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Old-ShatterhandOld-Shatterhand
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Update for setup on UdS HPC
1 parent a206cb7 commit 861d2f1

22 files changed

Lines changed: 793 additions & 242 deletions

‎configs/downstream/final_ml_small.yaml‎

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seed: [1234, 1337]
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root_dir: /scratch/SCRATCH_SAS/roman/Gothenburg/GIFFLAR/data_final_small
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logs_dir: /scratch/SCRATCH_SAS/roman/Gothenburg/GIFFLAR/logs_final_small
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datasets:
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#- name: Glycosylation
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# task: classification
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#- name: Tissue
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# task: multilabel
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- name: Taxonomy_Kingdom
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task: multilabel
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pre-transforms:
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GIFFLARTransform:
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GNNGLYTransform:
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ECFPTransform:
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SweetNetTransform:
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RGCNTransform:
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RandomWalkPE:
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dim: 20
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individual: False
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LaplacianPE:
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dim: 20
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individual: False
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model:
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- name: mlp
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feat_dim: 1024
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hidden_dim: 128
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batch_size: 32
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num_layers: 3
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epochs: 100
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patience: 30
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learning_rate: 0.001
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optimizer: Adam
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- name: sweetnet
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feat_dim: 128
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hidden_dim: 128
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batch_size: 32
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num_layers: 16
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epochs: 100
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patience: 30
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learning_rate: 0.001
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optimizer: Adam
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suffix:
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- name: gnngly
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feat_dim: 128
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hidden_dim: 128
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batch_size: 128
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num_layers: 32
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epochs: 100
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patience: 30
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learning_rate: 0.001
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optimizer: Adam
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suffix:
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# - name: rgcn
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# feat_dim: 128
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# hidden_dim: 128
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# batch_size: 32
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# num_layers: 8
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# epochs: 100
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# learning_rate: 0.001
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# optimizer: Adam
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# suffix:
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# - name: gifflar
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# feat_dim: 128
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# hidden_dim: 128
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# batch_size: 32
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# num_layers: 8
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# epochs: 100
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# learning_rate: 0.001
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# optimizer: Adam
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# pooling: global_mean
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# suffix:

‎configs/downstream/final_spectrum.yaml‎

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seed: [42, 1234, 1337]
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seed: 42
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root_dir: /scratch/SCRATCH_SAS/roman/Gothenburg/GIFFLAR/data_final
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logs_dir: /scratch/SCRATCH_SAS/roman/Gothenburg/GIFFLAR/logs_final
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datasets:
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dim: 20
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individual: False
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model:
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- name: mlp
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feat_dim: 1024
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hidden_dim: 1024
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batch_size: 16
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num_layers: 3
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epochs: 100
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patience: 30
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learning_rate: 0.001
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optimizer: Adam
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- name: sweetnet
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feat_dim: 128
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hidden_dim: 1024
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batch_size: 64
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num_layers: 16
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epochs: 100
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patience: 30
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learning_rate: 0.001
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optimizer: Adam
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suffix:
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# - name: mlp
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# feat_dim: 1024
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# hidden_dim: 1024
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# batch_size: 16
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# num_layers: 3
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# epochs: 100
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# patience: 30
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# learning_rate: 0.001
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# optimizer: Adam
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# # - name: sweetnet
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# # feat_dim: 128
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# # hidden_dim: 1024
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# # batch_size: 8
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# # num_layers: 16
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# # epochs: 100
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# # patience: 30
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# # learning_rate: 0.001
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# # optimizer: Adam
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# # suffix:
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- name: gnngly
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feat_dim: 128
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hidden_dim: 1024
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batch_size: 16
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batch_size: 8
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num_layers: 8
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epochs: 100
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patience: 30
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- name: rgcn
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feat_dim: 128
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hidden_dim: 1024
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batch_size: 16
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batch_size: 8
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num_layers: 8
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epochs: 100
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learning_rate: 0.001
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- name: gifflar
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feat_dim: 128
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hidden_dim: 1024
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batch_size: 16
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batch_size: 8
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num_layers: 8
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epochs: 100
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learning_rate: 0.001

‎configs/downstream/final_spectrum_small.yaml‎

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seed: [42, 1234, 1337]
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seed: 42
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root_dir: /scratch/SCRATCH_SAS/roman/Gothenburg/GIFFLAR/data_final_small
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logs_dir: /scratch/SCRATCH_SAS/roman/Gothenburg/GIFFLAR/logs_final_small
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datasets:
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dim: 20
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individual: False
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model:
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- name: mlp
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feat_dim: 1024
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hidden_dim: 1024
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batch_size: 256
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num_layers: 3
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epochs: 100
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patience: 30
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learning_rate: 0.001
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optimizer: Adam
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- name: sweetnet
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feat_dim: 128
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hidden_dim: 256
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batch_size: 256
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num_layers: 16
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epochs: 100
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patience: 30
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learning_rate: 0.001
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optimizer: Adam
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suffix:
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- name: gnngly
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feat_dim: 128
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hidden_dim: 256
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batch_size: 256
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num_layers: 8
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epochs: 100
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patience: 30
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learning_rate: 0.001
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optimizer: Adam
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suffix:
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#- name: mlp
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# feat_dim: 1024
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# hidden_dim: 128
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# batch_size: 32
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# num_layers: 3
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# epochs: 100
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# patience: 30
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# learning_rate: 0.001
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# optimizer: Adam
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#- name: sweetnet
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# feat_dim: 128
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# hidden_dim: 128
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# batch_size: 32
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# num_layers: 16
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# epochs: 100
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# patience: 30
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# learning_rate: 0.001
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# optimizer: Adam
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# suffix:
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#- name: gnngly
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# feat_dim: 128
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# hidden_dim: 128
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# batch_size: 128
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# num_layers: 32
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# epochs: 100
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# patience: 30
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# learning_rate: 0.001
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# optimizer: Adam
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# suffix:
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- name: rgcn
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feat_dim: 128
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hidden_dim: 256
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batch_size: 64
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hidden_dim: 128
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batch_size: 32
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num_layers: 8
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epochs: 100
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learning_rate: 0.001
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optimizer: Adam
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suffix:
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- name: gifflar
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feat_dim: 128
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hidden_dim: 256
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batch_size: 128
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hidden_dim: 128
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batch_size: 32
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num_layers: 8
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epochs: 100
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learning_rate: 0.001

‎configs/downstream/new_all.yaml‎

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seed: 42 # , 1234, 1227]
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root_dir: /scratch/SCRATCH_SAS/roman/Gothenburg/GIFFLAR/data_new
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logs_dir: /scratch/SCRATCH_SAS/roman/Gothenburg/GIFFLAR/logs_new
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datasets:
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- name: Glycosylation
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task: classification
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# - name: Tissue
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# task: multilabel
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# - name: Taxonomy_Kingdom
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# task: multilabel
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pre-transforms:
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GIFFLARTransform:
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GNNGLYTransform:
14+
ECFPTransform:
15+
SweetNetTransform:
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RGCNTransform:
17+
RandomWalkPE:
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dim: 20
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individual: False
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LaplacianPE:
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dim: 20
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individual: False
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model:
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# - name: rf
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# n_estimators: 500
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# n_jobs: -1
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# random_state: 42
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# - name: svm
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# random_state: 42
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# - name: xgb
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# random_state: 42
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# - name: mlp
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# feat_dim: 1024
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# hidden_dim: 1024
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# batch_size: 32
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# num_layers: 3
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# epochs: 100
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# patience: 30
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# learning_rate: 0.001
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# optimizer: Adam
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- name: sweetnet
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feat_dim: 128
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hidden_dim: 128
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batch_size: 32
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num_layers: 16
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epochs: 100
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patience: 30
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learning_rate: 0.001
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optimizer: Adam
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suffix:
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# - name: gnngly
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# feat_dim: 128
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# hidden_dim: 128
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# batch_size: 32
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# num_layers: 8
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# epochs: 100
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# patience: 30
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# learning_rate: 0.001
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# optimizer: Adam
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# suffix:
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# - name: rgcn
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# feat_dim: 128
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# hidden_dim: 128
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# batch_size: 32
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# num_layers: 8
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# epochs: 100
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# learning_rate: 0.001
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# optimizer: Adam
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# suffix:
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# - name: gifflar
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# feat_dim: 128
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# hidden_dim: 128
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# batch_size: 32
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# num_layers: 8
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# epochs: 100
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# learning_rate: 0.001
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# optimizer: Adam
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# pooling: global_mean
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# suffix:
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# - name: glylm
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# token_file: /scratch/SCRATCH_SAS/roman/Gothenburg/GIFFLAR/unique/GlyLM/bpe_glyles_2500.pkl
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# model_dir: /scratch/SCRATCH_SAS/roman/Gothenburg/GIFFLAR/unique/GlyLM/bpe_glyles_2500_t6/checkpoint-185120
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# hidden_dim: 320
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# epochs: 100
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# learning_rate: 0.001
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# batch_size: 256
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# optimizer: Adam
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# suffix: _bpe_glyles_25_t6_20

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