Clustering is a fundamental problem in machine learning and has been approached in many ways. Two general and quite different approaches include iteratively fitting a mixture model (e.g., using EM) and linking together pairs of training cases that have high affinity (e.g., using spectral methods). Pairwise clustering algorithms need not compute sufficient statistics and avoid poor solutions by directly placing similar examples in the same cluster. However, many applications require that each cluster of data be accurately described by a prototype or model, so affinity-based clustering - and its benefits - cannot be directly realized. We describe a technique called "affinity propagation", which combines the advantages of both approaches. The method learns a mixture model of the data by recursively propagating affinity messages. We demonstrate affinity propagation on the problems of clustering image patches for image segmentation and learning mixtures of gene expression models from microarray data. We find that affinity propagation obtains better solutions than mixtures of Gaussians, the K-medoids algorithm, spectral clustering and hierarchical clustering, and is both able to find a pre-specified number of clusters and is able to automatically determine the number of clusters. Interestingly, affinity propagation can be viewed as belief propagation in a graphical model that accounts for pairwise training case likelihood functions and the identification of cluster centers.

We address the problem of robust, computationally-efficient design of biological experiments. Classical optimal experiment design methods have not been widely adopted in biological practice, in part because the resulting designs can be very brittle if the nominal parameter estimates for the model are poor, and in part because of computational constraints. We present a method for robust experiment design based on a semidefinite programming relaxation. We present an application of this method to the design of experiments for a complex calcium signal transduction pathway, where we have found that the parameter estimates obtained from the robust design are better than those obtained from an "optimal" design.

Kernel methods make it relatively easy to define complex highdimensional feature spaces. This raises the question of how we can identify the relevant subspaces for a particular learning task. When two views of the same phenomenon are available kernel Canonical Correlation Analysis (KCCA) has been shown to be an effective preprocessing step that can improve the performance of classification algorithms such as the Support Vector Machine (SVM). This paper takes this observation to its logical conclusion and proposes a method that combines this two stage learning (KCCA followed by SVM) into a single optimisation termed SVM-2K. We present both experimental and theoretical analysis of the approach showing encouraging results and insights.

The Octopus arm is a highly versatile and complex limb. How the Octopus controls such a hyper-redundant arm (not to mention eight of them!) is as yet unknown. Robotic arms based on the same mechanical principles may render present day robotic arms obsolete. In this paper, we tackle this control problem using an online reinforcement learning algorithm, based on a Bayesian approach to policy evaluation known as Gaussian process temporal difference (GPTD) learning. Our substitute for the real arm is a computer simulation of a 2-dimensional model of an Octopus arm. Even with the simplifications inherent to this model, the state space we face is a high-dimensional one. We apply a GPTDbased algorithm to this domain, and demonstrate its operation on several learning tasks of varying degrees of difficulty.

Online learning algorithms are typically fast, memory efficient, and simple to implement. However, many common learning problems fit more naturally in the batch learning setting. The power of online learning algorithms can be exploited in batch settings by using online-to-batch conversions techniques which build a new batch algorithm from an existing online algorithm. We first give a unified overview of three existing online-to-batch conversion techniques which do not use training data in the conversion process. We then build upon these data-independent conversions to derive and analyze data-driven conversions. Our conversions find hypotheses with a small risk by explicitly minimizing datadependent generalization bounds. We experimentally demonstrate the usefulness of our approach and in particular show that the data-driven conversions consistently outperform the data-independent conversions.

The Perceptron algorithm, despite its simplicity, often performs well on online classification tasks. The Perceptron becomes especially effective when it is used in conjunction with kernels. However, a common difficulty encountered when implementing kernel-based online algorithms is the amount of memory required to store the online hypothesis, which may grow unboundedly. In this paper we present and analyze the Forgetron algorithm for kernel-based online learning on a fixed memory budget. To our knowledge, this is the first online learning algorithm which, on one hand, maintains a strict limit on the number of examples it stores while, on the other hand, entertains a relative mistake bound. In addition to the formal results, we also present experiments with real datasets which underscore the merits of our approach.

This paper addresses the issue of numerical computation in machine learning domains based on similarity metrics, such as kernel methods, spectral techniques and Gaussian processes. It presents a general solution strategy based on Krylov subspace iteration and fast N-body learning methods. The experiments show significant gains in computation and storage on datasets arising in image segmentation, object detection and dimensionality reduction. The paper also presents theoretical bounds on the stability of these methods.

This paper presents a rigorous statistical analysis characterizing regimes in which active learning significantly outperforms classical passive learning. Active learning algorithms are able to make queries or select sample locations in an online fashion, depending on the results of the previous queries. In some regimes, this extra flexibility leads to significantly faster rates of error decay than those possible in classical passive learning settings. The nature of these regimes is explored by studying fundamental performance limits of active and passive learning in two illustrative nonparametric function classes. In addition to examining the theoretical potential of active learning, this paper describes a practical algorithm capable of exploiting the extra flexibility of the active setting and provably improving upon the classical passive techniques. Our active learning theory and methods show promise in a number of applications, including field estimation using wireless sensor networks and fault line detection.

We present an efficient algorithm to actively select queries for learning the boundaries separating a function domain into regions where the function is above and below a given threshold. We develop experiment selection methods based on entropy, misclassification rate, variance, and their combinations, and show how they perform on a number of data sets. We then show how these algorithms are used to determine simultaneously valid 1 α confidence intervals for seven cosmological parameters. Experimentation shows that the algorithm reduces the computation necessary for the parameter estimation problem by an order of magnitude.

Topic models, such as latent Dirichlet allocation (LDA), can be useful tools for the statistical analysis of document collections and other discrete data. The LDA model assumes that the words of each document arise from a mixture of topics, each of which is a distribution over the vocabulary. A limitation of LDA is the inability to model topic correlation even though, for example, a document about genetics is more likely to also be about disease than x-ray astronomy. This limitation stems from the use of the Dirichlet distribution to model the variability among the topic proportions. In this paper we develop the correlated topic model (CTM), where the topic proportions exhibit correlation via the logistic normal distribution [1]. We derive a mean-field variational inference algorithm for approximate posterior inference in this model, which is complicated by the fact that the logistic normal is not conjugate to the multinomial. The CTM gives a better fit than LDA on a collection of OCRed articles from the journal Science. Furthermore, the CTM provides a natural way of visualizing and exploring this and other unstructured data sets.