feat: update 4track model

README.md

@@ -84,7 +84,7 @@ Here is example code
 # Sequence for short mRNA
 > seq=(
 'TCATCTGGATTATACATATTTCGCAATGAAAGAGAGGAAGAAAAGGAAGCAGCAAAATATGTGGAGGCCCA'
- 'ACAAAAGAGACTAGAAGCCTTATTCACTAAAATTCAGGAGGAATTTGAAGAACATGAAGTTACTTCCTCC
+ 'ACAAAAGAGACTAGAAGCCTTATTCACTAAAATTCAGGAGGAATTTGAAGAACATGAAGTTACTTCCTCC'
  'ACTGAAGTCTTGAACCCCCCAAAGTCATCCATGAGGGTTGGAATCAACTTCTGAAAACACAACAAAACCA'
  'TATTTACCATCACGTGCACTAACAAGACAGCAAGTTCGTGCTTTGCAAGATGGTGCAGAGCTTTATGAAG'
  'CAGTGAAGAATGCAGCAGACCCAGCTTACCTTGAGGGTTATTTCAGTGAAGAGCAGTTAAGAGCCTTGAA'

models/orthrus_base_4_track/epoch=18-step=20000.ckpt

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:58c38f75c8d253db481ddc0c910adaf8ae4d88ee42a993fc72b07e3ce1657302
-size 21415988
+oid sha256:157d60e0471bff00023376a4b29a1746b407ae919506baf2cf40e88d0009f8ce
+size 21409844

models/orthrus_base_4_track/lp_results/homo_lp_results_ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria_epoch=1-step=2000.ckpt_ridge.csv

@@ -0,0 +1,13 @@
+dataset,run_name,ckpt_name,lin_model,metric,split,mean_value,std_value
+go_mf,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=1-step=2000.ckpt,logistic,val_roc_auc,val,0.8220142525972354,
+go_mf,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=1-step=2000.ckpt,logistic,val_auprc,val,0.4625396927514182,
+mrfp,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=1-step=2000.ckpt,ridge,val_loss,val,0.41187612954069797,
+mrfp,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=1-step=2000.ckpt,ridge,val_r,val,0.4650231114299552,
+mrl,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=1-step=2000.ckpt,ridge,val_loss,val,0.7519351051859768,
+mrl,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=1-step=2000.ckpt,ridge,val_r,val,0.3815569357098566,
+protein_loc,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=1-step=2000.ckpt,logistic,val_roc_auc,val,0.8196707035908555,
+protein_loc,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=1-step=2000.ckpt,logistic,val_auprc,val,0.3503672527264725,
+hl_human,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=1-step=2000.ckpt,ridge,val_loss,val,0.7118696793044624,
+hl_human,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=1-step=2000.ckpt,ridge,val_r,val,0.508566975266374,
+hl_mouse,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=1-step=2000.ckpt,ridge,val_loss,val,0.7589341222101531,
+hl_mouse,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=1-step=2000.ckpt,ridge,val_r,val,0.47631361227244867,

models/orthrus_base_4_track/lp_results/homo_lp_results_ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria_epoch=10-step=12000.ckpt_ridge.csv

@@ -0,0 +1,13 @@
+dataset,run_name,ckpt_name,lin_model,metric,split,mean_value,std_value
+go_mf,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=10-step=12000.ckpt,logistic,val_roc_auc,val,0.8433483249915402,
+go_mf,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=10-step=12000.ckpt,logistic,val_auprc,val,0.5132275016061479,
+mrfp,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=10-step=12000.ckpt,ridge,val_loss,val,0.3924153336558653,
+mrfp,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=10-step=12000.ckpt,ridge,val_r,val,0.5055500181171051,
+mrl,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=10-step=12000.ckpt,ridge,val_loss,val,0.7462168153619977,
+mrl,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=10-step=12000.ckpt,ridge,val_r,val,0.3901367108773842,
+protein_loc,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=10-step=12000.ckpt,logistic,val_roc_auc,val,0.825789615510407,
+protein_loc,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=10-step=12000.ckpt,logistic,val_auprc,val,0.3624099056153837,
+hl_human,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=10-step=12000.ckpt,ridge,val_loss,val,0.6772307183584606,
+hl_human,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=10-step=12000.ckpt,ridge,val_r,val,0.541695841911757,
+hl_mouse,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=10-step=12000.ckpt,ridge,val_loss,val,0.7251545422958905,
+hl_mouse,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=10-step=12000.ckpt,ridge,val_r,val,0.5109326806495391,

models/orthrus_base_4_track/lp_results/homo_lp_results_ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria_epoch=12-step=14000.ckpt_ridge.csv

@@ -0,0 +1,13 @@
+dataset,run_name,ckpt_name,lin_model,metric,split,mean_value,std_value
+go_mf,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=12-step=14000.ckpt,logistic,val_roc_auc,val,0.8421522962237182,
+go_mf,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=12-step=14000.ckpt,logistic,val_auprc,val,0.5078808348506777,
+mrfp,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=12-step=14000.ckpt,ridge,val_loss,val,0.38159363235269134,
+mrfp,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=12-step=14000.ckpt,ridge,val_r,val,0.5210525632055019,
+mrl,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=12-step=14000.ckpt,ridge,val_loss,val,0.7449572004778382,
+mrl,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=12-step=14000.ckpt,ridge,val_r,val,0.39210775201429937,
+protein_loc,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=12-step=14000.ckpt,logistic,val_roc_auc,val,0.8253978288124967,
+protein_loc,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=12-step=14000.ckpt,logistic,val_auprc,val,0.35978864383790576,
+hl_human,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=12-step=14000.ckpt,ridge,val_loss,val,0.6759492269289844,
+hl_human,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=12-step=14000.ckpt,ridge,val_r,val,0.5430234153021989,
+hl_mouse,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=12-step=14000.ckpt,ridge,val_loss,val,0.7187604645312344,
+hl_mouse,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=12-step=14000.ckpt,ridge,val_r,val,0.5170162511471106,

models/orthrus_base_4_track/lp_results/homo_lp_results_ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria_epoch=14-step=16000.ckpt_ridge.csv

@@ -0,0 +1,13 @@
+dataset,run_name,ckpt_name,lin_model,metric,split,mean_value,std_value
+go_mf,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=14-step=16000.ckpt,logistic,val_roc_auc,val,0.8453107717715747,
+go_mf,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=14-step=16000.ckpt,logistic,val_auprc,val,0.51388271248823,
+mrfp,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=14-step=16000.ckpt,ridge,val_loss,val,0.38352797937787375,
+mrfp,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=14-step=16000.ckpt,ridge,val_r,val,0.5187762652770216,
+mrl,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=14-step=16000.ckpt,ridge,val_loss,val,0.7464369347298561,
+mrl,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=14-step=16000.ckpt,ridge,val_r,val,0.38989871864513437,
+protein_loc,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=14-step=16000.ckpt,logistic,val_roc_auc,val,0.825373574980663,
+protein_loc,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=14-step=16000.ckpt,logistic,val_auprc,val,0.3606313916724556,
+hl_human,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=14-step=16000.ckpt,ridge,val_loss,val,0.6729050049584757,
+hl_human,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=14-step=16000.ckpt,ridge,val_r,val,0.5458388693481175,
+hl_mouse,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=14-step=16000.ckpt,ridge,val_loss,val,0.7104695665288715,
+hl_mouse,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=14-step=16000.ckpt,ridge,val_r,val,0.5250332145677902,

models/orthrus_base_4_track/lp_results/homo_lp_results_ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria_epoch=16-step=18000.ckpt_ridge.csv

@@ -0,0 +1,13 @@
+dataset,run_name,ckpt_name,lin_model,metric,split,mean_value,std_value
+go_mf,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=16-step=18000.ckpt,logistic,val_roc_auc,val,0.8440424572851378,
+go_mf,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=16-step=18000.ckpt,logistic,val_auprc,val,0.5131805187647871,
+mrfp,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=16-step=18000.ckpt,ridge,val_loss,val,0.38003889341798525,
+mrfp,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=16-step=18000.ckpt,ridge,val_r,val,0.523477567510083,
+mrl,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=16-step=18000.ckpt,ridge,val_loss,val,0.7444410742413161,
+mrl,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=16-step=18000.ckpt,ridge,val_r,val,0.3930851174944151,
+protein_loc,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=16-step=18000.ckpt,logistic,val_roc_auc,val,0.8259117384044564,
+protein_loc,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=16-step=18000.ckpt,logistic,val_auprc,val,0.36113756335833136,
+hl_human,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=16-step=18000.ckpt,ridge,val_loss,val,0.6744663045562795,
+hl_human,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=16-step=18000.ckpt,ridge,val_r,val,0.5444030097422119,
+hl_mouse,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=16-step=18000.ckpt,ridge,val_loss,val,0.7113535602097519,
+hl_mouse,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=16-step=18000.ckpt,ridge,val_r,val,0.5241967682295874,

models/orthrus_base_4_track/lp_results/homo_lp_results_ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria_epoch=18-step=20000.ckpt_ridge.csv

@@ -0,0 +1,13 @@
+dataset,run_name,ckpt_name,lin_model,metric,split,mean_value,std_value
+go_mf,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=18-step=20000.ckpt,logistic,val_roc_auc,val,0.8446671447835594,
+go_mf,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=18-step=20000.ckpt,logistic,val_auprc,val,0.5141468969910018,
+mrfp,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=18-step=20000.ckpt,ridge,val_loss,val,0.3816430082054893,
+mrfp,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=18-step=20000.ckpt,ridge,val_r,val,0.520855720912494,
+mrl,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=18-step=20000.ckpt,ridge,val_loss,val,0.7437523843416108,
+mrl,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=18-step=20000.ckpt,ridge,val_r,val,0.39403218950488417,
+protein_loc,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=18-step=20000.ckpt,logistic,val_roc_auc,val,0.825946043024202,
+protein_loc,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=18-step=20000.ckpt,logistic,val_auprc,val,0.3617639617322508,
+hl_human,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=18-step=20000.ckpt,ridge,val_loss,val,0.6739744006625423,
+hl_human,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=18-step=20000.ckpt,ridge,val_r,val,0.544860645002531,
+hl_mouse,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=18-step=20000.ckpt,ridge,val_loss,val,0.7105890797238071,
+hl_mouse,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=18-step=20000.ckpt,ridge,val_r,val,0.5249681390195272,

models/orthrus_base_4_track/lp_results/homo_lp_results_ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria_epoch=3-step=4000.ckpt_ridge.csv

@@ -0,0 +1,13 @@
+dataset,run_name,ckpt_name,lin_model,metric,split,mean_value,std_value
+go_mf,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=3-step=4000.ckpt,logistic,val_roc_auc,val,0.8334827448623479,
+go_mf,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=3-step=4000.ckpt,logistic,val_auprc,val,0.48054142074091,
+mrfp,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=3-step=4000.ckpt,ridge,val_loss,val,0.3937403979375475,
+mrfp,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=3-step=4000.ckpt,ridge,val_r,val,0.5039354128857179,
+mrl,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=3-step=4000.ckpt,ridge,val_loss,val,0.7527737213090051,
+mrl,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=3-step=4000.ckpt,ridge,val_r,val,0.3806671640445604,
+protein_loc,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=3-step=4000.ckpt,logistic,val_roc_auc,val,0.8213135611439488,
+protein_loc,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=3-step=4000.ckpt,logistic,val_auprc,val,0.35596875648549375,
+hl_human,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=3-step=4000.ckpt,ridge,val_loss,val,0.7108028779272146,
+hl_human,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=3-step=4000.ckpt,ridge,val_r,val,0.5099485164455663,
+hl_mouse,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=3-step=4000.ckpt,ridge,val_loss,val,0.7471981375686599,
+hl_mouse,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=3-step=4000.ckpt,ridge,val_r,val,0.48843724229011504,

models/orthrus_base_4_track/lp_results/homo_lp_results_ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria_epoch=5-step=6000.ckpt_ridge.csv

@@ -0,0 +1,13 @@
+dataset,run_name,ckpt_name,lin_model,metric,split,mean_value,std_value
+go_mf,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=5-step=6000.ckpt,logistic,val_roc_auc,val,0.8378129434997147,
+go_mf,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=5-step=6000.ckpt,logistic,val_auprc,val,0.4930322732919934,
+mrfp,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=5-step=6000.ckpt,ridge,val_loss,val,0.42145942081505877,
+mrfp,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=5-step=6000.ckpt,ridge,val_r,val,0.46362110810253776,
+mrl,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=5-step=6000.ckpt,ridge,val_loss,val,0.7539863277031761,
+mrl,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=5-step=6000.ckpt,ridge,val_r,val,0.3786947841967137,
+protein_loc,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=5-step=6000.ckpt,logistic,val_roc_auc,val,0.822611781448217,
+protein_loc,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=5-step=6000.ckpt,logistic,val_auprc,val,0.3550260538018792,
+hl_human,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=5-step=6000.ckpt,ridge,val_loss,val,0.6853506444183269,
+hl_human,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=5-step=6000.ckpt,ridge,val_r,val,0.5338677108741229,
+hl_mouse,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=5-step=6000.ckpt,ridge,val_loss,val,0.7403810703891033,
+hl_mouse,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=5-step=6000.ckpt,ridge,val_r,val,0.49591840377848506,

models/orthrus_base_4_track/lp_results/homo_lp_results_ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria_epoch=7-step=8000.ckpt_ridge.csv

@@ -0,0 +1,13 @@
+dataset,run_name,ckpt_name,lin_model,metric,split,mean_value,std_value
+go_mf,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=7-step=8000.ckpt,logistic,val_roc_auc,val,0.838934161283643,
+go_mf,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=7-step=8000.ckpt,logistic,val_auprc,val,0.499202623569385,
+mrfp,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=7-step=8000.ckpt,ridge,val_loss,val,0.41299386356832335,
+mrfp,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=7-step=8000.ckpt,ridge,val_r,val,0.47458154750742787,
+mrl,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=7-step=8000.ckpt,ridge,val_loss,val,0.7506913875148472,
+mrl,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=7-step=8000.ckpt,ridge,val_r,val,0.3835651031902195,
+protein_loc,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=7-step=8000.ckpt,logistic,val_roc_auc,val,0.8234223639111674,
+protein_loc,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=7-step=8000.ckpt,logistic,val_auprc,val,0.35690103176614196,
+hl_human,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=7-step=8000.ckpt,ridge,val_loss,val,0.6861524146069266,
+hl_human,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=7-step=8000.ckpt,ridge,val_r,val,0.5330125034795364,
+hl_mouse,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=7-step=8000.ckpt,ridge,val_loss,val,0.734732230977574,
+hl_mouse,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=7-step=8000.ckpt,ridge,val_r,val,0.5014295583249777,

models/orthrus_base_4_track/lp_results/homo_lp_results_ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria_epoch=9-step=10000.ckpt_ridge.csv

@@ -0,0 +1,13 @@
+dataset,run_name,ckpt_name,lin_model,metric,split,mean_value,std_value
+go_mf,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=9-step=10000.ckpt,logistic,val_roc_auc,val,0.8419237597159581,
+go_mf,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=9-step=10000.ckpt,logistic,val_auprc,val,0.5067915793618881,
+mrfp,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=9-step=10000.ckpt,ridge,val_loss,val,0.3812646126826232,
+mrfp,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=9-step=10000.ckpt,ridge,val_r,val,0.5231334426937999,
+mrl,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=9-step=10000.ckpt,ridge,val_loss,val,0.7419690874136367,
+mrl,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=9-step=10000.ckpt,ridge,val_r,val,0.39632707952585045,
+protein_loc,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=9-step=10000.ckpt,logistic,val_roc_auc,val,0.8258357171939567,
+protein_loc,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=9-step=10000.ckpt,logistic,val_auprc,val,0.3602220156610885,
+hl_human,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=9-step=10000.ckpt,ridge,val_loss,val,0.6739133283342498,
+hl_human,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=9-step=10000.ckpt,ridge,val_r,val,0.5449821329643417,
+hl_mouse,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=9-step=10000.ckpt,ridge,val_loss,val,0.7232799553052773,
+hl_mouse,ssm_4t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=9-step=10000.ckpt,ridge,val_r,val,0.5127369847559508,

models/orthrus_base_4_track/lp_results/homo_lp_results_ssm_6t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria_epoch=18-step=20000.ckpt_ridge.csv

@@ -1,13 +0,0 @@
-dataset,run_name,ckpt_name,lin_model,metric,split,mean_value,std_value
-go_mf,ssm_6t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=18-step=20000.ckpt,logistic,val_roc_auc,val,0.8478578174637246,
-go_mf,ssm_6t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=18-step=20000.ckpt,logistic,val_auprc,val,0.5095139671888503,
-mrfp,ssm_6t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=18-step=20000.ckpt,ridge,val_loss,val,0.3546131256685185,
-mrfp,ssm_6t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=18-step=20000.ckpt,ridge,val_r,val,0.5707018777098897,
-mrl,ssm_6t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=18-step=20000.ckpt,ridge,val_loss,val,0.7273312686835766,
-mrl,ssm_6t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=18-step=20000.ckpt,ridge,val_r,val,0.41711144859054816,
-protein_loc,ssm_6t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=18-step=20000.ckpt,logistic,val_roc_auc,val,0.8337499171489103,
-protein_loc,ssm_6t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=18-step=20000.ckpt,logistic,val_auprc,val,0.3868738259700707,
-hl_human,ssm_6t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=18-step=20000.ckpt,ridge,val_loss,val,0.5510596183223497,
-hl_human,ssm_6t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=18-step=20000.ckpt,ridge,val_r,val,0.6528813736053247,
-hl_mouse,ssm_6t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=18-step=20000.ckpt,ridge,val_loss,val,0.5930341784262118,
-hl_mouse,ssm_6t_3_256_lr0.001_wd1e-05_mask0.15_splice_all_basic_eutheria,epoch=18-step=20000.ckpt,ridge,val_r,val,0.6290704100935987,

models/orthrus_base_4_track/model_config.json

@@ -1 +1 @@
-{"model_class": "ssm", "ssm_model_dim": 256, "ssm_n_layers": 3, "n_tracks": 6, "predict_splice_codon": false, "predict_masked": false}
+{"model_class": "ssm", "ssm_model_dim": 256, "ssm_n_layers": 3, "n_tracks": 4, "predict_splice_codon": false, "predict_masked": false}

notebooks/colab_prototye.ipynb

@@ -204,7 +204,8 @@
     "        t (gk.Transcript): The transcript object.\n",
     "    \"\"\"\n",
     "    seq = \"\".join([genome.dna(exon) for exon in t.exons])\n",
-    "    oh = seq_to_oh(seq)\n",
+    "    oh = \n",
+    "    _oh(seq)\n",
     "    return oh\n",
     "\n",
     "def create_six_track_encoding(t, channels_last=False):\n",

src/model.py

@@ -4,10 +4,25 @@ import os
 import json
 import torch
 import torch.nn as nn
+import numpy as np
 
 from mamba_ssm.modules.mamba_simple import Mamba, Block
 from huggingface_hub import PyTorchModelHubMixin
 
+# convert to one hot
+def seq_to_oh(seq):
+    oh = np.zeros((len(seq), 4), dtype=int)
+    for i, base in enumerate(seq):
+        if base == 'A':
+            oh[i, 0] = 1
+        elif base == 'C':
+            oh[i, 1] = 1
+        elif base == 'G':
+            oh[i, 2] = 1
+        elif base == 'T':
+            oh[i, 3] = 1
+    return oh
+
 def create_block(
     d_model,
     ssm_cfg=None,