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Amin Saberi

@amnsbr.bsky.social
154 followers 257 following 42 posts

Postdoc, Cognitive Neurogenerics Group at MPI-CBS & FZJ-INM7 | MD PhD aminsaberi.me

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Reposted by Amin Saberi
Andrea Luppi, PhD @loopyluppi.bsky.social · 02/10/2026
1/ 🚨 Just out in @natneuro.nature.com! 🧠 We profiled >6,000 features of brain dynamics across humans, macaques, marmosets, mice, fish and worms 🧑🐒🐒🐁🐟🪱 to find a shared neural endpoint of anaesthesia: spatiotemporal isolation of local activity 🧵👇 🔗 doi.org/10.1038/s41593-026-02460-4
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CMC Unit @cmc-unit.bsky.social · 27/09/2026
We, the Natural Decision Making Group and the Embodied Decision Making Group, are joining forces to establish the CMC Unit, a joint research unit to uncover computational, biological, and ecological principles underlying adaptive decision-making. You can read more about us here: cmc-unit.org
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Bratislav Misic @misicbata.bsky.social · 24/09/2026
netneurotools: a trainee-oriented approach to network neuroscience | doi.org/10.1038/s415... Our lab’s internal toolkit for accomplishing everyday tasks in brain imaging @natprot.nature.com ⤵️
doi.org
netneurotools: a trainee-oriented approach to network neuroscience - Nature Protocols
This is a Perspective covering a Python toolbox for neuroscience research that enables users to fetch datasets, construct networks and null models, estimate graph metrics, fit statistical models and v...
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Amin Saberi @amnsbr.bsky.social · 16/09/2026
Congratulations Andrea 👏🎉
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Sofie Valk @sofievalk.bsky.social · 20/08/2026
Brain structural variations across neurodevelopmental and psychiatric conditions are systematically constrained by the brain's intrinsic architecture > www.medrxiv.org/content/10.6...
medrxiv.org
Lifespan brain structural variation reveals shared organization across mental health conditions
Elucidating the neurobiological basis of neurodevelopmental and psychiatric conditions (NDPCs) remains challenging because brain alterations vary within diagnoses and overlap across them. Whether dive...
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Renato Duarte @rcfduarte.bsky.social · 11/03/2026
I tracked every keyword in 22 years of Cosyne abstracts to map how computational neuroscience evolved — from Bayesian brains to neural manifolds to LLMs — and where it's heading next.
open.substack.com
22 years of Brain Science: what CoSyNe tells us about the evolution of Neuroscience
Tracking the intellectual DNA of Computational and Systems Neuroscience through its flagship meeting
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Bratislav Misic @misicbata.bsky.social · 11/03/2026
Synaptome architecture shapes regional dynamics in the mouse brain | doi.org/10.1371/jour... How do diverse synapses relate to the spatial patterning of whole-brain dynamics? Justine Hansen explores @plosbiology.org ⤵️
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Alessandro Gozzi @gozziale.bsky.social · 12/03/2026
🚀 We are hiring: a PhD position is available in my lab (gozzilab.it) at @iitalk.bsky.social, Italy. Project: large-scale brain network mapping in behaving mice using functional ultrasound imaging (FUSI). 📅 Deadline: March 31 🔗 tinyurl.com/4jtetxa9 Reshares appreciated 😊
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Arman Behrad @armanbehrad.bsky.social · 08/01/2026
Wanna compare dynamics across neural data, RNNs, or dynamical systems? We got a fast and furious method🏎️ The 1st preprint of my PhD 🥳 fast dynamical similarity analysis (fastDSA): 📜: arxiv.org/abs/2511.22828 💻: github.com/CMC-lab/fast... I’ll be @cosynemeeting.bsky.social - happy to chat 😉
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Bratislav Misic @misicbata.bsky.social · 18/12/2025
netneurotools: a trainee-oriented approach to network neuroscience | doi.org/10.1101/2025... Our lab’s internal toolkit for accomplishing everyday tasks in brain imaging ⤵️
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Amin Saberi @amnsbr.bsky.social · 14/11/2025
Thanks for reading! Do reach out to us if you plan to use cuBNM in your study, we are happy to help 🙂 And many thanks to @sofievalk.bsky.social, @sbe.bsky.social, @borismontreal.bsky.social, @wanb.bsky.social and all the collaborators on this project 🙏🏻 21/21
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Amin Saberi @amnsbr.bsky.social · 14/11/2025
I’m now a bit obsessed with GPUs 🤓 They have great potential for scaling up neuroimaging and neuroscience analyses 📈 Coming up next: GPU-accelerated neuroimaging meta-analyses (work in progress 🚧: github.com/amnsbr/nimar...) 20/n
github.com
GitHub - amnsbr/nimare-gpu: GPU-accelerated activation likelihood estimation meta-analysis (a GPU wrapper for NiMARE)
GPU-accelerated activation likelihood estimation meta-analysis (a GPU wrapper for NiMARE) - amnsbr/nimare-gpu
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Amin Saberi @amnsbr.bsky.social · 14/11/2025
This started as a small weekend curiosity and turned into a very fun project. I learned a lot along the way, and I hope cuBNM helps others with their modeling studies. 19/n
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Amin Saberi @amnsbr.bsky.social · 14/11/2025
Community contributions are very welcome 🙌 If you’re interested to contribute new models, implement features, or help maintain the toolbox, visit the GitHub repo: github.com/amnsbr/cubnm 18/n
github.com
GitHub - amnsbr/cubnm: A toolbox for brain network modeling on GPUs
A toolbox for brain network modeling on GPUs. Contribute to amnsbr/cubnm development by creating an account on GitHub.
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Amin Saberi @amnsbr.bsky.social · 14/11/2025
A few technical details: The frontend is written in Python (for ease of use), but to optimize efficiency, the simulation core is written in CUDA and C++. And not just simulations, but also calculation of FC, FC dynamics and goodness of fit measures is done on GPUs 🚀 17/n
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Amin Saberi @amnsbr.bsky.social · 14/11/2025
As another example: An earlier version of this code was already used in our adolescent development study, where we found decreasing E-I ratio in association cortex with age: www.science.org/doi/full/10.... 16/n
science.org
Adolescent maturation of cortical excitation-inhibition ratio based on individualized biophysical network modeling
Individualized simulations reveal a decrease in excitation-inhibition ratio in association areas throughout adolescence.
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Amin Saberi @amnsbr.bsky.social · 14/11/2025
As examples of the utility of these individualized models, we investigated test-retest reliability and heritability of simulated (and empirical) measures in the HCP dataset, and found simulated features to be fairly reliable and heritable. 15/n
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Amin Saberi @amnsbr.bsky.social · 14/11/2025
This took a total of 1,426 hours on A100 GPUs (still considerable!) but multi-core supercomputer CPU nodes would have required 11x more time, 31x more cost and 14x more energy to do the same! 14/n
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Amin Saberi @amnsbr.bsky.social · 14/11/2025
A key advantage of cuBNM’s GPU implementation is to make it possible to fit large numbers of individualized BNMs, in batches! To demonstrate this, we built individualized models for 430 HCP participants, running >28 million simulations. 13/n
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Amin Saberi @amnsbr.bsky.social · 14/11/2025
cuBNM also supports regional heterogeneity of parameters, using map-based and node-based approaches. To demonstrate these approaches in the preprint, we applied them to fit group-level models of the HCP data, and as expected, found them to outperform the homogenous model. 12/n
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Amin Saberi @amnsbr.bsky.social · 14/11/2025
Two optimization approaches are included in cuBNM: 1️⃣ grid search 2️⃣ evolutionary optimizers (via pymoo, with CMA-ES as the featured method) We demonstrate both in the preprint by fitting the rWW model to the group-averaged HCP data. 11/n
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Amin Saberi @amnsbr.bsky.social · 14/11/2025
cuBNM currently includes five commonly used models (with rWW model featured in tutorials and the preprint). New models can be added via YAML model specification files. And a guide for contributing new models is included in the documentation. 10/n
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Amin Saberi @amnsbr.bsky.social · 14/11/2025
Check out our comprehensive tutorials cubnm.readthedocs.io/en/stable/tu... and read the preprint to learn how to 😊 And feel free to get in touch if you needed help. 9/n
cubnm.readthedocs.io
Tutorials - cubnm documentation
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Amin Saberi @amnsbr.bsky.social · 14/11/2025
Using cuBNM, if you have access to a few GPUs*, you can quickly and easily create individualized BNMs for your own dataset. All you need is: resting-state BOLD & structural connectivity (from each subject’s DWI, or a template SC). * CPUs are also supported, but are not our focus. 8/n
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Amin Saberi @amnsbr.bsky.social · 14/11/2025
Why are GPUs so much faster? GPUs are designed for parallel processing, so computations across both *simulations* and *nodes* can be massively parallelized 🧠⚙️ 7/n
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Amin Saberi @amnsbr.bsky.social · 14/11/2025
GPU implementation also makes it feasible to simulate denser networks with thousands of nodes: Compute time with number of nodes increases near-quadratically on CPUs, but near-linearly on GPUs. 6/n
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Amin Saberi @amnsbr.bsky.social · 14/11/2025
On GPU, compared to single-core CPU, simulations can run up to 1000+ times faster (typically: 400-800x faster). For example, running 32,768 simulations would take 3.8 *days* on a single-core CPU, but only 5.6 *minutes* on a data-center A100 GPU ⚡ 5/n
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Amin Saberi @amnsbr.bsky.social · 14/11/2025
So we thought: why not use GPUs to parallelize simulation calculations and make them faster? We tried it, and … it paid off really well 🥳Then we turned it into the cuBNM toolbox! 4/n
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Amin Saberi @amnsbr.bsky.social · 14/11/2025
We experienced this directly during my PhD work on adolescent maturation of E-I ratio. We needed to fit individualized models for several hundred subjects, using more complex models, and quickly ran into the limits of CPU-based implementations. 3/n
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Amin Saberi @amnsbr.bsky.social · 14/11/2025
Brain network models (BNMs) are great tools for investigating latent neural properties at micro-/mesoscale (such as excitation-inhibition ratio) using simulations. Despite their usefulness, the computational cost of simulation has limited their application at larger scales. 2/n
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Amin Saberi @amnsbr.bsky.social · 14/11/2025
✨ New preprint ✨ Introducing cuBNM, a toolbox we developed to run brain simulations *much* more efficiently on GPUs 🎉🚀 Preprint: www.biorxiv.org/content/10.1... Documentation: cubnm.readthedocs.io/en/stable/ GitHub: github.com/amnsbr/cubnm 1/n 🧵
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Kevin Mitchell @wiringthebrain.bsky.social · 16/10/2025
Great review on The Genetics of Human Handedness: Microtubules and Beyond www.cell.com/trends/genet... - handedness is such an interesting phenotype!
cell.com
Genetics of human handedness: microtubules and beyond
Handedness (i.e., the preference to use either the left or the right hand for fine motor tasks) is a widely investigated trait. Handedness heritability is consistently estimated to be 25%. After decad...
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Golia Shafiei @goliashf.bsky.social · 22/09/2025
Excited to share that our work introducing the Reproducible Brain Charts (RBC) data resource is now published in Neuron!! 🎉 📚 Read the paper: authors.elsevier.com/c/1lpaF3BtfH... 🧠 Explore the RBC dataset: reprobrainchart.github.io
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Bratislav Misic @misicbata.bsky.social · 10/09/2025
The effect of spherical projections on spin tests for brain maps | doi.org/10.1162/IMAG... Spin tests are the de facto null model for map-to-map comparisons in brain imaging. Why don't they perfectly control false positives? @vincebaz.bsky.social explores ⤵️
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Alessandro Gozzi @gozziale.bsky.social · 10/09/2025
🚨 Excited to share the latest preprint form the lab ➡️https://tinyurl.com/32d3be9f Here we tackle a long-standing chicken-or-egg 🐣🥚question in #autism and developmental neuroscience ➡️ Is excitation–inhibition (E:I) imbalance a "cause" or a "consequence" of #autism? Check out what we found! 🧵1/n
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Bratislav Misic @misicbata.bsky.social · 04/08/2025
Integrating and interpreting brain maps | doi.org/10.1016/j.ti... Imaging and recording technologies make it possible to map multiple biological features of the brain. How can these features be conceptually integrated into a coherent understanding of brain structure and function? ⤵️
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Sofie Valk @sofievalk.bsky.social · 21/06/2025
My lab is at @ohbmofficial.bsky.social in Brisbane! Find us at the @gradientsworkshop.bsky.social - great talks by @wanb.bsky.social Katerina Manoli (and others) Then we are at the educational sessions where @claraweber.bsky.social will present @amnsbr.bsky.social work on E/I balance.
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Amin Saberi @amnsbr.bsky.social · 06/06/2025
... and functional changes e.g., faster and stronger IPSCs, and an increase in parvalbumin expression which (at least in one study) was not mirrored by an increase in PV cell counts. I can recommend Caballero 2014 Brain Struct Func, Caballero 2016 Neuro Biobeh Rev, and Hoftman 2017 Biol Psychiatry.
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Amin Saberi @amnsbr.bsky.social · 06/06/2025
Thank you :) Interesting but difficult question! In our study we are focusing on simulted currents which one can argue is more closely related to synapses, but it's really difficult to tell from our data. But empirical evidence from animal studies to my knowledge is more in favor of synaptic ...
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Amin Saberi @amnsbr.bsky.social · 06/06/2025
Unfortunately not this year, but @sofievalk.bsky.social will be there. Also feel free to drop me an email/dm and we can talk more :)
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Amin Saberi @amnsbr.bsky.social · 06/06/2025
Thank you very much 😊 Yes cuBNM was the side product of this study. Happy to help if you're interested in using it!
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Sofie Valk @sofievalk.bsky.social · 05/06/2025
Very happy about this paper and what we learned from it!! Please see Amins thread for more juice 🧃 and let us know if you are also on the E/I journey and like to try our toolbox
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Leon Lotter @leondlotter.de · 05/06/2025
Amazing new paper on individual development of E/I balance during adolescence, first-authored by @amnsbr.bsky.social! Read @ Science Advances: www.science.org/doi/10.1126/... Bonus: Amin developed a tool to run biophysical network modelling on GPUs – because why shouldn't he? cubnm.readthedocs.io
science.org
Adolescent maturation of cortical excitation-inhibition ratio based on individualized biophysical network modeling
Individualized simulations reveal a decrease in excitation-inhibition ratio in association areas throughout adolescence.
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Rick Betzel @richardfbetzel.bsky.social · 05/06/2025
This is awesome!
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Amin Saberi @amnsbr.bsky.social · 05/06/2025
Haha, thank you 😁
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Amin Saberi @amnsbr.bsky.social · 05/06/2025
Thanks Rick 😊🙏
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Boris Bernhardt @borismontreal.bsky.social · 05/06/2025
⭐ new paper Maturation of cortical excitation-inhibition (EI) in adolescence now in Science Advances 💥 A true tour de force of multimodal MRI, connectomics & GPU-powered 🤖!! biophysical modelling by hiball superheroes 🦸‍♂️🦸‍♀️🦸‍♂️ @amnsbr.bsky.social @sofievalk.bsky.social @sbe.bsky.social
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Amin Saberi @amnsbr.bsky.social · 05/06/2025
Thank you 😊🎉
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Amin Saberi @amnsbr.bsky.social · 05/06/2025
... @linaschaare.bsky.social, @brainalien.bsky.social, @lifeofthemind.bsky.social, and many others not on BlueSky 🙏
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Amin Saberi @amnsbr.bsky.social · 05/06/2025
I spent most of my PhD on this study and while facing many difficulties, I am grateful to have learned so much. Huge thanks to @sofievalk.bsky.social for her incredible support, and to our co-authors, @sbe.bsky.social, @borismontreal.bsky.social, @juergendukart.bsky.social, @leondlotter.de, ...
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