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SX_spcas9_Lindel

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  1. indel_model/README.md +28 -28
  2. indel_model/config.json +0 -1
  3. indel_model/model.py +3 -0
  4. indel_model/runs/Oct28_11-56-11_ljw-System-Product-Name/events.out.tfevents.1730087772.ljw-System-Product-Name.78325.0 +3 -0
  5. indel_model/training_args.bin +1 -1
indel_model/README.md CHANGED
@@ -48,34 +48,34 @@ The following hyperparameters were used during training:
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  | Training Loss | Epoch | Step | Validation Loss |
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  |:-------------:|:-----:|:----:|:---------------:|
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- | 1022.9015 | 1.0 | 322 | 880.6259 |
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- | 710.5546 | 2.0 | 644 | 540.0049 |
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- | 420.3116 | 3.0 | 966 | 316.6203 |
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- | 244.25 | 4.0 | 1288 | 185.2686 |
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- | 144.4953 | 5.0 | 1610 | 113.2889 |
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- | 92.2283 | 6.0 | 1932 | 77.3025 |
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- | 66.9501 | 7.0 | 2254 | 60.5765 |
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- | 55.4647 | 8.0 | 2576 | 53.1402 |
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- | 50.3218 | 9.0 | 2898 | 49.8257 |
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- | 48.0615 | 10.0 | 3220 | 48.4087 |
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- | 47.063 | 11.0 | 3542 | 47.6446 |
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- | 46.608 | 12.0 | 3864 | 47.4013 |
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- | 46.3856 | 13.0 | 4186 | 47.2288 |
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- | 46.2889 | 14.0 | 4508 | 47.1595 |
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- | 46.2446 | 15.0 | 4830 | 47.0971 |
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- | 46.2194 | 16.0 | 5152 | 47.1161 |
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- | 46.2015 | 17.0 | 5474 | 47.1084 |
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- | 46.1923 | 18.0 | 5796 | 47.0945 |
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- | 46.1852 | 19.0 | 6118 | 47.1015 |
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- | 46.1783 | 20.0 | 6440 | 47.0496 |
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- | 46.1756 | 21.0 | 6762 | 47.0853 |
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- | 46.1676 | 22.0 | 7084 | 47.0705 |
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- | 46.1614 | 23.0 | 7406 | 47.1252 |
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- | 46.1549 | 24.0 | 7728 | 47.0727 |
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- | 46.1498 | 25.0 | 8050 | 47.0992 |
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- | 46.1441 | 26.0 | 8372 | 47.0982 |
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- | 46.1368 | 27.0 | 8694 | 47.0905 |
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- | 46.1308 | 28.0 | 9016 | 47.0622 |
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  | 46.1231 | 29.0 | 9338 | 47.0786 |
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  | 46.117 | 30.0 | 9660 | 47.0798 |
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  | Training Loss | Epoch | Step | Validation Loss |
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  |:-------------:|:-----:|:----:|:---------------:|
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+ | 1022.9014 | 1.0 | 322 | 880.6261 |
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+ | 710.5549 | 2.0 | 644 | 540.0052 |
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+ | 420.3118 | 3.0 | 966 | 316.6205 |
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+ | 244.2501 | 4.0 | 1288 | 185.2687 |
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+ | 144.4954 | 5.0 | 1610 | 113.2889 |
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+ | 92.2284 | 6.0 | 1932 | 77.3025 |
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+ | 66.9501 | 7.0 | 2254 | 60.5766 |
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+ | 55.4648 | 8.0 | 2576 | 53.1402 |
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+ | 50.3219 | 9.0 | 2898 | 49.8257 |
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+ | 48.0616 | 10.0 | 3220 | 48.4087 |
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+ | 47.0631 | 11.0 | 3542 | 47.6446 |
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+ | 46.6081 | 12.0 | 3864 | 47.4013 |
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+ | 46.3857 | 13.0 | 4186 | 47.2288 |
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+ | 46.2889 | 14.0 | 4508 | 47.1596 |
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+ | 46.2447 | 15.0 | 4830 | 47.0971 |
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+ | 46.2195 | 16.0 | 5152 | 47.1162 |
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+ | 46.2015 | 17.0 | 5474 | 47.1085 |
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+ | 46.1924 | 18.0 | 5796 | 47.0946 |
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+ | 46.1853 | 19.0 | 6118 | 47.1015 |
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+ | 46.1784 | 20.0 | 6440 | 47.0497 |
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+ | 46.1757 | 21.0 | 6762 | 47.0853 |
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+ | 46.1676 | 22.0 | 7084 | 47.0706 |
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+ | 46.1614 | 23.0 | 7406 | 47.1253 |
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+ | 46.155 | 24.0 | 7728 | 47.0727 |
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+ | 46.1499 | 25.0 | 8050 | 47.0992 |
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+ | 46.1442 | 26.0 | 8372 | 47.0982 |
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+ | 46.1369 | 27.0 | 8694 | 47.0905 |
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+ | 46.1309 | 28.0 | 9016 | 47.0622 |
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  | 46.1231 | 29.0 | 9338 | 47.0786 |
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  | 46.117 | 30.0 | 9660 | 47.0798 |
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indel_model/config.json CHANGED
@@ -1,5 +1,4 @@
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  {
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- "_name_or_path": "/home/ljw/sdc1/CRISPR_results/Lindel/SX_spcas9_Lindel_indel",
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  "architectures": [
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  "LindelModel"
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  ],
 
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  {
 
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  "architectures": [
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  "LindelModel"
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  ],
indel_model/model.py CHANGED
@@ -35,13 +35,16 @@ class LindelModel(PreTrainedModel):
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  self.reg_mode = config.reg_mode
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  self.reg_const = config.reg_const
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  if config.model == "indel":
 
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  feature_dim = 20 * 4 + 19 * 16
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  class_dim = 2
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  elif config.model == "ins":
 
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  feature_dim = 6 * 4 + 5 * 16
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  class_dim = 21
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  elif config.model == "del":
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  class_dim = (4 + 1 + 4 + config.dlen - 1) * (config.dlen - 1) // 2
 
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  feature_dim = class_dim * (config.mh_len + 1) + 20 * 4 + 19 * 16
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  self.linear = nn.Linear(in_features=feature_dim, out_features=class_dim)
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  self.initialize_weights()
 
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  self.reg_mode = config.reg_mode
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  self.reg_const = config.reg_const
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  if config.model == "indel":
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+ # onehotencoder(ref[cut-17:cut+3])
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  feature_dim = 20 * 4 + 19 * 16
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  class_dim = 2
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  elif config.model == "ins":
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+ # onehotencoder(ref[cut-3:cut+3])
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  feature_dim = 6 * 4 + 5 * 16
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  class_dim = 21
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  elif config.model == "del":
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  class_dim = (4 + 1 + 4 + config.dlen - 1) * (config.dlen - 1) // 2
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+ # concatenate get_feature and onehotencoder(ref[cut-17:cut+3])
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  feature_dim = class_dim * (config.mh_len + 1) + 20 * 4 + 19 * 16
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  self.linear = nn.Linear(in_features=feature_dim, out_features=class_dim)
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  self.initialize_weights()
indel_model/runs/Oct28_11-56-11_ljw-System-Product-Name/events.out.tfevents.1730087772.ljw-System-Product-Name.78325.0 ADDED
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indel_model/training_args.bin CHANGED
@@ -1,3 +1,3 @@
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