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AIDO.Protein-16B-dms-substitutions-Q53Z42_HUMAN_McShan_2019_binding-TAPBPR

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Caleb Ellington commited on
Commit
92a5ee5
·
1 Parent(s): 44482c5

update with major refactor

Browse files
Files changed (5) hide show
  1. fold0/config.yaml +5 -5
  2. fold1/config.yaml +5 -5
  3. fold2/config.yaml +5 -5
  4. fold3/config.yaml +5 -5
  5. fold4/config.yaml +5 -5
fold0/config.yaml CHANGED
@@ -141,10 +141,10 @@ trainer:
141
  reload_dataloaders_every_n_epochs: 0
142
  default_root_dir: logs
143
  model:
144
- class_path: genbio_finetune.tasks.SequenceRegression
145
  init_args:
146
  backbone:
147
- class_path: genbio_finetune.models.proteinfm_v1
148
  init_args:
149
  from_scratch: false
150
  use_peft: true
@@ -156,7 +156,7 @@ model:
156
  model_init_args: null
157
  max_length: 2048
158
  adapter:
159
- class_path: genbio_finetune.models.MLPPoolAdapter
160
  init_args:
161
  pooling: mean_pooling
162
  hidden_sizes:
@@ -180,13 +180,13 @@ model:
180
  differentiable: false
181
  fused: null
182
  lr_scheduler:
183
- class_path: genbio_finetune.lr_schedulers.CosineWithWarmup
184
  init_args:
185
  warmup_ratio: 0.05
186
  strict_loading: true
187
  reset_optimizer_states: false
188
  data:
189
- class_path: genbio_finetune.data.DMSFitnessPrediction
190
  init_args:
191
  path: genbio-ai/ProteinGYM-DMS
192
  train_split_files:
 
141
  reload_dataloaders_every_n_epochs: 0
142
  default_root_dir: logs
143
  model:
144
+ class_path: modelgenerator.tasks.SequenceRegression
145
  init_args:
146
  backbone:
147
+ class_path: modelgenerator.backbones.proteinfm_v1
148
  init_args:
149
  from_scratch: false
150
  use_peft: true
 
156
  model_init_args: null
157
  max_length: 2048
158
  adapter:
159
+ class_path: modelgenerator.adapters.MLPPoolAdapter
160
  init_args:
161
  pooling: mean_pooling
162
  hidden_sizes:
 
180
  differentiable: false
181
  fused: null
182
  lr_scheduler:
183
+ class_path: modelgenerator.lr_schedulers.CosineWithWarmup
184
  init_args:
185
  warmup_ratio: 0.05
186
  strict_loading: true
187
  reset_optimizer_states: false
188
  data:
189
+ class_path: modelgenerator.data.DMSFitnessPrediction
190
  init_args:
191
  path: genbio-ai/ProteinGYM-DMS
192
  train_split_files:
fold1/config.yaml CHANGED
@@ -141,10 +141,10 @@ trainer:
141
  reload_dataloaders_every_n_epochs: 0
142
  default_root_dir: logs
143
  model:
144
- class_path: genbio_finetune.tasks.SequenceRegression
145
  init_args:
146
  backbone:
147
- class_path: genbio_finetune.models.proteinfm_v1
148
  init_args:
149
  from_scratch: false
150
  use_peft: true
@@ -156,7 +156,7 @@ model:
156
  model_init_args: null
157
  max_length: 2048
158
  adapter:
159
- class_path: genbio_finetune.models.MLPPoolAdapter
160
  init_args:
161
  pooling: mean_pooling
162
  hidden_sizes:
@@ -180,13 +180,13 @@ model:
180
  differentiable: false
181
  fused: null
182
  lr_scheduler:
183
- class_path: genbio_finetune.lr_schedulers.CosineWithWarmup
184
  init_args:
185
  warmup_ratio: 0.05
186
  strict_loading: true
187
  reset_optimizer_states: false
188
  data:
189
- class_path: genbio_finetune.data.DMSFitnessPrediction
190
  init_args:
191
  path: genbio-ai/ProteinGYM-DMS
192
  train_split_files:
 
141
  reload_dataloaders_every_n_epochs: 0
142
  default_root_dir: logs
143
  model:
144
+ class_path: modelgenerator.tasks.SequenceRegression
145
  init_args:
146
  backbone:
147
+ class_path: modelgenerator.backbones.proteinfm_v1
148
  init_args:
149
  from_scratch: false
150
  use_peft: true
 
156
  model_init_args: null
157
  max_length: 2048
158
  adapter:
159
+ class_path: modelgenerator.adapters.MLPPoolAdapter
160
  init_args:
161
  pooling: mean_pooling
162
  hidden_sizes:
 
180
  differentiable: false
181
  fused: null
182
  lr_scheduler:
183
+ class_path: modelgenerator.lr_schedulers.CosineWithWarmup
184
  init_args:
185
  warmup_ratio: 0.05
186
  strict_loading: true
187
  reset_optimizer_states: false
188
  data:
189
+ class_path: modelgenerator.data.DMSFitnessPrediction
190
  init_args:
191
  path: genbio-ai/ProteinGYM-DMS
192
  train_split_files:
fold2/config.yaml CHANGED
@@ -141,10 +141,10 @@ trainer:
141
  reload_dataloaders_every_n_epochs: 0
142
  default_root_dir: logs
143
  model:
144
- class_path: genbio_finetune.tasks.SequenceRegression
145
  init_args:
146
  backbone:
147
- class_path: genbio_finetune.models.proteinfm_v1
148
  init_args:
149
  from_scratch: false
150
  use_peft: true
@@ -156,7 +156,7 @@ model:
156
  model_init_args: null
157
  max_length: 2048
158
  adapter:
159
- class_path: genbio_finetune.models.MLPPoolAdapter
160
  init_args:
161
  pooling: mean_pooling
162
  hidden_sizes:
@@ -180,13 +180,13 @@ model:
180
  differentiable: false
181
  fused: null
182
  lr_scheduler:
183
- class_path: genbio_finetune.lr_schedulers.CosineWithWarmup
184
  init_args:
185
  warmup_ratio: 0.05
186
  strict_loading: true
187
  reset_optimizer_states: false
188
  data:
189
- class_path: genbio_finetune.data.DMSFitnessPrediction
190
  init_args:
191
  path: genbio-ai/ProteinGYM-DMS
192
  train_split_files:
 
141
  reload_dataloaders_every_n_epochs: 0
142
  default_root_dir: logs
143
  model:
144
+ class_path: modelgenerator.tasks.SequenceRegression
145
  init_args:
146
  backbone:
147
+ class_path: modelgenerator.backbones.proteinfm_v1
148
  init_args:
149
  from_scratch: false
150
  use_peft: true
 
156
  model_init_args: null
157
  max_length: 2048
158
  adapter:
159
+ class_path: modelgenerator.adapters.MLPPoolAdapter
160
  init_args:
161
  pooling: mean_pooling
162
  hidden_sizes:
 
180
  differentiable: false
181
  fused: null
182
  lr_scheduler:
183
+ class_path: modelgenerator.lr_schedulers.CosineWithWarmup
184
  init_args:
185
  warmup_ratio: 0.05
186
  strict_loading: true
187
  reset_optimizer_states: false
188
  data:
189
+ class_path: modelgenerator.data.DMSFitnessPrediction
190
  init_args:
191
  path: genbio-ai/ProteinGYM-DMS
192
  train_split_files:
fold3/config.yaml CHANGED
@@ -141,10 +141,10 @@ trainer:
141
  reload_dataloaders_every_n_epochs: 0
142
  default_root_dir: logs
143
  model:
144
- class_path: genbio_finetune.tasks.SequenceRegression
145
  init_args:
146
  backbone:
147
- class_path: genbio_finetune.models.proteinfm_v1
148
  init_args:
149
  from_scratch: false
150
  use_peft: true
@@ -156,7 +156,7 @@ model:
156
  model_init_args: null
157
  max_length: 2048
158
  adapter:
159
- class_path: genbio_finetune.models.MLPPoolAdapter
160
  init_args:
161
  pooling: mean_pooling
162
  hidden_sizes:
@@ -180,13 +180,13 @@ model:
180
  differentiable: false
181
  fused: null
182
  lr_scheduler:
183
- class_path: genbio_finetune.lr_schedulers.CosineWithWarmup
184
  init_args:
185
  warmup_ratio: 0.05
186
  strict_loading: true
187
  reset_optimizer_states: false
188
  data:
189
- class_path: genbio_finetune.data.DMSFitnessPrediction
190
  init_args:
191
  path: genbio-ai/ProteinGYM-DMS
192
  train_split_files:
 
141
  reload_dataloaders_every_n_epochs: 0
142
  default_root_dir: logs
143
  model:
144
+ class_path: modelgenerator.tasks.SequenceRegression
145
  init_args:
146
  backbone:
147
+ class_path: modelgenerator.backbones.proteinfm_v1
148
  init_args:
149
  from_scratch: false
150
  use_peft: true
 
156
  model_init_args: null
157
  max_length: 2048
158
  adapter:
159
+ class_path: modelgenerator.adapters.MLPPoolAdapter
160
  init_args:
161
  pooling: mean_pooling
162
  hidden_sizes:
 
180
  differentiable: false
181
  fused: null
182
  lr_scheduler:
183
+ class_path: modelgenerator.lr_schedulers.CosineWithWarmup
184
  init_args:
185
  warmup_ratio: 0.05
186
  strict_loading: true
187
  reset_optimizer_states: false
188
  data:
189
+ class_path: modelgenerator.data.DMSFitnessPrediction
190
  init_args:
191
  path: genbio-ai/ProteinGYM-DMS
192
  train_split_files:
fold4/config.yaml CHANGED
@@ -141,10 +141,10 @@ trainer:
141
  reload_dataloaders_every_n_epochs: 0
142
  default_root_dir: logs
143
  model:
144
- class_path: genbio_finetune.tasks.SequenceRegression
145
  init_args:
146
  backbone:
147
- class_path: genbio_finetune.models.proteinfm_v1
148
  init_args:
149
  from_scratch: false
150
  use_peft: true
@@ -156,7 +156,7 @@ model:
156
  model_init_args: null
157
  max_length: 2048
158
  adapter:
159
- class_path: genbio_finetune.models.MLPPoolAdapter
160
  init_args:
161
  pooling: mean_pooling
162
  hidden_sizes:
@@ -180,13 +180,13 @@ model:
180
  differentiable: false
181
  fused: null
182
  lr_scheduler:
183
- class_path: genbio_finetune.lr_schedulers.CosineWithWarmup
184
  init_args:
185
  warmup_ratio: 0.05
186
  strict_loading: true
187
  reset_optimizer_states: false
188
  data:
189
- class_path: genbio_finetune.data.DMSFitnessPrediction
190
  init_args:
191
  path: genbio-ai/ProteinGYM-DMS
192
  train_split_files:
 
141
  reload_dataloaders_every_n_epochs: 0
142
  default_root_dir: logs
143
  model:
144
+ class_path: modelgenerator.tasks.SequenceRegression
145
  init_args:
146
  backbone:
147
+ class_path: modelgenerator.backbones.proteinfm_v1
148
  init_args:
149
  from_scratch: false
150
  use_peft: true
 
156
  model_init_args: null
157
  max_length: 2048
158
  adapter:
159
+ class_path: modelgenerator.adapters.MLPPoolAdapter
160
  init_args:
161
  pooling: mean_pooling
162
  hidden_sizes:
 
180
  differentiable: false
181
  fused: null
182
  lr_scheduler:
183
+ class_path: modelgenerator.lr_schedulers.CosineWithWarmup
184
  init_args:
185
  warmup_ratio: 0.05
186
  strict_loading: true
187
  reset_optimizer_states: false
188
  data:
189
+ class_path: modelgenerator.data.DMSFitnessPrediction
190
  init_args:
191
  path: genbio-ai/ProteinGYM-DMS
192
  train_split_files: