Biomedical subjects

Linyuan Lu

Publications and source records attributed to Linyuan Lu.

3 recordsLinked to original sources

PubMed2003

Spectra of random graphs with given expected degrees.

In the study of the spectra of power-law graphs, there are basically two competing approaches. One is to prove analogues of Wigner's semicircle law, whereas the other predicts that the eigenvalues follow a power-law distribution. Although the semicircle law and the power law have nothing in common, we will show that both approaches are essentially correct if one considers the appropriate matrices. We will prove that (under certain mild conditions) the eigenvalues of the (normalized) Laplacian of a random power-law graph follow the semicircle law, whereas the spectrum of the adjacency matrix of a power-law graph obeys the power law. Our results are based on the analysis of random graphs with given expected degrees and their relations to several key invariants. Of interest are a number of (new) values for the exponent beta, where phase transitions for eigenvalue distributions occur. The spectrum distributions have direct implications to numerous graph algorithms such as, for example, randomized algorithms that involve rapidly mixing Markov chains.

Journal Article↗

PubMed2003

Duplication models for biological networks.

Are biological networks different from other large complex networks? Both large biological and nonbiological networks exhibit power-law graphs (number of nodes with degree k, N(k) approximately k(-beta)), yet the exponents, beta, fall into different ranges. This may be because duplication of the information in the genome is a dominant evolutionary force in shaping biological networks (like gene regulatory networks and protein-protein interaction networks) and is fundamentally different from the mechanisms thought to dominate the growth of most nonbiological networks (such as the Internet). The preferential choice models used for nonbiological networks like web graphs can only produce power-law graphs with exponents greater than 2. We use combinatorial probabilistic methods to examine the evolution of graphs by node duplication processes and derive exact analytical relationships between the exponent of the power law and the parameters of the model. Both full duplication of nodes (with all their connections) as well as partial duplication (with only some connections) are analyzed. We demonstrate that partial duplication can produce power-law graphs with exponents less than 2, consistent with current data on biological networks. The power-law exponent for large graphs depends only on the growth process, not on the starting graph.

Internet↗

PubMed2002

The average distances in random graphs with given expected degrees.

Random graph theory is used to examine the "small-world phenomenon"; any two strangers are connected through a short chain of mutual acquaintances. We will show that for certain families of random graphs with given expected degrees the average distance is almost surely of order log nlog d, where d is the weighted average of the sum of squares of the expected degrees. Of particular interest are power law random graphs in which the number of vertices of degree k is proportional to 1kbeta for some fixed exponent beta. For the case of beta > 3, we prove that the average distance of the power law graphs is almost surely of order log nlog d. However, many Internet, social, and citation networks are power law graphs with exponents in the range 2 < beta < 3 for which the power law random graphs have average distance almost surely of order log log n, but have diameter of order log n (provided having some mild constraints for the average distance and maximum degree). In particular, these graphs contain a dense subgraph, which we call the core, having n(clog log n) vertices. Almost all vertices are within distance log log n of the core although there are vertices at distance log n from the core.

Journal Article↗