We consider the sparse inverse covariance regularization problem or graphical lasso with regularization parameter $\rho$. Suppose the co- variance graph formed by thresholding the entries of the sample covariance matrix at $\rho$ is decomposed into connected components. We show that the vertex-partition induced by the thresholded covariance graph is exactly equal to that induced by the estimated concentration graph. This simple rule, when used as a wrapper around existing algorithms, leads to enormous performance gains. For large values of $\rho$, our proposal splits a large graphical lasso problem into smaller tractable problems, making it possible to solve an otherwise infeasible large scale graphical lasso problem.

This paper tackles the problem of selecting among several linear estimators in non-parametric regression; this includes model selection for linear regression, the choice of a regularization parameter in kernel ridge regression, spline smoothing or locally weighted regression, and the choice of a kernel in multiple kernel learning. We propose a new algorithm which first estimates consistently the variance of the noise, based upon the concept of minimal penalty, which was previously introduced in the context of model selection. Then, plugging our variance estimate in Mallows' $C_L$ penalty is proved to lead to an algorithm satisfying an oracle inequality. Simulation experiments with kernel ridge regression and multiple kernel learning show that the proposed algorithm often improves significantly existing calibration procedures such as generalized cross-validation.

Boolean optimization finds a wide range of application domains, that motivated a number of different organizations of Boolean optimizers since the mid 90s. Some of the most successful approaches are based on iterative calls to an NP oracle, using either linear search, binary search or the identification of unsatisfiable sub-formulas. The increasing use of Boolean optimizers in practical settings raises the question of confidence in computed results. For example, the issue of confidence is paramount in safety critical settings. One way of increasing the confidence of the results computed by Boolean optimizers is to develop techniques for validating the results. Recent work studied the validation of Boolean optimizers based on branch-and-bound search. This paper complements existing work, and develops methods for validating Boolean optimizers that are based on iterative calls to an NP oracle. This entails implementing solutions for validating both satisfiable and unsatisfiable answers from the NP oracle. The work described in this paper can be applied to a wide range of Boolean optimizers, that find application in Pseudo-Boolean Optimization and in Maximum Satisfiability. Preliminary experimental results indicate that the impact of the proposed method in overall performance is negligible.

This paper presents algorithms for hierarchical, agglomerative clustering which perform most efficiently in the general-purpose setup that is given in modern standard software. Requirements are: (1) the input data is given by pairwise dissimilarities between data points, but extensions to vector data are also discussed (2) the output is a "stepwise dendrogram", a data structure which is shared by all implementations in current standard software. We present algorithms (old and new) which perform clustering in this setting efficiently, both in an asymptotic worst-case analysis and from a practical point of view. The main contributions of this paper are: (1) We present a new algorithm which is suitable for any distance update scheme and performs significantly better than the existing algorithms. (2) We prove the correctness of two algorithms by Rohlf and Murtagh, which is necessary in each case for different reasons. (3) We give well-founded recommendations for the best current algorithms for the various agglomerative clustering schemes.

The use of community detection algorithms is explored within the framework of cover song identification, i.e. the automatic detection of different audio renditions of the same underlying musical piece. Until now, this task has been posed as a typical query-by-example task, where one submits a query song and the system retrieves a list of possible matches ranked by their similarity to the query. In this work, we propose a new approach which uses song communities to provide more relevant answers to a given query. Starting from the output of a state-of-the-art system, songs are embedded in a complex weighted network whose links represent similarity (related musical content). Communities inside the network are then recognized as groups of covers and this information is used to enhance the results of the system. In particular, we show that this approach increases both the coherence and the accuracy of the system. Furthermore, we provide insight into the internal organization of individual cover song communities, showing that there is a tendency for the original song to be central within the community. We postulate that the methods and results presented here could be relevant to other query-by-example tasks.

Cross-validation on 7165 molecules yields a mean absolute error of 9.9 kcal/mol, which is an order of magnitude more accurate than counting bonds or semiempirical quantum chemistry. We use the GDB data base, a library of nearly one billion organic molecules that are stable and synthetically accessible according to organic chemistry rules [15]. While potentially applicable to any stoichiometry, as a proof of principle we restrict ourselves to small organic molecules. Specifically, we define a controlled test-bed consisting of all 7165 organic molecules from the GDB data base with up to seven "heavy" atoms that contain C, N, O, or S, being saturated with hydrogen atoms. Atomization energies range from -800 to -2000 kcal/mol.

A decision process in which rewards depend on history rather than merely on the current state is called a decision process with non-Markovian rewards (NMRDP). In decision-theoretic planning, where many desirable behaviours are more naturally expressed as properties of execution sequences rather than as properties of states, NMRDPs form a more natural model than the commonly adopted fully Markovian decision process (MDP) model. While the more tractable solution methods developed for MDPs do not directly apply in the presence of non-Markovian rewards, a number of solution methods for NMRDPs have been proposed in the literature. These all exploit a compact specification of the non-Markovian reward function in temporal logic, to automatically translate the NMRDP into an equivalent MDP which is solved using efficient MDP solution methods. This paper presents NMRDPP (Non-Markovian Reward Decision Process Planner), a software platform for the development and experimentation of methods for decision-theoretic planning with non-Markovian rewards. The current version of NMRDPP implements, under a single interface, a family of methods based on existing as well as new approaches which we describe in detail. These include dynamic programming, heuristic search, and structured methods. Using NMRDPP, we compare the methods and identify certain problem features that affect their performance. NMRDPPs treatment of non-Markovian rewards is inspired by the treatment of domain-specific search control knowledge in the TLPlan planner, which it incorporates as a special case. In the First International Probabilistic Planning Competition, NMRDPP was able to compete and perform well in both the domain-independent and hand-coded tracks, using search control knowledge in the latter.

Code optimization and high level synthesis can be posed as constraint satisfaction and optimization problems, such as graph coloring used in register allocation. Graph coloring is also used to model more traditional CSPs relevant to AI, such as planning, time-tabling and scheduling. Provably optimal solutions may be desirable for commercial and defense applications. Additionally, for applications such as register allocation and code optimization, naturally-occurring instances of graph coloring are often small and can be solved optimally. A recent wave of improvements in algorithms for Boolean satisfiability (SAT) and 0-1 Integer Linear Programming (ILP) suggests generic problem-reduction methods, rather than problem-specific heuristics, because (1) heuristics may be upset by new constraints, (2) heuristics tend to ignore structure, and (3) many relevant problems are provably inapproximable. Problem reductions often lead to highly symmetric SAT instances, and symmetries are known to slow down SAT solvers. In this work, we compare several avenues for symmetry breaking, in particular when certain kinds of symmetry are present in all generated instances. Our focus on reducing CSPs to SAT allows us to leverage recent dramatic improvement in SAT solvers and automatically benefit from future progress. We can use a variety of black-box SAT solvers without modifying their source code because our symmetry-breaking techniques are static, i.e., we detect symmetries and add symmetry breaking predicates (SBPs) during pre-processing. An important result of our work is that among the types of instance-independent SBPs we studied and their combinations, the simplest and least complete constructions are the most effective. Our experiments also clearly indicate that instance-independent symmetries should mostly be processed together with instance-specific symmetries rather than at the specification level, contrary to what has been suggested in the literature.

Tabu search is one of the most effective heuristics for locating high-quality solutions to a diverse array of NP-hard combinatorial optimization problems. Despite the widespread success of tabu search, researchers have a poor understanding of many key theoretical aspects of this algorithm, including models of the high-level run-time dynamics and identification of those search space features that influence problem difficulty. We consider these questions in the context of the job-shop scheduling problem (JSP), a domain where tabu search algorithms have been shown to be remarkably effective. Previously, we demonstrated that the mean distance between random local optima and the nearest optimal solution is highly correlated with problem difficulty for a well-known tabu search algorithm for the JSP introduced by Taillard. In this paper, we discuss various shortcomings of this measure and develop a new model of problem difficulty that corrects these deficiencies. We show that Taillards algorithm can be modeled with high fidelity as a simple variant of a straightforward random walk. The random walk model accounts for nearly all of the variability in the cost required to locate both optimal and sub-optimal solutions to random JSPs, and provides an explanation for differences in the difficulty of random versus structured JSPs. Finally, we discuss and empirically substantiate two novel predictions regarding tabu search algorithm behavior. First, the method for constructing the initial solution is highly unlikely to impact the performance of tabu search. Second, tabu tenure should be selected to be as small as possible while simultaneously avoiding search stagnation; values larger than necessary lead to significant degradations in performance.

Variable elimination is a general technique for constraint processing. It is often discarded because of its high space complexity. However, it can be extremely useful when combined with other techniques. In this paper we study the applicability of variable elimination to the challenging problem of finding still-lifes. We illustrate several alternatives: variable elimination as a stand-alone algorithm, interleaved with search, and as a source of good quality lower bounds. We show that these techniques are the best known option both theoretically and empirically. In our experiments we have been able to solve the n=20 instance, which is far beyond reach with alternative approaches.