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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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Amelie Stein @amelierocks.bsky.social · 18/09/2025

Deadline extended - last chance, second edition!

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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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jonathanziegler.bsky.social @jonathanziegler.bsky.social · 18/06/2025

🧬 I'm looking for a new colleague (machine learning researcher) to work on exciting research projects around protein engineering with our ML team in Zurich. Speaking from experience, this is an amazing gig! jobs.ashbyhq.com/cradlebio/92...

jobs.ashbyhq.com

Machine Learning Researcher in Protein Design (f/m/*)

Join a scaleup researching and operating ML-guided lead optimization of proteins. This means developing a combination of protein language models, and multi-property prediction and generation.

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Brian Hie @brianhie.bsky.social · 19/02/2025

We trained a genomic language model on all observed evolution, which we are calling Evo 2. The model achieves an unprecedented breadth in capabilities, enabling prediction and design tasks from molecular to genome scale and across all three domains of life.

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Patrick Kidger @patrickkidger.bsky.social · 11/02/2025

🚀 It's time for a new JAX ecosystem library! This time quite a small one: ESM2quinox. A #JAX + Equinox implementation of the ESM2 protein language model. GitHub: github.com/patrick-kidg... SciML is obviously my whole jam. My open source has largely focused on the differential equations ... [1/2]

github.com

GitHub - patrick-kidger/esm2quinox: An implementation of ESM2 in Equinox+JAX

An implementation of ESM2 in Equinox+JAX. Contribute to patrick-kidger/esm2quinox development by creating an account on GitHub.

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jonathanziegler.bsky.social @jonathanziegler.bsky.social · 13/02/2025

Still at AMLD in Lausanne today. If you’re around, let’s have a coffee! Also, we (Cradle) and our collaborators from Adaptyv are hosting a little conference after party. Stop by!

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jonathanziegler.bsky.social @jonathanziegler.bsky.social · 11/12/2024

Interestingly, our submission initially ranked between 300-600 on the competition leaderboard due to in-silico scoring mechanics that didn't normalize for sequence length. This highlights a crucial point: in-silico scores don't always tell the whole story when evaluating generative methods!

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jonathanziegler.bsky.social @jonathanziegler.bsky.social · 11/12/2024

Agreed that the full solution is a challenge! Adding variable length CDR edits expands the search space quite dramatically! Current experiments look quite promising, though!

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jonathanziegler.bsky.social @jonathanziegler.bsky.social · 11/12/2024

I‘d be curious to see the results! We’ve been playing around with CDR manipulation (including indels) and some of the ML models actually produce some pretty reasonable results! For diversification this is absolutely the way to go in my opinion. Most of the time binding got worse for us, though.

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jonathanziegler.bsky.social @jonathanziegler.bsky.social · 10/12/2024

Real-world example on how targeted protein sequence engineering can significantly outperform structurally informed de novo design. I strongly believe both methods have their place. This challenge by #AdaptyvBio was a good example of optimization>design. www.cradle.bio/blog/adaptyv...

Cradle takes home first place in Adaptyv Bio‘s Protein Design and Engineering competition

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jonathanziegler.bsky.social @jonathanziegler.bsky.social · 09/12/2024

Also, we will be talking about how our zero shot approach landed first in the #AdaptyvBio protein design competition. See you there @patrickkidger.bsky.social :)

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jonathanziegler.bsky.social @jonathanziegler.bsky.social · 09/12/2024

Off to #NeurIPS tomorrow with my lovely colleagues from #Cradle! Looking forward to new input and fun conversations! Ping me, let’s grab a coffee!

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jonathanziegler.bsky.social @jonathanziegler.bsky.social · 09/12/2024

Agreed! That being said, the models are trained to capture higher-order epistasis, and we generally try to avoid single-mutation datasets during training if possible.

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jonathanziegler.bsky.social @jonathanziegler.bsky.social · 09/12/2024

Thank you @klausenhauser.bsky.social ! We are currently working on some experiments for jointly optimizing Kon and Koff separately vs Kd as a singular metric. The former should give more fine-grained control of the trade offs of binding behavior without losing any signal for optimization.

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jonathanziegler.bsky.social @jonathanziegler.bsky.social · 08/12/2024

Adaptyv Bio hosted an antibody engineering competition to design/engineer binders to EGFR. Super stoked that we came in first place with the Cradle team! We’ll be talking about the methods used at #NeurIPS this coming week! Here are the full results foundry.adaptyvbio.com/competition

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