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Anton Bushuiev

@anton-bushuiev.bsky.social
219 followers 170 following 15 posts

PhD student at CTU Prague & IOCB Prague, machine learning for molecule discovery anton-bushuiev.github.io

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Reposted by Anton Bushuiev
Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 01/08/2026
Riboseek is a fast RNA/DNA search. More sensitive than nhmmer at 250x speed. Structure-aware realignment produces MSAs approaching rMSA quality. Plus 1.7M precomputed RNA MSAs, and an API to search your own 📄 www.biorxiv.org/content/10.6... 💾 github.com/steineggerla... 🌐 search.foldseek.com/riboseek
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Hannes Stark @hannes-stark.bsky.social · 05/03/2026
We have a little new paper at ICLR led by @AntonBushuiev. Test time training for proteins :) arxiv.org/abs/2411.02109 For example, you know the sequence that you want to fold, so fine-tune ESM on it at test time to get a better ESMFold structure prediction!
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Anton Bushuiev @anton-bushuiev.bsky.social · 05/03/2026
ProteinTTT is now easy to run on Hugging Face Spaces and Google Colab. We’ll also be presenting the paper at ICLR 2026 🇧🇷 🤗 Hugging Face Space: huggingface.co/spaces/pimen... ⚙️ Google Colab: colab.research.google.com/drive/1l_h7c... 🧵👇
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Milot Mirdita @milot.bsky.social · 20/01/2026
My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring! mirdita.org
mirdita.org
Mirdita Lab - Laboratory for Computational Biology & Molecular Machine Learning
Mirdita Lab builds scalable bioinformatics methods.
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Anton Bushuiev @anton-bushuiev.bsky.social · 03/01/2026
Amazing summary of our recent ProteinTTT paper youtube.com/shorts/XWueh...
youtube.com
【論文簡単解説】One protein is all you need簡単解説💨 #shorts #vtuber準備中 #澪乃ゆい
YouTube video by Miono Yui ch. | 澪乃ゆい
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Anton Bushuiev @anton-bushuiev.bsky.social · 27/10/2025
Very happy @roman-bushuiev.bsky.social and I joined the amazing team led by @hannes-stark.bsky.social to work on BoltzGen, a generative model for binder design based on Boltz-2. Excited what it will enable!
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Hannes Stark @hannes-stark.bsky.social · 26/10/2025
Excited to release BoltzGen which brings SOTA folding performance to binder design! The best part of this project is collaborating with a broad network of leading wetlabs that test BoltzGen at an unprecedented scale, showing success on many novel targets and pushing the model to its limits!
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Tomáš Pluskal @pluskal-lab.org · 25/10/2025
BIG BIG congratulations to our PhD student @roman-bushuiev.bsky.social for receiving the Google PhD Fellowship 2025 in Health Research! 🎉💰 goo.gle/43wJWw8
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Anton Bushuiev @anton-bushuiev.bsky.social · 23/10/2025
We train machine learning models on millions of proteins. But when it comes to making predictions, do we need them to understand all proteins at once? Often, we need an accurate model for the specific protein we are studying or designing. We address this with ProteinTTT arxiv.org/abs/2411.02109 1/🧵
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IOCB Prague @iocbprague.bsky.social · 28/05/2025
⚛️ @pluskal-lab.org from IOCB Prague, together with his student @roman-bushuiev.bsky.social and colleagues from #CIIRC CTU, Josef Šivic and @anton-bushuiev.bsky.social, have developed a machine learning model called #DreaMS – which accelerates the analysis of previously unknown molecules.
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Reposted by Anton Bushuiev
Roman Bushuiev @roman-bushuiev.bsky.social · 26/05/2025
Mass spectrometry is a key method to discover and identify molecules in biological and environmental samples. Yet, >90% of mass spectra remain hard to interpret. In our recent paper, we present DreaMS — a foundation model to interpret mass spectra of small molecules. www.nature.com/articles/s41...
nature.com
Self-supervised learning of molecular representations from millions of tandem mass spectra using DreaMS - Nature Biotechnology
A transformer model is used to construct the DreaMS Atlas—a molecular network of 201 million MS/MS spectra.
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Tomáš Pluskal @pluskal-lab.org · 24/05/2025
This paper represents a great effort by @roman-bushuiev.bsky.social and his brother @anton-bushuiev.bsky.social. The DreaMS foundation model for mass spectra of small molecules now opens lots of avenues for possible downstream applications. It might be a game changer for computational metabolomics.
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Nature Biotechnology @natbiotech.nature.com · 23/05/2025
Self-supervised learning of molecular representations from millions of tandem mass spectra using DreaMS - @pluskal-lab.org @iocbprague.bsky.social go.nature.com/4k1n5iC
go.nature.com
Self-supervised learning of molecular representations from millions of tandem mass spectra using DreaMS - Nature Biotechnology
A transformer model is used to construct the DreaMS Atlas—a molecular network of 201 million MS/MS spectra.
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Tomáš Pluskal @pluskal-lab.org · 11/04/2025
Back in July 2023 we organized a small bioML symposium at @iocbprague.bsky.social, and it turned out to be a very pleasant and successful event. This summer we are following up with a great line-up of speakers. Please register for free, deadline May 30. tinyurl.com/bioMLPrague25
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Roman Bushuiev @roman-bushuiev.bsky.social · 07/03/2025
🚀 Exciting MassSpecGym leaderboard update 🚀 Two new machine learning models achieve up to a 300% improvement in de novo molecular generation given mass spectra and corresponding chemical formulae. 🔥 1/n
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Reposted by Anton Bushuiev
Radoslav Krivak @rdkbio.bsky.social · 20/02/2025
MassSpecGym - the first comprehensive benchmark for the discovery and identification of molecules from MS/MS data. @roman-bushuiev.bsky.social @anton-bushuiev.bsky.social @josef-sivic.bsky.social @pluskal-lab.org NeurIPS 2024 paper: arxiv.org/abs/2410.23326 #ChemSky #MassSpec #AI4Science
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IOCB Prague @iocbprague.bsky.social · 20/02/2025
🤝 In April 2024, brothers Roman and Anton Bushuiev from the teams of @pluskal-lab.org @iocbprague.bsky.social and Josef Šivic #CIIRC_CTU initiated a collaboration among 14 research institutes across the globe to benchmark #AI methods for the discovery of molecules from mass spectrometry data. 1/2
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Polaris @polarishub.io · 24/01/2025
MassSpecGym is the largest publicly available collection of mass spectra data with 231K spectra for 29K unique molecular structures. 33% of the dataset was generated from newly measured, in-house data. 🛡️The dataset is now certified on Polaris! polarishub.io/datasets/rom... youtu.be/G8ZnVRm0ogc
youtu.be
MassSpecGym: A benchmark for the discovery and identification of molecules
YouTube video by PolarisHQ
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Tomáš Pluskal @pluskal-lab.org · 14/12/2024
The MassSpecGym team presenting the poster at #NeurIPS2024! Fei Wang, Adamo Young, @roman-bushuiev.bsky.social, @anton-bushuiev.bsky.social, Raman Samusevich
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Alfredo Canziani @alfcnz.bsky.social · 13/12/2024
Met the twins @roman-bushuiev.bsky.social @anton-bushuiev.bsky.social
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Roman Bushuiev @roman-bushuiev.bsky.social · 11/12/2024
Check out our NeurIPS 2024 spotlight poster on MassSpecGym, a dataset and benchmark for discovering new molecules from nature 🌿. If you work on generative models for graphs/molecules, plug your model into MassSpecGym and see how many molecules you can discover! 🚀 1/6
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Polaris @polarishub.io · 09/12/2024
What are the most interesting datasets and benchmark-related work for ML in drug discovery at NeurIPS? We’ll be at the conference doing short interviews with researchers and handing out some Polaris merch! Here’s who we have on the shortlist. 🧵
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Cas @caswognum.nl · 27/11/2024
Wow! 🤩 This may be the most carefully documented dataset on @polarishq.bsky.social. Great work by @roman-bushuiev.bsky.social! Do I have any #MassSpec researchers in my 🦋 network yet? I would love to hear what you think! github.com/polaris-hub/... #mass #spectrometry #dataset #benchmark
polarishub.io
massspecgym
roman-bushuiev
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