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Artur Szałata

@chatgtp.bsky.social
2K followers 4.7K following 56 posts

Research Scientist (ML) @ Isomorphic Labs | prev. @ Fabian Theis lab, intern @genentech.bsky.social & @novartis.bsky.social, MSc @icepfl.bsky.social. Opinions stated here are my own.

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Artur Szałata @chatgtp.bsky.social · 07/07/2026
I'm excited to share that a month ago, I joined Isomorphic Labs! It's hard to imagine a more pressing and motivating mission than reimagining drug discovery to solve all disease. I feel incredibly privileged to embark on it with such a stellar team!
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Artur Szałata @chatgtp.bsky.social · 24/06/2026
Using Starlink on a plane for the first time and the difference in unreal
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Mark Riedl @markriedl.bsky.social · 31/03/2026
Oh wow, Anthropic accidentally leaked Claude Code and it’s been cloned and made public github.com/instructkr/c...
github.com
GitHub - instructkr/claude-code: Claude Code Snapshot for Research. All original source code is the property of Anthropic.
Claude Code Snapshot for Research. All original source code is the property of Anthropic. - instructkr/claude-code
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Eugene Vinitsky 🍒 @eugenevinitsky.bsky.social · 28/03/2026
I love this. And right now atproto is the only place you could really scale up these changes
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Eugene Vinitsky 🍒 @eugenevinitsky.bsky.social · 15/03/2026
For a recent lab meeting, I wrote up a grab bag of ways to think about your development as a researcher during a PhD: emerge-lab.github.io/papers/an-un... Sharing in case folks find it useful or have feedback!
emerge-lab.github.io
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Artur Szałata @chatgtp.bsky.social · 03/03/2026
Paper alert 🚨 @ MLGenX @iclr-conf.bsky.social 2026! PertOmni - CLIP-style multimodal representation-learning framework for contrastive alignment of perturbation readouts and textual embeddings.
openreview.net
Learning Perturbation Effects Through Contrastive Alignment of...
Single-cell perturbation screens offer a scalable approach for characterizing the effects of genetic and chemical interventions on cellular state. However, most existing representation-learning...
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Artur Szałata @chatgtp.bsky.social · 03/03/2026
Paper alert 🚨 @ MLGenX @iclr-conf.bsky.social 2026! PerturBERT openreview.net/forum?id=ZsD... - Most transformers in single-cell omics (e.g. scGPT) learn gene co-expression through pre-training on masked gene expression levels.
openreview.net
PerturBERT: Learning Gene Co-Variation Embeddings from Perturbation...
Current foundation models for transcriptomic data are typically trained in a self-supervised manner to predict gene expression within a sample given other genes, thereby learning gene co-variation...
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Artur Szałata @chatgtp.bsky.social · 02/03/2026
Caris is launching a WGS+ML blood test for early cancer detection. Impressive sensitivity: 56% stage 1 and 70% stage 2 - if it holds, it would blow competitors out of the water
carislifesciences.com
Caris Completes Interim Readout of Achieve 1 Study Demonstrates Superior Sensitivity and Specificity of Caris Detect
Caris Life Sciences Completes Interim Readout of Achieve 1 Study Demonstrates Superior Sensitivity and Specificity of Caris Detect
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Artur Szałata @chatgtp.bsky.social · 27/02/2026
Nano Banana 2 test. Humans are still safe 😌
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Artur Szałata @chatgtp.bsky.social · 25/02/2026
"Constitution" is a bad name for model preference guidelines doc. It suggests, among others, public legitimacy, where there is none.
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Chris Paxton @cpaxton.bsky.social · 07/02/2026
How to fake a robotics result: a short blog post listing many sins which annoy me (many of which I am guilty of from time to time, to be fair) open.substack.com/pub/itcanthi...
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Eugene Vinitsky 🍒 @eugenevinitsky.bsky.social · 07/02/2026
Haha @cpaxton.bsky.social is on fire: open.substack.com/pub/itcanthi... Some useful tips in there even for non-roboticists looking to make their paper artificially look good
open.substack.com
How to Fake A Robotics Result
Since that deadline is coming up
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Ted Underwood @tedunderwood.com · 19/01/2026
And for a lot of Gen X journalists and academics, the answer to (a) — assuming existing skills and plans — is legit "no." AI can be useful, for sure, but the paths it differentially advantages are not the paths where they have accumulated momentum, expertise, and social capital. +
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Artur Szałata @chatgtp.bsky.social · 15/01/2026
A quick story on how we matched genes across two datasets with different Ensembl versions. 1. There must be a tool out there. Ensembl ID History converter ofc! 2. Doesn't match Ensembl search outcomes due to a bug 3. Lesson: use this client instead github.com/Ensembl/ense... !
github.com
Mapping of ENSG_IDs between different release of the Ensembl database · Issue #744 · Ensembl/ensembl
Dear members of the Ensembl team, I wasn’t sure who to contact, so I’m starting here. I am writing to ask you questions about the IDMapper tool presented on your website: https://www.ensembl.org/Ho...
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Artur Szałata @chatgtp.bsky.social · 13/01/2026
Also awesome for finding posters at a conference!
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Arc Institute @arcinstitute.org · 09/01/2026
Predicting cell state in previously unseen conditions has typically required retraining for each new biological context. Today, Arc is releasing Stack, a foundation model that learns to simulate cell state under novel conditions directly at inference time, no fine-tuning required.
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Sakana AI @sakanaai.bsky.social · 12/01/2026
Introducing DroPE: Extending Context by Dropping Positional Embeddings We found embeddings like RoPE aid training but bottleneck long-sequence generalization. Our solution’s simple: treat them as a temporary training scaffold, not a permanent necessity. arxiv.org/abs/2512.12167 pub.sakana.ai/DroPE
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Ethan Mollick @emollick.bsky.social · 11/01/2026
One very familiar pattern in AI and science right now is going from a lot of false starts on hard tasks (there have been near-misses where AI appears to solve an Erdos problem but just finds an old solution no one knew about) to actually doing the thing soon after. Three Erdos problems in 3 days.
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Andrew Gordon Wilson @andrewgwils.bsky.social · 07/01/2026
We introduce epiplexity, a new measure of information that provides a foundation for how to select, generate, or transform data for learning systems. We have been working on this for almost 2 years, and I cannot contain my excitement! arxiv.org/abs/2601.03220 1/7
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Ryan Moulton @moultano.bsky.social · 30/12/2025
Finished the essay. moultano.wordpress.com/2025/12/30/c...
moultano.wordpress.com
Children and Helical Time
In subjective time, childhood is half of life. Life, then, is the creation of childhoods. You have yours, and then you get to create them for others.
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Chris Paxton @cpaxton.bsky.social · 24/12/2025
Autonomous RIVR delivery robots in Pittsburgh
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Eugene Vinitsky 🍒 @eugenevinitsky.bsky.social · 14/12/2025
A quick sunday rewrite of an old blog post about how one should evaluate the effectiveness of an empirical paper: open.substack.com/pub/emergere...
open.substack.com
How much should I trust this paper?
Or how to build your castle on sand
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Nathan Lambert @natolambert.bsky.social · 06/12/2025
Good researchers obsess over evals The story of Olmo 3 (post-training), told through evals NeurIPS Talk tomorrow. Upper Level Room 2, 10:35AM. Slides: docs.google.com/presentation...
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Eugene Vinitsky 🍒 @eugenevinitsky.bsky.social · 17/11/2025
Elon’s power is that he offers a positive vision of the future. This attracts employees, funding, support. There’s a massive techno positive hole and he fills it.
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Artur Szałata @chatgtp.bsky.social · 23/10/2025
Active learning with DrugReflector beats SotA in phenotypic hit-rate for virtual screening. Includes a sc perturbation dataset with 10 lines and 104 compounds. Out in @science.org now! Grateful to Cellarity and @fabiantheis.bsky.social for the opportunity to contribute to this outstanding project!
science.org
Active learning framework leveraging transcriptomics identifies modulators of disease phenotypes
Phenotypic drug screening remains constrained by the vastness of chemical space and technical challenges scaling experimental workflows. To overcome these barriers, computational methods have been dev...
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Eugene Vinitsky 🍒 @eugenevinitsky.bsky.social · 23/10/2025
What if we did a single run and declared victory
Three panel thing. In the left panel we use error bars. In the second, we take statistical significance as the biggest number but still have error bars. In LLM science, we just have the biggest number
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Eugene Vinitsky 🍒 @eugenevinitsky.bsky.social · 13/10/2025
Community notes when
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Eugene Vinitsky 🍒 @eugenevinitsky.bsky.social · 11/10/2025
Yeah this is my biggest “AGI hype is not real” is that almost no one at these companies behaves like it’s real
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Eugene Vinitsky 🍒 @eugenevinitsky.bsky.social · 28/09/2025
My skepticism of LLM-as-scientist stems from how imbalanced the literature is. Median paper is mildly negative result presented as positive, it's unclear how to RLHF on good hypothesis vs. bad hypothesis, etc. We barely know how to teach this skill, how can we RLHF it
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Eugene Vinitsky 🍒 @eugenevinitsky.bsky.social · 25/09/2025
For folks considering grad school in ML, my advice is to explore programs that mix ML with a domain interest. ML programs are wildly oversubscribed while a lot of the fun right now is in figuring out what you can do with it
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Artur Szałata @chatgtp.bsky.social · 28/08/2025
A must-read before you jump on your first omics project - the top response here www.reddit.com/r/bioinforma...
reddit.com
Here0s0Johnny's comment on "Exemplary papers on multi-OMICS integration with solid storytelling"
Explore this conversation and more from the bioinformatics community
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Eugene Vinitsky 🍒 @eugenevinitsky.bsky.social · 23/08/2025
I think scientists thought people could tell apart the serious science from the bad fluff and ideological work that we all mostly ignore. We were not ready for people to start conflating all of them together
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Eugene Vinitsky 🍒 @eugenevinitsky.bsky.social · 17/08/2025
The more rigorous peer review happens in conversations and reading groups after the paper is out with reputational costs for publishing bad work
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Eugene Vinitsky 🍒 @eugenevinitsky.bsky.social · 23/07/2025
There are people, in tech (and now in the government!), who will mislead you about what current AI models are capable of. If we don't call them out, they'll drag us all down.
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Eugene Vinitsky 🍒 @eugenevinitsky.bsky.social · 22/07/2025
Oops I read my parrot a math textbook and now it keeps squawking out the answer to unseen math competitions
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Artur Szałata @chatgtp.bsky.social · 18/06/2025
Excited to share that I started my summer at @genentech.bsky.social BRAID Perturbation team in SF with Alex Wu! It's my first time on the West Coast - If you are around and would like to talk about ML and/or biology, hit me up! Looking fwd to the AI x Bio Unconference tomorrow 🚀
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Lisa Sikkema @lisasikkema.bsky.social · 03/06/2025
Analyzing your single-cell data by mapping to a reference atlas? Then how do you know the mapping actually worked, and you’re not analyzing mapping-induced artifacts? We developed mapQC, a mapping evaluation tool www.biorxiv.org/content/10.1... from the ‪@fabiantheis lab. Let’s dive in🧵
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dominik1klein.bsky.social @dominik1klein.bsky.social · 23/04/2025
From cell lines to full embryos, drug treatments to genetic perturbations, neuron engineering to virtual organoid screens — odds are there’s something in it for you! Built on flow matching, CellFlow can help guide your next phenotypic screen: biorxiv.org/content/10.1101/2025.04.11.648220v1
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Anshul Kundaje @anshulkundaje.bsky.social · 08/04/2025
Just a gentle reminder that deceptive hyping in scientific publications (which includes preprints) is actually antithetical to the core mission of the scientific process. We can stay grounded, truthful, humble while being ambitious. Revealing caveats, pitfalls & limitations speeds up progress.
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Luke Zappia @lazappi.bsky.social · 18/03/2025
Our paper benchmarking feature selection for scRNA-seq integration and reference usage is out now www.nature.com/articles/s41...! Keep reading for more about how we did the study and what we found out 🧵 👇 1/16
nature.com
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Artur Szałata @chatgtp.bsky.social · 25/02/2025
Exciting dataset! If you're looking for a complimentary scRNA-seq drug perturbations in healthy/primary tissue (PBMCs), check out our dataset with ~36% # drugs of Tahoe. proceedings.neurips.cc/paper_files/...
proceedings.neurips.cc
A benchmark for prediction of transcriptomic responses to chemical perturbations across cell types
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Nathan Lambert @natolambert.bsky.social · 11/02/2025
The fact that we seem to be marching straight towards another cold war, where AI is the defining technology, is hard to emotionally accept and even harder to deeply accept how hard some of the next few years can become.
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Quentin Gallouédec @qgallouedec.hf.co · 25/01/2025
Last moments of closed-source AI 🪦 : Hugging Face is openly reproducing the pipeline of 🐳 DeepSeek-R1. Open data, open training. open models, open collaboration. 🫵 Let's go! github.com/huggingface/...
github.com
GitHub - huggingface/open-r1: Fully open reproduction of DeepSeek-R1
Fully open reproduction of DeepSeek-R1. Contribute to huggingface/open-r1 development by creating an account on GitHub.
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Artur Szałata @chatgtp.bsky.social · 22/01/2025
Trying to identify preclinical models that resemble clinical tumors you work on? Check out our MOBER, now out in @science.org Advances! www.science.org/doi/10.1126/... . There's also a web app to explore the results mober.pythonanywhere.com
science.org
Biologically relevant integration of transcriptomics profiles from cancer cell lines, patient-derived xenografts, and clinical tumors using deep learning
A proposed deep learning method helps to bridge the gap between preclinical cancer models and clinical tumors.
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Itai Yanai @itaiyanai.bsky.social · 12/01/2025
When a paper is published, any data must be easily and completely accessible, or the publication is a sham and should be retracted editorially.
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Lisa Sikkema @lisasikkema.bsky.social · 13/12/2024
1/7 Planning to build a single-cell atlas? Or wondering how atlases can be useful to your research? Read our guide on single-cell atlases www.nature.com/articles/s41... published in Nature Methods, by @lisasikkema.bsky.social, @khrovatin.bsky.social, Malte Luecken, @fabiantheis.bsky.social et al.
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Fabian Theis @fabiantheis.bsky.social · 12/12/2024
1/🚀 Excited to share RegVelo, our new cell model combining RNA velocity with gene regulatory network (GRN) dynamics to model cellular changes and predict in silico perturbations. Here's how it works and why it matters! 🧵👇 biorxiv.org/content/10.1101/2024.12.11.627935v1
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Polaris @polarishub.io · 09/12/2024
4️⃣ “A benchmark for prediction of transcriptomic responses to chemical perturbations across cell types” @chatgtp.bsky.social neurips.cc/virtual/2024...
neurips.cc
NeurIPS Poster A benchmark for prediction of transcriptomic responses to chemical perturbations across cell typesNeurIPS 2024
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