities for the rotator include: 1) preservation of global and local image counts; 2) accurate count positioning; 3) a uniform and predictable amount of blurring due to the rotation. A new rotation method for iterative reconstruction is proposed which employs. Gaussian interpolation. This method was compared to standard rotation techniques and is shown to be superior to standard techniques when measured by these qualities. The computational cost was demonstrated to be only slightly more than bilinear interpolation.

Algorithms↗

Analysis of stereothresholds for stimuli below 2.5 c/deg.

We analyze published data on disparity detection thresholds for a wide range of conditions. This type of detection changes behavior dramatically at the spatial frequency of 2.5 c/deg; above this frequency threshold remains constant while below it threshold grows at a uniform rate. Many other types of threshold, such as upper disparity limits for depth perception and threshold amplitudes for stereo and monocular motion, show similar behavior. These data lead to the postulate that there are no foveal stereo channels peaking below 2.5 c/deg, so that foveal stimuli in the whole range below 2.5 c/deg are processed by a single channel tuned to this frequency. Consequently, disparity detection thresholds at frequencies below this frequency are controlled by the single parameter of effective contrast in the 2.5 c/deg channel, whose output depends jointly on the contrast and spatial frequency of the stimuli. We develop this idea to explain the relations between spatial and contrast tuning functions for disparity thresholds. To validate our conclusions, we describe an experiment with difference-of-Gaussian stimuli over a range of interocular widths and contrast differences. For a dichoptic width ratio of 2:1, the dichoptic contrast ratio required to minimize disparity detection thresholds was 1:4, just as predicted by the model.

Contrast Sensitivity↗

Human efficiency for recognizing 3-D objects in luminance noise.

The purpose of this study was to establish how efficiently humans use visual information to recognize simple 3-D objects. The stimuli were computer-rendered images of four simple 3-D objects--wedge, cone, cylinder, and pyramid--each rendered from 8 randomly chosen viewing positions as shaded objects, line drawings, or silhouettes. The objects were presented in static, 2-D Gaussian luminance noise. The observer's task was to indicate which of the four objects had been presented. We obtained human contrast thresholds for recognition, and compared these to an ideal observer's thresholds to obtain efficiencies. In two auxiliary experiments, we measured efficiencies for object detection and letter recognition. Our results showed that human object-recognition efficiency is low (3-8%) when compared to efficiencies reported for some other visual-information processing tasks. The low efficiency means that human recognition performance is limited primarily by factors intrinsic to the observer rather than the information content of the stimuli. We found three factors that play a large role in accounting for low object-recognition efficiency: stimulus size, spatial uncertainty, and detection efficiency. Four other factors play a smaller role in limiting object-recognition efficiency: observers' internal noise, stimulus rendering condition, stimulus familiarity, and categorization across views.

Contrast Sensitivity↗

Experimental and theoretical studies of the reaction of the OH radical with alkyl sulfides: 1. Direct observations of the formation of the OH-DMS adduct-pressure dependence of the forward rate of addition and development of a predictive expression at low temperature.

A pulsed laser photolysis-pulsed laser-induced fluorescence (PLP-PLIF) system was employed to study the kinetics and mechanisms of reactions (1) OH + h6-DMS --> products and (2) OH + d6-DMS --> products. We report direct observations of the rate coefficients for the formation and dissociation of the h6-OHDMS and d6-OHDMS adducts over the pressure range 50-650 Torr and between 240 and 245 K, together with measurements of the oxygen dependence of the effective rate coefficients for reactions 1 and 2 under similar conditions. The effective rate coefficients increased as a function of O2 concentration reaching their limiting values in each case. The values of the adduct formation rate, obtained from the O2 dependencies, were in excellent agreement with values determined from direct observation of adduct equilibration in N2. OH regeneration is insignificant. The rate coefficients for the formation of the adduct isotopomers showed slight differences in their falloff behavior and do not approach the high-pressure limit in either case. The equilibrium constants obtained show no dependence on isotopomer and are in good agreement with previous work. A "second-law" analysis of the temperature dependence of the equilibrium constant gives an adduct bond strength (DeltaH degrees =-10.9 +/- 1.0 kcal mol(-1)), also in good agreement with previously reported values. Using the entropy calculated from the ab initio vibrational frequencies, we obtain a "third-law" value for the reaction enthalpy at 240 K, DeltaH(240K) degrees = -10.5 kcal mol(-1) in good agreement with the other approach. The rate coefficient for the reactions of the adducts with O2 was obtained from an analysis of the O2 dependence and was determined to be 6.3 +/- 1.2 x 10(-13) cm3 molecule(-1) s(-1), with no dependence on pressure or isotopomer. The pressure and temperature dependence for all of the elementary processes in the initial steps of the dimethylsulfide (DMS) oxidation mechanism have been characterized in the range 238-245 K, allowing the formulation of an expression which can be used to calculate the effective rate coefficient for reaction 1 at any pressure and oxygen concentration. The expression can calculate the effective rate coefficient for reaction 1 to +/- 40% over the range 220-260 K, with the largest errors at the extremes of this range. Gaussian 03 has been used to calculate the structure of the OH-DMS adduct and its deuterated isotopomer. We find similar bound structures for both isotopomers. The calculated enthalpies of formation of the adducts are lower than the experimentally determined values.

Journal Article↗

Streamer initiation in atmospheric pressure gas discharges by direct particle simulation.

A two-dimensional particle code that simulates electrical breakdown of gases by modeling avalanche evolution from the initial ion-electron pair up to the development of a streamer is presented. Trajectories of individual particles are followed, the self-field is included consistently and collision processes are accurately modeled using experimentally determined cross sections. It is emphasized that the tadpolelike structure of well-formed streamer heads is present throughout the avalanche phase, and that the transition to the self-similar evolution characteristic of the streamer phase merely reflects the continued development of this structure. The importance of this for conventional fluid simulations of streamers, where the initial conditions for the streamer are taken to be a structureless Gaussian concentration of neutral plasma with significant density, is discussed. In the (realistic) situation where several avalanches are present simultaneously the large self-fields that rapidly develop lead to a strong interaction between them, in accord with the standard "cartoon" of streamer evolution.

Journal Article↗

Finding perceptually dominant orientations in natural textures.

An algorithm for detecting orientation in texture is developed and compared with results of humans detecting orientation in the same textures. The algorithm is based on the steerable filters of Freeman and Adelson (IEEE Trans. PAMI 13, 891-906, 1991), orientation-selective filters derived from derivatives of Gaussians. The filters are applied over multiple scales and their outputs non-linearly contrast-normalized. The data for humans were collected from forty subjects who were asked to identify 'the minimum number of dominant orientations' they perceived, and the 'strength' with which they perceived each orientation. Test data consisted of 111 grey-level images of natural textures taken from the Brodatz album, a standard collection used in computer vision and image processing. Results show that the computer and humans chose at least one of the same dominant orientations on 95 of the natural textures. Of these textures, 74 were also in 100% agreement on the location of all the dominant orientations chosen by both humans and computer. Disagreements are analyzed and possible causes are discussed. Some apparent limitations in the current filter shapes and sizes are illustrated, as well as some (surprisingly small) effects believed to be caused by semantic recognition and gestalt grouping.

Algorithms↗

On the influence of pigment-protein interactions on energy transfer processes in photosynthetic membrane structures. 3. The FMO complex of Chlorobium tepidum at high pressure.

The low-temperature absorption spectra of the Chlorobium tepidum FMO bacteriochlorophyll-protein complex at various pressures have been calculated within the framework of mini-exciton theory. The dependences of the Qy transition energies of the monomeric pigments on pressure have been found by means of functional minimization. This functional includes the parameters of both theoretical and experimental absorption spectra at low temperatures and various pressures. The dependences obtained are compared with those derived for the exciton transition energies, which have been obtained by deconvoluting absorption spectra with seven Gaussian components at each pressure. The pressure increase has been shown to result in the increased coupling energy between both the pigment molecules themselves and pigments and amino acid residues. The pigment molecules capable of binding histidines and water molecules have been shown to have the greatest and smallest responses to increased pressure, respectively. The couplings of Bchl molecules with the surrounding amino acid residues have been shown to change both the exciton delocalization index and the exciton distribution between the pigment molecules within the protein subunit; the increased pressure does not change these parameters significantly.

Bacterial Proteins↗

Volume-preserving smoothing of three-dimensional surfaces: application to intravascular ultrasound.

A volume-preserving three-dimensional smoothing approach is described that can be directly applied to 3D medical image data consisting of sets of 2D image slices, e.g., segmented intravascular ultrasound image sequences. Two local smoothing filters ℱ and 𝒢 were designed according to different smoothing goals and their performance was compared. Filtering with the ℱ filter of a relatively large frequency window keeps the important local characteristics of the object and results in little shrinkage while removing noise. Filtering with the Gaussian filter G that has an added volume compensation step results in no global shrinkage and may be used for multiscale filtering. The two filters can be easily extended to n-dimensional filtering.

Biomedical Engineering↗

Analysis of direction-tuning curves of neurons in the turtle's accessory optic system.

Visual-movement sensitivity of neurons in the turtle's accessory optic system was investigated. Neuronal responses to stimulus direction and speed were analyzed to determine whether they reflect processing by a one-dimensional encoder of visual motion or whether they indicate directional integration of presynaptic direction-sensitive responses whose maximal-response directions are distributed. Both of these mechanisms make predictions about the functional relationship between stimulus direction and response. The responses of single units in the basal optic nucleus to visual stimulation in different directions were described by both cosine and wrapped normal fitting functions. The wrapped normal function (a Gaussian curve mapped onto a circle) performed at least as well as the cosine function and described directional tuning curves of varying widths. Unlike cosines, the addition of two wrapped normals could describe multi-lobed directional data. Next, it was demonstrated that these neurons did not encode visual motion projected onto a single, spatial axis. Responses to the projected speed along the maximal-response direction were systematically lower than responses to the actual speed along that direction. Thus, for speeds above 1 degrees/s, neuronal response varies with respect to direction but not speed. Summation of presynaptic direction-sensitive responses with distributed maximal-response directions (referred to as directional integration) is discussed as a means of accounting for these results.

Animals↗

Stochastic resonance in the LIF models with input or threshold noise.

In this paper, two stochastic versions of the LIF neural model are considered: one with the noise signal applied to the firing threshold, the other having it added to the input current. Then, adopting a discontinuous stepwise noise whose innovations are uncorrelated and gaussian distributed, the behaviours of the two models pertaining to the stochastic resonance (SR) are analysed and compared. Furthermore, it is shown that introducing a suitable time correlation into the noise signal brings us from the first model to the second one.

Models, Biological↗

Unified segmentation.

A probabilistic framework is presented that enables image registration, tissue classification, and bias correction to be combined within the same generative model. A derivation of a log-likelihood objective function for the unified model is provided. The model is based on a mixture of Gaussians and is extended to incorporate a smooth intensity variation and nonlinear registration with tissue probability maps. A strategy for optimising the model parameters is described, along with the requisite partial derivatives of the objective function.

Algorithms↗

A parametric modeling of ionic channel current fluctuations using third-order statistics and its application to estimation of the kinetic parameters of single ionic channels.

A parametric modeling of stationary ionic-channel current fluctuations (SICF's) using third-order cumulants is presented and its application to estimation of the kinetic parameters of single ionic channels is discussed. We consider the case where third-order cumulants of SICF's are nonzero, and where SICF's are corrupted by an unobservable additive colored Gaussian noise that is independent of SICF's. First, we construct a virtual synthesizer that yields an output whose third-order cumulants are equivalent to those of SICF's on a specific slice. The synthesizer output is expressed by the sum of N5 - 1 first-order differential equation systems, where N8 denotes the number of states of single ionic channels. Next, discretizing the synthesizer output, we derive a discrete autoregressive (AR(N8 - 1)) process driven by the sum of N8 - 1 moving average (MA(N9 - 2)) processes. Then the AR coefficients are explicitly related to the kinetic parameters of single ionic channels, implying that the kinetic parameters can be estimated by identifying the ARMA coefficients using the third-order cumulants. In order to assess the validity of the proposed modeling and the accuracy of parameter estimates, Monte Carlo simulation is carried out in which the closed-open and closed-open-blocked schemes are treated as specific examples.

Ion Channels↗

Propagation of measurement noise through backprojection reconstruction in electrical impedance tomography.

A framework to analyze the propagation of measurement noise through backprojection reconstruction algorithms in electrical impedance tomography (EIT) is presented. Two measurement noise sources were considered: noise in the current drivers and in the voltage detectors. The influence of the acquisition system architecture (serial/semi-parallel) is also discussed. Three variants of backprojection reconstruction are studied: basic (unweighted), weighted and exponential backprojection. The results of error propagation theory have been compared with those obtained from simulated and experimental data. This comparison shows that the approach provides a good estimate of the reconstruction error variance. It is argued that the reconstruction error in EIT images obtained via backprojection can be approximately modeled as a spatially nonstationary Gaussian distribution. This methodology allows us to develop a spatial characterization of the reconstruction error in EIT images.

Algorithms↗

Feature selection and classifier performance in computer-aided diagnosis: the effect of finite sample size.

In computer-aided diagnosis (CAD), a frequently used approach for distinguishing normal and abnormal cases is first to extract potentially useful features for the classification task. Effective features are then selected from this entire pool of available features. Finally, a classifier is designed using the selected features. In this study, we investigated the effect of finite sample size on classification accuracy when classifier design involves stepwise feature selection in linear discriminant analysis, which is the most commonly used feature selection algorithm for linear classifiers. The feature selection and the classifier coefficient estimation steps were considered to be cascading stages in the classifier design process. We compared the performance of the classifier when feature selection was performed on the design samples alone and on the entire set of available samples, which consisted of design and test samples. The area Az under the receiver operating characteristic curve was used as our performance measure. After linear classifier coefficient estimation using the design samples, we studied the hold-out and resubstitution performance estimates. The two classes were assumed to have multidimensional Gaussian distributions, with a large number of features available for feature selection. We investigated the dependence of feature selection performance on the covariance matrices and means for the two classes, and examined the effects of sample size, number of available features, and parameters of stepwise feature selection on classifier bias. Our results indicated that the resubstitution estimate was always optimistically biased, except in cases where the parameters of stepwise feature selection were chosen such that too few features were selected by the stepwise procedure. When feature selection was performed using only the design samples, the hold-out estimate was always pessimistically biased. When feature selection was performed using the entire finite sample space, the hold-out estimates could be pessimistically or optimistically biased, depending on the number of features available for selection, the number of available samples, and their statistical distribution. For our simulation conditions, these estimates were always pessimistically (conservatively) biased if the ratio of the total number of available samples per class to the number of available features was greater than five.

Algorithms↗