Jakob Macke
@jakhmack.bsky.social
#AI4Science #CompNeuro #NeuroAI #SBI
www.mackelab.org @mackelab.bsky.social
· Prof Uni Tuebingen ML4Science BCCN tue.ai
· Adjunct MPI IS · Fellow ellis.eu
· currently hiring postdocs and PhD students
· sometimes goes for a run
www.mackelab.org @mackelab.bsky.social
· Prof Uni Tuebingen ML4Science BCCN tue.ai
· Adjunct MPI IS · Fellow ellis.eu
· currently hiring postdocs and PhD students
· sometimes goes for a run
Pinned
Jakob Macke
@jakhmack.bsky.social
· Nov 11
Alright: I develop ML/AI tools for scientific discovery with focus on neuroscience. In practice, currently: Simulation-based inference to discover data-compatible models, deep learning to optimise mechanistic models (flies!) and probabilistic ML to analyse + visualise high-d neural data (humans!)
Simulation-based inference has really become a commonly used tool for parameter inference across many fields and applications. We (finally...) got together to write a tutorial introduction and guide to (hopefully) help users get started and navigate the different methods and diagnostics!
Simulation-based inference (SBI) has transformed parameter inference across a wide range of domains. To help practitioners get started and make the most of these methods, we joined forces with researchers from many institutions and wrote a practical guide to SBI.
📄 Paper: arxiv.org/abs/2508.12939
📄 Paper: arxiv.org/abs/2508.12939
Simulation-Based Inference: A Practical Guide
A central challenge in many areas of science and engineering is to identify model parameters that are consistent with prior knowledge and empirical data. Bayesian inference offers a principled framewo...
arxiv.org
November 21, 2025 at 3:34 PM
Simulation-based inference has really become a commonly used tool for parameter inference across many fields and applications. We (finally...) got together to write a tutorial introduction and guide to (hopefully) help users get started and navigate the different methods and diagnostics!
Reposted by Jakob Macke
I am super happy to share that our project on training biophysical models with Jaxley is now published in Nature Methods: www.nature.com/articles/s41...
Jaxley: differentiable simulation enables large-scale training of detailed biophysical models of neural dynamics - Nature Methods
Jaxley is a versatile platform for biophysical modeling in neuroscience. It allows efficiently simulating large-scale biophysical models on CPUs, GPUs and TPUs. Model parameters can be optimized with ...
www.nature.com
November 13, 2025 at 12:38 PM
I am super happy to share that our project on training biophysical models with Jaxley is now published in Nature Methods: www.nature.com/articles/s41...
Reposted by 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...
November 13, 2025 at 4:56 PM
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!
Our work on training biophysical models with Jaxley is now out in @natmethods.nature.com. Led by @deismic.bsky.social, with @philipp.hertie.ai, @ppjgoncalves.bsky.social & @jakhmack.bsky.social et al.
Paper: www.nature.com/articles/s41...
Paper: www.nature.com/articles/s41...
Jaxley: differentiable simulation enables large-scale training of detailed biophysical models of neural dynamics - Nature Methods
Jaxley is a versatile platform for biophysical modeling in neuroscience. It allows efficiently simulating large-scale biophysical models on CPUs, GPUs and TPUs. Model parameters can be optimized with ...
www.nature.com
November 13, 2025 at 1:28 PM
Congrats to @deismic.bsky.social and everyone for getting this out!
Reposted by Jakob Macke
“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...
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...
www.biorxiv.org
October 6, 2025 at 6:25 PM
“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...
Reposted by Jakob Macke
🎉 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: 🧵 👇
October 17, 2025 at 1:30 PM
🎉 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: 🧵 👇
Reposted by Jakob Macke
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.
@bernsteinneuro.bsky.social 🚀🧠 #BernsteinConference
Thanks to @brainloops.bsky.social, @ekfstiftung.bsky.social and @cherish-msca.bsky.social for supporting these projects and our scholars.
September 30, 2025 at 2:19 PM
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.
@bernsteinneuro.bsky.social 🚀🧠 #BernsteinConference
Thanks to @brainloops.bsky.social, @ekfstiftung.bsky.social and @cherish-msca.bsky.social for supporting these projects and our scholars.
Reposted by Jakob Macke
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
September 30, 2025 at 2:06 PM
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
Reposted by Jakob Macke
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 🧵
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 🧵
September 9, 2025 at 3:00 PM
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 🧵
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 🧵
Reposted by Jakob Macke
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.
We were obviously very hungry while writing.
A retrospective on the 2025 SBI Hackathon
You walk into a bakery, take one bite of a still-warm pastry, and think: “Whoa - there’s rye flour, a hint of orange zest, maybe cardamom… and is that buckwheat honey?” From that single taste you begi...
mlcolab.org
July 31, 2025 at 11:54 AM
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.
We were obviously very hungry while writing.
Reposted by Jakob Macke
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 🧵
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 🧵
New preprint: SBI with foundation models!
Tired of training or tuning your inference network, or waiting for your simulations to finish? Our method NPE-PF can help: It provides training-free simulation-based inference, achieving competitive performance with orders of magnitude fewer simulations! ⚡️
Tired of training or tuning your inference network, or waiting for your simulations to finish? Our method NPE-PF can help: It provides training-free simulation-based inference, achieving competitive performance with orders of magnitude fewer simulations! ⚡️
July 23, 2025 at 6:45 PM
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 🧵
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!!
New preprint: SBI with foundation models!
Tired of training or tuning your inference network, or waiting for your simulations to finish? Our method NPE-PF can help: It provides training-free simulation-based inference, achieving competitive performance with orders of magnitude fewer simulations! ⚡️
Tired of training or tuning your inference network, or waiting for your simulations to finish? Our method NPE-PF can help: It provides training-free simulation-based inference, achieving competitive performance with orders of magnitude fewer simulations! ⚡️
July 23, 2025 at 2:37 PM
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!!
Reposted by Jakob Macke
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
July 16, 2025 at 12:47 PM
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
Reposted by Jakob Macke
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
July 16, 2025 at 1:14 PM
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
Reposted by Jakob Macke
👨💻 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
www.fens.org/careers/job-...
@neuromagendie.bsky.social
@neurobordeaux.bsky.social
July 10, 2025 at 3:13 PM
👨💻 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
www.fens.org/careers/job-...
@neuromagendie.bsky.social
@neurobordeaux.bsky.social
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!
Have I been to Antarctica? No. But my colleagues have, and we can learn a lot from the data they collected! Really happy to share that our work is now published!
Thrilled to share that our paper on using simulation-based inference for inferring ice accumulation and melting rates for Antarctic ice shelves is now published in Journal of Glaciology!
www.cambridge.org/core/journal...
www.cambridge.org/core/journal...
June 11, 2025 at 10:13 PM
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!
Reposted by Jakob Macke
I always find the figures from the @mackelab.bsky.social really clear and pretty!
For example in arxiv.org/abs/2404.09636.
For example in arxiv.org/abs/2404.09636.
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...
arxiv.org
June 3, 2025 at 6:17 AM
I always find the figures from the @mackelab.bsky.social really clear and pretty!
For example in arxiv.org/abs/2404.09636.
For example in arxiv.org/abs/2404.09636.
Reposted by Jakob Macke
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.
We just pushed “Memory by a 1000 rules” onto bioRxiv, where we use clever #ML to find #plasticity quadruplets (EE, EI, IE, II) that learn basic stability in spiking nets. Why is it cool? We find 1000s!! of solutions, and they don’t just stabilise. They #memorise! www.biorxiv.org/content/10.1...
Memory by a thousand rules: Automated discovery of functional multi-type plasticity rules reveals variety & degeneracy at the heart of learning
Synaptic plasticity is the basis of learning and memory, but the link between synaptic changes and neural function remains elusive. Here, we used automated search algorithms to obtain thousands of str...
www.biorxiv.org
June 4, 2025 at 1:40 PM
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.
magic, by magician @bconfavreux.bsky.social, using a magic SBI-wand conjured with Poornima Ramesh, under the auspices of the wise @tpvogels.bsky.social!
We just pushed “Memory by a 1000 rules” onto bioRxiv, where we use clever #ML to find #plasticity quadruplets (EE, EI, IE, II) that learn basic stability in spiking nets. Why is it cool? We find 1000s!! of solutions, and they don’t just stabilise. They #memorise! www.biorxiv.org/content/10.1...
Memory by a thousand rules: Automated discovery of functional multi-type plasticity rules reveals variety & degeneracy at the heart of learning
Synaptic plasticity is the basis of learning and memory, but the link between synaptic changes and neural function remains elusive. Here, we used automated search algorithms to obtain thousands of str...
www.biorxiv.org
June 2, 2025 at 7:11 PM
magic, by magician @bconfavreux.bsky.social, using a magic SBI-wand conjured with Poornima Ramesh, under the auspices of the wise @tpvogels.bsky.social!
Reposted by Jakob Macke
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?...
See the videos📣👇
Full playlist: youtube.com/playlist?lis... 🎥
Speaker: alleninstitute.org/odin-symposi...
youtu.be/N1IMki0RnIc?...
Opening remarks Karel Svoboda & Nima Dehghani
YouTube video by Allen Institute
youtu.be
May 8, 2025 at 3:48 PM
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?...
See the videos📣👇
Full playlist: youtube.com/playlist?lis... 🎥
Speaker: alleninstitute.org/odin-symposi...
youtu.be/N1IMki0RnIc?...
Reposted by Jakob Macke
📢 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
🙌 Host: @jakhmack.bsky.social
👉 Sign up: tinyurl.com/32ku5jth
May 12, 2025 at 11:09 AM
📢 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
🙌 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!!
It took more than a decade to trace the 130,000 connections in a fruit fly's brain. With the map in hand, researchers are turning to the next step in connectomics: building simulations.
By @ldattaro.bsky.social
#neuroskyence
www.thetransmitter.org/connectome/c...
By @ldattaro.bsky.social
#neuroskyence
www.thetransmitter.org/connectome/c...
Connectomics 2.0: Simulating the brain
With a complete fly connectome in hand, researchers are taking the next step to model how brain circuits fuel function.
www.thetransmitter.org
May 3, 2025 at 1:36 PM
Nice article in the transmitter about connectome-enabled brain models, covering @lappalainenjk.bsky.social’s work with @srinituraga.bsky.social and colleagues!!
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 ⬇️!
Excited to present our work on compositional SBI for time series at #ICLR2025 tomorrow!
If you're interested in simulation-based inference for time series, come chat with Manuel Gloeckler or Shoji Toyota
at Poster #420, Saturday 10:00–12:00 in Hall 3.
📰: arxiv.org/abs/2411.02728
If you're interested in simulation-based inference for time series, come chat with Manuel Gloeckler or Shoji Toyota
at Poster #420, Saturday 10:00–12:00 in Hall 3.
📰: arxiv.org/abs/2411.02728
Compositional simulation-based inference for time series
Amortized simulation-based inference (SBI) methods train neural networks on simulated data to perform Bayesian inference. While this strategy avoids the need for tractable likelihoods, it often requir...
arxiv.org
April 25, 2025 at 8:23 PM
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 ⬇️!
Reposted by Jakob Macke
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...
Also, a good reminder to share that our work is now out in Cell Reports 🙏🎊
⬇️
www.cell.com/cell-reports...
April 17, 2025 at 8:50 PM
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...
Also, a good reminder to share that our work is now out in Cell Reports 🙏🎊
⬇️
www.cell.com/cell-reports...