We use partial class memberships in soft classification to model uncertain labelling and mixtures of classes. Partial class memberships are not restricted to predictions, but may also occur in reference labels (ground truth, gold standard diagnosis) for training and validation data. Classifier performance is usually expressed as fractions of the confusion matrix, such as sensitivity, specificity, negative and positive predictive values. We extend this concept to soft classification and discuss the bias and variance properties of the extended performance measures. Ambiguity in reference labels translates to differences between best-case, expected and worst-case performance. We show a second set of measures comparing expected and ideal performance which is closely related to regression performance, namely the root mean squared error RMSE and the mean absolute error MAE. All calculations apply to classical crisp classification as well as to soft classification (partial class memberships and/or one-class classifiers). The proposed performance measures allow to test classifiers with actual borderline cases. In addition, hardening of e.g. posterior probabilities into class labels is not necessary, avoiding the corresponding information loss and increase in variance. We implement the proposed performance measures in the R package "softclassval", which is available from CRAN and at http://softclassval.r-forge.r-project.org. Our reasoning as well as the importance of partial memberships for chemometric classification is illustrated by a real-word application: astrocytoma brain tumor tissue grading (80 patients, 37000 spectra) for finding surgical excision borders. As borderline cases are the actual target of the analytical technique, samples which are diagnosed to be borderline cases must be included in the validation.

This paper summarizes efforts to computationally model two transitions in the evolution of human creativity: its origins about two million years ago, and the 'big bang' of creativity about 50,000 years ago. Using a computational model of cultural evolution in which neural network based agents evolve ideas for actions through invention and imitation, we tested the hypothesis that human creativity began with onset of the capacity for recursive recall. We compared runs in which agents were limited to single-step actions to runs in which they used recursive recall to chain simple actions into complex ones. Chaining resulted in higher diversity, open-ended novelty, no ceiling on the mean fitness of actions, and greater ability to make use of learning. Using a computational model of portrait painting, we tested the hypothesis that the explosion of creativity in the Middle/Upper Paleolithic was due to onset of con-textual focus: the capacity to shift between associative and analytic thought. This resulted in faster convergence on portraits that resembled the sitter, employed painterly techniques, and were rated as preferable. We conclude that recursive recall and contextual focus provide a computationally plausible explanation of how humans evolved the means to transform this planet.

Recent work has suggested reducing electricity generation cost by cutting the peak to average ratio (PAR) without reducing the total amount of the loads. However, most of these proposals rely on consumer's willingness to act. In this paper, we propose an approach to cut PAR explicitly from the supply side. The resulting cut loads are then distributed among consumers by the means of a multiunit auction which is done by an intelligent agent on behalf of the consumer. This approach is also in line with the future vision of the smart grid to have the demand side matched with the supply side. Experiments suggest that our approach reduces overall system cost and gives benefit to both consumers and the energy provider.

The goal of supervised feature selection is to find a subset of input features that are responsible for predicting output values. The least absolute shrinkage and selection operator (Lasso) allows computationally efficient feature selection based on linear dependency between input features and output values. In this paper, we consider a feature-wise kernelized Lasso for capturing non-linear input-output dependency. We first show that, with particular choices of kernel functions, non-redundant features with strong statistical dependence on output values can be found in terms of kernel-based independence measures. We then show that the globally optimal solution can be efficiently computed; this makes the approach scalable to high-dimensional problems. The effectiveness of the proposed method is demonstrated through feature selection experiments with thousands of features.

Motivation. Protein contact map describes the pairwise spatial and functional relationship of residues in a protein and contains key information for protein 3D structure prediction. Although studied extensively, it remains very challenging to predict contact map using only sequence information. Most existing methods predict the contact map matrix element-by-element, ignoring correlation among contacts and physical feasibility of the whole contact map. A couple of recent methods predict contact map based upon residue co-evolution, taking into consideration contact correlation and enforcing a sparsity restraint, but these methods require a very large number of sequence homologs for the protein under consideration and the resultant contact map may be still physically unfavorable. Results. This paper presents a novel method PhyCMAP for contact map prediction, integrating both evolutionary and physical restraints by machine learning and integer linear programming (ILP). The evolutionary restraints include sequence profile, residue co-evolution and context-specific statistical potential. The physical restraints specify more concrete relationship among contacts than the sparsity restraint. As such, our method greatly reduces the solution space of the contact map matrix and thus, significantly improves prediction accuracy. Experimental results confirm that PhyCMAP outperforms currently popular methods no matter how many sequence homologs are available for the protein under consideration. PhyCMAP can predict contacts within minutes after PSIBLAST search for sequence homologs is done, much faster than the two recent methods PSICOV and EvFold. See http://raptorx.uchicago.edu for the web server.

This paper investigates the control of an ML component within the Covariance Matrix Adaptation Evolution Strategy (CMA-ES) devoted to black-box optimization. The known CMA-ES weakness is its sample complexity, the number of evaluations of the objective function needed to approximate the global optimum. This weakness is commonly addressed through surrogate optimization, learning an estimate of the objective function a.k.a. surrogate model, and replacing most evaluations of the true objective function with the (inexpensive) evaluation of the surrogate model. This paper presents a principled control of the learning schedule (when to relearn the surrogate model), based on the Kullback-Leibler divergence of the current search distribution and the training distribution of the former surrogate model. The experimental validation of the proposed approach shows significant performance gains on a comprehensive set of ill-conditioned benchmark problems, compared to the best state of the art including the quasi-Newton high-precision BFGS method.

Modeling the purposeful behavior of imperfect agents from a small number of observations is a challenging task. When restricted to the single-agent decision-theoretic setting, inverse optimal control techniques assume that observed behavior is an approximately optimal solution to an unknown decision problem. These techniques learn a utility function that explains the example behavior and can then be used to accurately predict or imitate future behavior in similar observed or unobserved situations. In this work, we consider similar tasks in competitive and cooperative multi-agent domains. Here, unlike single-agent settings, a player cannot myopically maximize its reward; it must speculate on how the other agents may act to influence the game's outcome. Employing the game-theoretic notion of regret and the principle of maximum entropy, we introduce a technique for predicting and generalizing behavior.

As the amount and complexity of genetic information increases it is necessary that we explore some efficient ways of handling these data. This study takes the "divide and conquer" approach for analyzing high dimensional genomic data. Our aims include reducing the dimensionality of the problem that has to be dealt one at a time, improving the performance and interpretability of the models. We propose using the inherent structures in the genome; to divide the bigger problem into manageable parts. In plant and animal breeding studies a distinction is made between the commercial value (additive + epistatic genetic effects) and the breeding value (additive genetic effects) of an individual since it is expected that some of the epistatic genetic effects will be lost due to recombination. In this paper, we argue that the breeder can take advantage of some of the epistatic marker effects in regions of low recombination. The models introduced here aim to estimate local epistatic line heritability by using the genetic map information and combine the local additive and epistatic effects. To this end, we have used semi-parametric mixed models with multiple local genomic relationship matrices with hierarchical testing designs and lasso post-processing for sparsity in the final model and speed. Our models produce good predictive performance along with genetic association information.

A measure of dependence is said to be equitable if it gives similar scores to equally noisy relationships of different types. Equitability is important in data exploration when the goal is to identify a relatively small set of strongest associations within a dataset as opposed to finding as many non-zero associations as possible, which often are too many to sift through. Thus an equitable statistic, such as the maximal information coefficient (MIC), can be useful for analyzing high-dimensional data sets. Here, we explore both equitability and the properties of MIC, and discuss several aspects of the theory and practice of MIC. We begin by presenting an intuition behind the equitability of MIC through the exploration of the maximization and normalization steps in its definition. We then examine the speed and optimality of the approximation algorithm used to compute MIC, and suggest some directions for improving both. Finally, we demonstrate in a range of noise models and sample sizes that MIC is more equitable than natural alternatives, such as mutual information estimation and distance correlation.

As large-scale theft of data from corporate servers is becoming increasingly common, it becomes interesting to examine alternatives to the paradigm of centralizing sensitive data into large databases. Instead, one could use cryptography and distributed computation so that sensitive data can be supplied and processed in encrypted form, and only the final result is made known. In this paper, we examine how such a paradigm can be used to implement constraint satisfaction, a technique that can solve a broad class of AI problems such as resource allocation, planning, scheduling, and diagnosis. Most previous work on privacy in constraint satisfaction only attempted to protect specific types of information, in particular the feasibility of particular combinations of decisions. We formalize and extend these restricted notions of privacy by introducing four types of private information, including the feasibility of decisions and the final decisions made, but also the identities of the participants and the topology of the problem. We present distributed algorithms that allow computing solutions to constraint satisfaction problems while maintaining these four types of privacy. We formally prove the privacy properties of these algorithms, and show experiments that compare their respective performance on benchmark problems.