Scientist. Co-founder & CSO @ArcadiaScience. Head of Open Science @AsteraInstitute. Chasing unknown unknowns.

Joined September 2011
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For no reason at all, I made a simple one-page guide for self-publishing research without relying on journals or other centralized gatekeepers. It covers: – DOI deposits via Zenodo – FAIR repositories – crawlable HTML for Google AI systems – metadata, licenses, datasets, code, and protocols
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Prachee Avasthi retweeted
Lorenzo, NE a few days ago definitely did not suck. June 7th, 2 years in a row has pumped out epic colors and structure. #newx
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Cannot believe the capacity for the spurs to blow it in every game
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Disclosure Day kind of sucked
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Every scene without Emily Blunt was a waiting game until the next scene with Emily Blunt
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Jun 11
Announcement: @innovationwonk and I are hosting a session on Frontiers in Open Science June 18th at 2PM ET featuring the incredible folks behind ATProtoScience @rtk254 , Discourse Graphs @JoelChan86 , and openRxiv @cshperspectives Link below👇🏽
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Prachee Avasthi retweeted
I plan to live Anthropically. If someone asks me about something I don't like I'll just become a stupider version of myself
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My friend has a Hot Girls for Zohran t-shirt. I think there needs to be one that says Hot Girls for Jeff Dean This came up bc I just recommended to them the @AcquiredFM episode on Google AI, which was awesome acquired.fm/episodes/google-…
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There will be lots of narratives about this proposal to cap grants per NIH investigator given the fraught political climate but I’m glad the NIH is continuing to grapple with how best to responsibly distribute the public dollars still in its charge As with all requests for information on important policy proposals, I suspect there will be shockingly few respondents. And the responses that are sent will likely be dominated by backlash from those quite practiced and efficient at lobbying for their individual interests, even if they represent a vocal and powerful minority relative to a broader ecosystem that this would impact. If this affects you (though I’d argue distribution of resources by the largest public funder of health research in the world affects all of us), I’d do my homework and weigh in. grants.nih.gov/grants/guide/…

It is not insane IMO and can be about a lot of other things. You’ll remember that a decade ago the NIH proposed something similar, the grant support index, that was meant to also achieve the same: broader distribution of research dollars and higher funding rates instead of a Matthew effect of more grants to fewer investigators with diminishing returns. Many young PIs were in support. Back then, I submitted a letter in support of it on behalf of many signatories newpislack.wordpress.com/ope… The NIH-wide initiative had its roots in related capping policies that resulted in significantly increased funding rates at NIGMS relative to other ICs. The few and powerful at rich institutions (massive outliers in the grant recipient distribution) killed the initiative before it could even be thoroughly discussed. Back when the GSI was proposed, ~6% of NIH funded researchers had the support equivalent to 3 R01s. If going by RPGs not total dollars, I’d expect that to be an even smaller percentage of affected researchers now given the proliferation of R35 as a mechanism that consolidates multiple projects into a single award. IMO, the over-proliferation of completely unsustainable soft money positions is not a slam dunk justification to act as a sink for public research dollars distributed by an agency beholden to more than those researchers and institutions. This is not really my fight anymore, other than a vested interest in thriving federal funding for scientific research, responsibly deployed to support new ideas and institutions not just concentrate them … but I do think seeing this as entirely about a hostile administration threatens to dismiss a serious policy proposal that should be thoroughly considered on its merits
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Lol what year is this. This shit is decade out of date. Journals are a time machine to the past in every way nature.com/articles/d41586-0…

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🚨new job alert! If you’ve been following our efforts @ArcadiaScience, you know we’re interested in closing the gap between biological data and biological understanding. We’re hiring a Quantitative Biologist to help us develop new approaches for image and spectral analysis, design rigorous experiments, and apply statistical and machine learning methods to extract meaning from complex biological datasets across diverse organisms. If you get excited about experimental design, quantitative reasoning, and building new analytical methods, we’d love to hear from you! jobs.lever.co/arcadiascience…
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Prachee Avasthi retweeted
NEW PUBLICATION: "An interest-group theory of AI-tool governance in science", published in Public Choice. In this paper, I analyze one possible rationale for academics wanting to regulate and constrain the use of AI tools in scientific work: their own interest. Some researchers are less able than others to benefit from the new tools and therefore want to make it difficult for their competitors in academia to use them. rdcu.be/fl7PA
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Prachee Avasthi retweeted
I’m so excited about the launch of ESMFold2, ESMC, and the new ESM Atlas. This was a massive team effort, and I’m grateful to have worked with such an incredible group @biohub. A headline result I’m especially excited about: ESMFold2 can design minibinders and antibodies with nanomolar affinity, target selectivity, and functional activity against therapeutically relevant targets. Today, we’re sharing the full binder design protocol.
Today we're announcing ESMFold2, an open scientific engine to power prediction, design, and discovery across protein biology. The new model delivers state of the art performance on protein interactions, especially antibodies, a critical modality for therapeutics. We have designed and validated miniprotein binders and single chain antibodies across five therapeutic targets that are important in cancer and immunology. We are seeing very high success rates, and affinities at levels consistent with therapeutic activity. We’re also releasing an atlas of 6.8 billion proteins, and 1.1 billion predicted structures. ESMFold2 is built on a state of the art language model that has been trained on billions of protein sequences. A world model of protein biology emerges through language modeling. We’ve used the techniques of mechanistic interpretability developed to understand large language models to understand the concepts ESM uses to represent proteins. The model’s representation space has a compositional organization of features across scales, levels of complexity, and abstraction, that reflects and mirrors the understanding of protein biology developed through a century of empirical science. This understanding emerges without prior knowledge, just from language modeling of protein sequences. Language models are becoming a powerful substrate to understand and program biology. The design of protein interactions is one of the most fundamental problems in biophysics, and has critical implications for the discovery of new medicines. A simple gradient based search with the model was able to discover high-affinity protein binders. I'm excited by the potential this has to accelerate basic science and the understanding of proteins. And especially for the new avenues it opens up for therapeutic design and medicine.
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🚨New Job Alert We @ArcadiaScience are continuing to push the boundaries of high dimensional phenotyping across biological scales, favoring label-free approaches that can be applied across sample types. If you’re a creative, inventor type with the skills to prototype new optical technologies and methods, apply for the optical engineering role on our research team now! jobs.lever.co/arcadiascience…
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Note that the above is distinct from the hardware engineering role in our foundry, who will productionize prototyped optical instruments for broader internal and external use: jobs.lever.co/arcadiascience…
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Note that this is ALSO distinct from our imaging specialist role who operates/maintains in-house instruments and collaborates with our scientists to design imaging experiments that best suit their needs: jobs.lever.co/arcadiascience…
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I can’t endorse this enough. Bring back great puns
hey @meetgranola i think you should do an ad that goes granola the app for cereal entrepreneurs
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When you have an unambiguous and somewhat aggressive open science posture, you’ll never guess what percentage of people seeking unique opportunities swear up and down that they’re committed to open science. It’s ~100%. But it’s not enough to have a willingness (or even genuine enthusiasm) to behave differently when required to do so. That’s the absolute floor, not the bar. Actions speak louder than words by a mile. And there are people actually doing things that are way more believable than those who spent their lives as apologists for the status quo out of self-interest or paternalism (different intent, same outcome). Good news is acting without permission or cover…well, doesn’t need permission or cover. It’s never too late to do shit. Not because the world is changing and the playbook you were sold is/was hot garbage, but because it’s always ok to change your mind and newly do what you think is right. IME and IMO, the people looking for fearlessness are watching
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