Graph Theory and Networks in Biology

In this paper, we present a survey of the use of graph theoretical techniques in Biology. In particular, we discuss recent work on identifying and modelling the structure of bio-molecular networks, as well as the application of centrality measures to interaction networks and research on the hierarchical structure of such networks and network motifs. Work on the link between structural network properties and dynamics is also described, with emphasis on synchronization and disease propagation.Comment: 52 pages, 5 figures, Survey Pape

Network constraints on learnability of probabilistic motor sequences

Human learners are adept at grasping the complex relationships underlying incoming sequential input. In the present work, we formalize complex relationships as graph structures derived from temporal associations in motor sequences. Next, we explore the extent to which learners are sensitive to key variations in the topological properties inherent to those graph structures. Participants performed a probabilistic motor sequence task in which the order of button presses was determined by the traversal of graphs with modular, lattice-like, or random organization. Graph nodes each represented a unique button press and edges represented a transition between button presses. Results indicate that learning, indexed here by participants' response times, was strongly mediated by the graph's meso-scale organization, with modular graphs being associated with shorter response times than random and lattice graphs. Moreover, variations in a node's number of connections (degree) and a node's role in mediating long-distance communication (betweenness centrality) impacted graph learning, even after accounting for level of practice on that node. These results demonstrate that the graph architecture underlying temporal sequences of stimuli fundamentally constrains learning, and moreover that tools from network science provide a valuable framework for assessing how learners encode complex, temporally structured information.Comment: 29 pages, 4 figure

A Method for Reducing the Severity of Epidemics by Allocating Vaccines According to Centrality

One long-standing question in epidemiological research is how best to allocate limited amounts of vaccine or similar preventative measures in order to minimize the severity of an epidemic. Much of the literature on the problem of vaccine allocation has focused on influenza epidemics and used mathematical models of epidemic spread to determine the effectiveness of proposed methods. Our work applies computational models of epidemics to the problem of geographically allocating a limited number of vaccines within several Texas counties. We developed a graph-based, stochastic model for epidemics that is based on the SEIR model, and tested vaccine allocation methods based on multiple centrality measures. This approach provides an alternative method for addressing the vaccine allocation problem, which can be combined with more conventional approaches to yield more effective epidemic suppression strategies. We found that allocation methods based on in-degree and inverse betweenness centralities tended to be the most effective at containing epidemics.Comment: 10 pages, accepted to ACM BCB 201