https://arxiv.org/abs/1906.02691
Kingma, D. P., & Welling, M. (2019). An introduction to variational autoencoders. Foundations and Trends® in Machine Learning, 12(4), 307–392. https://doi.org/10.1561/2200000056
Posts Tagged ‘from’
1906.02691 An Introduction to Variational Autoencoders
February 18, 2025Diffusion Tutorial
February 17, 2025some tutorials on diffusion models:
[An Arxiv Tutorial]
https://arxiv.org/pdf/2403.18103
[Some Useful Blogs]
https://baincapitalventures.notion.site/Diffusion-Without-Tears-14e1469584c180deb0a9ed9aa6ff7a4c https://yang-song.net/blog/2021/score/
https://lilianweng.github.io/posts/2021-07-11-diffusion-models/
Suffix Array and BWT Explaination
February 11, 2025The book with a nice explanation of suffix array and BWT is
Bioinformatics Algorithms: An Active Learning Approach by Phillip Compeau & Pavel Pevzner. https://www.bioinformaticsalgorithms.org/
Conformational sampling and interpolation using language-based protein folding neural networks
February 7, 2025latex to rtf
February 1, 2025Paper on human reads in microbiome data
January 25, 2025Interesting paper on how the incomplete human genome can cause privacy issues in analyzing metagenomic data.
https://www.nature.com/articles/s41467-025-56077-5
Genome-wide association studies | Nature Reviews Methods Primers
January 25, 2025g accounts for the cumulative effect of all other variants on the phenotype besides the effect of the specific variant being tested (SNP s).
Although theoretically we should consider the effect of g when testing for GWAS associations, in practice don’t think this happens in standard GWAS tools, such as PLINK and REGENIE (see below).
PLINK: https://www.cog-genomics.org/plink/2.0/assoc
REGENIE: https://www.nature.com/articles/s41588-021-00870-7#Sec10
https://www.nature.com/articles/s43586-021-00056-9
Bats surf storm fronts, and public perception of preprints | Science | AAAS
January 18, 2025https://www.science.org/content/podcast/bats-surf-storm-fronts-and-public-perception-preprints
https://www.library.ucsb.edu/what-white-house-open-access-publishing-guidance-means-uc-researchers
QT:{{”
JB: Yeah. Actually all of the US agencies that fund research and spend more than a certain level a year have required since the year 2013 that their grantees host the manuscripts resulting from this funded work in public repositories. Because the research was funded with taxpayers money and the public had a right to read the results. There was a compromise reached in that year where the grantees and their publishers could request an embargo on the public release of these scientific papers of up to 12 months. And this was requested by the publishers for business reasons that they did not want to kind of lose their exclusivity that they have by putting these articles at least initially behind a paywall. Now there’s a new policy that is being finalized as we speak and will be go into effect by the end of this calendar year.
….
0:13:49.9
JB: 2025. And it will require the immediate release in a federal public repository of articles that result from federal funding. So that’s a big change in US policy and one that’s causing some ripples. Researchers and their institutions and publishers are all looking at significant changes to make this happen and not everybody’s happy about it but it’s gonna have potentially a big effect because something like 9% of all of the world’s scientific papers are funded by the US government.
“}}
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