Digital Drosophila Archive
111 lines
2.6 KiB
YAML
111 lines
2.6 KiB
YAML
phase: 4A
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paths:
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connectome_root: /data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only
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experiment_root: /data/digital-drosophila/experiments/phase4a-baseline
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expected_graph:
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neurons: 166700
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directed_edges: 25582938
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synaptic_contact_weight_sum: 124177617
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isolated_neurons: 217
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self_loops: 101
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device:
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required_name_substring: RTX 4090
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launcher_visible_gpu_uuid: GPU-79f3a85d-adce-7833-7003-6488140ca596
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mixed_multi_gpu: false
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model:
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integrator: forward_euler
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dt_ms: 0.1
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membrane_tau_ms: 20.0
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synaptic_tau_ms: 5.0
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refractory_ms: 2.2
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resting_potential_mv: -52.0
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reset_potential_mv: -52.0
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threshold_mv: -45.0
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synaptic_delay_ms: 1.8
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parameter_provenance: FlyWire-inspired 2024 LIF baseline; not MaleCNS measured single-cell parameters
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sign_policy:
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neurotransmitter_sign:
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acetylcholine: 1
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gaba: -1
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glutamate: -1
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dopamine: 1
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octopamine: 1
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serotonin: 1
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histamine: -1
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histamine_policy_note: explicitly configured inhibitory baseline assumption; not silently inferred
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unknown_sign: 0
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unclear_sign: 0
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unmapped_policy: error
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unmapped_sign: 0
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weights:
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transform: sqrt
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supported_transforms: [linear, sqrt, log1p]
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scale: 0.05
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chunk_edges: 2000000
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units: model synaptic-state increment per presynaptic spike
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formula: effective_weight = presynaptic_sign * scale * f(raw_synapse_count)
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preserve_raw_int64: true
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stimulations:
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single_neuron:
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kind: single_neuron_pulse
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neuron_idx: 0
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start_ms: 2.0
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duration_ms: 1.0
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amplitude_mv_equivalent: 400.0
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known_type_AMMC005:
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kind: known_type_pulse
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type_name: AMMC005
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max_neurons: 12
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start_ms: 5.0
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duration_ms: 1.0
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amplitude_mv_equivalent: 400.0
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sparse_poisson:
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kind: sparse_poisson
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target_fraction: 0.001
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rate_hz: 20.0
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event_amplitude_mv_equivalent: 1600.0
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smoke_tests:
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- name: smoke-10ms-single-neuron
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duration_ms: 10.0
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stimulation: single_neuron
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seed: 41001
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- name: smoke-100ms-known-type
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duration_ms: 100.0
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stimulation: known_type_AMMC005
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seed: 41002
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- name: smoke-1s-sparse-poisson
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duration_ms: 1000.0
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stimulation: sparse_poisson
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seed: 41003
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cpu_gpu_reference:
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seed: 41100
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subgraph_neurons: 512
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steps: 100
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pulse_start_step: 5
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pulse_steps: 10
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pulse_neurons: 4
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pulse_amplitude_mv_equivalent: 400.0
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absolute_tolerance: 1.0e-10
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validation:
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finite_check_interval_steps: 100
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explosive_step_fraction: 0.1
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memory_growth_tolerance_bytes: 10485760
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output:
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spike_representation: event_table_timestamp_ms_neuron_idx
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dense_time_by_neuron_forbidden: true
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rate_window_ms: 10.0
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reproducibility:
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seed: 41000
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deterministic_synthetic_inputs: true
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