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Ilenna Jones

@ilennaj.bsky.social
2.7K followers 409 following 37 posts

| Cellular/Molecular-turned-Computational Neuroscientist | | What do neurons even do?? | Neural Computation with Dendrites | | Biophysical Optimization | AI <-> Neuro | | Postdoctoral Research Fellow at the Harvard Kempner Institute | | www.ilenna.com

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Ilenna Jones @ilennaj.bsky.social · 31/07/2026
Where a synapse sits is a learned parameter that does computational work, and clusters support covariance discrimination. Built on a small core of Dendrinet, a dendritic modeling platform coming soon from @kempnerinstitute.bsky.social Preprint: arxiv.org/abs/2607.24503 10/
arxiv.org
Synaptic clustering emerges from learning and supports covariance discrimination
Functional synapse clusters (FSCs) are synapses with correlated presynaptic activity that are colocalized on the same neuronal dendritic branch. FSCs have been observed after learning in cortical and ...
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Ilenna Jones @ilennaj.bsky.social · 31/07/2026
Then, to do what pharmacology cannot, we shuffled learned synapse locations after training, keeping every weight and the nonlinearity intact. Excitatory shuffling drops performance to LDA. Inhibitory shuffling drops it to chance. 9/
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Ilenna Jones @ilennaj.bsky.social · 31/07/2026
As for how placement pays off, inhibition tracks excitation tightly for non-preferred classes, so shunting holds the branch subthreshold. For the preferred class the tracking is looser, excitation escapes, crosses threshold, and is amplified. 8/
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Ilenna Jones @ilennaj.bsky.social · 31/07/2026
Clusters emerge on their own, on distal branches, for excitatory and inhibitory synapses. Remove the NMDAR-like nonlinearity and excitatory clustering falls, matching the APV experiments, but inhibitory clustering rises. 7/
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Ilenna Jones @ilennaj.bsky.social · 31/07/2026
It solves the task and approaches QDA performance with depth. Collapse it to one compartment and performance falls to LDA. Removing any one biological component drops it toward chance. 6/
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Ilenna Jones @ilennaj.bsky.social · 31/07/2026
Dendrinet is a feedforward network of neurons with binary-branching dendritic trees, sparse conductance-based excitatory and inhibitory synapses, shunting inhibition, and an NMDAR-proxy nonlinearity. Nothing is clustered by hand. Synapses relocate during training. 5/
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Ilenna Jones @ilennaj.bsky.social · 31/07/2026
So no single channel is informative. LDA gets ~35%. QDA gets 100%. Any above-chance performance has to be second-order, which is exactly what neighboring synapses on a shared nonlinear branch are positioned to do. 4/
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Ilenna Jones @ilennaj.bsky.social · 31/07/2026
We needed a task where placement could matter. In Permuted Covariance Classification, 200 input channels follow a block correlation structure, and the four classes differ only in which channels co-vary. Means and variances are matched across classes. 3/
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Ilenna Jones @ilennaj.bsky.social · 31/07/2026
You cannot settle it in tissue, because the drug that blocks clustering also removes the dendritic nonlinearity that may be doing the computing. So we trained a dendritic network to place its own synapses, then ablated the placement while holding the nonlinearity fixed. 2/
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Ilenna Jones @ilennaj.bsky.social · 31/07/2026
When an animal learns, synapses carrying similar information end up next to each other on the same stretch of dendrite. We cannot say whether that arrangement does computational work, or merely coincides with learning. 1/
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Ilenna Jones @ilennaj.bsky.social · 31/07/2026
What does synapse position buy a neuron? We trained a dendritic network to place its own synapses on a covariance task. It clustered correlated inputs onto shared branches, and shuffling that placement destroyed performance while every weight stayed intact. Preprint: arxiv.org/abs/2607.24503 🧵-->
arxiv.org
Synaptic clustering emerges from learning and supports covariance discrimination
Functional synapse clusters (FSCs) are synapses with correlated presynaptic activity that are colocalized on the same neuronal dendritic branch. FSCs have been observed after learning in cortical and ...
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jordan @jordan.matelsky.com · 15/06/2026
so I just realized I forgot to #skeetprint my Contactomes paper... (is that what we're calling it?) www.biorxiv.org/content/10.6... @kordinglab.bsky.social @dacolon.bsky.social smithneurallab.weebly.com @jhuapl.bsky.social #academicsky #preprint #neuroscience
a single dendritic spine with a handful of synaptic partners but a HUGE number of contact partners
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Roy Eyono @royeyono.bsky.social · 19/03/2026
How do neural circuits in the brain implement normalization? 🧠 In our new paper, we show that just normalizing sensory input isn't enough. Crucially, we must also normalize the error signals! 🧵👇 Paper: arxiv.org/abs/2603.17676
arxiv.org
Inhibitory normalization of error signals improves learning in neural circuits
Normalization is a critical operation in neural circuits. In the brain, there is evidence that normalization is implemented via inhibitory interneurons and allows neural populations to adjust to chang...
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Ilenna Jones @ilennaj.bsky.social · 26/03/2026
All template files have explicit instructions for when not to edit the text. It's flexible too. As a special case, Daily Notes are hybrid because the top half is untouched raw text and the bottom half is collaborative with instructions to add relevant links to "Primary Node/Synthesis/Open Question"
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Ilenna Jones @ilennaj.bsky.social · 26/03/2026
I can imagine you can have two running at the same time for: 1) active dictation note-taking, 2) active refactoring the synthesis/relationship nodes I bet you could use a third agent to also make planning documents here that code dispatch could run and iterate on separately too. It's flexible
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Ilenna Jones @ilennaj.bsky.social · 26/03/2026
That's a good point. Each node template has instructions to keep date logs for each node that you produce, so changes can be tracked. In theory, you could also prompt the agent to make a relationship or synthesis node of your changing opinions, with links to the logged primary nodes and daily notes.
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Ilenna Jones @ilennaj.bsky.social · 25/03/2026
The Result: A living research vault that grows with your research. Not a graveyard of things you planned to read or a flat folder of notes. It's a fully customizable system that actually compounds. With dictation, it's frictionless too! github.com/ilennaj/obsidian-scientist-knowledge-template
github.com
GitHub - ilennaj/obsidian-scientist-knowledge-template: Template for keeping a living scientific knowledge database using obsidian and claude code.
Template for keeping a living scientific knowledge database using obsidian and claude code. - ilennaj/obsidian-scientist-knowledge-template
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Ilenna Jones @ilennaj.bsky.social · 25/03/2026
ME: Daily notes, reading journals, and dictated thoughts... these are all voice preserved and never touched by AI. That's the part that's actually mine. AI: Linking nodes, surfacing open questions, and updating project records are all the AI's job. The AI provides the glue.
Working Principles:

Primary Nodes are not interpretation zones — they contain only what the source material says, closely paraphrased or summarized.
Syntheses are explicitly marked as interpretation and cross-source integration.
Open Questions are parsimonious — one focused question per note, not a list of musings.
Relationship Nodes are flat and specific — they describe one relationship cluster at a time, not general "topics."
Skill Notes are honest about uncertainty — the "what's murky" section is as important as the objective content.
This vault evolves — nodes are updated, priority interests split, questions get answered, skills deepen.
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Ilenna Jones @ilennaj.bsky.social · 25/03/2026
My memory sucks. Note-taking is my superpower. I decided to upgrade this superpower by making a living knowledge base for research, powered by Claude Code (or any context agent). Here's a github template so you can do the same too. 🧵 github.com/ilennaj/obsidian-scientist-knowledge-template
github.com
GitHub - ilennaj/obsidian-scientist-knowledge-template: Template for keeping a living scientific knowledge database using obsidian and claude code.
Template for keeping a living scientific knowledge database using obsidian and claude code. - ilennaj/obsidian-scientist-knowledge-template
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Konrad Kording @kordinglab.bsky.social · 11/03/2026
In two hours we (with gunnar blohm and jordan matelsky) will run a webinar talking about our philosophy for doing good science and becoming good at science. And the tool planyourscience.com I wrote to help. If you want to join us you can sign up here:t.co/OJOQe1Ly18
planyourscience.com
Scientific Paper Planner - AI-Powered Research Planning
Structure your scientific research with AI-powered guidance. From hypothesis to methodology, plan your research paper with intelligent mentoring.
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Kempner Institute at Harvard University @kempnerinstitute.bsky.social · 10/03/2026
🧠What do neurons “want”?✨ Kempner researchers @binxuwang.bsky.social and Carlos Ponce have developed a way for neurons to train AI image models to match their “preferences.” Read more about the research, out now in @natneuro.nature.com, here: bit.ly/4bz47hw #neuroscience #NeuroAI
bit.ly
Kempner Researchers Harness Generative AI to Reveal What Neurons "Want" - Kempner Institute
How can scientists figure out what visual information a neuron really responds to? For decades, neuroscientists have tried to answer this question by showing animals pictures — of faces, trees, […]
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Maria Geffen @geffenlab.bsky.social · 27/02/2026
The deadline to apply for the Brain Prize Cajal summer course in Computational Neuroscience has been extended to March 9! We’re excited for you to join us in sunny Lisbon! Please do not hesitate to send in an application and learn about computational neuroscience! @gjorjulijana.bsky.social
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Ilenna Jones @ilennaj.bsky.social · 28/02/2026
Thanks for highlighting this interview Ben! At the Deep Learning Indaba 2025 (Urunana!) I chatted with the EIC of iafrikan.com about the importance of summer schools like Neuromatch Academy for accessing Comp Neuro and NeuroAI training! @deeplearningindaba.bsky.social @neuromatch.bsky.social
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The Transmitter @thetransmitter.bsky.social · 27/02/2026
Dendritic arbors provide neuroscience with an ideal opportunity to study how individual neurons interact with their broader circuitry and are the field’s best bet to bridge cellular and systems neuroscience, writes @justinkohare.bsky.social. #neuroskyence www.thetransmitter.org/dendrites/de...
thetransmitter.org
Dendrites help neuroscientists see the forest for the trees
Dendritic arbors provide just the right scale to study how individual neurons reciprocally interact with their broader circuitry—and are our best bet to bridge cellular and systems neuroscience.
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Konrad Kording @kordinglab.bsky.social · 26/02/2026
This paper on how the brain may do gradient descent is very cool: www.nature.com/articles/s41...
nature.com
Vectorized instructive signals in cortical dendrites - Nature
Mice learning a neurofeedback brain–computer interface task show neuron-specific teaching signals in cortical dendrites, consistent with a vectorized solution for credit assignment in the brain.
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willydorrell.bsky.social @willydorrell.bsky.social · 14/02/2026
Cosyne Viewing Parties Visas, costs, care responsibilities, and environmental concerns all limit Cosyne attendance. Luckily, the talks are livestreamed; but watching alone is the high road to an aneurism. Hence: viewing parties! Gather regionally to watch Cosyne talks! More info: shorturl.at/3DHZX.
shorturl.at
Will's Wild Website
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taylr @taylordahlin.com · 27/01/2026
brass solidarity band performing “stand by me” in the streets of whittier next to alex pretti’s memorial. the crowd started chanting “the people united will never be defeated” so they incorporated it into the song. i love minneapolis
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Simons Computational Neuroscience Imbizo @imbizo.bsky.social · 17/01/2026
A massive shoutout to our incredible mentors and TAs! 🙌 They delivered 6 wonderful tutorials. Their energy and dedication make this school special. 💻🧠 🇿🇦 @spiroschav.bsky.social | Will Dorrell | @kiradust.bsky.social | @isabelmaria-c.bsky.social | @colleenjg.bsky.social | @rherzoga.bsky.social
Mentors/TAs are giving their tutorials. Spiros Chavlis introduces Python with the LIF model, Will Dorrell on neural computation, Kira Düsterwald on Probability Theory, Isabel Cornacchia on Dynamical Systems, Colleen Gillon on Reinforcement learning, and Rubén Herzog on information theory applied to neural data.
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Spiros Chavlis @spiroschav.bsky.social · 10/01/2026
The venue is quiet tonight, but the anticipation is electric. ⚡️ Tomorrow, this space fills with students ready to gather and share knowledge. This is why we are here. We are Imbizo, and we love what we do. #imbizo2026
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Jakob Macke @jakhmack.bsky.social · 04/12/2025
Come work with us!!!
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Neuromatch @neuromatch.bsky.social · 02/12/2025
Today is #GivingTuesday! Join us in helping to make computational science education accessible to everyone, everywhere! Since, 2021, Neuromatch Academy and Climatematch Academy have supported nearly 14,000 learners from 135 countries. Your support makes this possible. neuromatch.io/donate/
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Kempner Institute at Harvard University @kempnerinstitute.bsky.social · 15/08/2025
Applications are now open for our #KempnerInstitute Research Fellowships! Postdocs studying the foundations of #intelligence or applications of #AI are encouraged to apply. Learn more and apply by Oct. 1: bit.ly/3UvpSpe #LLMs #NeuroAI #ML @shamkakade.bsky.social
bit.ly
Kempner Research Fellowship - Kempner Institute
The Kempner brings leading, early-stage postdoctoral scientists to Harvard to work on projects that advance the fundamental understanding of intelligence.
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Ilenna Jones @ilennaj.bsky.social · 23/08/2025
Finishing my 2 weeks of travel to #CCN2025 in Amsterdam, Netherlands and @deeplearningindaba.bsky.social #DLI2025 in Kigali, Rwanda. I saw tons o stellar research and ideas grounded in urgent real world applications of AI to improve people's lives. Now it's time to recuperate back home in Boston 😌🫠😊
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ML for Science @ml4science.bsky.social · 16/07/2025
Together with #AIMS, the African Institute for Mathematical Sciences, we have an exciting position to fill: The AIMS - Tübingen Junior Research Chair in Machine Learning for Science! 1/2
Formulas and numbers from the field of machine learning written in white chalk on a blackboard
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Ilenna Jones @ilennaj.bsky.social · 22/05/2025
The Harvard @kempnerinstitute.bsky.social spotlights me and my efforts there and at @imbizo.bsky.social in this article! Check it out!
kempnerinstitute.harvard.edu
With “Lunch and Learn,” the Kempner Offers a New Forum for Knowledge Building, Teaching, and Collaboration - Kempner Institute
Kempner Research Fellow Ilenna Jones studies dendrites, exploring how the computational properties of these structures in biological neurons can contribute to the next generation of brain-inspired AI....
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Ilenna Jones @ilennaj.bsky.social · 16/05/2025
Today, @hhmi.org stopped all competitions supporting ECRs when we needed it most. As an FGLI undergraduate 2014/2015 HHMI EXROP participant, a 2020 Gilliam Fellow, and applicant for the now paused 2025 HGF program - I was a consistently supported by HHMI throughout my career. Please reconsider!
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Kate Cavanaugh @katecavanaugh.bsky.social · 16/05/2025
I am a proud HHMI Gilliam Fellow alumn. The HHMI funded me at a critical time in my career - a real inflection point that made me realize that I had a place and future in science. I always looked to the HHMI as a safety net to those historically excluded by academia, 1/4
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Ilenna Jones @ilennaj.bsky.social · 16/05/2025
I'm so sad to hear this too - I gave so much time and effort into this application too. At the very least it helped give me the push to solidify ideas that I'm trying to push forward. We'll make it work somehow.
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Ilenna Jones @ilennaj.bsky.social · 15/05/2025
Testing this briefly felt like this gamifies the writing and planning process especially since there's a rating system that comes with the feedback- honestly fun to use to expand on fledgling projects!
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Konrad Kording @kordinglab.bsky.social · 15/05/2025
I have seen folks waste so much time by not properly planning research. Missed literature, missing controls, ignored hypotheses, etc. Lack of planning also produces bad science (e.g. analysis until significant). So I am writing an app. Looking for feedback. scientific-paper-planner-test.vercel.app
scientific-paper-planner-test.vercel.app
Scientific Paper Planner
Scientific Paper Planner Application
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Lisa Schmors @lisaschmors.bsky.social · 08/05/2025
🧠🤖 Computational Neuroscience summer school IMBIZO in Cape Town is open for applications again!   💻🧬 3 weeks of intense coursework & projects with support from expert tutors and faculty   📈Apply until July 1st! 🔗https://imbizo.africa/
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Ilenna Jones @ilennaj.bsky.social · 16/04/2025
It feels so good to see Imbizo students doing great things! @imbizo.bsky.social #imbizo
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Thomas Yeo @bttyeo.bsky.social · 11/04/2025
While the world burns, we cook up a new preprint! doi.org/10.1101/2025... Biophysical modeling is a key tool to derive mechanistic insights into the brain. These models are governed by biologically meaningful parameters (unlike artificial neural networks), but the dirty secret ... 1/N
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Roman Makarov @roman-makarov.bsky.social · 26/02/2025
We are thrilled to host a tutorial on biophysical modeling with Jaxley & DendroTweaks at #CNS2025! 📍 Florence, July 5 — looking forward to seeing you there! www.cnsorg.org/cns-2025 @cnsorg.bsky.social
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Mozes Jacobs @mozesjacobs.bsky.social · 10/03/2025
Traveling waves of neural activity are observed all over the brain. Can they be used to augment neural networks? I am thrilled to share our new work, "Traveling Waves Integrate Spatial Information Through Time" with @andykeller.bsky.social! 1/13
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cogscikid.bsky.social @cogscikid.bsky.social · 10/02/2025
Are you interested in comparing modern AI/RL agents to Humans? To make it easier for researchers spanning cognitive science, multi-agent RL, and HCI to do this, I've made nicewebrl github.com/wcarvalho/ni...
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Carl T. Bergstrom @carlbergstrom.com · 04/02/2025
Modern-Day Oracles or Bullshit Machines? Jevin West (@jevinwest.bsky.social) and I have spent the last eight months developing the course on large language models (LLMs) that we think every college freshman needs to take. thebullshitmachines.com
thebullshitmachines.com
INTRODUCTION
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Athena Akrami @athenaakrami.bsky.social · 30/01/2025
A bit late, but just to say how lucky I feel that I could spend a week at #Imbizo2025 summer school @imbizo.bsky.social, hanging out w/ this group of absolutely brilliant students, their dedicated TAs & other faculty. Watch out for this pool of talent! & consider applying/contributing next rounds
Group picture of students, TAs and faculty at the #imbizo2025 course
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Simons Computational Neuroscience Imbizo @imbizo.bsky.social · 30/01/2025
🎉 Exciting day at #Imbizo2025! Dr. Dan Wetmore & Dr. Garrick Orchard from Meta’s Reality Labs shared their industrial insights on designing top-notch AI/ML experiments, including innovative BCI applications 🤖💡 Students showcased creative solutions for EMG, sleep, wind, epilepsy monitoring & more! 🌟
Dr. Dan Wetmore giving a lecture Students at Imbizo working hard on their presentationStudent presentation on designing ML solutions to understand cardiac rhythms Student presentation on designing ML solutions to sleep paralysis
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