Caleb Ellington
commited on
Commit
•
c53050c
1
Parent(s):
2df10fb
update with major refactor
Browse files- fold0/config.yaml +5 -5
- fold1/config.yaml +5 -5
- fold2/config.yaml +5 -5
- fold3/config.yaml +5 -5
- fold4/config.yaml +5 -5
fold0/config.yaml
CHANGED
@@ -140,10 +140,10 @@ trainer:
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reload_dataloaders_every_n_epochs: 0
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default_root_dir: logs
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model:
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-
class_path:
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init_args:
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backbone:
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146 |
-
class_path:
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147 |
init_args:
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from_scratch: false
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use_peft: true
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@@ -155,7 +155,7 @@ model:
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model_init_args: null
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max_length: 2048
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adapter:
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158 |
-
class_path:
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init_args:
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pooling: mean_pooling
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hidden_sizes:
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@@ -179,13 +179,13 @@ model:
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differentiable: false
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fused: null
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lr_scheduler:
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182 |
-
class_path:
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init_args:
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warmup_ratio: 0.05
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185 |
strict_loading: true
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reset_optimizer_states: false
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data:
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-
class_path:
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init_args:
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path: genbio-ai/ProteinGYM-DMS
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mutation_type: indels
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reload_dataloaders_every_n_epochs: 0
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default_root_dir: logs
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model:
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+
class_path: modelgenerator.tasks.SequenceRegression
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144 |
init_args:
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145 |
backbone:
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146 |
+
class_path: modelgenerator.backbones.proteinfm
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147 |
init_args:
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148 |
from_scratch: false
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149 |
use_peft: true
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model_init_args: null
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max_length: 2048
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157 |
adapter:
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158 |
+
class_path: modelgenerator.adapters.MLPPoolAdapter
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159 |
init_args:
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pooling: mean_pooling
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hidden_sizes:
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|
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differentiable: false
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fused: null
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181 |
lr_scheduler:
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182 |
+
class_path: modelgenerator.lr_schedulers.CosineWithWarmup
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183 |
init_args:
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184 |
warmup_ratio: 0.05
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185 |
strict_loading: true
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reset_optimizer_states: false
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data:
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+
class_path: modelgenerator.data.DMSFitnessPrediction
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init_args:
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path: genbio-ai/ProteinGYM-DMS
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mutation_type: indels
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fold1/config.yaml
CHANGED
@@ -140,10 +140,10 @@ trainer:
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140 |
reload_dataloaders_every_n_epochs: 0
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141 |
default_root_dir: logs
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142 |
model:
|
143 |
-
class_path:
|
144 |
init_args:
|
145 |
backbone:
|
146 |
-
class_path:
|
147 |
init_args:
|
148 |
from_scratch: false
|
149 |
use_peft: true
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@@ -155,7 +155,7 @@ model:
|
|
155 |
model_init_args: null
|
156 |
max_length: 2048
|
157 |
adapter:
|
158 |
-
class_path:
|
159 |
init_args:
|
160 |
pooling: mean_pooling
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161 |
hidden_sizes:
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@@ -179,13 +179,13 @@ model:
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|
179 |
differentiable: false
|
180 |
fused: null
|
181 |
lr_scheduler:
|
182 |
-
class_path:
|
183 |
init_args:
|
184 |
warmup_ratio: 0.05
|
185 |
strict_loading: true
|
186 |
reset_optimizer_states: false
|
187 |
data:
|
188 |
-
class_path:
|
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:
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190 |
path: genbio-ai/ProteinGYM-DMS
|
191 |
mutation_type: indels
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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:
|
144 |
init_args:
|
145 |
backbone:
|
146 |
-
class_path:
|
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:
|
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:
|
183 |
init_args:
|
184 |
warmup_ratio: 0.05
|
185 |
strict_loading: true
|
186 |
reset_optimizer_states: false
|
187 |
data:
|
188 |
-
class_path:
|
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
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189 |
init_args:
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190 |
path: genbio-ai/ProteinGYM-DMS
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191 |
mutation_type: indels
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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:
|
144 |
init_args:
|
145 |
backbone:
|
146 |
-
class_path:
|
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:
|
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:
|
183 |
init_args:
|
184 |
warmup_ratio: 0.05
|
185 |
strict_loading: true
|
186 |
reset_optimizer_states: false
|
187 |
data:
|
188 |
-
class_path:
|
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:
|
144 |
init_args:
|
145 |
backbone:
|
146 |
-
class_path:
|
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:
|
159 |
init_args:
|
160 |
pooling: mean_pooling
|
161 |
hidden_sizes:
|
@@ -179,13 +179,13 @@ model:
|
|
179 |
differentiable: false
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180 |
fused: null
|
181 |
lr_scheduler:
|
182 |
-
class_path:
|
183 |
init_args:
|
184 |
warmup_ratio: 0.05
|
185 |
strict_loading: true
|
186 |
reset_optimizer_states: false
|
187 |
data:
|
188 |
-
class_path:
|
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
|