Many domains are naturally organized in an abstraction hierarchy or taxonomy, where the instances in "nearby" classes in the taxonomy are similar. In this paper, we provide a general probabilistic framework for clustering data into a set of classes organized as a taxonomy, where each class is associated with a probabilistic model from which the data was generated. The clustering algorithm simultaneously optimizes three things: the assignment of data instances to clusters, the models associated with the clusters, and the structure of the abstraction hierarchy. A unique feature of our approach is that it utilizes global optimization algorithms for both of the last two steps, reducing the sensitivity to noise and the propensity to local maxima that are characteristic of algorithms such as hierarchical agglomerative clustering that only take local steps. We provide a theoretical analysis for our algorithm, showing that it converges to a local maximum of the joint likelihood of model and data.

We propose the framework of mutual information kernels for learning covariance kernels, as used in Support Vector machines and Gaussian process classifiers, from unlabeled task data using Bayesian techniques. We describe an implementation of this framework which uses variational Bayesian mixtures of factor analyzers in order to attack classification problems in high-dimensional spaces where labeled data is sparse, but unlabeled data is abundant.

We investigate a learning algorithm for the classification of nonnegative data by mixture models. Multiplicative update rules are derived that directly optimize the performance of these models as classifiers. The update rules have a simple closed form and an intuitive appeal. Our algorithm retains the main virtues of the Expectation-Maximization (EM) algorithm--its guarantee of monotonic improvement, and its absence of tuning parameters--with the added advantage of optimizing a discriminative objective function. The algorithm reduces as a special case to the method of generalized iterative scaling for log-linear models. The learning rate of the algorithm is controlled by the sparseness of the training data. We use the method of nonnegative matrix factorization (NMF) to discover sparse distributed representations of the data. This form of feature selection greatly accelerates learning and makes the algorithm practical on large problems. Experiments show that discriminatively trained mixture models lead to much better classification than comparably sized models trained by EM.

We present an extension to the Mixture of Experts (ME) model, where the individual experts are Gaussian Process (GP) regression models. Using an input-dependent adaptation of the Dirichlet Process, we implement a gating network for an infinite number of Experts. Inference in this model may be done efficiently using a Markov Chain relying on Gibbs sampling. The model allows the effective covariance function to vary with the inputs, and may handle large datasets - thus potentially overcoming two of the biggest hurdles with GP models.

Bayesian belief propagation in graphical models has been recently shown to have very close ties to inference methods based in statistical physics. After Yedidia et al. demonstrated that belief propagation fixed points correspond to extrema of the so-called Bethe free energy, Yuille derived a double loop algorithm that is guaranteed to converge to a local minimum of the Bethe free energy. Yuille's algorithm is based on a certain decomposition of the Bethe free energy and he mentions that other decompositions are possible and may even be fruitful. In the present work, we begin with the Bethe free energy and show that it has a principled interpretation as pairwise mutual information minimization and marginal entropy maximization (MIME). Next, we construct a family of free energy functions from a spectrum of decompositions of the original Bethe free energy. For each free energy in this family, we develop a new algorithm that is guaranteed to converge to a local minimum. Preliminary computer simulations are in agreement with this theoretical development.

Motivated by our recent work on rooted tree matching, in this paper we provide a solution to the problem of matching two free (i.e., unrooted) trees by constructing an association graph whose maximal cliques are in one-to-one correspondence with maximal common subtrees. We then solve the problem using simple replicator dynamics from evolutionary game theory. Experiments on hundreds of uniformly random trees are presented. The results are impressive: despite the inherent inability of these simple dynamics to escape from local optima, they always returned a globally optimal solution.

We present Linear Relational Embedding (LRE), a new method of learning a distributed representation of concepts from data consisting of instances of relations between given concepts. Its final goal is to be able to generalize, i.e. infer new instances of these relations among the concepts. On a task involving family relationships we show that LRE can generalize better than any previously published method. We then show how LRE can be used effectively to find compact distributed representations for variable-sized recursive data structures, such as trees and lists.

For clustering points in Rna main application focus of this paper-one standard approach is based on generative models, in which algorithms such as EM are used to learn a mixture density. These approaches suffer from several drawbacks. First, to use parametric density estimators, harsh simplifying assumptions usually need to be made (e.g., that the density of each cluster is Gaussian). Second, the log likelihood can have many local minima and therefore multiple restarts are required to find a good solution using iterative algorithms. Algorithms such as K-means have similar problems.

Discriminative classifiers model the posterior p(ylx) directly, or learn a direct map from inputs x to the class labels. There are several compelling reasons for using discriminative rather than generative classifiers, one of which, succinctly articulated by Vapnik [6], is that "one should solve the [classification] problem directly and never solve a more general problem as an intermediate step [such as modeling p(xly)]." Indeed, leaving aside computational issues and matters such as handling missing data, the prevailing consensus seems to be that discriminative classifiers are almost always to be preferred to generative ones. Another piece of prevailing folk wisdom is that the number of examples needed to fit a model is often roughly linear in the number of free parameters of a model. This has its theoretical basis in the observation that for "many" models, the VC dimension is roughly linear or at most some low-order polynomial in the number of parameters (see, e.g., [1, 3]), and it is known that sample complexity in the discriminative setting is linear in the VC dimension [6]. In this paper, we study empirically and theoretically the extent to which these beliefs are true. A parametric family of probabilistic models p(x, y) can be fit either to optimize the joint likelihood of the inputs and the labels, or fit to optimize the conditional likelihood p(ylx), or even fit to minimize the 0-1 training error obtained by thresholding p(ylx) to make predictions.

The hierarchical hidden Markov model (HHMM) is a generalization of the hidden Markov model (HMM) that models sequences with structure at many length/time scales [FST98].