Archive MaleCNS research sources, provenance, bibliography and immutable data inventory
This commit is contained in:
Digital Drosophila Archive
+150
@@ -0,0 +1,150 @@
|
||||
{
|
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"CS_A_neuron_idx": [
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"CS_B_neuron_idx": [
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],
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||||
"CS_identity": "engineering split of sorted olfactory annotation_class population",
|
||||
"CS_populations_are_disjoint": true,
|
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"DAN_targets": {
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||||
"appetitive": [
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]
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||||
},
|
||||
"reward_interface": "artificial_unconditioned_signal_interface",
|
||||
"reward_value_is_dopamine_concentration": false
|
||||
}
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||||
+82
@@ -0,0 +1,82 @@
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{
|
||||
"all_passed": true,
|
||||
"controls": [
|
||||
{
|
||||
"checked": 4,
|
||||
"control": "/data/digital-drosophila/models/male-cns-lif/reference-v1/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/models/male-cns-lif/reference-v1"
|
||||
},
|
||||
{
|
||||
"checked": 7,
|
||||
"control": "/data/digital-drosophila/models/male-cns-lif/runtime-v1/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/models/male-cns-lif/runtime-v1"
|
||||
},
|
||||
{
|
||||
"checked": 5,
|
||||
"control": "/data/digital-drosophila/models/male-cns-lif/io-v1/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/models/male-cns-lif/io-v1"
|
||||
},
|
||||
{
|
||||
"checked": 73,
|
||||
"control": "/data/digital-drosophila/experiments/phase4c-runtime/manifests/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/experiments/phase4c-runtime"
|
||||
},
|
||||
{
|
||||
"checked": 43,
|
||||
"control": "/data/digital-drosophila/experiments/phase4d-io/manifests/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/experiments/phase4d-io"
|
||||
},
|
||||
{
|
||||
"checked": 166,
|
||||
"control": "/data/digital-drosophila/experiments/phase4e-visual-calibration/manifests/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/experiments/phase4e-visual-calibration"
|
||||
},
|
||||
{
|
||||
"checked": 15421,
|
||||
"control": "/data/digital-drosophila/experiments/phase4f-retinotopic-vision/manifests/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/experiments/phase4f-retinotopic-vision"
|
||||
},
|
||||
{
|
||||
"checked": 7,
|
||||
"control": "/data/digital-drosophila/models/male-cns-lif/visual-encoder-v1/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/models/male-cns-lif/visual-encoder-v1"
|
||||
},
|
||||
{
|
||||
"checked": 43,
|
||||
"control": "/data/digital-drosophila/experiments/phase4g-frozen-interface/manifests/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/experiments/phase4g-frozen-interface"
|
||||
},
|
||||
{
|
||||
"checked": 9,
|
||||
"control": "/data/digital-drosophila/models/male-cns-lif/frozen-interface-v1/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/models/male-cns-lif/frozen-interface-v1"
|
||||
},
|
||||
{
|
||||
"checked": 4,
|
||||
"control": "/data/digital-drosophila/models/learned/phase4g/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/models/learned/phase4g"
|
||||
}
|
||||
]
|
||||
}
|
||||
+82
@@ -0,0 +1,82 @@
|
||||
{
|
||||
"all_passed": true,
|
||||
"controls": [
|
||||
{
|
||||
"checked": 4,
|
||||
"control": "/data/digital-drosophila/models/male-cns-lif/reference-v1/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/models/male-cns-lif/reference-v1"
|
||||
},
|
||||
{
|
||||
"checked": 7,
|
||||
"control": "/data/digital-drosophila/models/male-cns-lif/runtime-v1/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/models/male-cns-lif/runtime-v1"
|
||||
},
|
||||
{
|
||||
"checked": 5,
|
||||
"control": "/data/digital-drosophila/models/male-cns-lif/io-v1/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/models/male-cns-lif/io-v1"
|
||||
},
|
||||
{
|
||||
"checked": 73,
|
||||
"control": "/data/digital-drosophila/experiments/phase4c-runtime/manifests/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/experiments/phase4c-runtime"
|
||||
},
|
||||
{
|
||||
"checked": 43,
|
||||
"control": "/data/digital-drosophila/experiments/phase4d-io/manifests/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/experiments/phase4d-io"
|
||||
},
|
||||
{
|
||||
"checked": 166,
|
||||
"control": "/data/digital-drosophila/experiments/phase4e-visual-calibration/manifests/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/experiments/phase4e-visual-calibration"
|
||||
},
|
||||
{
|
||||
"checked": 15421,
|
||||
"control": "/data/digital-drosophila/experiments/phase4f-retinotopic-vision/manifests/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/experiments/phase4f-retinotopic-vision"
|
||||
},
|
||||
{
|
||||
"checked": 7,
|
||||
"control": "/data/digital-drosophila/models/male-cns-lif/visual-encoder-v1/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/models/male-cns-lif/visual-encoder-v1"
|
||||
},
|
||||
{
|
||||
"checked": 43,
|
||||
"control": "/data/digital-drosophila/experiments/phase4g-frozen-interface/manifests/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/experiments/phase4g-frozen-interface"
|
||||
},
|
||||
{
|
||||
"checked": 9,
|
||||
"control": "/data/digital-drosophila/models/male-cns-lif/frozen-interface-v1/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/models/male-cns-lif/frozen-interface-v1"
|
||||
},
|
||||
{
|
||||
"checked": 4,
|
||||
"control": "/data/digital-drosophila/models/learned/phase4g/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/models/learned/phase4g"
|
||||
}
|
||||
]
|
||||
}
|
||||
+64
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phase: 4H
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||||
execution:
|
||||
mode: two-stage
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||||
stage1_only_entrypoint: phase4h_audit.py
|
||||
require_stage1_pass_before_conditioning: true
|
||||
|
||||
paths:
|
||||
connectome_root: /data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only
|
||||
model_root: /data/digital-drosophila/models/male-cns-lif/dopamine-plasticity-v1
|
||||
learned_root: /data/digital-drosophila/models/learned/phase4h
|
||||
experiment_root: /data/digital-drosophila/experiments/phase4h-dopamine-plasticity
|
||||
reference_root: /data/digital-drosophila/models/male-cns-lif/reference-v1
|
||||
runtime_root: /data/digital-drosophila/models/male-cns-lif/runtime-v1
|
||||
io_root: /data/digital-drosophila/models/male-cns-lif/io-v1
|
||||
phase4c_root: /data/digital-drosophila/experiments/phase4c-runtime
|
||||
phase4d_root: /data/digital-drosophila/experiments/phase4d-io
|
||||
phase4e_root: /data/digital-drosophila/experiments/phase4e-visual-calibration
|
||||
phase4f_root: /data/digital-drosophila/experiments/phase4f-retinotopic-vision
|
||||
phase4f_model_root: /data/digital-drosophila/models/male-cns-lif/visual-encoder-v1
|
||||
phase4g_root: /data/digital-drosophila/experiments/phase4g-frozen-interface
|
||||
phase4g_model_root: /data/digital-drosophila/models/male-cns-lif/frozen-interface-v1
|
||||
phase4g_learned_root: /data/digital-drosophila/models/learned/phase4g
|
||||
|
||||
expected_graph:
|
||||
neurons: 166700
|
||||
directed_edges: 25582938
|
||||
synaptic_contact_weight_sum: 124177617
|
||||
|
||||
audit:
|
||||
exact_class_values:
|
||||
KC: Kenyon_Cell
|
||||
MBON: MBON
|
||||
DAN: DAN
|
||||
pam_type_prefix: PAM
|
||||
ppl1_type_prefix: PPL1
|
||||
compartment_source_field: annotation_instance
|
||||
compartment_parser: single_parenthesized_substring_verbatim
|
||||
require_exact_compartment_string_match: true
|
||||
candidate_requires_actual_kc_mbon_edge: true
|
||||
candidate_requires_actual_dan_mbon_edge: true
|
||||
candidate_requires_exact_dan_mbon_compartment_match: true
|
||||
do_not_infer_missing_compartment_from_type: true
|
||||
|
||||
plasticity:
|
||||
base_connectome_mode: read_only
|
||||
overlay_equation: effective_weight = base_weight + plastic_delta
|
||||
rule: delta_w = polarity_compartment * eta * D_compartment(t) * eligibility_ij(t)
|
||||
first_version_rule_family: compartment_specific_dopamine_gated_anti_hebbian_depression
|
||||
default_confirmed_compartment_polarity: -1
|
||||
unknown_compartment_policy: exclude_from_plastic_mask
|
||||
pam_ppl1_cluster_valence_policy: prohibited
|
||||
reward_interface_interpretation: artificial_unconditioned_signal_not_dopamine_concentration
|
||||
polarity_provenance:
|
||||
- https://pubmed.ncbi.nlm.nih.gov/26637800/
|
||||
- https://pubmed.ncbi.nlm.nih.gov/25535793/
|
||||
- https://www.nature.com/articles/s41586-024-07819-w
|
||||
|
||||
prohibitions:
|
||||
modify_phase1_to_phase4g: false
|
||||
conditioning_during_stage1: false
|
||||
weight_update_during_stage1: false
|
||||
infer_unknown_mapping: false
|
||||
train_base_brain: false
|
||||
|
||||
+134
@@ -0,0 +1,134 @@
|
||||
phase: 4H
|
||||
names:
|
||||
reference: MaleCNS-LIF-reference-v1
|
||||
runtime: MaleCNS-LIF-runtime-v1
|
||||
io_api: MaleCNS-BrainIO-v1
|
||||
activity_stream: MaleCNS-ActivityStream-v1
|
||||
plasticity_candidate: MaleCNS-DopaminePlasticity-v1-candidate
|
||||
execution:
|
||||
mode: two-stage
|
||||
stage1_only_entrypoint: phase4h_audit.py
|
||||
require_stage1_pass_before_conditioning: true
|
||||
|
||||
paths:
|
||||
connectome_root: /data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only
|
||||
model_root: /data/digital-drosophila/models/male-cns-lif/dopamine-plasticity-v1
|
||||
learned_root: /data/digital-drosophila/models/learned/phase4h
|
||||
experiment_root: /data/digital-drosophila/experiments/phase4h-dopamine-plasticity
|
||||
reference_root: /data/digital-drosophila/models/male-cns-lif/reference-v1
|
||||
runtime_root: /data/digital-drosophila/models/male-cns-lif/runtime-v1
|
||||
io_root: /data/digital-drosophila/models/male-cns-lif/io-v1
|
||||
phase4c_root: /data/digital-drosophila/experiments/phase4c-runtime
|
||||
phase4d_root: /data/digital-drosophila/experiments/phase4d-io
|
||||
phase4e_root: /data/digital-drosophila/experiments/phase4e-visual-calibration
|
||||
phase4f_root: /data/digital-drosophila/experiments/phase4f-retinotopic-vision
|
||||
phase4f_model_root: /data/digital-drosophila/models/male-cns-lif/visual-encoder-v1
|
||||
phase4g_root: /data/digital-drosophila/experiments/phase4g-frozen-interface
|
||||
phase4g_model_root: /data/digital-drosophila/models/male-cns-lif/frozen-interface-v1
|
||||
phase4g_learned_root: /data/digital-drosophila/models/learned/phase4g
|
||||
|
||||
expected_graph:
|
||||
neurons: 166700
|
||||
directed_edges: 25582938
|
||||
synaptic_contact_weight_sum: 124177617
|
||||
|
||||
model:
|
||||
dt_ms: 0.1
|
||||
membrane_tau_ms: 20.0
|
||||
synaptic_tau_ms: 5.0
|
||||
refractory_ms: 2.2
|
||||
resting_potential_mv: -52.0
|
||||
reset_potential_mv: -52.0
|
||||
threshold_mv: -45.0
|
||||
synaptic_delay_ms: 1.8
|
||||
w_syn_mv_per_anatomical_synapse: 0.275
|
||||
|
||||
sign_policy:
|
||||
neurotransmitter_sign: {acetylcholine: 1, gaba: -1, glutamate: -1, dopamine: 1, octopamine: 1, serotonin: 1, histamine: -1}
|
||||
unknown_sign: 0
|
||||
unclear_sign: 0
|
||||
|
||||
readout:
|
||||
bins_ms: [1, 5, 10, 20, 50, 100]
|
||||
|
||||
audit:
|
||||
exact_class_values:
|
||||
KC: Kenyon_Cell
|
||||
MBON: MBON
|
||||
DAN: DAN
|
||||
pam_type_prefix: PAM
|
||||
ppl1_type_prefix: PPL1
|
||||
compartment_source_field: annotation_instance
|
||||
compartment_parser: single_parenthesized_substring_verbatim
|
||||
require_exact_compartment_string_match: true
|
||||
candidate_requires_actual_kc_mbon_edge: true
|
||||
candidate_requires_actual_dan_mbon_edge: true
|
||||
candidate_requires_exact_dan_mbon_compartment_match: true
|
||||
do_not_infer_missing_compartment_from_type: true
|
||||
|
||||
plasticity:
|
||||
base_connectome_mode: read_only
|
||||
overlay_equation: effective_weight = base_weight + plastic_delta
|
||||
rule: delta_w = polarity_compartment * eta * D_compartment(t) * eligibility_ij(t)
|
||||
first_version_rule_family: compartment_specific_dopamine_gated_anti_hebbian_depression
|
||||
default_confirmed_compartment_polarity: -1
|
||||
unknown_compartment_policy: exclude_from_plastic_mask
|
||||
pam_ppl1_cluster_valence_policy: prohibited
|
||||
reward_interface_interpretation: artificial_unconditioned_signal_not_dopamine_concentration
|
||||
polarity_provenance:
|
||||
- https://pubmed.ncbi.nlm.nih.gov/26637800/
|
||||
- https://pubmed.ncbi.nlm.nih.gov/25535793/
|
||||
- https://www.nature.com/articles/s41586-024-07819-w
|
||||
eligibility_tau_ms: 1000.0
|
||||
eta_effective_mv: 0.00275
|
||||
min_effective_weight_mv: 0.0
|
||||
max_fractional_depression_per_edge: 0.25
|
||||
training_trials: 3
|
||||
d_magnitude: 1.0
|
||||
|
||||
conditioning:
|
||||
cs_population: olfactory
|
||||
cs_rate_hz: 50.0
|
||||
cs_duration_ms: 100.0
|
||||
cs_targets_per_identity: 64
|
||||
cs_identity_rule: sorted_neuron_idx_disjoint_halves
|
||||
appetitive_compartment_verbatim: "y5B'2a"
|
||||
appetitive_dan_type_required: PAM15
|
||||
aversive_compartment_verbatim: "y2a'1"
|
||||
aversive_dan_type_required: PPL103
|
||||
delayed_reward_ms: 50.0
|
||||
train_seeds: [48001, 48002, 48003, 48004, 48005]
|
||||
evaluation_seeds: [48101, 48102, 48103, 48104, 48105]
|
||||
protocols:
|
||||
- appetitive-conditioning
|
||||
- aversive-conditioning
|
||||
- reversal-learning
|
||||
- delayed-reward
|
||||
- retention
|
||||
- d-zero-control
|
||||
- random-reward-control
|
||||
- frozen-brain-control
|
||||
reward_interface_label: artificial_unconditioned_signal_interface
|
||||
|
||||
success_gate:
|
||||
require_all_frozen_checksums_pass: true
|
||||
require_phase4c_reference_spike_events_exact: true
|
||||
require_no_nan_inf_or_runaway: true
|
||||
require_minimum_seed_majority: 3
|
||||
require_appetitive_and_aversive_mbon_separation_gain: true
|
||||
require_downstream_separation_gain: true
|
||||
require_reversal_signature: true
|
||||
require_retention_signature: true
|
||||
controls_must_not_equal_conditioning_effect: true
|
||||
weight_change_alone_is_never_sufficient: true
|
||||
|
||||
device:
|
||||
required_name_substring: RTX 4090
|
||||
launcher_visible_gpu_uuid: GPU-79f3a85d-adce-7833-7003-6488140ca596
|
||||
|
||||
prohibitions:
|
||||
modify_phase1_to_phase4g: false
|
||||
conditioning_during_stage1: false
|
||||
weight_update_during_stage1: false
|
||||
infer_unknown_mapping: false
|
||||
train_base_brain: false
|
||||
+35
@@ -0,0 +1,35 @@
|
||||
{
|
||||
"appetitive_protocol": {
|
||||
"caveat": "appetitive is a protocol label supported at the gamma5/beta-prime-2a reward-circuit level; it is not a claim that every PAM15 neuron or all PAM neurons have uniformly positive valence",
|
||||
"compartment_verbatim": "y5B'2a",
|
||||
"external_provenance": [
|
||||
"https://reiserlab.github.io/celltype-explorer-drosophila-male-cns/types/PAM15.html",
|
||||
"https://pmc.ncbi.nlm.nih.gov/articles/PMC7443709/",
|
||||
"https://pmc.ncbi.nlm.nih.gov/articles/PMC10632144/"
|
||||
],
|
||||
"local_evidence": "exact MaleCNS annotation_instance match plus actual DAN-to-MBON connectivity in the frozen neuron-level CSR",
|
||||
"male_cns_type": "PAM15"
|
||||
},
|
||||
"aversive_protocol": {
|
||||
"caveat": "aversive is a protocol label grounded in shock-responsive PPL1-gamma2alpha-prime-1 literature; it is not a blanket PPL1-negative rule",
|
||||
"compartment_verbatim": "y2a'1",
|
||||
"external_provenance": [
|
||||
"https://reiserlab.github.io/celltype-explorer-drosophila-male-cns/types/PPL103.html",
|
||||
"https://www.nature.com/articles/s41467-021-21388-w",
|
||||
"https://pubmed.ncbi.nlm.nih.gov/30332645/"
|
||||
],
|
||||
"local_evidence": "exact MaleCNS annotation_instance match plus actual DAN-to-MBON connectivity in the frozen neuron-level CSR",
|
||||
"male_cns_type": "PPL103"
|
||||
},
|
||||
"plasticity_polarity": {
|
||||
"caveat": "configured anti-Hebbian/LTD hypothesis; no sign was tuned to obtain a positive result",
|
||||
"provenance": [
|
||||
"https://pubmed.ncbi.nlm.nih.gov/26637800/",
|
||||
"https://pubmed.ncbi.nlm.nih.gov/25535793/",
|
||||
"https://www.nature.com/articles/s41586-024-07819-w"
|
||||
],
|
||||
"scope": "all four strictly confirmed compartments in this first-version hypothesis",
|
||||
"value": -1
|
||||
},
|
||||
"scope": "Phase 4H artificial unconditioned-signal interfaces; not measured dopamine concentration"
|
||||
}
|
||||
+213
@@ -0,0 +1,213 @@
|
||||
{
|
||||
"DAN_to_KC": {
|
||||
"edges": 129113,
|
||||
"synapse_weight": 225127
|
||||
},
|
||||
"DAN_to_MBON": {
|
||||
"actual_edges": 3160,
|
||||
"actual_synapse_weight": 39711,
|
||||
"confirmed_exact_compartment_edge_mappings": 95,
|
||||
"confirmed_unique_DAN_MBON_pairs": 95
|
||||
},
|
||||
"DAN_to_compartment": {
|
||||
"confirmed_neurons": 326,
|
||||
"unique_explicit_compartments": 20,
|
||||
"unknown_neurons": 14
|
||||
},
|
||||
"KC_to_MBON": {
|
||||
"edges": 61210,
|
||||
"synapse_weight": 463640
|
||||
},
|
||||
"MBON_to_downstream": {
|
||||
"edges": 39279,
|
||||
"synapse_weight": 263410,
|
||||
"unique_targets": 11342
|
||||
},
|
||||
"biological_basis_conclusion": "sufficient for a conservative, explicitly compartment-matched conditioning prototype",
|
||||
"compartment_polarity": [
|
||||
{
|
||||
"compartment_verbatim": "B2B'2a",
|
||||
"interpretation": "model hypothesis: coincident KC and compartmental DAN activity depresses eligible KC-to-MBON synapses",
|
||||
"not_interpreted_as": "PAM-positive/PPL1-negative cluster rule",
|
||||
"polarity_compartment": -1,
|
||||
"provenance": "https://pubmed.ncbi.nlm.nih.gov/26637800/;https://pubmed.ncbi.nlm.nih.gov/25535793/;https://www.nature.com/articles/s41586-024-07819-w",
|
||||
"rule_family": "compartment_specific_dopamine_gated_anti_hebbian_depression"
|
||||
},
|
||||
{
|
||||
"compartment_verbatim": "a1",
|
||||
"interpretation": "model hypothesis: coincident KC and compartmental DAN activity depresses eligible KC-to-MBON synapses",
|
||||
"not_interpreted_as": "PAM-positive/PPL1-negative cluster rule",
|
||||
"polarity_compartment": -1,
|
||||
"provenance": "https://pubmed.ncbi.nlm.nih.gov/26637800/;https://pubmed.ncbi.nlm.nih.gov/25535793/;https://www.nature.com/articles/s41586-024-07819-w",
|
||||
"rule_family": "compartment_specific_dopamine_gated_anti_hebbian_depression"
|
||||
},
|
||||
{
|
||||
"compartment_verbatim": "y2a'1",
|
||||
"interpretation": "model hypothesis: coincident KC and compartmental DAN activity depresses eligible KC-to-MBON synapses",
|
||||
"not_interpreted_as": "PAM-positive/PPL1-negative cluster rule",
|
||||
"polarity_compartment": -1,
|
||||
"provenance": "https://pubmed.ncbi.nlm.nih.gov/26637800/;https://pubmed.ncbi.nlm.nih.gov/25535793/;https://www.nature.com/articles/s41586-024-07819-w",
|
||||
"rule_family": "compartment_specific_dopamine_gated_anti_hebbian_depression"
|
||||
},
|
||||
{
|
||||
"compartment_verbatim": "y5B'2a",
|
||||
"interpretation": "model hypothesis: coincident KC and compartmental DAN activity depresses eligible KC-to-MBON synapses",
|
||||
"not_interpreted_as": "PAM-positive/PPL1-negative cluster rule",
|
||||
"polarity_compartment": -1,
|
||||
"provenance": "https://pubmed.ncbi.nlm.nih.gov/26637800/;https://pubmed.ncbi.nlm.nih.gov/25535793/;https://www.nature.com/articles/s41586-024-07819-w",
|
||||
"rule_family": "compartment_specific_dopamine_gated_anti_hebbian_depression"
|
||||
}
|
||||
],
|
||||
"frozen_checksum_audit": {
|
||||
"all_passed": true,
|
||||
"controls": [
|
||||
{
|
||||
"checked": 4,
|
||||
"control": "/data/digital-drosophila/models/male-cns-lif/reference-v1/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/models/male-cns-lif/reference-v1"
|
||||
},
|
||||
{
|
||||
"checked": 7,
|
||||
"control": "/data/digital-drosophila/models/male-cns-lif/runtime-v1/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/models/male-cns-lif/runtime-v1"
|
||||
},
|
||||
{
|
||||
"checked": 5,
|
||||
"control": "/data/digital-drosophila/models/male-cns-lif/io-v1/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/models/male-cns-lif/io-v1"
|
||||
},
|
||||
{
|
||||
"checked": 73,
|
||||
"control": "/data/digital-drosophila/experiments/phase4c-runtime/manifests/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/experiments/phase4c-runtime"
|
||||
},
|
||||
{
|
||||
"checked": 43,
|
||||
"control": "/data/digital-drosophila/experiments/phase4d-io/manifests/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/experiments/phase4d-io"
|
||||
},
|
||||
{
|
||||
"checked": 166,
|
||||
"control": "/data/digital-drosophila/experiments/phase4e-visual-calibration/manifests/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/experiments/phase4e-visual-calibration"
|
||||
},
|
||||
{
|
||||
"checked": 15421,
|
||||
"control": "/data/digital-drosophila/experiments/phase4f-retinotopic-vision/manifests/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/experiments/phase4f-retinotopic-vision"
|
||||
},
|
||||
{
|
||||
"checked": 7,
|
||||
"control": "/data/digital-drosophila/models/male-cns-lif/visual-encoder-v1/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/models/male-cns-lif/visual-encoder-v1"
|
||||
},
|
||||
{
|
||||
"checked": 43,
|
||||
"control": "/data/digital-drosophila/experiments/phase4g-frozen-interface/manifests/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/experiments/phase4g-frozen-interface"
|
||||
},
|
||||
{
|
||||
"checked": 9,
|
||||
"control": "/data/digital-drosophila/models/male-cns-lif/frozen-interface-v1/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/models/male-cns-lif/frozen-interface-v1"
|
||||
},
|
||||
{
|
||||
"checked": 4,
|
||||
"control": "/data/digital-drosophila/models/learned/phase4g/checksums.sha256",
|
||||
"failures": [],
|
||||
"passed": true,
|
||||
"root": "/data/digital-drosophila/models/learned/phase4g"
|
||||
}
|
||||
]
|
||||
},
|
||||
"graph": {
|
||||
"directed_edges": 25582938,
|
||||
"neurons": 166700,
|
||||
"synaptic_contact_weight_sum": 124177617
|
||||
},
|
||||
"input_sha256": {
|
||||
"indices": "ce20f7433f78442c717ad2a7b5394cf4a3b109d990b4be0788040b7b0f4ed150",
|
||||
"indptr": "fe43420f11e6242a11f8199ae7f097cab4b8a6db181d36f2a46b9e46670acbb4",
|
||||
"metadata": "922af16846a065c3dbfca7c11146b83ca217fcbd7392edc745f444a04eae8c63",
|
||||
"weights": "c7ae101451dd19c47fd976bcfacbc52d67193a68ffa04c5b4d2e911cfd52d99b"
|
||||
},
|
||||
"limitations": [
|
||||
"The neuron-level CSR has no synapse-level ROI/location, so candidate membership is conservative and does not prove that every KC-MBON contact lies inside the parsed compartment.",
|
||||
"Parenthesized annotation_instance tokens are preserved verbatim; missing or ambiguous tokens are not inferred from names.",
|
||||
"Direct DAN-to-MBON connectivity plus exact compartment-string equality is required; extrasynaptic dopamine is not inferred.",
|
||||
"polarity=-1 is an explicit anti-Hebbian/LTD model hypothesis with cited provenance, not a PAM/PPL1 valence rule."
|
||||
],
|
||||
"mapping_policy": {
|
||||
"candidate_requires_actual_dan_mbon_edge": true,
|
||||
"candidate_requires_actual_kc_mbon_edge": true,
|
||||
"candidate_requires_exact_dan_mbon_compartment_match": true,
|
||||
"compartment_parser": "single_parenthesized_substring_verbatim",
|
||||
"compartment_source_field": "annotation_instance",
|
||||
"do_not_infer_missing_compartment_from_type": true,
|
||||
"exact_class_values": {
|
||||
"DAN": "DAN",
|
||||
"KC": "Kenyon_Cell",
|
||||
"MBON": "MBON"
|
||||
},
|
||||
"pam_type_prefix": "PAM",
|
||||
"ppl1_type_prefix": "PPL1",
|
||||
"require_exact_compartment_string_match": true
|
||||
},
|
||||
"no_weight_update_or_conditioning_performed": true,
|
||||
"phase": "4H-stage1",
|
||||
"plastic_edge_candidate_mask": {
|
||||
"edge_ids_sha256": "8b0fb6eb2e6c31da4d17dc20d890aa3f367e514f05642de5bad6b42a1611c05b",
|
||||
"edges": 14232,
|
||||
"fraction_of_all_edges": 0.0005563082707701516,
|
||||
"full_edge_boolean_mask_sha256": "e8b7a439f07eae6e36729d6577a2c5e4a4c7aa4b15e97fc5266d7278db9e150e",
|
||||
"percent_of_all_edges": 0.05563082707701516,
|
||||
"synapse_weight": 105002
|
||||
},
|
||||
"population_counts": {
|
||||
"DAN_total": 340,
|
||||
"KC": 4064,
|
||||
"MBON": 97,
|
||||
"PAM": 316,
|
||||
"PPL1": 16,
|
||||
"other_DAN": 8
|
||||
},
|
||||
"reliable_mb_compartments": {
|
||||
"count": 4,
|
||||
"verbatim_values": [
|
||||
"B2B'2a",
|
||||
"a1",
|
||||
"y2a'1",
|
||||
"y5B'2a"
|
||||
]
|
||||
},
|
||||
"stage2_authorized_by_audit": true,
|
||||
"status": "PASS-AUDIT",
|
||||
"unknown": {
|
||||
"DAN_without_reliable_explicit_compartment": 14,
|
||||
"KC_to_MBON_edges_excluded_from_candidate_mask": 46978,
|
||||
"KC_to_MBON_target_MBONs_without_confirmed_DAN_match": 85,
|
||||
"MBON_without_reliable_explicit_compartment": 0,
|
||||
"actual_DAN_to_MBON_edges_not_exactly_compartment_matched": 3065,
|
||||
"reported_relationship_unknown_total_non_disjoint": 50142
|
||||
}
|
||||
}
|
||||
+213
@@ -0,0 +1,213 @@
|
||||
{
|
||||
"DAN_to_KC": {
|
||||
"edges": 129113,
|
||||
"synapse_weight": 225127
|
||||
},
|
||||
"DAN_to_MBON": {
|
||||
"actual_edges": 3160,
|
||||
"actual_synapse_weight": 39711,
|
||||
"confirmed_exact_compartment_edge_mappings": 95,
|
||||
"confirmed_unique_DAN_MBON_pairs": 95
|
||||
},
|
||||
"DAN_to_compartment": {
|
||||
"confirmed_neurons": 326,
|
||||
"unique_explicit_compartments": 20,
|
||||
"unknown_neurons": 14
|
||||
},
|
||||
"KC_to_MBON": {
|
||||
"edges": 61210,
|
||||
"synapse_weight": 463640
|
||||
},
|
||||
"MBON_to_downstream": {
|
||||
"edges": 39279,
|
||||
"synapse_weight": 263410,
|
||||
"unique_targets": 11342
|
||||
},
|
||||
"biological_basis_conclusion": "sufficient for a conservative, explicitly compartment-matched conditioning prototype",
|
||||
"compartment_polarity": [
|
||||
{
|
||||
"compartment_verbatim": "B2B'2a",
|
||||
"interpretation": "model hypothesis: coincident KC and compartmental DAN activity depresses eligible KC-to-MBON synapses",
|
||||
"not_interpreted_as": "PAM-positive/PPL1-negative cluster rule",
|
||||
"polarity_compartment": -1,
|
||||
"provenance": "https://pubmed.ncbi.nlm.nih.gov/26637800/;https://pubmed.ncbi.nlm.nih.gov/25535793/;https://www.nature.com/articles/s41586-024-07819-w",
|
||||
"rule_family": "compartment_specific_dopamine_gated_anti_hebbian_depression"
|
||||
},
|
||||
{
|
||||
"compartment_verbatim": "a1",
|
||||
"interpretation": "model hypothesis: coincident KC and compartmental DAN activity depresses eligible KC-to-MBON synapses",
|
||||
"not_interpreted_as": "PAM-positive/PPL1-negative cluster rule",
|
||||
"polarity_compartment": -1,
|
||||
"provenance": "https://pubmed.ncbi.nlm.nih.gov/26637800/;https://pubmed.ncbi.nlm.nih.gov/25535793/;https://www.nature.com/articles/s41586-024-07819-w",
|
||||
"rule_family": "compartment_specific_dopamine_gated_anti_hebbian_depression"
|
||||
},
|
||||
{
|
||||
"compartment_verbatim": "y2a'1",
|
||||
"interpretation": "model hypothesis: coincident KC and compartmental DAN activity depresses eligible KC-to-MBON synapses",
|
||||
"not_interpreted_as": "PAM-positive/PPL1-negative cluster rule",
|
||||
"polarity_compartment": -1,
|
||||
"provenance": "https://pubmed.ncbi.nlm.nih.gov/26637800/;https://pubmed.ncbi.nlm.nih.gov/25535793/;https://www.nature.com/articles/s41586-024-07819-w",
|
||||
"rule_family": "compartment_specific_dopamine_gated_anti_hebbian_depression"
|
||||
},
|
||||
{
|
||||
"compartment_verbatim": "y5B'2a",
|
||||
"interpretation": "model hypothesis: coincident KC and compartmental DAN activity depresses eligible KC-to-MBON synapses",
|
||||
"not_interpreted_as": "PAM-positive/PPL1-negative cluster rule",
|
||||
"polarity_compartment": -1,
|
||||
"provenance": "https://pubmed.ncbi.nlm.nih.gov/26637800/;https://pubmed.ncbi.nlm.nih.gov/25535793/;https://www.nature.com/articles/s41586-024-07819-w",
|
||||
"rule_family": "compartment_specific_dopamine_gated_anti_hebbian_depression"
|
||||
}
|
||||
],
|
||||
"frozen_checksum_audit": {
|
||||
"all_passed": true,
|
||||
"controls": [
|
||||
{
|
||||
"checked": 4,
|
||||
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||||
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||||
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||||
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||||
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Reference in New Issue
Block a user