We describe an efficient learning procedure for multilayer generative models that combine the best aspects of Markov random fields and deep, directed belief nets. The generative models can be learned one layer at a time and when learning is complete they have a very fast inference procedure for computing a good approximation to the posterior distribution in all of the hidden layers. Each hidden layer has its own MRF whose energy function is modulated by the top-down directed connections from the layer above. To generate from the model, each layer in turn must settle to equilibrium given its top-down input. We show that this type of model is good at capturing the statistics of patches of natural images.

We introduce a hierarchical Bayesian model for the discovery of putative regulators from gene expression data only. The hierarchy incorporates the knowledge that there are just a few regulators that by themselves only regulate a handful of genes. This is implemented through a so-called spike-and-slab prior, a mixture of Gaussians with different widths, with mixing weights from a hierarchical Bernoulli model. For efficient inference we implemented expectation propagation. Running the model on a malaria parasite data set, we found four genes with significant homology to transcription factors in an amoebe, one RNA regulator and three genes of unknown function (out of the top ten genes considered).

We consider the problem of Support Vector Machine transduction, which involves a combinatorial problem with exponential computational complexity in the number of unlabeled examples. Although several studies are devoted to Transductive SVM, they suffer either from the high computation complexity or from the solutions of local optimum. To address this problem, we propose solving Transductive SVM via a convex relaxation, which converts the NP-hard problem to a semi-definite programming. Compared with the other SDP relaxation for Transductive SVM, the proposed algorithm is computationally more efficient with the number of free parameters reduced from O(n2) to O(n) where n is the number of examples. Empirical study with several benchmark data sets shows the promising performance of the proposed algorithm in comparison with other state-of-the-art implementations of Transductive SVM.

We study the following question: is the two-dimensional structure of images a very strong prior or is it something that can be learned with a few examples of natural images? If someone gave us a learning task involving images for which the two-dimensional topology of pixels was not known, could we discover it automatically and exploit it? For example suppose that the pixels had been permuted in a fixed but unknown way, could we recover the relative two-dimensional location of pixels on images? The surprising result presented here is that not only the answer is yes but that about as few as a thousand images are enough to approximately recover the relative locations of about a thousand pixels. This is achieved using a manifold learning algorithm applied to pixels associated with a measure of distributional similarity between pixel intensities. We compare different topology-extraction approaches and show how having the two-dimensional topology can be exploited.

Empirical risk minimization offers well-known learning guarantees when training and test data come from the same domain. In the real world, though, we often wish to adapt a classifier from a source domain with a large amount of training data to different target domain with very little training data. In this work we give uniform convergence bounds for algorithms that minimize a convex combination of source and target empirical risk. The bounds explicitly model the inherent trade-off between training on a large but inaccurate source data set and a small but accurate target training set. Our theory also gives results when we have multiple source domains, each of which may have a different number of instances, and we exhibit cases in which minimizing a non-uniform combination of source risks can achieve much lower target error than standard empirical risk minimization.

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Statistical models on full and partial rankings of n items are often of limited practical usefor large n due to computational consideration. We explore the use of nonparametric models for partially ranked data and derive efficient procedures for their use for large n. The derivations are largely possible through combinatorial and algebraic manipulations based on the lattice of partial rankings. In particular, we demonstrate for the first time a nonparametric coherent and consistent model capable of efficiently aggregating partially ranked data of different types.

We study the relation between notions of game-theoretic equilibria which are based on stability under a set of deviations, and empirical equilibria which are reached by rational players. Rational players are modelled by players using no regret algorithms, which guarantee that their payoff in the long run is almost as much as the most they could hope to achieve by consistently deviating from the algorithm's suggested action. We show that for a given set of deviations over the strategy set of a player, it is possible to efficiently approximate fixed points of a given deviation if and only if there exist efficient no regret algorithms resistant to the deviations. Further, we show that if all players use a no regret algorithm, then the empirical distribution of their plays converges to an equilibrium.

When we have several related tasks, solving them simultaneously is shown to be more effective than solving them individually. This approach is called multi-task learning (MTL) and has been studied extensively. Existing approaches to MTL often treat all the tasks as \emph{uniformly related to each other and the relatedness of the tasks is controlled globally. For this reason, the existing methods can lead to undesired solutions when some tasks are not highly related to each other, and some pairs of related tasks can have significantly different solutions. In this paper, we propose a novel MTL algorithm that can overcome these problems. Our method makes use of a task network, which describes the relation structure among tasks. This allows us to deal with intricate relation structures in a systematic way. Furthermore, we control the relatedness of the tasks locally, so all pairs of related tasks are guaranteed to have similar solutions. We apply the above idea to support vector machines (SVMs) and show that the optimization problem can be cast as a second order cone program, which is convex and can be solved efficiently. The usefulness of our approach is demonstrated through simulations with protein super-family classification and ordinal regression problems.

We present a general boosting method extending functional gradient boosting to optimize complex loss functions that are encountered in many machine learning problems. Our approach is based on optimization of quadratic upper bounds of the loss functions which allows us to present a rigorous convergence analysis of the algorithm. More importantly, this general framework enables us to use a standard regression base learner such as single regression tree for £tting any loss function. We illustrate an application of the proposed method in learning ranking functions for Web search by combining both preference data and labeled data for training. We present experimental results for Web search using data from a commercial search engine that show signi£cant improvements of our proposed methods over some existing methods.