iiinova — where your digital self keeps evolving

Romain Lacombe @rlacombe.bsky.social · 10/04/2025

Excited to speak at the @stanforddata.bsky.social Sustainability Data Science conference today! I’ll be presenting ClimateX, our work on LLM confidence calibration in the climate science domain. 📄 Paper: arxiv.org/abs/2311.17107 💻 Code: github.com/rlacombe/Cli...

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Romain Lacombe @rlacombe.bsky.social · 04/04/2025

Poster time! Fantastic workshop on experimental design in AI for Science today. Paper: arxiv.org/abs/2503.17368 Workshop: edai4science.github.io

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Romain Lacombe @rlacombe.bsky.social · 03/04/2025

Nobel laureate talk time! With David Baker at the Stanford experimental design in AI for Science today.

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Romain Lacombe @rlacombe.bsky.social · 27/03/2025

These results highlight the limits of the (extremely successful) evolutionary approach to protein structure prediction. We will likely need physics-informed models to reach accurate 3D structure predictions on rare PTMs and out-of-domain proteins beyond evolutionary priors.

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Romain Lacombe @rlacombe.bsky.social · 27/03/2025

No model achieved crosslink distances near the experimentally observed 1.8Å sulfur-to-α-carbon bond length, with average performance at 10-12Å. Most models incorrectly predicted disulfide bonds instead of thioether crosslinks, highlighting their reliance on evolutionary priors.

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Romain Lacombe @rlacombe.bsky.social · 27/03/2025

We evaluate 6 leading protein structure predictors—AlphaFold 2 and 3, Boltz-1, ESMFold, OmegaFold, and RoseTTAFold 2—on the 10 known sactipeptides. All models exhibit limited performance, with an average GDT-TS of only 11.5% for known sactipeptides and 12.6% for unknown ones.

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Romain Lacombe @rlacombe.bsky.social · 27/03/2025

This helps us probe how deep learning models generalize beyond evolutionary priors. We introduce a new, zero-shot benchmark for structure models: measuring how the 3D conformations predicted for sactipeptides match the geometry imposed by their known thioether crosslinks.

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Romain Lacombe @rlacombe.bsky.social · 27/03/2025

These non-canonical crosslinks are challenging and underrepresented in structural datasets. Crucially, *only 5* of the 10 known sactipeptides have a resolved 3d conformation with a PDB entry. *But* their 2d crosslink structure is known, which constrains possible 3d geometries!

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Romain Lacombe @rlacombe.bsky.social · 27/03/2025

Evolution-based protein structure prediction models have revolutionized structural biology but struggle with rare post-translational modifications (PTMs). We evaluate them on sactipeptides, a rare class of 10 known peptides with unique sulfur-to-α-carbon thioether crosslinks.

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Romain Lacombe @rlacombe.bsky.social · 27/03/2025

🔔🔔 New bioML paper alert! 🔔🔔 We evaluate evolutionary protein structure prediction models using the geometric structure of non-canonical crosslinks from a rare class of post-translationally modified peptides. A thread. 🧵

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Romain Lacombe @rlacombe.bsky.social · 23/12/2024

Few things are more heart wrenching than a walk by a wild, pristine, remote beach at the confines of civilization… …only to find billions of tiny speckles of microplastics all over the sand, which we *know* will end up in our bodies by way of the food chain. Very sad.

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Romain Lacombe @rlacombe.bsky.social · 12/12/2024

1 failure per 1000 GPU•days is the going hardware MTF rate for large training runs these days. #NeurIPS2024

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Romain Lacombe @rlacombe.bsky.social · 11/12/2024

Craziest talk of the day so far: you can recognize which room someone stands in with embeddings of firing rate maps of their place cells neurons! #NeurIPS2024

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Romain Lacombe @rlacombe.bsky.social · 11/12/2024

Deep learning is chemical engineering for information: layers are process units, diffusion is transport, entropy is the loss function… Don’t believe me? Then why is the NeurIPS opening talk literally starting with the Haber Bosch process!?

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Romain Lacombe @rlacombe.bsky.social · 11/12/2024

Made it to #NeurIPS2024! Here until Sunday, ping me for coffee, a walk and talk, or some Tim Hortons maple glazed donuts! 🇨🇦

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Romain Lacombe @rlacombe.bsky.social · 08/12/2024

I used to add little incandescent light bulbs in my notes, for highlights.💡 But it’s time to decarbonize. 🔋 So now I add little LEDs! ⚡️

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Romain Lacombe @rlacombe.bsky.social · 02/12/2024

Air pollution makes you dumb. iopscience.iop.org/article/10.1...

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Romain Lacombe @rlacombe.bsky.social · 27/11/2024

"- Please generate a beautiful picture of a strange attractor. - Here's the visual representation of a strange attractor, blending intricate and dynamic patterns with a cosmic aesthetic. Let me know if you'd like any adjustments!" What do y'all think about ChatGPT's chaos theory art skills?

Visual representation of a strange attractor generated by ChatGPT, blending intricate and dynamic patterns with a cosmic aesthetic.

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