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Matthijs Pals

@matthijspals.bsky.social
963 followers 628 following 20 posts

Using deep learning to study neural dynamics @durstewitzlab

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Matthijs Pals @matthijspals.bsky.social · 28/09/2026
What are the dynamics underlying sequence working memory? To found out, we develop and analyse RNNs fitted to multi-session single-unit data of macaques. See my talk Wed 12:00, at @bernsteinneuro.bsky.social. With @jakhmack.bsky.social @mackelab.bsky.social Data from Chen et al., Neuron 2024.
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Roxana Zeraati @roxana-zeraati.bsky.social · 07/07/2026
Our paper "Neural timescales from a computational perspective" is finally out in @natneuro.nature.com: www.nature.com/articles/s41... We discuss how computational models and methods can distill empirical observations on neural timescales into quantitative, testable theories of brain computation.
nature.com
Neural timescales from a computational perspective - Nature Neuroscience
This review integrates computational approaches to provide a unified view on how data analysis methods, biophysical mechanistic models and machine learning approaches can help to uncover the origins a...
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Machine Learning in Science @mackelab.bsky.social · 02/07/2026
We congratulate @matthijspals.bsky.social on his successful PhD defense! During his time in the Mackelab, he used RNNs to link neural activity with underlying mechanisms. Now he moved on to a Postdoc position in @durstewitzlab.bsky.social at the ZI Mannheim and the University of Heidelberg.
Left to right: Philipp Berens, Anna Levina, Matthijs Pals, Peter Dayan, Jakob Macke.
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Louis Pezon @lpezon.bsky.social · 30/06/2026
Both brains and RNNs can re-use components of computation across similar tasks or contexts. But what exactly are those “shared components”? How can they be used to solve several tasks? We address these questions in a new preprint with @avm.bsky.social! Link: www.biorxiv.org/content/10.6...
biorxiv.org
Interpretable compositional computation with recurrent neural networks
Flexible cognition utilizes reusable components to enable rapid adaptation of behavior to different contexts or tasks. Analysis of artificial neural networks trained on multiple tasks suggested that t...
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Joao Barbosa @jbarbosa.org · 27/01/2026
Postdoc position in Paris: come help develop new generation human brain computer interfaces ⚡🧠💻 Interested? Contact me if you have experience with machine learning (e.g. simulation-based inference, RL, generative/diffusion models) or dynamical systems. See below for + details and retweet 🙏
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A Erdem Sagtekin @aesagtekin.bsky.social · 08/01/2026
1/7 How should feedback signals influence a network during learning? Should they first adjust synaptic weights, which then indirectly change neural activity (as in backprop.)? Or should they first adjust neural activity to guide synaptic updates (e.g., target prop.)? openreview.net/forum?id=xVI...
Diagram of a recurrent neural network: input goes into the network, output is compared to a target to produce an error, and dotted feedback arrows show updates to neural activity and to synaptic weights.
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Guillaume Bellec @bellecguill.bsky.social · 18/12/2025
Our paper on data constrained RNN that generalize to optogenetic perturbations now citable on eLife: doi.org/10.7554/eLif...
doi.org
Biologically informed cortical models predict optogenetic perturbations
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Richard Gao @rdgao.bsky.social · 03/12/2025
Finally got the job ad—looking for 2 PhD students to start spring next year: www.gao-unit.com/join-us/ If comp neuro, ML, and AI4Neuro is your thing, or you just nerd out over brain recordings, apply! I'm at neurips. DM me here / on the conference app or email if you want to meet 🏖️🌮
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Machine Learning in Science @mackelab.bsky.social · 28/11/2025
We are looking for a Research Engineer (E13 TV-L) to work at the intersection of #ML and #compneuro! 🤖🧠 Help us build large-scale bio-inspired neural networks, write high-quality research code, and contribute to open-source tools like jaxley, sbi, and flyvis 🪰. More info: www.mackelab.org/jobs/
mackelab.org
Jobs - mackelab
The MackeLab is a research group at the Excellence Cluster Machine Learning at Tübingen University!
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Machine Learning in Science @mackelab.bsky.social · 28/11/2025
MackeLab has grown! 🎉 Warm welcome to 5(!) brilliant and fun new PhD students / research scientists who joined our lab in the past year — we can’t wait to do great science and already have good times together! 🤖🧠 Meet them in the thread 👇 1/7
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Michael Deistler @deismic.bsky.social · 13/11/2025
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...
nature.com
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 ...
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Machine Learning in Science @mackelab.bsky.social · 13/11/2025
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...
nature.com
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 ...
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Machine Learning in Science @mackelab.bsky.social · 30/09/2025
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
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Richard Gao @rdgao.bsky.social · 23/09/2025
I've been waiting some years to make this joke and now it’s real: I conned somebody into giving me a faculty job! I’m starting as a W1 Tenure-Track Professor at Goethe University Frankfurt in a week (lol), in the Faculty of CS and Math and I'm recruiting PhD students 🤗
media.tenor.com
a man wearing a white shirt and tie smiles in front of a window
ALT: a man wearing a white shirt and tie smiles in front of a window
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DurstewitzLab @durstewitzlab.bsky.social · 21/09/2025
Our #AI #DynamicalSystems #FoundationModel DynaMix was accepted to #NeurIPS2025 with outstanding reviews (6555) – first model which can *zero-shot*, w/o any fine-tuning, forecast the *long-term statistics* of time series provided a context. Test it on #HuggingFace: huggingface.co/spaces/Durst...
huggingface.co
DynaMix - a Hugging Face Space by DurstewitzLab
Upload your time series data in CSV or NPY format and generate future forecasts. Configure the forecast length and settings, then download the results as CSV or NPY.
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sbi - Simulation-based inference @sbi-devs.bsky.social · 09/09/2025
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 🧵
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DurstewitzLab @durstewitzlab.bsky.social · 13/07/2025
Got prov. approval for 2 major grants in Neuro-AI & Dynamical Systems Reconstruction, on learning & inference in non-stationary environments, out-of-domain generalization, and DS foundation models. To all AI/math/DS enthusiasts: Expect job announcements (PhD/PostDoc) soon! Feel free to get in touch.
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Elkan Akyurek @elkanakyurek.bsky.social · 03/07/2025
Jelmer Borst and I are looking for a PhD candidate to build an EEG-based model of human working memory! This is a really cool project that I've wanted to kick off for a while, and I can't wait to see it happen. Please share and I'm happy to answer any Qs about the project! www.rug.nl/about-ug/wor...
rug.nl
Vacatures bij de RUG
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The Transmitter @thetransmitter.bsky.social · 30/06/2025
The neurons that encode sequential information into working memory do not fire in that same order during recall, a finding that is at odds with a long-standing theory. Read more in this month’s Null and Noteworthy. By @ldattaro.bsky.social #neuroskyence www.thetransmitter.org/null-and-not...
thetransmitter.org
Null and Noteworthy: Neurons tracking sequences don’t fire in order
Instead, neurons encode the position of sequential items in working memory based on when they fire during ongoing brain wave oscillations—a finding that challenges a long-standing theory.
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DurstewitzLab @durstewitzlab.bsky.social · 26/06/2025
How do animals learn new rules? By systematically testing diff. behavioral strategies, guided by selective attn. to rule-relevant cues: rdcu.be/etlRV Akin to in-context learning in AI, strategy selection depends on the animals' "training set" (prior experience), with similar repr. in rats & humans.
rdcu.be
Abstract rule learning promotes cognitive flexibility in complex environments across species
Nature Communications - Whether neurocomputational mechanisms that speed up human learning in changing environments also exist in other species remains unclear. Here, the authors show that both...
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Tatiana Engel @engeltatiana.bsky.social · 25/06/2025
Out today in @nature.com: we show that individual neurons have diverse tuning to a decision variable computed by the entire population, revealing a unifying geometric principle for the encoding of sensory and dynamic cognitive variables. www.nature.com/articles/s41...
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Valentin Schmutz @bio-emergent.bsky.social · 09/06/2025
Our new preprint 👀
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Tim Vogels @tpvogels.bsky.social · 02/06/2025
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...
biorxiv.org
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...
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sbi - Simulation-based inference @sbi-devs.bsky.social · 12/05/2025
Great news! Our March SBI hackathon in Tübingen was a huge success, with 40+ participants (30 onsite!). Expect significant updates soon: awesome new features & a revamped documentation you'll love! Huge thanks to our amazing SBI community! Release details coming soon. 🥁 🎉
A wide shot of approximately 30 individuals standing in a line, posing for a group photograph outdoors. The background shows a clear blue sky, trees, and a distant cityscape or hills.
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Joao Barbosa @jbarbosa.org · 10/05/2025
Please RT🙏 Reach out if you want to help understand cognition by modelling, analyzing and/or collect large scale intracortical data from 👩🐒🐁 We're a friendly, diverse group (n>25) w/ this terrace 😎 in the center of Paris! See👇 for + info about the lab We have funding to support your application!
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Machine Learning in Science @mackelab.bsky.social · 30/04/2025
🎓Hiring now! 🧠 Join us at the exciting intersection of ML and Neuroscience! #AI4science We’re looking for PhDs, Postdocs and Scientific Programmers that want to use deep learning to build, optimize and study mechanistic models of neural computations. Full details: www.mackelab.org/jobs/ 1/5
mackelab.org
Jobs - mackelab
The MackeLab is a research group at the Excellence Cluster Machine Learning at Tübingen University!
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Shervin Safavi @neuroprinciplist.bsky.social · 20/02/2025
Re-posting is appreciated: We have a fully funded PhD position in CMC lab @cmc-lab.bsky.social (at @tudresden_de). You can use forms.gle/qiAv5NZ871kv... to send your application and find more information. Deadline is April 30. Find more about CMC lab: cmclab.org and email me if you have questions.
forms.gle
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Machine Learning in Science @mackelab.bsky.social · 25/04/2025
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
arxiv.org
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...
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Amin Nejatbakhsh @aminejat.bsky.social · 22/04/2025
Excited to announce that our paper on "Comparing noisy neural population dynamics using optimal transport distances" has been selected for an oral presentation in #ICLR2025 (1.8% top papers). Check the thread for paper details (0/n). Presentation info: iclr.cc/virtual/2025....
iclr.cc
ICLR 2025 Comparing noisy neural population dynamics using optimal transport distances OralICLR 2025
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Matthijs Pals @matthijspals.bsky.social · 28/03/2025
Happening tomorrow morning :).
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Machine Learning in Science @mackelab.bsky.social · 27/03/2025
The @mackelab.bsky.social is represented at @cosynemeeting.bsky.social #cosyne2025 in Montreal with 3 posters, 2 workshop talks, and a main conference contributed talk (for the very first time in Mackelab history 🎉)!
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Jakob Macke @jakhmack.bsky.social · 24/03/2025
Out now 'in print'--- a true labor of love, in more ways than one. See the paper and press-release below! Also, go and see @matthijspals.bsky.social's talk at #Cosyne, where he will talk about related/follow up work! uni-tuebingen.de/en/research/...
uni-tuebingen.de
Deciphering the sequence of neuronal firing
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Matthijs Pals @matthijspals.bsky.social · 24/03/2025
Our study on sequence working memory using human spiking data and RNNs, is finally published :). Check it out! 👇
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T. Anderson Keller @andykeller.bsky.social · 10/03/2025
In the physical world, almost all information is transmitted through traveling waves -- why should it be any different in your neural network? Super excited to share recent work with the brilliant @mozesjacobs.bsky.social: "Traveling Waves Integrate Spatial Information Through Time" 1/14
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Michael Deistler @deismic.bsky.social · 28/02/2025
Together with @dendritesgr.bsky.social, we’ll be hosting a tutorial on constructing and optimizing biophysical models (via Jaxley & DendroTweaks) 🚀 Join us in Florence if you like dendrites, biophysics, or optimization!
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Auguste Schulz @auschulz.bsky.social · 03/02/2025
1) Some exciting science in turbulent times: How do mice distinguish self-generated vs. object-generated looming stimuli? Our new study combines VR and neural recordings from superior colliculus (SC) 🧠🐭 to explore this question. Check out our preprint doi.org/10.1101/2024... 🧵
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Melanie Tschiersch @mtschiersch.bsky.social · 20/01/2025
🚨Excited to share my first @biorxivpreprint.bsky.social🚨 with the amazing Smith lab, @jbarbosa.org and Albert Compte who made this work possible. We show that 🐒prefrontal hemispheres combine redundancy (for precision) & weak connections (for capacity) for supporting spatial working memory (WM). 1/🧵
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Guillaume Bellec @bellecguill.bsky.social · 08/01/2025
Pre-print 🧠🧪 Is mechanism modeling dead in the AI era? ML models trained to predict neural activity fail to generalize to unseen opto perturbations. But mechanism modeling can solve that. We say "perturbation testing" is the right way to evaluate mechanisms in data-constrained models 1/8
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Machine Learning in Science @mackelab.bsky.social · 13/12/2024
Talk to @vetterj.bsky.social and @gmoss13.bsky.social about sourcerer at #Neurips2024 today! 📍Poster #4006 (East; 11 am PT)
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Matthijs Pals @matthijspals.bsky.social · 11/12/2024
How to find all fixed points in piece-wise linear recurrent neural networks (RNNs)? A short thread 🧵 
In RNNs with N units with ReLU(x-b) activations the phase space is partioned in 2^N regions by hyperplanes at x=b 1/7
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sbi - Simulation-based inference @sbi-devs.bsky.social · 27/11/2024
The sbi package is growing into a community project 🌍 To reflect this and the many algorithms, neural nets, and diagnostics that have been added since its initial release, we have written a new software paper 📝 Check it out, and reach out if you want to get involved: arxiv.org/abs/2411.17337
arxiv.org
sbi reloaded: a toolkit for simulation-based inference workflows
Scientists and engineers use simulators to model empirically observed phenomena. However, tuning the parameters of a simulator to ensure its outputs match observed data presents a significant challeng...
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A Erdem Sagtekin @aesagtekin.bsky.social · 09/11/2024
This list likely reflects mainly my interests and circle, and I’m sure I’ve missed many people, but I gave it a try: (I’ll be slowly editing it until it reaches 150/150) go.bsky.app/7VFUkdn (also, I tried but couldn't remove my profile...)
go.bsky.app
Comp Neuro Starter Pack
Join the conversation
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Matthijs Pals @matthijspals.bsky.social · 14/11/2024
Seems like it's a good time to jump ship! I am working in @mackelab.bsky.social, on using deep learning (usually recurrent neural networks; RNNs) to study neural dynamics. A cool example is recent work where we show how to generate long sequences of realistic neural data: arxiv.org/abs/2406.16749
arxiv.org
Inferring stochastic low-rank recurrent neural networks from neural data
A central aim in computational neuroscience is to relate the activity of large populations of neurons to an underlying dynamical system. Models of these neural dynamics should ideally be both interpre...
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