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Bias correction #79

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0c9cbcd
adds bias intervention algorithm and test
micahwoodard May 3, 2026
f4adb53
specify delta
micahwoodard May 3, 2026
a8f4ff2
fixes comments and descriptions
micahwoodard May 3, 2026
dc0d022
regenerates
micahwoodard May 3, 2026
53561a2
Update src/aind_behavior_dynamic_foraging/task_logic/trial_generators…
micahwoodard May 3, 2026
4118245
regenerates
micahwoodard May 3, 2026
b4a0660
lints
micahwoodard May 3, 2026
65d65b3
rewrites bias calculation
micahwoodard May 3, 2026
46c741f
removes print
micahwoodard May 3, 2026
ec58e76
add metrics function
micahwoodard May 27, 2026
1376921
merges with main
micahwoodard May 27, 2026
a07b086
adds metrics function
micahwoodard May 28, 2026
e54ac89
lints
micahwoodard May 28, 2026
5a98537
integrates metrics into bonsai workflow
micahwoodard May 29, 2026
670b6f9
moves metrics update
micahwoodard May 29, 2026
46c0e06
adds TrialMetrics software event
micahwoodard May 29, 2026
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1 change: 1 addition & 0 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@ readme = {file = "README.md", content-type = "text/markdown"}
dependencies = [
"aind_behavior_services>=0.13.5",
"pydantic-settings",
"scikit-learn>=1.8.0",
]

[tool.uv.workspace]
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212 changes: 207 additions & 5 deletions schema/aind_behavior_dynamic_foraging.json
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Original file line number Diff line number Diff line change
Expand Up @@ -313,6 +313,56 @@
"type": "object",
"x-sgen-typename": "AllenNeuralDynamics.AindManipulator.AindManipulatorCalibration"
},
"AntiBiasParameters": {
"properties": {
"threshold": {
"$ref": "#/$defs/BiasThreshold",
"default": {
"upper": 0.7,
"lower": 0.3
},
"description": "Thresholds for bias correction intervention."
},
"intervention_interval": {
"default": 10,
"description": "Trials between bias intervention.",
"minimum": 0,
"title": "Intervention Interval",
"type": "integer"
},
"maximum_water_corrections": {
"default": 5,
"description": "Number of water correction to attempt.",
"minimum": 0,
"title": "Maximum Water Corrections",
"type": "integer"
},
"reward_fraction": {
"default": 0.8,
"description": "Fraction of full reward volume delivered during auto water (0=none, 1=full).",
"maximum": 1,
"minimum": 0,
"title": "Reward Fraction",
"type": "number"
},
"bias_window_length": {
"default": 200,
"description": "Trials to calculate bias over.",
"minimum": 0,
"title": "Bias Window Length",
"type": "integer"
},
"lickspout_offset_delta": {
"default": 0.05,
"description": "Distance (mm) to move the stage spouts by. This is a relative distance to the current value, not absolute.",
"minimum": 0,
"title": "Lickspout Offset Delta",
"type": "number"
}
},
"title": "AntiBiasParameters",
"type": "object"
},
"AuditorySecondaryReinforcer": {
"description": "Represents an auditory secondary reinforcer.",
"properties": {
Expand Down Expand Up @@ -511,7 +561,7 @@
"min_unrewarded_trials": 3,
"reward_fraction": 0.8
},
"description": "Auto water settings. If set, free water is delivered when the animal exceeds the ignored or unrewarded trial thresholds.",
"description": "Autowater settings. If set, free water is delivered when the animal exceeds the ignored or unrewarded trial thresholds.",
"oneOf": [
{
"$ref": "#/$defs/AutoWaterParameters"
Expand All @@ -521,6 +571,28 @@
}
]
},
"antibias_parameters": {
"default": {
"threshold": {
"lower": 0.3,
"upper": 0.7
},
"intervention_interval": 10,
"maximum_water_corrections": 5,
"reward_fraction": 0.8,
"bias_window_length": 200,
"lickspout_offset_delta": 0.05
},
"description": "Antibias settings. If set, trial generator will give water and move lickspouts to combat bias.",
"oneOf": [
{
"$ref": "#/$defs/AntiBiasParameters"
},
{
"type": "null"
}
]
},
"is_baiting": {
"default": false,
"description": "Whether uncollected rewards carry over to the next trial.",
Expand Down Expand Up @@ -656,6 +728,28 @@
"type": "object",
"x-sgen-typename": "AllenNeuralDynamics.AindBehaviorServices.Distributions.BetaDistributionParameters"
},
"BiasThreshold": {
"properties": {
"upper": {
"default": 0.7,
"description": "Absolute value of the upper bias threshold.",
"maximum": 1,
"minimum": 0,
"title": "Upper",
"type": "number"
},
"lower": {
"default": 0.3,
"description": "Absolute value of the lower bias threshold.",
"maximum": 1,
"minimum": 0,
"title": "Lower",
"type": "number"
}
},
"title": "BiasThreshold",
"type": "object"
},
"BinomialDistribution": {
"description": "A binomial probability distribution.\n\nModels the number of successes in a fixed number of independent\nBernoulli trials with constant success probability.",
"properties": {
Expand Down Expand Up @@ -811,7 +905,7 @@
"min_unrewarded_trials": 3,
"reward_fraction": 0.8
},
"description": "Auto water settings. If set, free water is delivered when the animal exceeds the ignored or unrewarded trial thresholds.",
"description": "Autowater settings. If set, free water is delivered when the animal exceeds the ignored or unrewarded trial thresholds.",
"oneOf": [
{
"$ref": "#/$defs/AutoWaterParameters"
Expand All @@ -821,6 +915,28 @@
}
]
},
"antibias_parameters": {
"default": {
"threshold": {
"lower": 0.3,
"upper": 0.7
},
"intervention_interval": 10,
"maximum_water_corrections": 5,
"reward_fraction": 0.8,
"bias_window_length": 200,
"lickspout_offset_delta": 0.05
},
"description": "Antibias settings. If set, trial generator will give water and move lickspouts to combat bias.",
"oneOf": [
{
"$ref": "#/$defs/AntiBiasParameters"
},
{
"type": "null"
}
]
},
"is_baiting": {
"default": false,
"description": "Whether uncollected rewards carry over to the next trial.",
Expand Down Expand Up @@ -1077,7 +1193,7 @@
"min_unrewarded_trials": 3,
"reward_fraction": 0.8
},
"description": "Auto water settings. If set, free water is delivered when the animal exceeds the ignored or unrewarded trial thresholds.",
"description": "Autowater settings. If set, free water is delivered when the animal exceeds the ignored or unrewarded trial thresholds.",
"oneOf": [
{
"$ref": "#/$defs/AutoWaterParameters"
Expand All @@ -1087,6 +1203,28 @@
}
]
},
"antibias_parameters": {
"default": {
"threshold": {
"lower": 0.3,
"upper": 0.7
},
"intervention_interval": 10,
"maximum_water_corrections": 5,
"reward_fraction": 0.8,
"bias_window_length": 200,
"lickspout_offset_delta": 0.05
},
"description": "Antibias settings. If set, trial generator will give water and move lickspouts to combat bias.",
"oneOf": [
{
"$ref": "#/$defs/AntiBiasParameters"
},
{
"type": "null"
}
]
},
"is_baiting": {
"default": false,
"description": "Whether uncollected rewards carry over to the next trial.",
Expand Down Expand Up @@ -1266,7 +1404,7 @@
"min_unrewarded_trials": 3,
"reward_fraction": 0.8
},
"description": "Auto water settings. If set, free water is delivered when the animal exceeds the ignored or unrewarded trial thresholds.",
"description": "Autowater settings. If set, free water is delivered when the animal exceeds the ignored or unrewarded trial thresholds.",
"oneOf": [
{
"$ref": "#/$defs/AutoWaterParameters"
Expand All @@ -1276,6 +1414,28 @@
}
]
},
"antibias_parameters": {
"default": {
"threshold": {
"lower": 0.3,
"upper": 0.7
},
"intervention_interval": 10,
"maximum_water_corrections": 5,
"reward_fraction": 0.8,
"bias_window_length": 200,
"lickspout_offset_delta": 0.05
},
"description": "Antibias settings. If set, trial generator will give water and move lickspouts to combat bias.",
"oneOf": [
{
"$ref": "#/$defs/AntiBiasParameters"
},
{
"type": "null"
}
]
},
"is_baiting": {
"const": true,
"default": true,
Expand Down Expand Up @@ -3403,6 +3563,26 @@
}
]
},
"TrialMetrics": {
"description": "Represents metrics of session",
"properties": {
"bias": {
"default": null,
"description": "Bias of session. Negative values correspond to left bias, positive right.",
"oneOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"title": "Bias"
}
},
"title": "TrialMetrics",
"type": "object"
},
"TrialOutcome": {
"description": "Represents the outcome of a single trial.",
"properties": {
Expand Down Expand Up @@ -3586,7 +3766,7 @@
"min_unrewarded_trials": 3,
"reward_fraction": 0.8
},
"description": "Auto water settings. If set, free water is delivered when the animal exceeds the ignored or unrewarded trial thresholds.",
"description": "Autowater settings. If set, free water is delivered when the animal exceeds the ignored or unrewarded trial thresholds.",
"oneOf": [
{
"$ref": "#/$defs/AutoWaterParameters"
Expand All @@ -3596,6 +3776,28 @@
}
]
},
"antibias_parameters": {
"default": {
"threshold": {
"lower": 0.3,
"upper": 0.7
},
"intervention_interval": 10,
"maximum_water_corrections": 5,
"reward_fraction": 0.8,
"bias_window_length": 200,
"lickspout_offset_delta": 0.05
},
"description": "Antibias settings. If set, trial generator will give water and move lickspouts to combat bias.",
"oneOf": [
{
"$ref": "#/$defs/AntiBiasParameters"
},
{
"type": "null"
}
]
},
"is_baiting": {
"default": false,
"description": "Whether uncollected rewards carry over to the next trial.",
Expand Down
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