PhD Student at @MeilerLab @UniLeipzig | Member of the PB³ Lab @pb3_lab | Biochem @Uchile | Founder @DataRoot_CL

Joined October 2011
I am thrilled to share my first article as a first author. Last semester while working as a T.A we implemented a set of 12 tutorials related to different bioinformatics topics within Jupyter Notebooks running on Google Colab. pubs.acs.org/doi/10.1021/acs… (1/4)
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Felipe Engelberger retweeted
Finally a more intuitive way to learn pLDDT/pAE? 😎 sokrypton.github.io/protein_… (Character idea from @HannesStaerk & Alex Waldherr)
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🚨New paper! Generative models are often “miscalibrated”. We calibrate diffusion models, LLMs, and more to meet desired distributional properties. E.g. we finetune protein models to better match the diversity of natural proteins. arxiv.org/abs/2510.10020 github.com/smithhenryd/cgm
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Excited to share work with @ZhidianZ, Milot Mirdita, Martin Steinegger, and @sokrypton biorxiv.org/content/10.1101/… TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling 🧵
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For every new technology (in this case engineered proteins) you have to first make a PoC.
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Thrilled to have shared my personal and scientific journey on the Baker Lab podcast! I hope it serves as an inspiration for aspiring scientists in Latin America.
NEW EPISODE 🎧 Susana Vazquez Torres crossed continents to become a scientist. In our lab, she's used AI to create new antitoxins for snakebites. Apple: podcasts.apple.com/us/podcas… Spotify: open.spotify.com/episode/580…
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Started teaching again! This time decided to try use #claude (@AnthropicAI) and @codesandbox for hosting to implement an interactive GREMLIN (Potts) model (w = coevolution, b = conservation) to show students how you go from MSA to contacts! 9kssnq.csb.app/
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Replying to @KevinKaichuang
The Google Colab version of RFdiffusion with the conditional fold generation option worked well! We successfully placed two helices in the beta barrel structure. The RMSD between prediction and X-ray is only 0.3 Å! colab.research.google.com/gi… colab.research.google.com/gi…
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7/ In particular, we showcase gLM2's ability to directly learn coevolutionary signal in protein-protein interfaces with no supervision! The learned contact maps can be extracted using @ZhidianZ et al's categorial Jacobian method.
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4/ Metagenomes feature significant bias and redundancies, but deduplicating large genomic databases can be computationally expensive. We implement *genomic SemDeDup*, an embedding-based deduplication for genomic sequences, resulting in tunable balancing and pruning of the corpus
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NEWS | Epic announcement coming tomorrow, thanks to @RosettaCommons @MeilerLab 🎉 Stay tuned!
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Amazing time at the @ImperialX_AI open day - super cool facilities and great content😆. Excited to receive a poster prize at the end! Electronic aspects inspired from @bradyajohnston who gave great advice to make sure the iPad stayed stuck! Animation code taken from @sokrypton 😎
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We recently created some new tools in Rosetta around ML protein design methods (including ProteinMPNN, ESM2, MIF-ST). You can run all of this using `docker run -it rosettacommons/rosetta:ml` (no python involved). We then benchmarked the different methods: biorxiv.org/content/10.1101/…
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Had a great time at the ML for Drug Discovery Summer School & MoML conference in Montréal (my first time in🇨🇦!) Kudos to the organizers for arranging such a great lineup of talks & labs! thanks to the hackathon, got some hands on experience with some concepts taught👨🏼‍💻
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Yesterday, I had the chance to present my first spotlight poster at #MoML2024 at @Mila_Quebec AI Institute! I presented joint work done with @luisa_kaermer and our amazing advisors, @JWestermayr and @MeilerLab. Huge thanks to @Esporascicomm for the amazing graphic design work!
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A 2D version of “AlphaFold pseudo Multi Dimensional Scaling” skills
New paper: How can you tell if a transformer has the right world model? We trained a transformer to predict directions for NYC taxi rides. The model was good. It could find shortest paths between new points But had it built a map of NYC? We reconstructed its map and found this:
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Amazing first week of #MoML2024 🇨🇦
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Replying to @SimonDBarnett
Honest question. Do we mean dynamics as in time-dependence, or as in conformational flexibility and variability ? Both are important, but in a sense, different things.
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sad but obvious realization, in the context of the recent gzip ~ llm scaling laws paper. LZ compression algorithms are optimal in the same way memorization is learning—only true with infinite data.
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Information geometry and optimal transport are cool in theory, but flow matching in the Fisher-Rao metric is even cooler in practice ! It was great to be part of this awesome team, thanks for having me!
Wonder how to generate discrete data with Riemannian Flow Matching? Well, here is our most recent work addressing this issue: Fisher Flow Matching 😎 ➡️ Available here: arxiv.org/abs/2405.14664 🔥 Let me break it down 🧵 (1/10) @bose_joey @mmbronstein @ismaililkanc @MirceaSci
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Our @NatRevPhys perspective article on neural operators and their ability to accelerate simulations and design is now out. rdcu.be/dD8BI @Nature 1. Neural operators learn mappings between functions, e.g. spatiotemporal processes and partial differential equations. Hence, they can extrapolate and predict solutions at new locations unseen during training. 2. They can be integrated with physics and other domain constraints enforced at finer resolutions to obtain high-fidelity solutions and good generalization. 3. They are differentiable, so they can directly optimize parameters for inverse design and other inverse problems. Neural operators can therefore augment, or even replace, existing numerical simulators in many applications, such as computational fluid dynamics, weather forecasting and material modeling, providing speedups of 4-5 orders of magnitude. @Azizzadenesheli @ZongyiLiCaltech @JeanKossaifi @caltech
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