The recording of 's talk on "OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization" (biorxiv.org/content/10.110) is now available here
youtube.com/watch?v=W92xVn
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OpenBioML
@openbioml
A collaborative research laboratory at the intersection of machine learning and biology supported by . Join us here: discord.gg/hq4BvpkGaW
openbioml.orgJoined August 2022
OpenBioML’s Tweets
Unfortunately, we have to move today's journal club to next week (Friday, January 13th, 9 PM CET). See you all next week!
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Join us next Friday (January 6th at 9 PM CET) for the OBML journal club as @gahdritz presents the recently released OpenFold pre-print (biorxiv.org/content/10.110). Come join if cutting edge open-source protein structure prediction sounds interesting to you!
discord.gg/HS6YmUuPmD
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Join us next Friday (January 6th at 9 PM CET) for the OBML journal club as presents the recently released OpenFold pre-print (biorxiv.org/content/10.110). Come join if cutting edge open-source protein structure prediction sounds interesting to you!
discord.gg/HS6YmUuPmD
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A good thread from community member & contributor on our ongoing DNA Diffusion project. Just one note: while the community is generally interested in conditioning the model through text, current experiments condition the model in other ways.
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At @openbioml, we are developing a diffusion model that can generate novel DNA regulatory sequences from a text prompt. Continue reading to learn more and discover how you can join this cutting-edge work at the intersection of machine learning and biology! 
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The recording of 's talk on "What if we just learn a language of model for all of life?" (hyperparameter.space/blog/what-if-w) and unifying objectives for machine learning models in computational biology more generally is now available here:
youtu.be/k_4yv6Eoef8
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Reminder that 's talk is tomorrow at 9 PM CET! Come join us if exploring novel learning objectives for foundation models in biology sounds interesting to you!
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Hi, today we are happy to announce the 11th edition of our journal club: join us on Friday, December 2nd at 9 PM CEST as @tsuname presents his essay "What if we just learn a language model for all of life?" and a discussion of what the "basis task" of biology might be.
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We are happy to have supported OpenFold, an effort to provide an open-source trainable reimplementation of 's AlphaFold2, and we look forward to continue supporting open-source computational biology research via our support of
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Our preprint on OpenFold, our trainable reproduction of AlphaFold2, is finally up (biorxiv.org/cgi/content/sh)! Since we open-sourced parameters in June, we've trained the model to high accuracy more than 50 times, on a variety of datasets. Here's what we learned (a lot) -> (1/19)
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Jotted down an idea on a quick blog post:
What if we just...modeled all what we know about life and biomedicine into one big language model?
hyperparameter.space/blog/what-if-w
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Hi, today we are happy to announce the 11th edition of our journal club: join us on Friday, December 2nd at 9 PM CEST as presents his essay "What if we just learn a language model for all of life?" and a discussion of what the "basis task" of biology might be.
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Great progress in over the last few weeks tackling some super important topics. Data and other areas will be key for this and very messy now.
Looking forward to taking it independent as a foundation out of incubation in due course for benefit of all.
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Finalising details for an independent #stablediffusion foundation as discussed on Monday talk with @eladgil,
Getting trademarks, governance etc set up with great input from open source experts
Looking forward to seeing this grow for the good of all 
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Unfortunately, today's journal club has been postponed due to Kevin being unwell. Please, join us on Friday November 4th at 9 PM CEST instead.
Event link:
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We will be providing all the resources necessary for the experiments themselves.
Join us in bringing the workshop ahead here: discord.gg/AMRdyPjwBb
We hope to see you soon! 🙂
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From experimenting with entirely new architectures and datasets to attempting to reproduce announced but currently closed-source protein structure prediction methods, we ask the wider community to get involved, from proposing improvements to helping implement them.
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We intend to run the workshop following the principles of open-science, releasing everything from model checkpoints to training logs, datasets and internal discussions.
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We have thoroughly tested OpenFold on the cluster and trained two different models to completion, one reproducing the exact AlphaFold2 setup and one ablating the effect of templates, and will be making both checkpoints available soon.
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These resources will allow the community to rapidly iterate on ideas as only the largest industrial research laboratories have up to now been able to.
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The project is only possible thanks to the support of , which has made available significant resources on its Ezra-1 cluster for the project, as well as to the development of the OpenFold codebase by AlQuraishi’s lab.
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The LibreFold workshop is inspired by the success of the BigScience language modeling research workshop and by what the structural biology community has built upon AlphaFold 2 following its release by DeepMind.
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Hi everyone, today we are announcing the start of the LibreFold project, a collaborative research workshop aiming to improve AlphaFold-like protein structure prediction methods.
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We are trying to create an open research laboratory, where developments in compbio research can be discussed. All journal club papers are proposed and voted by the community. If you'd like to contribute towards accelerating biology for the benefit of all, come join! :)
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And join us on Friday, October 28th at 9 PM CEST as presents his recent paper "Thermodynamics of evolution and the origin of life" (pnas.org/doi/abs/10.107).
Event link: discord.gg/HS6YmUuPmD?eve
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Join us on Friday, October 21st at 9 PM CEST as presents his most recent work "Protein structure generation via folding diffusion" (arxiv.org/abs/2209.15611).
Event link: discord.gg/HS6YmUuPmD?eve
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Hey everyone, today we are happy to announce the 9th and 10th edition of the OpenBioML Journal Club!
Find previous presentations on our YT channel: youtube.com/channel/UCJpyf
Join our community here: discord.com/invite/hq4Bvpk
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Furthermore, if you’d like to participate in an open & collaborative research laboratory at the intersection of AI and biology, do consider getting involved – we have access to large-scale resources, and would like to make the most of them. We look forward to hearing from you! 🙂
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If developing novel diffusion-based generative models of regulatory DNA sequences sounds interesting to you, consider joining Luca and his team in the dedicated DNA diffusion discord channel (discord.gg/6nB5yyfsmW).
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Hi, today we are happy to announce the DNA Diffusion OpenBioML community-initiated project!
"Understanding the code of life: generative models of regulatory DNA sequences based on diffusion models" (github.com/pinellolab/DNA) is spearheaded by and his team.
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Hi, today we are happy to announce the next edition of the OpenBioML Journal Club.
Join us next Friday (September 30th) at 9 PM CEST as presents "Deep Reinforcement Learning for Optimal Experimental Design in Biology" (biorxiv.org/content/10.110) and its broader context.
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Hi, today we are happy to announce the next edition of the OpenBioML Journal Club.
Join us next Friday (September 16th) at 9 PM CEST as presents his essay "A Future History of Biomedical Progress" (markov.bio/biomedical-pro).
Join us here: discord.gg/hq4BvpkGaW
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We are happy to announce the next edition of our journal club!
Join us on Friday September 2nd at 5 PM CEST as , and present "Disease variant prediction with deep generative models of evolutionary data" (nature.com/articles/s4158)!
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