In co-expression analysis, the correlation between pairs of genes is typically combined into a network model of the correlation structure, which facilitates secondary network analysis such as community structure or centrality [1]. However, the correlation between pairs of genes in a co-expression network typically is assumed to be uniform across all samples (e.g., tissue types, treatment conditions, disease status, etc.). Yet it is often inter-group differences in correlated data that are of biological or clinical interest. For example, a gene co-expression network in microarray data for chronic lymphocytic leukemia using known biomarkers was able to predict treatment outcomes in an independent sample [2]. A differential co-expression network approach that leverages the genetic network information may yield novel biomarkers and improved prediction. Differential expression methods compute the mean difference between groups for each gene but typically do not incorporate conditional variation from other genes in the data that may help explain the between-group variation.

In many cases of network analysis, it is more attractive to study how a network varies under different conditions than an individual static network. We propose a novel graphical model, namely Latent Differential Graph Model, where the networks under two different conditions are represented by two semiparametric elliptical distributions respectively, and the variation of these two networks (i.e., differential graph) is characterized by the difference between their latent precision matrices. We propose an estimator for the differential graph based on quasi likelihood maximization with nonconvex regularization. We show that our estimator attains a faster statistical rate in parameter estimation than the state-of-the-art methods, and enjoys oracle property under mild conditions. Thorough experiments on both synthetic and real world data support our theory.

Area under ROC (AUC) is a metric which is widely used for measuring the classification performance for imbalanced data. It is of theoretical and practical interest to develop online learning algorithms that maximizes AUC for large-scale data. A specific challenge in developing online AUC maximization algorithm is that the learning objective function is usually defined over a pair of training examples of opposite classes, and existing methods achieves on-line processing with higher space and time complexity. In this work, we propose a new stochastic online algorithm for AUC maximization. In particular, we show that AUC optimization can be equivalently formulated as a convex-concave saddle point problem. From this saddle representation, a stochastic online algorithm (SOLAM) is proposed which has time and space complexity of one datum. We establish theoretical convergence of SOLAM with high probability and demonstrate its effectiveness and efficiency on standard benchmark datasets.

The goal of minimizing misclassification error on a training set is often just one of several real-world goals that might be defined on different datasets. For example, one may require a classifier to also make positive predictions at some specified rate for some subpopulation (fairness), or to achieve a specified empirical recall. Other real-world goals include reducing churn with respect to a previously deployed model, or stabilizing online training. In this paper we propose handling multiple goals on multiple datasets by training with dataset constraints, using the ramp penalty to accurately quantify costs, and present an efficient algorithm to approximately optimize the resulting non-convex constrained optimization problem. Experiments on both benchmark and real-world industry datasets demonstrate the effectiveness of our approach.

Dimensionality reduction is one of the key issues in the design of effective machine learning methods for automatic induction. In this work, we introduce recursive maxima hunting (RMH) for variable selection in classification problems with functional data. In this context, variable selection techniques are especially attractive because they reduce the dimensionality, facilitate the interpretation and can improve the accuracy of the predictive models. The method, which is a recursive extension of maxima hunting (MH), performs variable selection by identifying the maxima of a relevance function, which measures the strength of the correlation of the predictor functional variable with the class label. At each stage, the information associated with the selected variable is removed by subtracting the conditional expectation of the process. The results of an extensive empirical evaluation are used to illustrate that, in the problems investigated, RMH has comparable or higher predictive accuracy than standard simensionality reduction techniques, such as PCA and PLS, and state-of-the-art feature selection methods for functional data, such as maxima hunting.

This study introduces a novel feature selection approach CMICOT, which is a further evolution of filter methods with sequential forward selection (SFS) whose scoring functions are based on conditional mutual information (MI). We state and study a novel saddle point (max-min) optimization problem to build a scoring function that is able to identify joint interactions between several features. This method fills the gap of MI-based SFS techniques with high-order dependencies. In this high-dimensional case, the estimation of MI has prohibitively high sample complexity. We mitigate this cost using a greedy approximation and binary representatives what makes our technique able to be effectively used. The superiority of our approach is demonstrated by comparison with recently proposed interaction-aware filters and several interaction-agnostic state-of-the-art ones on ten publicly available benchmark datasets.

New silicon technology is enabling large-scale electrophysiological recordings in vivo from hundreds to thousands of channels. Interpreting these recordings requires scalable and accurate automated methods for spike sorting, which should minimize the time required for manual curation of the results. Here we introduce KiloSort, a new integrated spike sorting framework that uses template matching both during spike detection and during spike clustering. KiloSort models the electrical voltage as a sum of template waveforms triggered on the spike times, which allows overlapping spikes to be identified and resolved. Unlike previous algorithms that compress the data with PCA, KiloSort operates on the raw data which allows it to construct a more accurate model of the waveforms. Processing times are faster than in previous algorithms thanks to batch-based optimization on GPUs. We compare KiloSort to an established algorithm and show favorable performance, at much reduced processing times. A novel post-clustering merging step based on the continuity of the templates further reduced substantially the number of manual operations required on this data, for the neurons with near-zero error rates, paving the way for fully automated spike sorting of multichannel electrode recordings.

Exemplar learning is a powerful paradigm for discovering visual similarities in an unsupervised manner. In this context, however, the recent breakthrough in deep learning could not yet unfold its full potential. With only a single positive sample, a great imbalance between one positive and many negatives, and unreliable relationships between most samples, training of convolutional neural networks is impaired. Given weak estimates of local distance we propose a single optimization problem to extract batches of samples with mutually consistent relations. Conflicting relations are distributed over different batches and similar samples are grouped into compact cliques. Learning exemplar similarities is framed as a sequence of clique categorization tasks. The CNN then consolidates transitivity relations within and between cliques and learns a single representation for all samples without the need for labels. The proposed unsupervised approach has shown competitive performance on detailed posture analysis and object classification.

We propose a criterion for discrimination against a specified sensitive attribute in supervised learning, where the goal is to predict some target based on available features. Assumingdata about the predictor, target, and membership in the protected group are available, we show how to optimally adjust any learned predictor so as to remove discrimination according to our definition. Our framework also improves incentives by shifting the cost of poor classification from disadvantaged groups to the decision maker, who can respond by improving the classification accuracy. We enourage readers to consult the more complete manuscript on the arXiv.

Calcium imaging is an important technique for monitoring the activity of thousands of neurons simultaneously. As calcium imaging datasets grow in size, automated detection of individual neurons is becoming important. Here we apply a supervised learning approach to this problem and show that convolutional networks can achieve near-human accuracy and superhuman speed. Accuracy is superior to the popular PCA/ICA method based on precision and recall relative to ground truth annotation by a human expert. These results suggest that convolutional networks are an efficient and flexible tool for the analysis of large-scale calcium imaging data.