Jakob Macke

Great new work from the labs of @jakhmack.bsky.social and @philipp.hertie.ai! The software Jaxley enables brain simulations which both imitate the processes in the brain in detail and can solve challenging cognitive tasks. Press release of @unituebingen.bsky.social: uni-tuebingen.de/en/universit...

Congrats to @deismic.bsky.social and everyone for getting this out!

An ion channel omnimodel for standardized biophysical neuron modelling Biophysical neuron modeling is an indispensable tool in neuroscience research, with the combination of diverse ion channel kinetics and morphologies being used to explain various single-neuron propert...

“Mapping ion channel function” doi.org/10.7554/eLif... isn’t exactly a citation slayer, but it’s still one of my favourites (& my first independent project). Today we push pt 2, where we trace code origin & unite almost all channel models in a common expression. Boom! www.biorxiv.org/content/10.1...

🎉 sbi participated in GSoC 2025 through @numfocus.bsky.social and it was a great success: our two students contributed major new features and substantial internal improvements: 🧵 👇

Hello Frankfurt 🇩🇪 - We are excited to share the latest result from our group and collaborators at
@bernsteinneuro.bsky.social 🚀🧠 #BernsteinConference

Thanks to @brainloops.bsky.social, @ekfstiftung.bsky.social and @cherish-msca.bsky.social for supporting these projects and our scholars.

The Macke lab is well-represented at the @bernsteinneuro.bsky.social conference in Frankfurt this year! We have lots of exciting new work to present with 7 posters (details👇) 1/9

From hackathon to release: sbi v0.25 is here! 🎉

What happens when dozens of SBI researchers and practitioners collaborate for a week? New inference methods, new documentation, lots of new embedding networks, a bridge to pyro and a bridge between flow matching and score-based methods 🤯

1/7 🧵

Sharing this here a bit late, but @vstaros.bsky.social and I wrote a little something about our experience contributing to the @sbi-devs.bsky.social (simulation-based inference) hackathon. @mlcolab.org @mackelab.bsky.social

We were obviously very hungry while writing.

My first paper on simulation-based inference (SBI) as part of @mackelab.bsky.social!

Exciting work on adapting state-of-the-art foundation models for posterior estimation. Almost plug-and-play, and surprisingly effective.

Paper/code in thread below 🧵

I have been genuinely amazed how well tabpfn works as a density estimator, and how helpful this is for SBI ... Great work by @vetterj.bsky.social, Manuel and @danielged.bsky.social!!

Formulas and numbers from the field of machine learning written in white chalk on a blackboard

Together with #AIMS, the African Institute for Mathematical Sciences, we have an exciting position to fill: The AIMS - Tübingen Junior Research Chair in Machine Learning for Science! 1/2

Mario Krenn (right) and eight members of his group stand next to each other for a group photo, with green plants in the background.

Come work with us in Tübingen! Our new professor @mariokrenn.bsky.social is looking for PhDs and postdocs! The group builds #AI systems for discovering new concepts, experiments and ideas in #physics. Find out more: uni-tuebingen.de/en/128980#c2... #AIforScience

👨‍💻 Open PI position in our institute 👨‍💻 !! If you are an expert in Computational Neuroscience and want to start your lab in Bordeaux, contact us !
www.fens.org/careers/job-...
@neuromagendie.bsky.social
@neurobordeaux.bsky.social

My point is not that you should include our work — but that more computational folks should actually tackle this wonderful data now that it is abailable, with ML or without (although we certainly have found ML useful)!

Sounds interesting! Loved how your pitch includes the availability of the drosophila connectome, unfortunately none of the abstracts seem to mention it?

Sbi can take you places … very proud about @gmoss13.bsky.social et als work, a wild and serendipitous collaboration made possible by @ml4science.bsky.social!

Oh I am more optimistic and even even excited, one can disect it, and it has interpretable units and sub circuits … we might need better tools though to make it easier for people to play with it!!

was our paper used as evidence for or against this thesis? (My biased view is that this approach shows how one can big data and mechanistic insights can be friends …)

All-in-one simulation-based inference Amortized Bayesian inference trains neural networks to solve stochastic inference problems using model simulations, thereby making it possible to rapidly perform Bayesian inference for any newly obser...

I always find the figures from the @mackelab.bsky.social really clear and pretty!

For example in arxiv.org/abs/2404.09636.

We’ve successfully automated part of the (neuro)scientific process. Now I may be out of a job. After a lot of iterations, here’s our framework for automatic discovery, built to embrace degeneracy and the realities of underconstrained modeling.

Thanks! Trying to make good figures is an important part of the @mackelab.bsky.social experience ;-). Indeed, this design was initiated by @janmatthis.bsky.social and then passed on and refined by @deismic.bsky.social and others! We still use it, although sometimes in white-on-black for talks ...

magic, by magician @bconfavreux.bsky.social, using a magic SBI-wand conjured with Poornima Ramesh, under the auspices of the wise @tpvogels.bsky.social!

YouTube video by Allen Institute Opening remarks Karel Svoboda & Nima Dehghani

Last month, we organized #ODIN2025 @alleninstitute.org (along w Karel, Saskia @sejdevries.bsky.social , David & Satra) with the theme "Integrating Scales & Modalities".
See the videos📣👇
Full playlist: youtube.com/playlist?lis... 🎥
Speaker: alleninstitute.org/odin-symposi...
youtu.be/N1IMki0RnIc?...

📢 Amazing speaker in our Neurocolloquium on Wed. May 21 at 4.15pm CEST: Marion Silies @unimainz.bsky.social‬ will talk about "From heterogeneous wiring to degenerative function in motion-detection circuit", live in Tübingen & in Zoom.
🙌 Host: @jakhmack.bsky.social
👉 Sign up: tinyurl.com/32ku5jth

Nice article in the transmitter about connectome-enabled brain models, covering @lappalainenjk.bsky.social’s work with @srinituraga.bsky.social and colleagues!!

We'll present our #ICLR2025 spotlight on ZAPBench this afternoon: 📍 Hall 3 #61!

Most simulators for time-series data (e.g., numerical solvers for differential equations) are Markovian-- this can be exploited for efficient simulation-based inference on time-series data! Talk to Manuel and Shoji at #ICLR2025, or read the paper ⬇️!

Thanks so much for the shout-out, and congrats on your exciting work!! 🎉 🙂

Also, a good reminder to share that our work is now out in Cell Reports 🙏🎊

⬇️

www.cell.com/cell-reports...

I am also not at Cosyne ;-). Then send us an email to mls-jobs@inf.uni-tuebingen.de, full instructions of what we need are here: www.mackelab.org/jobs/

I am not at Cosyne, but @rdgao.bsky.social @auschulz.bsky.social @matthijspals.bsky.social and Zinovia Stefanidi are-- talk to them about their awesome work (and ask them about open positions with us if you are interested...)!