Sponsored by Persistent Systems. Luis Rocha, Director of the Complex Systems PhD track in the School of Information and Computing at Indiana University Bloomington, explains the new software-driven approach to medical research. Big data generated through social media such as Twitter and Instragram provides a far deeper and fuller examination of the impact of medicines and diseases, leading to greater actionable insights to improve the efficacy of prevention and treatment.
Congratulations to CASCI alumnus Dr. Ahmed Abdeen Hamed who was recognized by FastCompany magazine, among the most creative people in the world, in 2016, for his research publication entitled: Twitter K-H networks in action: Advancing biomedical literature for drug search.Dr. Hamed completed his Computer Science MS degree at Indiana University in May 2005 and joined our Complex Networks & Systems track of the PhD in Informatics in the Fall of 2008. For personal reasons, he finished his PhD at the University of Vermont, but started his research in biomedical text mining with the CASCI group.
Network science has allowed us to understand the organization of complex systems across disciplines. However, there is a need to understand how to control them; for example, to identify strategies to revert a diseased cell to a healthy state in cancer treatment. Recent work in the field—based on linear control theory—suggests that the controllability of complex systems can be predicted solely from the graph of interactions between variables, without considering their dynamics. Such graph-based approaches have been used, for instance, to suggest that biological systems are harder to control and have appreciably different control profiles than social or technological systems. The methodology has also been increasingly used in many applications from financial to biochemical networks.
In work published today in Nature Scientific Reports, CNetS graduate student Alexander Gates and Professor Luis Rocha demonstrate that such graph-based methods fail to characterize controllability when dynamics are introduced. The study computed the control profiles of large ensembles of multivariate systems as well as existing Systems Biology models of biochemical regulation in various organisms.
Recent CASCI Complex Systems & Networks Phd program graduate Artemy Kolchinsky, is now a postdoc at the Santa Fe Institute. While at SFI, Kolchinsky is working with “David Wolpert on several projects related to optimal use of information and prediction. One is the problem of modeling and analyzing complicated dynamical systems that require large amounts of time and computational power to simulate. […] Another project investigates connections
between information processing and statistical physics. […] The two are [also] beginning to work on understanding why different social groups develop different organizations, whether the group is a prehistoric tribe or a business firm.” More details on the SFI update newsletter.
Congratulations to Luis Rocha, who has been awarded a Fulbright Scholarship devoted to developing Complex Systems methodologies for the Life Sciences. The 12-month sabbatical is to be pursued under the Fulbright program for educational exchanges between the United States and Portugal. It will focus on studying collective behavior and control in biochemical and social networks. The broader goal is to advance our ability to predict and control the dynamics of complex networks in three domain areas: biochemical, neurodyamic, and social systems. The scholarship will also be used to facilitate the design of a new doctoral program on complex networks and systems for the life sciences.
Update: On March 21st, 2016 the paper described below (PMC4720984) was highlighted by Russ Altman from Stanford University in his yearly review as one of 30 important papers of the year in translational bioinformatics.
Using complex networks analysis and social media mining, CNETS researchers from the CASCI team have found that Instagram, a growing social media platform among teens, can be used “to uncover drug-drug interactions (DDI) and adverse drug reactions (ADR).” The work shows that this popular social media service is “a very powerful source of data with great promise in the public-health domain”. The study, “Monitoring Potential Drug Interactions and Reactions via Network Analysis of Instagram User Timelines,” supported by an R01 grant from the National Institutes of Health as well as a gift from Persistent Inc., was recently published and presented at the Pacific Symposium on Biocomputing (PSB 2016), in Hawaii. (PubMed, arXiv). The results are based on almost 7.000 user timelines associated with depression drugs which combined have 5+ million posts.
Modularity in complex systems can be observed in networks and across dynamical states, time scales, and in response to different kinds of perturbations. In a paper published in Physical Review E (Rapid Communication), Kolchinsky, Gates & Rocha propose a principled alternative to detecting communities in static and dynamical networks. The method demonstrates that standard modularity measures on static networks can be seen as a special case of measuring the spread of perturbations in dynamical systems. Thus, the new method offers a powerful tool for exploring the modular organization of complex dynamical systems.
The CNetS poster “The Rise of Social Bots in Online Social Networks” by Emilio Ferrara, Onur Varol, Prashant Shiralkar, Clayton Davis, Filippo Menczer, and Alessandro Flammini won a Best Poster Award at CCS 2015. The poster was presented by Clayton Davis. The results will also appear in the paper “The Rise of Social Bots” to be published in Comm. ACM (in press, preprint).
The paper “Modularity and the Spread of Perturbations in Complex Dynamical Systems” by Artemy Kolchinsky, Alexander J. Gates and Luis M. Rocha, and the poster “Information Theoretic Structures of the French Revolution” by Alexander Barron, Simon DeDeo and Rebecca Spang won additional awards.
Finally, our former postdoctoral scientist Bruno Gonçalves (now tenured faculty member at Aix-Marseille Université) received a Junior Scientist Award from the Complex Systems Society for his contributions to the study of human social behavior from large-scale online attention and behavioral data. This is the second Junior Scientist Award for CNetS (the first was won by Filippo Radicchi).
Congratulations to the CNetS team!
Big success for CNetS researchers at the Conference on Complex Systems (CCS’15)! Here are the accepted talks from our center:
- Computational fact checking from knowledge networks by Giovanni Luca Ciampaglia, Prashant Shiralkar, Johan Bollen, Luis M Rocha, Filippo Menczer and Alessandro Flammini
- Control of complex networks requires structure and dynamics by Alexander Gates and Luis M. Rocha
- Darwin’s Semantic Voyage by Jaimie Murdock, Simon DeDeo, and Colin Allen
- Defining and Identifying Sleeping Beauties in Science by Qing Ke, Emilio Ferrara, Filippo Radicchi and Alessandro Flammini
- Detecting conflict in social unrest using Instagram* by Rion Brattig Correia, Kwan Nok Chan and Luis M. Rocha
- Detecting Campaigns in Social Media by Onur Varol, Emilio Ferrara, Filippo Menczer and Alessandro Flammini
- Discourse Polarization in the US Congress by Rion Brattig Correia, Kwan Nok Chan and Luis M. Rocha
- Eigenmood Twitter Analysis: measuring collective mood variation by Ian B. Wood, Joana Gonçalves-Sá, Johan Bollen and Luis M. Rocha
- Evolution of Online User Behavior During a Social Upheaval by Onur Varol, Emilio Ferrara, Christine Ogan, Filippo Menczer and Alessandro Flammini
- How human perception of the urban environment influences the abandonment process by Stefani Crabstree, Simon DeDeo
- Information theoretic structures of the French Revolution by Alexander Barron, Simon DeDeo, and Rebecca Spang
- Measuring Emotional Contagion in Online Social Networks by Zeyao Yang, Emilio Ferrara
- Modularity and the Spread of Perturbations in Complex Dynamical Systems* by Artemy Kolchinsky, Alexander J. Gates and Luis M. Rocha
- On Predictability of Rare Events Leveraging Social Media by Lei Le, Emilio Ferrara and Alessandro Flammini
- Optimal network modularity for information diffusion by Azadeh Nematzadeh, Emilio Ferrara, Alessandro Flammini and Yong-Yeol Ahn
- Redundancy and control in complex networks by Luis M. Rocha
- The Rise of Social Bots in Online Social Networks by Emilio Ferrara, Onur Varol, Prashant Shiralkar, Clayton Davis, Filippo Menczer and Alessandro Flammini
Simon DeDeo will also deliver one of the plenary talks. *Denotes papers “starred”, or designated as especially worthwhile by the CCS15 program committee.
Congratulations to Artemy Kolchinsky a brand new PhD in 2015 in the Complex Systems track of the Informatics PhD Program. Artemy’s PhD Dissertation is entittled “Measuring Scales: Integration and Modularity in Complex Systems“.