Image Congealing (IC) is a non-parametric method for the joint alignment of a col- lection of images affected by systematic and unwanted deformations. The method attempts to undo the deformations by minimizing a measure of complexity of the image ensemble, such as the averaged per-pixel entropy. This enables alignment without an explicit model of the aligned dataset as required by other methods (e.g. While IC is simple and general, it may intro- duce degenerate solutions when the transformations allow minimizing the com- plexity of the data by collapsing them to a constant. Such solutions need to be explicitly removed by regularization.

We propose a new method for constructing hyperkenels and define two promising special cases that can be computed in closed form. These we call the Gaussian and Wishart hyperkernels. The former is especially attractive in that it has an interpretable regularization scheme reminiscent of that of the Gaussian RBF kernel. We discuss how kernel learning can be used not just for improving the performance of classification and regression methods, but also as a stand-alone algorithm for dimensionality reduction and relational or metric learning.

Multinomial logistic regression provides the standard penalised maximum- likelihood solution to multi-class pattern recognition problems. More recently, the development of sparse multinomial logistic regression models has found ap- plication in text processing and microarray classification, where explicit identifi- cation of the most informative features is of value. In this paper, we propose a sparse multinomial logistic regression method, in which the sparsity arises from the use of a Laplace prior, but where the usual regularisation parameter is inte- grated out analytically. Evaluation over a range of benchmark datasets reveals this approach results in similar generalisation performance to that obtained using cross-validation, but at greatly reduced computational expense.

We present a novel algorithm called PG-means which is able to learn the number of clusters in a classical Gaussian mixture model. Our method is robust and efficient; it uses statistical hypothesis tests on one-dimensional projections of the data and model to determine if the examples are well represented by the model. In so doing, we are applying a statistical test for the entire model at once, not just on a per-cluster basis. We show that our method works well in difficult cases such as non-Gaussian data, overlapping clusters, eccentric clusters, high dimension, and many true clusters. Further, our new method provides a much more stable estimate of the number of clusters than existing methods.

The standard Support Vector Machine formulation does not provide its user with the ability to explicitly control the number of support vectors used to define the generated classifier. We present a modified version of SVM that allows the user to set a budget parameter B and focuses on minimizing the loss attained by the B worst-classified examples while ignoring the remaining examples. This idea can be used to derive sparse versions of both L1-SVM and L2-SVM. Technically, we obtain these new SVM variants by replacing the 1-norm in the standard SVM for- mulation with various interpolation-norms. We also adapt the SMO optimization algorithm to our setting and report on some preliminary experimental results.

Starting with the work of Jaakkola and Haussler, a variety of approaches have been proposed for coupling domain-specific generative models with statistical learning methods. The link is established by a kernel function which provides a similarity measure based inherently on the underlying model. In computational biology, the full promise of this framework has rarely ever been exploited, as most kernels are derived from very generic models, such as sequence profiles or hidden Markov models. Here, we introduce the MTreeMix kernel, which is based on a generative model tailored to the underlying biological mechanism. We compare this novel kernel to a standard, evolution-agnostic amino acid encoding in the prediction of HIV drug resistance from genotype, using support vector regression.

In this paper, we present a subspace method for learning nonlinear dynamical systems based on stochastic realization, in which state vectors are chosen using kernel canonical correlation analysis, and then state-space systems are identified through regression with the state vectors. We construct the theoretical underpinning and derive a concrete algorithm for nonlinear identification. The obtained algorithm needs no iterative optimization procedure and can be implemented on the basis of fast and reliable numerical schemes. The simulation result shows that our algorithm can express dynamics with a high degree of accuracy.

Semi-supervised SVMs (S3 VM) attempt to learn low-density separators by maximizing the margin over labeled and unlabeled examples. The associated optimization problem is non-convex. To examine the full potential of S3 VMs modulo local minima problems in current implementations, we apply branch and bound techniques for obtaining exact, global ly optimal solutions. Empirical evidence suggests that the globally optimal solution can return excellent generalization performance in situations where other implementations fail completely. While our current implementation is only applicable to small datasets, we discuss variants that can potentially lead to practically useful algorithms.

Data sets that characterize human activity over time through collections of timestamped events or counts are of increasing interest in application areas as humancomputer interaction, video surveillance, and Web data analysis. We propose a non-parametric Bayesian framework for modeling collections of such data. In particular, we use a Dirichlet process framework for learning a set of intensity functions corresponding to different categories, which form a basis set for representing individual time-periods (e.g., several days) depending on which categories the time-periods are assigned to. This allows the model to learn in a data-driven fashion what "factors" are generating the observations on a particular day, including (for example) weekday versus weekend effects or day-specific effects corresponding to unique (single-day) occurrences of unusual behavior, sharing information where appropriate to obtain improved estimates of the behavior associated with each category. Applications to realworld data sets of count data involving both vehicles and people are used to illustrate the technique.

We are at the beginning of the multicore era. Computers will have increasingly many cores (processors), but there is still no good programming framework for these architectures, and thus no simple and unified way for machine learning to take advantage of the potential speed up. In this paper, we develop a broadly applicable parallel programming method, one that is easily applied to many different learning algorithms. Our work is in distinct contrast to the tradition in machine learning of designing (often ingenious) ways to speed up a single algorithm at a time. Specifically, we show that algorithms that fit the Statistical Query model [15] can be written in a certain "summation form," which allows them to be easily parallelized on multicore computers.