CPNS LabUniversity of Exeter

A field guide for new BSc and MSc students

What is computational psychiatry?

A person reports what they feel. We can measure how they behave and how their brain responds. A computational model helps us ask what hidden processes might connect those observations.

Read straight through in about 20 minutes, or use the chapter list to dip in. No equations are required to begin.

THE CENTRAL QUESTION
01
ObserveSymptoms, choices, EEG and MEG
02
ExplainA model proposes how signals arise
03
TestCompare predictions with new data

Every arrow is a research question. The model gives us a way to make each one explicit.

01 / THE QUESTION

Why put a model between a symptom and a brain?

People with the same diagnosis may have different histories, symptoms and responses to treatment. Even the same symptom can have several plausible causes.

Imagine two people who both report poor concentration. For one, disrupted sleep may be central. For the other, altered responses to reward or uncertainty may matter more. Their experiences are real in both cases. A symptom score alone cannot tell us which account is right, so we need measurements and competing explanations.

Our question is often: what changed in the system that could have produced this observation?

Computational psychiatry makes explanations precise enough to simulate and test. The field includes cognitive tasks, reinforcement learning, statistics and machine learning. In CPNS, a major thread is mechanistic modelling of brain dynamics: we combine EEG or MEG with models of circuits, synapses and receptors. We also study how similar inference principles can guide intelligent agents.

DESCRIPTIVE QUESTION

Can a pattern distinguish groups?

Find a difference in a signal, or test whether a measured feature predicts an outcome in new people.

Example: does a spectral feature help predict treatment response?
GENERATIVE QUESTION

What could produce the pattern?

Specify hidden states and processes, generate predicted data, and fit the model to actual observations.

Example: which circuit parameters could account for the spectrum?

Both approaches are useful. A generative parameter is an inference under a particular model, not a direct measurement of an individual receptor or proof of causation.

02 / INFERENCE

The brain has to infer what caused its sensations

Sensory data are incomplete and noisy. We bring expectations to them, then update those expectations when evidence arrives.

Suppose you hear a faint tone in a noisy room. Whether a tone is probably present depends on how often tones occur, how often you hear a real one and how often noise sounds like one. Adjust those three ingredients below.

EXPERIMENT 01

Did you hear a tone?

A small, exact Bayesian example. “Heard a tone” is the observation; “tone really present” is the hidden state.

AFTER YOU HEAR A TONE

63%

Chance a tone was really there, given this simple model.

24 genuine detections ÷ (24 genuine + 14 false alarms) ≈ 63 in 100

Try making tones rare while keeping hearing accuracy high. A convincing sound can still be a false alarm. This exercise shows how prior probability and evidence reliability interact; it is not a model of hallucinations.

Predictive coding is a useful theoretical framework. Specific mappings from prediction errors to cell populations, oscillations or psychiatric symptoms remain hypotheses that experiments must test.

03 / OBSERVATIONS

What can we actually measure?

EEG records electrical potential at the scalp. MEG records magnetic fields produced by neural currents. Both track changes on a millisecond scale, but neither reads out a receptor directly.

We collect brain signals during rest, tasks, sleep or controlled pharmacological studies. Before interpreting them, we check timing, noisy channels and artefacts such as blinks or muscle activity. We can then examine event-related responses, frequency spectra and relationships between regions.

1ExperimentChoose an observation that can distinguish hypotheses.
2Clean dataInspect artefacts, trials and recording quality.
3DescribeLook at responses, rhythms and connections.
4ExplainFit candidate models and check predictions.

Three meanings of “connection”

Anatomical

Physical pathways between regions, often studied with structural MRI methods.

Functional

A statistical relationship between measured signals. Correlation alone does not give direction or mechanism.

Effective

A directed influence estimated within a specified model. Its interpretation depends on the model and data.

One signal can reflect many underlying processes. That is why the link from EEG/MEG to synapses requires a forward model of how proposed neural activity would generate the observed data, and careful checks for alternative explanations.

Want to understand a spectrum first?See waves become frequencies in the Fourier explainer
04 / MODELS

Try the central move: fit a model to data

A forward model turns chosen parameters into predicted observations. Inversion works backwards: which settings make the model's prediction resemble what we recorded?

The curves below are synthetic frequency spectra. Move the sliders until the teal model curve fits the dark observed curve. The toy model has a peak frequency, width and amplitude. These are visual properties of a curve, not receptor estimates or a DCM analysis.

EXPERIMENT 02

Fit the hidden spectrum

Observed data stay fixed while you change the model. Try a narrow peak, then a broad one.

Observed Your model
Observed and predicted synthetic spectra Two curves show power against frequency from 2 to 30 hertz. The model curve changes with the controls. 2122230 Hzrelative power

Adjust the sliders to improve the fit.

Curve mismatch—Smaller is better, on this illustrative scale.

A good fit does not prove that this is the process that generated a real brain signal. We also ask whether another model fits, whether parameters are identifiable, and whether predictions hold for new data.

What changes in a real CPNS model?

Instead of directly adjusting a peak, a neural mass model represents interacting populations of cells. Synaptic coupling, receptor-related time constants and transmission delays alter the modelled activity. A measurement model then predicts what EEG or MEG would look like. Dynamic Causal Modelling (DCM) is a framework for fitting and comparing such generative models.

01
Build the forward model

Write down the candidate circuit, its dynamics, inputs and observation process.

02
Invert it with Bayesian methods

Estimate probable parameter values and uncertainty. Variational Laplace is one approximation we develop and use.

03
Check and compare

Inspect whether simulated data resemble held-out or observed features, and compare plausible model variants.

04
Study the group

Use hierarchical methods such as Parametric Empirical Bayes (PEB) to ask how parameters vary with a group, symptom or intervention.

Show the compact mathematical version

Let θ denote hidden model parameters, u the experimental input and y the observation. A forward model predicts y ≈ g(θ, u) + ε. Bayesian inversion combines the likelihood of the observed data under those predictions with prior beliefs about plausible parameters: p(θ | y) ∝ p(y | θ) p(θ). Variational methods approximate that posterior and can compare candidate models through an evidence bound.

The numerical curve exercise above is only an analogy. Its peak, width and height do not implement neural mass dynamics or variational inversion.

Go deeper into the actual machineryCPNS modelling methodsInteractive PEB explainer
05 / RESEARCH

What has this approach taught us?

The lab's studies use the same logic on different questions: define a clinical contrast, record a signal, fit a mechanistic model, then ask what the parameter estimates can and cannot support.

DEPRESSION / PHARMACOLOGYPublished study · 2024

What changes in the brain during ketamine treatment?

Resting EEG was collected before and during a ketamine infusion in people with major depression. A model of frontal and parietal circuits found increased AMPA-mediated connectivity from parietal to frontal cortex and a shorter frontal GABAA time constant. Both parameter changes were associated with the degree of symptom change at 24 hours. The tested NMDA time-constant change did not survive correction for multiple comparisons.

Take away: the drug's known molecular target and the modelled brain changes associated with outcome need not be the same parameter. These associations are research findings, not an established individual treatment test.

Read the ketamine paper
SCHIZOPHRENIA / CIRCUITSPublished study · 2025

Which circuit explanations fit altered MEG rhythms?

A thalamo-cortical model was fit to MEG data from people with schizophrenia and controls. Within the selected model, the group comparison found stronger NMDA-mediated self-excitation of superficial pyramidal cells and weaker GABAB-mediated inhibition onto those cells. The authors also explored whether simulated adjustments to connections could bring modelled spectra closer to control patterns.

Take away: modelling turns a broad “dysconnectivity” idea into specific, testable candidate mechanisms. A simulated restoration is a hypothesis for further experiments, not evidence that a treatment will work.

Read the schizophrenia paper
SLEEP / DEVELOPMENTPublished study · 2026

Can sleep reveal mechanisms linked to psychiatric risk?

Sleep and wake EEG from children with 22q11.2 deletion syndrome and their siblings were fit with a conductance-based thalamo-cortical model. Changing NMDA-related model gain improved the match between group spectra, particularly during non-REM sleep. This provides a candidate circuit account of the observed sleep differences in a group with elevated psychiatric risk.

Take away: sleep offers a repeated window onto brain dynamics. Model perturbations can prioritise mechanisms, but independent experimental validation is still needed.

Read the sleep paper
THE THEORY BEHIND THE PROGRAMME

For a broad account of predictive coding, neural circuits and mental disorders, start with Shaw, Sumner and Berndt's review in Frontiers in Psychiatry. It is a framework for asking mechanistic questions, not a claim that one theory already explains every disorder.

06 / INTERPRETATION

What is the promise, and what would count as progress?

The ambition is to connect a person's experience to testable biological hypotheses and, eventually, better choices about intervention. The route from a fitted model to a useful clinical tool is long.

NOW

Explain a signal

Can a model reproduce data and point to plausible circuit processes?

NEXT

Test a prediction

Does a proposed mechanism survive a new task, cohort or pharmacological manipulation?

LATER

Help a decision

Can a validated measure improve an individual treatment choice beyond existing care?

Three checks we keep returning to

  • Model dependence. Could different circuits explain the same EEG or MEG pattern? What happens when we compare alternatives?
  • Generalisation. Does the finding hold across people, recording sessions, tasks and independent cohorts?
  • Clinical meaning. Does it predict an outcome in a way that is reliable and useful for someone outside the original study?

This is why good computational psychiatry needs careful experiments, strong data quality, uncertainty estimates and honest reporting of null or ambiguous results. Models make assumptions visible so we can improve them.

07 / YOUR ROUTE IN

Where should a new lab student start?

Pick a question you care about, then learn just enough of the toolkit to investigate it. You do not need to master the full maths before collecting or thinking clearly about data.

IF YOU ARE NEW TO THIS

A BSc starting route

  1. Try the tone experiment and explain how changing the prior alters the answer.
  2. Open the Fourier and Bayes visual explainers.
  3. Read one case above. Write down its question, observation and proposed mechanism.
  4. Think of an alternative explanation that the same data might allow.
IF YOU ALREADY ANALYSE DATA

An MSc starting route

  1. Fit the toy spectrum, then ask what the curve cannot identify.
  2. Explore predictive coding and the PEB group model.
  3. Read a methods section from one case and sketch its forward model and comparison.
  4. Propose a posterior predictive check, a competing model or a held-out test.

A useful question to bring to a meeting

“What observation would make us change our mind about this model?”