Rory Byrne
@rory.bio
Neuroscience PhD student, Cambridge UK. Confused but excited.
"Everything around me was somebody's lifework"
👋 https://rory.bio
🔨 https://flywhl.dev
🔧 https://compmotifs.com/
"Everything around me was somebody's lifework"
👋 https://rory.bio
🔨 https://flywhl.dev
🔧 https://compmotifs.com/
Pinned
Rory Byrne
@rory.bio
· Nov 29
Flywheel
Build momentum-preserving software tools for scientific progress
flywhl.dev
Hi friends, I'm Rory 👋 I study comp neuro at Cambridge with @timothyoleary.bsky.social, asking how neuronal biophysics contributes to network function, using tools from AI.
Speaking of tools, I also run a little org trying to create new incentives for building tools for science: flywhl.dev.
Speaking of tools, I also run a little org trying to create new incentives for building tools for science: flywhl.dev.
I built a link-sharing discussion website for (meta)science.
talk.amacrin.com
Scientific discourse here and elsewhere is a bit fragmented, so I made a space for centralised, casual discussion. You can log in with Bsky.
Still in testing mode. I'll move it to a new domain once I find a good name.
talk.amacrin.com
Scientific discourse here and elsewhere is a bit fragmented, so I made a space for centralised, casual discussion. You can log in with Bsky.
Still in testing mode. I'll move it to a new domain once I find a good name.
Science Talk
A forum for discussing metascience, tools, and scientific ideas. Share essays, ask questions, and connect with researchers.
talk.amacrin.com
November 10, 2025 at 8:35 AM
I built a link-sharing discussion website for (meta)science.
talk.amacrin.com
Scientific discourse here and elsewhere is a bit fragmented, so I made a space for centralised, casual discussion. You can log in with Bsky.
Still in testing mode. I'll move it to a new domain once I find a good name.
talk.amacrin.com
Scientific discourse here and elsewhere is a bit fragmented, so I made a space for centralised, casual discussion. You can log in with Bsky.
Still in testing mode. I'll move it to a new domain once I find a good name.
Answer: because seniors know the language of software architecture.
This enriches their LLM prompting significantly.
If you want to successfully use AI for coding, learn some software architecture!
This enriches their LLM prompting significantly.
If you want to successfully use AI for coding, learn some software architecture!
AI Was Supposed to Help Juniors Shine. Why Does It Mostly Make Seniors Stronger? | Discussion
AI Was Supposed to Help Juniors Shine. Why Does It Mostly Make Seniors Stronger? | <Can ELMA/>
AI was supposed to empower junior developers. In reality, it has become a tool that makes seniors more valuable while exposing the gaps in software culture.
elma.dev
September 21, 2025 at 7:08 AM
Answer: because seniors know the language of software architecture.
This enriches their LLM prompting significantly.
If you want to successfully use AI for coding, learn some software architecture!
This enriches their LLM prompting significantly.
If you want to successfully use AI for coding, learn some software architecture!
Proud to have been a part of this, a great example of distributed async science!
Huge thanks to @marcusghosh.bsky.social, @neuralreckoning.bsky.social, @tfiers.bsky.social, @krhab.bsky.social and others for putting in the bulk effort 🙌
Huge thanks to @marcusghosh.bsky.social, @neuralreckoning.bsky.social, @tfiers.bsky.social, @krhab.bsky.social and others for putting in the bulk effort 🙌
Is anarchist science possible? As an experiment, we got together a large group of computational neuroscientists from around the world to work on a single project without top down direction. Read on to find out what happened. 🤖🧠🧪
September 4, 2025 at 3:44 PM
Proud to have been a part of this, a great example of distributed async science!
Huge thanks to @marcusghosh.bsky.social, @neuralreckoning.bsky.social, @tfiers.bsky.social, @krhab.bsky.social and others for putting in the bulk effort 🙌
Huge thanks to @marcusghosh.bsky.social, @neuralreckoning.bsky.social, @tfiers.bsky.social, @krhab.bsky.social and others for putting in the bulk effort 🙌
A great piece from @ersatzben.bsky.social on the importance of bold, aesthetic, mission-oriented directions in publicly funded research.
betterscienceproject.substack.com/p/the-counte...
betterscienceproject.substack.com/p/the-counte...
The Counter-Reformation of science: how to make magnificence democratic
British research has perfected discipline and outsourced magnificence. The fix is to practise demonstration statecraft – visible proofs of capacity that pair theatre with delivery.
betterscienceproject.substack.com
September 1, 2025 at 1:46 PM
A great piece from @ersatzben.bsky.social on the importance of bold, aesthetic, mission-oriented directions in publicly funded research.
betterscienceproject.substack.com/p/the-counte...
betterscienceproject.substack.com/p/the-counte...
Reposted by Rory Byrne
How can we best use AI in science?
Myself and 9 other research fellows from @imperial-ix.bsky.social use AI methods in domains from plant biology (🌱) to neuroscience (🧠) and particle physics (🎇).
Together we suggest 10 simple rules @plos.org 🧵
doi.org/10.1371/jour...
Myself and 9 other research fellows from @imperial-ix.bsky.social use AI methods in domains from plant biology (🌱) to neuroscience (🧠) and particle physics (🎇).
Together we suggest 10 simple rules @plos.org 🧵
doi.org/10.1371/jour...
July 25, 2025 at 10:58 AM
How can we best use AI in science?
Myself and 9 other research fellows from @imperial-ix.bsky.social use AI methods in domains from plant biology (🌱) to neuroscience (🧠) and particle physics (🎇).
Together we suggest 10 simple rules @plos.org 🧵
doi.org/10.1371/jour...
Myself and 9 other research fellows from @imperial-ix.bsky.social use AI methods in domains from plant biology (🌱) to neuroscience (🧠) and particle physics (🎇).
Together we suggest 10 simple rules @plos.org 🧵
doi.org/10.1371/jour...
Reposted by Rory Byrne
New preprint for #neuromorphic and #SpikingNeuralNetwork folk (with @pengfei-sun.bsky.social).
arxiv.org/abs/2507.16043
Surrogate gradients are popular for training SNNs, but some worry whether they really learn complex temporal spike codes. TLDR: we tested this, and yes they can! 🧵👇
🤖🧠🧪
arxiv.org/abs/2507.16043
Surrogate gradients are popular for training SNNs, but some worry whether they really learn complex temporal spike codes. TLDR: we tested this, and yes they can! 🧵👇
🤖🧠🧪
Beyond Rate Coding: Surrogate Gradients Enable Spike Timing Learning in Spiking Neural Networks
We investigate the extent to which Spiking Neural Networks (SNNs) trained with Surrogate Gradient Descent (Surrogate GD), with and without delay learning, can learn from precise spike timing beyond fi...
arxiv.org
July 24, 2025 at 5:03 PM
New preprint for #neuromorphic and #SpikingNeuralNetwork folk (with @pengfei-sun.bsky.social).
arxiv.org/abs/2507.16043
Surrogate gradients are popular for training SNNs, but some worry whether they really learn complex temporal spike codes. TLDR: we tested this, and yes they can! 🧵👇
🤖🧠🧪
arxiv.org/abs/2507.16043
Surrogate gradients are popular for training SNNs, but some worry whether they really learn complex temporal spike codes. TLDR: we tested this, and yes they can! 🧵👇
🤖🧠🧪
Reposted by Rory Byrne
🟢 Applications are now open for two SSI Fellows' events: Niko Sirmpilatze's "Animals in Motion" and Alessandro Felder's "Big Imaging Data". These events will take place during the NIU Open Software Week running between Monday 11 and Friday 15 August in London.
www.software.ac.uk/news/ssi-fel...
www.software.ac.uk/news/ssi-fel...
April 28, 2025 at 10:45 AM
🟢 Applications are now open for two SSI Fellows' events: Niko Sirmpilatze's "Animals in Motion" and Alessandro Felder's "Big Imaging Data". These events will take place during the NIU Open Software Week running between Monday 11 and Friday 15 August in London.
www.software.ac.uk/news/ssi-fel...
www.software.ac.uk/news/ssi-fel...
Reposted by Rory Byrne
How do babies and blind people learn to localise sound without labelled data? We propose that innate mechanisms can provide coarse-grained error signals to boostrap learning. New preprint from @yang-chu.bsky.social. 🤖🧠🧪
arxiv.org/abs/2001.10605
arxiv.org/abs/2001.10605
Learning spatial hearing via innate mechanisms
The acoustic cues used by humans and other animals to localise sounds are subtle, and change during and after development. This means that we need to constantly relearn or recalibrate the auditory spa...
arxiv.org
April 24, 2025 at 4:57 PM
How do babies and blind people learn to localise sound without labelled data? We propose that innate mechanisms can provide coarse-grained error signals to boostrap learning. New preprint from @yang-chu.bsky.social. 🤖🧠🧪
arxiv.org/abs/2001.10605
arxiv.org/abs/2001.10605
Come build tools for science with us in London!
Food, cool people, great speakers (on both the science and toolmaking sides).
#neuroskyence #openscience #desci #openchem #bioinformatics #opensource #foss
Food, cool people, great speakers (on both the science and toolmaking sides).
#neuroskyence #openscience #desci #openchem #bioinformatics #opensource #foss
Following our successful SF event, we (www.compmotifs.com) are running another hackathon!
When? 7-8 June.
Where? London, UK.
Who? Builders and researchers from academia and industry.
What? Develop innovative computational tools to advance the natural sciences.
Join us: lu.ma/apsqlxlj?utm....
When? 7-8 June.
Where? London, UK.
Who? Builders and researchers from academia and industry.
What? Develop innovative computational tools to advance the natural sciences.
Join us: lu.ma/apsqlxlj?utm....
Science through Computation
Advancing the natural sciences
www.compmotifs.com
April 22, 2025 at 8:02 AM
Come build tools for science with us in London!
Food, cool people, great speakers (on both the science and toolmaking sides).
#neuroskyence #openscience #desci #openchem #bioinformatics #opensource #foss
Food, cool people, great speakers (on both the science and toolmaking sides).
#neuroskyence #openscience #desci #openchem #bioinformatics #opensource #foss
Reposted by Rory Byrne
How can we explore the space of computational models in #neuroscience 🧠?
Picture a mouse navigating an environment with light and dark areas.
🧵1/10
Picture a mouse navigating an environment with light and dark areas.
🧵1/10
Can LLMs be used to discover interpretable models of human and animal behavior?🤔
Turns out: yes!
Thrilled to share our latest preprint where we used FunSearch to automatically discover symbolic cognitive models of behavior.
1/12
Turns out: yes!
Thrilled to share our latest preprint where we used FunSearch to automatically discover symbolic cognitive models of behavior.
1/12
March 13, 2025 at 10:48 AM
How can we explore the space of computational models in #neuroscience 🧠?
Picture a mouse navigating an environment with light and dark areas.
🧵1/10
Picture a mouse navigating an environment with light and dark areas.
🧵1/10
If you’re in SF, come build tools-for-science with us later this month! 🛠️
#opensource #neuroskyence #openscience #machinelearning #compchem #chemsky
#opensource #neuroskyence #openscience #machinelearning #compchem #chemsky
We (www.compmotifs.com) are coming to SF!
Together with Pebblebed, we’re hosting a 2-day hackathon on 26-27 March for builders and scientists across disciplines to build new methods and tools for the computational and natural sciences. Join us: lu.ma/t5yik06g.
Reposts will be much appreciated!
Together with Pebblebed, we’re hosting a 2-day hackathon on 26-27 March for builders and scientists across disciplines to build new methods and tools for the computational and natural sciences. Join us: lu.ma/t5yik06g.
Reposts will be much appreciated!
Workshop: Science through Computation · Luma
The Computational Motifs Initiative is coming to San Francisco!
Together with Pebblebed, we’re hosting a 2-day hackathon on 26-27 March connecting builders and…
lu.ma
March 12, 2025 at 2:08 PM
If you’re in SF, come build tools-for-science with us later this month! 🛠️
#opensource #neuroskyence #openscience #machinelearning #compchem #chemsky
#opensource #neuroskyence #openscience #machinelearning #compchem #chemsky
Reposted by Rory Byrne
Just getting started @standupforscience.bsky.social
March 7, 2025 at 5:46 PM
Just getting started @standupforscience.bsky.social
Reposted by Rory Byrne
Scientific data and independence are at risk: We need to work with community-driven services and university libraries to create new multi-country organizations that are resilient to political interference.
By @neuralreckoning.bsky.social
#neuroskyence
www.thetransmitter.org/policy/scien...
By @neuralreckoning.bsky.social
#neuroskyence
www.thetransmitter.org/policy/scien...
Science must step away from nationally managed infrastructure
Scientific data and independence are at risk. We need to work with community-driven services and university libraries to create new multi-country organizations that are resilient to political…
www.thetransmitter.org
February 20, 2025 at 5:09 PM
Scientific data and independence are at risk: We need to work with community-driven services and university libraries to create new multi-country organizations that are resilient to political interference.
By @neuralreckoning.bsky.social
#neuroskyence
www.thetransmitter.org/policy/scien...
By @neuralreckoning.bsky.social
#neuroskyence
www.thetransmitter.org/policy/scien...
🔧 Logis - turn your git history into a searchable scientific log.
The `@commit` decorator auto-commits your code when your experiment runs - with metadata in the message.
Then you can find previous results by querying for commits with (e.g.) metrics.accuracy > 0.9.
github.com/flywhl/logis
The `@commit` decorator auto-commits your code when your experiment runs - with metadata in the message.
Then you can find previous results by querying for commits with (e.g.) metrics.accuracy > 0.9.
github.com/flywhl/logis
GitHub - flywhl/logis: Turn your git commit history into a scientific log
Turn your git commit history into a scientific log - flywhl/logis
github.com
February 16, 2025 at 2:10 PM
🔧 Logis - turn your git history into a searchable scientific log.
The `@commit` decorator auto-commits your code when your experiment runs - with metadata in the message.
Then you can find previous results by querying for commits with (e.g.) metrics.accuracy > 0.9.
github.com/flywhl/logis
The `@commit` decorator auto-commits your code when your experiment runs - with metadata in the message.
Then you can find previous results by querying for commits with (e.g.) metrics.accuracy > 0.9.
github.com/flywhl/logis
GitHub - flywhl/logis: Turn your git commit history into a scientific log
Turn your git commit history into a scientific log - flywhl/logis
github.com
February 16, 2025 at 1:34 PM
🔧 Logis - turn your git history into a searchable scientific log.
The `@commit` decorator auto-commits your code when your experiment runs - with metadata in the message.
Then you can find previous results by querying for commits with (e.g.) metrics.accuracy > 0.9.
github.com/flywhl/logis
The `@commit` decorator auto-commits your code when your experiment runs - with metadata in the message.
Then you can find previous results by querying for commits with (e.g.) metrics.accuracy > 0.9.
github.com/flywhl/logis
Reposted by Rory Byrne
Two Hard Things (2009) Discussion
bliki: Two Hard Things
There are only two hard things in Computer Science: cache invalidation and naming things -- Phil Karlton (bonus variations on the page)
martinfowler.com
January 20, 2025 at 2:40 AM
Two Hard Things (2009) Discussion
Reposted by Rory Byrne
Who likes categories anyway?
I wonder what this means for the concept of "areas"...
#neuroscience
www.thetransmitter.org/neural-codin...
I wonder what this means for the concept of "areas"...
#neuroscience
www.thetransmitter.org/neural-codin...
Most neurons in mouse cortex defy functional categories
The majority of cells in the cerebral cortex are unspecialized, according to an unpublished analysis—and scientists need to take care in naming neurons, the researchers warn.
www.thetransmitter.org
January 11, 2025 at 2:20 PM
Who likes categories anyway?
I wonder what this means for the concept of "areas"...
#neuroscience
www.thetransmitter.org/neural-codin...
I wonder what this means for the concept of "areas"...
#neuroscience
www.thetransmitter.org/neural-codin...
🔧 Cyantic v0.3.0 - a little library I wrote that builds complex Python objects (like Tensors) from simple blueprints using @pydantic.dev.
(The name comes from cyanotype photography, i.e. the "blueprint")
#opensource #python #openscience
github.com/flywhl/cyantic
(The name comes from cyanotype photography, i.e. the "blueprint")
#opensource #python #openscience
github.com/flywhl/cyantic
GitHub - flywhl/cyantic: Build complex types from simple blueprints via Pydantic
Build complex types from simple blueprints via Pydantic - flywhl/cyantic
github.com
January 9, 2025 at 11:11 AM
🔧 Cyantic v0.3.0 - a little library I wrote that builds complex Python objects (like Tensors) from simple blueprints using @pydantic.dev.
(The name comes from cyanotype photography, i.e. the "blueprint")
#opensource #python #openscience
github.com/flywhl/cyantic
(The name comes from cyanotype photography, i.e. the "blueprint")
#opensource #python #openscience
github.com/flywhl/cyantic
🔧 Re-sharing an old tool: a recursive function to generate hierarchical, modular, Dalean connectivity matrices in PyTorch.
Modules are locally dense, with increasingly sparse connections to more distal modules.
#neuroai #neuroskyence
gist.github.com/rorybyrne/dd...
Modules are locally dense, with increasingly sparse connections to more distal modules.
#neuroai #neuroskyence
gist.github.com/rorybyrne/dd...
January 8, 2025 at 10:27 AM
🔧 Re-sharing an old tool: a recursive function to generate hierarchical, modular, Dalean connectivity matrices in PyTorch.
Modules are locally dense, with increasingly sparse connections to more distal modules.
#neuroai #neuroskyence
gist.github.com/rorybyrne/dd...
Modules are locally dense, with increasingly sparse connections to more distal modules.
#neuroai #neuroskyence
gist.github.com/rorybyrne/dd...
I see the talks from Montreal AI and Neuroscience (MAIN) 2024 are now online:
www.youtube.com/@MAINConfere...
#neuroai #neuroskyence
www.youtube.com/@MAINConfere...
#neuroai #neuroskyence
MAIN Conference
Montreal AI and Neuroscience (MAIN) is an international conference organized by the UNIQUE Centre in collaboration with the Centre de Recherches Mathématiques (CRM) at the University of Montreal since...
www.youtube.com
January 6, 2025 at 2:07 PM
I see the talks from Montreal AI and Neuroscience (MAIN) 2024 are now online:
www.youtube.com/@MAINConfere...
#neuroai #neuroskyence
www.youtube.com/@MAINConfere...
#neuroai #neuroskyence
Forget LLMs, we need more good-old-fashioned code generation. Especially in science. I should be able to define models, analysis, wet-lab protocols, and figures in a declarative language (SQL is declarative), and use opinionated tools to generate the required code.
github.com/sqlc-dev/sqlc
github.com/sqlc-dev/sqlc
GitHub - sqlc-dev/sqlc: Generate type-safe code from SQL
Generate type-safe code from SQL. Contribute to sqlc-dev/sqlc development by creating an account on GitHub.
github.com
December 30, 2024 at 3:53 PM
Forget LLMs, we need more good-old-fashioned code generation. Especially in science. I should be able to define models, analysis, wet-lab protocols, and figures in a declarative language (SQL is declarative), and use opinionated tools to generate the required code.
github.com/sqlc-dev/sqlc
github.com/sqlc-dev/sqlc
Pleasantly surprised to see surrogate gradients used here to optimise over collision detection events (@ 18:28). Relevant for #NeuroAI since step functions can model lots of things in neurons beyond just spiking.
www.youtube.com/watch?v=L_Al...
www.youtube.com/watch?v=L_Al...
[Kevin Tracy Ph.D. Defense] Differentiable Convex Modeling for Robotic Motion Planning and Control
YouTube video by CMU Robotic Exploration Lab
www.youtube.com
December 30, 2024 at 1:20 PM
Pleasantly surprised to see surrogate gradients used here to optimise over collision detection events (@ 18:28). Relevant for #NeuroAI since step functions can model lots of things in neurons beyond just spiking.
www.youtube.com/watch?v=L_Al...
www.youtube.com/watch?v=L_Al...
Nice to see journals thinking about software tools, but I wonder if they can offer more to toolmakers than “here is a place to re-write your README in more opaque language”?
🛠️ November's most-read Tools and Resources paper presents a new method to identify dynamic causal interactions in complex systems: https://buff.ly/3Zldxpt
Learn more about publishing your tools or resources with us: https://buff.ly/4f2O0Ht
Learn more about publishing your tools or resources with us: https://buff.ly/4f2O0Ht
December 29, 2024 at 10:09 AM
Nice to see journals thinking about software tools, but I wonder if they can offer more to toolmakers than “here is a place to re-write your README in more opaque language”?
Reposted by Rory Byrne
