We provide preliminary evidence that eXlstmg algorithms for inferring small-scale gene regulation networks from gene expression data can be adapted to large-scale gene expression data coming from hybridization microarrays. The essential steps are (1) clustering many genes by their expression time-course data into a minimal set of clusters of co-expressed genes, (2) theoretically modeling the various conditions under which the time-courses are measured using a continious-time analog recurrent neural network for the cluster mean time-courses, (3) fitting such a regulatory model to the cluster mean time courses by simulated annealing with weight decay, and (4) analysing several such fits for commonalities in the circuit parameter sets including the connection matrices. This procedure can be used to assess the adequacy of existing and future gene expression time-course data sets for determ ining transcriptional regulatory relationships such as coregulation.

In this paper we define a probabilistic computational model which generalizes many noisy neural network models, including the recent work of Maass and Sontag [5]. We identify weak ergodicjty as the mechanism responsible for restriction of the computational power of probabilistic models to definite languages, independent of the characteristics of the noise: whether it is discrete or analog, or if it depends on the input or not, and independent of whether the variables are discrete or continuous. We give examples of weakly ergodic models including noisy computational systems with noise depending on the current state and inputs, aggregate models, and computational systems which update in continuous time. 1 Introduction Noisy neural networks were recently examined, e.g.

Local "belief propagation" rules of the sort proposed by Pearl [15] are guaranteed to converge to the correct posterior probabilities in singly connected graphical models. Recently, a number of researchers have empirically demonstrated good performance of "loopy belief propagation" using these same rules on graphs with loops. Perhaps the most dramatic instance is the near Shannon-limit performance of "Turbo codes", whose decoding algorithm is equivalent to loopy belief propagation. Except for the case of graphs with a single loop, there has been little theoretical understanding of the performance of loopy propagation. Here we analyze belief propagation in networks with arbitrary topologies when the nodes in the graph describe jointly Gaussian random variables.

The statistics of photographic images, when represented using multiscale (wavelet) bases, exhibit two striking types of non Gaussian behavior. First, the marginal densities of the coefficients have extended heavy tails. Second, the joint densities exhibit variance dependencies not captured by second-order models. We examine properties of the class of Gaussian scale mixtures, and show that these densities can accurately characterize both the marginal and joint distributions of natural image wavelet coefficients. This class of model suggests a Markov structure, in which wavelet coefficients are linked by hidden scaling variables corresponding to local image structure. We derive an estimator for these hidden variables, and show that a nonlinear "normalization" procedure can be used to Gaussianize the coefficients.

In the analysis of data recorded by optical imaging from intrinsic signals (measurement of changes of light reflectance from cortical tissue) the removal of noise and artifacts such as blood vessel patterns is a serious problem. Often bandpass filtering is used, but the underlying assumption that a spatial frequency exists, which separates the mapping component from other components (especially the global signal), is questionable. Here we propose alternative ways of processing optical imaging data, using blind source separation techniques based on the spatial decorre1ation of the data. We first perform benchmarks on artificial data in order to select the way of processing, which is most robust with respect to sensor noise. We then apply it to recordings of optical imaging experiments from macaque primary visual cortex. We show that our BSS technique is able to extract ocular dominance and orientation preference maps from single condition stacks, for data, where standard post-processing procedures fail. Artifacts, especially blood vessel patterns, can often be completely removed from the maps. In summary, our method for blind source separation using extended spatial decorrelation is a superior technique for the analysis of optical recording data.

Effective methods of capacity control via uniform convergence bounds for function expansions have been largely limited to Support Vector machines, where good bounds are obtainable by the entropy number approach. We extend these methods to systems with expansions in terms of arbitrary (parametrized) basis functions and a wide range of regularization methods covering the whole range of general linear additive models. This is achieved by a data dependent analysis of the eigenvalues of the corresponding design matrix.

We propose a new and efficient technique for incorporating contextual information into object classification. Most of the current techniques face the problem of exponential computation cost. In this paper, we propose a new general framework that incorporates partial context at a linear cost. This technique is applied to microscopic urinalysis image recognition, resulting in a significant improvement of recognition rate over the context free approach. This gain would have been impossible using conventional context incorporation techniques.

We formulate the problem of retrieving images from visual databases as a problem of Bayesian inference. This leads to natural and effective solutions for two of the most challenging issues in the design of a retrieval system: providing support for region-based queries without requiring prior image segmentation, and accounting for user-feedback during a retrieval session. We present a new learning algorithm that relies on belief propagation to account for both positive and negative examples of the user's interests.

Although one can derive the Gaussian noise assumption based on a maximum entropy approach, the main reason for this assumption is practicability: under the Gaussian noise assumption the maximum likelihood parameter estimate can simply be found by minimization of the squared error. Despite its common use it is far from clear that the Gaussian noise assumption is a good choice for many practical problems. A reasonable approach therefore would be a noise distribution which contains the Gaussian as a special case but which has a tunable parameter that allows for more flexible distributions.

We discuss an information theoretic approach for categorizing and modeling dynamic processes. The approach can learn a compact and informative statistic which summarizes past states to predict future observations. Furthermore, the uncertainty of the prediction is characterized nonparametrically by a joint density over the learned statistic and present observation. We discuss the application of the technique to both noise driven dynamical systems and random processes sampled from a density which is conditioned on the past. In the first case we show results in which both the dynamics of random walk and the statistics of the driving noise are captured. In the second case we present results in which a summarizing statistic is learned on noisy random telegraph waves with differing dependencies on past states. In both cases the algorithm yields a principled approach for discriminating processes with differing dynamics and/or dependencies. The method is grounded in ideas from information theory and nonparametric statistics.