We consider the problem of inferring direct neural network connections from Calcium imaging time series. Inverse covariance estimation has proven to be a fast and accurate method for learning macro-and micro-scale network connectivity in the brain and in a recent Kaggle Connectomics competition inverse covariance was the main component of several top ten solutions, including our own and the winning team's algorithm. However, the accuracy of inverse covariance estimation is highly sensitive to signal preprocessing of the Calcium fluorescence time series. Furthermore, brute force optimization methods such as grid search and coordinate ascent over signal processing parameters is a time intensive process, where learning may take several days and parameters that optimize one network may not generalize to networks with different size and parameters. In this paper we show how inverse covariance estimation can be dramatically improved using a simple convolution filter prior to applying sample covariance. Furthermore, these signal processing parameters can be learned quickly using a supervised optimization algorithm. In particular, we maximize a binomial log-likelihood loss function with respect to a convolution filter of the time series and the inverse covariance regularization parameter. Our proposed algorithm is relatively fast on networks the size of those in the competition (1000 neurons), producing AUC scores with similar accuracy to the winning solution in training time under 2 hours on a cpu. Prediction on new networks of the same size is carried out in less than 15 minutes, the time it takes to read in the data and write out the solution.

The success of machine learning, particularly in supervised settings, has led to numerous attempts to apply it in adversarial settings such as spam and malware detection. The core challenge in this class of applications is that adversaries are not static data generators, but make a deliberate effort to evade the classifiers deployed to detect them. We investigate both the problem of modeling the objectives of such adversaries, as well as the algorithmic problem of accounting for rational, objective-driven adversaries. In particular, we demonstrate severe shortcomings of feature reduction in adversarial settings using several natural adversarial objective functions, an observation that is particularly pronounced when the adversary is able to substitute across similar features (for example, replace words with synonyms or replace letters in words). We offer a simple heuristic method for making learning more robust to feature cross-substitution attacks. We then present a more general approach based on mixed-integer linear programming with constraint generation, which implicitly trades off overfitting and feature selection in an adversarial setting using a sparse regularizer along with an evasion model. Our approach is the first method for combining an adversarial classification algorithm with a very general class of models of adversarial classifier evasion. We show that our algorithmic approach significantly outperforms state-of-the-art alternatives.

Submodular optimization has found many applications in machine learning and beyond. We carry out the first systematic investigation of inference in probabilistic models defined through submodular functions, generalizing regular pairwise MRFs and Determinantal Point Processes.

We develop a scoring and classification procedure based on the PAC-Bayesian approach and the AUC (Area Under Curve) criterion. We focus initially on the class of linear score functions. We derive PAC-Bayesian non-asymptotic bounds for two types of prior for the score parameters: a Gaussian prior, and a spike-and-slab prior; the latter makes it possible to perform feature selection. One important advantage of our approach is that it is amenable to powerful Bayesian computational tools. We derive in particular a Sequential Monte Carlo algorithm, as an efficient method which may be used as a gold standard, and an Expectation-Propagation algorithm, as a much faster but approximate method. We also extend our method to a class of non-linear score functions, essentially leading to a nonparametric procedure, by considering a Gaussian process prior.

Modern applications in sensitive domains such as biometrics and medicine frequently require the use of non-decomposable loss functions such as precision@k, F-measure etc. Compared to point loss functions such as hinge-loss, these offer much more fine grained control over prediction, but at the same time present novel challenges in terms of algorithm design and analysis. In this work we initiate a study of online learning techniques for such non-decomposable loss functions with an aim to enable incremental learning as well as design scalable solvers for batch problems. To this end, we propose an online learning framework for such loss functions. Our model enjoys several nice properties, chief amongst them being the existence of efficient online learning algorithms with sublinear regret and online to batch conversion bounds. Our model is a provable extension of existing online learning models for point loss functions.

We present a theoretical analysis of F -measures for binary, multiclass and multilabel classification. These performance measures are non-linear, but in many scenarios they are pseudo-linear functions of the per-class false negative/false positive rate. Based on this observation, we present a general reduction of F - measure maximization to cost-sensitive classification with unknown costs. We then propose an algorithm with provable guarantees to obtain an approximately optimal classifier for the F -measure by solving a series of cost-sensitive classification problems. The strength of our analysis is to be valid on any dataset and any class of classifiers, extending the existing theoretical results on F -measures, which are asymptotic in nature. We present numerical experiments to illustrate the relative importance of cost asymmetry and thresholding when learning linear classifiers on various F -measure optimization tasks.

Even with the advent of more sophisticated, data-hungry methods, boosted decision trees remain extraordinarily successful for fast rigid object detection, achieving top accuracy on numerous datasets. While effective, most boosted detectors use decision trees with orthogonal (single feature) splits, and the topology of the resulting decision boundary may not be well matched to the natural topology of the data. Given highly correlated data, decision trees with oblique (multiple feature) splits can be effective. Use of oblique splits, however, comes at considerable computational expense. Inspired by recent work on discriminative decorrelation of HOG features, we instead propose an efficient feature transform that removes correlations in local neighborhoods. The result is an overcomplete but locally decorrelated representation ideally suited for use with orthogonal decision trees. In fact, orthogonal trees with our locally decorrelated features outperform oblique trees trained over the original features at a fraction of the computational cost. The overall improvement in accuracy is dramatic: on the Caltech Pedestrian Dataset, we reduce false positives nearly tenfold over the previous state-of-the-art.

We present the Bayesian Case Model (BCM), a general framework for Bayesian case-based reasoning (CBR) and prototype classification and clustering. BCM brings the intuitive power of CBR to a Bayesian generative framework. The BCM learns prototypes, the "quintessential" observations that best represent clusters in a dataset, by performing joint inference on cluster labels, prototypes and important features. Simultaneously, BCM pursues sparsity by learning subspaces, the sets of features that play important roles in the characterization of the prototypes. The prototype and subspace representation provides quantitative benefits in interpretability while preserving classification accuracy. Human subject experiments verify statistically significant improvements to participants' understanding when using explanations produced by BCM, compared to those given by prior art.

We study consistency properties of algorithms for non-decomposable performance measures that cannot be expressed as a sum of losses on individual data points, such as the F-measure used in text retrieval and several other performance measures used in class imbalanced settings. While there has been much work on designing algorithms for such performance measures, there is limited understanding of the theoretical properties of these algorithms. Recently, Ye et al. (2012) showed consistency results for two algorithms that optimize the F-measure, but their results apply only to an idealized setting, where precise knowledge of the underlying probability distribution (in the form of the'true' posterior class probability) is available to a learning algorithm. In this work, we consider plug-in algorithms that learn a classifier by applying an empirically determined threshold to a suitable'estimate' of the class probability, and provide a general methodology to show consistency of these methods for any non-decomposable measure that can be expressed as a continuous function of true positive rate (TPR) and true negative rate (TNR), and for which the Bayes optimal classifier is the class probability function thresholded suitably. We use this template to derive consistency results for plug-in algorithms for the F-measure and for the geometric mean of TPR and precision; to our knowledge, these are the first such results for these measures. In addition, for continuous distributions, we show consistency of plug-in algorithms for any performance measure that is a continuous and monotonically increasing function of TPR and TNR. Experimental results confirm our theoretical findings.

Performance metrics for binary classification are designed to capture tradeoffs between four fundamental population quantities: true positives, false positives, true negatives and false negatives. Despite significant interest from theoretical and applied communities, little is known about either optimal classifiers or consistent algorithms for optimizing binary classification performance metrics beyond a few special cases. We consider a fairly large family of performance metrics given by ratios of linear combinations of the four fundamental population quantities. This family includes many well known binary classification metrics such as classification accuracy, AM measure, F-measure and the Jaccard similarity coefficient as special cases. Our analysis identifies the optimal classifiers as the sign of the thresholded conditional probability of the positive class, with a performance metric-dependent threshold.