Coreference analysis, also known as record linkage or identity uncertainty, is a difficult and important problem in natural language processing, databases, citation matching and many other tasks. This paper introduces several discriminative, conditional-probability models for coreference analysis, all examples of undirected graphical models. Unlike many historical approaches to coreference, the models presented here are relational--they do not assume that pairwise coreference decisions should be made independently from each other. Unlike other relational models of coreference that are generative, the conditional model here can incorporate a great variety of features of the input without having to be concerned about their dependencies--paralleling the advantages of conditional random fields over hidden Markov models.

This paper analyzes generalization of the classic Rescorla-Wagner (R-W) learning algorithm and studies their relationship to Maximum Likelihood estimation of causal parameters. We prove that the parameters of two popular causal models, P and P C, can be learnt by the same generalized linear Rescorla-Wagner (GLRW) algorithm provided genericity conditions apply. We characterize the fixed points of these GLRW algorithms and calculate the fluctuations about them, assuming that the input is a set of i.i.d.

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.

Spike sorting involves clustering spike trains recorded by a microelectrode according to the source neuron. It is a complicated problem, which requires a lot of human labor, partly due to the non-stationary nature of the data. We propose an automated technique for the clustering of non-stationary Gaussian sources in a Bayesian framework. At a first search stage, data is divided into short time frames and candidate descriptions of the data as a mixture of Gaussians are computed for each frame. At a second stage transition probabilities between candidate mixtures are computed, and a globally optimal clustering is found as the MAP solution of the resulting probabilistic model. Transition probabilities are computed using local stationarity assumptions and are based on a Gaussian version of the Jensen-Shannon divergence. The method was applied to several recordings. The performance appeared almost indistinguishable from humans in a wide range of scenarios, including movement, merges, and splits of clusters.

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.

First-order Markov models have been successfully applied to many problems, for example in modeling sequential data using Markov chains, and modeling control problems using the Markov decision processes (MDP) formalism. If a first-order Markov model's parameters are estimated from data, the standard maximum likelihood estimator considers only the first-order (single-step) transitions. But for many problems, the firstorder conditional independence assumptions are not satisfied, and as a result the higher order transition probabilities may be poorly approximated. Motivated by the problem of learning an MDP's parameters for control, we propose an algorithm for learning a first-order Markov model that explicitly takes into account higher order interactions during training. Our algorithm uses an optimization criterion different from maximum likelihood, and allows us to learn models that capture longer range effects, but without giving up the benefits of using first-order Markov models. Our experimental results also show the new algorithm outperforming conventional maximum likelihood estimation in a number of control problems where the MDP's parameters are estimated from data.

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.

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 describe semi-Markov conditional random fields (semi-CRFs), a conditionally trained version of semi-Markov chains. Intuitively, a semi-CRF on an input sequence x outputs a "segmentation" of x, in which labels are assigned to segments (i.e., subsequences) of x rather than to individual elements x