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PubMed2006

Kernel least-squares models using updates of the pseudoinverse.

Sparse nonlinear classification and regression models in reproducing kernel Hilbert spaces (RKHSs) are considered. The use of Mercer kernels and the square loss function gives rise to an overdetermined linear least-squares problem in the corresponding RKHS. When we apply a greedy forward selection scheme, the least-squares problem may be solved by an order-recursive update of the pseudoinverse in each iteration step. The computational time is linear with respect to the number of the selected training samples.

Computer Simulation↗
PubMed2006

Computational framework for the prediction of transcription factor binding sites by multiple data integration.

Control of gene expression is essential to the establishment and maintenance of all cell types, and its dysregulation is involved in pathogenesis of several diseases. Accurate computational predictions of transcription factor regulation may thus help in understanding complex diseases, including mental disorders in which dysregulation of neural gene expression is thought to play a key role. However, biological mechanisms underlying the regulation of gene expression are not completely understood, and predictions via bioinformatics tools are typically poorly specific. We developed a bioinformatics workflow for the prediction of transcription factor binding sites from several independent datasets. We show the advantages of integrating information based on evolutionary conservation and gene expression, when tackling the problem of binding site prediction. Consistent results were obtained on a large simulated dataset consisting of 13050 in silico promoter sequences, on a set of 161 human gene promoters for which binding sites are known, and on a smaller set of promoters of Myc target genes. Our computational framework for binding site prediction can integrate multiple sources of data, and its performance was tested on different datasets. Our results show that integrating information from multiple data sources, such as genomic sequence of genes' promoters, conservation over multiple species, and gene expression data, indeed improves the accuracy of computational predictions.

Animals↗
PubMed2001

Monitoring task loading with multivariate EEG measures during complex forms of human-computer interaction.

Electroencephalographic (EEG) recordings were made while 16 participants performed versions of a personal-computer-based flight simulation task of low, moderate, or high difficulty. As task difficulty increased, frontal midline theta EEG activity increased and alpha band activity decreased. A participant-specific function that combined multiple EEG features to create a single load index was derived from a sample of each participant's data and then applied to new test data from that participant. Index values were computed for every 4 s of task data. Across participants, mean task load index values increased systematically with increasing task difficulty and differed significantly between the different task versions. Actual or potential applications of this research include the use of multivariate EEG-based methods to monitor task loading during naturalistic computer-based work.

Adult↗
PubMed2001

Neuronal population codes and the perception of object distance in weakly electric fish.

Weakly electric fish use an electric sense to navigate and capture prey in the dark. Objects in the surroundings of the fish produce distortions in their self-generated electric field; these distortions form a two-dimensional Gaussian-like electric image on the skin surface. To determine the distance of an object, the peak amplitude and width of its electric image must be estimated. These sensory features are encoded by a neuronal population in the early stages of the electrosensory pathway, but are not represented with classic bell-shaped neuronal tuning curves. In contrast, bell-shaped tuning curves do characterize the neuronal responses to the location of the electric image on the body surface, such that parallel two-dimensional maps of this feature are formed. In the case of such two-dimensional maps, theoretical results suggest that the width of neural tuning should have no effect on the accuracy of a population code. Here we show that although the spatial scale of the electrosensory maps does not affect the accuracy of encoding the body surface location of the electric image, maps with narrower tuning are better for estimating image width and those with wider tuning are better for estimating image amplitude. We quantitatively evaluate a two-step algorithm for distance perception involving the sequential estimation of peak amplitude and width of the electric image. This algorithm is best implemented by two neural maps with different tuning widths. These results suggest that multiple maps of sensory features may be specialized with different tuning widths, for encoding additional sensory features that are not explicitly mapped.

Algorithms↗
PubMed2001

Diagnosis supporting rules of the Hepar system.

The "Hepar" system comprises a clinical database and the shell of procedures that aim at data analysis and the support of diagnosis. The database consists of hepatological patient cases. Each case is described by about 200 medical findings and histopathologically verified diagnosis. The diagnosis supporting rules of "Hepar" are based on visualizing data transformations and on the similarity based techniques. The applied linear visualizing transformations of data sets on the plane aim at separating of the groups of patients associated with different diseases. The resulting diagnostic maps by the visual inspection allow to find such cases in the database that are similar to the previously diagnosed patients. This paper examines combining of data transformations with the nearest neighbors techniques in the support of diagnosis. We report the results on the experimental comparisons of different decision rules including the feature selection procedure.

Decision Support Techniques↗
PubMed2003

Measuring linear and quadratic contributions to neuronal response.

We present a method to dissociate the sign-dependent (linear or odd-order) response from the sign-independent (quadratic or even-order) response of a neuron to sequences of random orthonormal stimulus elements. The method is based on a modification of the classical linear-nonlinear model of neural response. The analysis produces estimates of the stimulus features to which the neuron responds in a sign-dependent manner, the stimulus features to which the neuron responds in a sign-independent manner and the relative weight of the sign-independent response. We propose that this method could be used to characterize simple and complex cells in the primary visual cortex.

Action Potentials↗
PubMed2004

[The chromosomal location of AD7C-NTP gene and the prediction of transmembrane domains of its deduced protein].

AIM: To characterize the chromosomal location of AD7C-NTP gene and predict the transmembrane domains and sub-cellular location of its deduced protein. METHODS: The AD7C-NTP mRNA sequence was alignmented with human genomic DNA sequence by Blat server. The transmembrane domains and sub-cellular location of AD7C-NTP protein were predicted by using PHDhtm, TMHMM2.0, HMMTOP2.0, SMART and PSORT servers, etc. RESULTS: The AD7C-NTP gene located in minus strand of 1p36.11, without intron. The AD7C-NTP protein was predicted to have 3 potential transmembrane domains and locate on peroxisome's membrane. CONCLUSION: Bioinformatics analysis of the AD7C-NTP gene and its deduced protein provides valuable clues for further gene cloning and study of function.

Alzheimer Disease↗
PubMed2004

[The research to the optimal calibration model for discrete scanning spectrometers].

For spectrometers which don't operate in consistently scanning mode such as fixed-filter spectrometer, diode arrays spectrometer and so on, how to find an optimal wavelengths combination rapidly and accurately has always been a key problem in NIR so far. The conventional methods to choose the optimal wavelengths for calibration are Forward Stepwise multiple linear Regression (FSR) and Backward Stepwise Regression (BSR), which choose the optimal wavelengths based on the t test result of all the calibration wavelengths. However, maybe the wavelength eliminated is very useful in application and the wavelength chosen may not be so useful as expected, as a result it is compulsory to make more tests to verify the truly applicable wavelength combination for calibration. In this paper the combination of the combination-making algorithm in combinatorics and computer languages which operate facing matrix is used to choose the optimal combination of wavelengths for calibration automatically and efficiently by computer. The most robust calibration equation can be obtained by making analysis of calibration regression that operates to find the minimum root mean standard error of calibration.

Calibration↗
PubMed2005

A universal learning rule that minimizes well-formed cost functions.

In this paper, we analyze stochastic gradient learning rules for posterior probability estimation using networks with a single layer of weights and a general nonlinear activation function. We provide necessary and sufficient conditions on the learning rules and the activation function to obtain probability estimates. Also, we extend the concept of well-formed cost function, proposed by Wittner and Denker, to multiclass problems, and we provide theoretical results showing the advantages of this kind of objective functions.

Algorithms↗
PubMed2006

The Self-Organizing Relationship (SOR) network employing fuzzy inference based heuristic evaluation.

When human beings acquire a new skill, this usually is accomplished by the summarization of numerous experiences based on their own evaluation criteria. Usually these experiences are obtained by trial and error. The criteria for success and failure are based on our own knowledge or advice given by others. The Self-Organizing Relationship (SOR) network has been inspired by this process and has been proposed to emulate this process computationally. In the previous applications of the SOR network for controller design, the evaluation criteria have been assigned by using mathematical expressions. Generally, however, mathematical expressions of the evaluation criteria become difficult as the complexity of a target system increases. On the other hand, human beings can contrive to express their knowledge for evaluation by using heuristic expressions, although a target system is complicated. In this study, we employ fuzzy inference in order to realize heuristic expressions of the evaluation criteria.

Algorithms↗
PubMed2004

Representation of number in animals and humans: a neural model.

This article addresses the representation of numerical information conveyed by nonsymbolic and symbolic stimuli. In a first simulation study, we show how number-selective neurons develop when an initially uncommitted neural network is given nonsymbolic stimuli as input (e.g., collections of dots) under unsupervised learning. The resultant network is able to account for the distance and size effects, two ubiquitous effects in numerical cognition. Furthermore, the properties of the network units conform in detail to the characteristics of recently discovered number-selective neurons. In a second study, we simulate symbol learning by presenting symbolic and nonsymbolic input simultaneously. The same number-selective neurons learn to represent the numerical meaning of symbols. In doing so, they show properties reminiscent of the originally available number-selective neurons, but at the same time, the representational efficiency of the neurons is increased when presented with symbolic input. This finding presents a concrete proposal on the linkage between higher order numerical cognition and more primitive numerical abilities and generates specific predictions on the neural substrate of number processing.

Animals↗
PubMed2004

Improving generalization performance of natural gradient learning using optimized regularization by NIC.

Natural gradient learning is known to be efficient in escaping plateau, which is a main cause of the slow learning speed of neural networks. The adaptive natural gradient learning method for practical implementation also has been developed, and its advantage in real-world problems has been confirmed. In this letter, we deal with the generalization performances of the natural gradient method. Since natural gradient learning makes parameters fit to training data quickly,the overfitting phenomenon may easily occur, which results in poor generalization performance. To solve the problem, we introduce the regularization term in natural gradient learning and propose an efficient optimizing method for the scale of regularization by using a generalized Akaike information criterion (network information criterion). We discuss the properties of the optimized regularization strength by NIC through theoretical analysis as well as computer simulations. We confirm the computational efficiency and generalization performance of the proposed method in real-world applications through computational experiments on benchmark problems.

Algorithms↗
PubMed2005

Exploring spike transfer through the thalamus using hybrid artificial-biological neuronal networks.

We use dynamic clamp to construct "hybrid" thalamic circuits by connecting a biological neuron in situ to silicon- or software-generated "neurons" through artificial synapses. The purpose is to explore cellular sensory gating mechanisms that regulate the transfer efficiency of signals during different sleep-wake states. Hybrid technology is applied in vitro to different paradigms such as: (1) simulating interactions between biological thalamocortical neurons, artificial reticular thalamic inhibitory interneurons and a simulated sensory input, (2) grafting an artificial sensory input to a wholly biological thalamic network that generates spontaneous sleep-like oscillations, (3) injecting in thalamocortical neurons a background synaptic bombardment mimicking the activity of corticothalamic inputs. We show that the graded control of the strength of intrathalamic inhibition, combined with the membrane polarization and the fluctuating synaptic noise in thalamocortical neurons, is able to govern functional shifts between different input/output transmission states of the thalamic gate.

Action Potentials↗
PubMed2004

A new information processing measure for adaptive complex systems.

This paper presents an implementation-independent measure of the amount of information processing performed by (part of) an adaptive system which depends on the goal to be performed by the overall system. This new measure gives rise to a theoretical framework under which several classical supervised and unsupervised learning algorithms fall and, additionally, new efficient learning algorithms can be derived. In the context of neural networks, the framework of information theory strives to design neurally inspired structures from which complex functionality should emerge. Yet, classical measures of information have not taken an explicit account of some of the fundamental concepts in brain theory and neural computation, namely that optimal coding depends on the specific task(s) to be solved by the system and that goal orientedness also depends on extracting relevant information from the environment to be able to affect it in the desired way. We present a new information processing measure that takes into account both the extraction of relevant information and the reduction of spurious information for the task to be solved by the system. This measure is implementation-independent and therefore can be used to analyze and design different adaptive systems. Specifically, we show its application for learning perceptrons, decision trees and linear autoencoders.

Algorithms↗