|
- # Train conda activate casanovo_env1
- exp_original bs=256
- exp_original_1 bs=32
- exp_original_2 bs=64
-
- python casanovo.py --mode train --pretrained "/userhome/xufan/peptide_data/zhipu_data/moco_mz/output_s1m1g1_6/checkpoint_0079_final.pth.tar" --peak_path "train_data/*" --peak_path_val "val_data/*" --output exp_small_1/log --config config.yaml
- python casanovo.py --mode train --peak_path "train_data/*" --peak_path_val "val_data/*" --output exp0/log --config config.yaml
- CUDA_VISIBLE_DEVICES=0
-
- python casanovo.py --mode train --pretrained "/userhome/xufan/peptide_data/zhipu_data/moco_mz/output_alls1m1g1_1/checkpoint_0001_final.pth.tar" --peak_path "train_data/*" --peak_path_val "val_data/*" --output exp_large/log --config config_large.yaml
-
- python casanovo.py --mode train --batch_size 64 --pretrained "/userhome/xufan/peptide_data/zhipu_data/moco_mz/output_alls1m1g1_1/checkpoint_0001_final.pth.tar" --peak_path "train_data/*" --peak_path_val "val_data/*" --output exp_large_2/log --config config_large.yaml
-
- python casanovo.py --mode train --batch_size 64 --peak_path "sample_data/*" --peak_path_val "sample_data/*" --output exp_original_2/log --config config.yaml
-
- python casanovo.py --mode train --batch_size 128 --pretrained "/userhome/xufan/peptide_data/zhipu_data/moco_mz/output_alls1m1g1_1/checkpoint_0001_final.pth.tar" --peak_path "train_data/*" --peak_path_val "val_data/*" --output exp_large_3/log --config config_large.yaml
-
- ++++++++++++++++++++++++++++++++++++++++++++++++
- lr_scheduler
- python casanovo.py --batch_size 32 --mode train --pretrained "/userhome/xufan/peptide_data/zhipu_data/moco_mz/output_s1m1g1_6/checkpoint_0079_final.pth.tar" --peak_path "train_data/*" --peak_path_val "val_data/*" --output exp_small_3/log --config config_small.yaml
-
- python casanovo.py --batch_size 32 --mode train --encoder_lr 0.0001 --pretrained "/userhome/xufan/peptide_data/zhipu_data/moco_mz/output_finetune1_lr0.03/checkpoint_0079_final.pth.tar" --peak_path "train_data/*" --peak_path_val "val_data/*" --output exp_small_4/log --config config_small.yaml
-
- python casanovo.py --batch_size 32 --mode train --encoder_lr 0.00005 --pretrained "/userhome/xufan/peptide_data/zhipu_data/moco_mz/output_finetune1_lr0.03/checkpoint_0079_final.pth.tar" --peak_path "train_data/*" --peak_path_val "val_data/*" --output exp_small_5/log --config config_small.yaml
- #
- python casanovo.py --batch_size 32 --mode train --encoder_lr 0.0001 --pretrained "/userhome/xufan/peptide_data/zhipu_data/moco_mz/output_finetune_m0/checkpoint_0079_final.pth.tar" --peak_path "train_data/*" --peak_path_val "val_data/*" --output exp_small_6/log --config config_small.yaml
-
- python casanovo.py --mode train --peak_path "train_data/*" --peak_path_val "val_data/*" --output exp_original_3/log --config config.yaml
-
- #
- python casanovo.py --batch_size 32 --mode train --encoder_lr 0.0001 --pretrained "/userhome/xufan/peptide_data/zhipu_data/moco_mz/output_finetune_large_m0.3/checkpoint_0079_final.pth.tar" --peak_path "train_data/*" --peak_path_val "val_data/*" --output exp_large_4/log --config config_large.yaml
-
- #### T5
- python casanovo.py --batch_size 32 --mode train --pretrained "/userhome/xufan/peptide_data/zhipu_data/moco_mz/output_finetune1_lr0.03/checkpoint_0079_final.pth.tar" --peak_path "train_data/*" --peak_path_val "val_data/*" --output exp_small_t5/log --config config_small_t5.yaml
-
- # eval
- python casanovo.py --mode eval --model "exp_original_3/epoch=29-step=1136640.ckpt" --peak_path "val_data/*" --peak_path_val "val_data/*" --output exp_original_3/log_eval --config config.yaml
-
- python casanovo.py --mode eval --model exp_small_3 --peak_path "val_data/*" --peak_path_val "val_data/*" --output exp_small_3/log_eval --config config_small.yaml
-
- python casanovo.py --mode eval --model "exp_large/epoch=15-step=150000.ckpt" --peak_path "val_data/*" --peak_path_val "val_data/*" --output exp_large/log_eval --config config_large.yaml
-
- python casanovo.py --mode eval --model exp_small_4 --peak_path "val_data/*" --peak_path_val "val_data/*" --output exp_small_4/log_eval --config config_small.yaml
-
- python casanovo.py --mode eval --model exp_original_3 --peak_path "val_data/*" --peak_path_val "val_data/*" --output exp_original_3/log_eval --config config.yaml
-
- python casanovo.py --mode eval --model "exp_large_4/epoch=18-step=719872.ckpt" --peak_path "val_data/*" --peak_path_val "val_data/*" --output exp_large_4/log_eval --config config_large.yaml
-
-
-
-
- #####
- {'G': 1, 'A': 2, 'S': 3, 'P': 4, 'V': 5, 'T': 6, 'C+57.021': 7, 'L': 8, 'I': 9, 'N': 10, 'D': 11, 'Q': 12, 'K': 13, 'E': 14, 'M': 15, 'H': 16, 'F': 17, 'R': 18, 'Y': 19, 'W': 20, 'M+15.995': 21, 'N+0.984': 22, 'Q+0.984': 23, '+42.011': 24, '+43.006': 25, '-17.027': 26, '+43.006-17.027': 27, '$': 28}
- {s, end ,unknow} [2..1...3]
|