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Francisco Pereira

@franciscopereira.bsky.social

410 followers 570 following 16 posts

Brain boffin / machine learning mercenary at NIMH. My opinions, not my employer's. @[email protected] @[email protected]

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Computer science 43%

Engineering 39%

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Reposted by Francisco C. Pereira

Sam Nastase @samnastase.bsky.social · 10d

I'm recruiting PhD students to join my new lab in Fall 2026! The Shared Minds Lab at @usc.edu will combine deep learning and ecological human neuroscience to better understand how we communicate our thoughts from one brain to another.

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Reposted by Francisco C. Pereira, Martin Wiener

Matthias Nau @matthiasnau.bsky.social · Aug 25

Excited to share our new paper w/ @cibaker.bsky.social in @natcomms.nature.com linking active vision & memory!

We provide evidence that gaze reinstatement & neural reactivation are deeply related phenomena that jointly reflect the experiences constructed during recall. doi.org/10.1038/s414...
🧵1/9

Neural and behavioral reinstatement jointly reflect retrieval of narrative events - Nature Communications

When people recall a movie, their eye movements and brain activity resemble those observed during the viewing. These behavioral and neural reactivations are linked through a common process, likely ref...

doi.org

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Reposted by Francisco C. Pereira

Grace Lindsay @neurograce.bsky.social · May 10

Because we must build good things while we scream about the bad, I have started a "Data for Good" team @data-for-good-team.bsky.social that partners with organizations needing short-term data science help. We have three projects ongoing & will add more as our capacity grows.
data-for-good-team.org

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Reposted by Francisco C. Pereira, Michael H. Fox

Thomas Yeo @bttyeo.bsky.social · Mar 26

It's finally here! Use the Network Correspondence Toolbox to help contextualize your neuroimaging findings 🧠

A network correspondence toolbox for quantitative evaluation of novel neuroimaging results - Nature Communications

Here, the authors present the Network Correspondence Toolbox, which enables researchers to examine and report spatial correspondence between their neuroimaging results and widely used brain atlases.

www.nature.com

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Reposted by Francisco C. Pereira

Gabe Loewinger @gabeloewinger.bsky.social · Mar 18

Test effects of behavior/events at every trial timepoint in photometry analyses! Paper with Erjia Cui, Dave Lovinger, Francisco Pereira. “A Statistical Framework for Analysis of Trial-Level Temporal Dynamics in Fiber Photometry Experiments.” Python+R packages! elifesciences.org/articles/95802. 1/13

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Reposted by Francisco C. Pereira, Talia Konkle

Martin Hebart @martinhebart.bsky.social · Mar 6

People talk a lot about objects, but what about the softness of a cushion, the greenness of an emerald, or the viscosity of oil? In our work just published @pnas.org, we shed light on how we make sense of the hundreds of materials around us.
www.pnas.org/doi/10.1073/...

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Reposted by Stanislas Dehaene, Francisco C. Pereira, Taku Ito

Jean-Rémi King @jeanremiking.bsky.social · Dec 12

🚨We're very excited to share our latest study, by Pablo Diego and team:

"A polar coordinate system represents syntax in large language models",

📄: Paper arxiv.org/abs/2412.05571
🪧: Poster tomorrow: neurips.cc/virtual/2024...
🧵: Thread 👇

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Reposted by Francisco C. Pereira

Matthias Nau @matthiasnau.bsky.social · Oct 22

Gaze reinstatement & neural reactivation may be linked through a common process that reinstates past experiences during memory retrieval! doi.org/10.1101/2024...

Check out our #Preprint that integrates eye tracking into the Sherlock fMRI Dataset! Postdoc work w/ @cibaker.bsky.social 🧠🟦 #PsychSciSky

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Reposted by Francisco C. Pereira

Peter Molfese @dcneuroscientist.bsky.social · Aug 21

The Center for Multimodal Neuroimaging (CMN) and the FMRIF are hosting a workshop September 4-5 on “Insights Into Cognitive And Neural Function Through Eye Tracking”.

The hybrid workshop will be streamed on zoom, info: cmn.nimh.nih.gov/cmnworkshop2...

#eyetracking #neuroscience #cognition

Center for Multimodal Neuroimaging

cmn.nimh.nih.gov

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Francisco Pereira @franciscopereira.bsky.social · May 13

The National Institute on Drug Abuse (NIDA) is seeking a Data Scientist and Senior Advisor to the NIDA Director and other leadership positions, on health informatics and data science, data management, emerging technologies, data standards and policy. More details at:
www.usajobs.gov/job/782086300

Data Scientist

This position serves as a Data Scientist and Senior Advisor to the NIDA Director and other leadership positions, on matters related to health informatics and data science, data management, and emergin...

www.usajobs.gov

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Francisco Pereira @franciscopereira.bsky.social · Mar 13

Thank you for the kind words, Sam! @gabeloewinger.bsky.social deserves most of the credit, both for spotting the need and then doing all the hard work to address it.

Francisco Pereira @franciscopereira.bsky.social · Feb 11

Interested in a researcher position studying the neural and computational bases of adaptive and maladaptive decision-making, and their relationship to mental health? Our colleague Silvia Lopez-Guzman is hiring a Data Scientist/Data Analyst, read more at cdn-lab.github.io .

Francisco Pereira @franciscopereira.bsky.social · Nov 10

We released a package implementing our framework. The methods can be applied to other neural data types too!

code: github.com/gloewing/pho...

Interested in learning more? Gabe Loewinger is giving a talk at SfN Monday 1pm in WCC-201
13/13

Francisco Pereira @franciscopereira.bsky.social · Nov 10

FLMM finds effects obscured by standard analyses! For example, FLMM reveals effects that "wash out" when analyzed with AUCs. In published work, Cue Period AUC finds no effects because it averages over time-windows (1) and (2) that have opposing effects. 12/13

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Francisco Pereira @franciscopereira.bsky.social · Nov 10

FLMM can disentangle components with distinct temporal dynamics. It can also be used to run analogues of standard hypothesis tests (e.g., ANOVAs, correlations) at each trial time-point. Below is an example akin to the FLMM version of a paired t-test. 11/13

Francisco Pereira @franciscopereira.bsky.social · Nov 10

Informally, functional random-effects allow one to model variability across animals in the signal "shape." 10/13

Francisco Pereira @franciscopereira.bsky.social · Nov 10

Including functional random-effects allow one to model how the dynamics of signal-covariate associations vary across animals. 9/13

Francisco Pereira @franciscopereira.bsky.social · Nov 10

FLMM plots can be conceptualized as pooling signal values (dF/F) at a given trial time-point (e.g., 1.7 sec) across animals and trials, correlating it with covariate(s) (e.g., Latency-to-press) and plotting the slope of the correlation. 8/13

Francisco Pereira @franciscopereira.bsky.social · Nov 10

FLMM outputs a coefficient estimate plot that shows how the signal–covariate association evolves across trial time-points. 7/13

Francisco Pereira @franciscopereira.bsky.social · Nov 10

FLMM exploits autocorrelation to construct *joint* 95% CIs (light grey) that show time windows where effects are statistically significant (any intervals that do not contain 0). All you need to do is visually inspect! 6/13

A plot showing the value of the model coefficient associated with a covariate, over the duration of a trial, time-locked to the lick event.

Francisco Pereira @franciscopereira.bsky.social · Nov 10

FLMM combines the benefits of 1) Mixed Models to account for between-animal heterogeneity, and 2) Functional Regression to model covariate effects at each trial-time point. 5/13

Francisco Pereira @franciscopereira.bsky.social · Nov 10

Solution: We propose an analysis framework based on Functional Linear Mixed Models (FLMM) that allows one to analyze signal–covariate associations at every trial time point. 4/13

Francisco Pereira @franciscopereira.bsky.social · Nov 10

Problem: Photometry is often applied in nested longitudinal experiments with multiple trials per session and sessions per animal. This induces correlation, missing data, etc., that can obscure effects if not accounted for statistically. 3/13

Francisco Pereira @franciscopereira.bsky.social · Nov 10

Problem: Common photometry analysis methods reduce detection of effects because, among other things, they average across trials and use summary statistics (e.g., AUC, peak amplitude). 2/13

Francisco Pereira @franciscopereira.bsky.social · Nov 10

If you use fiber photometry data and would like to test for the effects over time of stimuli, behavior, or any other variable, our new method may be of interest...

"A Statistical Framework for Analysis of Trial-Level Temporal Dynamics in Fiber Photometry Experiments"
www.biorxiv.org/content/10.1...

A plot showing fiber photometry time series for many trials.

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