Edoardo (Edo) Airoldi

Assistant Professor
Department of Statistics
FAS Center for Systems Biology
Faculty of Arts & Sciences
Harvard University

mailing address: Science Center, Harvard University, 1 Oxford Street, Cambridge, MA 02138, USA
phone: (617) 496-8318  
fax: (617) 496-8057
email: airoldi AT fas DOT harvard DOT edu

now.   My research interests encompass statistical methodology and theory with application to molecular biology and integrative genomics, computational social science, and statistical analysis of large biological and information networks. A few recent projects include (i) representation, sampling and inference methods for networks with rich node information, including the exchangeable graph model, (ii) metabolism and cellular proliferation, (iii) hypotheses testing and inference on signaling and metabolic pathways, including the map-kinase pathways, and the pathways regulating carbon and nitrogen metabolism, (iv) systems-level analyses of regulation and signaling dynamics with applications to stem cell development and cancer systems, (v) quantitation of alternative splicing events in human and mouse (vi) genome-wide quantitation of misreading and mistranslation events in yeast. Specific areas of technical interest include probabilitsic algorithms, approximation theorems, convex and combinatiorial optimization, and geometry.

brief bio.   In December 2006, I receved a Ph.D. from Carnegie Mellon, working on statistical machine learning and the analysis of complex systems with Stephen Fienberg and Kathleen Carley. My dissertation introduced statistical and computational elements of graph theory that support data analysis of complex systems and their evolution. Till December 2008, I was a postdoctoral fellow in the Lewis-Sigler Institute for Integrative Genomics of Princeton University working with Olga Troyanskaya, David Botstein, and James Broach. I developed mechanistic models to gain computational insights into aspects of the molecular and cellular biology that are not directly observable with experimental probes. I have been working closely with biologists and in the areas of cellular differentiation, cellular development and cancer, since.

  news   recent and upcoming talks
  • TBD. Penn State University (Statistics), Spring 2012, University Park, PA.

  • TBD. University of Chicago (Statistics Group at Booth Business School), Spring 2012, Chicago, IL.

  • TBD. Duke University (Institute for Genome Sciences), March 12, 2012, Durham, NC.

  • TBD. Brown University (Applied Mathematics), February 1, 2012, Providence, RI.

  • TBD. Duke University (Statistics), January 20, 2012, Durham, NC.

  • TBD. University of Texas at Austin (Statistics and Scientific Computing), November 11, 2011, Austin, TX.

  • TBD. University of Minnesota (Institute for Mathematics and its Applications), October 24, 2011, Minneapolis, MN.

  • Estimating latent processes on a graph from indirect measurements. MIT Lincoln Labs (Endicott House), August 9-10th 2011, Needham, MA.

  • Statistical models of complex networks. Joint Statistical Meetings, July 30th-August 4th, Miami Beach, FL.

  • A geometric approach to estimation of matrix-variate processes from indirect measurements. International Statistics Forum, July 17-19th 2011, Wu Xi, China.

  • Estimating latent processes on a graph from indirect data. Applied Statistics Symposium, June 29th 2011, New York, NY.

  • Social information, structure and interference. Universita degli Studi Federico II, June 25th 2011, Naples, Italy.

  • Evaluating topic models. Harvard Institute for Quantiative Social Sciences, May 20th 2011, Cambridge, MA.

  • Analysis and design of RNA sequencing experiments. MD Anderson Cancer Center, May 11th 2011, Houston, TX.

  • Estimating latent processes on a graph from indirect measurements. Boston University (Mathematics & Statistics), April 28th 2011, Boston, MA.

  • New tools for systems-level analysis of regulation and signaling dynamics. The Broad Institute, April 20th 2011, Cambridge, MA.

  • Deconvolution of mixing time series on a network. New England Statistics Symposium, April 16th 2011, Storrs, CT.

  • Estimating latent processes on a graph from indirect measurements. University of Massachusetts, Amherst (Statistics & Computational Social Science), April 8th 2011, Amherst, MA.

  • Deconvolution of mixing time series on a network. Massachusetts Insititute of Technology (McGovern & CBCL), March 28th 2011, Cambridge, MA.

  • New tools for systems-level analysis of regulation and signaling dynamics. Harvard School of Public Health, February 28th 2011, Boston, MA.

  • Systems-level analysis of regulation and signaling dynamics. Microsoft Research (Computational Aspects of Biological Information), December 8th 2010, Cambridge, MA.

  manuscripts
  • Blocker, AW & Airoldi, EM. (2011).   Deconvolution of mixing time series on a graph.   (pdf) (a shorter version appeared at UAI 2011) (Recipient of the IBM best student paper award, NESS 2011)

  • Hashimoto, T., Shieh, A. & Airoldi, EM. (2011).   Permutation-invariant Gaussian mixture models.   (pdf)

  • Airoldi, EM., Bassetti, F., Guindani, M. & Leisen, F. (2010).   Generalized species sampling priors with latent beta reinforcements.   (pdf)

  selected publications
  1. Shieh, A., Hashimoto, T. & Airoldi, EM. (2011).   Tree preserving embedding.   Proceedings of the National Academy of Sciences   (in press) (a shorter version appeared at ICML 2011)

  2. Choi, DS., Wolfe, PJ. & Airoldi, EM. (2011).   Stochastic blockmodels with growing number of classes.   Biometrika   (in press)

  3. Airoldi, EM., Choi, DS. & Wolfe, PJ. (2011).   Confidence sets for network structure.   Statistical Analysis and Data Mining   (in press)

  4. Airoldi, EM & Haas, B. (2011).   Polytope samplers for inferece in ill-posed inverse problems.   Journal of Machine Learning Research, W&CP (AiStat), 15, 110-118.  (pdf)

  5. Airoldi, EM., Heller, KA. & Silva, R. (2011).   Small sets of interacting proteins suggest functional linkage mechanisms via Bayesian analogical reasoning.   Bioinformatics   27, i374-i382. (pdf)

  6. Airoldi, EM., Bai, X., & Carley, KM. (2011).   Network sampling and classification: An investigation of network model representations.   Decision Support Systems   51, 506-518. (pdf)

  7. Airoldi, EM., Bai, X., & Malin, B. (2011).   An entropy approach to disclosure risk assessment: Lessons from real applications and simulated domains.   Decision Support Systems,   51, 10-20. (pdf)

  8. Markowetz, F., Mulder, K.W., Airoldi, E.M., Lemischka, I., & Troyanskaya, O.G. (2010).   Mapping dynamic histone acetylation patterns to gene expression in Nanog-depleted murine embryonic stem cells.   PLoS Computational Biology,   6, e1001034. (pdf)

  9. Airoldi, EM., Erosheva, EA., Fienberg, SE., Joutard, CJ., Love, TM., & Shringarpure S. (2010).   Reconceptualizing the classification of PNAS articles.   Proceedings of the National Academy of Sciences,   107, 20899-20904. (pdf) (editorial)

  10. Katz, Y., Wang, E., Airoldi*, EM., & Burge*, CB. (2010).   Analysis and design of RNA sequencing experiments for identifying mRNA isoform regulation.   Nature Methods,   7, 1009-1015. (pdf) (supplement)

  11. Silva, R., Heller, K.A., Ghahramani, Z., & Airoldi E.M. (2010).   Ranking relations using analogies in biological and information networks.   Annals of Applied Statistics,   4, 615-644. (pdf)

  12. Goldenberg, A., Zheng, A.X., Fienberg, S.E., & Airoldi E.M. (2009).   A survey of statistical network models.   Foundations and Trends in Machine Learning,   2, 129-233. (pdf)

  13. Lu, R., Markowetz, F., Unwin, R.D., Leek, J.T., Airoldi E.M., MacArthur, B.D., Lachmann, A., Rozov, R., Ma’ayan, A., Boyer, L.A., Troyanskaya, O.G., Whetton, A.D., & Lemischka, I.R (2009).   Systems-level dynamic analyses of fate change in murine embryonic stem cells.   Nature,   462, 358-362. (pdf)

  14. Barutcuoglu, Z., Airoldi, E.M., Dumeaux, V., Schapire, R.E., & Troyanskaya, O.G. (2009).   Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields.   Bioinformatics,   25, 1307-1313. (pdf)

  15. Airoldi, E.M., Huttenhower, C., Gresham, D., Lu, C., Caudy, A., Dunham, M., Broach, J., Botstein, D., & Troyanskaya, O.G. (2009).   Predicting cellular growth from gene expression signatures.   PLoS Computational Biology,   5, e1000257. (pdf)

  16. Airoldi, E.M., Blei, D.M., Fienberg, S.E., & Xing, E.P. (2008).   Mixed-membership stochastic blockmodels.   Journal of Machine Learning Research,   9, 1981-2014. (pdf) (a shorter version appeared at NIPS 2008)

  17. Warren, R., Airoldi, E.M., & Banks, D. (2008).   Network analysis of Wikipedia.   In: Statistical Methods in E-Commerce Research,   Jank & Shmueli, Eds., Wiley & Sons.

  18. Brauer, M.J., Huttenhower, C., Airoldi, E.M., Rosenstein, R., Matese, J.C., Gresham, D., Boer, V.M., Troyanskaya, O.G., & Botstein, D. (2008).   Coordination of growth rate, cell cycle, stress response and metabolic activity in yeast.   Molecular Biology of the Cell,   19, 352-367. (pdf)

  19. Airoldi, E.M. (2007).   Getting started in probabilistic graphical models.   PLoS Computational Biology,   3, e252. (pdf)

  20. Airoldi, E.M., Fienberg, S.E., Skinner, K.K. (2007).   Whose ideas? Whose words? Authorship of the Ronald Reagan radio addresses.   Political Science & Politics,   40, 501-506. (pdf)

  21. Airoldi, Blei, Fienberg, Goldenberg, Xing & Zheng, Eds. (2007).   Statistical Network Analysis: Models, Issues & New Directions.   Lecture Notes in Computer Science,   volume no. 4503. Springer-Verlag. (pdf)

  22. Airoldi, E.M. (2007).   Discussion on Handcock, Raftery and Tantrum 'Model-based clustering for social networks'.   Journal of the Royal Statistical Society, Series A,   170, Part 2, 30-31. (pdf)

  23. Malin, B., & Airoldi, E.M. (2007).   Confidentiality preserving audits of electronic medical record access.   World Congress on Health (Medical) Informatics (MEDINFO),   Brisbane, Australia. (pdf)

  24. Airoldi, E.M. (2006).   Bayesian mixed-membership models of complex and evolving networks.   Doctoral dissertation,   School of Computer Science, Carnegie Mellon University, PA USA. (pdf) (Recipient of the Savage award honorable mention, 2007)

  25. Airoldi, E.M., Anderson, A., Fienberg, S.E., Skinner, K.K. (2006).   Who wrote Ronald Reagan's radio addresses?   Bayesian Analysis,   1, 289-320. (pdf) (tr stat-03-789) (notes)

  26. Airoldi, E.M., & Carley, K.M. (2005).   Sampling algorithms for pure network topologies: Stability and separability of metric embeddings.   ACM KDD Explorations (Special Issue on Link Mining),   7, 13-22.

  27. Airoldi, E.M., Blei, D.M., Fienberg, S.E., & Xing, E.P. (2005).   A latent mixed-membership model for relational data.   ACM KDD Workshop on Link Analysis,   Chicago IL. (pdf) (Recipient of the John Van Ryzin award, 2006)

  28. Airoldi, E.M., Cohen, W.W., & Fienberg, S.E. (2005).   Bayesian methods for frequent terms in text: Models of contagion and the Delta square statistic.   CSNA & INTERFACE Annual Meetings,   St. Louis MI. (pdf)

  29. Malin, B., Airoldi, E.M., & Carley, K.M. (2005).   A social network analysis model for name disambiguation in lists.   Journal of Computational and Mathematical Organization Theory,   11, 119-139. (pdf)

  30. Gross, R., Airoldi, E.M., Malin, B., & Sweeney, L.A. (2005).   Integrating utility into face de-identification.   Privacy Enhancing Technologies (Revised Selected Papers),   Lecture Notes in Computer Science, vol. 3856, 227-242. (pdf)

  31. Malin, B., Airoldi, E.M., Edoho-Eket, S., & Li, Y. (2005).   Configurable security protocols for multi-party data analysis with malicious participants.   IEEE International Conference onf Data Engineering (ICDE),   Tokyo Japan. (pdf)

  32. Airoldi, E.M., Malin, B., & Sweeney, L.A. (2005).   Technologies to defeat fraudulent schemes related to email requests.   AAAI Symposium on Artificial Intelligence Technologies for Homeland Security,   Stanford CA. (pdf)

  33. Airoldi, E.M., & Faluotsos, C. (2004).   Recovering latent time series from their observed sums: Network tomography with particle filters.   ACM International Conference on Knowledge Discovery & Data Mining (KDD),   Seattle WA. (pdf) (tr cs-04-130) (Runner-up for best paper award)

  34. Airoldi, E.M. (2000).   Forecasts for Italian and Greek macroeconomic indicators.   Global Data Watch,   J.P. Morgan Economic Research. (issues of March 6-13-20-27, April 3-10-17-24, May 1-8)

  35. Fornari, I., & Airoldi, E.M. (1999).   Assessing Italy's inflation gap relative to the Euro area.   Global Data Watch,   J.P. Morgan Economic Research. (issue of December 20)

  36. Airoldi, E.M. (1999).   The theory of weak convergence of probability measures and its applications in statistics.   Dissertation,   Institute for Quantitative Methods, Bocconi University, Milan Italy. (Gold medal for best graduates, 1999)

  collaborators
  • David Banks (Duke), David Blei (Princeton), David Botstein (Princeton), Chris Burge (MIT), Kathleen Carley (Carnegie Mellon), Stephen Fienberg (Carnegie Mellon), Katherine Heller (University College London), Curtis Huttenhower (Princeton), Jure Leskovec (Carnegie Mellon), Xiodong Lin (University of Cincinnati), Bradley Malin (Vanderbilt), Florian Markowetz (Princeton), Erin O'Shea (Harvard), Aviv Regev (Broad Institute), Ricardo Silva (University College London), Olga Troyanskaya (Princeton), Eric Xing (Carnegie Mellon).