Hanbin Lee
@epigenci.bsky.social
PhD Student at UMich Statistics.
The account mostly trashes about urban planning and infrastructure.
Probability, Statistics, and Evolutionary Biology.
https://hanbin973.github.io
The account mostly trashes about urban planning and infrastructure.
Probability, Statistics, and Evolutionary Biology.
https://hanbin973.github.io
Pinned
Hanbin Lee
@epigenci.bsky.social
· Jul 19
Modelling complex traits with ancestral recombination graphs https://www.biorxiv.org/content/10.1101/2025.07.14.664631v1
My talk from this year's probgen is finally out.
Where do linear mixed models and random effects come from?
They emerge from *mutations* on Ancestral Recombination Graphs.
Where do linear mixed models and random effects come from?
They emerge from *mutations* on Ancestral Recombination Graphs.
The department coffee often tastes like sesame oil so I searched how close are the two plant species. Not even remotely close.
November 25, 2025 at 7:51 PM
The department coffee often tastes like sesame oil so I searched how close are the two plant species. Not even remotely close.
Doing all these intrinsic calculations feels like being disguised by some evil will.
November 25, 2025 at 6:47 PM
Doing all these intrinsic calculations feels like being disguised by some evil will.
www.biorxiv.org
November 25, 2025 at 3:38 PM
Reposted by Hanbin Lee
Unrelated to mim itself, but this is also the first preprint I've prepared in @typst.app rather than LaTeX. It was soooo much nicer. Folks; what are we doing? Why don't our journals accept manuscript sources in Typst!
Ok; mim (github.com/COMBINE-lab/...) preprint submitted! Excited for folks to see it and share thoughts. The key takeaway; mim allows the quick, one-time, building of a small auxiliary index that then allows scaling gzipped FASTQ parsing linearly in # of threads. 1/2
GitHub - COMBINE-lab/mim: A small, auxiliary index to massively improve parallel fastq parsing
A small, auxiliary index to massively improve parallel fastq parsing - COMBINE-lab/mim
github.com
November 25, 2025 at 2:38 PM
Unrelated to mim itself, but this is also the first preprint I've prepared in @typst.app rather than LaTeX. It was soooo much nicer. Folks; what are we doing? Why don't our journals accept manuscript sources in Typst!
Reposted by Hanbin Lee
Reposted by Hanbin Lee
There is beauty everywhere but especially in autumn in Philadelphia! 😻
November 24, 2025 at 5:32 PM
There is beauty everywhere but especially in autumn in Philadelphia! 😻
Pre-thanksgiving HW sets are a disaster.
November 24, 2025 at 9:36 PM
Pre-thanksgiving HW sets are a disaster.
Reposted by Hanbin Lee
"If you have to explain your sexuality when someone asks if you're dating anyone, you're queer."
February 4, 2024 at 7:15 PM
"If you have to explain your sexuality when someone asks if you're dating anyone, you're queer."
Reposted by Hanbin Lee
“queer not as being about who you’re having sex with (that can be a dimension of it); but queer as being about the self that is at odds with everything around it and has to invent and create and find a place to speak and to thrive and to live.” -bell hooks
February 3, 2024 at 3:21 PM
“queer not as being about who you’re having sex with (that can be a dimension of it); but queer as being about the self that is at odds with everything around it and has to invent and create and find a place to speak and to thrive and to live.” -bell hooks
The causal viewpoint is of course important, but the underlying population genetic setting has to be addressed in advance as it accounts for the ideal setting without causal complications.
1/n
1/n
I didn’t inhibit my argueing muscle enough. this is actually the right take, it’s eventually a case of “what’s your estimand?”. And it’s all observational, though it needs rigorous models before you can get to an answer (which can be, “these aren’t comparable ever”)
SNP h2 is not even h2 and even with we assume all these to be true, it all breaks up when there's selection and drift.
November 24, 2025 at 3:01 PM
The causal viewpoint is of course important, but the underlying population genetic setting has to be addressed in advance as it accounts for the ideal setting without causal complications.
1/n
1/n
Also, SNP heritability being similar across populations isn't even independent evidence because majority of common SNPs driving most of the signal are shared, thereby creating pseudoreplication.
November 24, 2025 at 2:01 AM
Also, SNP heritability being similar across populations isn't even independent evidence because majority of common SNPs driving most of the signal are shared, thereby creating pseudoreplication.
This is so funny.
November 23, 2025 at 8:31 PM
This is so funny.
I just keep reading this piece over and over again and...
arxiv.org/abs/1808.07717
arxiv.org/abs/1808.07717
Multiple Sequence Alignment is not a Solved Problem
Multiple sequence alignment is a basic procedure in molecular biology, and it is often treated as being essentially a solved computational problem. However, this is not so, and here I review the evide...
arxiv.org
November 23, 2025 at 6:09 PM
I just keep reading this piece over and over again and...
arxiv.org/abs/1808.07717
arxiv.org/abs/1808.07717
The wording is absolutely great.
WELKER: What is your message to Jewish New Yorkers who feel you won't be tough enough in your response to antisemitism?
MAMDANI: That I am looking forward to being the next mayor and fulfilling the commitment I've made to Jewish New Yorkers to not only protect them but to celebrate and cherish them
MAMDANI: That I am looking forward to being the next mayor and fulfilling the commitment I've made to Jewish New Yorkers to not only protect them but to celebrate and cherish them
November 23, 2025 at 5:51 PM
The wording is absolutely great.
I attended David Reich's talk this week and was genuinely surprised how good he is in describing demographic inference in plain language without any jargon.
November 23, 2025 at 5:01 PM
I attended David Reich's talk this week and was genuinely surprised how good he is in describing demographic inference in plain language without any jargon.
SNP h2 is not even h2 and even with we assume all these to be true, it all breaks up when there's selection and drift.
November 23, 2025 at 2:47 PM
SNP h2 is not even h2 and even with we assume all these to be true, it all breaks up when there's selection and drift.
Reposted by Hanbin Lee
How to Reproduce this Book Exactly with LaTeX - great resource for writing Latex #linkoftheday
github.com/BenjaminGor/...
github.com/BenjaminGor/...
GitHub - BenjaminGor/Latex_Notes_Tutorial: Latex Book/Note Writing Tutorial
Latex Book/Note Writing Tutorial. Contribute to BenjaminGor/Latex_Notes_Tutorial development by creating an account on GitHub.
github.com
November 22, 2025 at 5:58 PM
How to Reproduce this Book Exactly with LaTeX - great resource for writing Latex #linkoftheday
github.com/BenjaminGor/...
github.com/BenjaminGor/...
Reposted by Hanbin Lee
Simulation-based inference (SBI) has transformed parameter inference across a wide range of domains. To help practitioners get started and make the most of these methods, we joined forces with researchers from many institutions and wrote a practical guide to SBI.
📄 Paper: arxiv.org/abs/2508.12939
📄 Paper: arxiv.org/abs/2508.12939
Simulation-Based Inference: A Practical Guide
A central challenge in many areas of science and engineering is to identify model parameters that are consistent with prior knowledge and empirical data. Bayesian inference offers a principled framewo...
arxiv.org
November 21, 2025 at 3:08 PM
Simulation-based inference (SBI) has transformed parameter inference across a wide range of domains. To help practitioners get started and make the most of these methods, we joined forces with researchers from many institutions and wrote a practical guide to SBI.
📄 Paper: arxiv.org/abs/2508.12939
📄 Paper: arxiv.org/abs/2508.12939
Just learned that a famous causal inference guy is on Jeffrey's mail lol
November 21, 2025 at 1:17 PM
Just learned that a famous causal inference guy is on Jeffrey's mail lol
well.. vibe coding does work with some skills...?
November 21, 2025 at 1:27 AM
well.. vibe coding does work with some skills...?
Perhaps I'm too much of a old-fashioned person, but I hate all these new classroom formats and love the instructor just going straight in one-direction with few questions from students if needed.
November 20, 2025 at 4:34 PM
Perhaps I'm too much of a old-fashioned person, but I hate all these new classroom formats and love the instructor just going straight in one-direction with few questions from students if needed.
Am I the only person to read teaspoon as teasposons 😂😂
70 teaspoons placed in tearooms around the institute & observed weekly over 5 months. 80% of spoons disappeared; spoon halflife~81 days. Communal room halflife lower than in specific labs. 250 spoons annually required to maintain 70 spoon population.
pmc.ncbi.nlm.nih.gov/articles/PMC...
pmc.ncbi.nlm.nih.gov/articles/PMC...
The case of the disappearing teaspoons: longitudinal cohort study of the displacement of teaspoons in an Australian research institute
Objectives To determine the overall rate of loss of workplace teaspoons and whether attrition and displacement are correlated with the relative value of the teaspoons or type of tearoom. Design Longitudinal cohort study. Setting Research institute ...
pmc.ncbi.nlm.nih.gov
November 20, 2025 at 2:26 PM
Am I the only person to read teaspoon as teasposons 😂😂
Reposted by Hanbin Lee
70 teaspoons placed in tearooms around the institute & observed weekly over 5 months. 80% of spoons disappeared; spoon halflife~81 days. Communal room halflife lower than in specific labs. 250 spoons annually required to maintain 70 spoon population.
pmc.ncbi.nlm.nih.gov/articles/PMC...
pmc.ncbi.nlm.nih.gov/articles/PMC...
The case of the disappearing teaspoons: longitudinal cohort study of the displacement of teaspoons in an Australian research institute
Objectives To determine the overall rate of loss of workplace teaspoons and whether attrition and displacement are correlated with the relative value of the teaspoons or type of tearoom. Design Longitudinal cohort study. Setting Research institute ...
pmc.ncbi.nlm.nih.gov
November 20, 2025 at 3:44 AM
70 teaspoons placed in tearooms around the institute & observed weekly over 5 months. 80% of spoons disappeared; spoon halflife~81 days. Communal room halflife lower than in specific labs. 250 spoons annually required to maintain 70 spoon population.
pmc.ncbi.nlm.nih.gov/articles/PMC...
pmc.ncbi.nlm.nih.gov/articles/PMC...