Daniel Larremore

Daniel B. Larremore

Omidyar Fellow
Santa Fe Institute
Curriculum Vitae
larremore(at)santafe.edu
@danlarremore
Google Scholar Page
(gratuitous collaboration graph)

News

  • 2016 July 15 - I'll be at SIAM Network Science in Boston [NS16].
  • Talk: The ground truth about metadata and community detection in networks.
  • 2016 June 24 - I'll be at the Int'l Conf on Computational Social Science [IC2S2].
  • Talk: Gender, Productivity, and Prestige in Computer Science Faculty Hiring Networks
  • Talk (Sam Way): Trends and Gaps in Scholarly Productivity of Computer Science Faculty

Software and Code

  • webweb
  • webweb is a free software tool, for creating interactive network visualizations in MATLAB that are viewable in your web browser. The network at the top of this page is an example of webweb, with some modifications. Downloads and information can be found on the webweb page with a full set of examples and code too. Source code, written in javascript and d3, are found on the downloads page. Learn more about d3 at d3js.org. If you modify this code or use it to make figures, let me know and I'll be happy to post a link to your publication here.
  • [Download webweb]
  • percoVIS icon
  • PercoVIS is a free software tool, created to visualize the process of percolation on a network. It was developed with much inspiration and feedback from my collaborator, Dane Taylor. It includes Erdos-Renyi and Adjacent Edge decision rules for link addition, as well as the Social Climber attachment model. Documentation about these processes can be found on the download page. If you are interested in a similar tool to visualize Kuramoto oscillators, please check out Sebastian Skardal's Synched software.
  • [Download PercoVIS]
  • biSBM
  • biSBM is free and open-source code, created to apply the method described in the paper "Efficiently inferring community structure in bipartite networks". The code finds communities in a bipartite network using a maximum-likelihood approach stochastic block model. The code requires MATLAB as well as a C++ compiler. Details, and the publication on which this code is based, can be found through the link below.
  • [Download biSBM]
  • MATLAB Codes
    • findNetworkComponents - take an undirected network adjacency matrix and return the number of components, their sizes, and their membership lists.
    • [MATLAB File Exchange]

Research Interests

  • Networks and theory - The processes that generate complex networks leave hints about themselves in the patterns of edges, and the relationships between those patterns and vertex metadata. I work on mathematical descriptions of graph ensembles, inference of community structures, vertex ordering or ranking, and using metadata to better understand network formation.
  • With Bailey Fosdick, Johan Ugander, Joel Nishimura, Leto Peel, Aaron Clauset, Laurent Hébert-Dufresne, Eleanor A. Power.
  • Malaria's antigenic variation and evolution - The var genes of the malaria parasite P. falciparum evolve according to complicated and unknown rules, with selective pressures at multiple scales both within hosts and between hosts. I use tools from applied math and statistical physics to understand the structural and evolutionary constraints on var gene evolution, and its their relationships with parasite virulence, population structure, and epidemiology.
  • With Amy Bei, Caroline Buckee, Sesh Sundararaman, and the labs of Julian Rayner and Beatrice Hahn.
  • Academic labor market dynamics - PhDs become faculty each year, but the influences of prestige, advisor, gender, publication record, among other factors, on actual hiring outcomes are not well known, even within individual fields. I investigate inequalities and dynamics of the academic labor market through large-scale data collection and generative models.
  • With Aaron Clauset, Sam Way, Sam Arbesman, and Mirta Galesic.

Under Review / In Prep

  • 2016 "Uniform distributions in graph spaces: the many configuration models"
  • Bailey Fosdick, Daniel B. Larremore, Joel Nishimura, and Johan Ugander. In Prep.
  • 2016 "The ground truth about metadata and community detection in networks"
  • Leto Peel*, Daniel B. Larremore*, and Aaron Clauset. In Prep.
  • 2016 "Malaria population diversity influences expression dynamics and immune recognition among highly related genotypic clusters in Senegal"
  • Amy K. Bei, Kazutoyo Miura, Daniel B. Larremore, Ababacar Diouf , Nicholas Baro, Rachel F. Daniels, Allison Griggs, Eli L. Moss, Daniel E. Neafsey, Awa B. Deme, Mohammed Sy, Stephen Schaffner, Ambroise D. Ahouidi, Daouda Ndiaye , Tandakha Dieye, Souleymane Mboup, Caroline O. Buckee, Sarah K. Volkman, Carole A. Long, and Dyann F. Wirth. In Prep.
  • 2016 "Dynamics of Beneficial Epidemics"
  • Andrew Berdahl, Christa Brelsford, Caterina De Bacco, Marion Dumas, Vanessa Ferdinand, Joshua A. Grochow, Laurent Hébert-Dufresne, Yoav Kallus, Christopher P. Kempes, Artemy Kolchinsky, Daniel B. Larremore, Eric Libby, Eleanor A. Power, Caitlin A. Stern, Brendan Tracey. Undergoing Refinement ;D [arXiv]

Peer-reviewed publications

  • 2016 "Gender, Productivity, and Prestige in Computer Science Faculty Hiring Networks"
  • Samuel F. Way, Daniel B. Larremore, and Aaron Clauset. Proc. 2016 World Wide Web Conference (WWW), 1169-1179.
  • [WWW 2016][arXiv]
  • 2015 "Ape parasite origins of human malaria virulence genes"
  • Daniel B. Larremore, Sesh A. Sundararaman, Weimin Liu, William R. Proto, Aaron Clauset, Dorothy E. Loy, Sheri Speede, Lindsey J. Plenderleith, Paul M. Sharp, Beatrice H. Hahn, Julian C. Rayner*, and Caroline O. Buckee*. Nature Communications 6, 8368.
  • [Nature Comms.]
  • 2015 "Systematic inequality and hierarchy in faculty hiring networks"
  • Aaron Clauset, Samuel Arbesman, and Daniel B. Larremore, Science Advances. 1, e1400005.
  • [Science Advances] [code and data] [interactive data visualization]
  • 2015 "Immune characterization of P. falciparum parasites with a shared genetic signature in a region of decreasing transmission"
  • Amy K. Bei, Ababacar Diouf, Kazutoyo Miura, Daniel B. Larremore, Ulf Ribacke, Gregory Tullo, Eli L. Moss, Daniel E. Neafsey, Rachel F. Daniels, Amir E. Zeituni, Iguosadolo Nosamiefan, Sarah K. Volkman, Ambroise D. Ahouidi, Daouda Ndiaye, Tandakha Dieye, Souleymane Mboup, Caroline O. Buckee, Carole Long, and Dyann F. Wirth, Infection and Immunity 83(1), 276.
  • [PDF] [IAI]
  • 2014 "Efficiently inferring community structure in bipartite networks"
  • Daniel B. Larremore, Aaron Clauset, and Abigail Z. Jacobs, Physical Review E 90(1), 012805.
  • [PDF] [PRE] [code and data]
  • 2014 "Inhibition Causes Ceaseless Dynamics in Networks of Excitable Nodes"
  • Daniel B. Larremore, Woodrow L. Shew, Edward Ott, Francesco Sorrentino, and Juan G. Restrepo, Physical Review Letters 112, 138103.
  • [PDF] [PRL]
  • 2013 "A network approach to analyzing highly recombinant malaria parasite genes"
  • Daniel B. Larremore, Aaron Clauset, and Caroline O. Buckee. PLoS Computational Biology 9(10), e1003268.
  • [PDF] [PLoS Comp Bio] [interactive figures] [network and sequence data]
  • 2012 "Social Climber attachment in forming networks produces phase transition in a measure of connectivity"
  • Dane Taylor*, Daniel B. Larremore*. Physical Review E 86, 031140.
  • [PDF] [PRE]
  • 2012 "Statistical properties of avalanches in networks"
  • Daniel B. Larremore, Marshall Y. Carpenter, Edward Ott, and Juan G. Restrepo. Physical Review E 85, 066131.
  • [PDF] [PRE]
  • 2011 "Effects of network topology, transmission delays, and refractoriness on the response of coupled excitable systems to a stochastic stimulus"
  • Daniel B. Larremore, Woodrow L. Shew, Edward Ott, and Juan G. Restrepo. Chaos 21, 025117.
  • [PDF] [Chaos]
  • 2011 "Predicting criticality and dynamic range in complex networks: effects of topology"
  • Daniel B. Larremore, Woodrow L. Shew, and Juan G. Restrepo. Physical Review Letters 106, p. 058101.
  • [PDF] [PRL]

* denotes equal contribution.

Other Publications

  • 2014 Critical Dynamics in Complex Networks, chapter in Criticality in Neural Systems.
  • Daniel B. Larremore, Woodrow L. Shew, Juan G. Restrepo. Wiley, 365-392, 2014.
  • [Wiley]
  • 2012 "Progess Is Infectious"
  • Daniel E. Geer Jr., Daniel B. Larremore. IEEE Security & Privacy, 10(6), p. 94-95.
  • [PDF] [IEEE S&P]

Press

Teaching and Workshops

Workshops and Guest Lecturing
  • University of Colorado at Boulder
  • 2014 Oct 9, CSCI 5352. Network Analysis and Modeling
  • 2013 Nov 5-7, PHYS 7810 / CHEM 6711 / MCDB 6400. Foundations of Quantitative Biology
  • HSPH summer nanocourse: Modeling Infectious Disease
  • 2014 July 24 and 27. [details]
  • AMS Mathematics Research Community
  • 2014 June 24-30, Network Science. [details]
  • Oxford Tropical Disease Network Meeting, Kilifi, Kenya
  • 2013 Oct 3, Network Analysis Workshop.

I am not doing any teaching at this time.
Previous courses are listed below. See my FCQ evaluations.

  • University of Colorado at Boulder
  • 2012 Spring APPM 2350, Calculus III (Instructor)
  • 2011 Fall APPM 2350, Calculus III (Instructor)
  • 2009 - 2010 Applied Mathematics Lead TA
  • 2009 Fall - APPM 1360, Calculus II (TA)
  • 2009 Spring - APPM 2360, Ordinary Differential Equations (TA)
  • 2008 Fall - APPM 2350, Calculus III (TA)
  • 2008 Summer - APPM 2350, Calculus III (TA)
  • 2008 Spring - APPM 2360, Ordinary Differential Equations (TA)
  • 2007 Fall - APPM 2350, Calculus III (TA)

Contact Details

Santa Fe Institute
1399 Hyde Park Rd.
Santa Fe, NM, 87501
USA