Since the discovery of sophisticated fully polynomial randomized algorithms for a range of #P problems (Karzanov et al., 1991; Jerrum et al., 2001; Wilson, 2004), theoretical work on approximate inference in combinatorial spaces has focused on Markov chain Monte Carlo methods. Despite their strong theoretical guarantees, the slow running time of many of these randomized algorithms and the restrictive assumptions on the potentials have hindered the applicability of these algorithms to machine learning. Because of this, in applications to combinatorial spaces simple exact models are often preferred to more complex models that require approximate inference (Siepel et al., 2004). Variational inference would appear to provide an appealing alternative, given the success of variational methods for graphical models (Wainwright et al., 2008); unfortunately, however, it is not obvious how to develop variational approximations for combinatorial objects such as matchings, partial orders, plane partitions and sequence alignments. We propose a new framework that extends variational inference to a wide range of combinatorial spaces. Our method is based on a simple assumption: the existence of a tractable measure factorization, which we show holds in many examples. Simulations on a range of matching models show that the algorithm is more general and empirically faster than a popular fully polynomial randomized algorithm. We also apply the framework to the problem of multiple alignment of protein sequences, obtaining state-of-the-art results on the BAliBASE dataset (Thompson et al., 1999).

In multi-instance learning, there are two kinds of prediction failure, i.e., false negative and false positive. Current research mainly focus on avoding the former. We attempt to utilize the geometric distribution of instances inside positive bags to avoid both the former and the latter. Based on kernel principal component analysis, we define a projection constraint for each positive bag to classify its constituent instances far away from the separating hyperplane while place positive instances and negative instances at opposite sides. We apply the Constrained Concave-Convex Procedure to solve the resulted problem. Empirical results demonstrate that our approach offers improved generalization performance.

Recently, some variants of the $l_1$ norm, particularly matrix norms such as the $l_{1,2}$ and $l_{1,\infty}$ norms, have been widely used in multi-task learning, compressed sensing and other related areas to enforce sparsity via joint regularization. In this paper, we unify the $l_{1,2}$ and $l_{1,\infty}$ norms by considering a family of $l_{1,q}$ norms for $1 < q\le\infty$ and study the problem of determining the most appropriate sparsity enforcing norm to use in the context of multi-task feature selection. Using the generalized normal distribution, we provide a probabilistic interpretation of the general multi-task feature selection problem using the $l_{1,q}$ norm. Based on this probabilistic interpretation, we develop a probabilistic model using the noninformative Jeffreys prior. We also extend the model to learn and exploit more general types of pairwise relationships between tasks. For both versions of the model, we devise expectation-maximization~(EM) algorithms to learn all model parameters, including $q$, automatically. Experiments have been conducted on two cancer classification applications using microarray gene expression data.

We develop a deterministic single-pass algorithm for latent Dirichlet allocation (LDA) in order to process received documents one at a time and then discard them in an excess text stream. Our algorithm does not need to store old statistics for all data. The proposed algorithm is much faster than a batch algorithm and is comparable to the batch algorithm in terms of perplexity in experiments.

How are the spatial patterns of spontaneous and evoked population responses related? We study the impact of connectivity on the spatial pattern of fluctuations in the input-generated response of a neural network, by comparing the distribution of evoked and intrinsically generated activity across the different units. We develop a complementary approach to principal component analysis in which separate high-variance directions are typically derived for each input condition. We analyze subspace angles to compute the difference between the shapes of trajectories corresponding to different network states, and the orientation of the low-dimensional subspaces that driven trajectories occupy within the full space of neuronal activity. In addition to revealing how the spatiotemporal structure of spontaneous activity affects input-evoked responses, these methods can be used to infer input selectivity induced by network dynamics from experimentally accessible measures of spontaneous activity (e.g. from voltage- or calcium-sensitive optical imaging experiments). We conclude that the absence of a detailed spatial map of afferent inputs and cortical connectivity does not limit our ability to design spatially extended stimuli that evoke strong responses.

We extend Latent Dirichlet Allocation (LDA) by explicitly allowing for the encoding of side information in the distribution over words. This results in a variety of new capabilities, such as improved estimates for infrequently occurring words, as well as the ability to leverage thesauri and dictionaries in order to boost topic cohesion within and across languages. We present experiments on multi-language topic synchronisation where dictionary information is used to bias corresponding words towards similar topics. Results indicate that our model substantially improves topic cohesion when compared to the standard LDA model.

A number of objective functions in clustering problems can be described with submodular functions. In this paper, we introduce the minimum average cost criterion, and show that the theory of intersecting submodular functions can be used for clustering with submodular objective functions. The proposed algorithm does not require the number of clusters in advance, and it will be determined by the property of a given set of data points. The minimum average cost clustering problem is parameterized with a real variable, and surprisingly, we show that all information about optimal clusterings for all parameters can be computed in polynomial time in total. Additionally, we evaluate the performance of the proposed algorithm through computational experiments.

In this paper, we propose an efficient algorithm for estimating the natural policy gradient with parameter-based exploration; this algorithm samples directly in the parameter space. Unlike previous methods based on natural gradients, our algorithm calculates the natural policy gradient using the inverse of the exact Fisher information matrix. The computational cost of this algorithm is equal to that of conventional policy gradients whereas previous natural policy gradient methods have a prohibitive computational cost. Experimental results show that the proposed method outperforms several policy gradient methods.

A new algorithm for isotonic regression is presented based on recursively partitioning the solution space. We develop efficient methods for each partitioning subproblem through an equivalent representation as a network flow problem, and prove that this sequence of partitions converges to the global solution. These network flow problems can further be decomposed in order to solve very large problems. Success of isotonic regression in prediction and our algorithm's favorable computational properties are demonstrated through simulated examples as large as 2x10^5 variables and 10^7 constraints.

In this paper we consider the problem of learning an n x n Kernel matrix from m similarity matrices under general convex loss. Past research have extensively studied the m =1 case and have derived several algorithms which require sophisticated techniques like ACCP, SOCP, etc. The existing algorithms do not apply if one uses arbitrary losses and often can not handle m > 1 case. We present several provably convergent iterative algorithms, where each iteration requires either an SVM or a Multiple Kernel Learning (MKL) solver for m > 1 case. One of the major contributions of the paper is to extend the well known Mirror Descent(MD) framework to handle Cartesian product of psd matrices. This novel extension leads to an algorithm, called EMKL, which solves the problem in O(m^2 log n) iterations; in each iteration one solves an MKL involving m kernels and m eigen-decomposition of n x n matrices. By suitably defining a restriction on the objective function, a faster version of EMKL is proposed, called REKL, which avoids the eigen-decomposition. An alternative to both EMKL and REKL is also suggested which requires only an SVM solver. Experimental results on real world protein data set involving several similarity matrices illustrate the efficacy of the proposed algorithms.