A GLM-HMM deep dive

By Camilla Ucheoma Enwereuzor

As part of my MSc internship in the lab, I have spent the last couple of months diving into a paper by Ashwood et al. (2022), who investigated how observers switch between different strategies for perceptual decision-making over the course of long testing sessions. According to previous accounts (e.g., Wichmann & Hill, 2001), subjects maintain one main strategy during cognitive tasks, and any lapses (i.e., errors despite strong sensory evidence) arise independently of one another and of the time course of the experimental session. However, Ashwood et al. suggest that this view is not correct. Using a modelling approach based on Hidden Markov Models (HMMs), the authors found that mice switch between multiple strategies, or hidden “states”, during perceptual decision-making sessions (Figure 1). Importantly, the Markovian component of this approach implies that states are not independent of one another, but rather depend only on the state from the preceding trial, and can persist for many trials in a row. Let us look at how this modelling approach works in more detail.


Figure 1. Reprinted from Figure 1a-b of Histed and O’Rawe (2022). a. Schematic representation of the task for the IBL et al. (2021) mouse data. Mice turned a wheel to indicate whether a sinusoidal grating appeared on the left or right side of the screen. b. Recovered states according to a 3-state GLM-HMM: mice switched between an engaged state where they relied heavily on sensory evidence, to less engaged states that showed left or right biases.
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2023 in review

Another review of the year (here is 2022 and 2021), this time a bit late.

In 2023, I…

  • welcomed the lab’s first postdoc, Philippa Johnson;
  • started co-supervising Sarah Kusch, who will investigate pro-environmental behavior and cognitive effort at Ghent University;
  • was proud to see our lab’s projects presented at Cognitive Computational Neuroscience in Oxford, and NVP in Egmond aan Zee (see here, here and here);
  • published my opinion piece on academia & the climate crisis, and gave several workshops on the topic;
  • co-authored several preprints coming out of my postdoc time in the International Brain Laboratory;
  • applied for the Young Academy Leiden again, and was accepted this time;
  • took a course on mentoring organised at Princeton, and am still meeting regularly with a great mentoring circle;
  • taught courses on cognitive modelling, cognitive neuroscience and social dynamics;
  • read eclectically on systems neuroscience, mathematical psychology, dynamical systems in cognitive science, critical transitions, and social movements;
  • saw my beloved science Twitter collapse, and am attempting a fresh start on BlueSky;
  • participated in two hiring committees for the first time (turns out making good policies on such things is quite hard);
  • co-wrote a letter to Leiden University’s board, calling for an end to collaborations with the fossil fuel industry;
  • brought my toddler to a scientific workshop for the first time, and struggled to find a good balance between research trips and family life;
  • after losing my dad, learned the hard way how exhausting it is to grieve; that the administration after someone dies is a part-time job in and of itself; what a privilege it has been to have a mentor from another scientific field; and how lucky I am to have such supportive friends, family, lab members and colleagues.

Here’s to a 2024 with more mental calm, enough time to spend with the people most important to me, several exciting papers to write, insight and wisdom.

Anne joins Young Academy Leiden

Today, I was inaugurated as a member of the Young Academy Leiden, a group of early-career academics who think and work together on questions of research policy, outreach and interdisciplinary collaboration.

The theme of the inauguration was ‘Engagement’, and each incoming member made a short video on the topic. See below for my contribution.

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Climate action workshop @ CCN

By Eleanor Holton and Anne Urai

Do neuroscientists want to talk about climate change? Turns out they do, if we are to take anything from the CCN climate workshop which took place in Oxford a couple weeks ago. While a two-hour workshop after a days worth of packed neuroscience talks may not seem like a big draw, the event was packed.

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Comprehension of Data Visualisation

By Kasia Kruk

A radical social transition needs to take place to prevent the climate change from progressing as rapidly as it is now. In order to achieve that, we need good communication tools, which could spread the environmental awareness and improve the understanding of the current climate action urgency.

Over the past few months that was the focal point of this climate data visualisation project – how can we raise the awareness of the climate action’s urgency?

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Science as a gift economy

This post is inspired by my brother Max Urai, the better writer of the family – two steps ahead in his thinking, as always. Why literature is a gift-economy (Rekto:Verso, in Dutch). I shamelessly copied some quotations.

The pursuit of scientific knowledge works by virtue of the work of others. We stand on the shoulders of giants, re-mix and improve, discuss and critique; and we hope to leave our communities a bit better than we found them.

Such intellectual exchange can be characterised as a gift economy. This system operates very differently than the familiar market economy, where a trade of specified value is made, and both parties then go their own way. In the gift economy, on the other hand, our gifts cannot be precisely quantified. Rather, receiving gifts ties us the broader community, and commits us to return a gift – at some point, in some form, to someone (but never exactly).

Reciprocity in life and in the academy is a feature of infinite play. Reciprocity colonizes your future by enrolling you in longitudinal practices of giving and getting. When your child finishes college, you do not present them with a bill for all of the expenses they cost you growing up. If you do, you are planning to never see them again.

Bruce R. Caron, 2021
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Preprint review: behavioural state shifts are predicted by fluctuations in arousal

By Philippa Johnson

Review of: Daniel Hulsey, Kevin Zumwalt, Luca Mazzucato, David A. McCormick, Santiago Jaramillo. Decision-making dynamics are predicted by arousal and uninstructed movements. bioRxiv, doi: https://doi.org/10.1101/2023.03.02.530651

In a recent lab meeting, we discussed a preprint by Hulsey et al. (2023), which investigates whether fluctuations in arousal can account for some of the variability found in decision-making behaviour. In psychology experiments, we usually implicitly assume that people/animals perform the same cognitive task with the same strategy during an experimental ‘session’ – but more and more research shows that this is a bit naïve, and that we can draw false conclusions if we don’t take these nonstationarities into account. After all, the way we process information at the beginning of a boring lecture is surely very different to how we process information towards the end!

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Doughnut science: rethinking academia in a time of climate crisis

How to be an academic in a world on fire?

As scientists concerned about the climate crisis, we set out to rethink the role and goals of the university in tackling the 21st century’s challenges. Inspired by Raworth’s Doughnut Economics, we propose seven new ways to thinking – not only to help us think, but also to act.

Read the paper: Urai AE, Kelly C (2023) Rethinking academia in a time of climate crisis. eLife 12:e84991. https://doi.org/10.7554/eLife.84991
Join us for a discussion at Growing Up in Science Global on 11 April: https://nyu.zoom.us/meeting/register/tJIoc-GsqT8uGNXniBIHPo9u4ibfDwxysLkI

… and let us know your thoughts!

Update: our article has been translated into Spanish [link here].