We introduce a new Bayesian model for hierarchical clustering based on a prior over trees called Kingman's coalescent. We develop novel greedy and sequential Monte Carlo inferences which operate in a bottom-up agglomerative fashion. We show experimentally the superiority of our algorithms over the state-of-the-art, and demonstrate our approach in document clustering and phylolinguistics.

Although kernel measures of independence have been widely applied in machine learning (notably in kernel ICA), there is as yet no method to determine whether they have detected statistically significant dependence. We provide a novel test of the independence hypothesis for one particular kernel independence measure, the Hilbert-Schmidt independence criterion (HSIC).

This paper considers kernels invariant to translation, rotation and dilation. We show that no nontrivial positive definite (p.d.) kernels exist which are radial and dilation invariant, only conditionally positive definite (c.p.d.) ones. Accordingly, we discuss the c.p.d.

Semi-supervised methods use unlabeled data in addition to labeled data to construct predictors. While existing semi-supervised methods have shown some promising empirical performance, their development has been based largely based on heuristics. In this paper we study semi-supervised learning from the viewpoint of minimax theory. Our first result shows that some common methods based on regularization using graph Laplacians do not lead to faster minimax rates of convergence. Thus, the estimators that use the unlabeled data do not have smaller risk than the estimators that use only labeled data. We then develop several new approaches that provably lead to improved performance. The statistical tools of minimax analysis are thus used to offer some new perspective on the problem of semi-supervised learning.

Maximum entropy analysis of binary variables provides an elegant way for studying the role of pairwise correlations in neural populations. Unfortunately, these approaches suffer from their poor scalability to high dimensions. In sensory coding, however, high-dimensional data is ubiquitous. Here, we introduce a new approach using a near-maximum entropy model, that makes this type of analysis feasible for very high-dimensional data--the model parameters can be derived in closed form and sampling is easy. Therefore, our NearMaxEnt approach can serve as a tool for testing predictions from a pairwise maximum entropy model not only for low-dimensional marginals, but also for high dimensional measurements of more than thousand units. We demonstrate its usefulness by studying natural images with dichotomized pixel intensities. Our results indicate that the statistics of such higher-dimensional measurements exhibit additional structure that are not predicted by pairwise correlations, despite the fact that pairwise correlations explain the lower-dimensional marginal statistics surprisingly well up to the limit of dimensionality where estimation of the full joint distribution is feasible.

We study a pattern classification algorithm which has recently been proposed by Vapnik and coworkers. It builds on a new inductive principle which assumes that in addition to positive and negative data, a third class of data is available, termed the Universum. We assay the behavior of the algorithm by establishing links with Fisher discriminant analysis and oriented PCA, as well as with an SVM in a projected subspace (or, equivalently, with a data-dependent reduced kernel). We also provide experimental results.

Neural spike trains present challenges to analytical efforts due to their noisy, spiking nature. Many studies of neuroscientific and neural prosthetic importance rely on a smoothed, denoised estimate of the spike train's underlying firing rate. Current techniques to find time-varying firing rates require ad hoc choices of parameters, offer no confidence intervals on their estimates, and can obscure potentially important single trial variability. We present a new method, based on a Gaussian Process prior, for inferring probabilistically optimal estimates of firing rate functions underlying single or multiple neural spike trains. We test the performance of the method on simulated data and experimentally gathered neural spike trains, and we demonstrate improvements over conventional estimators.

A discriminative method is proposed for learning monotonic transformations of the training data while jointly estimating a large-margin classifier. In many domains such as document classification, image histogram classification and gene microarray experiments, fixed monotonic transformations can be useful as a preprocessing step. However, most classifiers only explore these transformations through manual trial and error or via prior domain knowledge. The proposed method learns monotonic transformations automatically while training a large-margin classifier without any prior knowledge of the domain. A monotonic piecewise linear function is learned which transforms data for subsequent processing by a linear hyperplane classifier. Two algorithmic implementations of the method are formalized. The first solves a convergent alternating sequence of quadratic and linear programs until it obtains a locally optimal solution. An improved algorithm is then derived using a convex semidefinite relaxation that overcomes initialization issues in the greedy optimization problem. The effectiveness of these learned transformations on synthetic problems, text data and image data is demonstrated.

Over the past few years, the notion of stability in data clustering has received growing attention as a cluster validation criterion in a sample-based framework. However, recent work has shown that as the sample size increases, any clustering model will usually become asymptotically stable. This led to the conclusion that stability is lacking as a theoretical and practical tool. The discrepancy between this conclusion and the success of stability in practice has remained an open question, which we attempt to address. Our theoretical approach is that stability, as used by cluster validation algorithms, is similar in certain respects to measures of generalization in a model-selection framework. In such cases, the model chosen governs the convergence rate of generalization bounds. By arguing that these rates are more important than the sample size, we are led to the prediction that stability-based cluster validation algorithms should not degrade with increasing sample size, despite the asymptotic universal stability. This prediction is substantiated by a theoretical analysis as well as some empirical results. We conclude that stability remains a meaningful cluster validation criterion over finite samples.

Clustering is often formulated as a discrete optimization problem. The objective is to find, among all partitions of the data set, the best one according to some quality measure. However, in the statistical setting where we assume that the finite data set has been sampled from some underlying space, the goal is not to find the best partition of the given sample, but to approximate the true partition of the underlying space. We argue that the discrete optimization approach usually does not achieve this goal. As an alternative, we suggest the paradigm of "nearest neighbor clustering". Instead of selecting the best out of all partitions of the sample, it only considers partitions in some restricted function class. Using tools from statistical learning theory we prove that nearest neighbor clustering is statistically consistent. Moreover, its worst case complexity is polynomial by construction, and it can be implemented with small average case complexity using branch and bound.