# The study's entry recipe: `tvbo run Bayesian_tvboptim.yaml`. Its directory is the study root.
tvbo_class: tvbo:SimulationStudy

citekey: Bayesian_tvboptim
title: "Recovering stimulus amplitude and excitability from one noisy recording"
label: "Bayesian inference of stimulation and excitability: three priors on one degenerate ridge"
description: >-
  Recovers both the amplitude of a 1 ms pulse and the excitability I of the Generic2dOscillator it
  drives, from a single noisy recording of V, by NUTS/MCMC. The two parameters trade off, so the
  posterior is a ridge rather than a point, and the three declared prior scenarios differ in nothing
  but how tightly they constrain each parameter. The recording is declared, not synthesised at run
  time: it is the forward run plus Gaussian measurement noise at a fixed seed, so every scenario is
  fitted to the same numbers and this recipe reproduces them.

experiments:
    - tvbo:experiment/Stimulation_Bayesian_Inference

figures:
    - name: bayesian_recovery
      label: "Bayesian recovery of stimulus amplitude and excitability"
      description: >-
        One noisy recording, three prior scenarios, and the degeneracy ridge that makes a point
        estimate misleading here.
      layout: |
          aaa
          aaa
          bcd
          bcd
      width: 180.0
      height: 105.0
      font_size: 7.0
      panel_numbers: true
      panels:
          a:
              kind: cartesian
              label: "The recording"
              description: >-
                The noiseless forward run at the true parameters (line) and the noisy recording the
                inference is given (points) — one trace, 50 samples. The rules mark the 1 ms pulse.
              layers:
                  - used: {experiment: 8, output: integration__recorded_ts}
                    mark: line
                    label: "Ground truth"
                    encoding: {x: time}
                    style: {color: "#003754", opts: {linewidth: 1.2}}
                  - used: {experiment: 8, output: integration__observed_ts}
                    mark: scatter
                    label: "Observed (noisy)"
                    encoding: {x: time}
                    style: {color: "#000000", opts: {s: 8, zorder: 3}}
              xlabel: "Time [ms]"
              ylabel: "V [a.u.]"
              legend: "upper right"
              xticks: [0, 50, 100, 150]
              rules:
                  - {orientation: vertical, at: [10.0]}
                  - {orientation: vertical, at: [11.0]}

          b:
              kind: cartesian
              label: "A — no hypothesis"
              description: >-
                Wide priors on both parameters. The draws fall on a line, not in a blob: a weak pulse
                into an excitable node and a strong pulse into a quiet one fit this recording equally
                well, and one trace cannot separate them. The rules cross at the truth.
              layers:
                  - used: {experiment: 8, output: inference__scenario_A__posterior__Generic2dOscillator.I}
                    mark: scatter
                    encoding: {x: inference__scenario_A__posterior__stimulus.amplitude}
                    style: {color: "#0a5170", opacity: 0.2, opts: {s: 3}}
              xlabel: "Stimulus amplitude"
              ylabel: "Excitability I"
              xlim: [0.18, 0.62]
              ylim: [-0.12, 0.42]
              xticks: [0.2, 0.3, 0.4, 0.5, 0.6]
              yticks: [-0.1, 0.0, 0.1, 0.2, 0.3, 0.4]
              rules:
                  - {orientation: vertical, at: [0.4]}
                  - {orientation: horizontal, at: [0.1]}

          c:
              kind: cartesian
              label: "B — tight amplitude prior"
              description: >-
                Pinning the amplitude does not shrink the posterior towards the truth: it slides along
                the same ridge, and the excitability takes up what the amplitude is no longer allowed
                to explain.
              layers:
                  - used: {experiment: 8, output: inference__scenario_B__posterior__Generic2dOscillator.I}
                    mark: scatter
                    encoding: {x: inference__scenario_B__posterior__stimulus.amplitude}
                    style: {color: "#3E8E68", opacity: 0.2, opts: {s: 3}}
              xlabel: "Stimulus amplitude"
              ylabel: ""
              xlim: [0.18, 0.62]
              ylim: [-0.12, 0.42]
              xticks: [0.2, 0.3, 0.4, 0.5, 0.6]
              yticks: [-0.1, 0.0, 0.1, 0.2, 0.3, 0.4]
              hide_yticklabels: true
              rules:
                  - {orientation: vertical, at: [0.4]}
                  - {orientation: horizontal, at: [0.1]}

          d:
              kind: cartesian
              label: "C — tight excitability prior"
              description: "The mirror image: pinning I moves the mass the other way along the ridge."
              layers:
                  - used: {experiment: 8, output: inference__scenario_C__posterior__Generic2dOscillator.I}
                    mark: scatter
                    encoding: {x: inference__scenario_C__posterior__stimulus.amplitude}
                    style: {color: "#d98a00", opacity: 0.2, opts: {s: 3}}
              xlabel: "Stimulus amplitude"
              ylabel: ""
              xlim: [0.18, 0.62]
              ylim: [-0.12, 0.42]
              xticks: [0.2, 0.3, 0.4, 0.5, 0.6]
              yticks: [-0.1, 0.0, 0.1, 0.2, 0.3, 0.4]
              hide_yticklabels: true
              rules:
                  - {orientation: vertical, at: [0.4]}
                  - {orientation: horizontal, at: [0.1]}