Learning probabilistic logic programming languages is receiving an increasing attention and systems are available for learning the parameters (PRISM, LeProbLog, LFI-ProbLog and EMBLEM) or both the structure and the parameters (SEM-CP-logic and SLIPCASE) of these languages. In this paper we present the algorithm SLIPCOVER for "Structure LearnIng of Probabilistic logic programs by searChing OVER the clause space". It performs a beam search in the space of probabilistic clauses and a greedy search in the space of theories, using the log likelihood of the data as the guiding heuristics. To estimate the log likelihood SLIPCOVER performs Expectation Maximization with EMBLEM. The algorithm has been tested on five real world datasets and compared with SLIPCASE, SEM-CP-logic, Aleph and two algorithms for learning Markov Logic Networks (Learning using Structural Motifs (LSM) and ALEPH++ExactL1). SLIPCOVER achieves higher areas under the precision-recall and ROC curves in most cases.

Statistical estimates can often be improved by fusion of data from several different sources. One example is so-called ensemble methods which have been successfully applied in areas such as machine learning for classification and clustering. In this paper, we present an ensemble method to improve community detection by aggregating the information found in an ensemble of community structures. This ensemble can found by re-sampling methods, multiple runs of a stochastic community detection method, or by several different community detection algorithms applied to the same network. The proposed method is evaluated using random networks with community structures and compared with two commonly used community detection methods. The proposed method when applied on a stochastic community detection algorithm performs well with low computational complexity, thus offering both a new approach to community detection and an additional community detection method.

Reshef & Reshef recently published a paper in which they present a method called the Maximal Information Coefficient (MIC) that can detect all forms of statistical dependence between pairs of variables as sample size goes to infinity. While this method has been praised by some, it has also been criticized for its lack of power in finite samples. We seek to modify MIC so that it has higher power in detecting associations for limited sample sizes. Here we present the Generalized Mean Information Coefficient (GMIC), a generalization of MIC which incorporates a tuning parameter that can be used to modify the complexity of the association favored by the measure. We define GMIC and prove it maintains several key asymptotic properties of MIC. Its increased power over MIC is demonstrated using a simulation of eight different functional relationships at sixty different noise levels. The results are compared to the Pearson correlation, distance correlation, and MIC. Simulation results suggest that while generally GMIC has slightly lower power than the distance correlation measure, it achieves higher power than MIC for many forms of underlying association. For some functional relationships, GMIC surpasses all other statistics calculated. Preliminary results suggest choosing a moderate value of the tuning parameter for GMIC will yield a test that is robust across underlying relationships. GMIC is a promising new method that mitigates the power issues suffered by MIC, at the possible expense of equitability. Nonetheless, distance correlation was in our simulations more powerful for many forms of underlying relationships. At a minimum, this work motivates further consideration of maximal information-based nonparametric exploration (MINE) methods as statistical tests of independence.

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.

Automatic mathematical solution assessment checks the equivalence of mathematical expressions in the user answer and standard solution. It is a challenging problem as the semantics of mathematical expressions are highly symbolic and equivalent mathematical expressions can be expressed in different forms. In this paper, we propose an effective Probabilistic Equivalence Verification (PEV) approach for automatic mathematical solution assessment. The proposed PEV approach is a randomized method based on the probabilistic numerical equivalence testing of two mathematical expressions. It can avoid false negative errors completely while guaranteeing a small probability of false positive errors to occur. The performance results have shown that the proposed PEV approach has outperformed other popular techniques in Computer Algebra Systems such as Maple and Mathematica.

In virtually all machine learning applications, hyper-parameter tuning is required to maximize predictive accuracy. Such tuning is computationally expensive, and the cost is further exacerbated by the need for multiple evaluations (via cross-validation or bootstrap) at each configuration setting to guarantee statistically significant results. This paper presents a simple, general technique for improving the efficiency of hyper-parameter tuning by minimizing the number of resampled evaluations at each configuration. We exploit the fact that train-test samples can easily be \emph{matched} across candidate hyper-parameter configurations. This permits the use of paired hypothesis tests and power analysis that allow for statistically sound early elimination of suboptimal candidates to minimize the number of evaluations. Results on synthetic and real-world datasets demonstrate that our method improves over competitors for discrete parameter settings, and enhances state-of-the-art techniques for continuous parameter settings.

The area under the ROC curve is widely used as a measure of performance of classification rules. However, it has recently been shown that the measure is fundamentally incoherent, in the sense that it treats the relative severities of misclassifications differently when different classifiers are used. To overcome this, Hand (2009) proposed the $H$ measure, which allows a given researcher to fix the distribution of relative severities to a classifier-independent setting on a given problem. This note extends the discussion, and proposes a modified standard distribution for the $H$ measure, which better matches the requirements of researchers, in particular those faced with heavily unbalanced datasets, the $Beta(\pi_1+1,\pi_0+1)$ distribution. [Preprint submitted at Pattern Recognition Letters]

We present an efficient algorithm for simultaneously training sparse generalized linear models across many related problems, which may arise from bootstrapping, cross-validation and nonparametric permutation testing. Our approach leverages the redundancies across problems to obtain significant computational improvements relative to solving the problems sequentially by a conventional algorithm. We demonstrate our fast simultaneous training of generalized linear models (FaSTGLZ) algorithm on a number of real-world datasets, and we run otherwise computationally intensive bootstrapping and permutation test analyses that are typically necessary for obtaining statistically rigorous classification results and meaningful interpretation. Code is freely available at http://liinc.bme.columbia.edu/fastglz.

We study a simple modification to the conventional time of flight mass spectrometry (TOFMS) where a \emph{variable} and (pseudo)-\emph{random} pulsing rate is used which allows for traces from different pulses to overlap. This modification requires little alteration to the currently employed hardware. However, it requires a reconstruction method to recover the spectrum from highly aliased traces. We propose and demonstrate an efficient algorithm that can process massive TOFMS data using computational resources that can be considered modest with today's standards. This approach can be used to improve duty cycle, speed, and mass resolving power of TOFMS at the same time. We expect this to extend the applicability of TOFMS to new domains.

In his seminal work, Schapire (1990) proved that weak classifiers could be improved to achieve arbitrarily high accuracy, but he never implied that a simple majority-vote mechanism could always do the trick. By comparing the asymptotic misclassification error of the majority-vote classifier with the average individual error, we discover an interesting phase-transition phenomenon. For binary classification with equal prior probabilities, our result implies that, for the majority-vote mechanism to work, the collection of weak classifiers must meet the minimum requirement of having an average true positive rate of at least 50% and an average false positive rate of at most 50%.