Reposted by MLSB (in San Diego + Copenhagen)David Ryan Koes @dkoes.compstruct.org · 07/12/2025Excited to be at the first independent @workshopmlsb.bsky.social 061
Reposted by MLSB (in San Diego + Copenhagen)Mile Sikic @msikic.bsky.social · 02/12/2025I’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 2/4mlsb.ioMLSB 2025 WorkshopWorkshop on Machine Learning in Structural Biology co-located with NeurIPS 2025 121
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 24/11/2025Hosted by EurIPS MLSB workshop organizers. RSVP below ⬇️ luma.com/e0avnsibluma.comMLSB @ EurIPS Happy Hour: Cradle x Adaptyv · LumaBrought 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… 022
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 130
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 25/09/2025Reminder that MLSB submissions for ✨BOTH✨ the Copenhagen and the San Diego MLSBs are due one week from now on October 1st 11:59pm AoE! 010
Reposted by MLSB (in San Diego + Copenhagen)jonathanziegler.bsky.social @jonathanziegler.bsky.social · 18/09/2025EuroMLSB 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! 022
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. 033
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 12/09/2025More information about speaker lineup coming soon 😎 None of this would have been possible without @patrickkidger.bsky.social and @jonathanziegler.bsky.social 🙌 010
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 12/09/2025Submissions 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. 100
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 12/09/2025You 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💫 2106
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 19/08/2025Information 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.ioMLSB 2025 WorkshopWorkshop on Machine Learning in Structural Biology co-located with NeurIPS 2025 010
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 100
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 28/07/2025Stay tuned for details on the 6th edition of MLSB, officially happening this December in downtown San Diego, CA! 0157
Reposted by MLSB (in San Diego + Copenhagen)Gina El Nesr @ginaelnesr.bsky.social · 07/07/2025Unfortunately, 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… 285
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 16/12/2024Brought to you by @ginaelnesr.bsky.social @gcorso.bsky.social @hkws.bsky.social @sesamedusa.bsky.social 010
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 16/12/2024Interested 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 160
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 16/12/2024Equally, 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! 020
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 16/12/2024Thank 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.comMLSB Post-Conference SurveyThank 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. 120
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024Leaderboard is graciously hosted by HuggingFace here: huggingface.co/spaces/MLSB/...huggingface.coLeaderboard2024 - a Hugging Face Space by MLSBDiscover amazing ML apps made by the community 010
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024Time 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 . 🔥 0122
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024PINDER: pinder.sh PLINDER: plinder.shpinder.shPINDER: Unlocking new discoveries through a scale-shift in data and real-world relevant and rigorous evaluationsPINDER is an academic-industry collaboration offering a gold standard dataset and evaluations for computational protein-protein interactions prediction. 120
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024Next up we're highlighting the results of the PINDER and PLINDER challenge. 130
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024Check out the paper here: www.mlsb.io/papers_2024/...mlsb.io 000
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024Next 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 131
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024Check out the paper: www.biorxiv.org/content/10.1...biorxiv.orgFlowPacker: Protein side-chain packing with torsional flow matchingAccurate 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... 000
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024Next up, contributed talk! FlowPacker: protein side-chain packing with torsional flow matching Jin Sub Lee, Philip Kim 121
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024Please check out the paper here: www.biorxiv.org/content/10.1...biorxiv.org 000
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024Next up - invited speaker! Boltz-1: Democratizing Biomolecular Interaction Modeling @jeremywohlwend.bsky.social 172
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024And the Foldseek webserver can be found here: search.foldseek.com/searchsearch.foldseek.comFoldseek Search ServerFoldseek Server offers fast and sensitive protein structure alignments against large protein structure collections 000
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024Check out the amazing codebase for MMseqs2-GPU here. github.com/soedinglab/M...github.comRelease MMseqs2 Release 16-747c6 · soedinglab/MMseqs2MMseqs2 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... 131
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024Next up, invited speaker! Challenges to metagenomic annotation with Foldseek and protein language models @milot.bsky.social 291
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024Check out the paper here: arxiv.org/abs/2406.10455arxiv.orgCryoSPIN: Improving Ab-Initio Cryo-EM Reconstruction with Semi-Amortized Pose InferenceCryo-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... 000
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024Check out the paper here: www.mlsb.io/papers_2024/...mlsb.io 010
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024Next up - Contributed Talk Improving Ab-Initio Cryo-EM Reconstruction with Semi-Amortized Pose Inference Shayan Shekarforoush @davelindell.bsky.social @marcusabrubaker.bsky.social David Fleet 120
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024Next 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 191
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024We're back from the break! The next talk is an invited speaker. Protein-Protein Interactions in Synthetic Co-Evolution & Other Stories Jennifer Listgarten 150
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024Check out the paper on Biorxiv! www.biorxiv.org/content/10.1...biorxiv.orgProtein Language Model Fitness Is a Matter of PreferenceLeveraging 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... 011
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024Check out the paper on biorxiv! www.biorxiv.org/content/10.1...biorxiv.orgGenerating All-Atom Protein Structure from Sequence-Only Training DataGenerative 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... 031
MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 15/12/2024Next up - Invited Speaker! Learning the determinants of protein folding energy landscapes from large-scale experiments @grocklin.bsky.social 191