Speaker: Alberto Pepe, Authorea                                                                                                                                                                                                                          
Title: Data-driven, Interactive Scientific Articles in a Collaborative Environment with Authorea
Date: 02/19/2016
Time: 3:30pm
Room: Informatics East 130
Abstract:  Most tools that scientists use for the preparation of scholarly manuscripts, such as Microsoft Word and LaTeX, function offline and do not account for the born-digital nature of research objects. Also, most authoring tools in use today are not designed for collaboration, and, as scientific collaborations grow in size, research transparency and the attribution of scholarly credit are at stake. In this talk, I will show how the Authorea platform allows scientists to collaboratively write rich data-driven manuscripts on the web — articles that would natively offer readers a dynamic, interactive experience with an article’s fulltext, images, data, and code — paving the road to increased data sharing, data reuse, research reproducibility, and Open Science.

Biography: Alberto Pepe is the co-founder of Authorea. He recently finished a Postdoctorate in Astrophysics at Harvard University. During his postdoctorate, Alberto was also a fellow of the Berkman Center for Internet and Society and the Institute for Quantitative Social Science. Alberto is the author of 30 publications in the fields of Information Science, Data Science, Computational Social Science, and Astrophysics. He obtained his Ph.D. in Information Science from the University of California, Los Angeles with a dissertation on scientific collaboration networks which was awarded with the Best Dissertation Award by the American Society for Information Science and Technology (ASIS&T). Prior to starting his Ph.D., Alberto worked in the Information Technology Department of CERN, in Geneva, Switzerland, where he worked on data repository software and also promoted Open Access among particle physicists. Alberto holds a M.Sc. in Computer Science and a B.Sc. in Astrophysics, both from University College London, U.K. Alberto was born and raised in the wine-making town of Manduria, in Puglia, Southern Italy.

Filippo Radicchi

Filippo Radicchi

Congratulations to Filippo Radicchi, who has been awarded a Faculty Early Career Development (CAREER) grant from the National Science Foundation to establish a research and education program devoted to studying critical infrastructures from the perspective of network theory. The $500,000 grant will focus on how physical networks, such as transportation, water, food supply, communications, and power generation and transmission, interact to deliver their assets as efficiently as possible. Transactional and relational infrastructures, such as financial and trade networks, also enter into the equation to serve as the backbone for modern society. Read more…

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.

“We build knowledge networks from what people are talking about on their public timelines. This enable us to visually graph and inspect how different drugs, symptoms and even natural products are connected to each other”, says Rion Brattig Correia, a doctoral student in the School of Informatics and Computing at IU Bloomington, who is first author on the study. “The universe of social media provides a very promising source of large-scale data that can help identify DDI and ADR in ways that have not been hitherto possible,” added the study’s senior author Luis M. Rocha, professor of informatics and computing, director of the Complex Networks and Systems PhD Program, and a member of the IU Network Science Institute. “Given the large number of users, analysis of social media data may be useful to identify under-reported, population-level pathology associated with DDI, thus further contributing to improvements in population health. Moreover, tapping into this data allows us to infer drug interactions with natural products – including cannabis – which constitute an array of DDI very poorly explored by biomedical research thus far.”

mediumModularity 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.

Optimized-IU_poster_5_botsThe 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!


Selection_879Predicting popularity and success in cultural markets is hard due to strong inequalities and inherent unpredictability. A good example comes from the world of fashion, where industry professionals face every season the difficult challenge of guessing who will be the next seasons’ top models. A recent study by CNetS graduate student Jaehyuk Park, research scientist Giovanni Luca Ciampaglia (also at the IU Network Science Institute), and research scientist Emilio Ferrara (now at the University of Southern California) is now showing that early success in modeling can be predicted from the digital traces left by the buzz on social media such as Instagram. The study has been accepted for presentation at the 19th ACM conference on Computer-Supported Cooperative Work and Social Computing (CSCW’16). The work has been covered in the media by the MIT Technology Review, Die Welt, Fusion, and iTNews.


Our understanding of how catastrophe propagates in multi-layered networks relies on theories that apply only to infinite systems. As a paper published in Nature Physics by Filippo Radicchi demonstrates, reducing an interconnected network of finite size to a multiset of decoupled graphs provides a route to understanding catastrophic events in real systems.


Big success for CNetS researchers at the Conference on Complex Systems (CCS’15)! Here are the accepted talks from our center:

  1. Computational fact checking from knowledge networks by Giovanni Luca Ciampaglia, Prashant Shiralkar, Johan Bollen, Luis M Rocha, Filippo Menczer and Alessandro Flammini
  2. Control of complex networks requires structure and dynamics by Alexander Gates and Luis M. Rocha
  3. Darwin’s Semantic Voyage by Jaimie Murdock, Simon DeDeo, and Colin Allen
  4. Defining and Identifying Sleeping Beauties in Science by Qing Ke, Emilio Ferrara, Filippo Radicchi and Alessandro Flammini
  5. Detecting conflict in social unrest using Instagram* by Rion Brattig Correia, Kwan Nok Chan and Luis M. Rocha
  6. Detecting Campaigns in Social Media by Onur Varol, Emilio Ferrara, Filippo Menczer and Alessandro Flammini
  7. Discourse Polarization in the US Congress by Rion Brattig Correia, Kwan Nok Chan and Luis M. Rocha
  8. Eigenmood Twitter Analysis: measuring collective mood variation by Ian B. Wood, Joana Gonçalves-Sá, Johan Bollen and Luis M. Rocha
  9. Evolution of Online User Behavior During a Social Upheaval by Onur Varol, Emilio Ferrara, Christine Ogan, Filippo Menczer and Alessandro Flammini
  10. How human perception of the urban environment influences the abandonment process by Stefani Crabstree, Simon DeDeo
  11. Information theoretic structures of the French Revolution by Alexander Barron, Simon DeDeo, and Rebecca Spang
  12. Measuring Emotional Contagion in Online Social Networks by Zeyao Yang, Emilio Ferrara
  13. Modularity and the Spread of Perturbations in Complex Dynamical Systems* by Artemy Kolchinsky, Alexander J. Gates and Luis M. Rocha
  14. On Predictability of Rare Events Leveraging Social Media by Lei Le, Emilio Ferrara and Alessandro Flammini
  15. Optimal network modularity for information diffusion by Azadeh Nematzadeh, Emilio Ferrara, Alessandro Flammini and Yong-Yeol Ahn
  16. Redundancy and control in complex networks by Luis M. Rocha
  17. 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.

In addition, CNetS researchers presented several papers at the recent NetSci, ICCSS, CAP 2015, CSCW, YTH Live, WWW, and ICCS conferences. Congratulations!

476706_w296Why do some research papers remain dormant for years and then suddenly explode with great impact upon the scientific community? These “sleeping beauties” are the subject of a new study by CNetS researchers Qing KeEmilio FerraraFilippo Radicchi, and Alessandro Flammini published in the Proceedings of the National Academy of Sciences. The study provides empirical evidence that a paper can truly be ahead of its time. A ‘premature’ topic may fail to attract attention even when it is introduced by authors who have already established a strong scientific reputation. The authors show that sleeping beauties can be dormant for many decades, and are more common than previously thought. The findings have been covered by media such as Nature and The New York Times. More…

The CNetS team

The CNetS team

LinkedIn announced that YY Ahn and his team of Ph.D. students from the Center for Complex Networks and Systems Research, including Yizhi Jing, Adazeh Nematzadeh, Jaehyuk Park, and Ian Wood, is one of the 11 winners of the LinkedIn Economic Graph Challenge.

Their project, “Forecasting large-scale industrial evolution,” aims to understand the macro-evolution of industries to track businesses and emerging skills. This data would be used to forecast economic trends and guide professionals toward promising career paths.

“This is a fascinating opportunity to study the network of industries and people with unprecedented details and size. All of us are very excited to collaborate with LinkedIn and our LinkedIn mentor, Mike Conover, who is a recent Informatics PhD alumnus, on this topic,” said Ahn. Read more…