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.
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.
TAKE THIS FURTHER
Prediction error and precision
A prediction is compared with incoming input. Precision describes how reliable an error signal is thought to be, and therefore how much it should influence an update. Predictive coding formalises that recurrent exchange across levels of a model.
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.
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
Adjust the sliders to improve the fit.
Curve mismatch—Smaller is better, on this illustrative scale.
The hidden curve was generated with a 12 Hz peak, width 2.4 and height 0.9. A close fit recovers properties of this chosen model.
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.
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.
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.
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.
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
Try the tone experiment and explain how changing the prior alters the answer.