MicroRNAs (miRNAs) are small non-coding RNAs which play a key role in the post-transcriptional regulation of many genes. Elucidating miRNA-regulated gene networks is crucial for the understanding of mechanisms and functions of miRNAs in many biological processes, such as cell proliferation, development, differentiation and cell homeostasis, as well as in many types of human tumors. To this aim, we have recently presented the biclustering method HOCCLUS2, for the discovery of miRNA regulatory networks. Experiments on predicted interactions revealed that the statistical and biological consistency of the obtained networks is negatively affected by the poor reliability of the output of miRNA target prediction algorithms. Recently, some learning approaches have been proposed to learn to combine the outputs of distinct prediction algorithms and improve their accuracy. However, the application of classical supervised learning algorithms presents two challenges: i) the presence of only positive examples in datasets of experimentally verified interactions and ii) unbalanced number of labeled and unlabeled examples.

Smart grids are power grids where clients may actively participate in energy production, storage and distribution. Smart grid management raises several challenges, including the possible changes and evolutions in terms of energy consumption and production, that must be taken into account in order to properly regulate the energy distribution. In this context, machine learning methods can be fruitfully adopted to support the analysis and to predict the behavior of smart grids, by exploiting the large amount of streaming data generated by sensor networks. In this paper, we propose a novel change detection method, called ECHAD (Embedding-based CHAnge Detection), that leverages embedding techniques, one-class learning, and a dynamic detection approach that incrementally updates the learned model to reflect the new data distribution. Our experiments show that ECHAD achieves optimal performances on synthetic data representing challenging scenarios. Moreover, a qualitative analysis of the results obtained on real data of a real power grid reveals the quality of the change detection of ECHAD. Specifically, a comparison with state-of-the-art approaches shows the ability of ECHAD in identifying additional relevant changes, not detected by competitors, avoiding false positive detections.

Motivation: The reconstruction of gene regulatory networks (GRNs) from gene expression data has received increasing attention in recent years, due to its usefulness in the understanding of regulatory mechanisms involved in human diseases. Most of the existing methods reconstruct the network through machine learning approaches, by analyzing known examples of interactions. However, (i) they often produce poor results when the amount of labeled examples is limited, or when no negative example is available and (ii) they are not able to exploit information extracted from GRNs of other (better studied) related organisms, when this information is available. Results: In this paper, we propose a novel machine learning method that overcomes these limitations, by exploiting the knowledge about the GRN of a source organism for the reconstruction of the GRN of the target organism, by means of a novel transfer learning technique. Moreover, the proposed method is natively able to work in the positive-unlabeled setting, where no negative example is available, by fruitfully exploiting a (possibly large) set of unlabeled examples. In our experiments, we reconstructed the human GRN, by exploiting the knowledge of the GRN of Mus musculus. Results showed that the proposed method outperforms state-of-the-art approaches and identifies previously unknown functional relationships among the analyzed genes. Availability and implementation: http://www.di.uniba.it/∼mignone/systems/biosfer/index.html. Supplementary information: Supplementary data are available at Bioinformatics online.

Recent developments in sensor networks and mobile computing led to a huge increase in data generated that need to be processed and analyzed efficiently. In this context, many distributed data mining algorithms have recently been proposed. Following this line of research, we propose the DENCAST system, a novel distributed algorithm implemented in Apache Spark, which performs density-based clustering and exploits the identified clusters to solve both single- and multi-target regression tasks (and thus, solves complex tasks such as time series prediction). Contrary to existing distributed methods, DENCAST does not require a final merging step (usually performed on a single machine) and is able to handle large-scale, high-dimensional data by taking advantage of locality sensitive hashing. Experiments show that DENCAST performs clustering more efficiently than a state-of-the-art distributed clustering algorithm, especially when the number of objects increases significantly. The quality of the extracted clusters is confirmed by the predictive capabilities of DENCAST on several datasets: It is able to significantly outperform (p-value $$<0.05$$ < 0.05 ) state-of-the-art distributed regression methods, in both single and multi-target settings.