LightDock: a new multi-scale approach to protein–protein docking

Computational prediction of protein–protein complex structure by docking can provide structural and mechanistic insights for protein interactions of biomedical interest. However, current methods struggle with difficult cases, such as those involving flexible proteins, low-affinity complexes or transient interactions. A major challenge is how to efficiently sample the structural and energetic landscape of the association at different resolution levels, given that each scoring function is often highly coupled to a specific type of search method. Thus, new methodologies capable of accommodating multi-scale conformational flexibility and scoring are strongly needed. We describe here a new multi-scale protein–protein docking methodology, LightDock, capable of accommodating conformational flexibility and a variety of scoring functions at different resolution levels. Implicit use of normal modes during the search and atomic/coarse-grained combined scoring functions yielded improved predictive results with respect to state-of-the-art rigid-body docking, especially in flexible cases.B.J-G was supported by a FPI fellowship from the Spanish Ministry of Economy and Competitiveness. This work was supported by I+D+I Research Project grants BIO2013-48213-R and BIO2016-79930-R from the Spanish Ministry of Economy and Competitiveness. This work is partially supported by the European Union H2020 program through HiPEAC (GA 687698), by the Spanish Government through Programa Severo Ochoa (SEV-2015-0493), by the Spanish Ministry of Science and Technology (TIN2015-65316-P) and the Departament d’Innovació, Universitats i Empresa de la Generalitat de Catalunya, under project MPEXPAR: Models de Programaciói Entorns d’Execució Paral·lels (2014-SGR-1051).Peer ReviewedPostprint (author's final draft

Multimodal estimation of distribution algorithms

Taking the advantage of estimation of distribution algorithms (EDAs) in preserving high diversity, this paper proposes a multimodal EDA. Integrated with clustering strategies for crowding and speciation, two versions of this algorithm are developed, which operate at the niche level. Then these two algorithms are equipped with three distinctive techniques: 1) a dynamic cluster sizing strategy; 2) an alternative utilization of Gaussian and Cauchy distributions to generate offspring; and 3) an adaptive local search. The dynamic cluster sizing affords a potential balance between exploration and exploitation and reduces the sensitivity to the cluster size in the niching methods. Taking advantages of Gaussian and Cauchy distributions, we generate the offspring at the niche level through alternatively using these two distributions. Such utilization can also potentially offer a balance between exploration and exploitation. Further, solution accuracy is enhanced through a new local search scheme probabilistically conducted around seeds of niches with probabilities determined self-adaptively according to fitness values of these seeds. Extensive experiments conducted on 20 benchmark multimodal problems confirm that both algorithms can achieve competitive performance compared with several state-of-the-art multimodal algorithms, which is supported by nonparametric tests. Especially, the proposed algorithms are very promising for complex problems with many local optima

Consumer satisfaction on the adoption of e-payment among millennials in Malaysia during Covid 19 pandemic

The Pandemic Covid-19 had hugely impacted businesses and economy in every sector of the world through the implementation of Lockdowns and Movement Control Order (MCO). This situation has unavoidably caused a worldwide monetary decline (Cheng, 2020 & UNDP, 2020). , The MCO situation has limited the normal face to face retailing activity and affected consumer goods and the retail industry. Stores of essential items along with meals, groceries, and healthcare experienced extended call for opportunities for serving purchasers at home, at the same time as facing demanding situations of stock, supply chain control, shipping, and maintaining their facility a secure environment (Roggeveen & Sethuraman, 2020)

Orthogonal learning particle swarm optimization

Particle swarm optimization (PSO) relies on its learning strategy to guide its search direction. Traditionally, each particle utilizes its historical best experience and its neighborhood’s best experience through linear summation. Such a learning strategy is easy to use, but is inefficient when searching in complex problem spaces. Hence, designing learning strategies that can utilize previous search information (experience) more efficiently has become one of the most salient and active PSO research topics. In this paper, we proposes an orthogonal learning (OL) strategy for PSO to discover more useful information that lies in the above two experiences via orthogonal experimental design. We name this PSO as orthogonal learning particle swarm optimization (OLPSO). The OL strategy can guide particles to fly in better directions by constructing a much promising and efficient exemplar. The OL strategy can be applied to PSO with any topological structure. In this paper, it is applied to both global and local versions of PSO, yielding the OLPSO-G and OLPSOL algorithms, respectively. This new learning strategy and the new algorithms are tested on a set of 16 benchmark functions, and are compared with other PSO algorithms and some state of the art evolutionary algorithms. The experimental results illustrate the effectiveness and efficiency of the proposed learning strategy and algorithms. The comparisons show that OLPSO significantly improves the performance of PSO, offering faster global convergence, higher solution quality, and stronger robustness

Crime Prediction and Analysis against women Using LRSRI-Missing Value Imputation and FIPSO - Optimum Feature Selection Methods

Data investigation is the method of considering crude measurements in arrange to draw conclusions around them. Many statistics evaluation techniques and tendencies had been automated into mechanical techniques and algorithms in such a manner that they provided raw statistics for human consumption. Machine learning could be a portion of artificial intelligence that permits computer frameworks to "analyze" their own statistics and improve them over time without being explicitly programmed. Machine learning algorithms can understand patterns in statistics and analyze them to make their own predictions. Lost esteem ascription is one of the foremost vital procedures in data pre-processing and it is additionally the most prepare of information examination. Ascription of lost information for a variable replaces lost information with a esteem inferred from an assess of the dispersion of that variable. Basic accusation employments as it were one suspicion. Numerous ascriptions employments diverse gauges to reflect the instability in evaluating this dispersion. In this article, The proposed method LRSRI used for impute the missing values on Crime against Women Data-set(CAW).The Linear Regression Imputation and Stochastic regression imputations are used in this method.Feature selection is another important data preprocessing techniques.This is often called attribute selection or feature selection. The most important problem in predictive modeling is the mechanical selection of features in the data. In this work,the proposed method FIPSO implemented for feature selection.This is feature importance and Particle Swarm Optimization based method.The main objective of this work is predict the crime rate against women in India based on 2001 to 2021 crime recorded against women in India.This Data set is collected from Data.gov.in.Finally The predicted result is compared with recent NCRB crime report.The proposed method LRSRI and FIPSO has given 98.34% accuracy of crime prediction.In feature,This outcome will be valuable for the crime office to control the CAW in India

A particle swarm based hybrid system for imbalanced medical data sampling

BackgroundMedical and biological data are commonly with small sample size, missing values, and most importantly, imbalanced class distribution. In this study we propose a particle swarm based hybrid system for remedying the class imbalance problem in medical and biological data mining. This hybrid system combines the particle swarm optimization (PSO) algorithm with multiple classifiers and evaluation metrics for evaluation fusion. Samples from the majority class are ranked using multiple objectives according to their merit in compensating the class imbalance, and then combined with the minority class to form a balanced dataset.ResultsOne important finding of this study is that different classifiers and metrics often provide different evaluation results. Nevertheless, the proposed hybrid system demonstrates consistent improvements over several alternative methods with three different metrics. The sampling results also demonstrate good generalization on different types of classification algorithms, indicating the advantage of information fusion applied in the hybrid system.ConclusionThe experimental results demonstrate that unlike many currently available methods which often perform unevenly with different datasets the proposed hybrid system has a better generalization property which alleviates the method-data dependency problem. From the biological perspective, the system provides indication for further investigation of the highly ranked samples, which may result in the discovery of new conditions or disease subtypes.<br /