Jamesb

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Jamesb

Jamesb

@experilearning

biocompute

London, UK Katılım Ekim 2020
475 Takip Edilen3.3K Takipçiler
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Jamesb
Jamesb@experilearning·
Left my job to focus 100% on math, CS and ML for a while. Haven't got a precise end goal in mind at the moment but I think something will emerge. Here's the stuff I am learning, learning process, etc: 1/n
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Seth Howes
Seth Howes@SethSHowes·
I’ve wanted to do this for a decade. But I never did - I refuse to give any company my DNA. It is me. So this week I sequenced my genome entirely at home. Literally on my kitchen table. I never exposed my DNA sequence to the internet. Not at any point. I used a MinION to do the sequencing (it’s smaller + weighs less than an iPhone). I used open-source DNA models for the analysis (Evo2 and AlphaGenome) running locally on a DGX Spark and Mac Studio. I traced mechanisms behind my family’s multigenerational autoimmune conditions that no clinician has been able to understand. When I set out to do this I didn’t know if it would actually work. It does. Your genome is the most private data you will ever have. You probably shouldn’t let it leave your house.
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Patrick Collison@patrickc

I'm lucky enough to have a great doctor and access to excellent Bay Area medical care. I've taken lots of standard screening tests over the years and have tried lots of "health tech" devices and tools. With all this said, by far the most useful preventative medical advice that I've ever received has come from unleashing coding agents on my genome, having them investigate my specific mutations, and having them recommend specific follow-on tests and treatments. Population averages are population averages, but we ourselves are not averages. For example, it turns out that I probably have a 30x(!) higher-than-average predisposition to melanoma. Fortunately, there are both specific supplements that help counteract the particular mutations I have, and of course I can significantly dial up my screening frequency. So, this is very useful to know. I don't know exactly how much the analysis cost, but probably less than $100. Sequencing my genome cost a few hundred dollars. (One often sees papers and articles claiming that models aren't very good at medical reasoning. These analyses are usually based on employing several-year-old models, which is a kind of ludicrous malpractice. It is true that you still have to carefully monitor the agents' reasoning, and they do on occasion jump to conclusions or skip steps, requiring some nudging and re-steering. But, overall, they are almost literally infinitely better for this kind of work than what one can otherwise obtain today.) There are still lots of questions about how this will diffuse and get adopted, but it seems very clear that medical practice is about to improve enormously. Exciting times!

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Jamesb
Jamesb@experilearning·
Science begins with myths becuase by the standards of the consensus "best current theory" which defines what we think of as "real" any deviation will appear like fantasy
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Jamesb
Jamesb@experilearning·
Top centaur-era skill = leveraging massive search. How fast can you spam attempts in parallel and trial and error your way to success. Make trials as fast+cheap as possible, learn from failure, apply computational approaches creatively to domains people aren't using them
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Jamesb
Jamesb@experilearning·
Daily progress #6 + utilisation rate is going up, the goblin is satisfied - but more can be done - the big unlock is going to be increasing walkaway time so I can run overnight with 100% confidence
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Jamesb
Jamesb@experilearning·
Daily progress #5 + made a script to track what % of the day our workcell is running + my sole aim is to make number go up + had fun benchmarking claude against himself at colour mixing optimisation + the system feels robust enough to leave running overnight 💪
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Jamesb@experilearning·
Friendship with opencv is over, CNN is my new best friend, 2x better well localisation than yeaterday
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Jamesb@experilearning·
Daily progress #4 - declared victory too soon w/ opencv well detector, it struggles with colours - thx @ZECTBynmo @Willqyu @dnbt777, gave me great ideas to fix - testing bioreactor dispensing w/ liquid handler pipetting - ready to cook some yeast i think lads
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Jamesb
Jamesb@experilearning·
@ZECTBynmo Very nice, someone DMd me suggesting this too, will give it a go
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Jamesb
Jamesb@experilearning·
manual data annotation... feeling extremely stupid doing this, there must be a better way
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Jamesb
Jamesb@experilearning·
@ReedSealFoss Am using opens atm but while it works great for empty/clear wells, it struggles with coloured wells 🤔
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r3333d
r3333d@ReedSealFoss·
@experilearning You can find circles in imagery with open cv. Ask Claude about it.
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Jamesb
Jamesb@experilearning·
@dnbt777 Mmmmm interesting I’ve not heard of moondream before
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danb
danb@dnbt777·
@experilearning you could make a moondream based annotation tool
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Jamesb
Jamesb@experilearning·
Daily progress #3 - fried gripper servo RIP - collecting some well images using colour mixing to make the opencv well detector more robust
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Jamesb
Jamesb@experilearning·
@tschwarz Haha! First step: buy a 3d printer. It will blow your mind
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tschwarz
tschwarz@tschwarz·
@experilearning mate you're making me wonder if there's more to life than web apps
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Jamesb
Jamesb@experilearning·
Daily progress #2 - got the gripper to place microplate lids back on plates - this is one of the trickier lab tasks because plates have quite unforgiving clearances - uses the same visual servo + CAD offset tricks from yesterday to make placement accurate
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Jamesb
Jamesb@experilearning·
@_ivyzhang ahhh awesome, I love this paper so much
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ivy
ivy@_ivyzhang·
@experilearning I think I have this same image somewhere in my Anki hahaha
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Jamesb
Jamesb@experilearning·
I spent a decade hoarding facts and ideas into a collection of 30,000 flashcards cards that I reviewed obsessively with spaced repetition algorithms. The great thing about these systems is that they get you to learn all kinds of fuzzy heuristics for what you value. 1/5
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Jamesb
Jamesb@experilearning·
I wonder if we could create synthetic re-discovery tasks for AI systems? Could we ablate certain concepts and see how much longer it takes to find the solution to problems? What might it tell us about knowledge itself? Full article here: experimentallearning.substack.com/p/whats-the-va… 5/5
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Jamesb
Jamesb@experilearning·
It suggests that one of the ways you can value a golden nugget is in how well it reduces the search space for problems you haven't encountered yet. 4/5
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