Markov Network Structure Learning via Ensemble-of-Forests Models

Real world systems typically feature a variety of different dependency types and topologies that complicate model selection for probabilistic graphical models. We introduce the ensemble-of-forests model, a generalization of the ensemble-of-trees model. Our model enables structure learning of Markov random fields (MRF) with multiple connected components and arbitrary potentials. We present two approximate inference techniques for this model and demonstrate their performance on synthetic data. Our results suggest that the ensemble-of-forests approach can accurately recover sparse, possibly disconnected MRF topologies, even in presence of non-Gaussian dependencies and/or low sample size. We applied the ensemble-of-forests model to learn the structure of perturbed signaling networks of immune cells and found that these frequently exhibit non-Gaussian dependencies with disconnected MRF topologies. In summary, we expect that the ensemble-of-forests model will enable MRF structure learning in other high dimensional real world settings that are governed by non-trivial dependencies.Comment: 13 pages, 6 figure

Adaptive Monotone Shrinkage for Regression

We develop an adaptive monotone shrinkage estimator for regression models with the following characteristics: i) dense coefficients with small but important effects; ii) a priori ordering that indicates the probable predictive importance of the features. We capture both properties with an empirical Bayes estimator that shrinks coefficients monotonically with respect to their anticipated importance. This estimator can be rapidly computed using a version of Pool-Adjacent-Violators algorithm. We show that the proposed monotone shrinkage approach is competitive with the class of all Bayesian estimators that share the prior information. We further observe that the estimator also minimizes Stein's unbiased risk estimate. Along with our key result that the estimator mimics the oracle Bayes rule under an order assumption, we also prove that the estimator is robust. Even without the order assumption, our estimator mimics the best performance of a large family of estimators that includes the least squares estimator, constant-$\lambda$ ridge estimator, James-Stein estimator, etc. All the theoretical results are non-asymptotic. Simulation results and data analysis from a model for text processing are provided to support the theory.Comment: Appearing in Uncertainty in Artificial Intelligence (UAI) 201

Fast Ridge Regression with Randomized Principal Component Analysis and Gradient Descent

We propose a new two stage algorithm LING for large scale regression problems. LING has the same risk as the well known Ridge Regression under the fixed design setting and can be computed much faster. Our experiments have shown that LING performs well in terms of both prediction accuracy and computational efficiency compared with other large scale regression algorithms like Gradient Descent, Stochastic Gradient Descent and Principal Component Regression on both simulated and real datasets

Improved Densification of One Permutation Hashing

The existing work on densification of one permutation hashing reduces the query processing cost of the $(K,L)$-parameterized Locality Sensitive Hashing (LSH) algorithm with minwise hashing, from $O(dKL)$ to merely $O(d + KL)$, where $d$ is the number of nonzeros of the data vector, $K$ is the number of hashes in each hash table, and $L$ is the number of hash tables. While that is a substantial improvement, our analysis reveals that the existing densification scheme is sub-optimal. In particular, there is no enough randomness in that procedure, which affects its accuracy on very sparse datasets. In this paper, we provide a new densification procedure which is provably better than the existing scheme. This improvement is more significant for very sparse datasets which are common over the web. The improved technique has the same cost of $O(d + KL)$ for query processing, thereby making it strictly preferable over the existing procedure. Experimental evaluations on public datasets, in the task of hashing based near neighbor search, support our theoretical findings

Efficient Bayesian Nonparametric Modelling of Structured Point Processes

This paper presents a Bayesian generative model for dependent Cox point processes, alongside an efficient inference scheme which scales as if the point processes were modelled independently. We can handle missing data naturally, infer latent structure, and cope with large numbers of observed processes. A further novel contribution enables the model to work effectively in higher dimensional spaces. Using this method, we achieve vastly improved predictive performance on both 2D and 1D real data, validating our structured approach.Comment: Presented at UAI 2014. Bibtex: @inproceedings{structcoxpp14_UAI, Author = {Tom Gunter and Chris Lloyd and Michael A. Osborne and Stephen J. Roberts}, Title = {Efficient Bayesian Nonparametric Modelling of Structured Point Processes}, Booktitle = {Uncertainty in Artificial Intelligence (UAI)}, Year = {2014}

Matroid Bandits: Fast Combinatorial Optimization with Learning

A matroid is a notion of independence in combinatorial optimization which is closely related to computational efficiency. In particular, it is well known that the maximum of a constrained modular function can be found greedily if and only if the constraints are associated with a matroid. In this paper, we bring together the ideas of bandits and matroids, and propose a new class of combinatorial bandits, matroid bandits. The objective in these problems is to learn how to maximize a modular function on a matroid. This function is stochastic and initially unknown. We propose a practical algorithm for solving our problem, Optimistic Matroid Maximization (OMM); and prove two upper bounds, gap-dependent and gap-free, on its regret. Both bounds are sublinear in time and at most linear in all other quantities of interest. The gap-dependent upper bound is tight and we prove a matching lower bound on a partition matroid bandit. Finally, we evaluate our method on three real-world problems and show that it is practical

Stochastic Discriminative EM

Stochastic discriminative EM (sdEM) is an online-EM-type algorithm for discriminative training of probabilistic generative models belonging to the exponential family. In this work, we introduce and justify this algorithm as a stochastic natural gradient descent method, i.e. a method which accounts for the information geometry in the parameter space of the statistical model. We show how this learning algorithm can be used to train probabilistic generative models by minimizing different discriminative loss functions, such as the negative conditional log-likelihood and the Hinge loss. The resulting models trained by sdEM are always generative (i.e. they define a joint probability distribution) and, in consequence, allows to deal with missing data and latent variables in a principled way either when being learned or when making predictions. The performance of this method is illustrated by several text classification problems for which a multinomial naive Bayes and a latent Dirichlet allocation based classifier are learned using different discriminative loss functions.Comment: UAI 2014 paper + Supplementary Material. In Proceedings of the Thirtieth Conference on Uncertainty in Artificial Intelligence (UAI 2014), edited by Nevin L. Zhang and Jian Tian. AUAI Pres

Combining predictions from linear models when training and test inputs differ

Methods for combining predictions from different models in a supervised learning setting must somehow estimate/predict the quality of a model's predictions at unknown future inputs. Many of these methods (often implicitly) make the assumption that the test inputs are identical to the training inputs, which is seldom reasonable. By failing to take into account that prediction will generally be harder for test inputs that did not occur in the training set, this leads to the selection of too complex models. Based on a novel, unbiased expression for KL divergence, we propose XAIC and its special case FAIC as versions of AIC intended for prediction that use different degrees of knowledge of the test inputs. Both methods substantially differ from and may outperform all the known versions of AIC even when the training and test inputs are iid, and are especially useful for deterministic inputs and under covariate shift. Our experiments on linear models suggest that if the test and training inputs differ substantially, then XAIC and FAIC predictively outperform AIC, BIC and several other methods including Bayesian model averaging.Comment: 12 pages, 2 figures. To appear in Proceedings of the 30th Conference on Uncertainty in Artificial Intelligence (UAI2014). This version includes the supplementary material (regularity assumptions, proofs