QuateXelero : an accelerated exact network motif detection algorithm

Finding motifs in biological, social, technological, and other types of networks has become a widespread method to gain more knowledge about these networks’ structure and function. However, this task is very computationally demanding, because it is highly associated with the graph isomorphism which is an NP problem (not known to belong to P or NP-complete subsets yet). Accordingly, this research is endeavoring to decrease the need to call NAUTY isomorphism detection method, which is the most time-consuming step in many existing algorithms. The work provides an extremely fast motif detection algorithm called QuateXelero, which has a Quaternary Tree data structure in the heart. The proposed algorithm is based on the well-known ESU (FANMOD) motif detection algorithm. The results of experiments on some standard model networks approve the overal superiority of the proposed algorithm, namely QuateXelero, compared with two of the fastest existing algorithms, G-Tries and Kavosh. QuateXelero is especially fastest in constructing the central data structure of the algorithm from scratch based on the input network

ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra

Background: Many biological systems are modeled qualitatively with discrete models, such as probabilistic Boolean networks, logical models, Petri nets, and agent-based models, with the goal to gain a better understanding of the system. The computational complexity to analyze the complete dynamics of these models grows exponentially in the number of variables, which impedes working with complex models. Although there exist sophisticated algorithms to determine the dynamics of discrete models, their implementations usually require labor-intensive formatting of the model formulation, and they are oftentimes not accessible to users without programming skills. Efficient analysis methods are needed that are accessible to modelers and easy to use. Method: By converting discrete models into algebraic models, tools from computational algebra can be used to analyze their dynamics. Specifically, we propose a method to identify attractors of a discrete model that is equivalent to solving a system of polynomial equations, a long-studied problem in computer algebra. Results: A method for efficiently identifying attractors, and the web-based tool Analysis of Dynamic Algebraic Models (ADAM), which provides this and other analysis methods for discrete models. ADAM converts several discrete model types automatically into polynomial dynamical systems and analyzes their dynamics using tools from computer algebra. Based on extensive experimentation with both discrete models arising in systems biology and randomly generated networks, we found that the algebraic algorithms presented in this manuscript are fast for systems with the structure maintained by most biological systems, namely sparseness, i.e., while the number of nodes in a biological network may be quite large, each node is affected only by a small number of other nodes, and robustness, i.e., small number of attractors

Competent genetic-evolutionary optimization of water distribution systems

A genetic algorithm has been applied to the optimal design and rehabilitation of a water distribution system. Many of the previous applications have been limited to small water distribution systems, where the computer time used for solving the problem has been relatively small. In order to apply genetic and evolutionary optimization technique to a large-scale water distribution system, this paper employs one of competent genetic-evolutionary algorithms - a messy genetic algorithm to enhance the efficiency of an optimization procedure. A maximum flexibility is ensured by the formulation of a string and solution representation scheme, a fitness definition, and the integration of a well-developed hydraulic network solver that facilitate the application of a genetic algorithm to the optimization of a water distribution system. Two benchmark problems of water pipeline design and a real water distribution system are presented to demonstrate the application of the improved technique. The results obtained show that the number of the design trials required by the messy genetic algorithm is consistently fewer than the other genetic algorithms

A Scalable VLSI Architecture for Soft-Input Soft-Output Depth-First Sphere Decoding

Multiple-input multiple-output (MIMO) wireless transmission imposes huge challenges on the design of efficient hardware architectures for iterative receivers. A major challenge is soft-input soft-output (SISO) MIMO demapping, often approached by sphere decoding (SD). In this paper, we introduce the - to our best knowledge - first VLSI architecture for SISO SD applying a single tree-search approach. Compared with a soft-output-only base architecture similar to the one proposed by Studer et al. in IEEE J-SAC 2008, the architectural modifications for soft input still allow a one-node-per-cycle execution. For a 4x4 16-QAM system, the area increases by 57% and the operating frequency degrades by 34% only.Comment: Accepted for IEEE Transactions on Circuits and Systems II Express Briefs, May 2010. This draft from April 2010 will not be updated any more. Please refer to IEEE Xplore for the final version. *) The final publication will appear with the modified title "A Scalable VLSI Architecture for Soft-Input Soft-Output Single Tree-Search Sphere Decoding

Triadic Measures on Graphs: The Power of Wedge Sampling

Graphs are used to model interactions in a variety of contexts, and there is a growing need to quickly assess the structure of a graph. Some of the most useful graph metrics, especially those measuring social cohesion, are based on triangles. Despite the importance of these triadic measures, associated algorithms can be extremely expensive. We propose a new method based on wedge sampling. This versatile technique allows for the fast and accurate approximation of all current variants of clustering coefficients and enables rapid uniform sampling of the triangles of a graph. Our methods come with provable and practical time-approximation tradeoffs for all computations. We provide extensive results that show our methods are orders of magnitude faster than the state-of-the-art, while providing nearly the accuracy of full enumeration. Our results will enable more wide-scale adoption of triadic measures for analysis of extremely large graphs, as demonstrated on several real-world examples

Compressed Representations of Conjunctive Query Results

Relational queries, and in particular join queries, often generate large output results when executed over a huge dataset. In such cases, it is often infeasible to store the whole materialized output if we plan to reuse it further down a data processing pipeline. Motivated by this problem, we study the construction of space-efficient compressed representations of the output of conjunctive queries, with the goal of supporting the efficient access of the intermediate compressed result for a given access pattern. In particular, we initiate the study of an important tradeoff: minimizing the space necessary to store the compressed result, versus minimizing the answer time and delay for an access request over the result. Our main contribution is a novel parameterized data structure, which can be tuned to trade off space for answer time. The tradeoff allows us to control the space requirement of the data structure precisely, and depends both on the structure of the query and the access pattern. We show how we can use the data structure in conjunction with query decomposition techniques, in order to efficiently represent the outputs for several classes of conjunctive queries.Comment: To appear in PODS'18; 35 pages; comments welcom

Coding-theorem Like Behaviour and Emergence of the Universal Distribution from Resource-bounded Algorithmic Probability

Previously referred to as `miraculous' in the scientific literature because of its powerful properties and its wide application as optimal solution to the problem of induction/inference, (approximations to) Algorithmic Probability (AP) and the associated Universal Distribution are (or should be) of the greatest importance in science. Here we investigate the emergence, the rates of emergence and convergence, and the Coding-theorem like behaviour of AP in Turing-subuniversal models of computation. We investigate empirical distributions of computing models in the Chomsky hierarchy. We introduce measures of algorithmic probability and algorithmic complexity based upon resource-bounded computation, in contrast to previously thoroughly investigated distributions produced from the output distribution of Turing machines. This approach allows for numerical approximations to algorithmic (Kolmogorov-Chaitin) complexity-based estimations at each of the levels of a computational hierarchy. We demonstrate that all these estimations are correlated in rank and that they converge both in rank and values as a function of computational power, despite fundamental differences between computational models. In the context of natural processes that operate below the Turing universal level because of finite resources and physical degradation, the investigation of natural biases stemming from algorithmic rules may shed light on the distribution of outcomes. We show that up to 60\% of the simplicity/complexity bias in distributions produced even by the weakest of the computational models can be accounted for by Algorithmic Probability in its approximation to the Universal Distribution.Comment: 27 pages main text, 39 pages including supplement. Online complexity calculator: http://complexitycalculator.com