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Nathaniel Blalock

@nathanielblalock.bsky.social
136 followers 425 following 20 posts

Graduate Research Assistant in Dr. Philip Romero's Lab at Duke/Wisconsin Reinforcement and Deep Learning for Protein Redesign | He/him

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Nathaniel Blalock @nathanielblalock.bsky.social · 25/05/2025
Let me know if you’d like me to clarify anything. I’m happy to talk!
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Nathaniel Blalock @nathanielblalock.bsky.social · 10/05/2025
Me too 🤪 It is really exciting to be submitting! We definitely learned a lot along the way
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Reposted by Nathaniel Blalock
Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 10/05/2025
Reinforcement learning with experimental feedback (RLXF) shifts protein language models so that they generate sequences with improved properties @nathanielblalock.bsky.social @philromero.bsky.social www.biorxiv.org/content/10.1...
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Nathaniel Blalock @nathanielblalock.bsky.social · 10/05/2025
Thank you for sharing our work @kevinkaichuang.bsky.social! It means a lot
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Nathaniel Blalock @nathanielblalock.bsky.social · 08/05/2025
Thank you for posting about our preprint!
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Nathaniel Blalock @nathanielblalock.bsky.social · 08/05/2025
and our open-source code at github.com/RomeroLab/RLXF
github.com
GitHub - RomeroLab/RLXF: Consolidated repository to perform RLXF
Consolidated repository to perform RLXF. Contribute to RomeroLab/RLXF development by creating an account on GitHub.
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Nathaniel Blalock @nathanielblalock.bsky.social · 08/05/2025
Want to learn more? Check out our preprint at www.biorxiv.org/content/10.1...
biorxiv.org
Functional alignment of protein language models via reinforcement learning
Protein language models (pLMs) enable generative design of novel protein sequences but remain fundamentally misaligned with protein engineering goals, as they lack explicit understanding of function a...
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Nathaniel Blalock @nathanielblalock.bsky.social · 08/05/2025
We apply RLXF across five diverse protein classes to demonstrate its generalizability and effectiveness at generating optimized sequences by learning functional constraints beyond those captured during pre-training
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Nathaniel Blalock @nathanielblalock.bsky.social · 08/05/2025
Experimental validation reveals the RLXF-aligned model generates a higher fraction of functional sequences, a greater number of sequences more fluorescent than CreiLOV, and the brightest oxygen-independent fluorescent protein variant reported to date
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Nathaniel Blalock @nathanielblalock.bsky.social · 08/05/2025
We align ESM-2 to experimental fluorescence data from the CreiLOV flavin-binding fluorescent protein. The aligned model learns to prioritize mutations that enhance fluorescence, many of which are missed by the base model
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Nathaniel Blalock @nathanielblalock.bsky.social · 08/05/2025
RLXF follows a two-phase strategy inspired by RLHF. Supervised Fine-Tuning initializes the model in the right region of sequence space. Proximal Policy Optimization directly aligns sequence generation with feedback from a reward function like a sequence-function predictor
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Nathaniel Blalock @nathanielblalock.bsky.social · 08/05/2025
Pre-trained pLMs generate highly diverse sequences mirroring statistical patterns from natural proteins. But here's the challenge: they lack an explicit understanding of function, often failing to generate proteins with enhanced or non-natural activities. RLXF bridges this gap!
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Nathaniel Blalock @nathanielblalock.bsky.social · 08/05/2025
We are excited in the @philromero.bsky.social lab to share our new preprint introducing RLXF for the functional alignment of protein language models (pLMs) with experimentally derived notions of biomolecular function!
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Nathaniel Blalock @nathanielblalock.bsky.social · 04/04/2025
Great article, simple reminder about the value of higher education! engineering.wisc.edu/blog/why-we-...
engineering.wisc.edu
Why we do research - College of Engineering - University of Wisconsin-Madison
At a time when the role and value of higher education are being questioned, it's imperative to reflect on the important benefits of research.
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Reposted by Nathaniel Blalock
Philip Romero @philromero.bsky.social · 24/03/2025
🎉Congrats to Chase on her new preprint! She developed OMEGA--a simple method for assembling custom gene panels for as little as $1.50 per gene. Big step forward protein engineering and design!🧬 www.biorxiv.org/content/10.1...
biorxiv.org
Scalable and cost-efficient custom gene library assembly from oligopools
Advances in metagenomics, deep learning, and generative protein design have enabled broad in silico exploration of sequence space, but experimental characterization is still constrained by the cost an...
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Reposted by Nathaniel Blalock
Alex Wild @alexwild.bsky.social · 28/01/2025
Post the amazing science things you have done with federal funding.
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Nathaniel Blalock @nathanielblalock.bsky.social · 20/12/2024
It was a pleasure meeting you! Y'all are doing super interesting and relevant work. It will be cool to see how we can continue to interact and maybe collaborate in the future!
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Nathaniel Blalock @nathanielblalock.bsky.social · 20/12/2024
Favorite foods! Tandoori chicken and chili momo's: everestkitchen.ca. Onigiri! www.onigiriya.ca. Pho: www.viethouserestaurant.com.
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Nathaniel Blalock @nathanielblalock.bsky.social · 20/12/2024
Papers #4: arxiv.org/abs/2406.17692 from the incredible @gregdnlp.bsky.social. I really like how explore what happens during the alignment of LLM's with RLHF. This was so cool to see having observed similar outcomes in my research.
arxiv.org
From Distributional to Overton Pluralism: Investigating Large Language Model Alignment
The alignment process changes several properties of a large language model's (LLM's) output distribution. We analyze two aspects of post-alignment distributional shift of LLM responses. First, we re-e...
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Nathaniel Blalock @nathanielblalock.bsky.social · 20/12/2024
Papers #2-3: arxiv.org/abs/2402.10210 and arxiv.org/abs/2405.00675 from the incredible @quanquangu.bsky.social. I really like how they explore new techniques for RLHF
arxiv.org
Self-Play Fine-Tuning of Diffusion Models for Text-to-Image Generation
Fine-tuning Diffusion Models remains an underexplored frontier in generative artificial intelligence (GenAI), especially when compared with the remarkable progress made in fine-tuning Large Language M...
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Nathaniel Blalock @nathanielblalock.bsky.social · 20/12/2024
Paper #1: arxiv.org/abs/2412.12979 Aligning autoregressive pLM's to generate EGFR binders via Direct Policy Optimization (DPO) from the incredible @noeliaferruz.bsky.social who gave a great talk as part of the MLSB workshop
arxiv.org
Guiding Generative Protein Language Models with Reinforcement Learning
Autoregressive protein language models (pLMs) have emerged as powerful tools to efficiently design functional proteins with extraordinary diversity, as evidenced by the successful generation of divers...
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Nathaniel Blalock @nathanielblalock.bsky.social · 20/12/2024
My 1st NeurIPS was a wonderful experience - incredible to see so much research in protein design and reinforcement learning. Here are my favorite papers (and favorite places I got food in Vancouver 😋):
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Nathaniel Blalock @nathanielblalock.bsky.social · 17/12/2024
Hey Kevin, could I be added? This is really helpful for joining Bluesky! Thank you for doing it
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Reposted by Nathaniel Blalock
Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 03/12/2024
Three BioML starter packs now! Pack 1: go.bsky.app/2VWBcCd Pack 2: go.bsky.app/Bw84Hmc Pack 3: go.bsky.app/NAKYUok DM if you want to be included (or nominate people who should be!)
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