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Merged
micahwoodard merged 2 commits into from
Sep 15, 2026
Merged

Slow anti-bias interventions for stage final and graduated #192

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fd088e2
slows bias intervention to 20 trials for final and graduated
micahwoodard Sep 15, 2026
12d3b32
fixes bias window length
micahwoodard Sep 15, 2026
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4 changes: 2 additions & 2 deletions schema/coupled_baiting.json
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Original file line number Diff line number Diff line change
Expand Up @@ -589,7 +589,7 @@
"upper": 0.5,
"lower": 0.0
},
"intervention_interval": 10,
"intervention_interval": 20,
"maximum_water_corrections": 2,
"bias_window_length": 200,
"lickspout_offset_delta": 0.05,
Expand Down Expand Up @@ -703,7 +703,7 @@
"upper": 0.5,
"lower": 0.0
},
"intervention_interval": 10,
"intervention_interval": 20,
"maximum_water_corrections": 2,
"bias_window_length": 200,
"lickspout_offset_delta": 0.05,
Expand Down
4 changes: 2 additions & 2 deletions schema/uncoupled.json
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Original file line number Diff line number Diff line change
Expand Up @@ -571,7 +571,7 @@
"upper": 0.5,
"lower": 0.0
},
"intervention_interval": 10,
"intervention_interval": 20,
"maximum_water_corrections": 2,
"bias_window_length": 200,
"lickspout_offset_delta": 0.05,
Expand Down Expand Up @@ -665,7 +665,7 @@
"upper": 0.5,
"lower": 0.0
},
"intervention_interval": 10,
"intervention_interval": 20,
"maximum_water_corrections": 2,
"bias_window_length": 200,
"lickspout_offset_delta": 0.05,
Expand Down
4 changes: 2 additions & 2 deletions schema/uncoupled_baiting.json
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Original file line number Diff line number Diff line change
Expand Up @@ -571,7 +571,7 @@
"upper": 0.5,
"lower": 0.0
},
"intervention_interval": 10,
"intervention_interval": 20,
"maximum_water_corrections": 2,
"bias_window_length": 200,
"lickspout_offset_delta": 0.05,
Expand Down Expand Up @@ -665,7 +665,7 @@
"upper": 0.5,
"lower": 0.0
},
"intervention_interval": 10,
"intervention_interval": 20,
"maximum_water_corrections": 2,
"bias_window_length": 200,
"lickspout_offset_delta": 0.05,
Expand Down
9 changes: 8 additions & 1 deletion ...aind_behavior_dynamic_foraging/task_logic/trial_generators/block_based_trial_generator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -192,7 +192,14 @@ def update(self, outcome: TrialOutcome | str):
# trial ignored so current baiting state retained
pass

self.bias = calculate_bias(outcomes=self.outcome_history)
self.bias = calculate_bias(
outcomes=self.outcome_history,
outcome_window_length=(
200
if not self.spec.bias_intervention_parameters
else self.spec.bias_intervention_parameters.bias_window_length
),
)

def next(self) -> Trial | None:
"""Generates the next trial in the session.
Expand Down
8 changes: 5 additions & 3 deletions src/aind_behavior_dynamic_foraging/task_logic/utils/calculate_bias.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
logger = logging.getLogger(__name__)


def calculate_bias(outcomes: List[TrialOutcome]) -> float:
def calculate_bias(outcomes: List[TrialOutcome], outcome_window_length: int = 200) -> float:
"""Estimate the side bias of an animal using logistic regression on recent trial history.

Fits a Su2022-style logistic regression model using rewarded and unrewarded choice
Expand All @@ -20,7 +20,9 @@ def calculate_bias(outcomes: List[TrialOutcome]) -> float:
----------
outcomes : List[TrialOutcome]
List of trial outcomes. Auto-response and ignored trials are excluded.
Only the most recent 200 trials are used.
Only the most recent `outcome_window_length` trials are used.
outcome_window_length : int
Number of recent trials to consider for bias calculation.

Returns
-------
Expand All @@ -34,7 +36,7 @@ def calculate_bias(outcomes: List[TrialOutcome]) -> float:
trial_window_length = 5
regularization_strength = 10

outcomes = outcomes[-200:]
outcomes = outcomes[-outcome_window_length:]

# exclude auto response and ignored trials
filtered = [t for t in outcomes if t.is_right_choice is not None]
Expand Down
4 changes: 2 additions & 2 deletions ...foraging_curricula/src/aind_behavior_dynamic_foraging_curricula/coupled_baiting/stages.py
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Original file line number Diff line number Diff line change
Expand Up @@ -336,7 +336,7 @@ def make_s_stage_final():
autowater_parameters=None,
bias_intervention_parameters=BiasInterventionParameters(
threshold=BiasThreshold(upper=0.5, lower=0.0),
intervention_interval=10,
intervention_interval=20,
maximum_water_corrections=2,
bias_window_length=200,
lickspout_offset_delta=0.05,
Expand Down Expand Up @@ -387,7 +387,7 @@ def make_s_stage_graduated():
autowater_parameters=None,
bias_intervention_parameters=BiasInterventionParameters(
threshold=BiasThreshold(upper=0.5, lower=0.0),
intervention_interval=10,
intervention_interval=20,
maximum_water_corrections=2,
bias_window_length=200,
lickspout_offset_delta=0.05,
Expand Down
4 changes: 2 additions & 2 deletions ...namic_foraging_curricula/src/aind_behavior_dynamic_foraging_curricula/uncoupled/stages.py
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Original file line number Diff line number Diff line change
Expand Up @@ -333,7 +333,7 @@ def make_s_stage_final():
reward_consumption_duration=3.0,
bias_intervention_parameters=BiasInterventionParameters(
threshold=BiasThreshold(upper=0.5, lower=0.0),
intervention_interval=10,
intervention_interval=20,
maximum_water_corrections=2,
bias_window_length=200,
lickspout_offset_delta=0.05,
Expand All @@ -357,7 +357,7 @@ def make_s_stage_graduated():
autowater_parameters=None,
bias_intervention_parameters=BiasInterventionParameters(
threshold=BiasThreshold(upper=0.5, lower=0.0),
intervention_interval=10,
intervention_interval=20,
maximum_water_corrections=2,
bias_window_length=200,
lickspout_offset_delta=0.05,
Expand Down
4 changes: 2 additions & 2 deletions ...raging_curricula/src/aind_behavior_dynamic_foraging_curricula/uncoupled_baiting/stages.py
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Original file line number Diff line number Diff line change
Expand Up @@ -333,7 +333,7 @@ def make_s_stage_final():
autowater_parameters=None,
bias_intervention_parameters=BiasInterventionParameters(
threshold=BiasThreshold(upper=0.5, lower=0.0),
intervention_interval=10,
intervention_interval=20,
maximum_water_corrections=2,
bias_window_length=200,
lickspout_offset_delta=0.05,
Expand Down Expand Up @@ -377,7 +377,7 @@ def make_s_stage_graduated():
autowater_parameters=None,
bias_intervention_parameters=BiasInterventionParameters(
threshold=BiasThreshold(upper=0.5, lower=0.0),
intervention_interval=10,
intervention_interval=20,
maximum_water_corrections=2,
bias_window_length=200,
lickspout_offset_delta=0.05,
Expand Down