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songlab
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TraitGym

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Tags:
dna
variant-effect-prediction
biology
genomics
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  1. mendelian_traits_matched_9/AUROC_by_chrom/all/Borzoi.LogisticRegression.chrom.csv +20 -0
  2. mendelian_traits_matched_9/AUROC_by_chrom/all/Borzoi_L2_L2.plus.all.csv +20 -0
  3. mendelian_traits_matched_9/AUROC_by_chrom/all/CADD+Borzoi.LogisticRegression.chrom.csv +20 -0
  4. mendelian_traits_matched_9/AUROC_by_chrom/all/CADD+GPN-MSA+Borzoi.LogisticRegression.chrom.csv +20 -0
  5. mendelian_traits_matched_9/AUROC_by_chrom/all/CADD+GPN-MSA.LogisticRegression.chrom.csv +20 -0
  6. mendelian_traits_matched_9/AUROC_by_chrom/all/CADD.LogisticRegression.chrom.csv +20 -0
  7. mendelian_traits_matched_9/AUROC_by_chrom/all/CADD.plus.RawScore.csv +20 -0
  8. mendelian_traits_matched_9/AUROC_by_chrom/all/Caduceus.LogisticRegression.chrom.csv +20 -0
  9. mendelian_traits_matched_9/AUROC_by_chrom/all/Caduceus_Embeddings.minus.inner_product.csv +20 -0
  10. mendelian_traits_matched_9/AUROC_by_chrom/all/Caduceus_Embeddings.plus.cosine_distance.csv +20 -0
  11. mendelian_traits_matched_9/AUROC_by_chrom/all/Caduceus_Embeddings.plus.euclidean_distance.csv +20 -0
  12. mendelian_traits_matched_9/AUROC_by_chrom/all/Caduceus_LLR.minus.score.csv +20 -0
  13. mendelian_traits_matched_9/AUROC_by_chrom/all/Caduceus_absLLR.plus.score.csv +20 -0
  14. mendelian_traits_matched_9/AUROC_by_chrom/all/Enformer.LogisticRegression.chrom.csv +20 -0
  15. mendelian_traits_matched_9/AUROC_by_chrom/all/Enformer_L2_L2.plus.all.csv +20 -0
  16. mendelian_traits_matched_9/AUROC_by_chrom/all/GPN-MSA+Borzoi.LogisticRegression.chrom.csv +20 -0
  17. mendelian_traits_matched_9/AUROC_by_chrom/all/GPN-MSA.LogisticRegression.chrom.csv +20 -0
  18. mendelian_traits_matched_9/AUROC_by_chrom/all/GPN-MSA_Embeddings.minus.inner_product.csv +20 -0
  19. mendelian_traits_matched_9/AUROC_by_chrom/all/GPN-MSA_Embeddings.plus.cosine_distance.csv +20 -0
  20. mendelian_traits_matched_9/AUROC_by_chrom/all/GPN-MSA_Embeddings.plus.euclidean_distance.csv +20 -0
  21. mendelian_traits_matched_9/AUROC_by_chrom/all/GPN-MSA_LLR.minus.score.csv +20 -0
  22. mendelian_traits_matched_9/AUROC_by_chrom/all/GPN-MSA_absLLR.plus.score.csv +20 -0
  23. mendelian_traits_matched_9/AUROC_by_chrom/all/GPN_final.LogisticRegression.chrom.csv +20 -0
  24. mendelian_traits_matched_9/AUROC_by_chrom/all/GPN_final_Embeddings.minus.inner_product.csv +20 -0
  25. mendelian_traits_matched_9/AUROC_by_chrom/all/GPN_final_Embeddings.plus.cosine_distance.csv +20 -0
  26. mendelian_traits_matched_9/AUROC_by_chrom/all/GPN_final_Embeddings.plus.euclidean_distance.csv +20 -0
  27. mendelian_traits_matched_9/AUROC_by_chrom/all/GPN_final_LLR.minus.score.csv +20 -0
  28. mendelian_traits_matched_9/AUROC_by_chrom/all/GPN_final_absLLR.plus.score.csv +20 -0
  29. mendelian_traits_matched_9/AUROC_by_chrom/all/HyenaDNA.LogisticRegression.chrom.csv +20 -0
  30. mendelian_traits_matched_9/AUROC_by_chrom/all/HyenaDNA_Embeddings.minus.inner_product.csv +20 -0
  31. mendelian_traits_matched_9/AUROC_by_chrom/all/HyenaDNA_Embeddings.plus.cosine_distance.csv +20 -0
  32. mendelian_traits_matched_9/AUROC_by_chrom/all/HyenaDNA_Embeddings.plus.euclidean_distance.csv +20 -0
  33. mendelian_traits_matched_9/AUROC_by_chrom/all/HyenaDNA_LLR.minus.score.csv +20 -0
  34. mendelian_traits_matched_9/AUROC_by_chrom/all/HyenaDNA_absLLR.plus.score.csv +20 -0
  35. mendelian_traits_matched_9/AUROC_by_chrom/all/NucleotideTransformer.LogisticRegression.chrom.csv +20 -0
  36. mendelian_traits_matched_9/AUROC_by_chrom/all/NucleotideTransformer_Embeddings.minus.inner_product.csv +20 -0
  37. mendelian_traits_matched_9/AUROC_by_chrom/all/NucleotideTransformer_Embeddings.plus.cosine_distance.csv +20 -0
  38. mendelian_traits_matched_9/AUROC_by_chrom/all/NucleotideTransformer_Embeddings.plus.euclidean_distance.csv +20 -0
  39. mendelian_traits_matched_9/AUROC_by_chrom/all/NucleotideTransformer_LLR.minus.score.csv +20 -0
  40. mendelian_traits_matched_9/AUROC_by_chrom/all/NucleotideTransformer_absLLR.plus.score.csv +20 -0
  41. mendelian_traits_matched_9/AUROC_by_chrom/all/Sei.LogisticRegression.chrom.csv +20 -0
  42. mendelian_traits_matched_9/AUROC_by_chrom/all/Sei.plus.seqclass_max_absdiff.csv +20 -0
  43. mendelian_traits_matched_9/AUROC_by_chrom_weighted_average/all/Borzoi.LogisticRegression.chrom.csv +2 -0
  44. mendelian_traits_matched_9/AUROC_by_chrom_weighted_average/all/CADD+Borzoi.LogisticRegression.chrom.csv +2 -0
  45. mendelian_traits_matched_9/AUROC_by_chrom_weighted_average/all/CADD+GPN-MSA+Borzoi.LogisticRegression.chrom.csv +2 -0
  46. mendelian_traits_matched_9/AUROC_by_chrom_weighted_average/all/CADD+GPN-MSA.LogisticRegression.chrom.csv +2 -0
  47. mendelian_traits_matched_9/AUROC_by_chrom_weighted_average/all/CADD.LogisticRegression.chrom.csv +2 -0
  48. mendelian_traits_matched_9/AUROC_by_chrom_weighted_average/all/CADD.plus.RawScore.csv +2 -0
  49. mendelian_traits_matched_9/AUROC_by_chrom_weighted_average/all/Caduceus.LogisticRegression.chrom.csv +2 -0
  50. mendelian_traits_matched_9/AUROC_by_chrom_weighted_average/all/Caduceus_Embeddings.minus.inner_product.csv +2 -0
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mendelian_traits_matched_9/AUROC_by_chrom/all/Borzoi_L2_L2.plus.all.csv ADDED
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mendelian_traits_matched_9/AUROC_by_chrom/all/CADD+Borzoi.LogisticRegression.chrom.csv ADDED
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mendelian_traits_matched_9/AUROC_by_chrom/all/CADD+GPN-MSA+Borzoi.LogisticRegression.chrom.csv ADDED
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mendelian_traits_matched_9/AUROC_by_chrom/all/Caduceus_Embeddings.minus.inner_product.csv ADDED
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mendelian_traits_matched_9/AUROC_by_chrom/all/Caduceus_Embeddings.plus.cosine_distance.csv ADDED
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1
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mendelian_traits_matched_9/AUROC_by_chrom/all/Caduceus_Embeddings.plus.euclidean_distance.csv ADDED
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1
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mendelian_traits_matched_9/AUROC_by_chrom/all/Caduceus_LLR.minus.score.csv ADDED
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mendelian_traits_matched_9/AUROC_by_chrom/all/Caduceus_absLLR.plus.score.csv ADDED
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mendelian_traits_matched_9/AUROC_by_chrom/all/Enformer.LogisticRegression.chrom.csv ADDED
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mendelian_traits_matched_9/AUROC_by_chrom/all/Enformer_L2_L2.plus.all.csv ADDED
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mendelian_traits_matched_9/AUROC_by_chrom/all/GPN-MSA+Borzoi.LogisticRegression.chrom.csv ADDED
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mendelian_traits_matched_9/AUROC_by_chrom/all/GPN-MSA.LogisticRegression.chrom.csv ADDED
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mendelian_traits_matched_9/AUROC_by_chrom/all/GPN-MSA_Embeddings.minus.inner_product.csv ADDED
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1
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mendelian_traits_matched_9/AUROC_by_chrom/all/GPN-MSA_Embeddings.plus.cosine_distance.csv ADDED
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1
+ chrom,n,Model,AUROC
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mendelian_traits_matched_9/AUROC_by_chrom/all/GPN-MSA_Embeddings.plus.euclidean_distance.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUROC
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mendelian_traits_matched_9/AUROC_by_chrom/all/GPN-MSA_LLR.minus.score.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
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+ X,500,GPN-MSA_LLR.minus.score,0.9062
mendelian_traits_matched_9/AUROC_by_chrom/all/GPN-MSA_absLLR.plus.score.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUROC
2
+ 1,210,GPN-MSA_absLLR.plus.score,0.7205845301083397
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mendelian_traits_matched_9/AUROC_by_chrom/all/GPN_final.LogisticRegression.chrom.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUROC
2
+ 1,210,GPN_final.LogisticRegression.chrom,0.652557319223986
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mendelian_traits_matched_9/AUROC_by_chrom/all/GPN_final_Embeddings.minus.inner_product.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUROC
2
+ 1,210,GPN_final_Embeddings.minus.inner_product,0.5054169816074578
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mendelian_traits_matched_9/AUROC_by_chrom/all/GPN_final_Embeddings.plus.cosine_distance.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUROC
2
+ 1,210,GPN_final_Embeddings.plus.cosine_distance,0.6397077349458301
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mendelian_traits_matched_9/AUROC_by_chrom/all/GPN_final_Embeddings.plus.euclidean_distance.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUROC
2
+ 1,210,GPN_final_Embeddings.plus.euclidean_distance,0.6336608717561099
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mendelian_traits_matched_9/AUROC_by_chrom/all/GPN_final_LLR.minus.score.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUROC
2
+ 1,210,GPN_final_LLR.minus.score,0.6477702191987906
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mendelian_traits_matched_9/AUROC_by_chrom/all/GPN_final_absLLR.plus.score.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUROC
2
+ 1,210,GPN_final_absLLR.plus.score,0.5947341899722852
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mendelian_traits_matched_9/AUROC_by_chrom/all/HyenaDNA.LogisticRegression.chrom.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUROC
2
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mendelian_traits_matched_9/AUROC_by_chrom/all/HyenaDNA_Embeddings.minus.inner_product.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUROC
2
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mendelian_traits_matched_9/AUROC_by_chrom/all/HyenaDNA_Embeddings.plus.cosine_distance.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUROC
2
+ 1,210,HyenaDNA_Embeddings.plus.cosine_distance,0.4454522549760645
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+ X,500,HyenaDNA_Embeddings.plus.cosine_distance,0.5174222222222222
mendelian_traits_matched_9/AUROC_by_chrom/all/HyenaDNA_Embeddings.plus.euclidean_distance.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUROC
2
+ 1,210,HyenaDNA_Embeddings.plus.euclidean_distance,0.4525069286974049
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+ X,500,HyenaDNA_Embeddings.plus.euclidean_distance,0.5195555555555555
mendelian_traits_matched_9/AUROC_by_chrom/all/HyenaDNA_LLR.minus.score.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUROC
2
+ 1,210,HyenaDNA_LLR.minus.score,0.4896699420508944
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+ X,500,HyenaDNA_LLR.minus.score,0.5074444444444445
mendelian_traits_matched_9/AUROC_by_chrom/all/HyenaDNA_absLLR.plus.score.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUROC
2
+ 1,210,HyenaDNA_absLLR.plus.score,0.5381708238851096
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mendelian_traits_matched_9/AUROC_by_chrom/all/NucleotideTransformer.LogisticRegression.chrom.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUROC
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+ 1,210,NucleotideTransformer.LogisticRegression.chrom,0.6389518770471152
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mendelian_traits_matched_9/AUROC_by_chrom/all/NucleotideTransformer_Embeddings.minus.inner_product.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUROC
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mendelian_traits_matched_9/AUROC_by_chrom/all/NucleotideTransformer_Embeddings.plus.cosine_distance.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUROC
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+ 1,210,NucleotideTransformer_Embeddings.plus.cosine_distance,0.564877802973041
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mendelian_traits_matched_9/AUROC_by_chrom/all/NucleotideTransformer_Embeddings.plus.euclidean_distance.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUROC
2
+ 1,210,NucleotideTransformer_Embeddings.plus.euclidean_distance,0.564877802973041
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+ X,500,NucleotideTransformer_Embeddings.plus.euclidean_distance,0.7382666666666666
mendelian_traits_matched_9/AUROC_by_chrom/all/NucleotideTransformer_LLR.minus.score.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUROC
2
+ 1,210,NucleotideTransformer_LLR.minus.score,0.5666414714033762
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+ X,500,NucleotideTransformer_LLR.minus.score,0.46684444444444445
mendelian_traits_matched_9/AUROC_by_chrom/all/NucleotideTransformer_absLLR.plus.score.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUROC
2
+ 1,210,NucleotideTransformer_absLLR.plus.score,0.5714285714285714
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+ X,500,NucleotideTransformer_absLLR.plus.score,0.44084444444444437
mendelian_traits_matched_9/AUROC_by_chrom/all/Sei.LogisticRegression.chrom.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUROC
2
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+ X,500,Sei.LogisticRegression.chrom,0.8018666666666667
mendelian_traits_matched_9/AUROC_by_chrom/all/Sei.plus.seqclass_max_absdiff.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUROC
2
+ 1,210,Sei.plus.seqclass_max_absdiff,0.5381708238851096
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mendelian_traits_matched_9/AUROC_by_chrom_weighted_average/all/Borzoi.LogisticRegression.chrom.csv ADDED
@@ -0,0 +1,2 @@
 
 
 
1
+ model,metric,score,se
2
+ Borzoi.LogisticRegression.chrom,AUROC,0.8065971866162441,0.021103589149458254
mendelian_traits_matched_9/AUROC_by_chrom_weighted_average/all/CADD+Borzoi.LogisticRegression.chrom.csv ADDED
@@ -0,0 +1,2 @@
 
 
 
1
+ model,metric,score,se
2
+ CADD+Borzoi.LogisticRegression.chrom,AUROC,0.8893582300725595,0.0192709349279206
mendelian_traits_matched_9/AUROC_by_chrom_weighted_average/all/CADD+GPN-MSA+Borzoi.LogisticRegression.chrom.csv ADDED
@@ -0,0 +1,2 @@
 
 
 
1
+ model,metric,score,se
2
+ CADD+GPN-MSA+Borzoi.LogisticRegression.chrom,AUROC,0.8934215272537339,0.016816618993044742
mendelian_traits_matched_9/AUROC_by_chrom_weighted_average/all/CADD+GPN-MSA.LogisticRegression.chrom.csv ADDED
@@ -0,0 +1,2 @@
 
 
 
1
+ model,metric,score,se
2
+ CADD+GPN-MSA.LogisticRegression.chrom,AUROC,0.9473345796526276,0.015185041415705083
mendelian_traits_matched_9/AUROC_by_chrom_weighted_average/all/CADD.LogisticRegression.chrom.csv ADDED
@@ -0,0 +1,2 @@
 
 
 
1
+ model,metric,score,se
2
+ CADD.LogisticRegression.chrom,AUROC,0.95856114498837,0.013203555700306433
mendelian_traits_matched_9/AUROC_by_chrom_weighted_average/all/CADD.plus.RawScore.csv ADDED
@@ -0,0 +1,2 @@
 
 
 
1
+ model,metric,score,se
2
+ CADD.plus.RawScore,AUROC,0.8925850098264585,0.016053941096174962
mendelian_traits_matched_9/AUROC_by_chrom_weighted_average/all/Caduceus.LogisticRegression.chrom.csv ADDED
@@ -0,0 +1,2 @@
 
 
 
1
+ model,metric,score,se
2
+ Caduceus.LogisticRegression.chrom,AUROC,0.5982808597501177,0.060088656273358895
mendelian_traits_matched_9/AUROC_by_chrom_weighted_average/all/Caduceus_Embeddings.minus.inner_product.csv ADDED
@@ -0,0 +1,2 @@
 
 
 
1
+ model,metric,score,se
2
+ Caduceus_Embeddings.minus.inner_product,AUROC,0.5436272633468365,0.04965723922381773