Pedro J. Goncalves
@ppjgoncalves.bsky.social
Computational Neuroscience and Machine Learning. Group Leader at VIB-NERF (https://nerf.be/en#/) and Associate Professor at KU Leuven (https://www.kuleuven.be/english/kuleuven). Affiliated with VIB.AI (vib.ai/en).
More details at goncalveslab.sites.vib.be
More details at goncalveslab.sites.vib.be
Reposted by Pedro J. Goncalves
New work out today by a collaborative team including @ppjgoncalves.bsky.social! 🙌
Introducing #JAXLEY, a differentiable simulator that brings biophysically detailed neural models into the realm of large‑scale, machine‑learning‑powered optimization.
https://doi.org/10.1038/s41592-025-02895-w
Introducing #JAXLEY, a differentiable simulator that brings biophysically detailed neural models into the realm of large‑scale, machine‑learning‑powered optimization.
https://doi.org/10.1038/s41592-025-02895-w
November 13, 2025 at 4:45 PM
New work out today by a collaborative team including @ppjgoncalves.bsky.social! 🙌
Introducing #JAXLEY, a differentiable simulator that brings biophysically detailed neural models into the realm of large‑scale, machine‑learning‑powered optimization.
https://doi.org/10.1038/s41592-025-02895-w
Introducing #JAXLEY, a differentiable simulator that brings biophysically detailed neural models into the realm of large‑scale, machine‑learning‑powered optimization.
https://doi.org/10.1038/s41592-025-02895-w
Super excited about this work led by the one and only @deismic.bsky.social!
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 4:07 PM
Super excited about this work led by the one and only @deismic.bsky.social!
Reposted by Pedro J. Goncalves
“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 Pedro J. Goncalves
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 🧵
Super exciting work led by @bconfavreux.bsky.social and @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 3, 2025 at 8:30 AM
Super exciting work led by @bconfavreux.bsky.social and @tpvogels.bsky.social!
Reposted by Pedro J. Goncalves
The @ppjgoncalves.bsky.social lab is recruiting a PhD student via the VIB.AI International PhD Call 2025!
Join to develop machine learning tools for neuroscience, focusing on simulation-based inference & neural circuit modeling.
📍 Leuven
🗓️ Apply by June 22 → https://tinyurl.com/53nc9vnd
Join to develop machine learning tools for neuroscience, focusing on simulation-based inference & neural circuit modeling.
📍 Leuven
🗓️ Apply by June 22 → https://tinyurl.com/53nc9vnd
May 21, 2025 at 8:57 AM
The @ppjgoncalves.bsky.social lab is recruiting a PhD student via the VIB.AI International PhD Call 2025!
Join to develop machine learning tools for neuroscience, focusing on simulation-based inference & neural circuit modeling.
📍 Leuven
🗓️ Apply by June 22 → https://tinyurl.com/53nc9vnd
Join to develop machine learning tools for neuroscience, focusing on simulation-based inference & neural circuit modeling.
📍 Leuven
🗓️ Apply by June 22 → https://tinyurl.com/53nc9vnd
Fantastic PhD opportunities at the intersection of machine learning and biology. Come join us at @vibai.bsky.social! More details at: vib.ai/en/vibai-int...
VIB.AI International PhD Call 2025
The VIB.AI International PhD Call 2025 is now open. We invite applicants from around the world to join an interdisciplinary research environment at the interface of AI, computational biology, and life...
vib.ai
May 8, 2025 at 8:07 PM
Fantastic PhD opportunities at the intersection of machine learning and biology. Come join us at @vibai.bsky.social! More details at: vib.ai/en/vibai-int...
Fantastic opportunity to establish your lab in ML for biology! Come join us!
We are looking for additional Group Leaders to join the growing computational biology community at VIB.
If you are excited about combining AI and machine learning with fundamental biology, we would love to hear from you!
https://vib.ai/en/opportunities#/job-description/110906
If you are excited about combining AI and machine learning with fundamental biology, we would love to hear from you!
https://vib.ai/en/opportunities#/job-description/110906
May 8, 2025 at 8:02 PM
Fantastic opportunity to establish your lab in ML for biology! Come join us!
Exciting project in Parkinson's disease! Patrik Verstreken's lab (verstrekenlab.sites.vib.be) and my lab are looking for a postdoc to develop and apply ML methods to the analysis of exciting brain-on-chip data. Please spread the word!
More details at: jobs.vib.be/j/110908/pos...
More details at: jobs.vib.be/j/110908/pos...
Postdoc position: Computational methods for neurodegeneration research - VIB
About the labs
The Verstreken Lab and the Gonçalves Lab are based in Leuven, Belgium and part of the
jobs.vib.be
April 24, 2025 at 7:43 PM
Exciting project in Parkinson's disease! Patrik Verstreken's lab (verstrekenlab.sites.vib.be) and my lab are looking for a postdoc to develop and apply ML methods to the analysis of exciting brain-on-chip data. Please spread the word!
More details at: jobs.vib.be/j/110908/pos...
More details at: jobs.vib.be/j/110908/pos...
Reposted by Pedro J. Goncalves
Hayden, Karthik & Nastya from the @ppjgoncalves.bsky.social lab joined the #SBI Hackathon in Tübingen in March, contributing to the open-source SBI package. Nastya gave a lightning talk on multifidelity inference for computationally expensive simulators. A great week of science & collaboration!
April 22, 2025 at 2:32 PM
Hayden, Karthik & Nastya from the @ppjgoncalves.bsky.social lab joined the #SBI Hackathon in Tübingen in March, contributing to the open-source SBI package. Nastya gave a lightning talk on multifidelity inference for computationally expensive simulators. A great week of science & collaboration!
Reposted by Pedro J. Goncalves
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...
Reposted by Pedro J. Goncalves
We apply our masked VAE approach to drosophila 🪰walking behavior, a macaque 🐒reach task & a synthetic dataset with access to the ground truth.
We propose calibration checks to evaluate the models’ uncertainty estimates, to avoid making confidently wrong predictions.
Check out the paper for more 🙂
We propose calibration checks to evaluate the models’ uncertainty estimates, to avoid making confidently wrong predictions.
Check out the paper for more 🙂
April 17, 2025 at 8:50 PM
We apply our masked VAE approach to drosophila 🪰walking behavior, a macaque 🐒reach task & a synthetic dataset with access to the ground truth.
We propose calibration checks to evaluate the models’ uncertainty estimates, to avoid making confidently wrong predictions.
Check out the paper for more 🙂
We propose calibration checks to evaluate the models’ uncertainty estimates, to avoid making confidently wrong predictions.
Check out the paper for more 🙂
Reposted by Pedro J. Goncalves
It's been a blast, thanks to @sbi-devs.bsky.social ! This week's hackathon was phenomenal! 🙏 😍 The sbi hackathon welcomed about 25 people in Tübingen with contributions spanning the globe , e.g. 🇺🇸🇯🇵🇧🇪🇩🇪. Wanna see, what we did? Check out the PRs👇
github.com/sbi-dev/sbi/...
github.com/sbi-dev/sbi/...
Pull requests · sbi-dev/sbi
sbi is a Python package for simulation-based inference, designed to meet the needs of both researchers and practitioners. Whether you need fine-grained control or an easy-to-use interface, sbi has ...
github.com
March 21, 2025 at 8:45 AM
It's been a blast, thanks to @sbi-devs.bsky.social ! This week's hackathon was phenomenal! 🙏 😍 The sbi hackathon welcomed about 25 people in Tübingen with contributions spanning the globe , e.g. 🇺🇸🇯🇵🇧🇪🇩🇪. Wanna see, what we did? Check out the PRs👇
github.com/sbi-dev/sbi/...
github.com/sbi-dev/sbi/...
Reposted by Pedro J. Goncalves
New work co-led by @ppjgoncalves.bsky.social introduces a powerful new approach to model conditional distributions of neural and behavioral data using masked variational autoencoders.
Congratulations to @auschulz.bsky.social et al.
https://www.cell.com/cell-reports/fulltext/S2211-1247(25)00109-3
Congratulations to @auschulz.bsky.social et al.
https://www.cell.com/cell-reports/fulltext/S2211-1247(25)00109-3
March 14, 2025 at 12:07 PM
New work co-led by @ppjgoncalves.bsky.social introduces a powerful new approach to model conditional distributions of neural and behavioral data using masked variational autoencoders.
Congratulations to @auschulz.bsky.social et al.
https://www.cell.com/cell-reports/fulltext/S2211-1247(25)00109-3
Congratulations to @auschulz.bsky.social et al.
https://www.cell.com/cell-reports/fulltext/S2211-1247(25)00109-3
Reposted by Pedro J. Goncalves
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... 🧵
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... 🧵
February 3, 2025 at 7:19 PM
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... 🧵
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... 🧵
Reposted by Pedro J. Goncalves
🎉 Just in time for the end of the year, we’ve released a new version of sbi!
📦 v0.23.3 comes packed with exciting features, bug fixes, and docs updates to make sbi smoother and more robust. Check it out! 👇
🔗 Full changelog: github.com/sbi-dev/sbi/...
📦 v0.23.3 comes packed with exciting features, bug fixes, and docs updates to make sbi smoother and more robust. Check it out! 👇
🔗 Full changelog: github.com/sbi-dev/sbi/...
December 30, 2024 at 2:57 PM
🎉 Just in time for the end of the year, we’ve released a new version of sbi!
📦 v0.23.3 comes packed with exciting features, bug fixes, and docs updates to make sbi smoother and more robust. Check it out! 👇
🔗 Full changelog: github.com/sbi-dev/sbi/...
📦 v0.23.3 comes packed with exciting features, bug fixes, and docs updates to make sbi smoother and more robust. Check it out! 👇
🔗 Full changelog: github.com/sbi-dev/sbi/...
Reposted by Pedro J. Goncalves
Cutting it a bit fine, but here’s my review of the year in neuroscience for 2024
The eighth of these, would you believe? We’ve got dark neurons, tiny monkeys, the most complete brain wiring diagram ever constructed, and much more…
Published on The Spike
Enjoy!
medium.com/the-spike/20...
The eighth of these, would you believe? We’ve got dark neurons, tiny monkeys, the most complete brain wiring diagram ever constructed, and much more…
Published on The Spike
Enjoy!
medium.com/the-spike/20...
2024: A Review of the Year in Neuroscience
Feeling a bit wired
medium.com
December 30, 2024 at 4:00 PM
Cutting it a bit fine, but here’s my review of the year in neuroscience for 2024
The eighth of these, would you believe? We’ve got dark neurons, tiny monkeys, the most complete brain wiring diagram ever constructed, and much more…
Published on The Spike
Enjoy!
medium.com/the-spike/20...
The eighth of these, would you believe? We’ve got dark neurons, tiny monkeys, the most complete brain wiring diagram ever constructed, and much more…
Published on The Spike
Enjoy!
medium.com/the-spike/20...
Reposted by Pedro J. Goncalves
1/ Excuse me, can I interest you in eliciting your beliefs as flexible probability distributions? No worries, we only need pairwise comparisons or rankings, no personal details.
Led by **Petrus Mikkola** and joint with **Arto Klami**, to be presented soon at @neuripsconf.bsky.social #NeurIPS2024
Led by **Petrus Mikkola** and joint with **Arto Klami**, to be presented soon at @neuripsconf.bsky.social #NeurIPS2024
December 4, 2024 at 9:06 AM
1/ Excuse me, can I interest you in eliciting your beliefs as flexible probability distributions? No worries, we only need pairwise comparisons or rankings, no personal details.
Led by **Petrus Mikkola** and joint with **Arto Klami**, to be presented soon at @neuripsconf.bsky.social #NeurIPS2024
Led by **Petrus Mikkola** and joint with **Arto Klami**, to be presented soon at @neuripsconf.bsky.social #NeurIPS2024
Reposted by Pedro J. Goncalves
We are launching an SBI Discord Server! 🎉
We want to use this server to further build a community around SBI, i.e., for sharing insights, questions and events around simulation-based inference in general and the sbi package in particular.
You are all invited to join! 🤗 github.com/sbi-dev/sbi/...
We want to use this server to further build a community around SBI, i.e., for sharing insights, questions and events around simulation-based inference in general and the sbi package in particular.
You are all invited to join! 🤗 github.com/sbi-dev/sbi/...
SBI Discord Server 🤖 · sbi-dev sbi · Discussion #1318
Dear all, we are launching an SBI Discord Server! 🎉 We want to use this server to further build a community around SBI, i.e., for sharing insights, questions and events around SBI in general and th...
github.com
December 3, 2024 at 8:54 AM
We are launching an SBI Discord Server! 🎉
We want to use this server to further build a community around SBI, i.e., for sharing insights, questions and events around simulation-based inference in general and the sbi package in particular.
You are all invited to join! 🤗 github.com/sbi-dev/sbi/...
We want to use this server to further build a community around SBI, i.e., for sharing insights, questions and events around simulation-based inference in general and the sbi package in particular.
You are all invited to join! 🤗 github.com/sbi-dev/sbi/...
Very privileged to be part of such an inspiring and fun community (effort)!
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
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...
arxiv.org
November 27, 2024 at 1:46 PM
Very privileged to be part of such an inspiring and fun community (effort)!
Reposted by Pedro J. Goncalves
Thrilled to contribute to this work led by David Frazier providing theory for NPE/NLE in simulation-based inference. These methods are known to match the accuracy of ABC and BSL with fewer simulations, this paper rigorously shows why this can be achieved.
arxiv.org/abs/2411.12068
arxiv.org/abs/2411.12068
The Statistical Accuracy of Neural Posterior and Likelihood Estimation
Neural posterior estimation (NPE) and neural likelihood estimation (NLE) are machine learning approaches that provide accurate posterior, and likelihood, approximations in complex modeling scenarios, ...
arxiv.org
November 21, 2024 at 6:04 AM
Thrilled to contribute to this work led by David Frazier providing theory for NPE/NLE in simulation-based inference. These methods are known to match the accuracy of ABC and BSL with fewer simulations, this paper rigorously shows why this can be achieved.
arxiv.org/abs/2411.12068
arxiv.org/abs/2411.12068
Reposted by Pedro J. Goncalves
Hello, world! We are a community-developed toolkit that performs Bayesian inference for simulators. We support a broad range of methods (NPE, NLE, NRE, amortized and sequential), neural network architectures (flows, diffusion models), samplers, and diagnostics. Join us!
November 18, 2024 at 7:26 AM
Hello, world! We are a community-developed toolkit that performs Bayesian inference for simulators. We support a broad range of methods (NPE, NLE, NRE, amortized and sequential), neural network architectures (flows, diffusion models), samplers, and diagnostics. Join us!
Reposted by Pedro J. Goncalves
First post!
New preprint led by @josepemanzano.bsky.social on amortised simulation-based inference #SBI to map orientation #uncertainty and perform brain #tractography. Great collaboration with @jakhmack.bsky.social, @ppjgoncalves.bsky.social, @deismic.bsky.social.
New preprint led by @josepemanzano.bsky.social on amortised simulation-based inference #SBI to map orientation #uncertainty and perform brain #tractography. Great collaboration with @jakhmack.bsky.social, @ppjgoncalves.bsky.social, @deismic.bsky.social.
November 21, 2024 at 2:06 PM
First post!
New preprint led by @josepemanzano.bsky.social on amortised simulation-based inference #SBI to map orientation #uncertainty and perform brain #tractography. Great collaboration with @jakhmack.bsky.social, @ppjgoncalves.bsky.social, @deismic.bsky.social.
New preprint led by @josepemanzano.bsky.social on amortised simulation-based inference #SBI to map orientation #uncertainty and perform brain #tractography. Great collaboration with @jakhmack.bsky.social, @ppjgoncalves.bsky.social, @deismic.bsky.social.