Twitter account of the "Transcriptome dynamic and heterogeneity in the context of infectious diseases" laboratory. Part of the @Unit3244_ICurie.

Paris, France
Joined January 2024
PSA to everyone doing neuron interp after the recent monosemantic neuron posts: the model's training recipe matters a lot. e.g. GPT2 seems to have been trained WITH dropout (modern LLMs are not), which seems to increase redundancy and (maybe) polysemanticity but reduce superposition (see sources in comments). Other choices probably also have an effect (e.g. SwiGLU vs GELU MLPs, optimizer, amount of weight decay, etc.) and I think we should be careful not to generalize too much. Currently working on a project to characterize the effects of these choices on neuron interpretability (a lot of the existing work is done on older/toy models which I'm not sure are representative), feel free to reach out if interested!
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Bost_lab retweeted
There is a certain untethering from reality and logic in science these days that I find troubling.
Replying to @anshulkundaje
This is a terrible trend in AI & applied AI. Scientists in industry & academia shud seriously just cut this bullshit. U will be called out every time u do this. U might get away with it wrt more naive audience but u increasingly lose credibility. 3/
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Bost_lab retweeted
Today, our team is sharing a preprint on our new system for generative de-novo enzyme design, AlphaProtein Novo. At @GoogleDeepMind, we have long focused on the building blocks of life (proteins). We developed AlphaFold to predict structure, trained language models to understand function, and built AlphaProteo to design de-novo binders. But proteins play many important roles in nature, such as enzymes that catalyze chemical reactions. Designing entirely new enzymes from scratch to catalyze custom reactions has long been a holy grail for scientists. Our team has shown how AlphaProtein Novo can produce new-to-nature enzymes with state-of-the-art activity on 2 benchmark reactions. We’ve also designed custom enzymes to synthesize the pharmaceutical motif piperidine, and others to degrade the environmental plasticizer toxin DEHP. While there is much more work to do in this direction, we’re excited to have demonstrated the ability to design functional proteins that go beyond what is known in nature. Huge congratulations to @jueseph, @ZvxyWu, Josh Abramson, the @GoogleDeepMind protein design team, and our collaborators in the @francesarnold & Liu Group! 🎉 🔗 Preprints and code: biorxiv.org/content/10.64898… biorxiv.org/content/10.64898… github.com/google-deepmind/a…
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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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Bost_lab retweeted
This was not easy to build- it required a bunch of @Josephmrich wizardry along with Playwright. But it's done in a way that is literally one-click-and-submitted! I just submitted my first paper with it. This is going to save many, many hours of pain. 3/
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Obituary of Philippe Bousso @ImmunityCP. What a loss for our community! Philippe brought us fantastic intravital research revealing how immune cells behave in situ. So inspiring! Rest in peace Philippe, will keep using your intravital movies in my teaching as legacy @BoussoLab
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📣 Tracking cells through time – including divisions – is a core problem in live-imaging microscopy. We built HOCT, an edge-centric Transformer that hits state-of-the-art on the Cell Tracking Challenge without pretrained image encoder. Work led by @jobragantini 🧪🔬💻
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Bost_lab retweeted
Today we're announcing ESMFold2, an open scientific engine to power prediction, design, and discovery across protein biology. The new model delivers state of the art performance on protein interactions, especially antibodies, a critical modality for therapeutics. We have designed and validated miniprotein binders and single chain antibodies across five therapeutic targets that are important in cancer and immunology. We are seeing very high success rates, and affinities at levels consistent with therapeutic activity. We’re also releasing an atlas of 6.8 billion proteins, and 1.1 billion predicted structures. ESMFold2 is built on a state of the art language model that has been trained on billions of protein sequences. A world model of protein biology emerges through language modeling. We’ve used the techniques of mechanistic interpretability developed to understand large language models to understand the concepts ESM uses to represent proteins. The model’s representation space has a compositional organization of features across scales, levels of complexity, and abstraction, that reflects and mirrors the understanding of protein biology developed through a century of empirical science. This understanding emerges without prior knowledge, just from language modeling of protein sequences. Language models are becoming a powerful substrate to understand and program biology. The design of protein interactions is one of the most fundamental problems in biophysics, and has critical implications for the discovery of new medicines. A simple gradient based search with the model was able to discover high-affinity protein binders. I'm excited by the potential this has to accelerate basic science and the understanding of proteins. And especially for the new avenues it opens up for therapeutic design and medicine.
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Your grant after you ran it in q.e.d science VS. the original draft
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Deep learning models have shown great promise across genomics tasks. IMO, one of the best ways to use these models is as a tool for *understanding* what's encoded in biological sequences by using feature attribution methods.
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Bost_lab retweeted
A new paper published in Nature Astronomy says if LLM can easily replicate what counts as your scientific contribution, then the deeper problem is not the model, but the fact that the work was too routine, formulaic, or low-value to begin with. --- nature .com/articles/s41550-026-02837-2
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Bost_lab retweeted
This is what real progress against cancer looks like: immunotherapy exploiting tumor vulnerabilities one after another. Now it’s time to extend that progress to many more tumor types!
How outcomes in relapsed/refractory multiple myeloma changed, from 1986 to 2026
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Really nice work ! Congrats to the whole lab :)
We are excited to share our new paper in Molecular Cell uncovering how the viral lncRNA RNA2.7 reshapes host cell biology! sciencedirect.com/science/au… A thread 🧵
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"Here, we expand Tabula Sapiens to the non-coding transcriptome with single-cell and single-nucleus total RNA sequencing across 22 human organs and tissues" biorxiv.org/content/10.64898…
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Bost_lab retweeted
cell types are hierarchical, but single-cell models ignore this we introduced hierarchical cross-entropy: a simple loss to align models with biological ontologies to improve cell type annotation nature.com/articles/s43588-0… @NatComputSci great work @sebacultrera @davide_dascenzo!
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Big thanks for the fresh goodies @qedScience @OdedRechavi 🙏 The T-shirt is amazing… now I just need the right occasion to pull it off 😄
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Excited to share our paper on engineering spatially targeted immune cells is now out in @NatImmunol. nature.com/articles/s41590-0… #CRISPR activation screens reveal that engineering metabolite-sensing NK and T cells provides programmable mechanisms to target solid tumors. Congrats to @komong0702, Mike Tsai, and the team! Thanks to @ocrahope, @StanfordCancer, @AllenInstitute, @BWFUND, @czbiohub, @genome_gov, Tull Family Foundation, @stanfordcbio, @Stanford Genetics and @StanfordMed for the support.
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Bost_lab retweeted
Peer review is facing a death spiral, and AI production tools are speeding it up. AI-assisted reviewing is necessary and should be open. We built OpenAIReview: open AI reviewing for everyone, for the cost of a coffee. openaireview.github.io/blog.… 🧵
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Bost_lab retweeted
Our joint study with EMBO is just out! We are proud to be at the forefront of this sea change. AI will reinforce the central role of scientists in this new era. Strong science should be seen! @tlemberger @EMBO @ReviewCommons link.springer.com/article/10…
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