patternAlchemist
@patternalchemist.bsky.social
Structural Immunology | Grad Student ⚙️🧬🌀🧩
Reposted by patternAlchemist
Thinking Machines wrote a superb blog post on determinism in LLMs and it is fascinating (if you like computer architecture otherwise you’re going to tear your hair out)
spoiler: did you know GPUs have instructions that aren’t deterministic?
thinkingmachines.ai/blog/defeati...
spoiler: did you know GPUs have instructions that aren’t deterministic?
thinkingmachines.ai/blog/defeati...
Defeating Nondeterminism in LLM Inference
Reproducibility is a bedrock of scientific progress. However, it’s remarkably difficult to get reproducible results out of large language models.
For example, you might observe that asking ChatGPT the...
thinkingmachines.ai
September 10, 2025 at 6:54 PM
Thinking Machines wrote a superb blog post on determinism in LLMs and it is fascinating (if you like computer architecture otherwise you’re going to tear your hair out)
spoiler: did you know GPUs have instructions that aren’t deterministic?
thinkingmachines.ai/blog/defeati...
spoiler: did you know GPUs have instructions that aren’t deterministic?
thinkingmachines.ai/blog/defeati...
Reposted by patternAlchemist
Let’s continue with the fresh new Greenland series 🙂.
Pastel late sunset with mountain style iceberg in background & our beautiful red sails 😌.
Pastel late sunset with mountain style iceberg in background & our beautiful red sails 😌.
August 21, 2025 at 12:53 PM
Let’s continue with the fresh new Greenland series 🙂.
Pastel late sunset with mountain style iceberg in background & our beautiful red sails 😌.
Pastel late sunset with mountain style iceberg in background & our beautiful red sails 😌.
Reposted by patternAlchemist
Henry has long been emphasizing that representative democracy is a method of thinking and decision-making, not just a way of extracting fixed preferences from a populace.
www.programmablemutter.com/p/the-ai-dem... "Crudely put, we suggest that many AI people would prefer a version of democracy that gets rid of the politics."
The AI democracy debate is weirdly narrow
There are plausible reasons for how it ended up that way
www.programmablemutter.com
August 5, 2025 at 2:13 PM
Henry has long been emphasizing that representative democracy is a method of thinking and decision-making, not just a way of extracting fixed preferences from a populace.
Reposted by patternAlchemist
Sometimes when you take a new path through the forest it peters out and you're left in dense woodland. Often though, you get a fine view for your efforts. I'm sure there's a life metaphor in there somewhere. 😀
#hiking #nature #photography #ForestFriday #EastCoastKin #Ireland
#hiking #nature #photography #ForestFriday #EastCoastKin #Ireland
July 4, 2025 at 11:05 AM
Sometimes when you take a new path through the forest it peters out and you're left in dense woodland. Often though, you get a fine view for your efforts. I'm sure there's a life metaphor in there somewhere. 😀
#hiking #nature #photography #ForestFriday #EastCoastKin #Ireland
#hiking #nature #photography #ForestFriday #EastCoastKin #Ireland
Reposted by patternAlchemist
Thrilled to announce Boltz-1, the first open-source and commercially available model to achieve AlphaFold3-level accuracy on biomolecular structure prediction! An exciting collaboration with Jeremy, Saro, and an amazing team at MIT and Genesis Therapeutics. A thread!
November 17, 2024 at 4:20 PM
Thrilled to announce Boltz-1, the first open-source and commercially available model to achieve AlphaFold3-level accuracy on biomolecular structure prediction! An exciting collaboration with Jeremy, Saro, and an amazing team at MIT and Genesis Therapeutics. A thread!
Reposted by patternAlchemist
AlphaFold is amazing but gives you static structures 🧊
In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃
Code: github.com/KULL-Centre/...
Colab: github.com/matteo-cagia...
In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃
Code: github.com/KULL-Centre/...
Colab: github.com/matteo-cagia...
April 17, 2025 at 7:11 PM
AlphaFold is amazing but gives you static structures 🧊
In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃
Code: github.com/KULL-Centre/...
Colab: github.com/matteo-cagia...
In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃
Code: github.com/KULL-Centre/...
Colab: github.com/matteo-cagia...
Reposted by patternAlchemist
🔥 Benchmark Alert! MotifBench sets a new standard for evaluating protein design methods in motif scaffolding.
Why does this matter? Reproducibility & fair comparison have been lacking—until now.
Paper: arxiv.org/abs/2502.12479 | Repo: github.com/blt2114/Moti...
A thread ⬇️
Why does this matter? Reproducibility & fair comparison have been lacking—until now.
Paper: arxiv.org/abs/2502.12479 | Repo: github.com/blt2114/Moti...
A thread ⬇️
February 19, 2025 at 8:50 PM
🔥 Benchmark Alert! MotifBench sets a new standard for evaluating protein design methods in motif scaffolding.
Why does this matter? Reproducibility & fair comparison have been lacking—until now.
Paper: arxiv.org/abs/2502.12479 | Repo: github.com/blt2114/Moti...
A thread ⬇️
Why does this matter? Reproducibility & fair comparison have been lacking—until now.
Paper: arxiv.org/abs/2502.12479 | Repo: github.com/blt2114/Moti...
A thread ⬇️
Reposted by patternAlchemist
📢📢 "Proteina: Scaling Flow-based Protein Structure Generative Models"
#ICLR2025 (Oral Presentation)
🔥 Project page: research.nvidia.com/labs/genair/...
📜 Paper: arxiv.org/abs/2503.00710
🛠️ Code and weights: github.com/NVIDIA-Digit...
🧵Details in thread...
(1/n)
#ICLR2025 (Oral Presentation)
🔥 Project page: research.nvidia.com/labs/genair/...
📜 Paper: arxiv.org/abs/2503.00710
🛠️ Code and weights: github.com/NVIDIA-Digit...
🧵Details in thread...
(1/n)
March 4, 2025 at 5:09 PM
📢📢 "Proteina: Scaling Flow-based Protein Structure Generative Models"
#ICLR2025 (Oral Presentation)
🔥 Project page: research.nvidia.com/labs/genair/...
📜 Paper: arxiv.org/abs/2503.00710
🛠️ Code and weights: github.com/NVIDIA-Digit...
🧵Details in thread...
(1/n)
#ICLR2025 (Oral Presentation)
🔥 Project page: research.nvidia.com/labs/genair/...
📜 Paper: arxiv.org/abs/2503.00710
🛠️ Code and weights: github.com/NVIDIA-Digit...
🧵Details in thread...
(1/n)
Reposted by patternAlchemist
RFDiffusion2: a diffusion model that scaffolds enzyme active sites at the atomic level enables the generation of functional de novo enzymes
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
April 11, 2025 at 7:54 PM
RFDiffusion2: a diffusion model that scaffolds enzyme active sites at the atomic level enables the generation of functional de novo enzymes
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by patternAlchemist
Excited to share our preprint “BoltzDesign1: Inverting All-Atom Structure Prediction Model for Generalized Biomolecular Binder Design” — a collaboration with
@martinpacesa.bsky.social, @Zhidian Zhang, @Bruno E. Correia, and @sokrypton.org
🧬 Code will be released in a couple weeks
@martinpacesa.bsky.social, @Zhidian Zhang, @Bruno E. Correia, and @sokrypton.org
🧬 Code will be released in a couple weeks
April 8, 2025 at 12:17 PM
Excited to share our preprint “BoltzDesign1: Inverting All-Atom Structure Prediction Model for Generalized Biomolecular Binder Design” — a collaboration with
@martinpacesa.bsky.social, @Zhidian Zhang, @Bruno E. Correia, and @sokrypton.org
🧬 Code will be released in a couple weeks
@martinpacesa.bsky.social, @Zhidian Zhang, @Bruno E. Correia, and @sokrypton.org
🧬 Code will be released in a couple weeks
Reposted by patternAlchemist
Protein function often depends on protein dynamics. To design proteins that function like natural ones, how do we predict their dynamics?
@hkws.bsky.social and I are thrilled to share the first big, experimental datasets on protein dynamics and our new model: Dyna-1!
🧵
@hkws.bsky.social and I are thrilled to share the first big, experimental datasets on protein dynamics and our new model: Dyna-1!
🧵
March 20, 2025 at 3:02 PM
Protein function often depends on protein dynamics. To design proteins that function like natural ones, how do we predict their dynamics?
@hkws.bsky.social and I are thrilled to share the first big, experimental datasets on protein dynamics and our new model: Dyna-1!
🧵
@hkws.bsky.social and I are thrilled to share the first big, experimental datasets on protein dynamics and our new model: Dyna-1!
🧵
Reposted by patternAlchemist
A post by @ncfrey.bsky.social and @amyxlu.bsky.social on repurposing ESMFold for protein design, featuring one of my favorite phrases in the field ncfrey.substack.com/p/hit-the-vi...
March 19, 2025 at 4:51 PM
A post by @ncfrey.bsky.social and @amyxlu.bsky.social on repurposing ESMFold for protein design, featuring one of my favorite phrases in the field ncfrey.substack.com/p/hit-the-vi...
Reposted by patternAlchemist
Structural biology is in an era of dynamics & assemblies but turning raw experimental data into atomic models at scale remains challenging. @minhuanli.bsky.social and I present ROCKET🚀: an AlphaFold augmentation that integrates crystallographic and cryoEM/ET data with room for more! 1/14.
February 24, 2025 at 12:23 PM
Structural biology is in an era of dynamics & assemblies but turning raw experimental data into atomic models at scale remains challenging. @minhuanli.bsky.social and I present ROCKET🚀: an AlphaFold augmentation that integrates crystallographic and cryoEM/ET data with room for more! 1/14.
Reposted by patternAlchemist
@science.org Cryo-EM reveals mechanisms of natural RNA multivalency | Science www.science.org/doi/10.1126/...
#RNAsky #RNAbiology #Cryo-EM
#RNAsky #RNAbiology #Cryo-EM
March 13, 2025 at 6:09 PM
@science.org Cryo-EM reveals mechanisms of natural RNA multivalency | Science www.science.org/doi/10.1126/...
#RNAsky #RNAbiology #Cryo-EM
#RNAsky #RNAbiology #Cryo-EM
Reposted by patternAlchemist
Awakening valley in the French Alps, with the Mt Blanc massif in background 🏔️
#photography #mountains #nature #art #landscape
#photography #mountains #nature #art #landscape
March 13, 2025 at 3:01 PM
Awakening valley in the French Alps, with the Mt Blanc massif in background 🏔️
#photography #mountains #nature #art #landscape
#photography #mountains #nature #art #landscape
Reposted by patternAlchemist
And now I'm not allowed in the store anymore.
Btw, that scale was very cold.
Btw, that scale was very cold.
February 17, 2025 at 2:56 PM
And now I'm not allowed in the store anymore.
Btw, that scale was very cold.
Btw, that scale was very cold.
Reposted by patternAlchemist
Grassley Thune and Mike Rounds are also publicly against the administration not respecting judicial orders
abcnews.go.com/Politics/rep...
thehill.com/regulation/c...
abcnews.go.com/Politics/rep...
thehill.com/regulation/c...
GOP senator: ‘We have to’ follow court decisions
Sen. Mike Rounds (R-S.D.) said “we have to” follow court decisions in the Trump administration’s various legal battles, even as top officials challenge the judicial actions. On Tuesday, Round…
thehill.com
February 12, 2025 at 1:38 AM
Grassley Thune and Mike Rounds are also publicly against the administration not respecting judicial orders
abcnews.go.com/Politics/rep...
thehill.com/regulation/c...
abcnews.go.com/Politics/rep...
thehill.com/regulation/c...
Reposted by patternAlchemist
The potential importance of reactivation of herpes simplex virus type 1 (HSV-1) as a contributing factor to developing Alzheimer's disease
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
January 7, 2025 at 7:39 PM
The potential importance of reactivation of herpes simplex virus type 1 (HSV-1) as a contributing factor to developing Alzheimer's disease
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by patternAlchemist
Here are some nice mushrooms
December 24, 2024 at 2:32 PM
Here are some nice mushrooms
Reposted by patternAlchemist
Scientists created a cellular "switch" that acts like a lock and key, precisely targeting cancer cells.
@natureportfolio.bsky.social
@piraner @KoleRoybal @Mohamad_Abedi @majo__duran
www.nature.com/articles/s41...
#ImmunoSky 🧪
@natureportfolio.bsky.social
@piraner @KoleRoybal @Mohamad_Abedi @majo__duran
www.nature.com/articles/s41...
#ImmunoSky 🧪
November 19, 2024 at 11:43 AM
Scientists created a cellular "switch" that acts like a lock and key, precisely targeting cancer cells.
@natureportfolio.bsky.social
@piraner @KoleRoybal @Mohamad_Abedi @majo__duran
www.nature.com/articles/s41...
#ImmunoSky 🧪
@natureportfolio.bsky.social
@piraner @KoleRoybal @Mohamad_Abedi @majo__duran
www.nature.com/articles/s41...
#ImmunoSky 🧪
Reposted by patternAlchemist
Tossed around like sea glass
And you rounded out my edges
I'll feel better when the headaches go away
And you rounded out my edges
I'll feel better when the headaches go away
October 24, 2024 at 10:38 AM
Tossed around like sea glass
And you rounded out my edges
I'll feel better when the headaches go away
And you rounded out my edges
I'll feel better when the headaches go away
Reposted by patternAlchemist
longing for South Dakota skies again.
November 17, 2024 at 6:00 PM
longing for South Dakota skies again.