@nklkhlr.bsky.social
Postdoc at Heidelberg University in the lab of Britta Velten working on ML for spatial omics data
🏠 nklkhlr.github.io
💻 github.com/nklkhlr
🏠 nklkhlr.github.io
💻 github.com/nklkhlr
Reposted
We have been working with Michal Klein on pushing a module to train *flow matching* models using JAX. This is shipped as part of our new release of the OTT-JAX toolbox (github.com/ott-jax/ott)
The tutorial to do so is here: ott-jax.readthedocs.io/tutorials/ne...
The tutorial to do so is here: ott-jax.readthedocs.io/tutorials/ne...
November 5, 2025 at 2:04 PM
We have been working with Michal Klein on pushing a module to train *flow matching* models using JAX. This is shipped as part of our new release of the OTT-JAX toolbox (github.com/ott-jax/ott)
The tutorial to do so is here: ott-jax.readthedocs.io/tutorials/ne...
The tutorial to do so is here: ott-jax.readthedocs.io/tutorials/ne...
Reposted
It's amazingly fast (< 𝟏𝐡 𝐟𝐨𝐫 𝐭𝐡𝐞 𝐟𝐮𝐥𝐥 𝐩𝐢𝐩𝐞𝐥𝐢𝐧𝐞, 𝐭𝐫𝐚𝐢𝐧𝐞𝐝 𝐨𝐧 𝐚 𝐠𝐚𝐦𝐢𝐧𝐠 𝐥𝐚𝐩𝐭𝐨𝐩) and high-quality.
Another Topological Deep Learning success story, coming soon to #NeurIPS2025!
🖥️ github.com/aidos-lab/in...
📜 arxiv.org/pdf/2410.18987
4/n
Another Topological Deep Learning success story, coming soon to #NeurIPS2025!
🖥️ github.com/aidos-lab/in...
📜 arxiv.org/pdf/2410.18987
4/n
October 29, 2025 at 8:19 AM
It's amazingly fast (< 𝟏𝐡 𝐟𝐨𝐫 𝐭𝐡𝐞 𝐟𝐮𝐥𝐥 𝐩𝐢𝐩𝐞𝐥𝐢𝐧𝐞, 𝐭𝐫𝐚𝐢𝐧𝐞𝐝 𝐨𝐧 𝐚 𝐠𝐚𝐦𝐢𝐧𝐠 𝐥𝐚𝐩𝐭𝐨𝐩) and high-quality.
Another Topological Deep Learning success story, coming soon to #NeurIPS2025!
🖥️ github.com/aidos-lab/in...
📜 arxiv.org/pdf/2410.18987
4/n
Another Topological Deep Learning success story, coming soon to #NeurIPS2025!
🖥️ github.com/aidos-lab/in...
📜 arxiv.org/pdf/2410.18987
4/n
Reposted
Extremely honoured to receive the Bayer foundation early excellence in science award. Thanks to all my team, colleagues, collaborators and mentors for making this possible!
Award for Heidelberg Data Scientist: The Early Excellence in Science Award goes to Britta Velten for innovative procedures in the analysis of complex data sets from the life sciences
www.uni-heidelberg.de/en/newsroom/...
www.uni-heidelberg.de/en/newsroom/...
October 16, 2025 at 3:18 PM
Extremely honoured to receive the Bayer foundation early excellence in science award. Thanks to all my team, colleagues, collaborators and mentors for making this possible!
Reposted
My take: Engineering *is* important. Ideas are cheap. Novelty is overrated. "Hyperparameter tuning" is a cynically dismissive term for something that is in fact the real, difficult problem.
Sometimes I’ll see a paper that implements an idea I’ve had but implements it poorly for engineering reasons. But then it’s hard to write a follow up paper because it’s not “novel” anymore
October 9, 2025 at 2:13 PM
My take: Engineering *is* important. Ideas are cheap. Novelty is overrated. "Hyperparameter tuning" is a cynically dismissive term for something that is in fact the real, difficult problem.
Reposted
After the coffee break ☕, we continue with the second part of practical session 5, with Nikolai Köhler and Wangjun Hu 🎓 going through the different materials: from storing spatial-omics data 💽 to learning spatial patterns using #MEFISTO 😎
September 17, 2025 at 10:20 AM
After the coffee break ☕, we continue with the second part of practical session 5, with Nikolai Köhler and Wangjun Hu 🎓 going through the different materials: from storing spatial-omics data 💽 to learning spatial patterns using #MEFISTO 😎
Reposted
Welcome to day 4 of #EMBOBioImage 🖥️
👉Happening right now: practical session 5, spatial statistics and omics integration, led by @brittavelten.bsky.social, assisted by Anna Klemm.
👉Happening right now: practical session 5, spatial statistics and omics integration, led by @brittavelten.bsky.social, assisted by Anna Klemm.
September 17, 2025 at 10:16 AM
Welcome to day 4 of #EMBOBioImage 🖥️
👉Happening right now: practical session 5, spatial statistics and omics integration, led by @brittavelten.bsky.social, assisted by Anna Klemm.
👉Happening right now: practical session 5, spatial statistics and omics integration, led by @brittavelten.bsky.social, assisted by Anna Klemm.
Reposted
I always find it funny that we obsess over sample size, yet peer review relies on the arbitrary opinions of just 2/3 people. That would be fine if editors were truly engaged, but given the workload, they don’t have the time, or don’t care enough. Anyway, I’m just glad it finally got published! 👏
1/ Everything that could go wrong in paper publishing… did.
A story of patience, absurdity, and persistence 🌀 <1min
From Alfonso Valencia’s lab and a very stubborn PhD student (me).
A story of patience, absurdity, and persistence 🌀 <1min
From Alfonso Valencia’s lab and a very stubborn PhD student (me).
September 3, 2025 at 3:09 PM
I always find it funny that we obsess over sample size, yet peer review relies on the arbitrary opinions of just 2/3 people. That would be fine if editors were truly engaged, but given the workload, they don’t have the time, or don’t care enough. Anyway, I’m just glad it finally got published! 👏
Reposted
@embl.org PhD programme just open - many interesting projects, including two with us @saezlab.bsky.social @ebi.embl.org - one on #host-microbiome interactions using #spatial omics, and one on #AI in #proteomics 👇
📢 Recruitment for the EMBL International PhD Programme is officially open!
At EMBL, we train young scientists to become skilled and creative future leaders in academia and other sectors. Join us and get a head start on your career in life sciences!
bit.ly/47mmiFF
At EMBL, we train young scientists to become skilled and creative future leaders in academia and other sectors. Join us and get a head start on your career in life sciences!
bit.ly/47mmiFF
September 2, 2025 at 6:55 PM
@embl.org PhD programme just open - many interesting projects, including two with us @saezlab.bsky.social @ebi.embl.org - one on #host-microbiome interactions using #spatial omics, and one on #AI in #proteomics 👇
Reposted
Very happy to share our latest publication unravelling how the #ERstress sensor ATF6 stirs up trouble (and tumors) in #colorectalcancer. ATF6 drives CRC by reshaping lipid #metabolism and the intestinal #microbiota. A huge thank you to all co-authors! #lifesciences
www.nature.com/articles/s42...
www.nature.com/articles/s42...
ATF6 activation alters colonic lipid metabolism causing tumour-associated microbial adaptation - Nature Metabolism
The transcription factor ATF6 causes an enrichment in long-chain fatty acids in the colonic epithelium, which leads to changes in the gut microbiota and contributes to the development of colorectal ca...
www.nature.com
September 2, 2025 at 7:01 PM
Very happy to share our latest publication unravelling how the #ERstress sensor ATF6 stirs up trouble (and tumors) in #colorectalcancer. ATF6 drives CRC by reshaping lipid #metabolism and the intestinal #microbiota. A huge thank you to all co-authors! #lifesciences
www.nature.com/articles/s42...
www.nature.com/articles/s42...
Reposted
We spent a year writing this review of low-dim embeddings and arguing about things like epistemic roles and best practices :-) 20+ authors are all participants of the Dagstuhl seminar we held last year: www.dagstuhl.de/24122. Led by @alexandr.bsky.social and Cyril de Bodt.
arxiv.org/abs/2508.15929
arxiv.org/abs/2508.15929
August 27, 2025 at 3:14 PM
We spent a year writing this review of low-dim embeddings and arguing about things like epistemic roles and best practices :-) 20+ authors are all participants of the Dagstuhl seminar we held last year: www.dagstuhl.de/24122. Led by @alexandr.bsky.social and Cyril de Bodt.
arxiv.org/abs/2508.15929
arxiv.org/abs/2508.15929
Reposted
#MachineLearning loves data. #Topology loves shape.
Let's bring them together!
👉The Euler Characteristic Transform (ECT) bridges both worlds, as I outline in a recent article in the Notices of the
@amermathsoc.bsky.social
Engage!
🧵1/n
Let's bring them together!
👉The Euler Characteristic Transform (ECT) bridges both worlds, as I outline in a recent article in the Notices of the
@amermathsoc.bsky.social
Engage!
🧵1/n
July 22, 2025 at 8:16 AM
#MachineLearning loves data. #Topology loves shape.
Let's bring them together!
👉The Euler Characteristic Transform (ECT) bridges both worlds, as I outline in a recent article in the Notices of the
@amermathsoc.bsky.social
Engage!
🧵1/n
Let's bring them together!
👉The Euler Characteristic Transform (ECT) bridges both worlds, as I outline in a recent article in the Notices of the
@amermathsoc.bsky.social
Engage!
🧵1/n
Reposted
Exciting kick-off meeting for our spatial omics seminar in and around Heidelberg organised with @tanevski.bsky.social and @denisschapiro.bsky.social. Was fun to see all the cool research happening here and connect. Reach out to us if you missed out and would like to join the next meetings!
July 3, 2025 at 11:03 AM
Exciting kick-off meeting for our spatial omics seminar in and around Heidelberg organised with @tanevski.bsky.social and @denisschapiro.bsky.social. Was fun to see all the cool research happening here and connect. Reach out to us if you missed out and would like to join the next meetings!
Reposted
🚀 Job opportunity: Bioinformatics Software Engineer
Join a young and passionate team at Heidelberg University to advance bioinformatics software that drive biological discovery.
Learn more & apply 👉 shorturl.at/GCpg7
Join a young and passionate team at Heidelberg University to advance bioinformatics software that drive biological discovery.
Learn more & apply 👉 shorturl.at/GCpg7
Bioinformatics Software Engineer
Post a job in 3min, or find thousands of job offers like this one at jobRxiv!
shorturl.at
June 25, 2025 at 1:21 PM
🚀 Job opportunity: Bioinformatics Software Engineer
Join a young and passionate team at Heidelberg University to advance bioinformatics software that drive biological discovery.
Learn more & apply 👉 shorturl.at/GCpg7
Join a young and passionate team at Heidelberg University to advance bioinformatics software that drive biological discovery.
Learn more & apply 👉 shorturl.at/GCpg7
Reposted
We're excited to be at the Kick Off Heidelberg Spatial-Omics Lunch Seminar Series with our very own @chiaraschiller.bsky.social presenting some of her PhD work!
July 1, 2025 at 9:52 AM
We're excited to be at the Kick Off Heidelberg Spatial-Omics Lunch Seminar Series with our very own @chiaraschiller.bsky.social presenting some of her PhD work!
Reposted
🌟We're glad to announce that the brand new EMBL Conference #EMBLSpatialBiology is now open for registration ➡️ https://s.embl.org/spb25-01-bl
Submit your abstract by 8 July and be part of the rapidly growing spatial biology community!
🗓️ 14 – 17 October
📍 EMBL Heidelberg and Virtual
#ESSB2025
Submit your abstract by 8 July and be part of the rapidly growing spatial biology community!
🗓️ 14 – 17 October
📍 EMBL Heidelberg and Virtual
#ESSB2025
April 29, 2025 at 9:00 AM
🌟We're glad to announce that the brand new EMBL Conference #EMBLSpatialBiology is now open for registration ➡️ https://s.embl.org/spb25-01-bl
Submit your abstract by 8 July and be part of the rapidly growing spatial biology community!
🗓️ 14 – 17 October
📍 EMBL Heidelberg and Virtual
#ESSB2025
Submit your abstract by 8 July and be part of the rapidly growing spatial biology community!
🗓️ 14 – 17 October
📍 EMBL Heidelberg and Virtual
#ESSB2025
Reposted
JOB OPPORTUNITY: Join us as a scientific programmer to advance tools for multi-omics data at Heidelberg University. Details can be found at shorturl.at/OcnOa and please spread the word!
Scientific programmer
Post a job in 3min, or find thousands of job offers like this one at jobRxiv!
shorturl.at
January 31, 2025 at 8:12 AM
JOB OPPORTUNITY: Join us as a scientific programmer to advance tools for multi-omics data at Heidelberg University. Details can be found at shorturl.at/OcnOa and please spread the word!