qishizhe/digital-drosophila
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Archive MaleCNS research sources, provenance, bibliography and immutable data inventory

Browse Source
This commit is contained in:
Digital Drosophila Archive
2026-09-29 03:38:32 +08:00
commit 3981628ff8
682 changed files with 161475 additions and 0 deletions
Download Patch File Download Diff File Expand all files Collapse all files
registry/catalog-20260929/evidence/phase4j-mb-physiology-repair/audit/base-sha256.json
+15
View File
@@ -0,0 +1,15 @@
{
"after": {
"/data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only/gpu/csr-indices.int32.npy": "ce20f7433f78442c717ad2a7b5394cf4a3b109d990b4be0788040b7b0f4ed150",
"/data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only/gpu/csr-indptr.int64.npy": "fe43420f11e6242a11f8199ae7f097cab4b8a6db181d36f2a46b9e46670acbb4",
"/data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only/gpu/csr-weights.int64.npy": "c7ae101451dd19c47fd976bcfacbc52d67193a68ffa04c5b4d2e911cfd52d99b",
"/data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only/neuron-index/unified-metadata.parquet": "922af16846a065c3dbfca7c11146b83ca217fcbd7392edc745f444a04eae8c63"
},
"before": {
"/data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only/gpu/csr-indices.int32.npy": "ce20f7433f78442c717ad2a7b5394cf4a3b109d990b4be0788040b7b0f4ed150",
"/data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only/gpu/csr-indptr.int64.npy": "fe43420f11e6242a11f8199ae7f097cab4b8a6db181d36f2a46b9e46670acbb4",
"/data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only/gpu/csr-weights.int64.npy": "c7ae101451dd19c47fd976bcfacbc52d67193a68ffa04c5b4d2e911cfd52d99b",
"/data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only/neuron-index/unified-metadata.parquet": "922af16846a065c3dbfca7c11146b83ca217fcbd7392edc745f444a04eae8c63"
},
"unchanged": true
}
registry/catalog-20260929/evidence/phase4j-mb-physiology-repair/audit/final-summary.json
+1039
View File
File diff suppressed because it is too large Load Diff
registry/catalog-20260929/evidence/phase4j-mb-physiology-repair/audit/frozen-after.json
+117
View File
@@ -0,0 +1,117 @@
{
"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"
},
{
"checked": 76,
"control": "/data/digital-drosophila/experiments/phase4h-dopamine-plasticity/manifests/checksums.sha256",
"failures": [],
"passed": true,
"root": "/data/digital-drosophila/experiments/phase4h-dopamine-plasticity"
},
{
"checked": 5,
"control": "/data/digital-drosophila/models/male-cns-lif/dopamine-plasticity-v1/checksums.sha256",
"failures": [],
"passed": true,
"root": "/data/digital-drosophila/models/male-cns-lif/dopamine-plasticity-v1"
},
{
"checked": 42,
"control": "/data/digital-drosophila/models/learned/phase4h/checksums.sha256",
"failures": [],
"passed": true,
"root": "/data/digital-drosophila/models/learned/phase4h"
},
{
"checked": 57,
"control": "/data/digital-drosophila/experiments/phase4i-mb-mechanistic-validation/manifests/checksums.sha256",
"failures": [],
"passed": true,
"root": "/data/digital-drosophila/experiments/phase4i-mb-mechanistic-validation"
},
{
"checked": 4,
"control": "/data/digital-drosophila/models/male-cns-lif/mb-mechanistic-v1/checksums.sha256",
"failures": [],
"passed": true,
"root": "/data/digital-drosophila/models/male-cns-lif/mb-mechanistic-v1"
}
]
}
registry/catalog-20260929/evidence/phase4j-mb-physiology-repair/audit/frozen-before.json
+117
View File
@@ -0,0 +1,117 @@
{
"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"
},
{
"checked": 76,
"control": "/data/digital-drosophila/experiments/phase4h-dopamine-plasticity/manifests/checksums.sha256",
"failures": [],
"passed": true,
"root": "/data/digital-drosophila/experiments/phase4h-dopamine-plasticity"
},
{
"checked": 5,
"control": "/data/digital-drosophila/models/male-cns-lif/dopamine-plasticity-v1/checksums.sha256",
"failures": [],
"passed": true,
"root": "/data/digital-drosophila/models/male-cns-lif/dopamine-plasticity-v1"
},
{
"checked": 42,
"control": "/data/digital-drosophila/models/learned/phase4h/checksums.sha256",
"failures": [],
"passed": true,
"root": "/data/digital-drosophila/models/learned/phase4h"
},
{
"checked": 57,
"control": "/data/digital-drosophila/experiments/phase4i-mb-mechanistic-validation/manifests/checksums.sha256",
"failures": [],
"passed": true,
"root": "/data/digital-drosophila/experiments/phase4i-mb-mechanistic-validation"
},
{
"checked": 4,
"control": "/data/digital-drosophila/models/male-cns-lif/mb-mechanistic-v1/checksums.sha256",
"failures": [],
"passed": true,
"root": "/data/digital-drosophila/models/male-cns-lif/mb-mechanistic-v1"
}
]
}
registry/catalog-20260929/evidence/phase4j-mb-physiology-repair/audit/phase4j.yaml
+136
View File
@@ -0,0 +1,136 @@
phase: 4J
name: MaleCNS-MB-physiology-repair-v1
paths:
connectome_root: /data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only
model_root: /data/digital-drosophila/models/male-cns-lif
phase4j_model_root: /data/digital-drosophila/models/male-cns-lif/mb-physiology-v1
experiment_root: /data/digital-drosophila/experiments/phase4j-mb-physiology-repair
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
phase4h_root: /data/digital-drosophila/experiments/phase4h-dopamine-plasticity
phase4h_model_root: /data/digital-drosophila/models/male-cns-lif/dopamine-plasticity-v1
phase4h_learned_root: /data/digital-drosophila/models/learned/phase4h
phase4i_root: /data/digital-drosophila/experiments/phase4i-mb-mechanistic-validation
phase4i_model_root: /data/digital-drosophila/models/male-cns-lif/mb-mechanistic-v1
names:
reference: MaleCNS-LIF-reference-v1
runtime: MaleCNS-LIF-runtime-v1
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]
device:
required_name_substring: RTX 4090
launcher_visible_gpu_uuid: GPU-79f3a85d-adce-7833-7003-6488140ca596
expected_graph:
neurons: 166700
directed_edges: 25582938
synaptic_contact_weight_sum: 124177617
phase4h_plastic_candidate_edges: 14232
plastic_mask_edges: 14232
stimuli:
targets_per_odor: 64
rate_hz: 50.0
duration_ms: 100.0
calibration_odor_count: 4
heldout_odor_count: 4
evaluation_seeds: [50101, 50102, 50103, 50104, 50105]
calibration_seed_base: 50000
formal_CS_seeds: [48101, 48102, 48103, 48104, 48105]
apl_overlay:
name: APL-Graded-Inhibition-v1
interpretation: experimental physiology overlay supplementing missing graded/non-spiking APL behavior in point-LIF
input_classes: [Kenyon_Cell, ALPN]
replace_spiking_APL_output_in_memory_only: true
calibration_reference_active_KC_fraction: [0.03, 0.09]
target_fraction_for_scoring: 0.06
tau_grid_ms: [20.0, 50.0, 100.0]
gain_grid_mv_per_state_step: [0.00001, 0.00003, 0.0001, 0.0003, 0.001, 0.003, 0.01, 0.03]
normalization_grid: [0.5, 1.0, 2.0]
heldout_max_mean_jaccard: 0.8
heldout_minimum_nonzero_fraction: 0.01
eligibility_v2:
name: causal-LTD-engineering-model
kc_trace_tau_ms: 100.0
trace_cap: 1.0
eta_effective_mv: 0.00275
polarity: -1
max_fractional_depression: 0.25
delta_t_ms: [-1000, -500, -250, -100, -50, 0, 50, 100, 250, 500, 1000]
pass_max_negative_LTD_fraction: 0.0
pass_plus_1000_to_zero_ratio: 0.01
provenance:
- https://pmc.ncbi.nlm.nih.gov/articles/PMC9012144/
- https://pubmed.ncbi.nlm.nih.gov/26637800/
bidirectional_branch:
name: order-sensitive-bidirectional-v1
kc_before_dan_tau_ms: 100.0
dan_before_kc_tau_ms: 100.0
kc_before_dan_polarity: -1
dan_before_kc_polarity: 1
eta_effective_mv: 0.00275
provenance:
- https://pmc.ncbi.nlm.nih.gov/articles/PMC9012144/
selection_policy: report_independently_never_select_by_memory_result
direct_kc:
ensemble_size: 64
target_compartment_verbatim: "y5B'2a"
matched_dan_type: PAM15
unrelated_compartment_verbatim: "y2a'1"
unrelated_dan_type: PPL103
pulse_times_ms: [10.0, 30.0, 50.0, 70.0, 90.0]
dan_time_ms: 90.0
duration_ms: 120.0
conditioning_trials: 3
train_seeds: [50201, 50202, 50203, 50204, 50205]
evaluation_seeds: [50301, 50302, 50303, 50304, 50305]
gates:
sparse_min_fraction: 0.03
sparse_max_fraction: 0.09
direct_seed_majority: 3
subthreshold_noise_floor: 0.0001
prohibitions:
modify_base_disk_artifacts: false
expand_plastic_mask: false
modify_global_or_KC_threshold: false
winner_take_all_or_top_k: false
tune_on_formal_CS: false
tune_plasticity_polarity_or_eta: false
modify_MBON_threshold_or_gain: false
decoder_or_classifier: false
game_visual_RL: false