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An efficient and reliable network alignment serves to find the mapping with maximum similarity between different networks, which is a way to improve our understanding of biology system and biological process. To build such network alignment is a foremost challenging task in computational biology because it involves the bipartite graph matching problem, which is an NP-hard problem. In this work, we...
Interactions among proteins are important mechanisms in living cells. The whole set of interactions is often referred to as a protein-protein interaction network (PIN). Comparison among such networks may discover conserved (or disrupted) patterns of interactions among species. Such comparison is performed using network alignment algorithms. They help analyse PPI networks for a better understanding...
Pebble game rigidity analysis is an efficient method for extracting rigidity and flexibility information of biomolecules without performing costly molecular dynamics simulations. The standard algorithm works on a multi-graph associated to a mechanical model constructed from an arbitrary atom-bond network. Motivated by large scale protein flexibility and simulated unfolding applications, we have developed...
Cluster computing combines the resources of multiple computers as they act like a single high-performance computer. In this study, a computer cluster consisting of Lustre distributed file system with one cluster server based on Slurm resource management system and thirteen calculation nodes were built by using available and inert computers that have different processors. Different bioinformatics algorithms...
In this paper an approach to information quantitative measuring is offered. This information is given as a fuzzy number. It is a particular case of the fuzzy set which is defined by a membership function. It should be noted that this function is determined on the basis of some segment on the set of real numbers. Therefore, a problem changes into construction of the fuzzy number membership function...
We report an experimental study that involves understanding how display (conventional or ecological) and system mode (profiting, neutral or losing) affect financial trading performance and risk preference. Twenty-four undergraduate and graduate student participants interacted with a financial trading simulator in the playback of a real market. Each participant completed a conventional display scenario...
Decision making support has become essential to conduct an effective management and operational system. It is considered an important part of operational research and management science. There are various decision issues concerning the good governance and management of a supply chain. In this paper, we focus on the conception problem of a supply chain, especially the geographical location implementation...
It is difficult to determine the folding structure of Escherichia coli chromosome by biological experiments and observation methods. However, the accumulation of a great deal of genetic data makes it possible to predict its folding boundaries distribution by computational biology methods. On the basis of fully understanding multiple sources of data, this paper proposes and implements a new folding...
This paper presents a prediction model to predict biogas production for anaerobic digestion process of food waste. There exist sophisticated biogas production models in published literature, but the application of these models in anaerobic digestion process of food waste is often impractical because of its high complexity. Considering the shortcomings of the accuracy of these biogas production prediction...
In this paper the problem of design optimization of a microwave wearable antenna is investigated. Reference is made to a specific antenna design that is wideband vee antenna which is characterized by 6 geometrical parameters. Those parameters were automatically adjusted with an evolution strategy based algorithm to obtain the impedance matching of antenna located in the proximity of the human body...
In order to understand the structure and folding of proteins, Hydrophobic-Polar (HP) model on 2D square lattice is one of the most explored models but parity problem of square lattice make it inefficient for biological applications. This work is dedicated to solve parity issues in 2D square lattice model. This work proposes a revised energy function and presents a case study for protein structure...
The Volterra model is a well-established option in nonlinear black-box system identification. However, the estimated model is often over-parametrized. This paper presents an approach to reducing the number of parameters of a Volterra model with the kernels parametrized in the orthonormal basis of Laguerre functions by estimating it with a sparse estimation algorithm subject to constraints. The resulting...
Species distribution modeling (SDM) calculates a species’ probabilistic distribution by combining Environmental raster layers with species datasets. Such models can help to answer complex questions in Ecology/Biology/Health, e.g., by calculating impacts of climate changes in Biodiversity, or the potential for a disease spread (vectors’ modeling). Machine learning is largely applied in SDM, being the...
In this paper, we describe a novel data model for online social networks based on hypergraphs. We show how an influence analysis problem can be properly faced leveraging the introduced network structure. In particular, we implemented a bio-inspired maximization algorithm on the top of the hypergraph model, exploiting the concept of influential path. Preliminary experiments using data of several social...
Credit scoring is explored to assess default risk of consumer behaviors for financial institutions, banks in particular. The advanced Bayesian algorithm is proposed for credit assessment. The new trial ensembles logistic regression analysis (LRA), cluster and MLP-NN in Bayesian approach as an advanced classifier. The investigation contain evidence that Bayesian ensemble technique optimizes LRA, cluster...
In this paper, a novel guidance-control scheme is presented for the unmanned surface vessel (USV) trajectory tracking. First, the guidance system is designed to give the reference speed and heading for the control system. Based on the SFLOS algorithm, the guidance system can track the desired curve in high precision. Then, control system is proposed based on backstepping technique and bio-inspired...
Sample preparation in digital microfluidics refers to the generation of droplets with target concentrations for onchip biochemical applications. In recent years, digital microfluidic biochips (DMFBs) have been adopted as a platform for sample preparation. However, there remain one major problem associated with sample preparation on a conventional DMFB. For conventional DMFBs, only a (1:1) mixing/splitting...
The Smith-Waterman algorithm, which produces the optimal local alignment between pairwise sequences, is universally used as a key component in bioinformatics fields. It is more sensitive than heuristic approaches, but also more time-consuming. To speed up the algorithm, Single-Instruction Multiple-Data (SIMD) instructions have been used to parallelize the algorithm by leveraging data parallel strategy...
Membrane computing also called P system, seeks to discover new computational models from the study of cellular membranes. In this study, we reported our initial efforts to classify Macao visitor expenditure profile using a membrane computing approach. Specifically, we designed a novel P system including specific membrane structure and membrane rules to realize an improved k-medoids clustering algorithm...
A service ecosystem, consisting of various kinds of services and mashups, evolves over time. Existing works on the evolution of service systems focus on either evaluating the impacts of services' changes on the usage of services and the stability of the whole ecosystem, or discovering co-occurrences between services, but fail to disclose any knowledge about the evolution of service composition patterns...
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