A virtual workspace for hybrid multidimensional scaling algorithms

In visualising multidimensional data, it is well known that different types of algorithms to process them. Data sets might be distinguished according to volume, variable types and distribution, and each of these characteristics imposes constraints upon the choice of applicable algorithms for their visualization. Previous work has shown that a hybrid algorithmic approach can be successful in addressing the impact of data volume on the feasibility of multidimensional scaling (MDS). This suggests that hybrid combinations of appropriate algorithms might also successfully address other characteristics of data. This paper presents a system and framework in which a user can easily explore hybrid algorithms and the data flowing through them. Visual programming and a novel algorithmic architecture let the user semi-automatically define data flows and the co-ordination of multiple views

A visual workspace for constructing hybrid MDS algorithms and coordinating multiple views

Data can be distinguished according to volume, variable types and distribution, and each of these characteristics imposes constraints upon the choice of applicable algorithms for their visualisation. This has led to an abundance of often disparate algorithmic techniques. Previous work has shown that a hybrid algorithmic approach can be successful in addressing the impact of data volume on the feasibility of multidimensional scaling (MDS). This paper presents a system and framework in which a user can easily explore algorithms as well as their hybrid conjunctions and the data flowing through them. Visual programming and a novel algorithmic architecture let the user semi-automatically define data flows and the co-ordination of multiple views of algorithmic and visualisation components. We propose that our approach has two main benefits: significant improvements in run times of MDS algorithms can be achieved, and intermediate views of the data and the visualisation program structure can provide greater insight and control over the visualisation process

Discrete Morse theory for computing cellular sheaf cohomology

Sheaves and sheaf cohomology are powerful tools in computational topology, greatly generalizing persistent homology. We develop an algorithm for simplifying the computation of cellular sheaf cohomology via (discrete) Morse-theoretic techniques. As a consequence, we derive efficient techniques for distributed computation of (ordinary) cohomology of a cell complex.Comment: 19 pages, 1 Figure. Added Section 5.

An Energy-driven Network Function Virtualization for Multi-domain Software Defined Networks

Network Functions Virtualization (NFV) in Software Defined Networks (SDN) emerged as a new technology for creating virtual instances for smooth execution of multiple applications. Their amalgamation provides flexible and programmable platforms to utilize the network resources for providing Quality of Service (QoS) to various applications. In SDN-enabled NFV setups, the underlying network services can be viewed as a series of virtual network functions (VNFs) and their optimal deployment on physical/virtual nodes is considered a challenging task to perform. However, SDNs have evolved from single-domain to multi-domain setups in the recent era. Thus, the complexity of the underlying VNF deployment problem in multi-domain setups has increased manifold. Moreover, the energy utilization aspect is relatively unexplored with respect to an optimal mapping of VNFs across multiple SDN domains. Hence, in this work, the VNF deployment problem in multi-domain SDN setup has been addressed with a primary emphasis on reducing the overall energy consumption for deploying the maximum number of VNFs with guaranteed QoS. The problem in hand is initially formulated as a "Multi-objective Optimization Problem" based on Integer Linear Programming (ILP) to obtain an optimal solution. However, the formulated ILP becomes complex to solve with an increasing number of decision variables and constraints with an increase in the size of the network. Thus, we leverage the benefits of the popular evolutionary optimization algorithms to solve the problem under consideration. In order to deduce the most appropriate evolutionary optimization algorithm to solve the considered problem, it is subjected to different variants of evolutionary algorithms on the widely used MOEA framework (an open source java framework based on multi-objective evolutionary algorithms).Comment: Accepted for publication in IEEE INFOCOM 2019 Workshop on Intelligent Cloud Computing and Networking (ICCN 2019

Maximizing Protein Translation Rate in the Ribosome Flow Model: the Homogeneous Case

Gene translation is the process in which intracellular macro-molecules, called ribosomes, decode genetic information in the mRNA chain into the corresponding proteins. Gene translation includes several steps. During the elongation step, ribosomes move along the mRNA in a sequential manner and link amino-acids together in the corresponding order to produce the proteins. The homogeneous ribosome flow model(HRFM) is a deterministic computational model for translation-elongation under the assumption of constant elongation rates along the mRNA chain. The HRFM is described by a set of n first-order nonlinear ordinary differential equations, where n represents the number of sites along the mRNA chain. The HRFM also includes two positive parameters: ribosomal initiation rate and the (constant) elongation rate. In this paper, we show that the steady-state translation rate in the HRFM is a concave function of its parameters. This means that the problem of determining the parameter values that maximize the translation rate is relatively simple. Our results may contribute to a better understanding of the mechanisms and evolution of translation-elongation. We demonstrate this by using the theoretical results to estimate the initiation rate in M. musculus embryonic stem cell. The underlying assumption is that evolution optimized the translation mechanism. For the infinite-dimensional HRFM, we derive a closed-form solution to the problem of determining the initiation and transition rates that maximize the protein translation rate. We show that these expressions provide good approximations for the optimal values in the n-dimensional HRFM already for relatively small values of n. These results may have applications for synthetic biology where an important problem is to re-engineer genomic systems in order to maximize the protein production rate