Readings matrices, spectra, random walks : Dan Spielman's spectral graph theory course. Eigenvalues of graphs. Eikmeier and D. KDD, Mathematics of Networks. Random walks and diffusion on networks. Masuda, M. Porter, and R. Physics Reports, Ugander et al. Kwak et al. WWW, Leskovec and E. Leskovec, J. Kleinberg, and C.
Watts and S. Travers and S. Sociometry, Scale-free networks are rare. Broido and A. Nature Communications, Tracing information flow on a global scale using Internet chain-letter data. Liben-Nowell and J. Using selection bias to explain the observed structure of Internet diffusions. Golub and M. The structure of positive interpersonal relations in small groups. Davis and S. Sociological Theories in Progress, Vol. Internet Mathematics, Power-Law Distributions in Empirical Data. Clauset, C. Shalizi, and M. Contemporary Physics, Fosdick, D.
Larremore, J. Nishimura, J. Stochastic blockmodels and community structure in networks. Karrer and M. PRE, Mixed Membership Stochastic Blockmodels. Airoldi, D. Blei, S. Fienberg, and E.
Affiliation Networks. Lattanzi and D. Coin-flipping, ball-dropping, and grass-hopping for generating random graphs from matrices of edge probabilities. Ramani, N. Eikmeier, and D. SIAM Review, to appear. Ulrike von Luxburg. Statistics and Computing, Mining Large Graphs Section 7. Lecture notes, On Clusterings: Good, Bad and Spectral. Kannan, S. Vempala, and A.
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On Spectral Clustering: Analysis and an Algorithm. Ng, Jordan, and Weiss. Kernel k-means, Spectral Clustering and Normalized Cuts. Dhillon, Guan, and Kulis.
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Peel, D. Larremore, and A. Science Advances, Zhu, Z. Ghahraman, and J. Transductive Learning via Spectral Graph Partitioning. Learning with Local and Global Consistency. Zhou et al. Monophily in social networks introduces similarity among friends-of-friends. Altenburger and J.
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Modeling of loops in proteins: a multi-method approach
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Higher-order clustering in networks. Yin, A. Ugander, L. Backstrom, and J. Modeling interactome: scale-free or geometric?
A hierarchical method for generating low‐energy conformers of a protein‐ligand complex
Corneil, and I. Bioinformatics, Structure and function of the feed-forward loop network motif.
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