Sparse Inverse Covariance Estimation via an Adaptive Gradient-Based Method

arXiv.org Machine Learning

We study the problem of estimating from data, a sparse approximation to the inverse covariance matrix. Estimating a sparsity constrained inverse covariance matrix is a key component in Gaussian graphical model learning, but one that is numerically very challenging. We address this challenge by developing a new adaptive gradient-based method that carefully combines gradient information with an adaptive step-scaling strategy, which results in a scalable, highly competitive method. Our algorithm, like its predecessors, maximizes an $\ell_1$-norm penalized log-likelihood and has the same per iteration arithmetic complexity as the best methods in its class. Our experiments reveal that our approach outperforms state-of-the-art competitors, often significantly so, for large problems.


The influence of feature selection methods on accuracy, stability and interpretability of molecular signatures

arXiv.org Machine Learning

Motivation: Biomarker discovery from high-dimensional data is a crucial problem with enormous applications in biology and medicine. It is also extremely challenging from a statistical viewpoint, but surprisingly few studies have investigated the relative strengths and weaknesses of the plethora of existing feature selection methods. Methods: We compare 32 feature selection methods on 4 public gene expression datasets for breast cancer prognosis, in terms of predictive performance, stability and functional interpretability of the signatures they produce. Results: We observe that the feature selection method has a significant influence on the accuracy, stability and interpretability of signatures. Simple filter methods generally outperform more complex embedded or wrapper methods, and ensemble feature selection has generally no positive effect. Overall a simple Student's t-test seems to provide the best results. Availability: Code and data are publicly available at http://cbio.ensmp.fr/~ahaury/.


Bound Propagation

arXiv.org Artificial Intelligence

In this article we present an algorithm to compute bounds on the marginals of a graphical model. For several small clusters of nodes upper and lower bounds on the marginal values are computed independently of the rest of the network. The range of allowed probability distributions over the surrounding nodes is restricted using earlier computed bounds. As we will show, this can be considered as a set of constraints in a linear programming problem of which the objective function is the marginal probability of the center nodes. In this way knowledge about the maginals of neighbouring clusters is passed to other clusters thereby tightening the bounds on their marginals. We show that sharp bounds can be obtained for undirected and directed graphs that are used for practical applications, but for which exact computations are infeasible.


Relative Density-Ratio Estimation for Robust Distribution Comparison

arXiv.org Machine Learning

Divergence estimators based on direct approximation of density-ratios without going through separate approximation of numerator and denominator densities have been successfully applied to machine learning tasks that involve distribution comparison such as outlier detection, transfer learning, and two-sample homogeneity test. However, since density-ratio functions often possess high fluctuation, divergence estimation is still a challenging task in practice. In this paper, we propose to use relative divergences for distribution comparison, which involves approximation of relative density-ratios. Since relative density-ratios are always smoother than corresponding ordinary density-ratios, our proposed method is favorable in terms of the non-parametric convergence speed. Furthermore, we show that the proposed divergence estimator has asymptotic variance independent of the model complexity under a parametric setup, implying that the proposed estimator hardly overfits even with complex models. Through experiments, we demonstrate the usefulness of the proposed approach.


Predictive Active Set Selection Methods for Gaussian Processes

arXiv.org Machine Learning

We propose an active set selection framework for Gaussian process classification for cases when the dataset is large enough to render its inference prohibitive. Our scheme consists of a two step alternating procedure of active set update rules and hyperparameter optimization based upon marginal likelihood maximization. The active set update rules rely on the ability of the predictive distributions of a Gaussian process classifier to estimate the relative contribution of a datapoint when being either included or removed from the model. This means that we can use it to include points with potentially high impact to the classifier decision process while removing those that are less relevant. We introduce two active set rules based on different criteria, the first one prefers a model with interpretable active set parameters whereas the second puts computational complexity first, thus a model with active set parameters that directly control its complexity. We also provide both theoretical and empirical support for our active set selection strategy being a good approximation of a full Gaussian process classifier. Our extensive experiments show that our approach can compete with state-of-the-art classification techniques with reasonable time complexity. Source code publicly available at http://cogsys.imm.dtu.dk/passgp.


VHPOP: Versatile Heuristic Partial Order Planner

arXiv.org Artificial Intelligence

VHPOP is a partial order causal link (POCL) planner loosely based on UCPOP. It draws from the experience gained in the early to mid 1990's on flaw selection strategies for POCL planning, and combines this with more recent developments in the field of domain independent planning such as distance based heuristics and reachability analysis. We present an adaptation of the additive heuristic for plan space planning, and modify it to account for possible reuse of existing actions in a plan. We also propose a large set of novel flaw selection strategies, and show how these can help us solve more problems than previously possible by POCL planners. VHPOP also supports planning with durative actions by incorporating standard techniques for temporal constraint reasoning. We demonstrate that the same heuristic techniques used to boost the performance of classical POCL planning can be effective in domains with durative actions as well. The result is a versatile heuristic POCL planner competitive with established CSP-based and heuristic state space planners.


On Polynomial Sized MDP Succinct Policies

arXiv.org Artificial Intelligence

Policies of Markov Decision Processes (MDPs) determine the next action to execute from the current state and, possibly, the history (the past states). When the number of states is large, succinct representations are often used to compactly represent both the MDPs and the policies in a reduced amount of space. In this paper, some problems related to the size of succinctly represented policies are analyzed. Namely, it is shown that some MDPs have policies that can only be represented in space super-polynomial in the size of the MDP, unless the polynomial hierarchy collapses. This fact motivates the study of the problem of deciding whether a given MDP has a policy of a given size and reward. Since some algorithms for MDPs work by finding a succinct representation of the value function, the problem of deciding the existence of a succinct representation of a value function of a given size and reward is also considered.


Translation of Pronominal Anaphora between English and Spanish: Discrepancies and Evaluation

arXiv.org Artificial Intelligence

This paper evaluates the different tasks carried out in the translation of pronominal anaphora in a machine translation (MT) system. The MT interlingua approach named AGIR (Anaphora Generation with an Interlingua Representation) improves upon other proposals presented to date because it is able to translate intersentential anaphors, detect co-reference chains, and translate Spanish zero pronouns into English---issues hardly considered by other systems. The paper presents the resolution and evaluation of these anaphora problems in AGIR with the use of different kinds of knowledge (lexical, morphological, syntactic, and semantic). The translation of English and Spanish anaphoric third-person personal pronouns (including Spanish zero pronouns) into the target language has been evaluated on unrestricted corpora. We have obtained a precision of 80.4% and 84.8% in the translation of Spanish and English pronouns, respectively. Although we have only studied the Spanish and English languages, our approach can be easily extended to other languages such as Portuguese, Italian, or Japanese.


SHOP2: An HTN Planning System

arXiv.org Artificial Intelligence

The SHOP2 planning system received one of the awards for distinguished performance in the 2002 International Planning Competition. This paper describes the features of SHOP2 which enabled it to excel in the competition, especially those aspects of SHOP2 that deal with temporal and metric planning domains.


Compiling Causal Theories to Successor State Axioms and STRIPS-Like Systems

arXiv.org Artificial Intelligence

We describe a system for specifying the effects of actions. Unlike those commonly used in AI planning, our system uses an action description language that allows one to specify the effects of actions using domain rules, which are state constraints that can entail new action effects from old ones. Declaratively, an action domain in our language corresponds to a nonmonotonic causal theory in the situation calculus. Procedurally, such an action domain is compiled into a set of logical theories, one for each action in the domain, from which fully instantiated successor state-like axioms and STRIPS-like systems are then generated. We expect the system to be a useful tool for knowledge engineers writing action specifications for classical AI planning systems, GOLOG systems, and other systems where formal specifications of actions are needed.