Mean Field Approaches to Independent Component Analysis

We develop mean field approaches for probabilistic independent component analysis (ICA). The sources are estimated from the mean of their posterior distribution and the mixing matrix (and noise level) is estimated by maximum a posteriori (MAP). The latter requires the computation of (a good approximation to) the correlations between sources. For this purpose we investigate three increasingly advanced mean field methods: variational, linear response and adaptive TAP and test the resulting algorithms on a number of problems. On synthetic data the advanced mean field approaches are able to recover the correct mixing matrix in cases where the variational mean field theory fails. For hand-written digits, sparse encoding is achieved using non-negative source and mixing priors. For speech, the mean field method is able to separate in the underdetermined (overcomplete) case of two sensors and three sources. One major advantage of the proposed method is its generality and implementational simplicity. Finally, we point out several possible extensions of the approaches developed here

Modulation Classification for MIMO-OFDM Signals via Approximate Bayesian Inference

The problem of modulation classification for a multiple-antenna (MIMO) system employing orthogonal frequency division multiplexing (OFDM) is investigated under the assumption of unknown frequency-selective fading channels and signal-to-noise ratio (SNR). The classification problem is formulated as a Bayesian inference task, and solutions are proposed based on Gibbs sampling and mean field variational inference. The proposed methods rely on a selection of the prior distributions that adopts a latent Dirichlet model for the modulation type and on the Bayesian network formalism. The Gibbs sampling method converges to the optimal Bayesian solution and, using numerical results, its accuracy is seen to improve for small sample sizes when switching to the mean field variational inference technique after a number of iterations. The speed of convergence is shown to improve via annealing and random restarts. While most of the literature on modulation classification assume that the channels are flat fading, that the number of receive antennas is no less than that of transmit antennas, and that a large number of observed data symbols are available, the proposed methods perform well under more general conditions. Finally, the proposed Bayesian methods are demonstrated to improve over existing non-Bayesian approaches based on independent component analysis and on prior Bayesian methods based on the `superconstellation' method.Comment: To be appear in IEEE Trans. Veh. Technolog

Mapping Spatial Variations of Structure and Function Parameters for Forest Condition Assessment of the Changbai Mountain National Nature Reserve

Forest condition is the baseline information for ecological evaluation and management. The National Forest Inventory of China contains structural parameters, such as canopy closure, stand density and forest age, and functional parameters, such as stand volume and soil fertility. Conventionally forest conditions are assessed through parameters collected from field observations, which could be costly and spatially limited. It is crucial to develop modeling approaches in mapping forest assessment parameters from satellite remote sensing. This study mapped structure and function parameters for forest condition assessment in the Changbai Mountain National Nature Reserve (CMNNR). The mapping algorithms, including statistical regression, random forests, and random forest kriging, were employed with predictors from Advanced Land Observing Satellite (ALOS)-2, Sentinel-1, Sentinel-2 satellite sensors, digital surface model of ALOS, and 1803 field sampled forest plots. Combined predicted parameters and weights from principal component analysis, forest conditions were assessed. The models explained spatial dynamics and characteristics of forest parameters based on an independent validation with all r values above 0.75. The root mean square error (RMSE) values of canopy closure, stand density, stand volume, forest age and soil fertility were 4.6%, 33.8%, 29.4%, 20.5%, and 14.3%, respectively. The mean assessment score suggested that forest conditions in the CMNNR are mainly resulted from spatial variations of function parameters such as stand volume and soil fertility. This study provides a methodology on forest condition assessment at regional scales, as well as the up-to-date information for the forest ecosystem in the CMNNR

Noisy independent component analysis of auto-correlated components

We present a new method for the separation of superimposed, independent, auto-correlated components from noisy multi-channel measurement. The presented method simultaneously reconstructs and separates the components, taking all channels into account and thereby increases the effective signal-to-noise ratio considerably, allowing separations even in the high noise regime. Characteristics of the measurement instruments can be included, allowing for application in complex measurement situations. Independent posterior samples can be provided, permitting error estimates on all desired quantities. Using the concept of information field theory, the algorithm is not restricted to any dimensionality of the underlying space or discretization scheme thereof

A stochastic algorithm for probabilistic independent component analysis

The decomposition of a sample of images on a relevant subspace is a recurrent problem in many different fields from Computer Vision to medical image analysis. We propose in this paper a new learning principle and implementation of the generative decomposition model generally known as noisy ICA (for independent component analysis) based on the SAEM algorithm, which is a versatile stochastic approximation of the standard EM algorithm. We demonstrate the applicability of the method on a large range of decomposition models and illustrate the developments with experimental results on various data sets.Comment: Published in at http://dx.doi.org/10.1214/11-AOAS499 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

From principal component to direct coupling analysis of coevolution in proteins: Low-eigenvalue modes are needed for structure prediction

Various approaches have explored the covariation of residues in multiple-sequence alignments of homologous proteins to extract functional and structural information. Among those are principal component analysis (PCA), which identifies the most correlated groups of residues, and direct coupling analysis (DCA), a global inference method based on the maximum entropy principle, which aims at predicting residue-residue contacts. In this paper, inspired by the statistical physics of disordered systems, we introduce the Hopfield-Potts model to naturally interpolate between these two approaches. The Hopfield-Potts model allows us to identify relevant 'patterns' of residues from the knowledge of the eigenmodes and eigenvalues of the residue-residue correlation matrix. We show how the computation of such statistical patterns makes it possible to accurately predict residue-residue contacts with a much smaller number of parameters than DCA. This dimensional reduction allows us to avoid overfitting and to extract contact information from multiple-sequence alignments of reduced size. In addition, we show that low-eigenvalue correlation modes, discarded by PCA, are important to recover structural information: the corresponding patterns are highly localized, that is, they are concentrated in few sites, which we find to be in close contact in the three-dimensional protein fold.Comment: Supporting information can be downloaded from: http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.100317

Are v1 simple cells optimized for visual occlusions? : A comparative study

Abstract: Simple cells in primary visual cortex were famously found to respond to low-level image components such as edges. Sparse coding and independent component analysis (ICA) emerged as the standard computational models for simple cell coding because they linked their receptive fields to the statistics of visual stimuli. However, a salient feature of image statistics, occlusions of image components, is not considered by these models. Here we ask if occlusions have an effect on the predicted shapes of simple cell receptive fields. We use a comparative approach to answer this question and investigate two models for simple cells: a standard linear model and an occlusive model. For both models we simultaneously estimate optimal receptive fields, sparsity and stimulus noise. The two models are identical except for their component superposition assumption. We find the image encoding and receptive fields predicted by the models to differ significantly. While both models predict many Gabor-like fields, the occlusive model predicts a much sparser encoding and high percentages of ‘globular’ receptive fields. This relatively new center-surround type of simple cell response is observed since reverse correlation is used in experimental studies. While high percentages of ‘globular’ fields can be obtained using specific choices of sparsity and overcompleteness in linear sparse coding, no or only low proportions are reported in the vast majority of studies on linear models (including all ICA models). Likewise, for the here investigated linear model and optimal sparsity, only low proportions of ‘globular’ fields are observed. In comparison, the occlusive model robustly infers high proportions and can match the experimentally observed high proportions of ‘globular’ fields well. Our computational study, therefore, suggests that ‘globular’ fields may be evidence for an optimal encoding of visual occlusions in primary visual cortex. Author Summary: The statistics of our visual world is dominated by occlusions. Almost every image processed by our brain consists of mutually occluding objects, animals and plants. Our visual cortex is optimized through evolution and throughout our lifespan for such stimuli. Yet, the standard computational models of primary visual processing do not consider occlusions. In this study, we ask what effects visual occlusions may have on predicted response properties of simple cells which are the first cortical processing units for images. Our results suggest that recently observed differences between experiments and predictions of the standard simple cell models can be attributed to occlusions. The most significant consequence of occlusions is the prediction of many cells sensitive to center-surround stimuli. Experimentally, large quantities of such cells are observed since new techniques (reverse correlation) are used. Without occlusions, they are only obtained for specific settings and none of the seminal studies (sparse coding, ICA) predicted such fields. In contrast, the new type of response naturally emerges as soon as occlusions are considered. In comparison with recent in vivo experiments we find that occlusive models are consistent with the high percentages of center-surround simple cells observed in macaque monkeys, ferrets and mice