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Hanbin Lee

@epigenci.bsky.social

690 followers 2.1K following 490 posts

PhD Student at UMich Statistics. The account mostly trashes about urban planning and infrastructure. Probability, Statistics, and Evolutionary Biology. https://hanbin973.github.io

hanbin973.github.io

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Hanbin Lee @epigenci.bsky.social · Jul 19

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.

bioRxiv Genomics @biorxiv-genomic.bsky.social · Jul 18

Modelling complex traits with ancestral recombination graphs https://www.biorxiv.org/content/10.1101/2025.07.14.664631v1

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Reposted by Hanbin Lee

April Wei @aprilwei.bsky.social · 4h

Method works from simple and complex scenarios in jointly estimating epoch time, population size, migration rate (symmetric or asymmetric), growth rate, and admixture proportion. Software integrated with msprime, demes, tsinfer/tsdate, relate, and singer. github.com/aprilweilab/...

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Reposted by Hanbin Lee

April Wei @aprilwei.bsky.social · 4h

Excited to preprint our latest work (w/ Drew DeHaas, Zhibai Jia, Leo Speidel) on using ARGs for demographic inference. w/ applications using data from 1000 Genomes Project. www.biorxiv.org/content/10.1...

Inference of complex demographic history using composite likelihood based on whole-genome genealogies

Accurate parametric inference on complex demographic models is a continuing challenge in population genetics. Ancestral recombination graphs (ARGs) provide richer information than simple population ge...

www.biorxiv.org

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Hanbin Lee @epigenci.bsky.social · 2d

github.com/jax-ml/jax/i... lol

JAX and TORCH · Issue #18032 · jax-ml/jax

Description When I only pip the latesd jax with cuda(pip install --upgrade "jax[cuda12_pip]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html), I can use the jax with gpu.But w...

github.com

Reposted by Hanbin Lee

Janne Pott @pottj.bsky.social · 2d

📣Preprint alert - a tricky one, as there are no significant results (and we all know null-results are hard to publish)
Do PCSK9 levels affect survival in breast cancer patients?
We tried to replicate findings in cell lines and mouse model using 3 Mendelian Randomization approaches, but failed.

medRxivpreprint @medrxivpreprint.bsky.social · 2d

PCSK9 and breast cancer survival: a Mendelian Randomization study https://www.medrxiv.org/content/10.1101/2025.10.03.25337270v1

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Hanbin Lee @epigenci.bsky.social · 2d

the biggest mystery of this school's computing cluster is that a more recent GPU has a shorter queue than the older one. People must be stuck at their default config script and never change it.

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Hanbin Lee @epigenci.bsky.social · 2d

downtown detroit got really nice over the past year

and AA is so damn overpriced.

Hanbin Lee @epigenci.bsky.social · 2d

genuinely considering moving to detroit after getting candidacy and only going to work 3 days a week

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Hanbin Lee @epigenci.bsky.social · 2d

midwest weather is so *hot* these days

Hanbin Lee @epigenci.bsky.social · 2d

cs.rice.edu/~ogilvie/com...

Likelihood of a tree

The likelihood of a tree is the probability of a multiple sequence alignment or matrix of trait states (commonly known as a character matrix) given a tree topology, branch lengths and substitution mod...

cs.rice.edu

Hanbin Lee @epigenci.bsky.social · 2d

tskit.dev/tskit/docs/s...

Python API — Tskit manual

tskit.dev

Hanbin Lee @epigenci.bsky.social · 3d

but don't math programs occasionally do this? they are generally small and funding is driven by undergrad teaching. Some including Cornell have done the same after Covid cus of graduation backlog.

Drug Monkey @drugmonkey.bsky.social · 4d

Another pause in graduate school admissions for 2026.
UCSD dept of math this time.

www.math.ucsd.edu/students/gra...

UCSD’s Department of Mathematics has paused PhD admissions -- we will not be able to admit new PhD students in Fall 2026.

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Hanbin Lee @epigenci.bsky.social · 3d

I looked up major road projects here and, of course, they look much better than rail counterparts, but the cost and the delays do look dire.

Hanbin Lee @epigenci.bsky.social · 4d

External validity is fundamentally a mechanistic component that statistics alone can never address.

Hanbin Lee @epigenci.bsky.social · 4d

I personally don't see big differences between attitudes towards RCTs and large language models.

Hanbin Lee @epigenci.bsky.social · 4d

Wouldn't manifold learning be easier if we restrict the function class to be factorable with respect to a quotient map?

Hanbin Lee @epigenci.bsky.social · 4d

Also, many drugs are tested on a very specific set of conditions specified in the eligibility criteria. Unfortunately, people seems to think these attributes as a global property of RCTs.

Hanbin Lee @epigenci.bsky.social · 4d

I think the idea implicitly hinges on the assumption that pharmaceutical interventions have a certain notion of *stable* treatment effect due to humans sharing a common biochemical/physiological mechanism.

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Hanbin Lee @epigenci.bsky.social · 4d

I just learned that \mathbb{CP} = \mathbb{C}\mathbb{P} and is turely mind blowing. How many \mathbb{} have been wasted for not knowing this so far?

Reposted by Hanbin Lee

Felicity Hannah @felicityhannah.bsky.social · 5d

This article manages to name her husband before it names… her.

Article reads:
Woman named as Archbishop of Canterbury in historic first

The 63-year-old archbishop-designate is married to Eamonn Mullally, with whom she has two children. Originally from Woking in Surrey, she was the UK's chief nursing officer from 1999 to 2004.

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Reposted by Hanbin Lee

Ana Ignatieva @anaignatieva.bsky.social · 5d

Delighted that our paper about the distribution of genomic spans of clades/edges in genealogies (ARGs), and using this for detecting inversions and other SVs (and other phenomena that cause local disruption of recombination) is out in MBE academic.oup.com/mbe/article/... (1/n)

The Length of Haplotype Blocks and Signals of Structural Variation in Reconstructed Genealogies

Abstract. Recent breakthroughs have enabled the accurate inference of large-scale genealogies. Through modelling the impact of recombination on the correla

academic.oup.com

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Hanbin Lee @epigenci.bsky.social · 5d

I was only aware of the two incidences in Bohemia but even more excited to learn that it dates far back to Rome. Wikipedia says that the term was coined after the event that sparked the 30 years war.

Hanbin Lee @epigenci.bsky.social · 5d

I'm always fascinated by the fact that there's a special word which means to throw a person out of a window.

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Reposted by Hanbin Lee

Patrick Dunleavy @patrickdunleavy.bsky.social · 6d

Elite school students end up in better universities than expected, based on their grades blogs.lse.ac.uk/politicsandp...

Elite school students end up in better universities than expected, based on their grades | British Politics and Policy at LSE

Students of private and grammar schools are over-represented in elite universities, but only part of that is explained by better grades.

blogs.lse.ac.uk

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Hanbin Lee @epigenci.bsky.social · 6d

but kinda surprising that a whole-nation level bailout costs less than simply building a fucking rail track in California.

Reposted by Hanbin Lee

Andrii Tarieiev @andriitarieiev.bsky.social · 6d

Jane Goodall died. Such news always sad but at least she left a huge legacy, lived a long life and had the possibility to stay in science for over 60 years. www.theguardian.com/science/2025...

Jane Goodall, world-renowned primatologist, dies aged 91

Jane Goodall Institute says ‘tireless advocate’ for natural world died in California during US speaking tour

www.theguardian.com

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