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

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...

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

The more rigorous peer review happens in conversations and reading groups after the paper is out with reputational costs for publishing bad work

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.

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 🚀

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🧵

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

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.

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

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/...

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.

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/...

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

When a paper is published, any data must be easily and completely accessible, or the publication is a sham and should be retracted editorially.

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.

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

4️⃣ “A benchmark for prediction of transcriptomic responses to chemical perturbations across cell types” @chatgtp.bsky.social neurips.cc/virtual/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. 🧵

I’m told burnout comes less from having too much to do but rather feeling like what you have to do is out of your control (and/or unpleasant work). So, working out substantial changes in what you’re obligated to be doing is the best way out. Thus making space for something new/interesting!

Public service announcement: Conference deadlines & other artificial deadlines are not excuses to put out half-baked work. If u want to put out half-baked work, u shud clearly state in the paper that results are preliminary & discuss areas of concern that might need careful verification. 1/

Here's a Cheminformatics Starter pack! Let me know if you would like to be added! And more importantly, do encourage people to join the blue skies :D

Three BioML starter packs now! Pack 1: go.bsky.app/2VWBcCd Pack 2: go.bsky.app/Bw84Hmc Pack 3: go.bsky.app/NAKYUok DM if you want to be included (or nominate people who should be!)

🚨 NeurIPS 2024 Spotlight Did you know we lack standards for AI benchmarks, despite their role in tracking progress, comparing models, and shaping policy? 🤯 Enter BetterBench–our framework with 46 criteria to assess benchmark quality: betterbench.stanford.edu 1/x

It's been a pleasure to work on the Human Neural Organoid Atlas. Congratulations to the great team across institutes 🎉 ! rdcu.be/d0VBH

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

Genomics, Evolution, and More @jlsteenwyk.bsky.social bsky.app/starter-pack...

If you're just coming in from Twitter, a great way to reconnect with your community is to find the people you were following there with the Sky Follower Bridge. It works really well! www.sky-follower-bridge.dev

Thrilled to share our paper on transformers in single cell omics out in @natureportfolio.bsky.social ! Check it out to learn about the latest models, how they are trained, applied, and their limitations. rdcu.be/dQuVW (🧵1/7)

AlphaMissense looks exciting, but I wish every published paper was reproducible and extensible. "we are not releasing the trained model weights, the code is not meant to be used to reproduce the AlphaMissense scores" www.science.org/doi/10.1126/... github.com/deepmind/alp...

The University Hospital in Greifswald is looking for an assistant professor in bioinformatics. Greifswald is a beautiful place and we would love to have you here! Please spread the word. #job #bioinformatics www.academics.de/jobs/w1-juni...