Lightnews — Scholar-powered news

Moritz Schaefer @moritzbaio.bsky.social · Jul 21

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!

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Moritz Schaefer @moritzbaio.bsky.social · Jun 18

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

Moritz Schaefer - BioMedical AI

moritzs.de

Moritz Schaefer @moritzbaio.bsky.social · May 6

Having fun at work... :)

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

Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · May 6

AI in medicine ready for takeoff 🤖🚁 We flew a drone through the Institute of Artificial Intelligence @MedUniWien. Join us for the trip and watch our team at "work". #AI #biomedicine #innovation #makingof (1/2)

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Moritz Schaefer @moritzbaio.bsky.social · Mar 25

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

Matching flows to data

Models that fit like water in a vessel.

hrovatin.github.io

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Moritz Schaefer @moritzbaio.bsky.social · Mar 12

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...

Google Image Result for https://cdn.prod.website-files.com/62375700635d76646ef2457f/67365276cca8746a8d6a232e_AD_4nXcwvKJAk8wseUsMhOovo63cjmXEXkqKM_RXxd1bqECb6M3LfWoMGc1sq2EAKsD8xmjzYW9icoFmPtxp8wwNKpn...

images.app.goo.gl

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Reposted by Moritz Schaefer

Scientists4Future Österreich @s4fat.bsky.social · Mar 7

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

Crowd of protestors at March for Science, Vienna

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Reposted by Moritz Schaefer

Stand Up for Science! @standupforscience.bsky.social · Mar 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

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)

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Moritz Schaefer @moritzbaio.bsky.social · Jan 26

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..

Moritz Schaefer @moritzbaio.bsky.social · Jan 16

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.

Ewan Birney @ewanbirney.bsky.social · Jan 3

The mistake from further away I think is to view AI through the lens of Large Language Models - these are great (well... at least very useful) for text, but so much in science (and in life!) is not text! The set of "tailored" or "narrow" AI in science will only increase

Moritz Schaefer @moritzbaio.bsky.social · Jan 10

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.

Moritz Schaefer @moritzbaio.bsky.social · Dec 30

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

This link will take you to a page that’s not on LinkedIn

lnkd.in

Reposted by Moritz Schaefer

Peter Koo @pkoo562.bsky.social · Dec 23

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!

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Reposted by Moritz Schaefer

Peter Gleick @petergleick.bsky.social · Dec 25

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...

Elon Musk takes aim at Wikipedia

The billionaire has become one of the most prominent supporters of President-elect Donald Trump.

www.newsweek.com

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Moritz Schaefer @moritzbaio.bsky.social · Dec 19

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...

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.

www.the-scientist.com

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Moritz Schaefer @moritzbaio.bsky.social · Nov 21

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!

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Moritz Schaefer @moritzbaio.bsky.social · Nov 19

How come everyone is joining Bluesky these days?

I thought it dead already.

Reposted by Moritz Schaefer

Stephanie Hicks @stephaniehicks.bsky.social · Nov 15

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 🧪🧬🖥️🧠📈

Cindy Fang presents her work at CSHL Biological Data Science

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Reposted by Moritz Schaefer

Andre Rendeiro @andre-rendeiro.com · Nov 16

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⬇️

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Moritz Schaefer @moritzbaio.bsky.social · Aug 15

"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...

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...

www.nature.com

Moritz Schaefer @moritzbaio.bsky.social · Jul 13

"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

Moritz Schaefer @moritzbaio.bsky.social · Jun 25

'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...

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.

www.cell.com

Moritz Schaefer @moritzbaio.bsky.social · Jun 10

"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... 🧬🖥️🧪

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...

www.nature.com

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Reposted by Moritz Schaefer

Richard M. Carpiano, PhD, MPH @rmcarpiano.medsky.social · Jun 7

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...

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...

www.nature.com

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Moritz Schaefer @moritzbaio.bsky.social · May 5

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 🧬 & 🖥️

openreview.net

Moritz Schaefer @moritzbaio.bsky.social · May 3

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..