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CTO and Chief Data Scientist at Foresite Labs. Lifter, runner, dog dad when I’m not working. Scientist, engineer, statistician when I am. Always a nerd

CA
Joined October 2008
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After years of building AI models to decode the language of cells, I’m thrilled to announce my next chapter: I will join Xaira Therapeutics as SVP and Head of Biomedical AI. Xaira’s vision is bold—and deeply aligned with my own: to build a virtual cell powered by AI, capable of unraveling the molecular basis of disease and matching the right therapy to the right patient. This is more than just drug discovery—it’s an opportunity to fundamentally rethink how we understand and treat human disease, from first principles to real-world cures. With a $1B+ war chest, an all-star team, and the long view in mind, we’re setting out to do something transformative: create foundation models that can reason over biology and bring precision and speed to every step of therapeutic development. At the same time, I’ll be maintaining my academic affiliations at University of Toronto, UHN, and Vector Institute during the next year to ensure a smooth transition—for my students, collaborators, and the many ongoing projects I deeply care about. Grateful to my mentors, collaborators, students for getting me here. The best is yet to come. Let’s build the future of medicine. #AI #DrugDiscovery #FoundationModels #VirtualCell #Xaira #scGPT #Biomedicine
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We're excited to welcome Paulo Fontoura to our team as chief medical officer! He brings a wealth of experience and deep insight to help advance our mission of leveraging AI to transform drug discovery. More info in today's announcement: bit.ly/3BxfbfO
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Congratulations to our co-founder, David Baker, and to John Jumper and @demishassabis of Google DeepMind, for sharing this year’s Nobel Prize in Chemistry! Their stunning breakthroughs have provided the foundation for our work at Xaira, and we couldn't be more proud.
“I got the phone call and my wife promptly started screaming.” The 2024 #NobelPrize in Chemistry gave David Baker’s household an early wake up call. We talk about the potential of building new proteins and the inspirational effect his fellow laureates have had on his field.
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If NVIDIA ever fails, it’s bc they got stuck at CUDA and never moved on to WUDA and SHUDA.
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Read the methods before reading the results Read the methods before reading the conclusions Read the methods before evaluating the conclusions Read the methods before making conclusions Read the methods!
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- Regulators should regulate applications, not technology. - Regulating basic technology will put an end to innovation. - Making technology developers liable for bad uses of products built from their technology will simply stop technology development. - It will certainly stop the distribution of open source AI platforms, which will kill the entire AI ecosystem, not just startups, but also academic research. - the strangest aspect of all this is that all of these regulations are based on completely hypothetical science fiction scenario that very, very few people in the field are plausible.
The effort to protect innovation and open source continues. I believe we’re all better off if anyone can carry out basic AI research and share their innovations. Right now, I’m deeply concerned about California's proposed law SB-1047. It’s a long, complex bill with many parts that require safety assessments, shutdown capability for models, and so on. There are many things wrong with this bill, but I’d like to focus here on just one: It defines an unreasonable “hazardous capability” designation that may make builders of large AI models liable if someone uses their models to do something that exceeds the bill’s definition of harm (such as causing $500 million in damage). That is practically impossible for any AI builder to ensure. If the bill is passed in its present form, it will stifle AI model builders, especially open source developers. Some AI applications, for example in healthcare, are risky. But as I wrote previously, regulators should regulate applications rather than technology. - Technology refers to tools that can be applied in many ways to solve various problems. - Applications are specific implementations of technologies designed to meet particular customer needs. For example, an electric motor is a technology. When we put it in a blender, an electric vehicle, dialysis machine, or guided bomb, it becomes an application. Imagine if we passed laws saying, if anyone uses a motor in a harmful way, the motor manufacturer is liable. Motor makers would either shut down or make motors so tiny as to be useless for most applications. If we pass such a law, sure, we might stop people from building guided bombs, but we’d also lose blenders, electric vehicles, and dialysis machines. In contrast, if we look at specific applications, like blenders, we can more rationally assess risks and figure out how to make sure they’re safe, and even ban classes of applications, like certain types of munitions. Safety is a property of the application, not a property of the technology (or model), as @random_walker and @sayashk have pointed out. Whether a blender is a safe one can’t be determined by examining the electric motor. A similar argument holds for AI. SB-1047 doesn’t account for this distinction. It ignores the reality that the number of beneficial uses of AI models is, like electric motors, vastly greater than the number of harmful ones. But, just as no one knows how to build a motor that can’t be used to cause harm, no one has figured out how to make sure an AI model can’t be adapted to harmful uses. In the case of open source models, there’s no known defense to fine-tuning to remove RLHF alignment. And jailbreaking work has shown that even closed-source, proprietary models that have been properly aligned can be attacked in ways that make them give harmful responses. Indeed, the sharp-witted @elder_plinius regularly tweets about jailbreaks for closed models. Kudos also to Anthropic’s @cem__anil and collaborators for publishing their work on many-shot jailbreaking, an attack that can get leading large language models to give inappropriate responses and is hard to defend against. California has been home to a lot of innovation in AI. I’m worried that this anti-competitive, anti-innovation proposal has gotten so much traction in the legislature. Worse, other jurisdictions often follow California, and it would be awful if they were to do so in this instance. SB-1047 passed in a key vote in the State Senate in May, but it still has additional steps before it becomes law. I hope you will speak out against it if you get a chance to do so. [Original text (with links): deeplearning.ai/the-batch/is… ]
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Love what this team’s doing. Awesome work
OpenFold developed by @gahdritz, @NazimBouatta, and @MoAlQuraishi is a trainable, open-source implementation of AlphaFold2. It is fast and memory efficient, and the code and training data are available under a permissive license. nature.com/articles/s41592-0…
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OpenFold developed by @gahdritz, @NazimBouatta, and @MoAlQuraishi is a trainable, open-source implementation of AlphaFold2. It is fast and memory efficient, and the code and training data are available under a permissive license. nature.com/articles/s41592-0…
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Fantastic lab!
🔥 Hiring a funded postdoctoral fellow position in human genetics! Come join us @CGM_MGH @broadinstitute @harvardmed! 🔥 Apply: partners.taleo.net/careersec…
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It is a pleasure to work with Vik Bajaj and his team at Foresite Labs and well as David Baker, Hetu Kamisetty, and their teams, Olivia Zetter from ARCH, and to back Marc Tessier Lavigne again. Excited to try to cure disease and fix the system.
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A landmark study. Adverse drug outcomes significantly lower in those with pharmacogenomically-guided therapy. It is time to make personalized prescribing a reality. sciencedirect.com/science/ar…
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Happy holidays from all of us at Foresite Labs. Wishing everyone a fantastic new year! As we begin the new year, we are looking to continue to grow our team. If you're interested in working with us or our incubated companies, check out our careers page: careers.foresitelabs.com/com…
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We are doing this for eQTLs and want to do for other types of molecular QTLs! Completely agree that most of the effort seems relatively boring, but the harmonised datasets are worth it and enable many new questions to be asked.
Replying to @anshulkundaje
Data standards, uniform processing pipelines, QC, metadata curation, reconciliation, harmonization are considered the most 'boring' components of doing individual or team science. Nobody wants to usually do it. This is because we don't realize the value of this boring investment.
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one of the most consistent oversights in platform development in biotech is not validating known biology this should be experiment #1. reproduce something that is already known on your platform before trying to discover something new
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New preprint from the lab! We made a software package to design indexing primers for high-throughput sequencing. Here's a link to the tweetorial from co-first author @OmarTariqBio
Have you ever done a double take after looking up the cost of commercial NGS prep kits? If so, you'll probably be interested our new preprint...(1/9)
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