Divya Nori
@divnori
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CS PhD @Stanford | @MIT alum | AI x Bio
Cambridge, Massachusetts
Joined July 2020
đź’» BECraft Code: Very grateful to work with Anisha Parsan, @CarolineUhler, and @WengongJin. Huge thank you to the original BindCraft creators, @MartinPacesa @sokrypton @befcorreia, for building a powerful foundation and making the code easy to extend.
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Beyond hallucination, pTMEnergy shines in virtual screening. It outperforms supervised, physics-based, and structure-based baselines at classifying miniprotein binders and RNA aptamers.
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By integrating pTMEnergy into the hallucination loop, we get BECraft, a drop-in extension to BindCraft that backprops through AlphaFold2 using this new energy. BECraft outperforms BindCraft, RFDiffusion, and ESM3 across 8 diverse targets 🚀.
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We fix this with pTMEnergy 💡. It reinterprets AlphaFold’s pAE logits as an energy-based model (EBM) which:.✅ Reflects the true statistical likelihood of the binder-target complex.✅ Enables dense gradients across the entire interface.
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BindCraft has become a go-to tool for protein binder design, using AlphaFold2 hallucination + ipTM-based backpropagation to optimize sequences. But ipTM has limitations:. ⚠️ It's a heuristic, not a proper likelihood. ⚠️ It yields sparse gradients, making optimization tricky.
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🔥 Introducing BindEnergyCraft (BECraft), the BindCraft pipeline you know and love, now enhanced with an energy-based loss to boost in silico binder success! Thrilled to present this as an oral at ICML @genbio_workshop next week. 📄 Paper: 🧵Thread⬇️
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RT @ml4proteins: We are excited to announce the launch of our new series of talks for early career scientists, including assistant professo….
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RT @SGRodriques: Today, we’re announcing the first major discovery made by our AI Scientist with the lab in the loop: a promising new treat….
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RT @cognition_labs: Introducing Devin 2.0: a new agent-native IDE experience. Generally available today starting at $20. 🧵👇 https://t.co/….
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RT @ml4proteins: This Tuesday, 1/7 @ 4 pm EST, we'll be back with the 2025 seminar series!. @SeyoneC will present "Mapping the combinatoria….
biorxiv.org
The sense of smell remains poorly understood, especially in contrast to visual and auditory coding. At the core of our sense of smell is the olfactory information flow, in which odorant molecules...
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RT @SGRodriques: FutureHouse is launching an independent postdoctoral fellowship program for exceptional researchers who want to apply our….
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RT @cognition_labs: Devin is generally available today! . Just tag Devin to fix frontend bugs, create first-draft PRs for backlog tasks, ma….
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RT @OwenDugan: 🚀 Exciting news! We're proud to announce OccamLLM, a novel method for exact language-model arithmetic in a single autoregres….
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RT @rishabh16_: 🚨🚨 I'm giving an Oral presentation at #MLCB2024 on RNA-FrameFlow this Friday, 6th September at 1:20pm PDT 🧬. 🔗: https://t.c….
arxiv.org
We introduce RNA-FrameFlow, the first generative model for 3D RNA backbone design. We build upon SE(3) flow matching for protein backbone generation and establish protocols for data preparation...
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Poster #109 at 1:30 pm today!.
Introducing RNAFlow, a protein-conditioned RNA🧬generative model for structure and sequence design. Excited to present this work, mentored by @WengongJin, @icmlconf in a few weeks!. Paper: Thread: ⬇️🧵
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We evaluate whether RNAFlow can design the sequence and structure of an aptamer that binds to GRK2, a target of interest for chronic heart failure. We provide a known binding motif of 4-nucleotides. RNAFlow’s predictions resemble the true aptamer’s sequence and structure!
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