Expectation Maximization
Proof of the EM algorithm
- bioinformatics 26
- math 8
- python 5
- mathematics 5
- machine-learning 3
- clustering 3
- mitochondria 2
- music 1
- rna-seq 1
- bayesian 1
- tsne 1
bioinformatics
Counting Haplotypes using Expectation Maximzation
notes on the 1995 paper by Excoffier and Slatkin
Estimating genotypes and testing HWE from sequences
Continuing discussion of the Li paper Inference using sequencing data…
Genotyping from sequence data
Reading H. Li, Inference using sequencing data… Bioinformatics 2011.
Samtools and Pysam
Reconciling output from samtools mpileup and pysam mpileup
The mem in bwa and what it means
MEM means Maximal Exact Match – and it can trip you up.
More mitochondrial links
References to look into later
Mitochondria
Scattered info on the mitochondrial genome
Some fundamental terminology on time series
Stationarity, autocorrelation, ergodicity, …
Computing Autocorrelation
Computing autocorrelation of long sequences
Amplification Bias - 2
See Calibrating genomic and allelic coverage… by Zhang, et. al.
Amplification Bias
See Calibrating genomic and allelic coverage… by Zhang, et. al.
Notes on sequencing files
Some details on SAM/BAM files and related topics
PdfPages builds a pdf document from matplotlib figures
How to combine matplotlib plots into a pdf document
Python normalizations of Gamma-Poisson and Negative Binomial Distributions
keeping the parameters straight
Bayesian Online Changepoint Detection
Notes on the Adams-MacKay algorithm
FPKM and TPM Units for RNA Seq after Pachter
Pachter explains units of expression
A few references for today
A few interesting links that showed up today
CBS on real data
An example of cbs on real data
Circular Binary Segmentation
A look at the Circular Binary Segmentation algorithm
GC Bias correction in ginkgo and cnvkit
Comparison of GC bias correction in ginkgo and cnvkit
ENCODE mappability tracks
ENCODE mappability tracks
Mapping to bins for cnvkit
cnvkit uses samtools bedcov for mapping
Binning in CNVkit
How bins are constructed in CNVkit
Binning And Mapping In Gingko Fixed
Binning and mapping reads in Ginkgo
Ginkgo and CNVkit
Notes on ginkgo and cnvkit
math
Polya’s Urn
an app that simulates Polya’s Urn
deFinetti’s Theorem Part II
some links to follow up results on deFinetti’s Theorem
deFinetti’s Theorem
some notes on deFinetti’s Theorem and related topics
tSNE animation
animation of tsne on 2500 MNIST digits
Expectation Maximization
Proof of the EM algorithm
Counting Haplotypes using Expectation Maximzation
notes on the 1995 paper by Excoffier and Slatkin
Wold’s Decomposition
Notes on Wold’s decomposition
Math Test
As the following beautiful equation shows, I can now render TeX in this site:
python
Check of automatic differentiation
code that verifies that pytorch automatically computed gradient from KL divergence agrees with the formula in the tSNE paper.
Samtools and Pysam
Reconciling output from samtools mpileup and pysam mpileup
PdfPages builds a pdf document from matplotlib figures
How to combine matplotlib plots into a pdf document
Python normalizations of Gamma-Poisson and Negative Binomial Distributions
keeping the parameters straight
A few references for today
A few interesting links that showed up today
mathematics
ICERM workshop on scientific machine learning
Some highlights from the workshop 1/28/2019-1/30/2019
Enumerating Trees
Ordered trees and Catalan Numbers
Remarks on the Marchenko-Pastur Distribution
Some remarks on the moments of the Marchenko-Pastur distribution
The Wigner Distribution for a Random Symmetric Matrix
a picture of the wigner semi-circle distribution
Python normalizations of Gamma-Poisson and Negative Binomial Distributions
keeping the parameters straight
machine-learning
Check of automatic differentiation
code that verifies that pytorch automatically computed gradient from KL divergence agrees with the formula in the tSNE paper.
ICERM workshop on scientific machine learning
Some highlights from the workshop 1/28/2019-1/30/2019
A few references for today
A few interesting links that showed up today
clustering
Gaussian Mixture in Stan
Fitting a gaussian mixture in Stan
Carlsson-Memoli on Hierarchical Clustering
Carlsson and Memoli show that single-linkage hierarchical clustering has good properties (and other types do not)
Kleinberg’s Impossibility Theorem for Clustering
Kleinberg shows that it’s impossible to find a clustering algorithm that satisfies three simple properties.
mitochondria
More mitochondrial links
References to look into later
Mitochondria
Scattered info on the mitochondrial genome
music
Rainy Sunday Playlist Fixed
A playlist for a rainy Sunday
rna-seq
FPKM and TPM Units for RNA Seq after Pachter
Pachter explains units of expression
bayesian
Bayesian Online Changepoint Detection
Notes on the Adams-MacKay algorithm
tsne
Vantage Point Trees
A discussion and implementation of “vantage point trees”