Artur Szałata @chatgtp.bsky.social · 07/07/2026I'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! 070
Artur Szałata @chatgtp.bsky.social · 24/06/2026Using Starlink on a plane for the first time and the difference in unreal 030
Reposted by Artur SzałataMark Riedl @markriedl.bsky.social · 31/03/2026Oh wow, Anthropic accidentally leaked Claude Code and it’s been cloned and made public github.com/instructkr/c...github.comGitHub - 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 412332
Reposted by Artur SzałataEugene Vinitsky 🍒 @eugenevinitsky.bsky.social · 28/03/2026I love this. And right now atproto is the only place you could really scale up these changes 2402
Reposted by Artur SzałataEugene Vinitsky 🍒 @eugenevinitsky.bsky.social · 15/03/2026For 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 610112
Artur Szałata @chatgtp.bsky.social · 03/03/2026Paper alert 🚨 @ MLGenX @iclr-conf.bsky.social 2026! PertOmni - CLIP-style multimodal representation-learning framework for contrastive alignment of perturbation readouts and textual embeddings.openreview.netLearning 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... 151
Artur Szałata @chatgtp.bsky.social · 03/03/2026Paper 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.netPerturBERT: 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... 120
Artur Szałata @chatgtp.bsky.social · 02/03/2026Caris 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 watercarislifesciences.comCaris Completes Interim Readout of Achieve 1 Study Demonstrates Superior Sensitivity and Specificity of Caris DetectCaris Life Sciences Completes Interim Readout of Achieve 1 Study Demonstrates Superior Sensitivity and Specificity of Caris Detect 000
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. 120
Reposted by Artur SzałataChris Paxton @cpaxton.bsky.social · 07/02/2026How 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... 1285
Reposted by Artur SzałataEugene Vinitsky 🍒 @eugenevinitsky.bsky.social · 07/02/2026Haha @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 goodopen.substack.comHow to Fake A Robotics ResultSince that deadline is coming up 2293
Reposted by Artur SzałataTed Underwood @tedunderwood.com · 19/01/2026And 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. + 1142
Artur Szałata @chatgtp.bsky.social · 15/01/2026A 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.comMapping of ENSG_IDs between different release of the Ensembl database · Issue #744 · Ensembl/ensemblDear 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... 141
Reposted by Artur SzałataArc Institute @arcinstitute.org · 09/01/2026Predicting 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. 1116
Reposted by Artur SzałataSakana AI @sakanaai.bsky.social · 12/01/2026Introducing 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 211821
Reposted by Artur SzałataEthan Mollick @emollick.bsky.social · 11/01/2026One 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. 310812
Reposted by Artur SzałataAndrew Gordon Wilson @andrewgwils.bsky.social · 07/01/2026We 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 814234
Reposted by Artur SzałataRyan Moulton @moultano.bsky.social · 30/12/2025Finished the essay. moultano.wordpress.com/2025/12/30/c...moultano.wordpress.comChildren and Helical TimeIn 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. 1714428
Reposted by Artur SzałataChris Paxton @cpaxton.bsky.social · 24/12/2025Autonomous RIVR delivery robots in Pittsburgh 2019844
Reposted by Artur SzałataEugene Vinitsky 🍒 @eugenevinitsky.bsky.social · 14/12/2025A 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.comHow much should I trust this paper?Or how to build your castle on sand 1183
Reposted by Artur SzałataNathan Lambert @natolambert.bsky.social · 06/12/2025Good 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... 1306
Reposted by Artur SzałataEugene Vinitsky 🍒 @eugenevinitsky.bsky.social · 17/11/2025Elon’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. 7585
Artur Szałata @chatgtp.bsky.social · 23/10/2025Active 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.orgActive learning framework leveraging transcriptomics identifies modulators of disease phenotypesPhenotypic 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... 1112
Reposted by Artur SzałataEugene Vinitsky 🍒 @eugenevinitsky.bsky.social · 23/10/2025What if we did a single run and declared victory 1333570
Reposted by Artur SzałataEugene Vinitsky 🍒 @eugenevinitsky.bsky.social · 13/10/2025Community notes when 2415
Reposted by Artur SzałataEugene Vinitsky 🍒 @eugenevinitsky.bsky.social · 11/10/2025Yeah this is my biggest “AGI hype is not real” is that almost no one at these companies behaves like it’s real 0152
Reposted by Artur SzałataEugene Vinitsky 🍒 @eugenevinitsky.bsky.social · 28/09/2025My 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 812210
Reposted by Artur SzałataEugene Vinitsky 🍒 @eugenevinitsky.bsky.social · 25/09/2025For 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 815217
Artur Szałata @chatgtp.bsky.social · 28/08/2025A must-read before you jump on your first omics project - the top response here www.reddit.com/r/bioinforma...reddit.comHere0s0Johnny's comment on "Exemplary papers on multi-OMICS integration with solid storytelling"Explore this conversation and more from the bioinformatics community 030
Reposted by Artur SzałataEugene Vinitsky 🍒 @eugenevinitsky.bsky.social · 23/08/2025I 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 6362
Reposted by Artur SzałataEugene Vinitsky 🍒 @eugenevinitsky.bsky.social · 17/08/2025The more rigorous peer review happens in conversations and reading groups after the paper is out with reputational costs for publishing bad work 2485
Reposted by Artur SzałataEugene Vinitsky 🍒 @eugenevinitsky.bsky.social · 23/07/2025There 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. 3206
Reposted by Artur SzałataEugene Vinitsky 🍒 @eugenevinitsky.bsky.social · 22/07/2025Oops I read my parrot a math textbook and now it keeps squawking out the answer to unseen math competitions 5583
Artur Szałata @chatgtp.bsky.social · 18/06/2025Excited 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 🚀 030
Reposted by Artur SzałataLisa Sikkema @lisasikkema.bsky.social · 03/06/2025Analyzing 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🧵 22410
Reposted by Artur Szałatadominik1klein.bsky.social @dominik1klein.bsky.social · 23/04/2025From 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 1187
Reposted by Artur SzałataAnshul Kundaje @anshulkundaje.bsky.social · 08/04/2025Just 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. 39216
Reposted by Artur SzałataLuke Zappia @lazappi.bsky.social · 18/03/2025Our 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 🧵 👇 1/16nature.com 64017
Artur Szałata @chatgtp.bsky.social · 25/02/2025Exciting 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.ccA benchmark for prediction of transcriptomic responses to chemical perturbations across cell types 082
Reposted by Artur SzałataNathan Lambert @natolambert.bsky.social · 11/02/2025The 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. 1274
Reposted by Artur SzałataQuentin Gallouédec @qgallouedec.hf.co · 25/01/2025Last 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.comGitHub - huggingface/open-r1: Fully open reproduction of DeepSeek-R1Fully open reproduction of DeepSeek-R1. Contribute to huggingface/open-r1 development by creating an account on GitHub. 0347
Artur Szałata @chatgtp.bsky.social · 22/01/2025Trying 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.comscience.orgBiologically relevant integration of transcriptomics profiles from cancer cell lines, patient-derived xenografts, and clinical tumors using deep learningA proposed deep learning method helps to bridge the gap between preclinical cancer models and clinical tumors. 1182
Reposted by Artur SzałataItai Yanai @itaiyanai.bsky.social · 12/01/2025When a paper is published, any data must be easily and completely accessible, or the publication is a sham and should be retracted editorially. 3393
Reposted by Artur SzałataLisa Sikkema @lisasikkema.bsky.social · 13/12/20241/7 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. 15017
Reposted by Artur SzałataFabian Theis @fabiantheis.bsky.social · 12/12/20241/🚀 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 311247
Reposted by Artur SzałataPolaris @polarishub.io · 09/12/20244️⃣ “A benchmark for prediction of transcriptomic responses to chemical perturbations across cell types” @chatgtp.bsky.social neurips.cc/virtual/2024...neurips.ccNeurIPS Poster A benchmark for prediction of transcriptomic responses to chemical perturbations across cell typesNeurIPS 2024 141