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Prediction mechanisms of the brain: a computational taxonomy

Lead Research Organisation: UNIVERSITY OF OXFORD
Department Name: Clinical Neurosciences

Abstract

Our brains receive a continuous torrent of unsorted, noisy data from the senses - changing patterns of light, distributions of sound frequencies, and signals from our skin and muscles about the position and movements of the body. Yet we perceive an ordered and meaningful world of objects, speech and music (not patterns of light and sound energy), in which we produce actions directed towards behavioural goals (rather than outputting jumble of limb locations and muscle tensions). To create order from chaos, the brain is continually constructing and refining models of the sensory world and the animal's or person's actions in it. These models simplify information processing by capturing the meaningful structure in the external world and ignoring information that is unstructured, meaningless or irrelevant. In this sense we can think of brains almost like scientists, actively trying to understand and predict the world around them by simplifying it down to its core elements.
In my research, I am trying to answer some rather general questions about how the brain constructs internal models that accurately capture the structure of the external world. I will be targeting three information processing challenges that brains face again and again in different contexts, and trying to work out if the brain has dedicated systems for solving these problems, and if so, how those systems work:
- How does the brain focus on relevant variation in stimuli (such as the rate at which cars are approaching a pedestrian crossing) and filter out irrelevant variation (such as the colour of the cars)?
- How does the brain optimise processing of relevant stimuli (for example, focussing attention on stimuli where similar stimuli have very different meanings, and so careful processing is required?
- How does the brain determine how much to change its expectations about the world, as the environment changes? If I experience a surprising event (such as an increase in traffic on my route to work), how much should I update my expectations for future occasions? Can I voluntarily set my brain to learn faster (for example, if I expect a change in traffic flow because I know that construction work is taking place) and to forget again (when the construction work is over)?

My approach to understanding how the brain meets these challenges is to develop algorithms (implemented in computer programmes) that behave in a similar way to human brains in solving these challenges, and then to work out how these algorithms could be computed by populations of neurons in a real brain. Then to test whether the algorithms are correct (that is, whether the brain really works that way), I use my neural network models to generate new predictions about how people will behave in experiments, and how their brain activity will change in different circumstances. I measure brain activity using non-invasive imaging techniques such as MRI.
Some of my models also make predictions about how different brain chemicals (neurotransmitters and neuromodulators) affect the processing of information by the brain. To test these hypotheses, I will give healthy volunteers small doses of drugs that affect neurotransmitter concentrations and observe the resulting changes in their behaviour and brain activity.

Technical Summary

The proposed research aims to develop a computational characterization of the roles of different brain systems in the formation and tuning of predictive models of the environment. The central theme of the research is to investigate the notion that the involvement of certain brain structures in a diverse range of cognitive processes can be understood in terms of formally equivalent computational functions provided in a range of superficially different cognitive contexts.
I will focus on three computational challenges that the brain faces when forming predictive internal models of the environment, and which arguably cut across multiple behavioural and cognitive contexts: How to focus on the relevant dimensions of content and ignore irrelevant variation (computation 1: marginalization)? How to focus processing resources within a dimension to reflect the structure of the perceptual world, or task demands (computation 2: reparameterization)? How to balance the need for stability in predictive models with the need to incorporate new information about a changing environment (computation 3: stability/malleability of representations)?
For each identified challenge, I will develop models of the core computational processes at both an algorithmic level to predict behaviour, and a biophysical level to predict brain activity. An important part of the biophysical modelling will be to incorporate physiological characteristics specific to the brain systems underlying each computation, to explain why these particular brain structures are suited for the computations they perform. To test the models, I will use a combination of imaging paradigms (using fMRI and MEG) that are carefully designed to test hypotheses about the neural code underlying brain activity (e.g. MVPA and cross-stimulus suppression techniques). I will also test specific hypotheses about the roles of neuromodulators by combining brain imaging with pharmacological manipulations in healthy volunteers.

Planned Impact

The proposed research is basic (non-applied) science and therefore the impact beyond academia will be realized over the longer term. However through laying down basic theory in the field of neuroscience, the intention is to create a robust foundation for applied work which will have value for many years to come.

In addition to the academic impacts of the work (see academic beneficiaries) the intended impacts are as follows:

Health
Disorders of brain function, both in psychiatry and neurology, represent an important and increasing proportion of health problems in the Western world. The proposed research is basic science directed towards understanding the relationships between brain physiology and brain function. Although the research is not directed towards modeling any particular disorder, it is very likely that the models developed during the fellowship could be applied in clinical research. For example, models of the role of acetylcholine in category formation and maintenance in prefrontal cortex could have applications for the understanding of diverse disorders including Alzheimer's disease and ADHD (both of which have a cholinergic aspect and elements of their symptomology that could be characterized in terms of disordered categorical processing). Models of the role of dopamine and noradrenaline in determining the stability of internal models could similarly have applications in the understanding of psychological disorders in which these neuromodulators are disordered, including depression, anxiety and schizophrenia. I note that CDA fellows are encouraged to apply for further grant support during the course of their award and therefore once some of the basic modeling and validation work is underway, I will be looking to develop clinical collaborations to test the application of these models to clinical populations.

Society
Neuroscience research is, quite simply, interesting to the general public. Findings in neuroscience continue to attract media attention (for example, at the time of writing a paper in social neuroscience [Mascaro et al 2013 doi: 10.1073/pnas.1305579110] using methods developed here at FMRIB has been the top hit for all news on the BBC website for 48 hours straight). Whilst recognizing the need to report research responsibly and without over-sensationalizing findings to attract maximal media attention, I do believe it is important to maintain public interest in science as a valuable part of society and culture. Several of my recent studies [CV refs 10,11,13,17] were ranked in the top 5% of published articles in terms of interest in new and social media [www.altmetric.com].

Economic
Education and research are thriving export sectors for the UK, in which our small country punches well above its weight internationally. By basing the fellowship in a university environment in which I am actively involved in teaching, I will contribute to this economic benefit.

Publications

10 25 50
 
Description BBSRC SLOLA
Amount £2,911,000 (GBP)
Funding ID BB/W003392/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 03/2022 
End 04/2027
 
Description Inhibitory engrams in learning and memory consolidation (research grant)
Amount £613,000 (GBP)
Funding ID MR/W01971X/1 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 03/2022 
End 04/2025
 
Title Data from: Control of entropy in neural models of environmental state 
Description Humans and animals construct internal models of their environment in order to select appropriate courses of action. The representation of uncertainty about the current state of the environment is a key feature of these models that controls the rate of learning as well as directly affecting choice behaviour. To maintain flexibility, given that uncertainty naturally decreases over time, most theoretical inference models include a dedicated mechanism to drive up model uncertainty. Here we probe the long-standing hypothesis that noradrenaline is involved in determining the entropy, and thus flexibility, of neural models. Pupil diameter, which indexes neuromodulatory state including noradrenaline release, predicted increases (but not decreases) in entropy in a neural state model encoded in human medial orbitofrontal cortex, as measured using multivariate functional MRI. Activity in anterior cingulate cortex predicted pupil diameter. These results provide evidence for top-down, neuromodulatory control of entropy in neural state models. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
URL https://datadryad.org/stash/dataset/doi:10.5061/dryad.jk17vk0
 
Title Decision-making in dynamic, continuously evolving environments: Quantifying the flexibility of human choice 
Description # Decision-making in dynamic, continuously evolving environments: Quantifying the flexibility of human choice [https://doi.org/10.5061/dryad.02v6wwq6b](https://doi.org/10.5061/dryad.02v6wwq6b) This repository contains EEG and behavioural data from a study of continuous decision making in a random-dot kinteogram paradigm, in which participants aim to detect consistent periods of motion ('response periods') in background noise. Participants complete 6 blocks, each consisting of 4 conditions (different 'environments'). Each condition lasts 5 minutes. Full details of the paradigm are given in the preprint at [https://www.biorxiv.org/content/10.1101/2022.08.18.504278.abstract](https://www.biorxiv.org/content/10.1101/2022.08.18.504278.abstract). *** ## Description of the data and file structure The location of data files in the repository are highlighted in **bold**, and the relevant MATLAB functions to load/explore the data are given in *italics*. Code to analyse this data is stored at our online code respository, [https://github.com/CCNHuntLab/ruesseler-eeg-analysis](https://github.com/CCNHuntLab/ruesseler-eeg-analysis). ### A. Participant information. **participantInfo.xlsx** is an Excel spreadsheet that gives information about participants IDs and who is pilot, study, control. You will see that the IDs are not consecutive numbers -- this is because we always gave everyone interested in the study (and receiving participant information sheet) a number and put them on a separate excel sheet with contact details etc (this is a separate, locked file which is not included with this dataset). The initial participants were pilot subjects from our lab, several of whom trained themselves on their own computers and for whom we don't have their training data (until subject 7). We also include in this spreadsheet some info on people excluded because they were unable to do the task, and/or several which have a bad EEG channel problem that were also excluded from further analysis. ### B. Behavioural and EEG data. There are 4 folders that contain the data. 1. Preprocessed data: * Behaviour: 1 matlab file for main study and also vertical: has response info (see code) and all stimuli saved in cells (easier and faster to read in than to do separately for each subject) (ruesseler-eeg-analysis: behaviouralAnalysis: function: *read\_in\_behav\_data\_with\_new\_response\_matrix.m*) * **preprocessedData/behaviour/behav\_data\_all\_subjs\_all3.mat** contains behavioural data for 28 subjects who completed the main task; 24 for whom EEG data was successfully acquired and a further 4 participants for whom there were technical issues with the data acquisition. The naming conventions of the different variables provided in these two data files are given in ***Appendix A***. * **preprocessedData/behaviour/behav\_data\_all\_subjs\_allVertical.mat** contains behavioural data for the 6 subjects who completed the task with simultaneous vertical and horizontal dot motion stimuli that were superimposed on one another. The naming conventions for these variables are similarly given in ***Appendix A***. * EEG: Folder for each subject with spm files containing raw eeg data for each session for LMRM = left mastoid/right mastoid as reference, downsampled to 100Hz. There are additional preprocessing steps that can be run. (ruesseler-eeg-analysis preprocessing functions: *EyeblinkCopy\_of\_run\_preprocessing\_for\_all\_subjects*) * **preprocessedData/[subjID]/LMRM/Mdspmeeg\_[subjID]\_sess00X\_eeg.mat** contains the EEG data for subject **[subjID]** for session **[X]** (of 6 sessions). This file is in SPM12 format, and has a partner **[.dat]** file with the same filename (all SPM12 files consist of a header .mat file and a data .dat file). The EEG data in this file is after minimal pre-processing has been performed (conversion to SPM12 format, downsampling to 100Hz, and re-referencing of the data using *spm\_eeg\_montage* to a left mastoid/right mastoid reference (hence **[LMRM]** is the folder name)). If you want to perform any analysis with the raw data, we suggest that you use this file (virtually any analysis can be performed with this file, except looking at high-frequency EEG responses). Note that the naming convention Mdspmeeg\_ refers to the fact that the file is in SPM format, and has been downsampled and montaged. Details of the structure of these .mat and .dat files can be understood by referencing the SPM12 manual, available at [https://www.fil.ion.ucl.ac.uk/spm/](https://www.fil.ion.ucl.ac.uk/spm/) * Please note: we also have stored versions of SPM12 files from the different stages of preprocessing, *en route* from the raw downsampled EEG data to the results from the convolutional GLM analyses (see next point). These intermediate preprocessing files are quite large (\~193GB), and so are ***not*** included in this repository. It should be possible to recreate them with the code and the methods from the paper, but please contact us directly if you think you need any of our copies of the intermediate preprocessing stages of the data. 2. convGLM * **convGLM/matchedEegData/LMRM/[subjID]\_EEGdat.mat** are files in MATLAB format, with EEG data matched to stimulus stream (for processing information, look in ruesseler-eeg-analysis repository for: *run\_match\_of\_eeg\_and\_stimulus\_for\_all\_subjects.m*). Note that these include two datafiles for each subject, both before and after current source density analysis (CSD) - the latter is **[subjID]\_csdEEGdat.mat**. The naming conventions for these variables are similarly given in ***Appendix B***. * **convGLM/betasGLMData/LMRM/[subjID]\_[model\_name].mat** are files in MATLAB format that contain the betas for each subject for a range of different convolutional GLMs that have been applied to the data (for details of the different models, look in ruesseler-eeg-analysis for: *run\_convolutional\_GLM\_for\_all\_subjects.m*). The naming conventions for these variables are similarly given in ***Appendix C***. 3. conventionalEEG analysis * **conventionalEEGAnalysis/LMRM/[epoching\_type]\_[subjID].mat** EEG data that have been epoched into trials, either locked to trial start or response, and with/without CSD transform applied (for the different types of epoching, look in ruesseler-eeg-analysis for: *all\_subjects\_create\_single\_trial\_data.m*). The naming conventions for these variables are similarly given in ***Appendix D***. * Note that the folder *averageReference* is intentionally empty, as we only include data that has been re-referenced to a left mastoid/right mastoid reference in this repository (hence the 'LMRM' naming convention throughout). 4. Raw data -- ***removed from this repository.*** * Please note: the *raw* data before conversion to SPM format have been removed from this repository, as Dryad has an upper limit of 300GB per repository. Most analyses should instead be possible with the "lightly preprocessed" data (see point 1), and certainly all analyses that were included in the paper. Please contact us directly if you think you need access to the *raw* data (\~560GB). * Training: folder for each subject with stim and behavioural folders * Experiment: folder for each subject and subfolders for stim (MATLAB format), behaviour (MATLAB), eeg (Curry format), eye (Eyelink) **Maria Ruesseler ([maria.ruesseler@gmail.com](mailto:maria.ruesseler@gmail.com)) and Laurence Hunt ([laurence.hunt@psy.ox.ac.uk](mailto:laurence.hunt@psy.ox.ac.uk))** *** ## Appendix A: Structure of behavioural data files The following variables are stored in the matlab files: **preprocessedData/behaviour/behav\_data\_all\_subjs\_all3.mat** and **preprocessedData/behaviour/behav\_data\_all\_subjs\_allVertical.mat** ### "All\_responses" variable *all\_responses* is a large matrix of *all responses made by allsubjects* \- useful for plotting psychometric functions etc: 1 = points won on current trial or for current response (correct = +3, incorrect = -3, false alarm = -1.5, missed trial = -1.5) 2 = reaction time in secs 3 = choice: 0 left, 1 right 4 = current (mean) coherence of dots 5 = choice: correct 1, incorrect 0 6 = frame on which response occured (for *missed* responses: 500ms after the end of response period) 7 = flag for *type* of response: * 0: incorrect response during coherent motion, * 1: for correct response during coherent motion, * 2: response during incoherent motion, * 3: missed response to coherent motion 8 = total number of trials per block 9 = block ID (which of 4 blocks was currently being completed) * 1: frequent and short response periods * 2: frequent and long response periods * 3: rare and short response periods * 4: rare and long response periods 10 = session id (which of 6 sessions (each session consisted of 4 blocks)) 11 = subject number (running number, starting with 1, used for indexing) 12 = subject ID. Corresponds to *subject ID* column in **participantInfo.xlsx** ### "Streams" variables Variables ending in *streams* are cell arrays indexed with {*subject,session*}(:,*block*). (Note that *subject* here = running subject number (i.e. column 11 in *all\_responses*)) * *stim\_streams:* the actual coherence that participants saw on each frame * *stim\_streams\_org:* what was created before the experimental session-- compare to *stim\_streams*, below * *stim\_streams*: trial periods have been filled with noise after a response is made and the participant detected a trial (and thus contain the actual coherence the participant was exposed to) * *mean\_stim\_streams:* has the mean coherence with which the stimulus was created (0 for baseline periods, 0.3,0.4,0.5 for trials) * *mean\_stim\_streams\_org:* same distinction as for *stim\_streams* * *noise\_streams:* a stream of coherences generated with a mean coherence of 0 over the whole block (used to fill up remaining trial time during the experiment) * *trigger\_streams:* stream of triggers that were attempted to be sent at each frame for EEG recording (not relevant for behavioural analysis) n.b. for all *streams* variables (except *trigger\_streams*): values >1 are set to 1 and values <-1 are set to -1 (as motion coherence can't be greater(smaller) than 1 (-1). Note that stimulus was presented at 100Hz, in blocks of 5min --> \~30,000 frames/block. *** ## Appendix B: Structure of files with EEG data matched to stimulus stream The following two variables are stored in the files **convGLM/matchedEegData/LMRM/[subjID]\_EEGdat.mat:** * *EEGdat{sessionID}{blockID}*: each of these cells contains a channels\*time matrix of EEG data, after the triggers have been matched so that the EEG data corresponds to the same samples in the stimulus streams * *badSamples{sessionID}{blockID}*: each of these cells contains a channels\*time logical index of whether the channel is marked as **bad** in preprocessing (1) or not (0) *** ## Appendix C: Structure of files with betas from convolutional GLM The following variables are stored in the files **convGLM/betasGLMData/LMRM/[subjID]\_[model\_name].mat:** * betas\_subject{regressorNumber}: each of these cells contains a four-dimensional matrix with regression coefficients from the corresponding model fit: dimensions nChannels\*nPeriEventTimepoints\*nSessions\*nBlocks. The ordering of the betas is given by *continuous\_RDK\_set\_options*, which is called by *run\_convolutional\_GLM\_for\_all\_subjects.m* in *ruesseler-eeg-analysis* * chanlabels{channelNumber}: each of these cells contains the label for each of the EEG channels, using 10-20 convention *** ## Appendix D: Structure of files with conventionally epoched EEG data The following variables are stored in the files **conventionalEEGAnalysis/LMRM/[epoching\_type]\_[subjID].mat** * dataAppend: a structure containing epoched data, stored in *FieldTrip* format, for exploratory epoch-based analyses. For details of FieldTrip format visit https://www.fieldtriptoolbox.org 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
URL https://datadryad.org/stash/dataset/doi:10.5061/dryad.02v6wwq6b
 
Title Human behavioural and eye-tracking data from inference task with targeted memory reactivation 
Description Raw behavioural data is available for 32 participants in .mat (MATLAB) files. Raw eye-tracking data is available for 30 participants in .edf (EyeLink Data file) and .mat formats. Preprocessed data for 27 (behavioural) and 25 (eye-tracking) participants is available in .mat files. Eye-tracking data includes gaze position and pupillometry data for both eyes recorded at 1000Hz. 
Type Of Material Database/Collection of data 
Year Produced 2024 
Provided To Others? Yes  
URL https://data.mrc.ox.ac.uk/data-set/human-behavioural-and-eye-tracking-data-inference-task-targeted-m...