week 8. homework 7 2 state hmm state 1: neutral state 2: conserved emissions: alignment columns ...
DESCRIPTION
Homework 7 tips Do just one Viterbi parse (no training). Ambiguous bases have been changed to "A". Make sure you look up hg18 positions. AATAAT 1 2 A-AA-A 1 2 CCCCCC human dog mouseTRANSCRIPT
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Week 8
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Homework 7• 2 state HMM– State 1: neutral– State 2: conserved
• Emissions: alignment columns – Alignment of human, dog, mouse sequences
AAT
1
2
A-A
1
2
CCC
1
2
0
humandogmouse
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Homework 7 tips• Do just one Viterbi parse (no training).• Ambiguous bases have been changed to "A".• Make sure you look up hg18 positions.
AAT
1
2
A-A
1
2
CCC
1
2
0
humandogmouse
![Page 4: Week 8. Homework 7 2 state HMM State 1: neutral State 2: conserved Emissions: alignment columns Alignment of human, dog, mouse sequences AATAAT](https://reader035.vdocuments.us/reader035/viewer/2022062600/5a4d1b8c7f8b9ab0599bf2d3/html5/thumbnails/4.jpg)
Homework 8• Use logistic regression to predict gene
expression using genomics assays in GM12878.• Train using gradient descent.• Label: CAGE gene expression --
"expressed"/"non-expressed"• Features: Histone modifications and DNA
accessibility.
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Homework 8 backstory
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Homework 8 backstory
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Homework 8 backstory
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Model complexity: interpretation and generalization
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Two goals for machine learning: prediction or interpretation
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Generative methods model the joint distribution of features and labels
A G A C A A G G
Translation start sites:
Background:
Generative models are usually more interpretable.
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Generative methods model the conditional distribution of the label given the features.
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Discriminative models are more data-efficient
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Simpler models generalize better and are more interpretable
Simple models have "strong inductive bias"
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Regularization decreases the complexity of a model
L2 regression improves the generalizability of a model:
L1 regression improves the interpretability of a model:
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L2 regularization
True
True+noise
lambda=8
lambda=3
lambda=1
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L2 regularization
True
True+noise
lambda=10
lambda=7
lambda=4
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L1 regularization
True
True+noise
lambda=10
lambda=8
lambda=5