Digital Drosophila Archive
137 lines
4.8 KiB
YAML
137 lines
4.8 KiB
YAML
phase: 4J
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name: MaleCNS-MB-physiology-repair-v1
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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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model_root: /data/digital-drosophila/models/male-cns-lif
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phase4j_model_root: /data/digital-drosophila/models/male-cns-lif/mb-physiology-v1
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experiment_root: /data/digital-drosophila/experiments/phase4j-mb-physiology-repair
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reference_root: /data/digital-drosophila/models/male-cns-lif/reference-v1
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runtime_root: /data/digital-drosophila/models/male-cns-lif/runtime-v1
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io_root: /data/digital-drosophila/models/male-cns-lif/io-v1
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phase4c_root: /data/digital-drosophila/experiments/phase4c-runtime
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phase4d_root: /data/digital-drosophila/experiments/phase4d-io
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phase4e_root: /data/digital-drosophila/experiments/phase4e-visual-calibration
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phase4f_root: /data/digital-drosophila/experiments/phase4f-retinotopic-vision
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phase4f_model_root: /data/digital-drosophila/models/male-cns-lif/visual-encoder-v1
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phase4g_root: /data/digital-drosophila/experiments/phase4g-frozen-interface
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phase4g_model_root: /data/digital-drosophila/models/male-cns-lif/frozen-interface-v1
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phase4g_learned_root: /data/digital-drosophila/models/learned/phase4g
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phase4h_root: /data/digital-drosophila/experiments/phase4h-dopamine-plasticity
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phase4h_model_root: /data/digital-drosophila/models/male-cns-lif/dopamine-plasticity-v1
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phase4h_learned_root: /data/digital-drosophila/models/learned/phase4h
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phase4i_root: /data/digital-drosophila/experiments/phase4i-mb-mechanistic-validation
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phase4i_model_root: /data/digital-drosophila/models/male-cns-lif/mb-mechanistic-v1
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names:
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reference: MaleCNS-LIF-reference-v1
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runtime: MaleCNS-LIF-runtime-v1
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model:
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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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w_syn_mv_per_anatomical_synapse: 0.275
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sign_policy:
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neurotransmitter_sign: {acetylcholine: 1, gaba: -1, glutamate: -1, dopamine: 1, octopamine: 1, serotonin: 1, histamine: -1}
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unknown_sign: 0
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unclear_sign: 0
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readout:
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bins_ms: [1, 5, 10, 20, 50, 100]
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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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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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phase4h_plastic_candidate_edges: 14232
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plastic_mask_edges: 14232
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stimuli:
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targets_per_odor: 64
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rate_hz: 50.0
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duration_ms: 100.0
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calibration_odor_count: 4
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heldout_odor_count: 4
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evaluation_seeds: [50101, 50102, 50103, 50104, 50105]
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calibration_seed_base: 50000
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formal_CS_seeds: [48101, 48102, 48103, 48104, 48105]
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apl_overlay:
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name: APL-Graded-Inhibition-v1
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interpretation: experimental physiology overlay supplementing missing graded/non-spiking APL behavior in point-LIF
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input_classes: [Kenyon_Cell, ALPN]
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replace_spiking_APL_output_in_memory_only: true
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calibration_reference_active_KC_fraction: [0.03, 0.09]
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target_fraction_for_scoring: 0.06
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tau_grid_ms: [20.0, 50.0, 100.0]
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gain_grid_mv_per_state_step: [0.00001, 0.00003, 0.0001, 0.0003, 0.001, 0.003, 0.01, 0.03]
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normalization_grid: [0.5, 1.0, 2.0]
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heldout_max_mean_jaccard: 0.8
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heldout_minimum_nonzero_fraction: 0.01
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eligibility_v2:
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name: causal-LTD-engineering-model
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kc_trace_tau_ms: 100.0
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trace_cap: 1.0
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eta_effective_mv: 0.00275
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polarity: -1
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max_fractional_depression: 0.25
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delta_t_ms: [-1000, -500, -250, -100, -50, 0, 50, 100, 250, 500, 1000]
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pass_max_negative_LTD_fraction: 0.0
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pass_plus_1000_to_zero_ratio: 0.01
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provenance:
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- https://pmc.ncbi.nlm.nih.gov/articles/PMC9012144/
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- https://pubmed.ncbi.nlm.nih.gov/26637800/
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bidirectional_branch:
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name: order-sensitive-bidirectional-v1
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kc_before_dan_tau_ms: 100.0
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dan_before_kc_tau_ms: 100.0
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kc_before_dan_polarity: -1
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dan_before_kc_polarity: 1
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eta_effective_mv: 0.00275
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provenance:
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- https://pmc.ncbi.nlm.nih.gov/articles/PMC9012144/
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selection_policy: report_independently_never_select_by_memory_result
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direct_kc:
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ensemble_size: 64
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target_compartment_verbatim: "y5B'2a"
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matched_dan_type: PAM15
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unrelated_compartment_verbatim: "y2a'1"
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unrelated_dan_type: PPL103
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pulse_times_ms: [10.0, 30.0, 50.0, 70.0, 90.0]
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dan_time_ms: 90.0
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duration_ms: 120.0
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conditioning_trials: 3
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train_seeds: [50201, 50202, 50203, 50204, 50205]
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evaluation_seeds: [50301, 50302, 50303, 50304, 50305]
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gates:
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sparse_min_fraction: 0.03
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sparse_max_fraction: 0.09
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direct_seed_majority: 3
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subthreshold_noise_floor: 0.0001
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prohibitions:
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modify_base_disk_artifacts: false
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expand_plastic_mask: false
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modify_global_or_KC_threshold: false
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winner_take_all_or_top_k: false
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tune_on_formal_CS: false
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tune_plasticity_polarity_or_eta: false
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modify_MBON_threshold_or_gain: false
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decoder_or_classifier: false
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game_visual_RL: false
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