Existing algorithms for discrete partially observable Markov decision processes can at best solve problems of a few thousand states due to two important sources of intractability: the curse of dimensionality and the policy space complexity. This paper describes a new algorithm (VDCBPI) that mitigates both sources of intractability by combining the Value Directed Compression (VDC) technique [13] with Bounded Policy Iteration (BPI) [14]. The scalability of VDCBPI is demonstrated on synthetic network management problems with up to 33 million states.

De novo Sequencing of peptides is a challenging task in proteome research. While there exist reliable DNAsequencing methods, the highthroughput de novo sequencing of proteins by mass spectrometry is still an open problem. Current approaches suffer from a lack in precision to detect mass peaks in the spectrograms. In this paper we present a novel method for de novo peptide sequencing based on a hidden Markov model. Experiments effectively demonstrate that this new method significantly outperforms standard approaches in matching quality.

We introduce a computationally efficient method to estimate the validity of the BP method as a function of graph topology, the connectivity strength, frustration and network size. We present numerical results that demonstrate the correctness of our estimates for the uniform random model and for a real-world network ("C.

Classification algorithms typically induce population-wide models that are trained to perform well on average on expected future instances. We introduce a Bayesian framework for learning instance-specific models from data that are optimized to predict well for a particular instance. Based on this framework, we present a lazy instance-specific algorithm called ISA that performs selective model averaging over a restricted class of Bayesian networks. On experimental evaluation, this algorithm shows superior performance over model selection. We intend to apply such instance-specific algorithms to improve the performance of patient-specific predictive models induced from medical data.

We propose a new method for clustering based on finding maximum margin hyperplanes through data. By reformulating the problem in terms of the implied equivalence relation matrix, we can pose the problem as a convex integer program. Although this still yields a difficult computational problem, the hard-clustering constraints can be relaxed to a soft-clustering formulation which can be feasibly solved with a semidefinite program. Since our clustering technique only depends on the data through the kernel matrix, we can easily achieve nonlinear clusterings in the same manner as spectral clustering. Experimental results show that our maximum margin clustering technique often obtains more accurate results than conventional clustering methods. The real benefit of our approach, however, is that it leads naturally to a semi-supervised training method for support vector machines. By maximizing the margin simultaneously on labeled and unlabeled training data, we achieve state of the art performance by using a single, integrated learning principle.

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.

In the context of binary classification, we define disagreement as a measure of how often two independently-trained models differ in their classification of unlabeled data. We explore the use of disagreement for error estimation and model selection. We call the procedure co-validation, since the two models effectively (in)validate one another by comparing results on unlabeled data, which we assume is relatively cheap and plentiful compared to labeled data. We show that per-instance disagreement is an unbiased estimate of the variance of error for that instance. We also show that disagreement provides a lower bound on the prediction (generalization) error, and a tight upper bound on the "variance of prediction error", or the variance of the average error across instances, where variance is measured across training sets.

It has been demonstrated that basic aspects of human visual motion perception are qualitatively consistent with a Bayesian estimation framework, where the prior probability distribution on velocity favors slow speeds. Here, we present a refined probabilistic model that can account for the typical trial-to-trial variabilities observed in psychophysical speed perception experiments. We also show that data from such experiments can be used to constrain both the likelihood and prior functions of the model. Specifically, we measured matching speeds and thresholds in a two-alternative forced choice speed discrimination task. Parametric fits to the data reveal that the likelihood function is well approximated by a LogNormal distribution with a characteristic contrast-dependent variance, and that the prior distribution on velocity exhibits significantly heavier tails than a Gaussian, and approximately follows a power-law function.

We prove generalization error bounds for predicting entries in a partially observed matrix by fitting the observed entries with a low-rank matrix. In justifying the analysis approach we take to obtain the bounds, we present an example of a class of functions of finite pseudodimension such that the sums of functions from this class have unbounded pseudodimension.

We describe an algorithm for support vector machines (SVM) that can be parallelized efficiently and scales to very large problems with hundreds of thousands of training vectors. Instead of analyzing the whole training set in one optimization step, the data are split into subsets and optimized separately with multiple SVMs. The partial results are combined and filtered again in a'Cascade' of SVMs, until the global optimum is reached. The Cascade SVM can be spread over multiple processors with minimal communication overhead and requires far less memory, since the kernel matrices are much smaller than for a regular SVM. Convergence to the global optimum is guaranteed with multiple passes th rough the Cascade, but already a single pass provides good generalization. A single pass is 5x - 10x faster than a regular SVM for problems of 100,000 vectors when implemented on a single processor. Parallel implementations on a cluster of 16 processors were tested with over 1 million vectors (2-class problems), converging in a day or two, while a regular SVM never converged in over a week.