SUMMARY: The advent of high-throughput technologies has provided researchers with measurements of thousands of molecular entities and enable the investigation of the internal regulatory apparatus of the cell. However, network inference from high-throughput data is far from being a solved problem. While a plethora of different inference methods have been proposed, they often lead to non-overlapping predictions, and many of them lack user-friendly implementations to enable their broad utilization. Here, we present Consensus Interaction Network Inference Service (COSIFER), a package and a companion web-based platform to infer molecular networks from expression data using state-of-the-art consensus approaches. COSIFER includes a selection of state-of-the-art methodologies for network inference and different consensus strategies to integrate the predictions of individual methods and generate robust networks. AVAILABILITY AND IMPLEMENTATION: COSIFER Python source code is available at https://github.com/PhosphorylatedRabbits/cosifer. The web service is accessible at https://ibm.biz/cosifer-aas. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

In this paper, the problem of one-bit compressed sensing (OBCS) is formulated as a problem in probably approximately correct (PAC) learning. It is shown that the Vapnik-Chervonenkis (VC-) dimension of the set of half-spaces in $\R^n$ generated by $k$-sparse vectors is bounded below by $k ( \lfloor\lg (n/k) \rfloor +1 )$ and above by $\lfloor 2k \lg (en) \rfloor $. By coupling this estimate with well-established results in PAC learning theory, we show that a consistent algorithm can recover a $k$-sparse vector with $O(k \lg n)$ measurements, given only the signs of the measurement vector. This result holds for \textit{all} probability measures on $\R^n$. The theory is also applicable to the case of noisy labels, where the signs of the measurements are flipped with some unknown probability.

Ensemble methods that aggregate predictions from a set of diverse base learners consistently outperform individual classifiers. Many such popular strategies have been developed in a supervised setting, where the sample labels have been provided to the ensemble algorithm. However, with the rising interest in unsupervised algorithms for machine learning and growing amounts of uncurated data, the reliance on labeled data precludes the application of ensemble algorithms to many real world problems. To this end we develop a new theoretical framework for ensemble learning, the Strategy for Unsupervised Multiple Method Aggregation (SUMMA), that estimates the performances of base classifiers and uses these estimates to form an ensemble classifier. SUMMA also generates an ensemble ranking of samples based on the confidence score it assigns to each sample. We illustrate the performance of SUMMA using a synthetic example as well as two real world problems.

In this paper we introduce a new optimization formulation for sparse regression and compressed sensing, called CLOT (Combined L-One and Two), wherein the regularizer is a convex combination of the $\ell_1$- and $\ell_2$-norms. This formulation differs from the Elastic Net (EN) formulation, in which the regularizer is a convex combination of the $\ell_1$- and $\ell_2$-norm squared. It is shown that, in the context of compressed sensing, the EN formulation does not achieve robust recovery of sparse vectors, whereas the new CLOT formulation achieves robust recovery. Also, like EN but unlike LASSO, the CLOT formulation achieves the grouping effect, wherein coefficients of highly correlated columns of the measurement (or design) matrix are assigned roughly comparable values. It is already known LASSO does not have the grouping effect. Therefore the CLOT formulation combines the best features of both LASSO (robust sparse recovery) and EN (grouping effect). The CLOT formulation is a special case of another one called SGL (Sparse Group LASSO) which was introduced into the literature previously, but without any analysis of either the grouping effect or robust sparse recovery. It is shown here that SGL achieves robust sparse recovery, and also achieves a version of the grouping effect in that coefficients of highly correlated columns belonging to the same group of the measurement (or design) matrix are assigned roughly comparable values.