Andrew Kern
@pastramimachine
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Evolution, population genetics, machine learning. rhythm section.
Eugene, Oregon
Joined December 2011
unit tests take all the freedom out of programming. feels un-american.
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One thing that rules about academia is you can go with your lab up a rather insane mountain and no one blinks an eye.
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RT @stoolpresidente: Top 1 American moment when Joey Chestnut beat up a protestor mid hot dog eating contest.
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only one thing could make driving in Boston worse.
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Okay i'm not going to show all the results in this thread-- go read the paper! . What I will say is this is very exciting to me, and I think the first use of a LLM framework specifically for population genetics.
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5) because of the generative nature of cxt, we can do multiple decoding passes and treat those passes as an approximate posterior sample. Incredibly such samples are quite well calibrated, meaning we can rapidly get a sense of uncertainty
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4) cxt, because it is a deep language model, has the capacity to be trained on huge corpus. we decided to train it on the entire v0.2 stdpopsim catalog-- it does really well
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@KevinKorfmann 3) our method -- that we call cxt -- is highly accurate. in benchmark comparisons against Singer and gamma-SMC, cxt looks very good
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@KevinKorfmann 2) the model is small (for a language model) -- 10-20M parameters -- so it trains in minutes or hours, not days. and prediction is blazing fast (decoding human chroms in minutes).
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@KevinKorfmann there are a few things to highlight: . 1) we perform generative training using the task of 'next coalescence prediction' where the model is asked to predict the next time moving across a chromosome. this is akin to next token prediction in natural language
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Really excited about our lab's latest paper led by @KevinKorfmann. Here, Kevin has developed a deep, transformer-based language model for population genetics for inferring coalescent times (times of common ancestry) along recombining chromosomes.
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"AI is crap" i whisper to myself as i scrape the wrong code block from stackoverflow.
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AI agents at the command line make me so pumped for a future with robots at home.
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RT @leo_speidel: Postdoc position in my group in Tokyo! .Please get in touch if you are interested. And happy to discuss projects - rang….
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Any plant pathologists who can diagnose what happened to this dahlia?
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RT @robertsietsema: Here's my idea of the five best pastrami sandwiches in NYC in Monday's free Substack [link in first comment] https://t.….
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