All posts by rocha_luis

Canalization and Control in Automata Networks

Dynamical Modularity
Dynamical Modularity

Read our latest paper titled Canalization and Control in Automata Networks: Body Segmentation in Drosophila melanogaster in PLoS ONE. Authors Manuel Marques-Pita & Luis Rocha ask, How do cells and tissues ‘compute’? Schema redescription is presented as a methodology to characterize canalization in automata networks used to model biochemical regulation and signalling. Canalization becomes synonymous with redundancy present in the logic of automata. This results in straightforward measures to quantify canalization in an automaton (micro-level), which is in turn integrated into a highly scalable framework to characterize the collective dynamics of large-scale automata networks (macro-level). Several new results ensue from this methodology developed as part of the CASCI collective dynamics project: uncovering of dynamical modularity (modules in the dynamics rather than in the structure of networks), identification of minimal conditions and critical nodes to control the convergence to attractors, simulation of dynamical behaviour from incomplete information about initial conditions, and measures of macro-level canalization and robustness to perturbations. The methodology is applicable to any complex network that can be modelled using automata, but this work focuses on biochemical regulation and signalling, with a well-known model of the intra- and inter cellular genetic regulation of body segmentation in Drosophila melanogaster.

Highly accessed paper in BMC Bioinformatics


The pharmacokinetics ontology and corpus for text mining developed in collaboration with Li’s lab at IUPUI, part of CASCI Biomedical Literature Mining work, has been reported in BMC Bioinformatics where it has become a Highly Accessed paper:

Wu, Hengyi, S. Karnik, A. Subhadarshini, Z. Wang, S. Philips, X. Han, C. Chiang, L. Liu, M. Boustani, L.M. Rocha, S.K. Quinney, D.A. Flockhart and L. Li [2013]. “An Integrated Pharmacokinetics Ontology and Corpus for Text Mining”. BMC Bioinformatics. 14:35. DOI:10.1186/1471-2105-14-35.

IARPA contract to study new ways to forecast critical societal events

University and industry scientists are determining how to forecast significant societal events, ranging from violent protests to nationwide credit-rate crashes, by analyzing the billions of pieces of information in the ocean of public communications, such as tweets, web queries, oil prices, and daily stock market activity.

“We are automating the generation of alerts, so that intelligence analysts can focus on interpreting the discoveries rather than on the mechanics of integrating information,” said Naren Ramakrishnan, the Thomas L. Phillips Professor of Engineering in the computer science department at Virginia Tech. He is leading the team of computer scientists and subject-matter experts from Virginia Tech, the University of Maryland, Cornell University, Children’s Hospital of Boston, San Diego State University, University of California at San Diego, and Indiana University, and from the companies, CACI International Inc., and Basis Technology.

CNetS Professors Bollen and Rocha from the School of Informatics and Computing at Indiana University are members of this project. Prof. Bollen, has devised a way to evaluate the tone of tweets – calm, alert, vital, etc. — to predict stock market trends. Prof. Rocha, has developed bio-inspired methods to predict associations in biochemical, social, and knowledge networks, including web and e-mail systems.

Additional details: Researchers study new ways to forecast critical societal events.