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Phylogenetic analysis using Machine learning (1)

The interpretation of the phylogenetic tree is an essential yet challenging aspect of evolutionary studies. To conduct an evolutionary study of the organisms is the core of biological research. The resulting phylogeny is then subjected to a plethora of analyses essential for further genomic research (Azouri 2021). The phylogenetic analysis involves several methods that can be used to interpret data. Recently, researchers have begun studying the use of machine learning in inferring phylogenetic trees.<br><br>Contact:<br>ud83cudf10: www.tutorsindia.com<br>ud83dudce7: info@tutorsindia.com<br>ud83dudcac(WA): 91-8754446690 <br>

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Phylogenetic analysis using Machine learning (1)

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  1. PHYLOGENETICANALYSIS USINGMACHINELEARNING AnAcademicpresentationby Dr.NancyAgnes,Head,TechnicalOperations,TutorsIndia Group www.tutorsindia.com Email:info@tutorsindia.com

  2. Today'sDiscussion OUTLINE Introduction PhylogeneticAnalysis Currently available methods for inference Applicationof machine learning Futurescope

  3. INTRODUCTION The interpretation of the phylogenetic tree is an essentialyetchallengingaspectofevolutionarystudies. Toconductanevolutionarystudyoftheorganismsisthe coreof biologicalresearch. Theresultingphylogenyisthensubjectedtoaplethoraof analyses essential for further genomic research (Azouri 2021). The phylogenetic analysisinvolves several methods thatcanbeusedtointerpretdata.Recently,researchers havebegunstudyingtheuseofmachinelearningin inferringphylogenetictrees. Contd...

  4. PHYLOGENETIC ANALYSIS The study of the evolutionary history of a species or a groupoforganismsisknownasphylogeneticanalysis. Here,theevolutionaryrelationshipbetweendifferent species or organisms having a common ancestor is representedwiththehelpofbranchingdiagrams. Thisdiagramiscalledthephylogenetictree,whichcanbe eitherrooted orunrooted. Phylogenetic analysis can also be used to study the relationshipbetweencharacteristicsofanorganism, includinggenesand proteins. Contd...

  5. Theapplicationsofphylogeneticanalysisarenumerous. These include – reconstruction of the ancestral gene for the derivation of extant genes,studyofhumandiseaseandepidemiology,interpretationoftheevolutionof ecological and behavioural traits, estimation of historical biogeographic relationships,and many more. InterestingBlog:PerformanceEvaluationMetricsforMachine-LearningBased Dissertation

  6. CURRENTLY AVAILABLE METHODSFOR INFERENCE Previously,morphologicalfeatureswereusedinthe assessment of similarities among species and in phylogeneticanalysis. It has drastically changed over time. Nowadays, this analysisusesinformationextractedfromDNA,RNAor protein. Thegenerationofaphylogenetictreeinvolvesthe alignmentof sequences. Themostwidely-usedtoolforthisisthealignment-based methodology. Contd...

  7. Inthismethod,thetwosequencesarestackedinawaytohighlighttheircommon symbolsand substrings. Thiscomparisonofsequenceshelpstoidentifypatternsofsharedancestrybetween species. (Munjal2019).However,exploitingtheselarge-scalemoleculardataposes significantchallenges. Oneofthemostdifficulttasksistodevelopeffectivetechniquesfortheextractionof missingdata. Contd...

  8. The Maximum likelihood or Markov Chain Monte Carlo (MCMC) methods and probabilisticmodelsofsequenceevolutionarehighlyreliablestatisticalmethodsused forthe reconstruction ofgene and speciestrees. Evenso,manyoftheseapproachesarenotscalableenoughtostudyphylogenomic datasetsof hundredsor thousands ofgenes and taxa. Thus,thedevelopmentofaquickandefficientmethodistheneedofthehour( Bhattacharjee2020).

  9. APPLICATIONOF MACHINE LEARNING Machinelearninghasfoundvariousapplicationsinthe fieldoftechnology-drivenresearch. Onesuchusageofmachinelearningisinthe inferenceofthephylogenetictree. Inarecentstudy,researchersutilizedthemachine learningmethodtopredictthebestmodelforthemost common prediction task: phylogenetic tree reconstruction for a given collection of sequences (Abadi2020). Contd...

  10. A research study gave a detailed analysis of plant diversity trends to date, demonstratingthatusingmachine learningtoforecastfuturediversitycouldbe tremendouslybeneficial. Theyappliedmachinelearningapproachestophylogeneticdiversityinvascularplants (Park2020). Bhattacharjee et al., fortheveryfirsttime,demonstratedthepotentialandfeasibilityofusingdeeplearning techniquesto compute distancematrices. Thestudyevaluatedbothmatrixfactorization(ME)andautoencoder(AE)andaimedto developimprovised models forbetter results. Contd...

  11. Theyshowedthatboththesemethodsarereliableandcanbeappliedforhandling large-scaledatasets. Theyalsohighlightedtheabilityofthesetechniquesovertheheuristic-based techniquestoautomaticallylearncomplicatedinter-variableassociations. Theirresearchcanalsobeusedasamodelforapplyingmachinelearningmethodsto thephylogenetic analysis (Bhattacharjee2020). Inanotherresearch,amachinelearningframeworkwasdevelopedtorankthe neighbouringtreesinaccordancewiththeirprosperitytoincreasethelikelihood. Contd...

  12. Theyappliedmultiplefeaturesandutilizedmachinelearningtoimproveanoptimal tool. The study suggested specific ways to practice machine learning algorithms in phylogeneticanalysis. Furthermore,theypresentedamethodologythatcansignificantlyspeeduptree- searchalgorithmswithoutsacrificingaccuracy(Azouri 2021). Arecentreviewfocusedontheapplicationofmachinelearning-basedtechniquesin thedata analysis ofthe human microbiome. Itprovidedaninsightintotheplethoraofadvantagesthatmachinelearninghasto offerover classical methods. Contd...

  13. ThemostcommontechniquescoveredinthisreviewinvolvedSupportVector Machines,RandomForest, k-NNand LogisticRegression. This review suggested how machine learning can contribute to the development of newmodelsthatcanbeusefulinpredictingclassificationsinthefieldofmicrobiology, inferring host phenotypes to predict diseases and characterization of state-specific microbialsignaturesusing microbialcommunities(Macros 2021). Contd...

  14. Contd...

  15. FUTURESCOPE Machinelearninghasfoundvariousapplicationsinthe fieldoftechnology-driven research. Onesuchusageofmachinelearningisinthe inferenceofthephylogenetictree. Inarecentstudy,researchersutilizedthemachine learningmethodtopredictthebestmodelforthemost common prediction task: phylogenetic tree reconstruction for a given collection of sequences (Abadi2020).Future scope Contd...

  16. Contd...

  17. CONTACTUS UNITEDKINGDOM +44-1143520021 INDIA +91-4448137070 EMAIL info@tutorsindia.com

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