Scalable Inference of Gene Regulatory Networks with the Spark Distributed Computing Platform Cristo

Inference of Gene Regulatory Networks (GRNs) remains an important open challenge in computational biology. The goal of bio-model inference is to, based on time-series of gene expression data, obtain the sparse topological structure and the parameters that quantitatively understand and reproduce the dynamics of biological system. Nevertheless, the inference of a GRN is a complex optimization problem that involve processing S-System models, which include large amount of gene expression data from hundreds (even thousands) of genes in multiple time-series (essays). This complexity, along with the amount of data managed, make the inference of GRNs to be a computationally expensive task. Therefore, the genera- tion of parallel algorithmic proposals that operate efficiently on distributed processing platforms is a must in current reconstruction of GRNs. In this paper, a parallel multi-objective approach is proposed for the optimal inference of GRNs, since min- imizing the Mean Squared Error using S-System model and Topology Regularization value. A flexible and robust multi-objective cellular evolutionary algorithm is adapted to deploy parallel tasks, in form of Spark jobs. The proposed approach has been developed using the framework jMetal, so in order to perform parallel computation, we use Spark on a cluster of distributed nodes to evaluate candidate solutions modeling the interactions of genes in biological networks.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Spark solutions for discovering fuzzy association rules in Big Data

The research reported in this paper was partially supported the COPKIT project from the 8th Programme Framework (H2020) research and innovation programme (grant agreement No 786687) and from the BIGDATAMED projects with references B-TIC-145-UGR18 and P18-RT-2947.The high computational impact when mining fuzzy association rules grows significantly when managing very large data sets, triggering in many cases a memory overflow error and leading to the experiment failure without its conclusion. It is in these cases when the application of Big Data techniques can help to achieve the experiment completion. Therefore, in this paper several Spark algorithms are proposed to handle with massive fuzzy data and discover interesting association rules. For that, we based on a decomposition of interestingness measures in terms of α-cuts, and we experimentally demonstrate that it is sufficient to consider only 10equidistributed α-cuts in order to mine all significant fuzzy association rules. Additionally, all the proposals are compared and analysed in terms of efficiency and speed up, in several datasets, including a real dataset comprised of sensor measurements from an office building.COPKIT project from the 8th Programme Framework (H2020) research and innovation programme 786687BIGDATAMED projects B-TIC-145-UGR18 P18-RT-294