We propose a "soft greedy" learning algorithm for building small conjunctions of simple threshold functions, called rays, defined on single real-valued attributes. We also propose a PAC-Bayes risk bound which is minimized for classifiers achieving a nontrivial tradeoff between sparsity (the number of rays used) and the magnitude of the separating margin of each ray. Finally, we test the soft greedy algorithm on four DNA micro-array data sets.

Multiple realizations of continuous-valued time series from a stochastic process often contain systematic variations in rate and amplitude. To leverage the information contained in such noisy replicate sets, we need to align them in an appropriate way (for example, to allow the data to be properly combined by adaptive averaging). We present the Continuous Profile Model (CPM), a generative model in which each observed time series is a non-uniformly subsampled version of a single latent trace, to which local rescaling and additive noise are applied. After unsupervised training, the learned trace represents a canonical, high resolution fusion of all the replicates. As well, an alignment in time and scale of each observation to this trace can be found by inference in the model. We apply CPM to successfully align speech signals from multiple speakers and sets of Liquid Chromatography-Mass Spectrometry proteomic data.

Areas of the brain involved in various forms of memory exhibit patterns of neural activity quite unlike those in canonical computational models. We show how to use well-founded Bayesian probabilistic autoassociative recall to derive biologically reasonable neuronal dynamics in recurrently coupled models, together with appropriate values for parameters such as the membrane time constant and inhibition. We explicitly treat two cases. One arises from a standard Hebbian learning rule, and involves activity patterns that are coded by graded firing rates. The other arises from a spike timing dependent learning rule, and involves patterns coded by the phase of spike times relative to a coherent local field potential oscillation. Our model offers a new and more complete understanding of how neural dynamics may support autoassociation.

The correction of bias in magnetic resonance images is an important problem in medical image processing. Most previous approaches have used a maximum likelihood method to increase the likelihood of the pixels in a single image by adaptively estimating a correction to the unknown image bias field. The pixel likelihoods are defined either in terms of a preexisting tissue model, or non-parametrically in terms of the image's own pixel values. In both cases, the specific location of a pixel in the image is not used to calculate the likelihoods. We suggest a new approach in which we simultaneously eliminate the bias from a set of images of the same anatomy, but from different patients. We use the statistics from the same location across different images, rather than within an image, to eliminate bias fields from all of the images simultaneously. The method builds a "multi-resolution" nonparametric tissue model conditioned on image location while eliminating the bias fields associated with the original image set.

We present a graphical model for beat tracking in recorded music. Using a probabilistic graphical model allows us to incorporate local information and global smoothness constraints in a principled manner. We evaluate our model on a set of varied and difficult examples, and achieve impressive results. By using a fast dual-tree algorithm for graphical model inference, our system runs in less time than the duration of the music being processed.

We study a method of optimal data-driven aggregation of classifiers in a convex combination and establish tight upper bounds on its excess risk with respect to a convex loss function under the assumption that the solution of optimal aggregation problem is sparse. We use a boosting type algorithm of optimal aggregation to develop aggregate classifiers of activation patterns in fMRI based on locally trained SVM classifiers. The aggregation coefficients are then used to design a "boosting map" of the brain needed to identify the regions with most significant impact on classification.

The structural similarity of neural networks and genetic regulatory networks to digital circuits, and hence to each other, was noted from the very beginning of their study [1, 2]. In this work, we propose a simple biochemical system whose architecture mimics that of genetic regulation and whose components allow for in vitro implementation of arbitrary circuits. We use only two enzymes in addition to DNA and RNA molecules: RNA polymerase (RNAP) and ribonuclease (RNase). We develop a rate equation for in vitro transcriptional networks, and derive a correspondence with general neural network rate equations [3]. As proof-of-principle demonstrations, an associative memory task and a feedforward network computation are shown by simulation. A difference between the neural network and biochemical models is also highlighted: global coupling of rate equations through enzyme saturation can lead to global feedback regulation, thus allowing a simple network without explicit mutual inhibition to perform the winner-take-all computation. Thus, the full complexity of the cell is not necessary for biochemical computation: a wide range of functional behaviors can be achieved with a small set of biochemical components.

In this paper we propose to combine two powerful ideas, boosting and manifold learning.

We present a competitive analysis of Bayesian learning algorithms in the online learning setting and show that many simple Bayesian algorithms (such as Gaussian linear regression and Bayesian logistic regression) perform favorably when compared, in retrospect, to the single best model in the model class. The analysis does not assume that the Bayesian algorithms' modeling assumptions are "correct," and our bounds hold even if the data is adversarially chosen. For Gaussian linear regression (using logloss), our error bounds are comparable to the best bounds in the online learning literature, and we also provide a lower bound showing that Gaussian linear regression is optimal in a certain worst case sense. We also give bounds for some widely used maximum a posteriori (MAP) estimation algorithms, including regularized logistic regression.

We examine the marriage of recent probabilistic generative models for social networks with classical frameworks from mathematical economics. We are particularly interested in how the statistical structure of such networks influences global economic quantities such as price variation. Our findings are a mixture of formal analysis, simulation, and experiments on an international trade data set from the United Nations.