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README.md

@@ -1,3 +1,18 @@
----
-license: mit
----
+---
+license: mit
+---
+
+# Gyrokinetics compression validation dataset
+Subsampled 5D gyrokinetics dataset to reproduce Table 1 from the paper: __Physics-Informed Neural Compression of High-Dimensional Plasma Data__.
+
+
+| Method        | CR        | PSNR ↑           | EPE ↓            | L1(Q) ↓           | PSNR($\phi$) ↑        | WD($k_y^{\text{spec}}$) ↓ | WD($Q^{\text{spec}}$) ↓ |
+|---------------|-----------|------------------|------------------|-------------------|------------------|------------------|------------------|
+| ZFP           | 901×      | 28.97 ± 1.09     | 0.169 ± 0.10     | 107.48 ± 49.35    | −16.20 ± 7.09    | 0.020 ± 0.01    | 0.116 ± 0.20    |
+| Wavelet       | 936×      | 33.07 ± 1.18     | 0.063 ± 0.04     | 107.74 ± 49.51    | −13.24 ± 9.20    | 0.020 ± 0.01    | **0.010 ± 0.00** |
+| PCA           | 1020×     | 32.09 ± 0.98     | 0.091 ± 0.06     | 67.60 ± 36.08     | −10.22 ± 6.89    | 0.020 ± 0.01    | 0.011 ± 0.00    |
+| JPEG2000      | 1000×     | 34.33 ± 0.95     | 0.062 ± 0.05     | 103.91 ± 44.12    | −20.85 ± 6.50    | 0.020 ± 0.01    | 0.035 ± 0.03    |
+| NF            | 1167×     | **36.91 ± 0.93** | **0.039 ± 0.03** | 61.50 ± 16.91     | 1.24 ± 5.99      | 0.017 ± 0.01    | 0.017 ± 0.00    |
+| PINC-NF       | 1167×     | _35.76 ± 1.38_   | _0.046 ± 0.03_   | **2.18 ± 8.33**   | **13.50 ± 4.44** | **0.006 ± 0.00**| 0.015 ± 0.00    |
+| AE + EVA      | 716×      | 35.64 ± 2.03     | 0.093 ± 0.09     | _15.01 ± 16.42_   | 6.72 ± 4.98      | 0.016 ± 0.01    | 0.012 ± 0.01    |
+| VQ-VAE + EVA  | 301×      | 32.61 ± 1.58     | 0.101 ± 0.08     | 44.26 ± 40.97     | _7.66 ± 3.75_    | _0.015 ± 0.01_  | 0.013 ± 0.01    |

autoencoders/ae/best.pth

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autoencoders/ae/config.yaml

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+stage: peft
+experiment_id: test
+seed: 0
+output_path: /local00/bioinf/gyrokinetics/debug/20251109_180156
+ddp:
+  enable: false
+  n_nodes: 1
+amp:
+  enable: true
+  bfloat: true
+eval: true
+device: cuda
+ae_checkpoint: /system/user/publicwork/gyrokinetics_checkpoints/diff_ae/20251015_182239
+diff_checkpoint: null
+dataset:
+  name: cyclone
+  path: /local00/bioinf/gyrokinetics/preprocessed
+  normalization: zscore
+  normalization_scope: dataset
+  minmax_beta1: 8
+  minmax_beta2: 4
+  offset: 0
+  subsample: 1
+  spatial_ifft: true
+  separate_zf: true
+  real_potens: true
+  split_into_bands: null
+  log_transform: false
+  num_workers: 4
+  active_keys:
+  - re
+  - im
+  input_fields:
+  - df
+  - phi
+  - flux
+  training_trajectories: iteration_{0-5,7-12,14-31,33-58,60-67,69-82,84-99}.h5
+  validation_trajectories:
+  - iteration_13.h5
+  - iteration_59.h5
+  - iteration_68.h5
+  partial_holdouts: null
+  training_cond_filters:
+    last_fluxes:
+    - 1.0
+    - .inf
+    first_fluxes:
+    - 1.0
+    - .inf
+  eval_cond_filters:
+    last_fluxes:
+    - 1.0
+    - .inf
+    first_fluxes:
+    - 1.0
+    - .inf
+  augment: null
+autoencoder:
+  name: ae
+  model_type: ae
+  bundle_seq_length: 1
+  latent_dim: 1024
+  act_fn: GELU
+  decouple_mu: true
+  conditioning:
+  - itg
+  - dg
+  - s_hat
+  - q
+  extra_zf_loss: false
+  init_weights: xavier_uniform
+  patching_init_weights: xavier_uniform
+  cond_init_weights: xavier_uniform
+  loss_scheduler:
+    df:
+      start: 0.1
+      end: 1.0
+      start_fraction: 0.0
+      end_fraction: 0.1
+    flux_int:
+      start: 0.0
+      end: 1.0
+      start_fraction: ${var.start_fraction_int}
+      end_fraction: ${var.end_fraction_int}
+    phi_int:
+      start: 0.0
+      end: 1.0
+      start_fraction: ${var.start_fraction_int}
+      end_fraction: ${var.end_fraction_int}
+    kyspec:
+      start: 0.0
+      end: 1.0
+      start_fraction: ${var.start_fraction_spec}
+      end_fraction: ${var.end_fraction_spec}
+    kxspec:
+      start: 0.0
+      end: 1.0
+      start_fraction: ${var.start_fraction_spec}
+      end_fraction: ${var.end_fraction_spec}
+    qspec:
+      start: 0.0
+      end: 1.0
+      start_fraction: ${var.start_fraction_spec}
+      end_fraction: ${var.end_fraction_spec}
+    phi_zf:
+      start: 0.0
+      end: 1.0
+      start_fraction: ${var.start_fraction_spec}
+      end_fraction: ${var.end_fraction_spec}
+    mass:
+      start: 0.0
+      end: 1.0
+      start_fraction: ${var.start_fraction_spec}
+      end_fraction: ${var.end_fraction_spec}
+    qspec_monotonicity:
+      start: 0.0
+      end: 1.0
+      start_fraction: ${var.start_fraction_mono}
+      end_fraction: ${var.end_fraction_mono}
+    kyspec_monotonicity:
+      start: 0.0
+      end: 1.0
+      start_fraction: ${var.start_fraction_mono}
+      end_fraction: ${var.end_fraction_mono}
+  loss_weights:
+    df: 10.0
+  extra_loss_weights:
+    flux_int: 0.5
+    phi_int: 0.5
+    kxspec: 0.001
+    kyspec: 0.001
+    qspec: 0.001
+    phi_zf: 0.01
+    mass: 0.1
+    qspec_monotonicity: 0.8
+    kyspec_monotonicity: 0.8
+  patch:
+    patch_size:
+    - 6
+    - 0
+    - 3
+    - 5
+    - 6
+    window_size:
+    - 6
+    - 0
+    - 6
+    - 9
+    - 6
+    merging_hidden_ratio: 1.0
+    unmerging_hidden_ratio: 1.0
+    c_multiplier: 1.0
+  vit:
+    num_heads:
+    - 16
+    depth:
+    - 4
+    gradient_checkpoint: true
+    use_abs_pe: false
+    use_rpb: true
+    use_rope: true
+    gated_attention: true
+    modulation: dit
+    drop_path: 0.1
+    mid_norm_learnable: false
+    norm_layer: LayerNorm
+  bottleneck:
+    dim: 128
+    norm_learnable: true
+    num_heads: 2
+    depth: 2
+    use_linear: true
+  peft:
+    method: eva
+    lora:
+      r: 32
+      lora_alpha: 1
+      lora_dropout: 0.0
+      bias: none
+      strategy: mlp_only
+    eva:
+      r: 32
+      lora_alpha: 1
+      lora_dropout: 0.0
+      bias: none
+      strategy: mlp_only
+      rho: 2.0
+      tau: 0.99
+      use_label_mask: true
+      whiten: false
+      adjust_scaling_factors: true
+    save:
+      save_lora_only: true
+      save_full_model: false
+diffusion:
+  model:
+    name: dit
+    latent_dim: 256
+    conditioning:
+    - itg
+    - dg
+    - s_hat
+    - q
+    vit:
+      num_heads: 8
+      depth: 4
+      gradient_checkpoint: false
+      patch_skip: true
+      modulation: film
+      drop_path: 0.1
+    act_fn: GELU
+    use_rpb: true
+    use_rope: false
+  scheduler:
+    name: ddpm
+    train_timesteps: 20
+    num_inference_timesteps: 20
+    beta_start: 0.0001
+    beta_end: 0.01
+    beta_schedule: linear
+    prediction_type: epsilon
+logging:
+  writer: wandb
+  mode: online
+  entity: ukaea-mhd
+  project: diffusion
+  run_id: peft_ae_20251109_180156
+  tqdm: true
+  model_summary: false
+  tags:
+  - peft
+  - eva
+  - AE
+  - cr1080
+  - v8
+  - COMPRESSION
+  compression_ratio: false
+  name_suffix: eva_AE_cr1080_BIG_v8_v5
+training:
+  batch_size: 16
+  n_epochs: 200
+  num_workers: 4
+  pin_memory: true
+  optimizer: muon
+  learning_rate: 0.0002
+  weight_decay: 1.0e-05
+  scheduler: cosine_with_min_lr
+  min_lr: 4.0e-06
+  clip_grad: true
+  clip_to: 1.0
+  use_latest_checkpoint: false
+  gradnorm_balancer: none
+  loss_type: complex_l1
+  exclude_from_wd:
+  - cond
+  integral_loss_type: int_norm_l1
+  spectral_loss_type: energy_normalized_log_l1
+  ds: 0.01
+  eval_loss_type: mse
+  eval_integral_loss_type: mse
+  eval_spectral_loss_type: l1
+validation:
+  batch_size: 16
+  n_eval_steps: 2
+  validate_every_n_epochs: 10
+  eval_integrals: true
+  tracked_val_losses:
+  - df
+  - flux_int
+  - phi_int
+var:
+  start_fraction_int: 0.0
+  end_fraction_int: 0.3
+  start_fraction_spec: 0.3
+  end_fraction_spec: 0.5
+  start_fraction_mono: 0.5
+  end_fraction_mono: 0.7

autoencoders/vapor/best.pth

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autoencoders/vqvae/best.pth

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autoencoders/vqvae/config.yaml

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+stage: peft
+experiment_id: test
+seed: 0
+output_path: /local00/bioinf/gyrokinetics/debug/20250919_073133
+ddp:
+  enable: false
+  n_nodes: 1
+amp:
+  enable: true
+  bfloat: true
+eval: true
+device: cuda
+ae_checkpoint: /system/user/publicwork/gyrokinetics_checkpoints/compression_ckpts/20250911_143815
+diff_checkpoint: null
+dataset:
+  name: cyclone
+  path: /local00/bioinf/gyrokinetics/preprocessed
+  normalization: zscore
+  normalization_scope: dataset
+  minmax_beta1: 8
+  minmax_beta2: 4
+  offset: 0
+  subsample: 1
+  spatial_ifft: true
+  separate_zf: true
+  real_potens: false
+  split_into_bands: null
+  log_transform: false
+  num_workers: 4
+  active_keys:
+  - re
+  - im
+  input_fields:
+  - df
+  - phi
+  - flux
+  training_trajectories: iteration_{0-5,7-12,14-31,33-58}.h5
+  validation_trajectories:
+  - iteration_13.h5
+  - iteration_59.h5
+  - iteration_68.h5
+  partial_holdouts: null
+  training_cond_filters:
+    last_fluxes:
+    - 1.0
+    - .inf
+    first_fluxes:
+    - 1.0
+    - .inf
+  eval_cond_filters:
+    last_fluxes:
+    - 1.0
+    - .inf
+    first_fluxes:
+    - 1.0
+    - .inf
+  augment: null
+autoencoder:
+  name: vqvae
+  model_type: vqvae
+  bundle_seq_length: 1
+  latent_dim: 1024
+  act_fn: GELU
+  decouple_mu: true
+  conditioning:
+  - itg
+  - dg
+  - s_hat
+  - q
+  extra_zf_loss: false
+  init_weights: xavier_uniform
+  patching_init_weights: xavier_uniform
+  cond_init_weights: xavier_uniform
+  vq:
+    codebook_size: 8192
+    embedding_dim: 128
+    commitment_weight: 0.3
+    codebook_type: euclidean
+    ema_decay: 0.99
+    entropy_loss_weight: 0.01
+    threshold_ema_dead_code: 2
+    rotation_trick: false
+  loss_scheduler:
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+    phi_int: null
+    kyspec: null
+  loss_weights:
+    df: 10.0
+    vq_commit: 10.0
+  extra_loss_weights:
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+    phi_int: 1.0
+    kxspec: 1.0
+    kyspec: 1.0
+    qspec: 1.0
+    phi_zf: 1.0
+    mass: 1.0
+    qspec_monotonicity: 0.0
+    kyspec_monotonicity: 0.0
+  patch:
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+    - 4
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+    - 4
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+    - 4
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+    unmerging_hidden_ratio: 1.0
+    c_multiplier: 1.0
+  vit:
+    num_heads:
+    - 16
+    depth:
+    - 4
+    gradient_checkpoint: true
+    use_abs_pe: true
+    use_rpb: true
+    use_rope: true
+    gated_attention: true
+    modulation: dit
+    drop_path: 0.1
+    mid_norm_learnable: false
+    norm_layer: LayerNorm
+  gfm:
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+    high_freq_num: 5
+    low_freq_num: 5
+    phi_num: 32
+    alpha: 0.01
+    use_bias: true
+    mode: reshape
+    max_spatial_dims: 32
+  bottleneck:
+    dim: 128
+    norm_learnable: true
+    num_heads: 2
+    depth: 2
+    use_linear: true
+  peft:
+    method: eva
+    lora:
+      r: 32
+      lora_alpha: 1
+      lora_dropout: 0.0
+      bias: none
+      strategy: attention_mlp
+    eva:
+      r: 32
+      lora_alpha: 1
+      lora_dropout: 0.0
+      bias: none
+      strategy: attention_mlp
+      rho: 2.0
+      tau: 0.99
+      use_label_mask: true
+      whiten: false
+      adjust_scaling_factors: true
+      num_batches: 0
+    save:
+      save_lora_only: true
+      save_full_model: false
+diffusion:
+  model:
+    name: dit
+    latent_dim: 256
+    conditioning:
+    - itg
+    - dg
+    - s_hat
+    - q
+    vit:
+      num_heads: 8
+      depth: 4
+      gradient_checkpoint: false
+      patch_skip: true
+      modulation: film
+      drop_path: 0.1
+    act_fn: GELU
+    use_rpb: true
+    use_rope: false
+  scheduler:
+    name: ddpm
+    train_timesteps: 20
+    num_inference_timesteps: 20
+    beta_start: 0.0001
+    beta_end: 0.01
+    beta_schedule: linear
+    prediction_type: epsilon
+logging:
+  writer: wandb
+  mode: online
+  entity: ukaea-mhd
+  project: diffusion
+  run_id: peft_vqvae_20250919_073133
+  tqdm: true
+  model_summary: false
+  tags:
+  - peft
+  - v7
+  - eva
+  - DLcL1
+  - SLlogRl1
+  - v6_v2
+  - VQVAE
+  compression_ratio: false
+  name_suffix: peft_VQVAEcr40960_ep100_DLcL1_SLlogRl1_lr2e-4_eva_r32_attmlp_rho2_tau099_v2
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+  n_epochs: 100
+  num_workers: 4
+  pin_memory: true
+  optimizer: muon
+  learning_rate: 0.0002
+  weight_decay: 1.0e-05
+  scheduler: cosine_with_min_lr
+  min_lr: 4.0e-06
+  clip_grad: true
+  clip_to: 1.0
+  gradnorm_balancer: none
+  loss_type: complex_l1
+  exclude_from_wd:
+  - cond
+  integral_loss_type: int_norm_l1
+  spectral_loss_type: log_relative_l1
+  ds: 0.01
+  eval_loss_type: mse
+  eval_integral_loss_type: mse
+  eval_spectral_loss_type: l1
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