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Reposted by Salar Nouri

Shervin Safavi @neuroprinciplist.bsky.social · 07/04/2026

If you need a method to infer causality from neural data, even when the signal is short, check our recent paper: Paper: joss.theoj.org/papers/10.21... Code: github.com/CMC-lab/Tran...

joss.theoj.org

TranCIT: Transient Causal Interaction Toolbox

Nouri et al., (2025). TranCIT: Transient Causal Interaction Toolbox. Journal of Open Source Software, 10(116), 9302, https://doi.org/10.21105/joss.09302

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Reposted by Salar Nouri

CMC Unit @cmc-unit.bsky.social · 07/04/2026

Thrilled to see the second paper of the lab out 🤩 Check it out if you need a method to infer causality from neural data, even when the signal is short! Paper: joss.theoj.org/papers/10.21... Code: github.com/CMC-lab/Tran...

joss.theoj.org

TranCIT: Transient Causal Interaction Toolbox

Nouri et al., (2025). TranCIT: Transient Causal Interaction Toolbox. Journal of Open Source Software, 10(116), 9302, https://doi.org/10.21105/joss.09302

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Salar Nouri @sanouri.bsky.social · 07/04/2026

Go ahead and pip install trancit, and let us know what you think! If you are analyzing ripples, spindles, or bursts, give it a spin. 🌪️ Issues and PRs are welcome on GitHub! github.com/CMC-lab/Tran...

github.com

GitHub - CMC-lab/TranCIT: Transient Causal Interaction estimator

Transient Causal Interaction estimator. Contribute to CMC-lab/TranCIT development by creating an account on GitHub.

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Salar Nouri @sanouri.bsky.social · 07/04/2026

This work was a fantastic collaboration! 🤝 Big thanks to my collaborators Kaidi Shao and Shervin Safavi (@neuroprinciplist.bsky.social) for their guidance. Proud to kick off my journey with this release! 🎉

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Salar Nouri @sanouri.bsky.social · 07/04/2026

There is a growing interest in understanding transient dynamics! For related approaches to bursty cognition, check out the work of Mikael Lundqvist (www.sciencedirect.com/science/arti...) and recent work on large-scale interactions by Martin Vinck. Exciting times for dynamic analysis! 🌊

sciencedirect.com

Beta: bursts of cognition

Beta oscillations are linked to the control of goal-directed processing of sensory information and the timing of motor output. Recent evidence demonst…

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Salar Nouri @sanouri.bsky.social · 07/04/2026

What about real brains? 🐀 We analyzed Hippocampal LFP during Sharp-Wave Ripples (SWRs). Using rDCS (relative DCS), we correctly identified the transient information flow from CA3 ➡️ CA1. Critically, this only works if you align data to the cause—a key feature our toolbox handles automatically.

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Salar Nouri @sanouri.bsky.social · 07/04/2026

Does it work? We simulated coupled oscillators to test the "Synchrony Pitfall." As synchrony spikes (right panel), TE (blue line) crashes to zero (oops! 🙈). DCS (yellow line) correctly maintains the causal link. It doesn't blink even when signals lockstep.

DCS successfully captures causal influence during high synchrony, where TE fails.

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Salar Nouri @sanouri.bsky.social · 07/04/2026

Why SCMs? 🤯 Unlike predictive methods, SCM-based DCS uses "interventional" logic. It mathematically "cuts the causal arrow" to quantify direct influence. This makes it robust to the "Synchrony Pitfall"—a trap in which standard TE drops to zero when signals become too synchronized. 🕳️

Conceptualizing the intervention for rDCS.

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Salar Nouri @sanouri.bsky.social · 07/04/2026

Enter TranCIT. 🛠️ We provide an open-source pipeline designed specifically for transient dynamics. It implements not only GC and TE but also the novel DCS and rDCS (relative DCS) methods based on Structural Causal Models (SCMs).

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Salar Nouri @sanouri.bsky.social · 07/04/2026

The problem: Traditional methods such as Granger causality and transfer entropy (TE) assume stationarity and require long data segments. 📉 But the brain doesn't wait! 🛑 Neural interactions often happen in short, intense bursts (ripples, beta bursts) where these methods fail.

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Salar Nouri @sanouri.bsky.social · 07/04/2026

The foundation of this work lies in the powerful "Dynamic Causal Strength" (DCS) methodology originally developed by Kaidi Shao, Nikos Logothetis, and Michel Besserve (www.frontiersin.org/articles/10....). We brought it to the Python ecosystem and supercharged it! 🐍🚀

frontiersin.org

Frontiers | Information theoretic measures of causal influences during transient neural events

Transient phenomena play a key role in coordinating brain activity at multiple scales, however their underlying mechanisms remain largely unknown. A key chal...

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Salar Nouri @sanouri.bsky.social · 07/04/2026

Wanna infer causal interactions during brief, transient neural events? 🧠⚡ Many methods struggle with such non-stationarities, but we got a robust solution for you! 📦 My recent publication with @cmc-lab.bsky.social 🥳: TranCIT: Transient Causal Interaction Toolbox 📜 JOSS: bsky.app/profile/joss...

Conceptualizing the intervention for DCS

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Reposted by Salar Nouri

Journal of Open Source Software @joss-openjournals.bsky.social · 30/12/2025

Just published in JOSS: 'TranCIT: Transient Causal Interaction Toolbox' doi.org/10.21105/joss.09302

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Reposted by Salar Nouri

Lioba Enk @liobaenk.bsky.social · 11/03/2026

At #MBBS2026, Shervin Safavi @neuroprinciplist.bsky.social @cmc-lab.bsky.social presents their in-silico findings of #oscillator dynamics in #brainbody #embodied agents, stressing the role of #homeostatic state in #RL! ⭐️ #MBB #MindBrainBody #neuroskyence

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