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ABC and IFC: Modules Detection Method for PPI Network
2014
BioMed Research International
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Then the cluster centers are updated through different functions of bees in ABC algorithm; then the clustering result is obtained through IFC method based on the new optimized cluster center. ...
A novel clustering model which combines the optimization mechanism of artificial bee colony (ABC) with the fuzzy membership matrix is proposed in this paper. ...
Functional flow clustering algorithm [17, 18] is a new clustering method for PPI networks, which regards each node as a "reservoir" and passes on the flow to the next node by the connecting edge. ...
doi:10.1155/2014/968173
pmid:24991575
pmcid:PMC4060787
fatcat:bj32eqdk25ejpkkdk7bqsnbtdm
A Review on Artificial Bee Colony Algorithms and Their Applications to Data Clustering
2017
Cybernetics and Information Technologies
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Artificial Bee Colony (ABC) algorithm is one of the popular swarm based algorithm inspired by intelligent foraging behaviour of honeybees that helps to minimize these shortcomings. ...
However, the popular conventional clustering algorithms have shortcomings such as dependency on center initialization, slow convergence rate, local optima trap, etc. ...
Lei, T i a n and W u [168] proposed a new clustering model for PPI networks by use of ABC search mechanism to find the cluster centers and then performing clustering through Intuitionistic Fuzzy Clustering ...
doi:10.1515/cait-2017-0027
fatcat:evxefbetd5gv3enuc7fiulyewm
Clustering PPI Data Based on Bacteria Foraging Optimization Algorithm
2011
2011 IEEE International Conference on Bioinformatics and Biomedicine
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This paper proposed a novel method using Bacteria Foraging Optimization(BFO) algorithm to avoid the influence of cluster number on experimental result of clustering PPI networks. ...
Keywords-bacteria foraging optimization algorithm; PPI networks; accumulation coefficient of edge I. IEEE International Conference on Bioinformatics and Biomedicine 978-0-7695-4574-5/11 $26.00 ...
Our research team [8] had adopted artificial bee colony and particle swarm optimization algorithms to predict functional modules. ...
doi:10.1109/bibm.2011.18
dblp:conf/bibm/LeiWGZ11
fatcat:hp67mo2zhnat3olntrjaq5texa
Detecting protein complexes from DPINs by density based clustering with Pigeon-Inspired Optimization Algorithm
2016
Science China Information Sciences
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BFO clustering model is based on BFO mechanism and intuitionistic fuzzy set while PMABC-ACE is based on the propagating mechanism of artificial bee colony. ...
protein backbone based on Ant Colony Optimization Algorithm [23] . ...
PPI network of its improved version 2.2.1 Basic DBSCAN algorithm DBSCAN, introduced by Ester et al. [19] , is a clustering algorithm based on dense area for spatial datasets. ...
doi:10.1007/s11432-016-5578-9
fatcat:suinh4xgevdjdlluvcmd64q4di
Smell Detection Agent Optimisation Framework and Systems Biology Approach to Detect Dys-Regulated Subnetwork in Cancer Data
2021
Biomolecules
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Then, a nature-inspired Smell Detection Agent (SDA) optimisation algorithm is designed with multiple agents traversing through various paths in the network. ...
Moreover, based on the weight values assigned to nodes in the subnetwork, PLK1, CTNNB1, IGF1, AURKA, PCNA, HSPA4 and GAPDH are proposed as drug targets for further studies. ...
Table 1 . 1 Comparing performance of the proposed algorithm and Artificial Bee Colony (ABC) algorithm. ...
doi:10.3390/biom12010037
pmid:35053185
pmcid:PMC8774275
fatcat:ycf4kepkcndutnr33mak5k4vre
Elephant Herding Optimization: Variants, Hybrids, and Applications
2020
Mathematics
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Elephant herding optimization (EHO) is a nature-inspired metaheuristic optimization algorithm based on the herding behavior of elephants. ...
A comprehensive review for the EHO-based algorithms and their applications are presented in this paper. ...
(MBO) [48] [49] [50] [51] [52] , artificial bee optimization (MBO) [48] [49] [50] [51] [52] , artificial bee colonies (ABCs) [53] , earthworm optimization algorithms (EWAs) [54] , ant colony optimization ...
doi:10.3390/math8091415
fatcat:ihbpefqhhnclxehnketfovfehm
Clustering of high throughput gene expression data
2012
Computers & Operations Research
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However, this paper presents a review of the current clustering algorithms designed especially for analyzing gene expression data. ...
Clustering is one of the methods used to gain insight into biological processes, particularly at the genomics level. Clearly, clustering can be used in many areas of biological data analysis. ...
[91] proposed an algorithm to find functional modules from large biological networks. The algorithm assigns nodes to the same cluster based on how they share common neighbors. ...
doi:10.1016/j.cor.2012.03.008
pmid:23144527
pmcid:PMC3491664
fatcat:zfc3l22vmvfvlphpqmoox5ka54
Scale invariance in natural and artificial collective systems: a review
2017
Journal of the Royal Society Interface
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If the degree of collective integration of a system does not depend on size, its level of robustness and adaptivity is typically increased and we refer to it as scale-invariant. ...
Self-organized collective coordinated behaviour is an impressive phenomenon, observed in a variety of natural and artificial systems, in which coherent global structures or dynamics emerge from local interactions ...
The authors thank Ozan Catal, Matthias Langhendries, Stiaan Uyttersprot and Wout Van Hauwermeiren for their efforts in discussing a subset of the presented works on a very early version of this review ...
doi:10.1098/rsif.2017.0662
pmid:29093130
pmcid:PMC5721168
fatcat:wotdj7ugh5ahth4hwlf47fqn4a
Multi-AUV collaborative operation based on time-varying navigation map and dynamic grid model
2020
IEEE Access
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evacuation in buildings based on improved artificial bee colony
2）. ...
The fusion of the two
method based on BISOM and VS algorithms. ...
doi:10.1109/access.2020.3020629
fatcat:okeqrfk6qvcczp3cfajb57uivm
Are There Biomimetic Lessons from Genetic Regulatory Networks for Developing a Lunar Industrial Ecology?
2021
Biomimetics
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We examine the prospect for employing a bio-inspired architecture for a lunar industrial ecology based on genetic regulatory networks. ...
The lunar industrial ecology resembles a metabolic system in that it comprises multiple chemical processes interlinked through waste recycling. ...
The expression dynamics of an artificial genome may be modelled graphically as a Boolean network encoded through promoters with evolution implemented through a genetic algorithm selecting according to ...
doi:10.3390/biomimetics6030050
fatcat:yglsxb2mzzc75bbiqlx2rlzkha
A Review of Mathematical and Computational Methods in Cancer Dynamics
[article]
2022
arXiv
pre-print
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Cancers are complex adaptive diseases regulated by the nonlinear feedback systems between genetic instabilities, environmental signals, cellular protein flows, and gene regulatory networks. ...
However, the time-series analysis of these complex networks remains vastly absent in cancer research. ...
Jacek Majewski of McGill University, for the knowledge he granted on glioma epigenetics and computational epigenetic modelling. ...
arXiv:2201.02055v5
fatcat:hxhvnvagcbdeldwsb3zet3wavu
Engineering, Technology & Applied Science Research (ETASR), Vol. 12, No. 1, pp. 7974-8227
2022
Zenodo
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ETASR is indexed in the Web of Science Core Collection (former Web of Science/Thomson Reuters Master Journal List), through the Emerging Sources Citation Index, is a Crossref member (DOI prefix: 10.48084 ...
The authors in [65] used the protein homology model along with 28 DL models and Reinforcement Learning (RL) techniques to evaluate drugs based on some predefined metrics. ...
Lympertos for providing background information regarding the available geospatial data of the power distribution network of Patras Area. ...
doi:10.5281/zenodo.6369694
fatcat:nvdnhvh53rcvhiic5lij7azjka
Poster Presentation
2022
Experimental animals
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…Contrary…to… my…expectations,…nine…mutants…were…fertile.… Mir465… cluster… is… one… of… HS… candidates.… Mir465… cluster… consist… of… Mir465a,… b-1,… c-1,… c-2,… and… d.… Recent… study… reported… next ...
…To…identify…the…causal…gene,…we…first…investigated… … As… a… result… of… PCR-based… genotyping… in… our… FVB/NJcl… colony,… all… the… affected… mice… were… homozygous… for… the… Slc7a9…mutant…allele,… ...
doi:10.1538/expanim.71suppl-p
pmid:35705295
pmcid:PMC9242873
fatcat:gunvhrcr4bemjl2bon3np2q3ky
SK3 Channel Overexpression in Mice Causes Hippocampal Shrinkage Associated with Cognitive Impairments
2016
Molecular Neurobiology
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this model system. ...
Based on the mRNA expansion profiles we observed, we predict that transgenic mice that overexpress the murine SK3 gene may represent a research model for neuropsychiatric disorders, even though the symptoms ...
Sabine Martin and Saju Balakrishnan were funded through the Cluster of Excellence and DFG Research Center Nanoscale Microscopy and Molecular Physiology of the Brain. ...
doi:10.1007/s12035-015-9680-6
pmid:26803493
pmcid:PMC5310555
fatcat:lyjjllxfjzc6nkni2fe4zf6h2y
IRCHLB-IV-Abstracts of Presentations at the 4th International Research Conference on Huanglongbing
2015
Journal of citrus pathology
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Then, these networks were partitioned into functional modules by the Markov Cluster Algorithm. 154 modules (38.8%) in these networks had some degree of Gene Ontology biological process enrichment, and ...
Through cluster analysis and spatial statistics, we have developed maps that organize plantings based on the spatial pattern and dynamics of ACP populations and HLB risk. ...
the vascular flow. ...
doi:10.5070/c421030222
fatcat:pk5cm3rzbzasracphhmg3qmaga
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