Benjamin Cowley
@benjocowley.bsky.social
Assistant Professor in computational neuroscience at Cold Spring Harbor Laboratory. Think cortically, act neuronally.
cowleygroup.cshl.edu
cowleygroup.cshl.edu
Reposted by Benjamin Cowley
🔬 Exciting PostDoc Opportunity! 🐁🧠
We - the @sinzlab.bsky.social (sinzlab.org) and @trose-neuro.bsky.social (troselab.de) Labs - are seeking an experimental postdoc to work at @unibonn.bsky.social with cutting-edge miniature 2-photon microscopy and gaze tracking in freely behaving mice.
We - the @sinzlab.bsky.social (sinzlab.org) and @trose-neuro.bsky.social (troselab.de) Labs - are seeking an experimental postdoc to work at @unibonn.bsky.social with cutting-edge miniature 2-photon microscopy and gaze tracking in freely behaving mice.
November 21, 2025 at 5:05 PM
🔬 Exciting PostDoc Opportunity! 🐁🧠
We - the @sinzlab.bsky.social (sinzlab.org) and @trose-neuro.bsky.social (troselab.de) Labs - are seeking an experimental postdoc to work at @unibonn.bsky.social with cutting-edge miniature 2-photon microscopy and gaze tracking in freely behaving mice.
We - the @sinzlab.bsky.social (sinzlab.org) and @trose-neuro.bsky.social (troselab.de) Labs - are seeking an experimental postdoc to work at @unibonn.bsky.social with cutting-edge miniature 2-photon microscopy and gaze tracking in freely behaving mice.
Reposted by Benjamin Cowley
As a longtime fan of cool papers in @currentbiology.bsky.social, I am really thrilled to see this out!
This study sets the stage for understanding the origins of novel (vocal) behaviors.
Big shout out to the main architects of this work @xmikezheng20.bsky.social and @cliffscience.bsky.social
This study sets the stage for understanding the origins of novel (vocal) behaviors.
Big shout out to the main architects of this work @xmikezheng20.bsky.social and @cliffscience.bsky.social
Great @currentbiology.bsky.social study by @xmikezheng20.bsky.social @cliffscience.bsky.social @arkarupbanerjee.bsky.social 🧪🧠🐭🎶
Vocal repertoire expansion in singing mice by co-opting a conserved midbrain circuit node
www.cell.com/current-biol...
Vocal repertoire expansion in singing mice by co-opting a conserved midbrain circuit node
www.cell.com/current-biol...
Vocal repertoire expansion in singing mice by co-opting a conserved midbrain circuit node
Zheng and Harpole et al. show that singing mice produce two major vocal modes: ancestral
USVs and novel songs that follow a linearly decelerating rhythm. Although acoustically
distinct, songs and USVs...
www.cell.com
November 19, 2025 at 6:42 PM
As a longtime fan of cool papers in @currentbiology.bsky.social, I am really thrilled to see this out!
This study sets the stage for understanding the origins of novel (vocal) behaviors.
Big shout out to the main architects of this work @xmikezheng20.bsky.social and @cliffscience.bsky.social
This study sets the stage for understanding the origins of novel (vocal) behaviors.
Big shout out to the main architects of this work @xmikezheng20.bsky.social and @cliffscience.bsky.social
Reposted by Benjamin Cowley
🔔 NEW PREPRINT FROM THE LAB ‼️
We introduce a new ML model, LoRAX, for predicting olfactory responses from chemical features, a tricky problem that benefits from progress in ML for biochem. We combine LoRA fine-tuning with protein and chemical foundation models, www.biorxiv.org/content/10.1...
We introduce a new ML model, LoRAX, for predicting olfactory responses from chemical features, a tricky problem that benefits from progress in ML for biochem. We combine LoRA fine-tuning with protein and chemical foundation models, www.biorxiv.org/content/10.1...
Low rank adaptation of chemical foundation models generate effective odorant representations
Featurizing odorants to enable robust prediction of their properties is difficult due to the complex activation patterns that odorants evoke in the olfactory system. Structurally similar odorants can ...
www.biorxiv.org
November 20, 2025 at 1:38 PM
🔔 NEW PREPRINT FROM THE LAB ‼️
We introduce a new ML model, LoRAX, for predicting olfactory responses from chemical features, a tricky problem that benefits from progress in ML for biochem. We combine LoRA fine-tuning with protein and chemical foundation models, www.biorxiv.org/content/10.1...
We introduce a new ML model, LoRAX, for predicting olfactory responses from chemical features, a tricky problem that benefits from progress in ML for biochem. We combine LoRA fine-tuning with protein and chemical foundation models, www.biorxiv.org/content/10.1...
Reposted by Benjamin Cowley
First published paper from the depaqlab, led by the supernatural @ryguy.io! Glad to add a new software resource to the neuro community for fitting SSMs, including hierarchical models and switching GLMs, and many others! If you love Julia and SSMs, this is for you!
🚨🚨🚨NEW PAPER ALERT🚨🚨🚨
We present StateSpaceDynamics.jl, an open-source Julia package for fitting probabilistic state-space models (SSMs)—including non-conjugate models like Poisson LDS and switching variants (SLDS). Python has had existing packages that have given this functionality...
We present StateSpaceDynamics.jl, an open-source Julia package for fitting probabilistic state-space models (SSMs)—including non-conjugate models like Poisson LDS and switching variants (SLDS). Python has had existing packages that have given this functionality...
Just published in JOSS: 'StateSpaceDynamics.jl: A Julia package for probabilistic state space models (SSMs)' https://doi.org/10.21105/joss.08077
November 15, 2025 at 2:26 AM
First published paper from the depaqlab, led by the supernatural @ryguy.io! Glad to add a new software resource to the neuro community for fitting SSMs, including hierarchical models and switching GLMs, and many others! If you love Julia and SSMs, this is for you!
Reposted by Benjamin Cowley
Our new paper in @natcomms.nature.com introduces improv, a flexible software platform that integrates models with experiments in real-time. Traditional experiments collect all data first, then analyze it later. With improv, models analyze data as it streams in and actively guide what to do next.
November 13, 2025 at 3:45 PM
Our new paper in @natcomms.nature.com introduces improv, a flexible software platform that integrates models with experiments in real-time. Traditional experiments collect all data first, then analyze it later. With improv, models analyze data as it streams in and actively guide what to do next.
Reposted by Benjamin Cowley
The Flatiron Institute is #hiring! View our numerous open computational researcher positions: https://www.simonsfoundation.org/flatiron/careers/ #science
Careers
Careers on Simons Foundation
www.simonsfoundation.org
November 7, 2025 at 4:04 PM
The Flatiron Institute is #hiring! View our numerous open computational researcher positions: https://www.simonsfoundation.org/flatiron/careers/ #science
Reposted by Benjamin Cowley
Note: this has a computational scientist track! It’s for you, too, math nerds!
Applications for our Fellows-to-Faculty Award are now open! This program supports early career scientists in #autism or #neuroscience research by facilitating their transition into tenure-track faculty positions. Apply by 1/14/2026: www.simonsfoundation.org/2025/10/31/a... #science
Applications for Fellows-to-Faculty Awards Now Open
Applications for Fellows-to-Faculty Awards Now Open on Simons Foundation
www.simonsfoundation.org
October 31, 2025 at 4:30 PM
Note: this has a computational scientist track! It’s for you, too, math nerds!
Reposted by Benjamin Cowley
Thrilled that our paper is out today in Nature!
www.nature.com/articles/s4...
www.nature.com/articles/s4...
Sensory expectations shape neural population dynamics in motor circuits
Nature - Experiments with human volunteers and macaques show that expectations produced by probabilistic cueing of future sensory inputs shape motor circuit dynamics in order to increase the...
www.nature.com
October 29, 2025 at 4:11 PM
Thrilled that our paper is out today in Nature!
www.nature.com/articles/s4...
www.nature.com/articles/s4...
Reposted by Benjamin Cowley
Bifurcations—an underexplored concept in neuroscience—can help explain how small differences in neural circuits give rise to entirely novel functions, writes Xiao-Jing Wang.
#neuroskyence
www.thetransmitter.org/neural-dynam...
#neuroskyence
www.thetransmitter.org/neural-dynam...
The missing half of the neurodynamical systems theory
Bifurcations—an underexplored concept in neuroscience—can help explain how small differences in neural circuits give rise to entirely novel functions.
www.thetransmitter.org
October 27, 2025 at 1:51 PM
Bifurcations—an underexplored concept in neuroscience—can help explain how small differences in neural circuits give rise to entirely novel functions, writes Xiao-Jing Wang.
#neuroskyence
www.thetransmitter.org/neural-dynam...
#neuroskyence
www.thetransmitter.org/neural-dynam...
Reposted by Benjamin Cowley
Please repost!!:
We are searching for new AI-Bio faculty at Duke to be part of a new Discovery AI center. Looking for faculty who focus on pushing boundaries in ML model development in a highly interactive environment. DEADLINE for applications- Nov 1st!!
www.nature.com/naturecareer...
We are searching for new AI-Bio faculty at Duke to be part of a new Discovery AI center. Looking for faculty who focus on pushing boundaries in ML model development in a highly interactive environment. DEADLINE for applications- Nov 1st!!
www.nature.com/naturecareer...
Tenure-Track Assistant Professor Position –AI/ML for Cell Biology - Durham, North Carolina (US) job with Duke University School of Medicine | 12844591
Tenure-Track Assistant Professor Position –AI/ML for Cell Biology
www.nature.com
October 25, 2025 at 3:11 PM
Please repost!!:
We are searching for new AI-Bio faculty at Duke to be part of a new Discovery AI center. Looking for faculty who focus on pushing boundaries in ML model development in a highly interactive environment. DEADLINE for applications- Nov 1st!!
www.nature.com/naturecareer...
We are searching for new AI-Bio faculty at Duke to be part of a new Discovery AI center. Looking for faculty who focus on pushing boundaries in ML model development in a highly interactive environment. DEADLINE for applications- Nov 1st!!
www.nature.com/naturecareer...
Reposted by Benjamin Cowley
Our work with @pawa-pawa.bsky.social is out in Nature Machine Intelligence! The choice of activation function affects the representations, dynamics, and circuit solutions that emerge in RNNs trained on cognitive tasks. Activation matters!
www.nature.com/articles/s42...
www.nature.com/articles/s42...
October 24, 2025 at 7:18 PM
Our work with @pawa-pawa.bsky.social is out in Nature Machine Intelligence! The choice of activation function affects the representations, dynamics, and circuit solutions that emerge in RNNs trained on cognitive tasks. Activation matters!
www.nature.com/articles/s42...
www.nature.com/articles/s42...
Reposted by Benjamin Cowley
Come join us as a CSHL-Simons Fellow!
supporting bold research programs aimed at tackling fundamental questions across all Neuroscience areas, from NeuroAI to brain body interactions. CSHL Fellows are appointed for 3-5 years and direct their own research groups.
www.cshl.edu/about-us/car...
supporting bold research programs aimed at tackling fundamental questions across all Neuroscience areas, from NeuroAI to brain body interactions. CSHL Fellows are appointed for 3-5 years and direct their own research groups.
www.cshl.edu/about-us/car...
Fellows Positions | Cold Spring Harbor Laboratory
CSHL Simons Fellow in NEUROSCIENCE Cold Spring Harbor Laboratory (CSHL) is seeking to fill a Cold Spring Harbor Laboratory Fellow position in the area of NEUROSCIENCE (experimental and/or computationa...
www.cshl.edu
October 25, 2025 at 1:17 PM
Come join us as a CSHL-Simons Fellow!
supporting bold research programs aimed at tackling fundamental questions across all Neuroscience areas, from NeuroAI to brain body interactions. CSHL Fellows are appointed for 3-5 years and direct their own research groups.
www.cshl.edu/about-us/car...
supporting bold research programs aimed at tackling fundamental questions across all Neuroscience areas, from NeuroAI to brain body interactions. CSHL Fellows are appointed for 3-5 years and direct their own research groups.
www.cshl.edu/about-us/car...
Reposted by Benjamin Cowley
Apply to become a CSHL-Simons Fellow in Neuroscience!
Run your own lab, pursue bold ideas, join a highly collaborative community!
All areas including experimental or computational neuro, including NeuroAI & systems
PhD required; ≤~1 yr postdoc
www.cshl.edu/about-us/car...
Run your own lab, pursue bold ideas, join a highly collaborative community!
All areas including experimental or computational neuro, including NeuroAI & systems
PhD required; ≤~1 yr postdoc
www.cshl.edu/about-us/car...
Fellows Positions | Cold Spring Harbor Laboratory
CSHL Simons Fellow in NEUROSCIENCE Cold Spring Harbor Laboratory (CSHL) is seeking to fill a Cold Spring Harbor Laboratory Fellow position in the area of NEUROSCIENCE (experimental and/or computationa...
www.cshl.edu
October 24, 2025 at 7:16 PM
Apply to become a CSHL-Simons Fellow in Neuroscience!
Run your own lab, pursue bold ideas, join a highly collaborative community!
All areas including experimental or computational neuro, including NeuroAI & systems
PhD required; ≤~1 yr postdoc
www.cshl.edu/about-us/car...
Run your own lab, pursue bold ideas, join a highly collaborative community!
All areas including experimental or computational neuro, including NeuroAI & systems
PhD required; ≤~1 yr postdoc
www.cshl.edu/about-us/car...
Cold Spring Harbor Laboratory is now offering a new BioAI PhD program!
We aim to train bright computational students to solve real-world biological questions.
A strong focus is in neuroAI--models of the brain, embodied agents, evolutionary algos.
Come join us!
www.cshl.edu/phd-program/...
We aim to train bright computational students to solve real-world biological questions.
A strong focus is in neuroAI--models of the brain, embodied agents, evolutionary algos.
Come join us!
www.cshl.edu/phd-program/...
BioAI PhD Program | Cold Spring Harbor Laboratory
Since 1890, Cold Spring Harbor Laboratory (CSHL) has been a global leader in research and education. The international scientific community at CSHL provides a unique and stimulating atmosphere for doc...
www.cshl.edu
October 23, 2025 at 2:00 PM
Cold Spring Harbor Laboratory is now offering a new BioAI PhD program!
We aim to train bright computational students to solve real-world biological questions.
A strong focus is in neuroAI--models of the brain, embodied agents, evolutionary algos.
Come join us!
www.cshl.edu/phd-program/...
We aim to train bright computational students to solve real-world biological questions.
A strong focus is in neuroAI--models of the brain, embodied agents, evolutionary algos.
Come join us!
www.cshl.edu/phd-program/...
Reposted by Benjamin Cowley
Apply to the new CSHL grad program in BioAI/neuroAI!
(Masters degree or equivalent required in a quantitative area such as computer science, physics, mathematics, or engineering)
www.cshl.edu/phd-program/...
(Masters degree or equivalent required in a quantitative area such as computer science, physics, mathematics, or engineering)
www.cshl.edu/phd-program/...
October 22, 2025 at 11:59 PM
Apply to the new CSHL grad program in BioAI/neuroAI!
(Masters degree or equivalent required in a quantitative area such as computer science, physics, mathematics, or engineering)
www.cshl.edu/phd-program/...
(Masters degree or equivalent required in a quantitative area such as computer science, physics, mathematics, or engineering)
www.cshl.edu/phd-program/...
Reposted by Benjamin Cowley
#Cosyne2026 deadline is just around the corner:
🧠📜 **16 October 2025! 📜🧠
See below for more on key dates and abstract submission:
www.cosyne.org/abstracts-su...
🧠📜 **16 October 2025! 📜🧠
See below for more on key dates and abstract submission:
www.cosyne.org/abstracts-su...
Abstract Submission — COSYNE
Submit your COSYNE 2026 abstract; double‑blind, 2-page PDF. Opens Sept 5, 2025. Deadline and guidelines inside.
www.cosyne.org
October 7, 2025 at 8:19 PM
#Cosyne2026 deadline is just around the corner:
🧠📜 **16 October 2025! 📜🧠
See below for more on key dates and abstract submission:
www.cosyne.org/abstracts-su...
🧠📜 **16 October 2025! 📜🧠
See below for more on key dates and abstract submission:
www.cosyne.org/abstracts-su...
Reposted by Benjamin Cowley
A study led by Cina Aghamohammadi is now out in @natcomms.nature.com! We developed a mathematical framework for partitioning spiking variability, which revealed that spiking irregularity is nearly invariant for each neuron and decreases along the cortical hierarchy.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
October 12, 2025 at 12:42 AM
A study led by Cina Aghamohammadi is now out in @natcomms.nature.com! We developed a mathematical framework for partitioning spiking variability, which revealed that spiking irregularity is nearly invariant for each neuron and decreases along the cortical hierarchy.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Benjamin Cowley
🧠 New preprint: we show that model-guided microstimulation can steer monkey visual behavior.
Paper: arxiv.org/abs/2510.03684
🧵
Paper: arxiv.org/abs/2510.03684
🧵
October 7, 2025 at 3:22 PM
🧠 New preprint: we show that model-guided microstimulation can steer monkey visual behavior.
Paper: arxiv.org/abs/2510.03684
🧵
Paper: arxiv.org/abs/2510.03684
🧵
Reposted by Benjamin Cowley
We're very proud to be releasing the complete male fly CNS connectome!
It's the product of a huge team effort here at Janelia in partnership with the Cambridge Fly Connectomics group (@jefferis.bsky.social and colleagues), plus invaluable collaborators.
More soon...
www.janelia.org/project-team...
It's the product of a huge team effort here at Janelia in partnership with the Cambridge Fly Connectomics group (@jefferis.bsky.social and colleagues), plus invaluable collaborators.
More soon...
www.janelia.org/project-team...
Male CNS Connectome
A team of researchers has unveiled the complete connectome of a male fruit fly central nervous system —a seamless map of all the neurons in the brain and nerve cord of a single male fruit fly and the ...
www.janelia.org
October 5, 2025 at 6:02 PM
We're very proud to be releasing the complete male fly CNS connectome!
It's the product of a huge team effort here at Janelia in partnership with the Cambridge Fly Connectomics group (@jefferis.bsky.social and colleagues), plus invaluable collaborators.
More soon...
www.janelia.org/project-team...
It's the product of a huge team effort here at Janelia in partnership with the Cambridge Fly Connectomics group (@jefferis.bsky.social and colleagues), plus invaluable collaborators.
More soon...
www.janelia.org/project-team...
Reposted by Benjamin Cowley
I've been arguing that #NeuroAI should model the brain in health *and* in disease -- very excited to share a first step from Melika Honarmand: inducing dyslexia in vision-language-models via targeted perturbations of visual-word-form units (analogous to human VWFA) 🧠🤖🧪 arxiv.org/abs/2509.24597
October 2, 2025 at 12:10 PM
I've been arguing that #NeuroAI should model the brain in health *and* in disease -- very excited to share a first step from Melika Honarmand: inducing dyslexia in vision-language-models via targeted perturbations of visual-word-form units (analogous to human VWFA) 🧠🤖🧪 arxiv.org/abs/2509.24597
Reposted by Benjamin Cowley
A pair of papers on using holographic optogenetics and compressed sensing for connectomics:
Rapid learning of neural circuitry from holographic ensemble stimulation enabled by model-based compressed sensing
www.nature.com/articles/s41...
Rapid learning of neural circuitry from holographic ensemble stimulation enabled by model-based compressed sensing
www.nature.com/articles/s41...
Rapid learning of neural circuitry from holographic ensemble stimulation enabled by model-based compressed sensing - Nature Neuroscience
The authors develop a new computational system for high-throughput mapping of synaptic connectivity using two-photon holographic optogenetics and intracellular recordings.
www.nature.com
September 19, 2025 at 4:15 AM
A pair of papers on using holographic optogenetics and compressed sensing for connectomics:
Rapid learning of neural circuitry from holographic ensemble stimulation enabled by model-based compressed sensing
www.nature.com/articles/s41...
Rapid learning of neural circuitry from holographic ensemble stimulation enabled by model-based compressed sensing
www.nature.com/articles/s41...
Reposted by Benjamin Cowley
👁️🧠 New preprint: We demonstrate the first data-driven neural control framework for a visual cortical implant in a blind human!
TL;DR Deep learning lets us synthesize efficient stimulation patterns that reliably evoke percepts, outperforming conventional calibration.
www.biorxiv.org/content/10.1...
TL;DR Deep learning lets us synthesize efficient stimulation patterns that reliably evoke percepts, outperforming conventional calibration.
www.biorxiv.org/content/10.1...
September 27, 2025 at 2:52 AM
👁️🧠 New preprint: We demonstrate the first data-driven neural control framework for a visual cortical implant in a blind human!
TL;DR Deep learning lets us synthesize efficient stimulation patterns that reliably evoke percepts, outperforming conventional calibration.
www.biorxiv.org/content/10.1...
TL;DR Deep learning lets us synthesize efficient stimulation patterns that reliably evoke percepts, outperforming conventional calibration.
www.biorxiv.org/content/10.1...
Reposted by Benjamin Cowley
(1/n) How can we infer single-trial communication between 🧠 regions? Check out our ICML 2025 paper: “Accurate Identification of Communication Between Multiple Interacting Neural Populations,” by Belle Liu and @jsacks.bsky.social in my lab: arxiv.org/abs/2506.19094
Accurate identification of communication between multiple interacting neural populations
Neural recording technologies now enable simultaneous recording of population activity across many brain regions, motivating the development of data-driven models of communication between brain region...
arxiv.org
September 25, 2025 at 10:26 PM
(1/n) How can we infer single-trial communication between 🧠 regions? Check out our ICML 2025 paper: “Accurate Identification of Communication Between Multiple Interacting Neural Populations,” by Belle Liu and @jsacks.bsky.social in my lab: arxiv.org/abs/2506.19094
Reposted by Benjamin Cowley
New preprint! How can you remember an image you saw once, even after seeing thousands of them? We find a role for humble mid-level visual cortex in high-capacity, one-shot learning. doi.org/10.1101/2025.09.22.677855 🧵🧪1/
Neuronal signatures of successful one-shot memory in mid-level visual cortex
High-capacity, one-shot visual recognition memory challenges theories of learning and neural coding because it requires rapid, robust, and durable representations. Most studies have focused on the hip...
doi.org
September 23, 2025 at 3:09 PM
New preprint! How can you remember an image you saw once, even after seeing thousands of them? We find a role for humble mid-level visual cortex in high-capacity, one-shot learning. doi.org/10.1101/2025.09.22.677855 🧵🧪1/
Reposted by Benjamin Cowley
🛑 Attention researchers who train freely-moving rodents!
Jess Breda and I developed a protocol for training center-port nose fixation 61% faster than a previous curriculum while keeping violation rates low.
Preprint here: www.biorxiv.org/content/10.1...
Jess Breda and I developed a protocol for training center-port nose fixation 61% faster than a previous curriculum while keeping violation rates low.
Preprint here: www.biorxiv.org/content/10.1...
FixGrower: An efficient and robust curriculum for shaping fixation behavior in rodents
Center-port fixation is a common prerequisite for many freely-moving rodent tasks in neuroscience and psychology. However, typical protocols for shaping this behavior are non-standardized and ineffici...
www.biorxiv.org
September 22, 2025 at 2:59 PM
🛑 Attention researchers who train freely-moving rodents!
Jess Breda and I developed a protocol for training center-port nose fixation 61% faster than a previous curriculum while keeping violation rates low.
Preprint here: www.biorxiv.org/content/10.1...
Jess Breda and I developed a protocol for training center-port nose fixation 61% faster than a previous curriculum while keeping violation rates low.
Preprint here: www.biorxiv.org/content/10.1...