SVP Compute at @insitro. Previously at Myriad and Counsyl. Interested in compbio, phylogenetics, pop gen, data eng (redun), note-taking (KeepNote).

San Francisco, CA
Joined December 2011
Today, I'm excited to share some work our team has been doing over the last few years at @insitro. It's a new tool for data science called redun. We describe the motivation and contributions in this post. github.com/insitro/redun/
We're excited to announce the open sourcing of redun, an expressive, efficient, and easy-to-use workflow framework designed to deal with complex, rapidly evolving scientific workflows spanning multiple data types. Read more here: insitro.medium.com/8b06b707a…
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We’re thrilled to share that Lamin is now generally available! With just a few clicks, anyone can create a database on lamin.ai In 2022, we set out to build an open-source data management tool that’d make it easier to scale AI workflows in the life sciences. Over the past few years, we’ve served research labs and enterprises of all sizes with what used to take a dozen tools: - Data lineage - Format-agnostic lakehouse - Notes, ELN, LIMS, ontologies - Versioning, branching - Data lake, catalog - Agents, workflows, notebooks - Feature store, MLOps With Lamin, it’s just Postgres and storage in a Python package, plus an optional GitHub-like web platform. Give it a try: pip install lamindb Thanks to @_DimensionCap and @ycombinator and many others who made this possible
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Honored to be selected as a STAT Wunderkind this year, alongside so many incredible and inspiring scientists!
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Trying out X articles, decided to at last explain my criticisms graph libraries properly. Graphs are dead, long live graphs.
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Shared some notes on Python 3.15, using it with uv, and features from Python 3.11 I'm excited to use now that 3.10 is no longer the minimum supported version for my own projects simonwillison.net/2026/Oct/1…
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Welcome to our Monday Meditations! 🌞 Today @badlogicgames and @mitsuhiko are talking why we built Pi Durable, a harness build around a small task-based workflow engine so long-running, multiplayer agents can suspend and resume anywhere. Also: why not Temporal or Effect.ts.
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🗞️ an application in lisp you grow by talking to it Why is software built the way it is now, rather than grown through iterative use of LLMs? What if you could develop your application just by chatting with it? Live and interactive, with no compilation steps. ghuntley.com/lisp/
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A lot of the long-running persistent sandbox stuff today feels like lift-and-shift. I suspect sandboxes will evolve from being “devboxes in the cloud” to something much more ephemeral. One environment for every _command_. And snapshotting in between so you can pause/resume/clone.
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In light of the progress in mathematics, we at Edison Scientific and FutureHouse have assembled a set of Millennium Problems for Biology. They are chosen to be very hard to solve but very easy to validate in a simple laboratory environment. Any of these, if solved, would mark a major advance in biotechnology, and most of them would contribute materially towards curing disease. These are, in some sense, the “last reasonable eval” for AI in biology. This was work primarily by @MichaelaThinks and myself, with contributions from many others. Short descriptions below. The full descriptions of the problems with acceptance criteria are at the Bio Millennium Problems website, linked in the next post. Share more if you have ideas. If they meet our criteria, we’ll add them to our list (with attribution and permission).
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In the next ty release, we have full support for recursive implicit type aliases (at arbitrary depths). For the type theorists among us, this is implemented using mu types.
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So excited that the DeepMind Institute has launched today! I am leading Post-AGI Interaction Research for DMI, to ensure that the future is one in with safe, delightful, agency-preserving Human-AI Interactions.
My journey to develop AGI spans 25 yrs, including 10+ yrs thinking about technical & societal perspectives at Google DeepMind. AGI is on the horizon - we need deeper understanding of its implications. To help, we've created the DeepMind Institute.
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it’s hilarious how everyone keeps reinventing Erlang supervision trees tech from the 80s, people
Cursor's harness for thousands of coding agents went through four designs Each got better by removing a role: the planner, then the judge, then the integrator What survived: a recursive planner tree, workers that never talk to each other, one handoff message flowing up 5-min animated walkthrough of the whole post:
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I asked my AI to solve this long-standing problem before you asked yours.
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I shared before that my only paper as a PhD student was published in @GenomeResearch 20 years ago. I'm delighted to share that I recently joined the journal as an editor genome.cshlp.org/about. This feels very personal. As a student, I learned genome biology partly by reading papers by Rick Myers, Evan Eichler, Aravinda Chakravarti, Richard Gibbs, and Anne Ferguson-Smith, and I took Kateryna Makova's evolutionary genomics class in grad school. Now I get to join them in weekly editorial meetings - It still feels a bit surreal. One thing that makes @GenomeResearch special is that its 7 editors are active scientists who discuss new submissions and make editorial suggestions together. We meet every week on Zoom - and yes, we look at submissions over the weekend. I am new - but some editors have served the journal for decades. I've been struck by the seriousness, care, and sense of stewardship they bring to every paper and to the journal as a whole. @GenomeResearch is a nonprofit journal that has published landmark papers and helped shape genomics for decades, while remaining deeply committed to the research community. I am honored to play a small part in what come next. We all have many choices about where to submit our work. Whether you work in comp biology, AI for genomics, genomic technologies, disease genomics, genomic variation, evolutionary genomics, or other areas of genome biology, I hope you continue sending your exciting work to @GenomeResearch
20 years ago today, on April 7, 2006, I submitted the only paper I published during my PhD to @genomeresearch. By today's standards, the work feels too simple, and every figure looks plain. Science has moved fast, and I am working on completely different problems now. That era is gone. genome.cshlp.org/content/16/…
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I'm so freakin sick of how Claude talks. It's not just annoying, it's infuriating. The honest evaluation: it's the precise mechanism driving my current headache. It's the load-bearing root cause of my daily stress. It's genuinely painful, and that matters.
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🚨 New pub alert! At @ArcadiaScience, we just released this open-source system for capturing instrumentation data, processing it, uploading to cloud storage, and making it available for humans, workflows, and autonomous agents. We hope you can adapt it for your own internal instrumentation! thestacks.org/publications/r…
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My hunch is that ~95% of venture capital deployed into Bio x AI is funding better bullets, not identifying targets worth shooting at. Hard to believe that alone will transform healthcare. We need AI that can decode biological function.
Was chatting with a wet-lab experimentalist friend doing cancer stuff back at Yale and she told me something along the lines of "yah using AI for binder design is cool and all but idk where exactly to use it when so much is unknown about the underlying pathways that control disease progression" Helped put a ton of things into perspective on how experimentalists currently view such tools and what they'd actually like to see
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Fabulous essay from one of the OGs of AI x bio "Drug Discovery Has No Magic Wands" Everyone should read it and digest it.
Only about a quarter of human diseases have an approved therapy. By some estimates it's a few percent. Most of those treatments slow a disease rather than stop it. Closing that gap is what the AI-cures-everything story promises. Build a system smart enough and the cures hidden in what we already know will fall out. I have worked at the intersection of machine learning and biology for three decades, and I believe #AI will eventually transform human health. The capabilities arriving now are extraordinary. But the promise rests on an assumption that is simply false: that we already understand human biology well enough for a clever enough reasoner to find the answers in it. We don't. More than 90% of drugs entering clinical trials fail, a number that has barely moved in decades. In the large majority of those failures the molecule was engineered just fine. The mechanism it targeted was wrong. We are doing a pretty good job at manufacturing keys, but they are generally for the wrong locks. And because nobody wants to fail in the clinic, the industry has retreated to the locks it already trusts: 38 targets now have more than 50 programs against each of them, while the number of novel targets advanced per year fell from roughly 100 in 2015 to about 30 in 2024. AI will not reason its way past this. Biology wasn't engineered. It is the product of billions of years of messy, stochastic evolution, and the variation that produced is too vast and too idiosyncratic to work out in the abstract. You have to measure it. Aimed at a biology this thinly sampled, AI will mostly help us generate failures faster. I founded @insitro because getting to the right locks requires a different kind of system. We generate multimodal human and cellular data at scale, use machine learning to find causal drivers of disease, and test those hypotheses experimentally. Virtual Human™ is built for causal discovery; TherML™ turns what it finds into the right therapeutic intervention. It is working: first-in-class programs internally and with partners, three #ALS targets that Virtual Human™ identified and @bmsnews nominated, and additional collaborations with @EliLillyandCo and @GileadSciences . Today we are launching Deep Phenotype: Scaled Biology, Deep Causality. Issue one is "Drug Discovery Has No Magic Wands," the first half of a two-part essay on the magical thinking currently running through our field and what I think it will actually take. After that you will hear from insitro's own scientists and engineers, people who work across computation and experiment because the problem requires both. Getting this right is hard, and we do not have all of it worked out. I hope you will follow along and think it through with us. DeepPhenotype.Substack.com
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Matt Rasmussen retweeted
Only about a quarter of human diseases have an approved therapy. By some estimates it's a few percent. Most of those treatments slow a disease rather than stop it. Closing that gap is what the AI-cures-everything story promises. Build a system smart enough and the cures hidden in what we already know will fall out. I have worked at the intersection of machine learning and biology for three decades, and I believe #AI will eventually transform human health. The capabilities arriving now are extraordinary. But the promise rests on an assumption that is simply false: that we already understand human biology well enough for a clever enough reasoner to find the answers in it. We don't. More than 90% of drugs entering clinical trials fail, a number that has barely moved in decades. In the large majority of those failures the molecule was engineered just fine. The mechanism it targeted was wrong. We are doing a pretty good job at manufacturing keys, but they are generally for the wrong locks. And because nobody wants to fail in the clinic, the industry has retreated to the locks it already trusts: 38 targets now have more than 50 programs against each of them, while the number of novel targets advanced per year fell from roughly 100 in 2015 to about 30 in 2024. AI will not reason its way past this. Biology wasn't engineered. It is the product of billions of years of messy, stochastic evolution, and the variation that produced is too vast and too idiosyncratic to work out in the abstract. You have to measure it. Aimed at a biology this thinly sampled, AI will mostly help us generate failures faster. I founded @insitro because getting to the right locks requires a different kind of system. We generate multimodal human and cellular data at scale, use machine learning to find causal drivers of disease, and test those hypotheses experimentally. Virtual Human™ is built for causal discovery; TherML™ turns what it finds into the right therapeutic intervention. It is working: first-in-class programs internally and with partners, three #ALS targets that Virtual Human™ identified and @bmsnews nominated, and additional collaborations with @EliLillyandCo and @GileadSciences . Today we are launching Deep Phenotype: Scaled Biology, Deep Causality. Issue one is "Drug Discovery Has No Magic Wands," the first half of a two-part essay on the magical thinking currently running through our field and what I think it will actually take. After that you will hear from insitro's own scientists and engineers, people who work across computation and experiment because the problem requires both. Getting this right is hard, and we do not have all of it worked out. I hope you will follow along and think it through with us. DeepPhenotype.Substack.com
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The data we need to understand human biology is about 1000x the quantity we've collected Full piece from @insitro founder and CEO @DaphneKoller: a16z.news/p/drug-discovery-h…
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Matt Rasmussen retweeted
Asking "what have note-taking apps accomplished?" is like asking "what have spreadsheets accomplished?" or "what have cameras accomplished?". A tool doesn't accomplish anything on its own. A tool is a means to an end. A few days ago, someone jokingly asked if Henry Ford had a personal knowledge base in Obsidian. Well, sort of! He had something he called "jot books", where he journaled, kept notes, grocery lists, etc... Not dissimilar to how people use Obsidian. The Henry Ford Museum has fifty of these notebooks. How should we quantify the impact of Henry Ford's notebooks? How should we quantify the impact of spreadsheets? Most people who accomplish anything take notes in some form, because writing is a way of thinking. We love to mythologize the tools and methods of accomplished people because we hope it will let us absorb a bit of their genius. But a good camera doesn't make a good photographer. Taking lots of photos helps. Should you take notes? Probably. Does it matter what your method is? Probably not. Whatever works for you. Obsidian (or any other form of notetaking) is successful if it disappears and lets you accomplish your work.
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