MLSB (in San Diego + Copenhagen)

Reminder that MLSB submissions for ✨BOTH✨ the Copenhagen and the San Diego MLSBs are due one week from now on October 1st 11:59pm AoE!

EuroMLSB at EurIPS is confirmed and the submission deadline is set to Oct 1st. This is **earlier than the EurIPS-suggested workshop deadline** for a reason: we have a shared submission process with MLSB in SanDiego for which the deadline is now also extended to Oct 1st!

🚨To accommodate the addition of EuroMLSB, we have extended the submission deadline to October 1, 2025 11:59pm AoE.

Find information on paper guidelines at mlsb.io. Submissions will be made through CMT.

More information about speaker lineup coming soon 😎

None of this would have been possible without
@patrickkidger.bsky.social and @jonathanziegler.bsky.social 🙌

Submissions will use the same system, and all papers—regardless of location preference—will receive the same level of review and be evaluated under identical acceptance criteria.

You asked and we listened... @workshopmlsb.bsky.social is excited to be expanding to Copenhagen, DK at @euripsconf.bsky.social 🎉

Two workshops (San Diego & Copenhagen) will run concurrently to support broader attendance. You can indicate your location preference(s) in the submission portal💫

Information on submission guidelines are on our website at mlsb.io/call-for-papers

Specifically, we ask all authors to adhere to the NeurIPS Rules on use of LLMs!

📢The submission portal for MLSB 2025 is live! Submissions are due September 26, 2025 11:59 pm AoE. cmt3.research.microsoft.com/MLSB2025

updated!

Stay tuned for details on the 6th edition of MLSB, officially happening this December in downtown San Diego, CA!

Unfortunately, the MLSB Workshop @ NeurIPS (@workshopmlsb.bsky.social) was rejected this year.

Feedback from the deciding committee indicates it was a coin flip decision, with 283 proposals & a number related to “computational biology”

More on the future of MLSB soon…

Brought to you by @ginaelnesr.bsky.social @gcorso.bsky.social @hkws.bsky.social @sesamedusa.bsky.social

Interested in turning your workshop paper into a publication? MLSB has partnered with PRX Life to start a new special collection! Submission is free and open access -

Editorial: tinyurl.com/mlsbeditorial
Collection: go.aps.org/4fWvbHe
Submission: go.aps.org/3Znaux5

Equally, big thank you to our sponsors whom without would not have made MLSB possible. If you or your team is interested in sponsoring MLSB next year, please reach out!

MLSB Post-Conference Survey Thank you for taking a few minutes to complete this survey about your experience at MLSB 2024 @ NeurIPS! Your feedback is valuable and ensures that we run a smooth workshop each year.

Thank you to everyone who came to MLSB this year!!

We are collecting feedback in a short 2 minute survey (and more data means maybe next year we'll train a new model... or just get a bigger room 😄)

forms.gle/WHFNfvxVh3Qx...

Leaderboard2024 - a Hugging Face Space by MLSB Discover amazing ML apps made by the community

Leaderboard is graciously hosted by HuggingFace here: huggingface.co/spaces/MLSB/...

Time for the MLSB Panel 🎛️ We're welcoming @grocklin.bsky.social @noeliaferruz.bsky.social Erika Alden DeBenedictis @milot.bsky.social Jennifer Listgarten
to the panel, hosted by the wonderful @hkws.bsky.social . 🔥

PINDER: pinder.sh
PLINDER: plinder.sh

Next up we're highlighting the results of the PINDER and PLINDER challenge.

Check out the paper here: www.mlsb.io/papers_2024/...

Next up - contributed talk.

HelixFlow, SE(3)–equivariant Full-atom Design of Peptides With Flow-matching Models

Xuezhi Xie, Pedro A Valiente, Jisun Kim, Jin Sub Lee, Philip Kim

FlowPacker: Protein side-chain packing with torsional flow matching Accurate prediction of protein side-chain conformations is necessary to understand protein folding, proteinprotein interactions and facilitate de novo protein design. Here we apply torsional flow matc...

Check out the paper: www.biorxiv.org/content/10.1...

Next up, contributed talk!

FlowPacker: protein side-chain packing with torsional flow matching

Jin Sub Lee, Philip Kim

Please check out the paper here: www.biorxiv.org/content/10.1...

Next up - invited speaker!

Boltz-1: Democratizing Biomolecular Interaction Modeling

@jeremywohlwend.bsky.social

And the Foldseek webserver can be found here:

search.foldseek.com/search