Moritz Schaefer

Just presented our new multimodal histopathology method "SpotWhisperer" at ICML, one of the largest AI conference.

SpotWhisperer enables spatially resolved annotation of histopathology images using natural language. We achieved this by "transferring" annotations from transcriptomic data. More soon!

After an exciting 3.5 years at CeMM and the AI Institute, it's time for me to move on to the next adventure.
I am grateful for the friendships I made and the science I got to contribute to.

I also wrote a brief recap of my science and activities during that time. Enjoy! moritzs.de/cemm

Having fun at work... :)

Made possible by an amazing bunch of colleagues at my institute.

Matching flows to data Models that fit like water in a vessel.

Great behind-the-scenes overview on 'Flow matching and OT in cell biology'
hrovatin.github.io/posts/sc_flo...

The "record presentation" feature of PowerPoint shows presentation notes in a teleprompter style (e.g. directly under the camera).

It's a pity there is no way to configure the "presenter view" window that way though.

images.app.goo.gl/otejMV2qCaBf...

Crowd of protestors at March for Science, Vienna

THANK YOU to everyone who joined the #March for #Science in #Vienna today! 💐💐💐
>500 people in front of @univie.ac.at, ~1000 people at Votivpark! 💚💚💚
Science is for everyone!
#standupforscience2025
#scienceforall
#sciencenotsilence

Speaker lineup for stand up for science - Bill Nye, Dr. Atul Gawande, Dr. Phil Plait, Dr. Michael Mann, Dr. Itai Yanai Dr. Francis Collins, Dr. Victor Ambros, Dr. Nate Brought, Bill Nelson, JD Dr. Ticora V Jones, Dr. Gretchen Goldman, Dr. Haley Chatelaine Dr. Bonnielinn Swenor, Dr. Allison Agwu, Dr. Patrick Sullivan, Andrew Eneim Dr. Nathaniel Kupperman, Bridget Nelson, MPH, Samantha Jade Duran Denali Kincaid, Connor Phillips, Gabriella Amaya, Emily Whitehead Sarah Aleman
Senator  Chris Van Hollen (MD), Rep. Bill Foster (IL-11) Rep. Suhas Subramanyam (VA-10), Rep. Jamie Raskin (MD-8) Rep. Glenn Ivey (MD-4), Former Rep. Fred Upton (MI-6)

SPEAKER LINEUP FOR STAND UP FOR SCIENCE ☀️

Here's our list of current speakers—and it's still growing! Come tomorrow to hear some amazing speakers talk about science, their experiences, and the future.

#standupforscience2025

The question is, "for how long will Bluesky be better?". Let's hope for the best, but decentralization promises of the platform need yet to materialize..

Yes.

LLMs should rather be seen as "interface modules" of more complex AI systems: Their core role will be to *translate* between AI language (bits and bytes) and human-readable language.

Really cool work! Keep us posted, if you automate more things
E.g. What about automatically scanning new literature and sending reminders if it relates to currently running lab projects.

Visiting the #38C3 conference was an absolute blast again! Four days of great interactions and talks around politics, society, information security and science

- My highlights post on LinkedIn:
www.linkedin.com/posts/moritz...
- I gave a talk too: lnkd.in/dXRF2mai
- All talks here: media.ccc.de

I'm hiring:

1. Research associate (wet-lab w/ phd) to generate mpra perturbation data

2. ML postdoc to build multimodal generative AI for DNA (eg diffusion and LLMs)

3. Bioinformatician (any level) to process and harmonize functional genomics data to train foundation models

DM me if interested!

Elon Musk takes aim at Wikipedia The billionaire has become one of the most prominent supporters of President-elect Donald Trump.

If you've never donated to Wikipedia, now's the time. Elon Musk is attacking it because it's one of the only sources of honest, curated information that he can't control.
www.newsweek.com/elon-musk-ta...

An AI Lab Partner Helps Sift Through Transcriptomics Data Big omics datasets can be overwhelming for researchers with limited programming skills, but texting with a new AI chatbot could help them wade through their results.

Thrilled to see our work with the @bocklab.bsky.social featured in 'The Scientist'!

It's a really great read and builds on an interview I had with the @kamalnahas.bsky.social.

www.the-scientist.com/an-ai-lab-pa...

Had a fantastic time last week at CSHL's #biodata24, with amazing discussions around AI and bioinformatics and presenting my work on CellWhisperer.
Thanks @mike_schatz and all organizers, looking forward to being back in 2026!

How come everyone is joining Bluesky these days?

I thought it dead already.

Cindy Fang presents her work at CSHL Biological Data Science

Congratulations to @findycang.bsky.social from @jhubiostat.bsky.social who did an amazing job presenting her work at #biodata24 tonight! Preprint coming soon. ☺️

#ProudPI #stats #spatial #omics #transferlearning 🧪🧬🖥️🧠📈

What if we could look at a human tissue image🔬and quantify its biological age?🧬 And how could we get the same insights without collecting the tissue sample? In our new @biorxivpreprint, we create "tissue clocks" ⏳to do just that! www.biorxiv.org/content/10.1... 📝 #aging #tissue thread below⬇️

Contextual AI models for single-cell protein biology - Nature Methods PINNACLE is a context-specific geometric deep learning model for generating protein representations. Leveraging single-cell transcriptomics combined with networks of protein–protein interactions, cell...

"Contextual AI models for single-cell protein biology" 🧪🧬🖥️
- Protein embeddings are powerful.
- But: they are usually cell-type agnostic
- This paper: Embedding cell-type-aware protein representations via GNNs on scRNA-seq-pruned protein interaction graphs

www.nature.com/articles/s41...

"Transformers need glasses!
Information over-squashing in language tasks"
- In typical LLMs every token only 'sees' previous tokens (causal attention)
- This leads to information inbalance across tokens
- Thereby, later tokens 'vanish' in long sequences
arxiv.org/pdf/2406.04267

The primitive endoderm supports lineage plasticity to enable regulative development Although generally considered a simple support tissue, extra-embryonic primitive endoderm has the capacity to regenerate a complete blastocyst and continue post-implantation development.

'The primitive endoderm (PrE) supports lineage plasticity to enable regulative development' 🧬️🧪
- PrE is extra-embryonic tissue (at day 4) but can still recreate a full blastocyst (i.e. also embryo)
- JAK/STAT supports this plasticity
- www.cell.com/cell/abstrac...

Why is exercise good for you? Scientists are finding answers in our cells Decades of evidence shows that exercise leads to healthier, longer lives. Researchers are just starting to work out what it does to cells to reap this reward. Decades of evidence shows that exercise l...

"Why is exercise good for you?"

- Humans, as hunter-gatherers, evolved to 'always move'
- Exercise alters gene expression throughout the body
- With exercise, muscles contribute to anti-inflammation through IL-6 production

www.nature.com/articles/d41... 🧬🖥️🧪

Post-January 6th deplatforming reduced the reach of misinformation on Twitter - Nature Difference-in-differences analysis indicates that the decision by Twitter to deplatform 70,000 users following the events at the US Capitol on 6 January 2021 had wider effects on the spread of mi...

Cool study... Post-January 6th deplatforming on Twitter reduced the reach of misinformation
Hats off to my UCR colleagues Kevin Esterling and Diogo Ferrari and their co-authors...
🧪sociology polisky policysky
www.nature.com/articles/s41...

openreview.net/pdf?id=KIeU4...

- Most drug design methods assume rigid proteins -
Simple docking experiments show: Flexible side chains enhance modeling
- New method FlexFlow: Flow matching of small molecules in addition to side chain configurations

Looking forward to full release 🧬 & 🖥️

I go 90% with the stated opinion about OpenAI etc. Yet, it's a real pity that some arguments needed to be overdrawn. I use GPT-4 daily and find it extremely useful. Also, highly unlikely that LLMs will worsen due to data pollution.

One more example of how polarisation wins the attention market..

Enhancing generative perturbation models with LLM-informed gene... Genetic perturbations are key to understanding how genes regulate cell behavior, yet the ability to predict responses to these perturbations remains a significant challenge. While numerous...

- A common problem in ML is to generalize to cases unseen during training
- Here, GPT- and protein embeddings enable perturbation effect prediction for unseen genes
- My take: Great direction and I anticipate more 'embedding arithmetics' (e.g. 'gene1-gene2' for overexpression and KO)

On the Bottleneck of Graph Neural Networks and its Practical Implications Since the proposal of the graph neural network (GNN) by Gori et al. (2005) and Scarselli et al. (2008), one of the major problems in training GNNs was their struggle to propagate information...

The original 'oversquashing' paper is very accessibly written:

- In GNNs, when data needs to pass many nodes, the data gets exponentially 'diluted'
- Adding a simply fully-connected edge layer, improved upon QM9 by 42%
- This foundational and simple concept is only from 3 years ago

Cell subtype-specific effects of genetic variation in the Alzheimer’s disease brain - Nature Genetics Single-nucleus RNA sequencing from the dorsolateral prefrontal cortex of 424 aging individuals, and mapping the effect of genetic variation on gene expression, identified a large number of cis-express...

"Cell subtype-specific effects of genetic variation in the Alzheimer’s disease brain"

- scRNA-seq 🧬 allows high-throughput variant effect description 🖥️
- Here: brain tissue from 424 individuals, revealing unprecedented number of eQTLs
- Analysis mostly promoter-driven. More Hi-C data needed?

- AI models are not suited for disoveries followig the common deductive-nomological model (e.g. via laws)
- Yet they allow discovery through information compression, dimensionality reduction and feature correlation
- Example case studies: Protein structure prediction and single cell RNA-seq analyses

"Understanding Biology in the Age of Artificial Intelligence"
arxiv.org/abs/2403.04106

AI models are uncommon to uncover strict "laws" in biology. How are they still useful? An epistemological perspective

3-bullet-point review in the comment below