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Deep Learning in Bioinformatics Artem Bachynskyi 02.12.2016

Deep Learning in BioinformaticsProtein structure prediction: • 1-dimensional structural properties • contactmap • structure modelquality assessment Gene expressionregulation:

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Page 1: Deep Learning in BioinformaticsProtein structure prediction: • 1-dimensional structural properties • contactmap • structure modelquality assessment Gene expressionregulation:

DeepLearninginBioinformatics

Artem Bachynskyi02.12.2016

Page 2: Deep Learning in BioinformaticsProtein structure prediction: • 1-dimensional structural properties • contactmap • structure modelquality assessment Gene expressionregulation:
Page 3: Deep Learning in BioinformaticsProtein structure prediction: • 1-dimensional structural properties • contactmap • structure modelquality assessment Gene expressionregulation:

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OrdinaryNNvsConvolutionalNN

Source:http://cs231n.github.io/convolutional-networks/

Page 4: Deep Learning in BioinformaticsProtein structure prediction: • 1-dimensional structural properties • contactmap • structure modelquality assessment Gene expressionregulation:

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Convolutionprocedure

Source:https://ujjwalkarn.me/2016/08/11/intuitive-explanation-convnets/

Page 5: Deep Learning in BioinformaticsProtein structure prediction: • 1-dimensional structural properties • contactmap • structure modelquality assessment Gene expressionregulation:

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Pullingprocedure

Source:http://cs231n.stanford.edu/slides/winter1516_lecture1.pdf

Page 6: Deep Learning in BioinformaticsProtein structure prediction: • 1-dimensional structural properties • contactmap • structure modelquality assessment Gene expressionregulation:

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Source:http://cs231n.github.io/convolutional-networks/

Page 7: Deep Learning in BioinformaticsProtein structure prediction: • 1-dimensional structural properties • contactmap • structure modelquality assessment Gene expressionregulation:

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FirstsuccessfulapplicationofCNN

Source:http://cs231n.stanford.edu/slides/winter1516_lecture1.pdf

Page 8: Deep Learning in BioinformaticsProtein structure prediction: • 1-dimensional structural properties • contactmap • structure modelquality assessment Gene expressionregulation:

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Stateoftheartmodel

Source:http://cs231n.stanford.edu/slides/winter1516_lecture1.pdf

Page 9: Deep Learning in BioinformaticsProtein structure prediction: • 1-dimensional structural properties • contactmap • structure modelquality assessment Gene expressionregulation:

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DNNbyGoogle

Page 10: Deep Learning in BioinformaticsProtein structure prediction: • 1-dimensional structural properties • contactmap • structure modelquality assessment Gene expressionregulation:

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RecurrentNN

Page 11: Deep Learning in BioinformaticsProtein structure prediction: • 1-dimensional structural properties • contactmap • structure modelquality assessment Gene expressionregulation:

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Genetic dataInputdata

1. sequencingdata(DNA-seq,RNA-seq,ChIP-seq,DNase-seq)

2. featuresfromgenomicsequence:• positionspecificscoringmatrix(PSSM)• physicochemicalproperties(stericparameter,

volume)• Atchley factors(FAC)• 1-dimensionalstructuralproperties

3. contactmap(distanceofaminoacidpairsin3Dstructure)

4. microarraygeneexpression

Results

Protein structure prediction:• 1-dimensional structural properties• contact map• structure model quality assessment

Gene expression regulation:• splice junction• genetic variants affecting splicing• sequence specificity

Protein classification:• super family• subcellular localization

Anomaly classification:• cancer

Page 12: Deep Learning in BioinformaticsProtein structure prediction: • 1-dimensional structural properties • contactmap • structure modelquality assessment Gene expressionregulation:

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A

B

Source:http://www.nature.com/nbt/journal/v33/n8/fig_tab/nbt.3300_F2.html

scoretheeffectofnovelmutation

identifybinding

Page 13: Deep Learning in BioinformaticsProtein structure prediction: • 1-dimensional structural properties • contactmap • structure modelquality assessment Gene expressionregulation:

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Biomedical imagingInputdata

• magneticresonanceimage(MRI)

• radiographicimagepositronemissiontomography(PET)

• histopathology image

• volumetricelectronmicroscopyimage

• retinalimage

• insituhybridization(ISH)image

• X-rayimages

Results

Anomalyclassification• geneexpressionpattern• cancer• Alzheimer'sdisease• Schizophrenia

Segmentation• cellstructure• neuronalstructure• vesselmap• braintumor

Recognition• cellnuclei• fingerjoint• anatomicalstructure

Braindecoding• behavior

Page 14: Deep Learning in BioinformaticsProtein structure prediction: • 1-dimensional structural properties • contactmap • structure modelquality assessment Gene expressionregulation:

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Source:https://pdfs.semanticscholar.org/b8e6/6cb1544e5bb53400ad6c3a2a4c3748b118b5.pdf

Page 15: Deep Learning in BioinformaticsProtein structure prediction: • 1-dimensional structural properties • contactmap • structure modelquality assessment Gene expressionregulation:

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BiomedicalsignalprocessingInputdata

ECoG, ECG, EMG, EOG

EEG:• raw• wavelet• frequency• differential entropy

extracted features from EEG:• normalized decay• peak variation

Results

Brain decoding• behavior• emotion

Anomaly classification• Alzheimer's disease• seizure• sleep stage

Page 16: Deep Learning in BioinformaticsProtein structure prediction: • 1-dimensional structural properties • contactmap • structure modelquality assessment Gene expressionregulation:

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Source:https://pdfs.semanticscholar.org/b8e6/6cb1544e5bb53400ad6c3a2a4c3748b118b5.pdf

Page 17: Deep Learning in BioinformaticsProtein structure prediction: • 1-dimensional structural properties • contactmap • structure modelquality assessment Gene expressionregulation:

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HeartdiseasedetectionusingCNN

ECG ECGwavelets CNN

DiseasePrediction

Page 18: Deep Learning in BioinformaticsProtein structure prediction: • 1-dimensional structural properties • contactmap • structure modelquality assessment Gene expressionregulation:

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Kaggle competition

CNN

Predictionofdiseasestage

Page 19: Deep Learning in BioinformaticsProtein structure prediction: • 1-dimensional structural properties • contactmap • structure modelquality assessment Gene expressionregulation:

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Page 20: Deep Learning in BioinformaticsProtein structure prediction: • 1-dimensional structural properties • contactmap • structure modelquality assessment Gene expressionregulation:

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[email protected],10:00am

Page 21: Deep Learning in BioinformaticsProtein structure prediction: • 1-dimensional structural properties • contactmap • structure modelquality assessment Gene expressionregulation:

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Homework1. VisitthisonlineCNNplatform:http://cs.stanford.edu/people/karpathy/convnetjs/demo/mnist.html2. Byvariating learning rate,momentum, batchsize,weightdecay,trytoachieve0.96accuracy.3. Provideascreenshotofyourresult,please.4. Afterreaching0.96accuracy,press“pause”buttonandscrolldownto“ExamplepredictionsonTestset”,report2-3worstpredictedexamples(withscreenshots).

Additionally, youcanmodifynetworkbychanging JSONfile.

Page 22: Deep Learning in BioinformaticsProtein structure prediction: • 1-dimensional structural properties • contactmap • structure modelquality assessment Gene expressionregulation:

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