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Rory Byrne

@rory.bio
538 followers 1.4K following 74 posts

Neuroscience PhD student, Cambridge UK. Confused but excited. "Everything around me was somebody's lifework" 👋 rory.bio 🔧 compmotifs.com

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Reposted by Rory Byrne
Marcus Ghosh @marcusghosh.bsky.social · 22/12/2025
Toy models, just in time for Christmas! Excited to share my first article for @thetransmitter.bsky.social #neuroskyence
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Rory Byrne @rory.bio · 10/11/2025
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
Science Talk
A forum for discussing metascience, tools, and scientific ideas. Share essays, ask questions, and connect with researchers.
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Rory Byrne @rory.bio · 21/09/2025
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!
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Rory Byrne @rory.bio · 04/09/2025
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 🙌
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Rory Byrne @rory.bio · 01/09/2025
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
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.
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Rory Byrne @rory.bio · 25/07/2025
open.substack.com/pub/learning...
open.substack.com
Backpropagation is older than you think
AI Histories #6: Backprop begins in the Second World War, not with Werbos or Rumelhart
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Marcus Ghosh @marcusghosh.bsky.social · 25/07/2025
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...
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Dan Goodman @neural-reckoning.org · 24/07/2025
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
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...
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Institute for Research Software @softwaresaved.bsky.social · 28/04/2025
🟢 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...
NIU Open Software Week
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Dan Goodman @neural-reckoning.org · 24/04/2025
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
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...
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Rory Byrne @rory.bio · 22/04/2025
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
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Marcus Ghosh @marcusghosh.bsky.social · 13/03/2025
How can we explore the space of computational models in #neuroscience 🧠? Picture a mouse navigating an environment with light and dark areas. 🧵1/10
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Rory Byrne @rory.bio · 12/03/2025
If you’re in SF, come build tools-for-science with us later this month! 🛠️ #opensource #neuroskyence #openscience #machinelearning #compchem #chemsky
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Grace Lindsay @neurograce.bsky.social · 07/03/2025
Just getting started @standupforscience.bsky.social
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The Transmitter @thetransmitter.bsky.social · 20/02/2025
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...
thetransmitter.org
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…
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Rory Byrne @rory.bio · 16/02/2025
#opensource #python #openscience #neuroskyence #machinelearning #neuroai
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Rory Byrne @rory.bio · 16/02/2025
🔧 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
github.com
GitHub - flywhl/logis: Turn your git commit history into a scientific log
Turn your git commit history into a scientific log - flywhl/logis
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Hacker News Top Stories @hackernewsbot.bsky.social · 20/01/2025
Two Hard Things (2009) Discussion
martinfowler.com
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)
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PessoaBrain @pessoabrain.bsky.social · 11/01/2025
Who likes categories anyway? I wonder what this means for the concept of "areas"... #neuroscience www.thetransmitter.org/neural-codin...
thetransmitter.org
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.
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Rory Byrne @rory.bio · 09/01/2025
🔧 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
github.com
GitHub - flywhl/cyantic: Build complex types from simple blueprints via Pydantic
Build complex types from simple blueprints via Pydantic - flywhl/cyantic
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Rory Byrne @rory.bio · 08/01/2025
🔧 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...
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Rory Byrne @rory.bio · 06/01/2025
I see the talks from Montreal AI and Neuroscience (MAIN) 2024 are now online: www.youtube.com/@MAINConfere... #neuroai #neuroskyence
youtube.com
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...
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Rory Byrne @rory.bio · 30/12/2024
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
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.
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Rory Byrne @rory.bio · 30/12/2024
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...
youtube.com
[Kevin Tracy Ph.D. Defense] Differentiable Convex Modeling for Robotic Motion Planning and Control
YouTube video by CMU Robotic Exploration Lab
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Rory Byrne @rory.bio · 29/12/2024
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”?
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Gaël Varoquaux @gaelvaroquaux.bsky.social · 22/12/2024
If you work with Python dataframes (pandas, @pola.rs) and are not using skrub.TableReport, you're missing out 😀 We keep improving it
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Rory Byrne @rory.bio · 19/12/2024
86% of OSS contributions from organisations are in the form of employee labour.
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The Alchemist Zero One @the-alchemist-01.bsky.social · 17/12/2024
Unconscious mind rules the roost. "According to the researchers, this theory is important because it explains that all our decisions and actions are actually made unconsciously, although we fool ourselves into believing that we consciously made them." www.bumc.bu.edu/camed/2022/1...
bumc.bu.edu
New Explanation for Consciousness | Chobanian & Avedisian School of Medicine
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Rory Byrne @rory.bio · 16/12/2024
And if my grandmother had wheels she’d be a bicycle.
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Proceedings of the National Academy of Sciences @pnas.org · 13/12/2024
We highlighted member Susan Goldin-Meadow's groundbreaking research on language origins. Her @uofchicago.bsky.social work reveals how deaf children create communication, transforming our understanding of human linguistic creativity. Read more: www.pnas.org/doi/10.1073/...
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Lorenzo Lorenzo-Luaces, PhD @lluaces.bsky.social · 13/12/2024
I love this especially for research study designs
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Grace Lindsay @neurograce.bsky.social · 06/12/2024
I love this idea of a "call for problems"
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Rory Byrne @rory.bio · 10/12/2024
🔧 I built a tool today (alpha). github.com/flywhl/cast Cast is a small lib, using @pydantic.dev to build complex Python objects from parameter specs. E.g. write a pydantic model with a tensor, pass in _parameters_, receive the built tensor. #opensource #openscience #neuroskyence #machinelearning
github.com
GitHub - flywhl/cast: Parameter-driven instantiation for Pydantic types
Parameter-driven instantiation for Pydantic types. Contribute to flywhl/cast development by creating an account on GitHub.
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Rory Byrne @rory.bio · 06/12/2024
I would greatly appreciate submissions and shares of this, to help us motivate funders to support open source toolmaking for academic science. 🙏 #neuroskyence #neuroscience #neuroai #chemsky #compchem #compbio #hpc #machinelearning #ai
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NumFOCUS @numfocus.bsky.social · 05/12/2024
Open-source allows research to move from theory to practice, leading to new scientific breakthroughs that rely on the power of several NumFOCUS projects to complete their research. You can help projects continue pushing boundaries by donating today! hubs.la/Q02-nBzP0 #OpenCode4BetterScience
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Robert Aboukhalil @robert.bio · 04/12/2024
“We don’t value software, data, and methods in the same way we value papers, even though those resources empower millions of scientists” 💯 www.statnews.com/sponsor/2024...
statnews.com
New report highlights the scientific impact of open source software
Two of the scientists who won this year’s Nobel Prize for cracking the code of proteins’ intricate structures relied, in part, on a series of computing
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Elisa Galliano @elisagalliano.bsky.social · 03/12/2024
Migration from the Bad Place completed, the whole lab is on 🦋💙! Roll call to follow, in the meantime have a look at our website: lots of pics of pretty neurons & some occasional science content and, importantly, strongly worded opinions about open science and research culture gallianolab.org
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Rory Byrne @rory.bio · 03/12/2024
Great example of “last mile” tooling needed to bridge AI to scientific workflows. It’s hard to get these built in academia because they require a traditional software eng skillset (eg. building UIs) that scientists rarely have.
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Rory Byrne @rory.bio · 03/12/2024
NESTML: A declarative language for writing neuron models, build by @poojanbabu.bsky.social. github.com/nest/nestml
github.com
GitHub - nest/nestml: A domain specific language for neuron and synapse models in spiking neural network simulation
A domain specific language for neuron and synapse models in spiking neural network simulation - nest/nestml
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Rory Byrne @rory.bio · 03/12/2024
Thanks Jascha 🫶 We’re working hard to create sustainable funding mechanisms for open source scientific tooling - understanding the challenge landscape is a key first step!
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Rory Byrne @rory.bio · 02/12/2024
I am now @rory.bio - cool. A very clever (partial-)solution to the authenticity problem over at Twitter.
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Rory Byrne @rory.bio · 01/12/2024
Just found out there’s a name for the way I structure my notes: Discourse Graph. www.protocol.ai/blog/discour... #toolsforscience #openscience
protocol.ai
Discourse Graphs and the Future of Science
Interview between Tom Kalil, Chief Innovation Officer of Schmidt Futures, Dr. Evan Miyazono, Research Team Lead at Protocol Labs, and Dr. Matt Akamatsu, Assistant Professor of Biology at the Universit...
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Dan Goodman @neural-reckoning.org · 29/11/2024
I propose we switch from saying preprint / published paper to saying publish / reprint. "I published my paper on arxiv and I'm hoping to get it reprinted in Nature"
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Rory Byrne @rory.bio · 29/11/2024
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.
flywhl.dev
Flywheel
Build momentum-preserving software tools for scientific progress
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