DavidVivancos/NeuraxonLife2.1-TimeSeries

NeuraxonLife2-DeepTimeSeries: Artificial Life Neuraxon Neural Network Simulation Deep Time Series Dataset

Dataset Description

The NeuraxonLife 2.1 Deep Time Series Dataset is a comprehensive collection of simulation data from the Neuraxon Game of Life environment, where autonomous agents ("NxErs") evolve biologically-plausible neural networks under survival pressures. This dataset includes detailed time series, event logs, neural states, and behavioral data across thousands of simulation runs, enabling deep exploration of neural dynamics, plasticity, synchronization, and evolutionary processes. It is designed for validating the Neuraxon paper: 'A New Neural Growth & Computation Blueprint' by David Vivancos & Dr. Jose Sanchez for Qubic Science.

From a Neuraxon neural network (https://www.researchgate.net/publication/397331336_Neuraxon )

This version emphasizes temporal data with high-resolution time series (per-tick metrics) and event tables, capturing phenomena like multi-timescale synaptic plasticity, neuromodulation thresholds, dendritic spikes, phase coherence, and ITU (Intelligent Tissue Unit) evolution.

Dataset Summary

This dataset provides insights into emergent neural computation in an artificial life setting. Each NxEr features:

• Neuraxon neural networks with dendritic branches and multi-timescale weights (fast, slow, meta)
• Four neuromodulators (dopamine, serotonin, acetylcholine, norepinephrine) influencing trinary states
• Behavioral interactions (foraging, mating, exploration) in a grid world
• Evolutionary mechanisms via ITU hybridization
• High-frequency time series for network activity, branching ratios, cross-frequency coupling (CFC), autocorrelation windows (ACW), and more

Key highlights:

• 1983 simulation games
• Over 9 million time series rows
• Detailed events for plasticity, spontaneous firings, threshold modulations, etc.
• Mapped to paper sections for targeted validation (e.g., Section 1: Trinary Neuromodulation)

Supported Tasks

• Temporal Dynamics Analysis: Study oscillator frequencies, phase coherence, and CFC over time
• Plasticity Modeling: Analyze LTP/LTD rates, associativity, and weight evolution
• Neuromodulation Research: Examine threshold crossings and spatial variance of modulators
• Behavioral Correlation: Link neural states to agent actions via I/O patterns
• Evolutionary Fitness Prediction: Predict ITU fitness from temporal and energy metrics
• Criticality Assessment: Evaluate branching ratios and self-organized criticality
• Synchronization Studies: Investigate PAC (phase-amplitude coupling) and mean phase velocity

Dataset Structure

The dataset consists of 28 interconnected tables stored as Parquet files, plus metadata:

/
├── games.parquet                  # Game metadata
├── nxers.parquet                  # Agent data
├── network_params.parquet         # Network configurations
├── neurons.parquet                # Neuron states
├── synapses.parquet               # Synapse details
├── foods.parquet                  # Food sources
├── time_series.parquet            # Core time series data
├── plasticity_events.parquet      # LTP/LTD events
├── nxer_events.parquet            # Agent lifecycle events
├── io_patterns.parquet            # Input/output patterns
├── itu_fitness.parquet            # ITU fitness history
├── neuromodulator_events.parquet  # Modulator threshold crossings
├── phase_events.parquet           # Phase synchronization events
├── dendritic_events.parquet       # Dendritic spikes
├── homeostatic_events.parquet     # Homeostatic adjustments
├── weight_evolution_events.parquet# Weight changes
├── world_grids.parquet            # World terrain
├── food_progress.parquet          # Harvest progress
├── nxer_visited_history.parquet   # Exploration paths
├── neuron_state_history.parquet   # Neuron state deques
├── synapse_neighbor_ids.parquet   # Associativity neighbors
├── silent_synapse_events.parquet  # Silent synapse transitions
├── spontaneous_events.parquet     # Spontaneous firings
├── autoreceptor_events.parquet    # Autoreceptor modulations
├── subthreshold_events.parquet    # Near-threshold integrations
├── threshold_modulation_events.parquet # Threshold breakdowns
├── associativity_events.parquet   # Cooperative LTP events
├── hall_of_fame.parquet           # Top performers
├── manifest.json                  # Dataset metadata
└── README.md                      # This file

Data Tables

1. Games Table (games.parquet)
   Rows: 1983 | Columns: 53 | Size: 399 KB
   Description: Main game metadata including summary statistics, neuromodulator peaks, and NxEr summaries. Key for paper validation across all sections.
   Columns: (All types inferred: int/string/float) game_id, round_number, status, file_timestamp, source_file, created_at, step_tick, global_time_steps, births_count, deaths_count, game_index, world_size, world_grid_hash, log_level, logger_version, start_timestamp, end_timestamp, duration_seconds, total_ticks, total_neurons_created, total_neurons_died, total_synapses_created, total_synapses_pruned, total_plasticity_events, total_ltp_events, total_ltd_events, peak_network_activity, average_branching_ratio, branching_ratio_samples, peak_dopamine, peak_serotonin, peak_acetylcholine, peak_norepinephrine, total_silent_synapse_activations, total_spontaneous_events, total_dendritic_spikes, total_homeostatic_adjustments, peak_phase_coherence, total_threshold_modulations, total_associativity_events, total_metabotropic_activations, total_ionotropic_activations, peak_autocorrelation_window, mean_weight_change_rate, total_subthreshold_integrations, nxer_total_born, nxer_total_died, nxer_max_food_found, nxer_max_time_lived, nxer_max_mates, nxer_max_explored, num_nxers_in_file, num_foods_in_file.

2. NxErs Table (nxers.parquet)
   Rows: 40557 | Columns: 52 | Size: 19 MB
   Description: Individual NxEr data including identity, position, state, sensory attributes, statistics, and I/O history. Essential for behavioral analysis.
   Columns: game_id, round_number, nxer_id, name, color_r, color_g, color_b, is_male, clan_id, pos_x, pos_y, can_land, can_sea, food, alive, born_ts, died_ts, vision_range, smell_radius, heading, ticks_per_action, tick_accum, harvesting, mating_with, mating_end_tick, dopamine_boost_ticks, mating_intent_until_tick, mate_cooldown_until_tick, last_move_tick, last_input_0 to last_input_5, last_output_0 to last_output_4, parent_0, parent_1, stats_food_found, stats_food_taken, stats_explored, stats_time_lived_s, stats_mates_performed, stats_energy_efficiency, stats_temporal_sync_score, stats_fitness_score, visited_count, visited_json.

3. Network Params Table (network_params.parquet)
   Rows: 40557 | Columns: 82 | Size: 17 MB
   Description: Complete network parameters for each NxEr including architecture, topology, neuron properties, synaptic time constants, plasticity rates, neuromodulation baselines, oscillator frequencies, and ITU config.
   Columns: game_id, round_number, nxer_id, nxer_name, network_name, num_input_neurons, num_hidden_neurons, num_output_neurons, connection_probability, small_world_k, small_world_rewire_prob, preferential_attachment, membrane_time_constant, firing_threshold_excitatory, firing_threshold_inhibitory, adaptation_rate, spontaneous_firing_rate, neuron_health_decay, num_dendritic_branches, branch_threshold, plateau_decay, tau_fast, tau_slow, tau_meta, tau_ltp, tau_ltd, w_fast_init_min, w_fast_init_max, w_slow_init_min, w_slow_init_max, w_meta_init_min, w_meta_init_max, learning_rate, stdp_window, learning_rate_mod, plasticity_threshold, associativity_strength, synapse_integrity_threshold, synapse_formation_prob, synapse_death_prob, neuron_death_threshold, dopamine_baseline, dopamine_high_affinity_threshold, dopamine_low_affinity_threshold, serotonin_baseline, serotonin_high_affinity_threshold, serotonin_low_affinity_threshold, acetylcholine_baseline, acetylcholine_high_affinity_threshold, acetylcholine_low_affinity_threshold, norepinephrine_baseline, norepinephrine_high_affinity_threshold, norepinephrine_low_affinity_threshold, neuromod_decay_rate, diffusion_rate, oscillator_low_freq, oscillator_mid_freq, oscillator_high_freq, oscillator_strength, phase_coupling_strength, energy_baseline, firing_energy_cost, plasticity_energy_cost, metabolic_rate, recovery_rate, target_firing_rate, homeostatic_plasticity_rate, itu_circle_radius, evolution_interval, fitness_temporal_weight, fitness_energy_weight, fitness_pattern_weight, max_axonal_delay, dt, simulation_steps, activity_threshold, net_time, net_step_count, net_energy_consumed, net_branching_ratio, net_num_synapses, net_num_neurons.

4. Neurons Table (neurons.parquet)
   Rows: 1,499,241 | Columns: 33 | Size: 579 MB
   Description: Individual neuron state snapshots including membrane potential, trinary state, adaptation, autoreceptor levels, energy, phase, and individualized parameters. Relevant to Sections 1, 2, 6.
   Columns: game_id, round_number, nxer_id, neuron_id, neuron_type, membrane_potential, trinary_state, adaptation, autoreceptor, health, is_active, energy_level, phase, natural_frequency, intrinsic_timescale, fitness_score, circle_id, last_firing_time, membrane_time_constant, firing_threshold_excitatory, firing_threshold_inhibitory, adaptation_rate, spontaneous_firing_rate, neuron_health_decay, energy_baseline, firing_energy_cost, plasticity_energy_cost, metabolic_rate, recovery_rate, num_dendritic_branches, state_history_json, state_history_length, dendritic_branches_json.

5. Synapses Table (synapses.parquet)
   Rows: 1,179,169 | Columns: 28 | Size: 132 MB
   Description: Synapse data including multi-timescale weights, traces, integrity, and time constants. Key for Sections 3 and 4.
   Columns: game_id, round_number, nxer_id, pre_id, post_id, w_fast, w_slow, w_meta, is_silent, is_modulatory, integrity, axonal_delay, learning_rate_mod, synapse_type, potential_delta_w, tau_fast, tau_slow, tau_meta, tau_ltp, tau_ltd, learning_rate, plasticity_threshold, pre_trace, post_trace, pre_trace_ltd, associative_strength, neighbor_synapse_ids_json, neighbor_count.

6. Foods Table (foods.parquet)
   Rows: 59,490 | Columns: 11 | Size: 475 KB
   Description: Food source state including position, remaining amount, and respawn status.
   Columns: game_id, round_number, food_id, anchor_x, anchor_y, pos_x, pos_y, alive, respawn_at_tick, remaining, progress_json.

7. Time Series Table (time_series.parquet)
   Rows: 9,170,708 | Columns: 82 | Size: 1.56 GB
   Description: Comprehensive time series data including network activity, branching ratio, neuromodulator levels, oscillator components, CFC metrics, trinary distributions, synaptic statistics, dendritic metrics, ACW estimates, and ITU fitness. Essential for all sections.
   Columns: game_id, round_number, tick, timestamp, network_activity, branching_ratio, total_energy, average_energy, energy_efficiency, temporal_sync, dopamine, serotonin, acetylcholine, norepinephrine, oscillator_drive, oscillator_low, oscillator_mid, oscillator_high, phase_coherence, cfc_low_mid, cfc_mid_high, excitatory_fraction, inhibitory_fraction, neutral_fraction, autoreceptor_mean, autoreceptor_std, adaptation_mean, spontaneous_firing_count, driven_firing_count, silent_synapse_count, active_synapse_count, modulatory_synapse_count, mean_synapse_integrity, mean_plateau_potential, mean_branch_potential, dendritic_spike_count, mean_intrinsic_timescale, timescale_heterogeneity, membrane_potential_mean, membrane_potential_std, mean_w_fast, mean_w_slow, mean_w_meta, std_w_fast, std_w_slow, std_w_meta, mean_pre_trace, mean_post_trace, mean_pre_trace_ltd, std_pre_trace, mean_delta_w, ltp_rate, ltd_rate, mean_associativity_contribution, associativity_event_count, mean_learning_rate_mod, std_learning_rate_mod, mean_autocorrelation_window, std_autocorrelation_window, autocorrelation_coefficient_mean, mean_threshold_excitatory_effective, mean_threshold_inhibitory_effective, threshold_modulation_by_ach, threshold_modulation_by_autoreceptor, ionotropic_contribution_mean, metabotropic_contribution_mean, modulator_grid_entropy, modulator_grid_gradient_magnitude, dopamine_spatial_variance, serotonin_spatial_variance, silent_synapse_fraction, silent_to_active_transitions, active_to_silent_transitions, subthreshold_integration_count, near_threshold_fraction, pac_theta_gamma, pac_delta_theta, mean_phase_velocity, itu_mean_fitness, itu_fitness_variance, itu_mutation_events, itu_pruning_events.

8. Plasticity Events Table (plasticity_events.parquet)
   Rows: 517,662 | Columns: 8 | Size: 6.6 MB
   Description: LTP and LTD events with timing and weight changes. Key for Section 4.
   Columns: game_id, round_number, tick, event_type, pre_id, post_id, delta_w, details_json.

9. NxEr Events Table (nxer_events.parquet)
   Rows: 237,628 | Columns: 6 | Size: 1.1 MB
   Description: NxEr lifecycle events including birth, death, mating, and stealing attempts.
   Columns: game_id, round_number, tick, event_type, nxer_id, details_json.

10. I/O Patterns Table (io_patterns.parquet)
    Rows: 991,500 | Columns: 6 | Size: 3.6 MB
    Description: Input/output patterns for each NxEr per tick. Useful for behavioral analysis.
    Columns: game_id, round_number, tick, nxer_id, inputs_json, outputs_json.

11. ITU Fitness Table (itu_fitness.parquet)
    Rows: 138,367 | Columns: 5 | Size: 132 KB
    Description: ITU fitness history over time. Key for Section 8.
    Columns: game_id, round_number, tick, circle_id, fitness.

12. Neuromodulator Events Table (neuromodulator_events.parquet)
    Rows: 594,900 | Columns: 7 | Size: 4 MB
    Description: Neuromodulator threshold crossing events. Key for Section 1.
    Columns: game_id, round_number, tick, modulator, level, crossed_threshold, effect.

13. Phase Events Table (phase_events.parquet)
    Rows: 216,269 | Columns: 6 | Size: 2.7 MB
    Description: Phase synchronization events including coherence measurements. Key for Section 7.
    Columns: game_id, round_number, tick, event_type, phase_coherence, details_json.

14. Dendritic Events Table (dendritic_events.parquet)
    Rows: 418,097 | Columns: 8 | Size: 7.1 MB
    Description: Dendritic spike events with branch potential and calcium influx. Related to Sections 1 and 5.
    Columns: game_id, round_number, tick, neuron_id, branch_id, branch_potential, plateau_potential, ca_influx.

15. Homeostatic Events Table (homeostatic_events.parquet)
    Rows: 396,600 | Columns: 8 | Size: 6.5 MB
    Description: Homeostatic plasticity threshold adjustments. Related to Section 4.
    Columns: game_id, round_number, tick, neuron_id, old_threshold, new_threshold, activity_level, direction.

16. Weight Evolution Events Table (weight_evolution_events.parquet)
    Rows: 991,500 | Columns: 8 | Size: 29 MB
    Description: Multi-timescale weight changes. Key for Section 3.
    Columns: game_id, round_number, tick, pre_id, post_id, w_fast_delta, w_slow_delta, w_meta_delta.

17. World Grids Table (world_grids.parquet)
    Rows: 1983 | Columns: 4 | Size: 1.5 MB
    Description: Full 2D world grid terrain data. Required for game resumption.
    Columns: game_id, round_number, world_size, grid_json.

18. Food Progress Table (food_progress.parquet)
    Rows: 48,056 | Columns: 5 | Size: 132 KB
    Description: Food harvest progress tracking. Required for game resumption.
    Columns: game_id, round_number, food_id, nxer_id, harvest_progress.

19. NxEr Visited History Table (nxer_visited_history.parquet)
    Rows: 40,557 | Columns: 6 | Size: 17 MB
    Description: Full coordinate history of cells visited by each NxEr. Required for game resumption.
    Columns: game_id, round_number, nxer_id, nxer_name, visited_coords_json, visited_count.

20. Neuron State History Table (neuron_state_history.parquet)
    Rows: 1,499,241 | Columns: 7 | Size: 6.3 MB
    Description: Last 50 states for each neuron. Required for intrinsic timescale calculation (Section 6).
    Columns: game_id, round_number, nxer_id, neuron_id, neuron_type, state_history_json, history_length.

21. Synapse Neighbor IDs Table (synapse_neighbor_ids.parquet)
    Rows: 429,649 | Columns: 7 | Size: 3.7 MB
    Description: Neighbor synapse IDs for associativity. Required for cooperative LTP (Section 4).
    Columns: game_id, round_number, nxer_id, synapse_pre_id, synapse_post_id, neighbor_synapse_ids_json, neighbor_count.

22. Silent Synapse Events Table (silent_synapse_events.parquet)
    Rows: 19,342 | Columns: 9 | Size: 74 KB
    Description: Events for synapses becoming active/silent.
    Columns: game_id, round_number, tick, pre_id, post_id, event_type, previous_state, new_state, trigger.

23. Spontaneous Events Table (spontaneous_events.parquet)
    Rows: 321,977 | Columns: 7 | Size: 3.5 MB
    Description: Spontaneous firing events. Detailed for Section 6.
    Columns: game_id, round_number, tick, neuron_id, neuron_type, membrane_potential, spontaneous_rate.

24. Autoreceptor Events Table (autoreceptor_events.parquet)
    Rows: 396,600 | Columns: 8 | Size: 125 KB
    Description: Autoreceptor modulation events. Detailed for Section 1.
    Columns: game_id, round_number, tick, neuron_id, modulator_type, autoreceptor_level, release_inhibition, threshold_change.

25. Subthreshold Events Table (subthreshold_events.parquet)
    Rows: 594,900 | Columns: 8 | Size: 18 MB
    Description: Near-threshold integrations. Detailed for Section 5.
    Columns: game_id, round_number, tick, neuron_id, membrane_potential, threshold, distance_to_threshold, input_sum.

26. Threshold Modulation Events Table (threshold_modulation_events.parquet)
    Rows: 594,900 | Columns: 9 | Size: 10 MB
    Description: Breakdown of Ach vs autoreceptor on thresholds.
    Columns: game_id, round_number, tick, neuron_id, base_threshold, ach_contribution, autoreceptor_contribution, final_threshold, acetylcholine_level.

27. Associativity Events Table (associativity_events.parquet)
    Rows: 594,900 | Columns: 7 | Size: 112 KB
    Description: Cooperative LTP events. For Section 4 validation.
    Columns: game_id, round_number, tick, post_neuron_id, participating_synapses, cooperative_boost, total_weight_change.

28. Hall of Fame Table (hall_of_fame.parquet)
    Rows: 59,264 | Columns: 16 | Size: 849 KB
    Description: Top performing NxErs by category.
    Columns: game_id, round_number, category, rank, name, is_male, can_land, can_sea, stats_food_found, stats_food_taken, stats_explored, stats_time_lived_s, stats_mates_performed, stats_energy_efficiency, stats_temporal_sync_score, stats_fitness_score.

Relationships Between Tables

• Most tables join on game_id and round_number.
• Agent-level: nxers → network_params, neurons, synapses (via nxer_id).
• Neuron-level: neurons → dendritic_events, homeostatic_events, spontaneous_events, etc. (via neuron_id).
• Synapse-level: synapses → plasticity_events, weight_evolution_events (via pre_id, post_id).
• Time series: time_series → event tables (via tick for correlation).
• Behavioral: nxers → io_patterns, nxer_events, nxer_visited_history.
• World: games → world_grids, foods, food_progress.

Usage

Loading with Python (pandas)

import pandas as pd

# Load tables
games = pd.read_parquet('games.parquet')
time_series = pd.read_parquet('time_series.parquet')

# Example: Filter time series for a specific game
game_ts = time_series[time_series['game_id'] == 'some_game_id']

Loading with Hugging Face Datasets

from datasets import load_dataset

# Load from Hugging Face Hub (assuming uploaded as 'DavidVivancos/NeuraxonLife2-DeepTimeSeries')
dataset = load_dataset("DavidVivancos/NeuraxonLife2-DeepTimeSeries")

# Access tables
time_series = dataset['time_series']

Example Analyses

1. Branching Ratio Over Time

import matplotlib.pyplot as plt
import pandas as pd

ts = pd.read_parquet('time_series.parquet')
game_ts = ts[ts['game_id'] == ts['game_id'].unique()[0]]
plt.plot(game_ts['tick'], game_ts['branching_ratio'])
plt.xlabel('Tick')
plt.ylabel('Branching Ratio')
plt.title('Network Criticality Over Time')
plt.show()

2. Plasticity Event Analysis

events = pd.read_parquet('plasticity_events.parquet')
ltp_count = events[events['event_type'] == 'LTP'].shape[0]
ltd_count = events[events['event_type'] == 'LTD'].shape[0]
print(f"LTP/LTD Ratio: {ltp_count / ltd_count:.2f}")

3. Fitness Correlation

from sklearn.linear_model import LinearRegression
import numpy as np

nxers = pd.read_parquet('nxers.parquet')
X = nxers[['stats_temporal_sync_score']].values
y = nxers['stats_fitness_score'].values
model = LinearRegression().fit(X, y)
print(f"R²: {model.score(X, y):.3f}")

Dataset Creation

Generated from 1983 Neuraxon Game of Life JSON save files using converter version 1.0.0:

1. Scanned and processed JSON files.
2. Extracted hierarchical data into tables.
3. Converted to Parquet with Snappy compression.
4. Validated row counts and relationships.

Citation

@dataset{NeuraxonLife2.1-TimeSeries
  title={Neuraxon Game of Life 2.1 Research Dataset Deep Time Series Exploration},
  author={Vivancos, David and Sanchez, Jose},
  year={2026},
  publisher={Hugging Face},
  url={https://huggingface.co/datasets/DavidVivancos/NeuraxonLife2.1-TimeSeries}
}

License

This dataset is released under the CC BY 4.0 license.

Additional Information

Authors

• David Vivancos / Artificiology Research https://artificiology.com/ - Qubic Science https://qubic.org/
• Dr. Jose Sanchez / UNIR - Qubic Science https://qubic.org/

Dataset Curators

• David Vivancos / Artificiology Research https://artificiology.com/ - Qubic Science https://qubic.org/
• Dr. Jose Sanchez / UNIR - Qubic Science https://qubic.org/

Version History

• v2.1.0 (January 4th 2026): Initial release with deep time series focus.

Contact

For questions or issues, please open a GitHub issue at https://github.com/DavidVivancos/Neuraxon or contact [[email protected]].