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MLSB (in San Diego + Copenhagen)

@workshopmlsb.bsky.social
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Machine Learning in Structural Biology workshop co-located with NeurIPS 2025 & at EurIPS 2025. Dec 7. San Diego, CA mlsb.io

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Reposted by MLSB (in San Diego + Copenhagen)
David Ryan Koes @dkoes.compstruct.org · 07/12/2025
Excited to be at the first independent @workshopmlsb.bsky.social
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Reposted by MLSB (in San Diego + Copenhagen)
Mile Sikic @msikic.bsky.social · 02/12/2025
I’ll also be giving a keynote on Dec 7 at @workshopmlsb.bsky.social (co-located with NeurIPS), speaking about the next wave of RNA structure prediction. 🔗 mlsb.io 2/4
mlsb.io
MLSB 2025 Workshop
Workshop on Machine Learning in Structural Biology co-located with NeurIPS 2025
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 24/11/2025
Hosted by EurIPS MLSB workshop organizers. RSVP below ⬇️ luma.com/e0avnsib
luma.com
MLSB @ EurIPS Happy Hour: Cradle x Adaptyv · Luma
Brought to you by Machine Learning in Structural Biology (MLSB) at EurIPS 2025! Join Cradle and Adaptyv Bio for drinks and conversation at the intersection of…
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 24/11/2025
🧬 Attending EurIPS in Copenhagen? Come join us for ML×SBio Drinks! Join CradleBio & @adaptyv.bio for an evening of conversation at the intersection of machine learning and structural biology. 📍 Copenhagen | EurIPS week 🎟️ Space limited—RSVP to secure your spot
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 25/09/2025
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!
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Reposted by MLSB (in San Diego + Copenhagen)
jonathanziegler.bsky.social @jonathanziegler.bsky.social · 18/09/2025
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!
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 17/09/2025
🚨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.
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 12/09/2025
More information about speaker lineup coming soon 😎 None of this would have been possible without @patrickkidger.bsky.social and @jonathanziegler.bsky.social 🙌
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 12/09/2025
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.
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 12/09/2025
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💫
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 19/08/2025
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!
mlsb.io
MLSB 2025 Workshop
Workshop on Machine Learning in Structural Biology co-located with NeurIPS 2025
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 19/08/2025
📢The submission portal for MLSB 2025 is live! Submissions are due September 26, 2025 11:59 pm AoE. cmt3.research.microsoft.com/MLSB2025
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 28/07/2025
updated!
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 28/07/2025
Stay tuned for details on the 6th edition of MLSB, officially happening this December in downtown San Diego, CA!
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Reposted by MLSB (in San Diego + Copenhagen)
Gina El Nesr @ginaelnesr.bsky.social · 07/07/2025
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…
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 16/12/2024
Brought to you by @ginaelnesr.bsky.social @gcorso.bsky.social @hkws.bsky.social @sesamedusa.bsky.social
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 16/12/2024
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
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 16/12/2024
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!
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 16/12/2024
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...
docs.google.com
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.
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024
Leaderboard is graciously hosted by HuggingFace here: huggingface.co/spaces/MLSB/...
huggingface.co
Leaderboard2024 - a Hugging Face Space by MLSB
Discover amazing ML apps made by the community
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024
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 . 🔥
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024
PINDER: pinder.sh PLINDER: plinder.sh
pinder.sh
PINDER: Unlocking new discoveries through a scale-shift in data and real-world relevant and rigorous evaluations
PINDER is an academic-industry collaboration offering a gold standard dataset and evaluations for computational protein-protein interactions prediction.
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024
Next up we're highlighting the results of the PINDER and PLINDER challenge.
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024
Check out the paper here: www.mlsb.io/papers_2024/...
mlsb.io
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024
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
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024
Check out the paper: www.biorxiv.org/content/10.1...
biorxiv.org
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...
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024
Next up, contributed talk! FlowPacker: protein side-chain packing with torsional flow matching Jin Sub Lee, Philip Kim
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024
Please check out the paper here: www.biorxiv.org/content/10.1...
biorxiv.org
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024
Next up - invited speaker! Boltz-1: Democratizing Biomolecular Interaction Modeling @jeremywohlwend.bsky.social
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024
And the Foldseek webserver can be found here: search.foldseek.com/search
search.foldseek.com
Foldseek Search Server
Foldseek Server offers fast and sensitive protein structure alignments against large protein structure collections
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024
Check out the amazing codebase for MMseqs2-GPU here. github.com/soedinglab/M...
github.com
Release MMseqs2 Release 16-747c6 · soedinglab/MMseqs2
MMseqs2 Release 16 introduces support for GPU-accelerated searches [1]. Additionally, we fixed numerous bugs and relicensed MMseqs2 under the MIT license. [1] Kallenborn F, Chacon A, Hundt C, Sirel...
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024
Next up, invited speaker! Challenges to metagenomic annotation with Foldseek and protein language models @milot.bsky.social
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024
Check out the paper here: arxiv.org/abs/2406.10455
arxiv.org
CryoSPIN: Improving Ab-Initio Cryo-EM Reconstruction with Semi-Amortized Pose Inference
Cryo-EM is an increasingly popular method for determining the atomic resolution 3D structure of macromolecular complexes (eg, proteins) from noisy 2D images captured by an electron microscope. The com...
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024
Check out the paper here: www.mlsb.io/papers_2024/...
mlsb.io
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024
Next up - Contributed Talk Improving Ab-Initio Cryo-EM Reconstruction with Semi-Amortized Pose Inference Shayan Shekarforoush @davelindell.bsky.social @marcusabrubaker.bsky.social David Fleet
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024
Next up - Contributed Talk! Generative modeling of protein ensembles guided by crystallographic electron densities Sai Advaith Maddipatla · Nadav Sellam · @sankethvedula.bsky.social · Ailie Marx · Alex Bronstein
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024
We're back from the break! The next talk is an invited speaker. Protein-Protein Interactions in Synthetic Co-Evolution & Other Stories Jennifer Listgarten
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024
Check out the paper on Biorxiv! www.biorxiv.org/content/10.1...
biorxiv.org
Protein Language Model Fitness Is a Matter of Preference
Leveraging billions of years of evolution, scientists have trained protein language models (pLMs) to understand the sequence and structure space of proteins aiding in the design of more functional pro...
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024
Check out the paper on biorxiv! www.biorxiv.org/content/10.1...
biorxiv.org
Generating All-Atom Protein Structure from Sequence-Only Training Data
Generative models for protein design are gaining interest for their potential scientific impact. However, protein function is mediated by many modalities, and simultaneously generating multiple modali...
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024
Next up - Invited Speaker! Learning the determinants of protein folding energy landscapes from large-scale experiments @grocklin.bsky.social
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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024
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