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Chaitanya K. Joshi

@chaitjo.bsky.social
1.1K followers 178 following 131 posts

AI researcher excited about biomolecule design 🧬 PhD student at the University of Cambridge Prev. at FAIR, Prescient Design, and MRC LMB 📝 chaitjo.substack.com

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Chaitanya K. Joshi @chaitjo.bsky.social · 14/04/2026
Excited to have Edric Choi present his latest work on RNA chemical mapping at the CASP Nucleic Acids Reading Group! Thursday April 16 2026 on Zoom; Pacific Daylight Saving Time 8 am / Eastern Daylight Saving Time 11 am -- free to attend and full of interactive discussions.
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Chaitanya K. Joshi @chaitjo.bsky.social · 06/02/2026
I recently joined The Pauling Principle podcast to discuss our research on RNA design, hot takes on architecture research in BioML, origins of life, and being in a wet lab! Feels pretty surreal that I'm interesting enough to be on a podcast (?) www.youtube.com/watch?v=ftrQ...
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Chaitanya K. Joshi @chaitjo.bsky.social · 08/01/2026
Four years of research on Geometric Deep Learning & Molecular Design, summarized in 3 questions: - How expressive are our models? (Theory) - Can we build foundation models for molecules? (Architecture) - Can AI design RNA in the real world? (Application)
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Chaitanya K. Joshi @chaitjo.bsky.social · 08/01/2026
New blog 💙: I reflect on why I worked on what I worked on... I think a PhD is a very special time. You get to challenge yourself, push your boundaries, and grow. My thoughts go against the current AI/academia narrative online, so I hope you find it interesting. chaitjo.substack.com/p/phd-thesis...
chaitjo.substack.com
A Cambridge PhD thesis in three research questions
Geometric Deep Learning for Molecular Modelling and Design: A personal scientific journey
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Chaitanya K. Joshi @chaitjo.bsky.social · 04/01/2026
It relies on new algorithms for template search, invented by Kagglers such as G. John Rao. If no templates are found, the model can still work and works decently well without templates, too.
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Chaitanya K. Joshi @chaitjo.bsky.social · 02/01/2026
The main takeaway from the Kaggle competition was how powerful RNA template modeling can be — it was kind of shocking to us 🤯 RNAPro integrates 3D templates into Protenix/the AF3 architecture, and this moves the needle on automated RNA structure prediction!
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Chaitanya K. Joshi @chaitjo.bsky.social · 02/01/2026
Happy new year! A step change in RNA structure prediction, powered by top Kaggle-ers in a collaboration lead by Stanford University and NVIDIA Happy to have played a small part in the new RNAPro model, significantly outperforming AlphaFold 3 as well as VFold (CASP winners)
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Chaitanya K. Joshi @chaitjo.bsky.social · 26/12/2025
The video was largely created using AI text-to-video, and I must say the results are pretty impressive! There's huge potential for this technology to make science more approachable, just like Google's NotebookLM.
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Chaitanya K. Joshi @chaitjo.bsky.social · 26/12/2025
Merry Christmas!🎄🌟 Sharing something interesting: Friso van de Stadt created a pretty neat explainer video for our gRNAde paper and "AlphaGo moment for RNA design" blogpost! www.youtube.com/watch?v=wDeZ...
youtube.com
AI vs. Humans: The "AlphaGo Moment" for RNA Design
YouTube video by Chaitanya K. Joshi
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Chaitanya K. Joshi @chaitjo.bsky.social · 18/12/2025
I wrote some personal reflections about being physically embedded in a world-leading molecular biology lab @mrclmb.bsky.social, learning to communicate with experimentalists, back-breaking wet lab work, scientific rigour, and skin in the game! 💌: chaitjo.substack.com/p/an-ai-rese...
chaitjo.substack.com
An AI Researcher in the Cathedral of Molecular Biology
How we designed catalytic RNA functions, and what I learned holding a pipette at the MRC Laboratory of Molecular Biology.
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Chaitanya K. Joshi @chaitjo.bsky.social · 15/12/2025
- How to set up the design prompt just right? - How many sequences to sample and how to make them diverse? - How exactly is filtering done step-by-step? - How to analyze wet-lab results and create figures? You can find out all of that in our GitHub codebase! 💻: github.com/chaitjo/geom...
github.com
GitHub - chaitjo/geometric-rna-design: gRNAde is a Generative AI framework for inverse design of 3D RNA structure and function
gRNAde is a Generative AI framework for inverse design of 3D RNA structure and function - chaitjo/geometric-rna-design
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Chaitanya K. Joshi @chaitjo.bsky.social · 15/12/2025
With this release, we are fully openly releasing all the tacit knowledge for getting biomolecule design models to actually work in wet labs! Seemingly small-but-critical details are often missing in flagship papers, and it took us a while to finetune our pipeline:
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Chaitanya K. Joshi @chaitjo.bsky.social · 15/12/2025
Many papers have built their RNA design pipelines using the gRNAde code & data from our ICLR 2025 spotlight paper - that's been exciting to see! Especially the attempt at biologically meaningful benchmarks 🤗 But how to take ML conference papers to wet-lab validated results?
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Chaitanya K. Joshi @chaitjo.bsky.social · 15/12/2025
Excited to release the fully open-source code for gRNAde - our wet-lab validated, generative AI framework for 3D RNA inverse design 🚀⭐️ I pride myself on open-science & this is probably the most intense release I've done!
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Rocío Mercado Oropeza @rociomer.bsky.social · 09/12/2025
Happy to have contributed to and now finally share LeMat-GenBench, a new open benchmark + leaderboard for generative crystalline materials models! ⚛️✨ It provides standardised metrics for validity, stability, & much more. Already includes results for 12 models! 🔗 Paper: arxiv.org/abs/2512.04562 1/4
arxiv.org
LeMat-GenBench: A Unified Evaluation Framework for Crystal Generative Models
Generative machine learning (ML) models hold great promise for accelerating materials discovery through the inverse design of inorganic crystals, enabling an unprecedented exploration of chemical spac...
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Arc Institute @arcinstitute.org · 07/12/2025
Thank you to everyone who made the inaugural Virtual Cell Challenge a success. Over 5,000 participants from 114 countries competed to build AI models that predict cellular responses to genetic perturbations. Today we're announcing the winners and reflecting on what we learned.
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Chaitanya K. Joshi @chaitjo.bsky.social · 08/12/2025
I think the term ‘Virtual cell’ will have the same trajectory as ‘AGI’ or ‘Foundation models’: Initially opposed by rigorous scientists, while the Bay Area and Demis Hassabis are the only ones comfortable using it → becoming a mainstream term in academia soon, in few years (Overton window)
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Chaitanya K. Joshi @chaitjo.bsky.social · 04/12/2025
Thankful for the tireless work and motivation from yourself and the Eterna team!
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Jill Townley @jilltownley.bsky.social · 03/12/2025
An AI researcher interested in biochemistry modeling successfully improved his RNA language model through participation in the Eterna pseudoknot design competition. Congratulations, Chaitanya! 🧬🧪 #RNAsky The polymerase ribozyme results are pretty cool too. 😎
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Erik Poppleton @poppleton.phd · 03/12/2025
Enumerating possible pseudoknots that a sequence can form with nearest-neighbor models is an NP-hard problem. Even evaluating these structures is challenging, let alone designing them. So it’s great to see data-based models starting to crack the RNA structural design problem! 🧬🧪
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Chaitanya K. Joshi @chaitjo.bsky.social · 03/12/2025
5/ Want the story behind the science? 🏰 I wrote a blog post about our "AlphaGo Moment" and what it was like being an AI researcher embedded at the legendary @mrclmb.bsky.social (holding a pipette for the first time!) Read it on Substack: chaitjo.substack.com/p/alphago-mo...
chaitjo.substack.com
An AlphaGo moment for RNA design
How our AI system, gRNAde, matched human experts at the complex game of RNA folding—and why it matters.
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Chaitanya K. Joshi @chaitjo.bsky.social · 03/12/2025
4/ This was a massive team effort bridging AI and biology, from one end of Cambridge to another 🤗🚲 Thanks to Edo Gianni* @edogia.bsky.social, Sam Kwok*, @simonmathis.bsky.social, Pietro Liò, and @philholliger.bsky.social for this journey! 📄 Preprint: tinyurl.com/gRNAde-paper
tinyurl.com
Generative inverse design of RNA structure and function with gRNAde
The design of RNA molecules with bespoke three-dimensional structures and functions is a central goal in synthetic biology and biotechnology. However, progress has been limited by the challenges of de...
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Chaitanya K. Joshi @chaitjo.bsky.social · 03/12/2025
3/ The Mechanistic Insight 👽 What did gRNAde learn? Humans stick close to nature, but gRNAde changes ~70% vs. WT sequence. And it "sees" invisible 3D constraints that rational methods miss, allowing us to make "generative jumps" to new functional islands in sequence space 🏝️
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Chaitanya K. Joshi @chaitjo.bsky.social · 03/12/2025
2/ The Function Challenge ⚙️ But can we move from static shape to dynamic RNA machines? We show how with a complex RNA Polymerase Ribozyme. Rational design failed (3% success). gRNAde succeeded (31.5% active), discovering improved variants 15-20 mutations away from nature.
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Chaitanya K. Joshi @chaitjo.bsky.social · 03/12/2025
1/ The Structure Challenge 🧩 We entered gRNAde into Eterna OpenKnot: a CASP-style blinded, wet-lab competition by @eternagame.org The result? Parity with the world's best humans, and big gains over Rosetta, RFdiffusion. We can automate expert intuition for complex RNA folding!
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Chaitanya K. Joshi @chaitjo.bsky.social · 03/12/2025
Introducing gRNAde: our own little "AlphaGo Moment" for RNA design! 🧬🚀 📝: tinyurl.com/gRNAde-paper Unlike proteins, RNA design has long relied on "wisdom of the crowd" (human experts) or the slow crawl of directed evolution — gRNAde changes that! 🧵👇
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Chaitanya K. Joshi @chaitjo.bsky.social · 03/12/2025
Wow thank you, Jamie, for sharing! 🤗
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Jamie Cate @jhdcate.bsky.social · 15/11/2025
To make future progress it’s worth revisiting the past. From Olke Uhlenbeck, “Keeping RNA Happy” pmc.ncbi.nlm.nih.gov/articles/PMC...
pmc.ncbi.nlm.nih.gov
Keeping RNA happy
An official website of the United States government
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Chaitanya K. Joshi @chaitjo.bsky.social · 15/11/2025
🚀🧬 Beyond Structure-based Biomolecule Design Its an important moment for structure-based biomolecule design: models starting to work and action shifting from academia to industry. So what are the next scientific problems academia could be thinking about? chaitjo.substack.com/p/beyond-str...
chaitjo.substack.com
Beyond structure-based biomolecule design
Dynamics, black-box data, and the antedisciplinary frontier of biomolecule design
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Chaitanya K. Joshi @chaitjo.bsky.social · 18/10/2025
And at big industrial labs with large budgets, the scientists are just able to do a lot more intuition-building. They are able to try ideas a lot faster, and get a 'feel' for what ideas will work much faster as a result.
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Chaitanya K. Joshi @chaitjo.bsky.social · 18/10/2025
Why do 'frontier' labs train the best models? I think its because training deep learning models is less like science/engineering, and more like cooking. It takes some time to develop the intuitions around learning dynamics of big models.
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Das Lab @rdaslab.bsky.social · 24/09/2025
The results are in: top codes in Stanford #RNA 3D Folding @kaggle.com competition are competitive with CASP16-leading humans Vfold, beat AlphaFold 3. Top team’s trick was template-based modeling, not #DeepLearning. Congrats: john, odat, Eigen, + all 1706 participants! www.kaggle.com/competitions...
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 17/09/2025
🚨To accommodate the addition of EuroMLSB, we have extended the submission deadline to October 1, 2025 11:59pm AoE. Find information on paper guidelines at mlsb.io. Submissions will be made through CMT.
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 17/09/2025
Genome language models can generate new, high-fitness bacteriophages! @samuelhking.bsky.social @claudiadriscoll.bsky.social @david-li.bsky.social @danguo.bsky.social @adititm.bsky.social Garyk Brixi @maxewilkinson.bsky.social @brianhie.bsky.social www.biorxiv.org/content/10.1...
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Samuel King @samuelhking.bsky.social · 17/09/2025
Many of the most complex and useful functions in biology emerge at the scale of whole genomes. Today, we share our preprint “Generative design of novel bacteriophages with genome language models”, where we validate the first, functional AI-generated genomes 🧵
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Jase Gehring @skyjase.bsky.social · 18/09/2025
very cool work and a milestone in synthetic biology. how impressive are the new phage genomes? with generative bioML, i'm always looking at how similar the generated sequences are to known sequences. let's take a look
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 12/09/2025
You asked and we listened... @workshopmlsb.bsky.social is excited to be expanding to Copenhagen, DK at @euripsconf.bsky.social 🎉 Two workshops (San Diego & Copenhagen) will run concurrently to support broader attendance. You can indicate your location preference(s) in the submission portal💫
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Chaitanya K. Joshi @chaitjo.bsky.social · 05/09/2025
The 3D structure of biomolecules are nature's 'thinking tokens' enroute to the output that we actually truly want to understand: Function. (Slide from Denny Zhou's Stanford talk on LLM Reasoning)
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Rachael Kretsch @rachael-kretsch.bsky.social · 02/09/2025
We have restarted our global Nucleic Acid Strcuture webinar series to bring the expiremental and computational communities together to discuss new developments in the field. Join us this Thursday for the next webinar. Sign up to our mailing list here: groups.google.com/g/casp-rna-sig
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Chaitanya K. Joshi @chaitjo.bsky.social · 31/08/2025
Scaling laws for BioML and wet lab data will eventually work out in the right setting! After all, language data for LLMs was acquired by the largest wet lab experiment ever conducted: Human civilisation 🤯
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Nate Corley @ncorley.bsky.social · 15/08/2025
(1/7) Training biomolecular foundation models shouldn't be so hard. And open-source structure prediction is important. So today we're releasing two software packages: AtomWorks and RosettaFold3 (RF3) [www.biorxiv.org/content/10.1101/202…...)
biorxiv.org
Accelerating Biomolecular Modeling with AtomWorks and RF3
Deep learning methods trained on protein structure databases have revolutionized biomolecular structure prediction, but developing and training new models remains a considerable challenge. To facilita...
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Chaitanya K. Joshi @chaitjo.bsky.social · 16/08/2025
It can train foundation models, but can it train frontier models too? ;)
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Chaitanya K. Joshi @chaitjo.bsky.social · 15/08/2025
📢 Submissions for MLSB 2025 are officially open! We invite researchers to submit their work on the intersection of AI and structural biology. 🗓️ Deadline: September 26, 2025 🔗 More info: cmt3.research.microsoft.com/MLSB2025
mlsb.io
MLSB 2025 Workshop
Workshop on Machine Learning in Structural Biology co-located with NeurIPS 2025
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Chaitanya K. Joshi @chaitjo.bsky.social · 15/08/2025
RosettaFold 3 is here! 🧬🚀 AtomWorks (the foundational data pipeline powering it) is perhaps the really most exciting part of this release! Congratulations @simonmathis.bsky.social and team!!! ❤️ bioRxiv preprint: www.biorxiv.org/content/10.1...
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Chaitanya K. Joshi @chaitjo.bsky.social · 05/08/2025
Great image of organizers space group symmetry!
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Chaitanya K. Joshi @chaitjo.bsky.social · 01/08/2025
Really insightful post and responses - this is why I keep coming back to science social media!
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Chaitanya K. Joshi @chaitjo.bsky.social · 31/07/2025
Alex’s explainer thread is a heartfelt one: x.com/Alex__Abruda... And the preprint is on arXiv link: www.arxiv.org/abs/2507.21938
x.com
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Chaitanya K. Joshi @chaitjo.bsky.social · 31/07/2025
🧬 Protein designers: we keep saying we're getting really good at making static, rock-like proteins... Introducing Dynamic MPNN - our first step towards truly multi-state and 'programmable' protein design! Great collaboration led by Alex Abrudan and Sebastian Pujalte!
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Martin Pacesa @martinpacesa.bsky.social · 25/07/2025
I am super excited to announce that I will be starting my lab at the Department of Pharmacology of the University of Zurich in Switzerland next year!
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Eterna @eternagame.org · 23/07/2025
Coming up this weekend, Eternacon will feature presentations about fellow #citsci platform @zooniverse.bsky.social and how participants of both Zooniverse and Eterna have created #machinelearning tools for projects. @noirlabastro.bsky.social Register for free at eternagame.org/eternacon/2025
Blue image of ROOL nanocage made of RNA with text on top noting Eternacon dates as July 26 and 27.
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