
Founder of Geodesic Intelligence @Geodesiclab | Professor @UCLA | Opinions are my own
Los Angeles, CA
Joined August 2017
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Quanquan Gu retweeted
Hi all, I have a new result I'm excited to share. It turns out that *all existing implementations* of softmax and cross-entropy (that's JAX, PyTorch, textbooks, etc) have a subtle bug --- two bugs, actually. A simple rewrite fixes both, and eliminates "slingshots" when grokking:
Since when did mathematical rigor become optional in interpreting neural networks?
interpretability might be the most important scientific problem in the world right now, as I don't think we can solve alignment if we don't know what we're building. I think I have good news about it. I co-authored early work in mechanistic interpretability at OpenAI and came away pessimistic, because neural networks appeared to fold into arbitrary tangled knots. years later, I started openai's first large-scale automated interpretability project, finding about 2% of neurons legible with the primitive tools we had
with modern agentic tools and a much closer look, the picture looks totally different. the vast majority in models up to trillions of parameters are legible, and their circuits beautiful. many famous examples of tangled neurons turned out to be misunderstood. The roadblocks I expected mostly aren't there. I now think ambitious interpretability will be solved by the time we need it most, and possibly quite soon, as automated scientists keep improving. it may be a bitter lesson for interpretability: the simple thing, at absurd scale, works
already-clean.goodfire.com/
This is AI for AI at its finest. LFG! 🚀
Biology could be AI’s next recursive self-improvement frontier.
Design in silico → test in the lab → turn experimental feedback into semi-synthetic training data → improve the model → repeat.
At @Geodesiclab , we’re building toward that flywheel.
The wet lab becomes part of the learning algorithm.
AI Drug Discovery Is Becoming a Bottleneck Trade
I get excited when an industry starts going through a real regime change. AI drug discovery (“AIDD”) increasingly looks like one of those moments.
Two things are happening:
1/ Upstream: the frontier AI labs are piling in.
2/ Downstream: The supply chain is clearly moving.
Supply-chain checks suggest the upstream picks-and-shovels of discovery and early preclinical R&D are starting to feel the increase in experimental volume.
DNA → protein → assays → sequencing → automation → preclinical testing
Names across that stack include $TWST , @GenScript , $ILMN , $TXG , lab-automation vendors and CROs.
$TWST expects triple-digit percentage growth in AI-enabled drug-discovery orders in FY26, and another year of triple-digit order growth in FY27.
@GenScript's AIDD business doubled YoY in 1H26. Its current platform advertises industrial-scale validation of 4,000+ designs/day, with integrated sequence-to-data workflows. Our channel checks suggest the ramp is moving even faster: roughly 8,000 designs/day currently, with a path toward ~16,000/day by YE26.
---
Why does AI drive more wet-lab demand?
1/ AI makes hypothesis generation almost free → way more shots on goal.
The bottleneck is moving from expert-driven design to biological validation.
2/ AI models need continuous experimental feedback — and both good and bad data are useful.
Traditionally, only the highest-conviction A+ candidates might get pushed into expensive validation. With AI, even the B/C candidates can be valuable because failed experiments generate training data.
@GenScript has said its sequence-to-binding workflow can return data in 4–7 days, and that faster cycle times matter because AI models depend on continuous experimental feedback.
@Anthropic is a clean example. @claudeai designed 1,320 protein binders. @adaptyvbio converted those digital sequences into DNA, expressed the proteins and tested binding. Only 354 actually bound. And the 966 failures are not wasted. They are useful negative labels: what does not express, what does not bind, what has poor affinity. Those results help train the next model iteration.
3/ Wet labs are no longer just making drugs. They are making training data.
$TWST / @GenScript increasingly look like biological data foundries.
$TWST explicitly talks about generating model-ready data from AI-designed sequences. In some workflows, the customer may care less about receiving the physical protein than about getting structured experimental results back into the model.
Traditional drug discovery asks: “Does candidate X work?”
AI drug discovery also asks: “What can this experiment teach the model?”
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TAM of AIDD
If AI is simply a better R&D tool, the relevant spending pool is the $300–400B of annual global pharma R&D. If AI meaningfully increases the number of viable drug programs, the opportunity is larger because it expands downstream demand for DNA synthesis, protein production, assays, and preclinical work.
Near term, we can also size demand from AI-company spending. If Anthropic reaches $80B of ARR in 2026 and spends just 1% on AIDD, that alone would imply ~$800M of annual investment.
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Trade setup
This is a trade that could have long legs. It’s hard to really stop working until PhaseI/II results (2028+)
It smells a lot like the bottleneck trade we just saw in semis: GPUs → HBM → networking → power/cooling. In biology, It basically follows the drug discovery process downstream: AI models → designs → DNA/protein → assays → preclinical capacity.
After the upstream picks-and-shovels, animal testing could become the next bottleneck. Monkey prices are already near prior highs and CRO capacity is tight. AIDD pushing more candidates into preclinical development would only add demand.
?? But clinical trials are still the bottleneck?
This is the biggest pushback I keep coming back to. No matter how fast discovery becomes, drugs still need to go through preclinical → Phase I → Phase II → Phase III → approval. You still need patients, time and capital.
But that doesn’t mean the bottleneck trade won’t work. More viable candidates — especially with higher success rates — still means more demand throughout the development process.
And who knows: clinical trials themselves may eventually be optimized by AI.
?? What breaks the trade?
Near term, the picks-and-shovels trade breaks if experimental budgets stop growing, AI-generated designs don’t translate into useful wet-lab hits, or capacity catches up too quickly.
Longer term, the thesis breaks if AI drugs look great in discovery / Phase I but fail at normal rates in Phase II/III. That is why Phase II matters so much.
?? Milestones
Late 2026–2027: first Isomorphic-designed drugs enter human trials; more AI-native programs move into IND-enabling work / tox.
2028–2030: clinical trial results start telling us whether AI-designed drugs actually perform better than conventional drugs.
Calling all the "bottleneck bros". :) @jukan05 @zephyr_z9 @aleabitoreddit @ParadisLabs
+++
More comprehensive analysis: robonomics.substack.com/p/ai…
Quanquan Gu retweeted
What does an AI-native workflow for protein binder design look like in practice?
In our latest post, we walk through a pilot design run using NovaDDE:
Given a target, the AI agent analyzes the design problem, helps select an epitope and design approach, submits the job, and guides the computational evaluation of the resulting candidates.
We also share some of the directions we’re exploring as we continue to develop the workflow.
A closer look at NovaDDE and where we’re taking it next:
geodesiclab.com/news/novadde…
The future of drug discovery will be built by scientists and AI agents working together.
We’re opening up Geodesic’s models and capabilities through APIs, so scientists, developers, and AI agents can build directly on top of them.
This is another step toward making AI a native part of how medicines are discovered.
Today, we’re launching the Geodesic API Platform.
geodesiclab.com/api
For the first time, Geodesic is making our AI models and drug discovery capabilities available through APIs.
At its core is NovaAtom, our in-house model for predicting the structures of proteins, small molecules, nucleic acids, and their interactions.
Now available in Lite Preview, this is the first time NovaAtom has been made available beyond Geodesic’s own discovery platform.
Alongside NovaAtom, we’ve integrated the field’s core models — carefully curated and continuously updated.
To use the API:
curl -X POST platform.geodesiclab.com/api… \
-H "Authorization: Bearer $GEODESIC_API_KEY" \
-F "model=novaatom" \
-F 'params={"jobName":"rbd-nanobody","sequences":">rbd\nTNLCPFGEVFNATRFASV...\n>nb\nQVQLVESGGGLVQAGGSLR..."}'
Poll the job, pull the results, and feed them directly into the next model.
Your AI assistant can use the platform directly, too. Connect Claude Code, Codex, or your own agent with one URL and an API key.
We manage the integrations and handoffs. You focus on the science.
Understand biology. Predict structures. Design proteins. Discover molecules.
One key. One interface.
Start building today!
Quanquan Gu retweeted
ʙɪɴᴅᴄʀᴀꜰᴛ2 is out, and we're not waiting for the paper. The full code drops today, free for academic and industry use.
We're releasing it early so you can start designing right now, and bring its full power to the current Adaptyv competition.
github.com/PacesaLab/BindCra…
Quanquan Gu retweeted
Near-perfect score on the WebMCP benchmark combining Jev with Mercury 2.5!
Similar to Mercury 2.5, I suspect Jev itself is a diffusion LLM. Generating structured outputs like JSON in parallel is akin to infilling while sampling from a dLLM.
We just ran Jev on our WebMCP benchmark.
The result: basically broke the benchmark.
Jev + Mercury 2.5 (a fast, low-cost LLM) using WebMCP solved 100% of the tasks at roughly 112× lower model cost than GPT-6 Astra using computer use with code execution. Compared to Astra using screenshot-based computer use, the model cost was 245× lower (!).
We also compared Jev operating the browser with and without WebMCP.
We used Browser Use’s open-source Ultrafast, with some improvements to the harness to make it more reliable across the benchmark.
Jev’s browser-control accuracy on its own was not amazing - adding WebMCP nearly doubled the number of solved tasks, from 25/49 to 49/49, while reducing model cost by 18% (more on why below).
The benchmark and methodology are fully open and reproducible.
Full results: webmcp.com/benchmark
A few words on how the Jev + WebMCP harness works and why this is exciting:
Jev receives text as input and a set of discrete options it can choose from. With WebMCP, those options are the tools exposed by the website. At each step, Jev sees the task, the available tools and previous results, then picks what to do next.
The limitation is that Jev can’t generate arbitrary text, which you need for tool arguments. For example, it can choose the search_products tool, but it can’t generate the search query itself.
So we split the work: Jev picks the tool and Mercury 2.5 generates the arguments if needed.
This works well because turns out most of the cognitive load in these tasks is around choosing the right action. The argument generation itself is relatively simple, so we can delegate to a small and very fast model. We used Mercury, which outputs 1,000+ tokens/sec and is very cheap.
The result is a pretty simple combination: Jev for tool selection + Mercury for arguments + WebMCP for the interface. It ends up being very reliable, very fast, and very cheap.
A few words about Ultrafast and why do we think it underperforms:
Without WebMCP, Jev chooses from the page’s controls: which button to click, which field to fill, or which option to select.
But choosing a valid button is different from choosing the right next step. The agent still has to navigate menus, understand forms, recover from errors and recognize when the task is actually complete.
Our hypothesis is that WebMCP makes the decision space much simpler. Instead of figuring out a sequence of clicks through a website, Jev chooses explicit actions that directly advance the task.
@typesafeai itself documents weaker accuracy on questions requiring multiple reasoning steps. WebMCP moves much of that complexity into the website’s tools, leaving Jev with clearer decisions and fewer opportunities to go wrong (in a sense WebMCP "compresses" a sequence of clicks into one tool call).
Our modified Ultrafast setup solved 25/49 tasks - that is a result for our particular implementation and benchmark, not a universal limit on Jev or Browser Use. We are open to more harness optimization to get this result to perform better, feel free to directly contribute to the benchmark here: github.com/nekuda-ai/WindTun…
Browser-use ultrafast: github.com/browser-use/jev-u…
Quanquan Gu retweeted
Our wet-lab validation campaign for Proteina-Complexa is now on bioRxiv! It includes some new exciting experimental results, from large protein structures (fully codesigned!) to functional carbohydrate binders.
biorxiv.org/content/10.64898…
Thread with some of the additions 🧵1/n
The future of drug discovery is AI-native.
Our goal is to give every scientist the tools to explore more ideas, run more experiments, and discover better medicines faster.
NovaDDE Plus is one more step in that direction.
NovaDDE Plus is now live!
Built for scientists who use AI for drug discovery every day — more compute, priority access, concurrent runs, API access, and end-to-end campaign execution.
$30/month and sign up by September 25 to get your first month free.
Our goal is simple: put the most powerful AI for drug discovery into the hands of every scientist.
geodesiclab.com/pricing
Quanquan Gu retweeted
honestly the kind of millennium prize problems that are justified.
We’re launching the Geodesic Grand Challenges.
What are the hardest questions in drug discovery that, if solved, could change what’s possible over the next 5–10 years?
We’re asking you to help define them.
Selected questions will become official Geodesic Grand Challenges. Each selected contributor receives 10,000 Geodesic credits.
Once the challenges are selected, we’ll open a call for solutions, with a $1 million prize for a verified solution to each challenge.
The next breakthrough starts with the right question.
Submit yours!
geodesiclab.com/grand-challe…
Some problems are worth solving as fast as we possibly can.
Drug discovery is one of them.
Let’s find the hardest problems and solve them together!
We’re launching the Geodesic Grand Challenges.
What are the hardest questions in drug discovery that, if solved, could change what’s possible over the next 5–10 years?
We’re asking you to help define them.
Selected questions will become official Geodesic Grand Challenges. Each selected contributor receives 10,000 Geodesic credits.
Once the challenges are selected, we’ll open a call for solutions, with a $1 million prize for a verified solution to each challenge.
The next breakthrough starts with the right question.
Submit yours!
geodesiclab.com/grand-challe…
This is the direction I’m most excited about for AI for Science: closing the loop between models and real-world experiments!
We built high-throughput materials labs in Menlo Park to create a loop between experiments and models. The labs generate fresh data, the models learn from it, and then help us decide what to try next.
Using only 1,300 H200s, plus months of our experimental data, we mid-trained and RL’d an open-source model to surpass GPT-6 Astra on our analysis benchmark. We call it Neon.
This is real footage from our lab. We’re focusing first on hard problems in materials science, including superconductors, magnets, and semiconductor materials.
Read our blog posts below.
Quanquan Gu retweeted
I don't trust anyone's AI risk assessment. I don't think we know what awaits us.
Given that, I'm choosing to be optimistic, betting an existence more extraordinary than we can imagine sits on the other side and it's worth fighting for.
Quanquan Gu retweeted
Well said. Very compact. Sums it all up. I'm optimistic though that while the profession changes, the thirst for knowledge and understanding will not dry up.
Quanquan Gu retweeted
It’s easy to tell whether Muon was used to train a model just by looking at the empirical spectral distribution of its hidden layer weights. Compared with SGD/Adam, Muon leaves a very distinctive spectral signature in W^T W. This is because Muon updates low-magnitude directions more aggressively.
Just got this incredible news from UCLA Math Circle.
Two high school students, Aayush Bathija and Prince Rohatgi, working with postdoc Daniel Soskin through the UCLA Math Circle, have solved a problem that Fields Medalist June Huh had previously worked on without solving.
The paper was heavily AI-assisted.
Whatever your view on AI in mathematics, enabling high school students to push the frontier of mathematical research is something worth celebrating.
arxiv.org/abs/2609.05341
Mathematicians are increasingly using AI themselves to solve problems. If a problem is genuinely solved, with a rigorous proof that can be independently verified, why should it matter whether the AI was operated by a mathematician, an enthusiast, a university, or an AI company?
I’m happy to see pharma and many leading scientists taking a much more open view of AI for drug discovery.
If AI can help us understand biology faster, design better therapeutics, and get medicines to patients years earlier, accelerating discovery is exactly the point.
Many problems are just too important to solve slowly.


























