BioE PhD student @stanford and @arcinstitute in the Hie Lab // AI for biological design
Joined April 2020
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Biological engineering has long aimed to design living systems with the programmability of software, but the tools to do so rarely fit together.
Today, we’re sharing our preprint introducing Proto, a high-level programming language for generative biology that composes models and design tools across DNA, RNA, and proteins to optimize towards user-specified functional objectives.
Aditi Merchant retweeted
Today in @Nature, we introduce SynthID Bio, a family of watermarking methods for protein sequences and structures, that we believe will contribute to responsible development of AI for biology. Learn more in our blog and this thread 🧵 - deepmind.google/blog/introdu…
A truly beautiful paper by the always inspiring (and wise🦉) @_David_Li and @garykbrixi! Check out how you can leverage learned co-evolutionary relationships for biological discovery with Minerva!
Excited to share Minerva, our approach using genome language models for biological discovery! Using Minerva, we find that UG27 reverse transcriptase systems encode variable arrays of diverse ncRNAs with a shared structure, each templating a short DNA hairpin. With @garykbrixi.
Aditi Merchant retweeted
As with biological design, AI can also accelerate biological discovery.
In new work led by @_David_Li and @garykbrixi with @mfgrp, we show how genome language models enable systematic discovery of genetic elements, revealing a new class of reverse-transcriptase mechanisms.
Aditi Merchant retweeted
Genomes are full of dark matter of unknown functions.
We present Minerva, a new method for discovery guided by genome language models. Minerva reveals the interactions hidden in non-coding DNA, pointing to hundreds of new putative RNAs and repetitive elements per bacterial genome. Minerva allows us to find and study elements invisible to traditional methods at orders of magnitude greater scale than before.
You can now run Proto’s suite of 100+ Bio AI, database search, and bioinformatics tools directly from ChatGPT! Excited to see what everyone builds 🧬
More features and updates coming soon, stay tuned :)
Learn more about the Rosalind Workbench research preview below!
Rosalind Workbench connects scientific questions to specialized models, tools, and reviewable outputs in one workflow, from protein structure and sequence analysis to sequencing pipelines.
developers.openai.com/blog/r…
Aditi Merchant retweeted
You can now use Proto in ChatGPT!
Here is de novo nanobody design with Germinal (chatgpt.com/share/6a919bda-e…) and semantic design with Evo 2 (chatgpt.com/share/6a90a552-c…).
Check out the Rosalind Workbench Research Preview: developers.openai.com/blog/r…
Rosalind Workbench connects scientific questions to specialized models, tools, and reviewable outputs in one workflow, from protein structure and sequence analysis to sequencing pipelines.
developers.openai.com/blog/r…
Aditi Merchant retweeted
Excited to share the final version of ProteinDPO is out today in @naturemethods! New in the paper is application of the model to stabilization of the pre-fusion state of hemagglutinin, the primary component of flu vaccines. 1/8
🔗nature.com/articles/s41592-0…
📑rdcu.be/fzUc2
Aditi Merchant retweeted
Our work led by @talaldotpdb on aligning protein generative models to experimental fitness with ProteinDPO is now published in @naturemethods!
New in the published paper includes stabilizing mutations to H5 hemagglutinin, a component of flu vaccines.
nature.com/articles/s41592-0…
Aditi Merchant retweeted
Following the publication of our phage gen paper, I wrote some personal thoughts on biosafety and biosecurity as generative biology improves.
Given the trajectory of progress, there should be concern and urgency -- but also optimism.
brianhie.com/present_and_fut…
Aditi Merchant retweeted
At Therna we treat RNA as a language you can read, score, and rewrite.
Our new post: designing a glucagon mRNA for HepG2, with Evo 2, PARADE, EnCodon and ViennaRNA in one loop using Proto.
Illustrative only. Public models, no wet lab validation.
Link in the comments
Happening today! Tune in to learn more about Proto and how to use it for your own biological design goals 🧬
We’re excited to host @aditimerch on Tuesday, July 21, for a presentation on her recent work, “A High-Level Programming Language for Generative Biology with Proto.” The talk will take place from 6:00–7:00 p.m. ET / 3:00–4:00 p.m. PT
Aditi Merchant retweeted
Check out our website proto.evodesign.org, which visualizes our designs and provides open access to 120+ biological AI models and tools!
To learn how to navigate the UI and start designing with our Proto agent, check out youtu.be/8UnOrC_0jmo?si=rq-Q…
We've received amazing feedback over the past day and we're excited to see what the community builds! proto.evodesign.org
Huge congrats to the Germinal team on their beautiful paper! An exciting day in AI for biological design!
Germinal is out today in Nature Biotechnology! Important additions to VHH design from the preprint: we demonstrate scFv design, evaluate binder polyreactivity, and characterise epitope specificity by alanine mutagenesis and a beautiful cryo-EM structure… nature.com/articles/s41587-0…
Aditi Merchant retweeted
Imagine programming protein, DNA, and RNA systems like you would write computer code, or even by natural language prompting of an AI agent. @brianhie and team just made this a reality with Proto: a high-level programming language for generative biology.
And check out Daniel’s post to learn a bit more about the language abstraction Proto introduces and how to run Proto for your design campaigns from your browser!
Biological engineering has long aimed to make biological systems designable, composable, and programmable across scales and modalities. However, existing biological AI models and tools are siloed and difficult to compose.
Today, we’re proud to share our preprint for Proto, a high-level programming language and open infrastructure layer generative biology.
*This thread is centered around the Proto Language. For the full paper thread, check out: xitter.cf/aditimerch/status/2069…
Check out Ben’s post to learn more about how to access Proto’s comprehensive suite of models and tools!
Performing bioinformatics analysis and building biological design pipelines can mean a lot of infrastructure fighting: fragmented tools, idiosyncratic formats, and APIs that are hard to compose. That friction slows researchers down, and as this Anthropic blog post lays out, it's now a major bottleneck for modern agents as well.
Today, we're releasing Proto, a design platform for generative biology. This thread is on the layer that makes it work: proto-tools, a universal open-source infrastructure layer for biological models and tools.
Aditi Merchant retweeted
In new work, we lay out a vision for a high-level programming language for generative biology, called Proto.
Proto composes generative and predictive models spanning DNA, RNA, proteins, ligands, and their interactions, which we use to design complex biological functions. 1/n
None of this would have been possible without the support of @BrianHie, my brilliant co-first authors @dan_guo_ and @bviggiano_13, and the rest of the Proto team, @leba1127, @ev_hur, @tinabmai, @peteryin21, and @samuelhking! Incredibly grateful to have spent the last few months working alongside these incredible people in our small corner of Arc!
And of course, Proto wouldn’t exist without the countless researchers and experimentalists whose tools, models, and datasets made this work possible.
To learn more, check out the preprint here:
biorxiv.org/content/10.64898…
