Lightnews — Scholar-powered news

Reposted by Nathan C. Frey

Evan Spotte-Smith (they/them) @ewcspottesmith.bsky.social · May 14

It's finally done (enough for a preprint)! Today, in collaboration with so many folks at Meta (shout-out Daniel Levine and Muhammed Shuaibi, who put in superhuman levels of work), Berkeley, Stanford, NYU, and more, I'm proud to announce the Open Molecules 2025 (OMol25) dataset!
#CompChem #ML 🧪 ⚗️

The Open Molecules 2025 (OMol25) Dataset, Evaluations, and Models

Machine learning (ML) models hold the promise of transforming atomic simulations by delivering quantum chemical accuracy at a fraction of the computational cost. Realization of this potential would en...

arxiv.org

1 10 39

Reposted by Nathan C. Frey

Diego del Alamo @delalamo.xyz · Mar 19

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...

The phrase "pathologically disorganized" is used to describe a neural network trained to predict protein structure from sequence embeddings

4 14

Reposted by Nathan C. Frey

briantrippe.bsky.social @briantrippe.bsky.social · Feb 19

🔥 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 ⬇️

1 17 40

Nathan C. Frey @ncfrey.bsky.social · Feb 26

This was a massive, 3+ effort with 60+ collaborators, and we're still only scratching the surface of what's possible in biology, drug design, and ML. Incredibly proud of this team and honored to be a part of this research and sharing it with the world.

1

Nathan C. Frey @ncfrey.bsky.social · Feb 26

We @prescientdesign.bsky.social Genentech pre-printed our "Lab-in-the-loop for therapeutic antibody design." We built a general ML system to accelerate molecule design for challenging, therapeutically relevant targets.

www.biorxiv.org/content/10.1...

www.biorxiv.org

1 8 23

Reposted by Nathan C. Frey

NYU Center for Data Science @nyudatascience.bsky.social · Jan 15

CDS PhD student @angie-chen.bsky.social presents LLOME, using LLMs to optimize synthetic sequences with potential applications for drug design.

Co-led by @activelearner.bsky.social & @ncfrey.bsky.social and others at @prescientdesign.bsky.social

nyudatascience.medium.com/language-mod...

Language Models Optimize Biologically Realistic Synthetic Sequences, Potentially Helping Drug…

CDS researchers unveil LLOME, which optimizes biologically realistic synthetic sequences with potential applications for drug discovery.

nyudatascience.medium.com

3 9

Nathan C. Frey @ncfrey.bsky.social · Dec 12

New blog post with Aya Ismail on our recent work, which introduces a fundamentally new way to build foundation models that are interpretable by design for scientific discovery.

tinyurl.com/cb-plm-blog

1 3 8

Nathan C. Frey @ncfrey.bsky.social · Dec 11

My team @prescientdesign.bsky.social is hiring! 🎉

Join me, @stephenra.com, @keunwoochoi.bsky.social, @kyunghyuncho.bsky.social, and the Large Molecule Drug Discovery AI/ML and LLM teams to work on basic research and applications of LLMs to drug discovery.

Link to apply: tinyurl.com/prescient-lmdd

6

Nathan C. Frey @ncfrey.bsky.social · Dec 9

Join us in NYC as a graduate student intern at Prescient Design, Genentech this summer to work on fundamental research in 3D generative models, with applications to protein design!

Apply directly, and please share with anyone who may be interested!
roche.wd3.myworkdayjobs.com/en-US/ROG-A2...

2025 Summer Intern - Frontiers Research and Large Molecule Drug Discovery AI/ML, Prescient Design

Department Summary Prescient Design is seeking exceptional graduate student interns with a strong research background in machine learning (ML), a passion for independent exploration, and the ability t...

roche.wd3.myworkdayjobs.com

1 10 18

Nathan C. Frey @ncfrey.bsky.social · Dec 6

Incredible work led by @amyxlu.bsky.social introducing PLAID, an all-atom co-generation method for proteins that requires only sequence inputs for training data! Read Amy's thread below, with links to the preprint, code, and model weights!

👇

Amy Lu @amyxlu.bsky.social · Dec 6

1/🧬 Excited to share PLAID, our new approach for co-generating sequence and all-atom protein structures by sampling from the latent space of ESMFold. This requires only sequences during training, which unlocks more data and annotations:

bit.ly/plaid-proteins
🧵

6

Nathan C. Frey @ncfrey.bsky.social · Dec 4

get in early on the best podcast for bio, chem, and ML. fill the void in your life of entertaining, technical content made by experts for experts (and enthusiasts!).

owl @owlposting1.bsky.social · Dec 4

Can AI improve the current state of molecular simulation?

www.owlposting.com/p/can-ai-imp...

in my first podcast, I spend 2 hours interviewing Corin Wagen and Ari Wagen, two brothers who are building the next generation of molecular simulation for drug discovery and material science

Can AI improve the current state of molecular simulation? (Corin & Ari Wagen, Ep #1)

2.1 hours listening time

www.owlposting.com

6

Reposted by Nathan C. Frey

ruiqigao.bsky.social @ruiqigao.bsky.social · Dec 2

A common question nowadays: Which is better, diffusion or flow matching? 🤔

Our answer: They’re two sides of the same coin. We wrote a blog post to show how diffusion models and Gaussian flow matching are equivalent. That’s great: It means you can use them interchangeably.

6 58 250

Reposted by Nathan C. Frey

Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · Nov 25

BioM3: a model that generates proteins conditioned on text prompts, with wet-lab validation!

www.biorxiv.org/content/10.1...

Overview of the BioM3 framework for protein design via natural language prompts.

1 15 81

Reposted by Nathan C. Frey

Simon Mathis @simonmathis.bsky.social · Nov 25

A weekend project from a while back -- this little package (with no dependencies) allows you to interact with pymol remotely.

I use it a lot for my protein design workflows together with @biotite.bsky.social.

Just `pip install pymol-remote`

4 13 47

Reposted by Nathan C. Frey

Willie Neiswanger @willieneis.bsky.social · Nov 20

The first list filled up, so here's a second list of AI for Science researchers on bluesky.

Let me know if I missed you / if you'd like to join!

bsky.app/starter-pack...

58 29 70

Reposted by Nathan C. Frey

Willie Neiswanger @willieneis.bsky.social · Nov 10

I'm making a list of AI for Science researchers on bluesky — let me know if I missed you / if you'd like to join!

go.bsky.app/AcP9Lix

160 90 250

Reposted by Nathan C. Frey

Simon Mathis @simonmathis.bsky.social · Nov 20

🧪 For people interested in AI & enzymes (enzyme engineering, design, discovery, ...), I'm assembling a starter pack for us.

DM if you'd like to be included!

go.bsky.app/MhfaQBh

6 8 36

Nathan C. Frey @ncfrey.bsky.social · Nov 19

bsky.app/profile/kevi...

Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · Nov 18

Two BioML starter packs now:

Pack 1: go.bsky.app/2VWBcCd
Pack 2: go.bsky.app/Bw84Hmc

DM if you want to be included (or nominate people who should be!)

Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · Nov 11

I tried to make a bioml starter pack. DM if you want me to add or remove you?

go.bsky.app/2VWBcCd

4

Reposted by Nathan C. Frey

Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · Nov 18

Two BioML starter packs now:

Pack 1: go.bsky.app/2VWBcCd
Pack 2: go.bsky.app/Bw84Hmc

DM if you want to be included (or nominate people who should be!)

Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · Nov 11

I tried to make a bioml starter pack. DM if you want me to add or remove you?

go.bsky.app/2VWBcCd

Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · Nov 11

Anybody have a bioml starter pack?

10 56 120

Reposted by Nathan C. Frey

Sander Dieleman @sedielem.bsky.social · Nov 15

In a gratuitous attempt to acquire more followers myself 😁, I've made a start on a "starter pack". Hopefully as more people from 🐦 make it over to 🦋, we can extend this a bit. Suggestions welcome!

I've noticed not all accounts seem to be eligible to be added, anyone know what's up with that? 🤔