Showing papers by "Center for Discrete Mathematics and Theoretical Computer Science published in 2010"

Modularity map of the network of human cell differentiation.

Abstract: Cell differentiation in multicellular organisms is a complex process whose mechanism can be understood by a reductionist approach, in which the individual processes that control the generation of different cell types are identified. Alternatively, a large-scale approach in search of different organizational features of the growth stages promises to reveal its modular global structure with the goal of discovering previously unknown relations between cell types. Here, we sort and analyze a large set of scattered data to construct the network of human cell differentiation (NHCD) based on cell types (nodes) and differentiation steps (links) from the fertilized egg to a developed human. We discover a dynamical law of critical branching that reveals a self-similar regularity in the modular organization of the network, and allows us to observe the network at different scales. The emerging picture clearly identifies clusters of cell types following a hierarchical organization, ranging from sub-modules to super-modules of specialized tissues and organs on varying scales. This discovery will allow one to treat the development of a particular cell function in the context of the complex network of human development as a whole. Our results point to an integrated large-scale view of the network of cell types systematically revealing ties between previously unrelated domains in organ functions.

Systems approach to studying animal sociality: individual position versus group organization in dynamic social network models.

Abstract: Social networks can be used to represent group structure as a network of interacting components, and also to quantify both the position of each individual and the global properties of a group. In a series of simulation experiments based on dynamic social networks, we test the prediction that social behaviors that help individuals reach prominence within their social group may conflict with their potential to benefit from their social environment. In addition to cases where individuals were able to benefit from improving both their personal relative importance and group organization, using only simple rules of social affiliation we were able to obtain results in which individuals would face a trade-off between these factors. While selection would favor (or work against) social behaviors that concordantly increase (or decrease, respectively) fitness at both individual and group level, when these factors conflict with each other the eventual selective pressure would depend on the relative returns individuals get from their social environment and their position within it. The presented results highlight the importance of a systems approach to studying animal sociality, in which the effects of social behaviors should be viewed not only through the benefits that those provide to individuals, but also in terms of how they affect broader social environment and how in turn this is reflected back on an individual's fitness.

Disproportional effects in populations of concern for pandemic influenza: insights from seasonal epidemics in Wisconsin, 1967-2004.

Abstract: Please cite this paper as: Lofgren et al. (2010) Disproportional effects in populations of concern for pandemic influenza: insights from seasonal epidemics in Wisconsin, 1967–2004. Influenza and Other Respiratory Viruses 4(4), 205–212. Background Influenza infections pose a serious burden of illness in the United States. We explored age, influenza strains, and seasonal epidemic curves in relation to influenza-associated mortality. Methods The state of Wisconsin death records for the years 1967–2004 were analyzed for three distinct populations: children, general population, and elderly. Yearly parameters of duration, intensity, and peak timing were obtained from Annual Harmonic Regression coefficients. Results Overall, elderly had the highest rate and intensity of influenza mortality. The children and infant subpopulations showed an earlier and wider range in duration of peak timing than elderly. During A/Hong Kong/1/68 pandemic years, the elderly subpopulation showed no change in mortality rates while a sharp increase was observed for the children and infant subpopulations. In epidemic years such as 1966–1969, children and infants showed a dramatic decrease in the severity of influenza outbreaks over time. The elderly had increased baseline mortality in years (1986–1987) where predominant strain was characterized as A/Singapore/6/86. Conclusions Our findings indicate that the younger populations may have benefited from the lack of a major shift in viral strains for a number of decades. Furthermore, we demonstrate considerable heterogeneity in the spread of seasonal influenza across age categories, with implications both for the modeling of influenza seasonality, risk assessment, and effective distribution and timing of vaccine and prophylactic interventions.

A hybrid genetic algorithm for VLSI floorplanning

Abstract: Floorplanning is the first stage of the very large scale integrated-circuit (VLSI) physical design process, the resultant quality of this stage is very important for successive design stages. From the computational point of view, VLSI floorplanning is an NP-hard problem. In this paper, a hybrid genetic algorithm (HGA) for a non-slicing and hard-module VLSI floorplanning problem is presented. This HGA uses an effective genetic search method to explore the search space and an efficient local search method to exploit information in the search region. Experimental results on MCNC benchmarks [16] show that the HGA is effective and promising in building block layout application.

A GRASP based algorithm for multi-constraint circuit partitioning

Abstract: We study the circuit partitioning problem with area and delay constraints to optimize the circuit performance. We integrate delay constraints into the greedy randomized adaptive search procedure (GRASP), so that GRASP can be used to deal with delay problems. The GRASP with area and delay constraints can generate better initial partitions. Then the initial partition is iteratively improved by an extended FM algorithm. Finally we obtain the partition satisfying area and delay constraints. Our hybrid algorithm can solve bi-partition with area and delay constraints successfully. The experimental results indicate that, compared with FM algorithm and clustering algorithm, our hybrid algorithm improves the solution quality in a reasonable computational time, and obtains a better partition, especially in terms of the minimum cut-size and the average cut-size.

Real-time streaming media playout algorithm based on RBF delay prediction

Abstract: Analyzing two important indicators of real-time streaming media system, and then aiming at the drawbacks of the conventional real-time streaming media playout algorithm and the playout algorithm based on Differencing AR, a real-time streaming media playout algorithm based on RBF (radial basis function) delay prediction is proposed. The algorithm takes the initiative to adjust the time interval to ensure the continuity of playout and reduce average buffer delay in different situation with time-based forecasts by predicting the receive time and playout time. Finally, compared with other algorithms, the experiment result shows that this algorithm is effective.

TT-STUN protocol design for effective TCP NAT traversal

Abstract: For the NAT gateway widely used in the computer network, PC can not connect to another one through NAT gateway using TCP directly. Despite there are many methods like UPNP and Port prediction which can resolve the problems, it is difficult to be used for the Low penetration rate. In this article, we design TT-STUN protocol using TCP To Stun To TCP's design for effective TCP NAT traversal. According to reliable data, its penetration can reach 90%.

A network access control mechanism based on role and behavior

Abstract: Current Role-Based Access Control (RBAC) can't assign permissions dynamically and can't update access control policies automatically. In this paper we present a new network access control (NAC) mechanism based on role and behavior (RB-NAC) which enhances role-based access control by establishing clusters of behavior to limit permissions of user dynamically and incorporating an incremental-learning algorithm to update the policies without manual intervention. RB-NAC as an enhanced access control mechanism shows its efficient flexibility and scalability in access control.

New foundations to geometry

Abstract: Leyton's books in MIT Press, Springer and Birkhauser have developed New Foundations to Geometry which are opposed to the Standard Foundations to Geometry. In the Standard Foundations, a geometric object is defined as an invariant, which, Leyton argues, destroys memory storage. In contrast, in Leyton's New Foundations, a geometric object is defined as a memory store, and he has created the corresponding mathematics, which has fundamental differences from standard mathematics. Leyton's mathematics has been applied by scientists in over 40 disciplines, which shows their interoperability. Furthermore, because, he argues that this mathematics gives the structure of memory stores, it is appropriate for the history-based parametrics program of ISO. Since, in the New Foundations, the geometry is generative, it is also called Generative Geometry. Two basic principles of this geometry are maximisation of transfer and maximisation of recoverability of the generative operations. Leyton's geometry invents the mathematics of transfer and recoverability.

A dynamic convexized method for the TSP

Abstract: This paper describes a dynamic convexized method for solving the symmetric traveling salesman problem (TSP). We construct an auxiliary function and design an algorithm based on this function. The possibility of sinking into a previous local minimizer can be reduced by adjusting the value of the parameter in the auxiliary function. We have verified the correctness of this approach both in theory and experiment. Computational tests show that the algorithm is effective.