Samuel Scarpino bio photo

Samuel Scarpino

Assistant Professor in the Network Science Institute at Northeastern University.

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Welcome!

I am an Assistant Professor in the Network Science Institute at Northeastern University--with appointments in Marine & Environmental Sciences, Physics, and Health Sciences (starting Sept. 2018)--and am also the Chief Data Scientist at Dharma.ai. My research spans a broad range of topics in complex systems and network science, including: infectious disease dynamics, forecasting and predictive modeling, complex network analysis, disease genomics and transcriptomics, outbreak surveillance, social networks, gene network evolution, and decision making under uncertainty. Our group, the Emergent Epidemics Lab, approaches these topics by investigating questions using mathematical and computational methods from biology, statistics, physics, applied mathematics, and computer science.

Through collaboration with laboratory, field, and public health researchers, the mathematical and computational models we develop are interrogated with novel experiments, evaluated on new data sources, and applied to public health and clincal problems. Our surveillance research, for example, is done in close association with state, national, and international public health agencies and has led to substantive changes in surveillance practices. I believe this type of collaboration between scientists and public health decision makers is critical for efficient, effective outbreak preparedness and response.

Beyond disease, the group's research has focused on a variety of topics, including animal movement and group dynamics; traffic routing; the effects of environmental toxins on behavior and neural biology; and models of spatiotemporal variation in tree density and fruiting phenology. If you’re interested in working with us, please contact me via email. For more detailed information, please see full-text versions of our articles and my current curriculum vitae. Lastly, for those interested in Big Data, read my philosophy here.

Affiliations

Network Science Institute, Northeastern University

Department of Marine and Environmental Sciences, Northeastern University

Department of Physics, Northeastern University

Department of Health Sciences, Northeastern University

Fellow, ISI Foundation, Turin Italy

News

12/17/18: I am excited to participate in the Complex Networks Winter Workshop in Quebec City! You can find the slides for my lecture here.

12/07/18: I am participating in the International Workshop on Theoretical perspectives in Network Science at Seoul National University and organized by the Asia Pacific Center for Theoretical Physics. Learn more about the workshop here.

11/25/18: We posted a pre-print describing how the "Proteostasis environment shapes higher-order epistasis operating on antibiotic resistance" to the bioRxiv.

11/05/18: The Network Science Institute at Northeastern University is recruiting for an open rank, tenure-track professor in network science and human health. Learn more and apply here.

10/25/18: Chia-Hung and I are both speaking at the First Annual Northeastern University Network Science Student Research Symposium. See the schedule here and join us on Nov. 1st!

10/11/18: What are the information theoretical limits to forecasting disease spread? Giovanni Petri and I have just posted an updated version of our manuscript, "On the predictability of infectious disease outbreaks" to the arXiv.

10/04/18: I was named to the Scientific Steering Committee for BioFire's Trend surveillance system. See the data in action here.

09/26/18: I participated in a World Economic Forum meeting on data sharing during outbreaks in NYC.

09/01/18: Wan He joined our lab as new PhD student in Network Science! We're very excited to have her join our group.

08/16/18: I collaborated on an analysis of how the participatory surveillance systems, FluNearYou, can augment existing influenza surveillance in the US. Read it here.

08/13/18: Our paper on neonatal intensive care networks in the US, led by Munik Shrestha and in collaboration with the Vermont Oxford Network, is online at EPJ Data Science. Read it here.

08/07/18: I interviewed by the Northeastern Univ. undergraduate science magazine, NUSci, about Nipah, Ebola, Zika, and other emerging infectious diseases. Read the article here.

07/26/18: Caitlin Rivers and I published a Correspondence in Nature on predicting outbreak trajectories. Read it here.

07/09/18: Chia-Hung Yang and I both attended the Society for Molecular Biology and Evolution meeting in Yokohama, Japan. Preprints describing the work we presented are coming very soon.

06/11/18: I'm giving an invited lecture on predictability and network dynamics at the annual NetSci meeting in Paris later this week.

05/25/18: I used data curated by Prof. Caitlin Rivers at Johns Hopkins, imported into Dharma.ai, to write a short post about the ongoing Ebola outbreak in the DRC.

05/05/18: The schedule for our satellite at NetSci 2018, Networks and Contagion, is live. Check it out here.

04/25/18: I debated about data privacy at the 2018 Digital Health meeting in Lyon. Learn more about the conference here.

04/10/18: My interview on the Important Not Important podcast about algorithms, disease modeling, & why interdisciplinary approaches to science are so critical is online. You can listen to the podcast here.

04/03/18: Our new manuscript on a socioeconomic bias in influenza surveillance is on the arXiv. If you're looking for the supplment, see my Publications page.

03/28/18: Both Munik and Chia-Hung had manuscripts accepted for podium presentations at conferences this summer. We're looking forward to seeing everyone and learning about new and exciting science later this year! Learn more about what our group is up to here.

03/17/18: I participated in Brown University's Hack for Humanity Event. Learn more about this amazing event here.

03/12/18: I spoke at the Harvard School of Public Health's Center for Communicable Disease Dynamics on the Predictability of Infectious Disease Outbreaks. Watch it here.

02/25/18: We had two exciting papers on next generation surveillance systems accepted. Read them on the Publications page.

02/14/18: Our latest pre-print, "The Interhospital Transfer Network for Very Low Birth Weight Infants in the United States" is on the arXiv.

02/04/18: Have you had a manuscript delayed at the arXiv due to how your work was classified? If so, try out the Moderator Buster tool I built using 20,000 pre-prints and deep learining.

01/12/18: I was interviewed about our work on Zika virus sexual transmission by Infectious Disease News.

01/01/18: Don't close the gates is a News and Views I just published in Nature Physics. You can read it here.

12/19/17: I just published an essay on influenza vaccination. You can read it on Medium.

11/21/17: I was interviewed by Northeastern University about my reseach interests and ended up also discussing my love for cooking and interest in creativity.

11/08/17: I am speaking at the Workshop on Data and Algorithm Bias during CIKM 2017 in Singapore. More information here.

10/27/17: I was name a Fellow of the ISI Foundation in Turin Italy. You can read about the fellows program and the exciting complex systems work being done at ISI here.

10/17/17: I'm on the program committee for NERCCS 2018: the First Northeast Regional Conference on Complex Systems. Learn more and submit your abtracts here.


10/01/17: I was interviewed by fivethirtyeight .com about how power outages in Puerto Rico might increase mosquito-born disease incidence. You can read the full article here.


09/25/17: Our manuscript on how the risk of Zika virus sexual transmission may be dramatically underestimated is now early online at PLoS Pathogens.


09/17/17: I'm honored and humbled to recieve one of two Junior Researcher Awards from the Complex Systems Society. Our wonderful community makes us all stronger. Thank you all!


08/20/17: I'm giving a keynote address at CompleNet18. Submit your contributed talks here.


08/07/17: Our manuscript on Zika virus sexual transmission is early online at PNAS.


07/25/17: A paper describing a novel use of BioFire data for disease surveillance is on bioRxiv.


07/02/17: Our paper on how asymmetric percolation drives a double transition in sexual contact networks is on the arXiv.


06/15/17: Our paper on the topology of gene expression networks is out in Proceedings of the Royal Society. Read it here.


05/28/17: Excited to announce that my group is moving to the Network Science Insitute at Northeastern this fall! Im grateful for everyone at UVM & thrilled to join the team Northeastern University.


05/15/17: Our paper on Estimating trait heritability in highly fecund species was selected for the 2016 G3: Genes|Genomes|Genetics Spotlight. Read about it here.


04/17/17: I spoke at the Gund Institute Research Slam about the predictability of disease outbreaks. You can watch the four minute talk here.


04/03/17: The code and data for our work on gene networks and local adaptation are on GitHub.


03/21/17: What are the information theoretical limits to forecasting disease spread? Giovanni Petri and I explore this topic in our new pre-print, which is now live on the arXiv.


03/01/17: Our work on designing arbovirus surveillance systems is early online at Emerging Infectious Diseases. Read it here.


02/09/17: Munik and my collaborative paper with the Vermont Oxford Network on the Interhospital Transfer Network for Very Low Birth Weight Infants in the United States was just accepted for a podium presentation at the Pediatric Academic Societies annual meeting. We are very excited about this new direction for the lab!


01/25/17: Our satellite on Networks and Contagion was selected for NetSci 2017. More details, and a link to abstract submission, here.


01/16/17: Stat 201: Computational Statistics is starting this week! Head over to my teaching page for more information.


12/22/16: Our work on designing arbovirus surveillance systems was just accepted at Emerging Infectious Diseases.


12/05/16: There are three faculty members from the Complex Systems Center at UVM on the SIAM Workshop on Network Science program committee. We're looking forward to reading your best new work! Submit here.


11/30/16: Are we underestimating the Zika sexual transmission risk? My collaborators and I think so. Read our new pre-print on bioRxiv.


11/10/16: I am now a Deputy Editor at PLoS Neglected Tropical Diseases. I'm looking forward to reading your best work on advancing our scientific, public health, and medical understanding of neglected pathogens.


10/15/16: We just posted a pre-print for our work on the topology of local adaptation. Read it on bioRxiv.


10/07/16: Our manuscript "On the young age of intraspecific herbaceous taxa" is early online at New Phytologist.


09/26/16: Presenting tonight at the Burlington Data Science Meet-up on socioeconomic biases in influenza surveillance. Visit the organization website for more information.


09/12/16: Submit to the new session on health, data, and computation at WWW 2017. Details here.


08/31/16: I'm currently teaching a class on statistical learning. All of the material will be posted to the teaching page on this website.


08/09/16: Lots of exciting press coverage of our paper in Nature Physics. You can find most of them here.


08/03/16: Great article in Smithsonian Magazine discussing our new paper on how replacing sick workers can accelerate disease transmission.


08/01/16: Our paper on how replacing key members of society during an outbreak can accelerate transmission is out in Nature Physics. Read it here here.


06/15/16: Sophia Navarre has joined our group and will be working on a study of how climate variables affect the persistence and spread of arboviruses.


06/08/16: I'm giving a seminar to the Mathematics & Foundation of Complex Systems group at the ISI foundation in Turin Italy on fundamental limits to disease prediction.


05/13/16: George Chrisafis, an undergraduate in our group, was awarded UVM's Common Good Internship award and will spend the summer at the Hutch in Seattle. Read more here here.


04/19/16: Our paper on the cost-effectiveness of next-generation vaccines: the case of pertussis is early online at Vaccine. Read it here here.


04/15/16: Presenting on how high tech surveillance systems overlook the poor during the Institute for Disease Modeling's annual research symposium.


04/04/16: Presented on the challenges of forecasting infectious diseases with Alessandro Vespignani at the Vermont Complex Systems Center's "Big Spread, Big Dead" event. See my talk here.


03/28/16: Our paper on the economic benefit of priming children with the whole-cell pertussis vaccine is online first at JAMA pediatrics. Read it here and the editorial here.


03/22/16: Co-organized a workshop at the Santa Fe Institute on the resurgence of whooping cough. Read the press release here.


03/01/16: Munik Shrestha joined the Emergent Epidemics Lab as our first postdoctoral researcher. Learn more about Munik and his research here.


02/11/16: I attended a Chatham House roundtable discussion on Strengthening Data Sharing for Public Health. Read more here.


01/10/16: The Santa Fe Reporter wrote a nice article on the whooping cough resurgence that featured our recent pertussis paper. Read it here.


12/15/15: I am co-organizing a workshop at the Santa Fe Institute on the re-emergence of pertussis.


11/07/15: The talk I gave on poverty and disease at Creative Mornings Santa Fe is now online. Watch it here.


10/11/15: Our paper on paper on the challenges and opportunities of using novel data streams for disease surveillance is in press at EPJ Data Science. Read it here.


9/30/15: I'll be speaking at Creative Mornings Santa Fe on Wed. Oct. 14th at 9am. Details here.


9/3/15: Our paper on how a prudent behavior can drive accelerating disease transmission is on the arXiv. Read it here.


8/27/15: Our paper on Dynamic Message Passing for recurrent state epidemics on networks is out in PRE. Read it here.


8/01/15: I'm co-organizing a workshop called EpiHack: Analytics on data analytics for public health with the Skoll Global Threats Fund.


6/30/15: The New York Times wrote a nice article about our recent pertussis paper. Read it here.


6/23/15: Our paper on asymptomatic transmission and the resurgence of whooping cough is now online at BMC Medicine. Read it here.


5/13/15: A new version of my R package, binequality, is available on GitHub. Find it here.


3/30/15: Our paper on robust estimation of inequality from binned income data was just accepted at Sociological Methodology. Read the pre-print here and check out the accompanying R package.


3/16/15: Our workshop, "Non-equilibrium versus optimization approaches to the origin of social groups," has been funded for summer 2016 by IMeRA - Aix Marseille Universite.


3/7/15: Excited to announce that I'll be starting as an Assistant Professor in the Department of Mathematics and Statistics and the Complex Systems Center at the University of Vermont in Jan. 2016. I'm looking for graduate students and postdocs, so please send me an email if you are interested in joining our group.


1/12/15: Poverty and Ebola: Why Ebola Goes Viral or Dies Out - see my new article in Nautilus.


1/1/15: Our paper, "Epidemiological and Viral Genomic Sequence Analysis of the 2014 Ebola Outbreak Reveals Clustered Transmission," was published in
Clinical Infectious Diseases and covered by the New York Times and The Economist, among others.


12/10/14: I was interviewed about the ongoing Ebola outbreak by Mary-Charlotte on KSFR's Science Radio Cafe, listen
here.