Hybrid Simulated Annealing for Data Clustering

2017 ◽  
Vol 40 (2) ◽  
pp. 92-98
Author(s):  
Sung-Soo Kim ◽  
◽  
Jun-Young Baek ◽  
Beom-Soo Kang
Keyword(s):  
Simulated Annealing ◽  
Data Clustering ◽  
Hybrid Simulated Annealing

scholarly journals A Peptides Prediction Methodology for Tertiary Structure Based on Simulated Annealing

2021 ◽  
Vol 26 (2) ◽  
pp. 39
Author(s):  
Juan P. Sánchez-Hernández ◽  
Juan Frausto-Solís ◽  
Juan J. González-Barbosa ◽  
Diego A. Soto-Monterrubio ◽  
Fanny G. Maldonado-Nava ◽  
...  
Keyword(s):  
Simulated Annealing ◽  
Ab Initio ◽  
Primary Structure ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Secondary Structure Prediction ◽  
Golden Ratio ◽  
Small Peptides ◽  
Hybrid Simulated Annealing ◽  
Ab Initio Models

The Protein Folding Problem (PFP) is a big challenge that has remained unsolved for more than fifty years. This problem consists of obtaining the tertiary structure or Native Structure (NS) of a protein knowing its amino acid sequence. The computational methodologies applied to this problem are classified into two groups, known as Template-Based Modeling (TBM) and ab initio models. In the latter methodology, only information from the primary structure of the target protein is used. In the literature, Hybrid Simulated Annealing (HSA) algorithms are among the best ab initio algorithms for PFP; Golden Ratio Simulated Annealing (GRSA) is a PFP family of these algorithms designed for peptides. Moreover, for the algorithms designed with TBM, they use information from a target protein’s primary structure and information from similar or analog proteins. This paper presents GRSA-SSP methodology that implements a secondary structure prediction to build an initial model and refine it with HSA algorithms. Additionally, we compare the performance of the GRSAX-SSP algorithms versus its corresponding GRSAX. Finally, our best algorithm GRSAX-SSP is compared with PEP-FOLD3, I-TASSER, QUARK, and Rosetta, showing that it competes in small peptides except when predicting the largest peptides.

scholarly journals Improved Bidirectional CABOSFV Based on Multi-Adjustment Clustering and Simulated Annealing

2016 ◽  
Vol 16 (6) ◽  
pp. 27-42 ◽  
Author(s):  
Minghan Yang ◽  
Xuedong Gao ◽  
Ling Li
Keyword(s):  
Simulated Annealing ◽  
Data Clustering ◽  
Time Complexity ◽  
Clustering Algorithm ◽  
Feature Vector ◽  
Parameter Determination ◽  
Data Sets ◽  
Parameter Vector ◽  
Clustering Validity

Abstract Although Clustering Algorithm Based on Sparse Feature Vector (CABOSFV) and its related algorithms are efficient for high dimensional sparse data clustering, there exist several imperfections. Such imperfections as subjective parameter designation and order sensibility of clustering process would eventually aggravate the time complexity and quality of the algorithm. This paper proposes a parameter adjustment method of Bidirectional CABOSFV for optimization purpose. By optimizing Parameter Vector (PV) and Parameter Selection Vector (PSV) with the objective function of clustering validity, an improved Bidirectional CABOSFV algorithm using simulated annealing is proposed, which circumvents the requirement of initial parameter determination. The experiments on UCI data sets show that the proposed algorithm, which can perform multi-adjustment clustering, has a higher accurateness than single adjustment clustering, along with a decreased time complexity through iterations.

A Hybrid Simulated Annealing and Simplex Method for Fixed-Cost Capacitated Multicommodity Network Design

2012 ◽  
pp. 17-31 ◽  
Author(s):  
Masoud Yaghini ◽  
Mohammad Karimi ◽  
Mohadeseh Rahbar ◽  
Rahim Akhavan
Keyword(s):  
Simulated Annealing ◽  
Network Design ◽  
Simplex Method ◽  
Minimum Cost ◽  
Parameter Tuning ◽  
Fixed Cost ◽  
Hybrid Simulated Annealing ◽  
Np Hard Problem ◽  
Multicommodity Network Design ◽  
Opening And Closing

The fixed-cost Capacitated Multicommodity Network Design (CMND) problem is a well known NP-hard problem. This paper presents a matheuristic algorithm combining Simulated Annealing (SA) metaheuristic and Simplex method for CMND problem. In the proposed algorithm, a binary array is considered as solution representation and the SA algorithm manages open and closed arcs. Several strategies for opening and closing arcs are proposed and evaluated. In this matheuristic approach, for a given design vector, CMND becomes a Capacitated Multicommodity minimum Cost Flow (CMCF) problem. The exact evaluation of the CMCF problem is performed using the Simplex method. The parameter tuning for the proposed algorithm is done by means of design of experiments approach. The performance of the proposed algorithm is evaluated by solving different benchmark instances. The results of the proposed algorithm show that it is able to obtain better solutions in comparison with previous methods in the literature.

Sign in / Sign up

Export Citation Format

Share Document