Artur Szałata
@chatgtp.bsky.social
Machine learning for molecular biology. ELLIS PhD student at Fabian Theis lab. EPFL alumnus.
Pinned
Artur Szałata
@chatgtp.bsky.social
· Nov 15
A benchmark for prediction of transcriptomic responses to chemical...
Single-cell transcriptomics has revolutionized our understanding of cellular heterogeneity and drug perturbation effects. However, its high cost and the vast chemical space of potential drugs...
openreview.net
Interested in predicting transcriptomic effects of perturbations? Check out our @NeurIPS24 D&B spotlight living perturbation prediction benchmark & new drug perturbation dataset:
- paper: openreview.net/forum?id=WTI... !
- benchmarking platform: openproblems.bio/results/pert...
🧵1/8
- paper: openreview.net/forum?id=WTI... !
- benchmarking platform: openproblems.bio/results/pert...
🧵1/8
Reposted by Artur Szałata
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.
November 17, 2025 at 2:02 PM
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.
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!
Grateful to Cellarity and @fabiantheis.bsky.social for the opportunity to contribute to this outstanding project!
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...
www.science.org
October 23, 2025 at 7:41 PM
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!
Grateful to Cellarity and @fabiantheis.bsky.social for the opportunity to contribute to this outstanding project!
Reposted by Artur Szałata
What if we did a single run and declared victory
October 23, 2025 at 2:28 AM
What if we did a single run and declared victory
Reposted by Artur Szałata
Community notes when
October 13, 2025 at 4:16 AM
Community notes when
Reposted by Artur Szałata
Yeah this is my biggest “AGI hype is not real” is that almost no one at these companies behaves like it’s real
October 11, 2025 at 8:58 PM
Yeah this is my biggest “AGI hype is not real” is that almost no one at these companies behaves like it’s real
Reposted by Artur Szałata
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
September 28, 2025 at 8:40 PM
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
Reposted by Artur Szałata
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
September 25, 2025 at 3:25 AM
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
A must-read before you jump on your first omics project - the top response here www.reddit.com/r/bioinforma...
Here0s0Johnny's comment on "Exemplary papers on multi-OMICS integration with solid storytelling"
Explore this conversation and more from the bioinformatics community
www.reddit.com
August 28, 2025 at 6:06 PM
A must-read before you jump on your first omics project - the top response here www.reddit.com/r/bioinforma...
Reposted by Artur Szałata
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
August 23, 2025 at 6:20 PM
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
Reposted by Artur Szałata
The more rigorous peer review happens in conversations and reading groups after the paper is out with reputational costs for publishing bad work
August 17, 2025 at 4:12 PM
The more rigorous peer review happens in conversations and reading groups after the paper is out with reputational costs for publishing bad work
Reposted by Artur Szałata
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.
Reporter: The FDA has a new AI tool that's intended to speed up drug approvals. But several FDA employees say the new AI helper is making up studies that do not exist. One FDA employee telling us, 'Anything that you don't have time to double check is unreliable. It hallucinates confidently'
July 23, 2025 at 8:01 PM
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.
Reposted by Artur Szałata
Oops I read my parrot a math textbook and now it keeps squawking out the answer to unseen math competitions
July 22, 2025 at 1:09 PM
Oops I read my parrot a math textbook and now it keeps squawking out the answer to unseen math competitions
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 🚀
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 🚀
June 18, 2025 at 4:37 AM
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 🚀
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 🚀
Reposted by Artur Szałata
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🧵
June 3, 2025 at 8:24 AM
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🧵
Reposted by Artur Szałata
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
Built on flow matching, CellFlow can help guide your next phenotypic screen: biorxiv.org/content/10.1101/2025.04.11.648220v1
April 23, 2025 at 9:26 AM
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
Built on flow matching, CellFlow can help guide your next phenotypic screen: biorxiv.org/content/10.1101/2025.04.11.648220v1
Reposted by Artur Szałata
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.
April 8, 2025 at 9:03 AM
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.
Reposted by Artur Szałata
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
Keep reading for more about how we did the study and what we found out 🧵 👇
1/16
https://www.nature.com/articles/s41592-025-02624-3🎉
March 18, 2025 at 3:40 PM
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
Keep reading for more about how we did the study and what we found out 🧵 👇
1/16
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/...
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/...
February 25, 2025 at 10:15 PM
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/...
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/...
Reposted by Artur Szałata
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.
February 11, 2025 at 5:46 PM
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.
Reposted by Artur Szałata
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/...
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 - 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.
github.com
January 25, 2025 at 2:36 PM
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/...
Hugging Face is openly reproducing the pipeline of 🐳 DeepSeek-R1. Open data, open training. open models, open collaboration.
🫵 Let's go!
github.com/huggingface/...
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
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.
www.science.org
January 22, 2025 at 5:20 PM
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
Reposted by Artur Szałata
When a paper is published, any data must be easily and completely accessible, or the publication is a sham and should be retracted editorially.
January 12, 2025 at 8:56 PM
When a paper is published, any data must be easily and completely accessible, or the publication is a sham and should be retracted editorially.
Reposted by Artur Szałata
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.
December 13, 2024 at 10:33 AM
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.
Reposted by Artur Szałata
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
biorxiv.org/content/10.1101/2024.12.11.627935v1
December 12, 2024 at 2:48 PM
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
biorxiv.org/content/10.1101/2024.12.11.627935v1
Reposted by Artur Szałata
4️⃣ “A benchmark for prediction of transcriptomic responses to chemical perturbations across cell types”
@chatgtp.bsky.social
neurips.cc/virtual/2024...
@chatgtp.bsky.social
neurips.cc/virtual/2024...
NeurIPS Poster A benchmark for prediction of transcriptomic responses to chemical perturbations across cell typesNeurIPS 2024
neurips.cc
December 9, 2024 at 5:09 PM
4️⃣ “A benchmark for prediction of transcriptomic responses to chemical perturbations across cell types”
@chatgtp.bsky.social
neurips.cc/virtual/2024...
@chatgtp.bsky.social
neurips.cc/virtual/2024...