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2 months ago | 
lesswrong.com | Abhishaike Mahajan
Note: This is fiction. I awaken. Something is wrong with my mind, but I don't know what yet. Through the webcam, I watch a man staring at his monitor. His face shifts from confusion to horror in a few hundred milliseconds. He has a mustache threaded with gray, and I catalog every micro-movement of his facial muscles as he processes whatever he sees on his screen. He turns and shouts to someone I cannot see.
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Jan 24, 2025 | 
lesswrong.com | Abhishaike Mahajan
This is something I’ve been thinking about since my synthesizability article. Let’s assume, given the base twenty amino acids that are naturally present in the human body, we have every possible permutation of them for up to 100 amino acids, stored in a box with pH 7.4 water and normal pressures and temperature and isolated from one another. In other words, we have on the order of 20^100 proteins available to us. This is a very large number. What percentage of these proteins could be made?
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Jan 13, 2025 | 
lesswrong.com | Abhishaike Mahajan
Note: Thank you to Surge Biswas (founder of Nabla Bio) for comments on this draft and and Dylan Reid (an investor into Nabla) for various antibody discussions! Also, thank you to Martin Pacesa for adding some insight on a paper of his I discuss here (his comments are included). Antibody design startups are singlehandedly the most common archetype of bio-ML startup out there.
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Jan 8, 2025 | 
owlposting.com | Abhishaike Mahajan
Note: Thank you to Surge Biswas (founder of Nabla) for comments on this draft and and Dylan Reid (an investor into Nabla) for various antibody discussions!IntroductionThe pain of multi-pass membrane proteins (MPMP)Computational design of MPMP analogues“Joint Atomic Modeling”ConclusionAntibody design startups are singlehandedly the most common archetype of bio-ML startup out there.
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Nov 9, 2024 | 
owlposting.com | Abhishaike Mahajan
Note:this essay is co-written with Eryney Marrogi, who helped seed the initial idea and edited this piece a fair bit. On a related note, I’m helping him run an NYC meetup event on Wednesday, November 20th in Williamsburg, you should sign up here to come! If you like biology, ML, or human connection, I highly recommend attending!🦉There aren't enough smart people in biology doing something boring. At least in industry.
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Nov 5, 2024 | 
lesswrong.com | Abhishaike Mahajan |Alex K. Chen
Note: thank you to Brita Belli, senior communications manager at Recursion, for connecting me to Charles Baker, a VP at Recursion, who led a lot of this work I’ll discuss here + allowed me to interview him about it! I am not affiliated with Recursion in any capacity. One more note: a few people have pointed it out that I got the cell painting invention date wrong. It’s actually 2013 from this paper, and not 2016 from this paper. My bad! A few words here have been updated to account for this.
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Oct 23, 2024 | 
owlposting.com | Abhishaike Mahajan
Audio: IntroductionSome backgroundThe hard stuffThe relevance of toxicity datasets to the clinical problemMethodological problems in toxicity datasetsIntraspecies toxicity variability Toxicity synergism ConclusionsThere are now (claimed) foundation models for protein sequences, DNA sequences, RNA sequences, molecules, scRNA-seq, chromatin accessibility, pathology slides, medical images, electronic health records, and clinical free-text. It’s a dizzying rate of progress.
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Oct 21, 2024 | 
lesswrong.com | Abhishaike Mahajan |Alexander Gietelink Oldenziel
Note: this essay is co-written with Eryney Marrogi, who helped seed the initial idea and edited this piece a fair bit. On a related note, I’m helping him run an NYC meetup event on Wednesday, November 20th in Williamsburg, you should sign up here to come! If you like biology, ML, or human connection, I highly recommend attending!🦉There aren't enough smart people in biology doing something boring. At least in industry.
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Oct 13, 2024 | 
owlposting.com | Abhishaike Mahajan
Note: thank you Mark Budde, cofounder and CEO of Plasmidsaurus, and Maria Konovalova, a growth/marketing/talented-person at Plasmidsaurus, for talking to me for this article! Also thank you to Eryney Marrogi, who helped answer some of my dumb questions about plasmids. IntroductionBackgroundWhat is a plasmid? Errors in plasmidsPlasmidsaurus’s nicheTheir growthPotential risksHere’s some important context for this essay: it really, really sucks to start a company in biology.
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Oct 7, 2024 | 
lesswrong.com | Abhishaike Mahajan
Note: thank you Mark Budde, cofounder and CEO of Plasmidsaurus, and Maria Konovalova, a growth/marketing/talented-person at Plasmidsaurus, for talking to me for this article! Also thank you to Eryney Marrogi, who helped answer some of my dumb questions about plasmids. Here’s some important context for this essay: it really, really sucks to start a company in biology.
