Moritz Schaefer
@moritzbaio.bsky.social
My Bio? AI Bio!
Currently in the Bock lab@CeMM talking to single cells with LLMs.
Here: paper reviews in 3 lines
Mastodon (inactive): @moritzschaefer@qoto.org
Twitter: @muronglizi
Currently in the Bock lab@CeMM talking to single cells with LLMs.
Here: paper reviews in 3 lines
Mastodon (inactive): @moritzschaefer@qoto.org
Twitter: @muronglizi
📝Finally out: Chat with your cells in English language - right in the browser. ✨
Try it yourself: cellwhisperer.bocklab.org and check out our tweetorial.
Huge shout-out to to all the other contributors for the amazing teamwork!
Try it yourself: cellwhisperer.bocklab.org and check out our tweetorial.
Huge shout-out to to all the other contributors for the amazing teamwork!
November 11, 2025 at 3:04 PM
📝Finally out: Chat with your cells in English language - right in the browser. ✨
Try it yourself: cellwhisperer.bocklab.org and check out our tweetorial.
Huge shout-out to to all the other contributors for the amazing teamwork!
Try it yourself: cellwhisperer.bocklab.org and check out our tweetorial.
Huge shout-out to to all the other contributors for the amazing teamwork!
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!
SpotWhisperer enables spatially resolved annotation of histopathology images using natural language. We achieved this by "transferring" annotations from transcriptomic data. More soon!
July 21, 2025 at 1:24 AM
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!
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
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
Moritz Schaefer - BioMedical AI
moritzs.de
June 18, 2025 at 11:13 AM
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
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.
Made possible by an amazing bunch of colleagues at my institute.
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)
May 6, 2025 at 12:12 PM
Having fun at work... :)
Made possible by an amazing bunch of colleagues at my institute.
Made possible by an amazing bunch of colleagues at my institute.
Great behind-the-scenes overview on 'Flow matching and OT in cell biology'
hrovatin.github.io/posts/sc_flo...
hrovatin.github.io/posts/sc_flo...
Matching flows to data
Models that fit like water in a vessel.
hrovatin.github.io
March 25, 2025 at 2:38 PM
Great behind-the-scenes overview on 'Flow matching and OT in cell biology'
hrovatin.github.io/posts/sc_flo...
hrovatin.github.io/posts/sc_flo...
Reposted by Moritz Schaefer
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
>500 people in front of @univie.ac.at, ~1000 people at Votivpark! 💚💚💚
Science is for everyone!
#standupforscience2025
#scienceforall
#sciencenotsilence
March 7, 2025 at 4:21 PM
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
>500 people in front of @univie.ac.at, ~1000 people at Votivpark! 💚💚💚
Science is for everyone!
#standupforscience2025
#scienceforall
#sciencenotsilence
Reposted by Moritz Schaefer
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
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
March 6, 2025 at 1:07 PM
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
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
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.
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.
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
January 16, 2025 at 5:12 AM
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.
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.
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
- My highlights post on LinkedIn:
www.linkedin.com/posts/moritz...
- I gave a talk too: lnkd.in/dXRF2mai
- All talks here: media.ccc.de
LinkedIn
This link will take you to a page that’s not on LinkedIn
lnkd.in
December 30, 2024 at 4:26 PM
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
- My highlights post on LinkedIn:
www.linkedin.com/posts/moritz...
- I gave a talk too: lnkd.in/dXRF2mai
- All talks here: media.ccc.de
Reposted by Moritz Schaefer
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!
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!
December 23, 2024 at 8:04 PM
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!
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!
Reposted by Moritz Schaefer
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...
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
December 25, 2024 at 3:54 AM
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...
www.newsweek.com/elon-musk-ta...
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...
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
December 19, 2024 at 2:37 PM
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...
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!
Thanks @mike_schatz and all organizers, looking forward to being back in 2026!
November 21, 2024 at 2:52 PM
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!
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.
I thought it dead already.
November 19, 2024 at 11:09 AM
How come everyone is joining Bluesky these days?
I thought it dead already.
I thought it dead already.
Reposted by Moritz Schaefer
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 🧪🧬🖥️🧠📈
#ProudPI #stats #spatial #omics #transferlearning 🧪🧬🖥️🧠📈
November 15, 2024 at 4:07 AM
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 🧪🧬🖥️🧠📈
#ProudPI #stats #spatial #omics #transferlearning 🧪🧬🖥️🧠📈
Reposted by Moritz Schaefer
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⬇️
November 16, 2024 at 3:15 PM
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" 🧪🧬🖥️
- 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...
- 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
August 15, 2024 at 1:20 PM
"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...
- 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
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
July 13, 2024 at 7:35 PM
"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
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 (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...
- 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
June 25, 2024 at 10:13 AM
'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...
- 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?"
- 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... 🧬🖥️🧪
- 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
June 10, 2024 at 6:08 AM
"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... 🧬🖥️🧪
- 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... 🧬🖥️🧪
Reposted by Moritz Schaefer
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...
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
June 7, 2024 at 1:34 AM
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...
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 🧬 & 🖥️
- 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
May 5, 2024 at 4:36 AM
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 🧬 & 🖥️
- 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..
One more example of how polarisation wins the attention market..
May 3, 2024 at 6:46 AM
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..
One more example of how polarisation wins the attention market..
- 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)
- 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)
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...
openreview.net
April 10, 2024 at 6:57 AM
- 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)
- 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)
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
- 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
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...
arxiv.org
April 8, 2024 at 6:08 AM
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
- 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