We develop and test new machine learning methods for the prediction of topological representations of protein structures in the form of coarse-or fine-grained contact or distance maps that are translation and rotation invariant. The methods are based on generalized input-output hidden Markov models (GIOHMMs) and generalized recursive neural networks (GRNNs). The methods are used to predict topology directly in the fine-grained case and, in the coarsegrained case, indirectly by first learning how to score candidate graphs and then using the scoring function to search the space of possible configurations. Computer simulations show that the predictors achieve state-of-the-art performance.

The problem of super-resolution involves generating feasible higher resolution images, which are pleasing to the eye and realistic, from a given low resolution image. This might be attempted by using simple filters for smoothing out the high resolution blocks or through applications where substantial prior information is used to imply the textures and shapes which will occur in the images. In this paper we describe an approach which lies between the two extremes. It is a generic unsupervised method which is usable in all domains, but goes beyond simple smoothing methods in what it achieves. We use a dynamic treelike architecture to model the high resolution data. Approximate conditioning on the low resolution image is achieved through a mean field approach.

Machine learning has reached a point where many probabilistic methods can be understood as variations, extensions and combinations of a much smaller set of abstract themes, e.g., as different instances of the EM algorithm. This enables the systematic derivation of algorithms customized for different models.

This paper presents a kernel method that allows to combine color and shape information for appearance-based object recognition. It doesn't require to define a new common representation, but use the power of kernels to combine different representations together in an effective manner. These results are achieved using results of statistical mechanics of spin glasses combined with Markov random fields via kernel functions. Experiments show an increase in recognition rate up to 5.92% with respect to conventional strategies.

We consider data which are images containing views of multiple objects. Our task is to learn about each of the objects present in the images. This task can be approached as a factorial learning problem, where each image must be explained by instantiating a model for each of the objects present with the correct instantiation parameters. A major problem with learning a factorial model is that as the number of objects increases, there is a combinatorial explosion of the number of configurations that need to be considered. We develop a method to extract object models sequentially from the data by making use of a robust statistical method, thus avoiding the combinatorial explosion, and present results showing successful extraction of objects from real images.

We examine the problem of generating state-space compressions of POMDPs in a way that minimally impacts decision quality. We analyze the impact of compressions on decision quality, observing that compressions that allow accurate policy evaluation (prediction of expected future reward) will not affect decision quality. We derive a set of sufficient conditions that ensure accurate prediction in this respect, illustrate interesting mathematical properties these confer on lossless linear compressions, and use these to derive an iterative procedure for finding good linear lossy compressions. We also elaborate on how structured representations of a POMDP can be used to find such compressions.

This paper focuses on people's short-run behavior by examining dynamical versions of these three theories, and comparing their predictions to a real-world dataset.

Greedy importance sampling is an unbiased estimation technique that reduces the variance of standard importance sampling by explicitly searching for modes in the estimation objective. Previous work has demonstrated the feasibility of implementing this method and proved that the technique is unbiased in both discrete and continuous domains. In this paper we present a reformulation of greedy importance sampling that eliminates the free parameters from the original estimator, and introduces a new regularization strategy that further reduces variance without compromising unbiasedness. The resulting estimator is shown to be effective for difficult estimation problems arising in Markov random field inference. In particular, improvements are achieved over standard MCMC estimators when the distribution has multiple peaked modes.

In this paper, we propose a Bayesian framework, which constructs shared-state triphone HMMs based on a variational Bayesian approach, and recognizes speech based on the Bayesian prediction classification; variational Bayesian estimation and clustering for speech recognition (VBEC). An appropriate model structure with high recognition performance can be found within a VBEC framework. Unlike conventional methods, including BIC or MDL criterion based on the maximum likelihood approach, the proposed model selection is valid in principle, even when there are insufficient amounts of data, because it does not use an asymptotic assumption. In isolated word recognition experiments, we show the advantage of VBEC over conventional methods, especially when dealing with small amounts of data.

Classification trees are one of the most popular types of classifiers, with ease of implementation and interpretation being among their attractive features. Despite the widespread use of classification trees, theoretical analysis of their performance is scarce. In this paper, we show that a new family of classification trees, called dyadic classification trees (DCTs), are near optimal (in a minimax sense) for a very broad range of classification problems. This demonstrates that other schemes (e.g., neural networks, support vector machines) cannot perform significantly better than DCTs in many cases. We also show that this near optimal performance is attained with linear (in the number of training data) complexity growing and pruning algorithms. Moreover, the performance of DCTs on benchmark datasets compares favorably to that of standard CART, which is generally more computationally intensive and which does not possess similar near optimality properties. Our analysis stems from theoretical results on structural risk minimization, on which the pruning rule for DCTs is based.