Caleb Ellington commited on
Commit
c53050c
1 Parent(s): 2df10fb

update with major refactor

Browse files
fold0/config.yaml CHANGED
@@ -140,10 +140,10 @@ trainer:
140
  reload_dataloaders_every_n_epochs: 0
141
  default_root_dir: logs
142
  model:
143
- class_path: genbio_finetune.tasks.SequenceRegression
144
  init_args:
145
  backbone:
146
- class_path: genbio_finetune.models.proteinfm
147
  init_args:
148
  from_scratch: false
149
  use_peft: true
@@ -155,7 +155,7 @@ model:
155
  model_init_args: null
156
  max_length: 2048
157
  adapter:
158
- class_path: genbio_finetune.models.MLPPoolAdapter
159
  init_args:
160
  pooling: mean_pooling
161
  hidden_sizes:
@@ -179,13 +179,13 @@ model:
179
  differentiable: false
180
  fused: null
181
  lr_scheduler:
182
- class_path: genbio_finetune.lr_schedulers.CosineWithWarmup
183
  init_args:
184
  warmup_ratio: 0.05
185
  strict_loading: true
186
  reset_optimizer_states: false
187
  data:
188
- class_path: genbio_finetune.data.DMSFitnessPrediction
189
  init_args:
190
  path: genbio-ai/ProteinGYM-DMS
191
  mutation_type: indels
 
140
  reload_dataloaders_every_n_epochs: 0
141
  default_root_dir: logs
142
  model:
143
+ class_path: modelgenerator.tasks.SequenceRegression
144
  init_args:
145
  backbone:
146
+ class_path: modelgenerator.backbones.proteinfm
147
  init_args:
148
  from_scratch: false
149
  use_peft: true
 
155
  model_init_args: null
156
  max_length: 2048
157
  adapter:
158
+ class_path: modelgenerator.adapters.MLPPoolAdapter
159
  init_args:
160
  pooling: mean_pooling
161
  hidden_sizes:
 
179
  differentiable: false
180
  fused: null
181
  lr_scheduler:
182
+ class_path: modelgenerator.lr_schedulers.CosineWithWarmup
183
  init_args:
184
  warmup_ratio: 0.05
185
  strict_loading: true
186
  reset_optimizer_states: false
187
  data:
188
+ class_path: modelgenerator.data.DMSFitnessPrediction
189
  init_args:
190
  path: genbio-ai/ProteinGYM-DMS
191
  mutation_type: indels
fold1/config.yaml CHANGED
@@ -140,10 +140,10 @@ trainer:
140
  reload_dataloaders_every_n_epochs: 0
141
  default_root_dir: logs
142
  model:
143
- class_path: genbio_finetune.tasks.SequenceRegression
144
  init_args:
145
  backbone:
146
- class_path: genbio_finetune.models.proteinfm
147
  init_args:
148
  from_scratch: false
149
  use_peft: true
@@ -155,7 +155,7 @@ model:
155
  model_init_args: null
156
  max_length: 2048
157
  adapter:
158
- class_path: genbio_finetune.models.MLPPoolAdapter
159
  init_args:
160
  pooling: mean_pooling
161
  hidden_sizes:
@@ -179,13 +179,13 @@ model:
179
  differentiable: false
180
  fused: null
181
  lr_scheduler:
182
- class_path: genbio_finetune.lr_schedulers.CosineWithWarmup
183
  init_args:
184
  warmup_ratio: 0.05
185
  strict_loading: true
186
  reset_optimizer_states: false
187
  data:
188
- class_path: genbio_finetune.data.DMSFitnessPrediction
189
  init_args:
190
  path: genbio-ai/ProteinGYM-DMS
191
  mutation_type: indels
 
140
  reload_dataloaders_every_n_epochs: 0
141
  default_root_dir: logs
142
  model:
143
+ class_path: modelgenerator.tasks.SequenceRegression
144
  init_args:
145
  backbone:
146
+ class_path: modelgenerator.backbones.proteinfm
147
  init_args:
148
  from_scratch: false
149
  use_peft: true
 
155
  model_init_args: null
156
  max_length: 2048
157
  adapter:
158
+ class_path: modelgenerator.adapters.MLPPoolAdapter
159
  init_args:
160
  pooling: mean_pooling
161
  hidden_sizes:
 
179
  differentiable: false
180
  fused: null
181
  lr_scheduler:
182
+ class_path: modelgenerator.lr_schedulers.CosineWithWarmup
183
  init_args:
184
  warmup_ratio: 0.05
185
  strict_loading: true
186
  reset_optimizer_states: false
187
  data:
188
+ class_path: modelgenerator.data.DMSFitnessPrediction
189
  init_args:
190
  path: genbio-ai/ProteinGYM-DMS
191
  mutation_type: indels
fold2/config.yaml CHANGED
@@ -140,10 +140,10 @@ trainer:
140
  reload_dataloaders_every_n_epochs: 0
141
  default_root_dir: logs
142
  model:
143
- class_path: genbio_finetune.tasks.SequenceRegression
144
  init_args:
145
  backbone:
146
- class_path: genbio_finetune.models.proteinfm
147
  init_args:
148
  from_scratch: false
149
  use_peft: true
@@ -155,7 +155,7 @@ model:
155
  model_init_args: null
156
  max_length: 2048
157
  adapter:
158
- class_path: genbio_finetune.models.MLPPoolAdapter
159
  init_args:
160
  pooling: mean_pooling
161
  hidden_sizes:
@@ -179,13 +179,13 @@ model:
179
  differentiable: false
180
  fused: null
181
  lr_scheduler:
182
- class_path: genbio_finetune.lr_schedulers.CosineWithWarmup
183
  init_args:
184
  warmup_ratio: 0.05
185
  strict_loading: true
186
  reset_optimizer_states: false
187
  data:
188
- class_path: genbio_finetune.data.DMSFitnessPrediction
189
  init_args:
190
  path: genbio-ai/ProteinGYM-DMS
191
  mutation_type: indels
 
140
  reload_dataloaders_every_n_epochs: 0
141
  default_root_dir: logs
142
  model:
143
+ class_path: modelgenerator.tasks.SequenceRegression
144
  init_args:
145
  backbone:
146
+ class_path: modelgenerator.backbones.proteinfm
147
  init_args:
148
  from_scratch: false
149
  use_peft: true
 
155
  model_init_args: null
156
  max_length: 2048
157
  adapter:
158
+ class_path: modelgenerator.adapters.MLPPoolAdapter
159
  init_args:
160
  pooling: mean_pooling
161
  hidden_sizes:
 
179
  differentiable: false
180
  fused: null
181
  lr_scheduler:
182
+ class_path: modelgenerator.lr_schedulers.CosineWithWarmup
183
  init_args:
184
  warmup_ratio: 0.05
185
  strict_loading: true
186
  reset_optimizer_states: false
187
  data:
188
+ class_path: modelgenerator.data.DMSFitnessPrediction
189
  init_args:
190
  path: genbio-ai/ProteinGYM-DMS
191
  mutation_type: indels
fold3/config.yaml CHANGED
@@ -140,10 +140,10 @@ trainer:
140
  reload_dataloaders_every_n_epochs: 0
141
  default_root_dir: logs
142
  model:
143
- class_path: genbio_finetune.tasks.SequenceRegression
144
  init_args:
145
  backbone:
146
- class_path: genbio_finetune.models.proteinfm
147
  init_args:
148
  from_scratch: false
149
  use_peft: true
@@ -155,7 +155,7 @@ model:
155
  model_init_args: null
156
  max_length: 2048
157
  adapter:
158
- class_path: genbio_finetune.models.MLPPoolAdapter
159
  init_args:
160
  pooling: mean_pooling
161
  hidden_sizes:
@@ -179,13 +179,13 @@ model:
179
  differentiable: false
180
  fused: null
181
  lr_scheduler:
182
- class_path: genbio_finetune.lr_schedulers.CosineWithWarmup
183
  init_args:
184
  warmup_ratio: 0.05
185
  strict_loading: true
186
  reset_optimizer_states: false
187
  data:
188
- class_path: genbio_finetune.data.DMSFitnessPrediction
189
  init_args:
190
  path: genbio-ai/ProteinGYM-DMS
191
  mutation_type: indels
 
140
  reload_dataloaders_every_n_epochs: 0
141
  default_root_dir: logs
142
  model:
143
+ class_path: modelgenerator.tasks.SequenceRegression
144
  init_args:
145
  backbone:
146
+ class_path: modelgenerator.backbones.proteinfm
147
  init_args:
148
  from_scratch: false
149
  use_peft: true
 
155
  model_init_args: null
156
  max_length: 2048
157
  adapter:
158
+ class_path: modelgenerator.adapters.MLPPoolAdapter
159
  init_args:
160
  pooling: mean_pooling
161
  hidden_sizes:
 
179
  differentiable: false
180
  fused: null
181
  lr_scheduler:
182
+ class_path: modelgenerator.lr_schedulers.CosineWithWarmup
183
  init_args:
184
  warmup_ratio: 0.05
185
  strict_loading: true
186
  reset_optimizer_states: false
187
  data:
188
+ class_path: modelgenerator.data.DMSFitnessPrediction
189
  init_args:
190
  path: genbio-ai/ProteinGYM-DMS
191
  mutation_type: indels
fold4/config.yaml CHANGED
@@ -140,10 +140,10 @@ trainer:
140
  reload_dataloaders_every_n_epochs: 0
141
  default_root_dir: logs
142
  model:
143
- class_path: genbio_finetune.tasks.SequenceRegression
144
  init_args:
145
  backbone:
146
- class_path: genbio_finetune.models.proteinfm
147
  init_args:
148
  from_scratch: false
149
  use_peft: true
@@ -155,7 +155,7 @@ model:
155
  model_init_args: null
156
  max_length: 2048
157
  adapter:
158
- class_path: genbio_finetune.models.MLPPoolAdapter
159
  init_args:
160
  pooling: mean_pooling
161
  hidden_sizes:
@@ -179,13 +179,13 @@ model:
179
  differentiable: false
180
  fused: null
181
  lr_scheduler:
182
- class_path: genbio_finetune.lr_schedulers.CosineWithWarmup
183
  init_args:
184
  warmup_ratio: 0.05
185
  strict_loading: true
186
  reset_optimizer_states: false
187
  data:
188
- class_path: genbio_finetune.data.DMSFitnessPrediction
189
  init_args:
190
  path: genbio-ai/ProteinGYM-DMS
191
  mutation_type: indels
 
140
  reload_dataloaders_every_n_epochs: 0
141
  default_root_dir: logs
142
  model:
143
+ class_path: modelgenerator.tasks.SequenceRegression
144
  init_args:
145
  backbone:
146
+ class_path: modelgenerator.backbones.proteinfm
147
  init_args:
148
  from_scratch: false
149
  use_peft: true
 
155
  model_init_args: null
156
  max_length: 2048
157
  adapter:
158
+ class_path: modelgenerator.adapters.MLPPoolAdapter
159
  init_args:
160
  pooling: mean_pooling
161
  hidden_sizes:
 
179
  differentiable: false
180
  fused: null
181
  lr_scheduler:
182
+ class_path: modelgenerator.lr_schedulers.CosineWithWarmup
183
  init_args:
184
  warmup_ratio: 0.05
185
  strict_loading: true
186
  reset_optimizer_states: false
187
  data:
188
+ class_path: modelgenerator.data.DMSFitnessPrediction
189
  init_args:
190
  path: genbio-ai/ProteinGYM-DMS
191
  mutation_type: indels