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Biomedical subjects

S Amari

Publications and source records attributed to S Amari.

At least 19 recordsLinked to original sources

Polytype distribution in circumstellar silicon carbide.

The inferred crystallographic class of circumstellar silicon carbide based on astronomical infrared spectra is controversial. We have directly determined the polytype distribution of circumstellar SiC from transmission electron microscopy of presolar silicon carbide from the Murchison carbonaceous meteorite. Only two polytypes (of a possible several hundred) were observed: cubic 3C and hexagonal 2H silicon carbide and their intergrowths. We conclude that this structural simplicity is a direct consequence of the low pressures in circumstellar outflows and the corresponding low silicon carbide condensation temperatures.

Astronomical Phenomena↗

Essential role of the nonreducing terminal alpha-mannosyl residues of the N-linked carbohydrate chain of bovine zona pellucida glycoproteins in sperm-egg binding.

It has been proposed that mammalian sperm bind species-specifically to carbohydrate chains of zona pellucida glycoproteins at fertilization. Although the sperm ligand carbohydrate chains have been characterized in mice and pigs, the existence of the ligands of other mammals remains unclear. In order to explore the bovine sperm ligand, two in vitro competition assay methods were applied. As a result, a high-mannose-type carbohydrate chain, Manalpha1-6(Manalpha1-3)Manalpha1-6(Manalpha1-3)Manbeta1-4GlcNAcbeta1-4GlcNAc, which is the major neutral chain in bovine egg zona glycoproteins, was shown to possess bovine sperm ligand activity. When nonreducing terminal alpha-mannosyl residues were eliminated from the zona glycoproteins by alpha-mannosidase digestion, the ligand activity was reduced, indicating that the alpha-mannosyl residues play an essential role in bovine sperm-egg binding. The number of sperm binding to eggs was reduced to about one-half after fertilization. The ligand-active high-mannose-type chain may be buried after fertilization, since its amount remains unchanged. Pretreatment of bovine sperm with the sperm ligand-carbohydrate chain significantly inhibited penetration of the sperm into oocyte and the male pronucleus formation. Thus, a correlation between the sperm ligand activity and in vitro fertilization rate was observed.

Animals↗

Unified stabilization approach to principal and minor components extraction algorithms.

Principal component and minor component extractions provide powerful techniques in many information processing fields. There have been proposed a number of algorithms for principal and minor component (or subspace) extraction, which have different dynamical behaviors. In this paper, we give rigorous stability analysis of these algorithms, obtaining a unified insight view on the dynamical behaviors of various algorithms.

Algorithms↗

Population coding with correlation and an unfaithful model.

This study investigates a population decoding paradigm in which the maximum likelihood inference is based on an unfaithful decoding model (UMLI). This is usually the case for neural population decoding because the encoding process of the brain is not exactly known or because a simplified decoding model is preferred for saving computational cost. We consider an unfaithful decoding model that neglects the pair-wise correlation between neuronal activities and prove that UMLI is asymptotically efficient when the neuronal correlation is uniform or of limited range. The performance of UMLI is compared with that of the maximum likelihood inference based on the faithful model and that of the center-of-mass decoding method. It turns out that UMLI has advantages of decreasing the computational complexity remarkably and maintaining high-level decoding accuracy. Moreover, it can be implemented by a biologically feasible recurrent network (Pouget, Zhang, Deneve, & Latham, 1998). The effect of correlation on the decoding accuracy is also discussed.

Algorithms↗

Attention modulation of neural tuning through peak and base rate.

This study investigates the influence of attention modulation on neural tuning functions. It has been shown in experiments that attention modulation alters neural tuning curves. Attention has been considered at least to serve to resolve limiting capacities and to increase the sensitivity to attended stimulus, while the exact functions of attention are still under debate. Inspired by recent experimental results on attention modulation, we investigate the influence of changes in the height and base rate of the tuning curve on the encoding accuracy, using the Fisher information. Under an assumption of stimulus-conditional independence of neural responses, we derive explicit conditions that determine when the height and base rate should be increased or decreased to improve encoding accuracy. Notably, a decrease in the tuning height and base rate can improve the encoding accuracy in some cases. Our theoretical results can predict the effective size of attention modulation on the neural population with respect to encoding accuracy. We discuss how our method can be used quantitatively to evaluate different aspects of attention function.

Animals↗

Local minima and plateaus in hierarchical structures of multilayer perceptrons.

Local minima and plateaus pose a serious problem in learning of neural networks. We investigate the hierarchical geometric structure of the parameter space of three-layer perceptrons in order to show the existence of local minima and plateaus. It is proved that a critical point of the model with H - 1 hidden units always gives many critical points of the model with H hidden units. These critical points consist of many lines in the parameter space, which can cause plateaus in learning of neural networks. Based on this result, we prove that a point in the critical lines corresponding to the global minimum of the smaller model can be a local minimum or a saddle point of the larger model. We give a necessary and sufficient condition for this, and show that this kind of local minima exist as a line segment if any. The results are universal in the sense that they do not require special properties of the target, loss functions and activation functions, but only use the hierarchical structure of the model.

Models, Neurological↗

The presence of a glycosyl phosphatidylinositol-anchored alpha-mannosidase in boar sperm.

alpha-Mannosidase and beta-galactosidase were released from boar sperm into the medium by treatment with calcium ionophore A23187 or by 0.2% Brij-35/2% acetic acid. About half as much alpha-mannosidase activity as that in the acid extract was recovered by digestion with phosphatidylinositol-specific phospholipase C (PI-PLC), whereas the liberation rate of beta-galactosidase treated with PI-PLC was low. These results suggest that some alpha-mannosidase is anchored in the plasma membrane of the acrosomal region by attachment to the lipid phosphatidylinositol and that beta-galactosidase is localized mainly in the acrosome or integrated in the plasma membrane by a spanning stretch of hydrophobic peptides. beta-Galactosidase, which is present as an oligomers in the acid extract of sperm, dissociated into monomers under weakly alkaline conditions; under acidic conditions, the monomers associated again. No pH-sensitive association-dissociation of alpha-mannosidase was observed.

Acrosome↗

Estimating functions of independent component analysis for temporally correlated signals.

This article studies a general theory of estimating functions of independent component analysis when the independent source signals are temporarily correlated. Estimating functions are used for deriving both batch and on-line learning algorithms, and they are applicable to blind cases where spatial and temporal probability structures of the sources are unknown. Most algorithms proposed so far can be analyzed in the framework of estimating functions. An admissible class of estimating functions is derived, and related efficient on-line learning algorithms are introduced. We analyze dynamical stability and statistical efficiency of these algorithms. Different from the independently and identically distributed case, the algorithms work even when only the second-order moments are used. The method of simultaneous diagonalization of cross-covariance matrices is also studied from the point of view of estimating functions.

Algorithms↗

Adaptive method of realizing natural gradient learning for multilayer perceptrons.

The natural gradient learning method is known to have ideal performances for on-line training of multilayer perceptrons. It avoids plateaus, which give rise to slow convergence of the backpropagation method. It is Fisher efficient, whereas the conventional method is not. However, for implementing the method, it is necessary to calculate the Fisher information matrix and its inverse, which is practically very difficult. This article proposes an adaptive method of directly obtaining the inverse of the Fisher information matrix. It generalizes the adaptive Gauss-Newton algorithms and provides a solid theoretical justification of them. Simulations show that the proposed adaptive method works very well for realizing natural gradient learning.

Algorithms↗

Nonholonomic orthogonal learning algorithms for blind source separation.

Independent component analysis or blind source separation extracts independent signals from their linear mixtures without assuming prior knowledge of their mixing coefficients. It is known that the independent signals in the observed mixtures can be successfully extracted except for their order and scales. In order to resolve the indeterminacy of scales, most learning algorithms impose some constraints on the magnitudes of the recovered signals. However, when the source signals are nonstationary and their average magnitudes change rapidly, the constraints force a rapid change in the magnitude of the separating matrix. This is the case with most applications (e.g., speech sounds, electroencephalogram signals). It is known that this causes numerical instability in some cases. In order to resolve this difficulty, this article introduces new nonholonomic constraints in the learning algorithm. This is motivated by the geometrical consideration that the directions of change in the separating matrix should be orthogonal to the equivalence class of separating matrices due to the scaling indeterminacy. These constraints are proved to be nonholonomic, so that the proposed algorithm is able to adapt to rapid or intermittent changes in the magnitudes of the source signals. The proposed algorithm works well even when the number of the sources is overestimated, whereas the existent algorithms do not (assuming the sensor noise is negligibly small), because they amplify the null components not included in the sources. Computer simulations confirm this desirable property.

Algorithms↗

Natural gradient learning for over- and under-complete bases In ICA.

Independent component analysis or blind source separation is a new technique of extracting independent signals from mixtures. It is applicable even when the number of independent sources is unknown and is larger or smaller than the number of observed mixture signals. This article extends the natural gradient learning algorithm to be applicable to these overcomplete and undercomplete cases. Here, the observed signals are assumed to be whitened by preprocessing, so that we use the natural Riemannian gradient in Stiefel manifolds.

Learning↗

Blind separation of a mixture of uniformly distributed source signals: A novel approach.

A new, efficient algorithm for blind separation of uniformly distributed sources is proposed. The mixing matrix is assumed to be orthogonal by prewhitening the observed signals. The learning rule adaptively estimates the mixing matrix by conceptually rotating a unit hypercube so that all output signal components are contained within or on the hypercube. Under some ideal constraints, it has been theoretically shown that the algorithm is very similar to an ideal O(1/T2) convergent algorithm, which is much faster than the existing O(1/T) convergent algorithms. The algorithm has been generalized to take care of the noisy signals by adaptively dilating the hypercube in conjunction with its rotation.

Algorithms↗

A positive selection for plasmid loss in Saccharomyces cerevisiae using galactose-inducible growth inhibitory sequences.

Counter-selections for the loss of introduced plasmid sequences are useful for gene manipulations in yeast. We have used GAL10 promoter-mediated overexpression of GIN sequences, which inhibit the growth of cells, to develop a novel counter-selection system. Yeast cells carrying a GIN sequence grow normally on glucose medium but are unable to grow on galactose medium, whereas derivatives that have lost the GIN sequence are able to grow in the presence of galactose. We constructed autonomously replicating, integrating, and disruption plasmids carrying GIN sequences and tested their use to select for loss of the plasmid. The results showed that the GIN sequences provide a selection for efficient loss of plasmids or integrated constructs from yeast during growth on galactose medium, indicating that this system can be used for plasmid shuffling, gene replacements and marker gene recycling. This counter-selection system has wide application, because any Gal+ strain and a wide variety of marker genes can be used. In addition, counter-selection systems using growth-inhibitory sequences should be applicable to other yeasts and possibly to other organisms.

Galactose↗

Improving support vector machine classifiers by modifying kernel functions.

We propose a method of modifying a kernel function to improve the performance of a support vector machine classifier. This is based on the structure of the Riemannian geometry induced by the kernel function. The idea is to enlarge the spatial resolution around the separating boundary surface, by a conformal mapping, such that the separability between classes is increased. Examples are given specifically for modifying Gaussian Radial Basis Function kernels. Simulation results for both artificial and real data show remarkable improvement of generalization errors, supporting our idea.

Journal Article↗

Complexity issues in natural gradient descent method for training multilayer perceptrons.

The natural gradient descent method is applied to train an n-m-1 multilayer perceptron. Based on an efficient scheme to represent the Fisher information matrix for an n-m-1 stochastic multilayer perceptron, a new algorithm is proposed to calculate the natural gradient without inverting the Fisher information matrix explicitly. When the input dimension n is much larger than the number of hidden neurons m, the time complexity of computing the natural gradient is O(n).

Learning↗

Multiple tuning of birdcage resonators.

A theoretical framework is presented for designing birdcage resonators for MRI and MR spectroscopy. The analogy between the birdcage problem and the phonon problem in solid-state physics is used to achieve multiple tuning. Allowing that the capacitances in the columns of the cage assume unequal values, it is possible to achieve multiple tuning and simultaneously preserve the sinusoidal current distribution necessary to set a homogeneous magnetic field. Given the physical dimensions of the columns and branches of the cage as well as the desired resonant frequencies, the corresponding values of the capacitances can be calculated exactly. Closed-form expressions for the capacitances are given in terms of the mutual inductances and the desired resonant frequencies. A detailed analysis for a symmetrical low-pass birdcage is presented. The expressions for the resonant frequencies reduce to those given by other authors when only nearest-neighbor mutual inductances are included.

Algorithms↗

A numerical study on learning curves in stochastic multilayer feedforward networks.

The universal asymptotic scaling laws proposed by Amari et al. are studied in large scale simulations using a CM5. Small stochastic multilayer feedforward networks trained with backpropagation are investigated. In the range of a large number of training patterns t, the asymptotic generalization error scales as 1/t as predicted. For a medium range t a faster 1/t2 scaling is observed. This effect is explained by using higher order corrections of the likelihood expansion. It is shown for small t that the scaling law changes drastically, when the network undergoes a transition from strong overfitting to effective learning.

Learning↗