Molecular Network Control Through Boolean Canalization

Boolean networks are an important class of computational models for molecular interaction networks. Boolean canalization, a type of hierarchical clustering of the inputs of a Boolean function, has been extensively studied in the context of network modeling where each layer of canalization adds a degree of stability in the dynamics of the network. Recently, dynamic network control approaches have been used for the design of new therapeutic interventions and for other applications such as stem cell reprogramming. This work studies the role of canalization in the control of Boolean molecular networks. It provides a method for identifying the potential edges to control in the wiring diagram of a network for avoiding undesirable state transitions. The method is based on identifying appropriate input-output combinations on undesirable transitions that can be modified using the edges in the wiring diagram of the network. Moreover, a method for estimating the number of changed transitions in the state space of the system as a result of an edge deletion in the wiring diagram is presented. The control methods of this paper were applied to a mutated cell-cycle model and to a p53-mdm2 model to identify potential control targets

The Density Matrix Renormalization Group in Nuclear Physics: A Status Report

We report on the current status of recent efforts to develop the Density Matrix Renormalization Group method for use in large-scale nuclear shell-model calculations.Comment: 6 pages, 8 figures, $^*$ Talk presented at the XXVI$^{th}$ Symposium on Nuclear Physics, 6 pages, 8 figures, Talk presented at the XXVIth Symposium on Nuclear Physics,6-9 January 2003, Taxco, Mexic

Automatic, computer aided geometric design of free-knot, regression splines

A new algorithm for Computer Aided Geometric Design of least squares (LS) splines with variable knots, named GeDS, is presented. It is based on interpreting functional spline regression as a parametric B-spline curve, and on using the shape preserving property of its control polygon. The GeDS algorithm includes two major stages. For the first stage, an automatic adaptive, knot location algorithm is developed. By adding knots, one at a time, it sequentially "breaks" a straight line segment into pieces in order to construct a linear LS B-spline fit, which captures the "shape" of the data. A stopping rule is applied which avoids both over and under fitting and selects the number of knots for the second stage of GeDS, in which smoother, higher order (quadratic, cubic, etc.) fits are generated. The knots appropriate for the second stage are determined, according to a new knot location method, called the averaging method. It approximately preserves the linear precision property of B-spline curves and allows the attachment of smooth higher order LS B-spline fits to a control polygon, so that the shape of the linear polygon of stage one is followed. The GeDS method produces simultaneously linear, quadratic, cubic (and possibly higher order) spline fits with one and the same number of B-spline regression functions. The GeDS algorithm is very fast, since no deterministic or stochastic knot insertion/deletion and relocation search strategies are involved, neither in the first nor the second stage. Extensive numerical examples are provided, illustrating the performance of GeDS and the quality of the resulting LS spline fits. The GeDS procedure is compared with other existing variable knot spline methods and smoothing techniques, such as SARS, HAS, MDL, AGS methods and is shown to produce models with fewer parameters but with similar goodness of fit characteristics, and visual quality

Two-Body Density Matrix for Closed s-d Shell Nuclei

The two-body density matrix for $^{4}He,^{16}O$ and $^{40}Ca$ within the Low-order approximation of the Jastrow correlation method is considered. Closed analytical expressions for the two-body density matrix, the center of mass and relative local densities and momentum distributions are presented. The effects of the short-range correlations on the two-body nuclear characteristics are investigated.Comment: 13 pages(LaTeX), 4 figures (ps

Adaptive notifications to support knowledge sharing in virtual communities

Social web-groups where people with common interests and goals communicate, share resources, and construct knowledge, are becoming a major part of today’s organisational practice. Research has shown that appropriate support for effective knowledge sharing tailored to the needs of the community is paramount. This brings a new challenge to user modelling and adaptation, which requires new techniques for gaining sufficient understanding of a virtual community (VC) and identifying areas where the community may need support. The research presented here addresses this challenge presenting a novel computational approach for community-tailored support underpinned by organisational psychology and aimed at facilitating the functioning of the community as a whole (i.e. as an entity). A framework describing how key community processes—transactive memory (TM), shared mental models (SMMs), and cognitive centrality (CCen)—can be utilised to derive knowledge sharing patterns from community log data is described. The framework includes two parts: (i) extraction of a community model that represents the community based on the key processes identified and (ii) identification of knowledge sharing behaviour patterns that are used to generate adaptive notifications. Although the notifications target individual members, they aim to influence individuals’ behaviour in a way that can benefit the functioning of the community as a whole. A validation study has been performed to examine the effect of community-adapted notifications on individual members and on the community as a whole using a close-knit community of researchers sharing references. The study shows that notification messages can improve members’ awareness and perception of how they relate to other members in the community. Interesting observations have been made about the linking between the physical and the VC, and how this may influence members’ awareness and knowledge sharing behaviour. Broader implications for using log data to derive community models based on key community processes and generating community-adapted notifications are discussed

Computing the Kolmogorov-Smirnov Distribution when the Underlying cdf is Purely Discrete, Mixed or Continuous

The distribution of the Kolmogorov-Smirnov (K-S) test statistic has been widely studied under the assumption that the underlying theoretical cdf, F(x), is continuous. However, there are many real-life applications in which fitting discrete or mixed distributions is required. Nevertheless, due to inherent difficulties, the distribution of the K-S statistic when F(x) has jump discontinuities has been studied to a much lesser extent and no exact and efficient computational methods have been proposed in the literature. In this paper, we provide a fast and accurate method to compute the (complementary) cdf of the K-S statistic when F(x) is discontinuous, and thus obtain exact p values of the K-S test. Our approach is to express the complementary cdf through the rectangle probability for uniform order statistics, and to compute it using Fast Fourier Transform(FFT). Secondly, we provide a C++ and an R implementation of the proposed method, which fills in the existing gap in statistical software. We give also a useful extension of the Schmid’s asymptotic formula for the distribution of the K-S statistic, relaxing his requirement for F(x) to be increasing between jumps and thus allowing for any general mixed or purely discrete F(x). The numerical performance of the proposed FFT-based method, implemented both in C++ and in the R package KSgeneral, is illustrated when F(x) is mixed, purely discrete, and continuous. The performance of the general asymptotic formula is also studied