Systematic Definition of Protein Constituents along the Major Polarization Axis Reveals an Adaptive Reuse of the Polarization Machinery in Pheromone-Treated Budding Yeast

Polarizing cells extensively restructure cellular components in a spatially and temporally coupledmanner along the major axis of cellular extension. Budding yeast are a useful model of polarized growth, helping to define many molecular components of this conserved process. Besides budding, yeast cells also differentiate upon treatment with pheromone from the opposite mating type, forming a mating projection (the ‘shmoo’) by directional restructuring of the cytoskeleton, localized vesicular transport and overall reorganization of the cytosol. To characterize the proteomic localization changes ac-companying polarized growth, we developed and implemented a novel cell microarray-based imaging assay for measuring the spatial redistribution of a large fraction of the yeast proteome, and applied this assay to identify proteins localized along the mating projection following pheromone treatment. We further trained a machine learning algorithm to refine the cell imaging screen, identifying additional shmoo-localized proteins. In all, we identified 74 proteins that specifically localize to the mating projection, including previously uncharacterized proteins (Ycr043c, Ydr348c, Yer071c, Ymr295c, and Yor304c-a) and known polarization complexes such as the exocyst. Functional analysis of these proteins, coupled with quantitative analysis of individual organelle movements during shmoo formation, suggests a model in which the basic machinery for cell polarization is generally conserved between processe

Random Feature Maps via a Layered Random Projection (LaRP) Framework for Object Classification

The approximation of nonlinear kernels via linear feature maps has recently gained interest due to their applications in reducing the training and testing time of kernel-based learning algorithms. Current random projection methods avoid the curse of dimensionality by embedding the nonlinear feature space into a low dimensional Euclidean space to create nonlinear kernels. We introduce a Layered Random Projection (LaRP) framework, where we model the linear kernels and nonlinearity separately for increased training efficiency. The proposed LaRP framework was assessed using the MNIST hand-written digits database and the COIL-100 object database, and showed notable improvement in object classification performance relative to other state-of-the-art random projection methods.Comment: 5 page

Nonlinear Hebbian learning as a unifying principle in receptive field formation

The development of sensory receptive fields has been modeled in the past by a variety of models including normative models such as sparse coding or independent component analysis and bottom-up models such as spike-timing dependent plasticity or the Bienenstock-Cooper-Munro model of synaptic plasticity. Here we show that the above variety of approaches can all be unified into a single common principle, namely Nonlinear Hebbian Learning. When Nonlinear Hebbian Learning is applied to natural images, receptive field shapes were strongly constrained by the input statistics and preprocessing, but exhibited only modest variation across different choices of nonlinearities in neuron models or synaptic plasticity rules. Neither overcompleteness nor sparse network activity are necessary for the development of localized receptive fields. The analysis of alternative sensory modalities such as auditory models or V2 development lead to the same conclusions. In all examples, receptive fields can be predicted a priori by reformulating an abstract model as nonlinear Hebbian learning. Thus nonlinear Hebbian learning and natural statistics can account for many aspects of receptive field formation across models and sensory modalities

ELM regime classification by conformal prediction on an information manifold

Characterization and control of plasma instabilities known as edge-localized modes (ELMs) is crucial for the operation of fusion reactors. Recently, machine learning methods have demonstrated good potential in making useful inferences from stochastic fusion data sets. However, traditional classification methods do not offer an inherent estimate of the goodness of their prediction. In this paper, a distance-based conformal predictor classifier integrated with a geometric-probabilistic framework is presented. The first benefit of the approach lies in its comprehensive treatment of highly stochastic fusion data sets, by modeling the measurements with probability distributions in a metric space. This enables calculation of a natural distance measure between probability distributions: the Rao geodesic distance. Second, the predictions are accompanied by estimates of their accuracy and reliability. The method is applied to the classification of regimes characterized by different types of ELMs based on the measurements of global parameters and their error bars. This yields promising success rates and outperforms state-of-the-art automatic techniques for recognizing ELM signatures. The estimates of goodness of the predictions increase the confidence of classification by ELM experts, while allowing more reliable decisions regarding plasma control and at the same time increasing the robustness of the control system

Representing complex data using localized principal components with application to astronomical data

Often the relation between the variables constituting a multivariate data space might be characterized by one or more of the terms: ``nonlinear'', ``branched'', ``disconnected'', ``bended'', ``curved'', ``heterogeneous'', or, more general, ``complex''. In these cases, simple principal component analysis (PCA) as a tool for dimension reduction can fail badly. Of the many alternative approaches proposed so far, local approximations of PCA are among the most promising. This paper will give a short review of localized versions of PCA, focusing on local principal curves and local partitioning algorithms. Furthermore we discuss projections other than the local principal components. When performing local dimension reduction for regression or classification problems it is important to focus not only on the manifold structure of the covariates, but also on the response variable(s). Local principal components only achieve the former, whereas localized regression approaches concentrate on the latter. Local projection directions derived from the partial least squares (PLS) algorithm offer an interesting trade-off between these two objectives. We apply these methods to several real data sets. In particular, we consider simulated astrophysical data from the future Galactic survey mission Gaia.Comment: 25 pages. In "Principal Manifolds for Data Visualization and Dimension Reduction", A. Gorban, B. Kegl, D. Wunsch, and A. Zinovyev (eds), Lecture Notes in Computational Science and Engineering, Springer, 2007, pp. 180--204, http://www.springer.com/dal/home/generic/search/results?SGWID=1-40109-22-173750210-

Fast Selection of Spectral Variables with B-Spline Compression

The large number of spectral variables in most data sets encountered in spectral chemometrics often renders the prediction of a dependent variable uneasy. The number of variables hopefully can be reduced, by using either projection techniques or selection methods; the latter allow for the interpretation of the selected variables. Since the optimal approach of testing all possible subsets of variables with the prediction model is intractable, an incremental selection approach using a nonparametric statistics is a good option, as it avoids the computationally intensive use of the model itself. It has two drawbacks however: the number of groups of variables to test is still huge, and colinearities can make the results unstable. To overcome these limitations, this paper presents a method to select groups of spectral variables. It consists in a forward-backward procedure applied to the coefficients of a B-Spline representation of the spectra. The criterion used in the forward-backward procedure is the mutual information, allowing to find nonlinear dependencies between variables, on the contrary of the generally used correlation. The spline representation is used to get interpretability of the results, as groups of consecutive spectral variables will be selected. The experiments conducted on NIR spectra from fescue grass and diesel fuels show that the method provides clearly identified groups of selected variables, making interpretation easy, while keeping a low computational load. The prediction performances obtained using the selected coefficients are higher than those obtained by the same method applied directly to the original variables and similar to those obtained using traditional models, although using significantly less spectral variables