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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. complex_traits_matched_9/AUROC_by_chrom/all/Borzoi.LogisticRegression.chrom.csv +23 -0
  2. complex_traits_matched_9/AUROC_by_chrom/all/Borzoi_L2_L2.plus.all.csv +23 -0
  3. complex_traits_matched_9/AUROC_by_chrom/all/CADD+Borzoi.LogisticRegression.chrom.csv +23 -0
  4. complex_traits_matched_9/AUROC_by_chrom/all/CADD+GPN-MSA+Borzoi.LogisticRegression.chrom.csv +23 -0
  5. complex_traits_matched_9/AUROC_by_chrom/all/CADD+GPN-MSA.LogisticRegression.chrom.csv +23 -0
  6. complex_traits_matched_9/AUROC_by_chrom/all/CADD.LogisticRegression.chrom.csv +23 -0
  7. complex_traits_matched_9/AUROC_by_chrom/all/CADD.plus.RawScore.csv +23 -0
  8. complex_traits_matched_9/AUROC_by_chrom/all/Caduceus.LogisticRegression.chrom.csv +23 -0
  9. complex_traits_matched_9/AUROC_by_chrom/all/Caduceus_Embeddings.minus.inner_product.csv +23 -0
  10. complex_traits_matched_9/AUROC_by_chrom/all/Caduceus_Embeddings.plus.cosine_distance.csv +23 -0
  11. complex_traits_matched_9/AUROC_by_chrom/all/Caduceus_Embeddings.plus.euclidean_distance.csv +23 -0
  12. complex_traits_matched_9/AUROC_by_chrom/all/Caduceus_LLR.minus.score.csv +23 -0
  13. complex_traits_matched_9/AUROC_by_chrom/all/Caduceus_absLLR.plus.score.csv +23 -0
  14. complex_traits_matched_9/AUROC_by_chrom/all/Enformer.LogisticRegression.chrom.csv +23 -0
  15. complex_traits_matched_9/AUROC_by_chrom/all/Enformer_L2_L2.plus.all.csv +23 -0
  16. complex_traits_matched_9/AUROC_by_chrom/all/GPN-MSA+Borzoi.LogisticRegression.chrom.csv +23 -0
  17. complex_traits_matched_9/AUROC_by_chrom/all/GPN-MSA.LogisticRegression.chrom.csv +23 -0
  18. complex_traits_matched_9/AUROC_by_chrom/all/GPN-MSA_Embeddings.minus.inner_product.csv +23 -0
  19. complex_traits_matched_9/AUROC_by_chrom/all/GPN-MSA_Embeddings.plus.cosine_distance.csv +23 -0
  20. complex_traits_matched_9/AUROC_by_chrom/all/GPN-MSA_Embeddings.plus.euclidean_distance.csv +23 -0
  21. complex_traits_matched_9/AUROC_by_chrom/all/GPN-MSA_LLR.minus.score.csv +23 -0
  22. complex_traits_matched_9/AUROC_by_chrom/all/GPN-MSA_absLLR.plus.score.csv +23 -0
  23. complex_traits_matched_9/AUROC_by_chrom/all/GPN_final.LogisticRegression.chrom.csv +23 -0
  24. complex_traits_matched_9/AUROC_by_chrom/all/GPN_final_Embeddings.minus.inner_product.csv +23 -0
  25. complex_traits_matched_9/AUROC_by_chrom/all/GPN_final_Embeddings.plus.cosine_distance.csv +23 -0
  26. complex_traits_matched_9/AUROC_by_chrom/all/GPN_final_Embeddings.plus.euclidean_distance.csv +23 -0
  27. complex_traits_matched_9/AUROC_by_chrom/all/GPN_final_LLR.minus.score.csv +23 -0
  28. complex_traits_matched_9/AUROC_by_chrom/all/GPN_final_absLLR.plus.score.csv +23 -0
  29. complex_traits_matched_9/AUROC_by_chrom/all/HyenaDNA.LogisticRegression.chrom.csv +23 -0
  30. complex_traits_matched_9/AUROC_by_chrom/all/HyenaDNA_Embeddings.minus.inner_product.csv +23 -0
  31. complex_traits_matched_9/AUROC_by_chrom/all/HyenaDNA_Embeddings.plus.cosine_distance.csv +23 -0
  32. complex_traits_matched_9/AUROC_by_chrom/all/HyenaDNA_Embeddings.plus.euclidean_distance.csv +23 -0
  33. complex_traits_matched_9/AUROC_by_chrom/all/HyenaDNA_LLR.minus.score.csv +23 -0
  34. complex_traits_matched_9/AUROC_by_chrom/all/HyenaDNA_absLLR.plus.score.csv +23 -0
  35. complex_traits_matched_9/AUROC_by_chrom/all/NucleotideTransformer.LogisticRegression.chrom.csv +23 -0
  36. complex_traits_matched_9/AUROC_by_chrom/all/NucleotideTransformer_Embeddings.minus.inner_product.csv +23 -0
  37. complex_traits_matched_9/AUROC_by_chrom/all/NucleotideTransformer_Embeddings.plus.cosine_distance.csv +23 -0
  38. complex_traits_matched_9/AUROC_by_chrom/all/NucleotideTransformer_Embeddings.plus.euclidean_distance.csv +23 -0
  39. complex_traits_matched_9/AUROC_by_chrom/all/NucleotideTransformer_LLR.minus.score.csv +23 -0
  40. complex_traits_matched_9/AUROC_by_chrom/all/NucleotideTransformer_absLLR.plus.score.csv +23 -0
  41. complex_traits_matched_9/AUROC_by_chrom/all/Sei.LogisticRegression.chrom.csv +23 -0
  42. complex_traits_matched_9/AUROC_by_chrom/all/Sei.plus.seqclass_max_absdiff.csv +23 -0
  43. complex_traits_matched_9/AUROC_by_chrom_weighted_average/all/Borzoi.LogisticRegression.chrom.csv +2 -0
  44. complex_traits_matched_9/AUROC_by_chrom_weighted_average/all/Borzoi_L2_L2.plus.all.csv +2 -0
  45. complex_traits_matched_9/AUROC_by_chrom_weighted_average/all/CADD+Borzoi.LogisticRegression.chrom.csv +2 -0
  46. complex_traits_matched_9/AUROC_by_chrom_weighted_average/all/CADD+GPN-MSA.LogisticRegression.chrom.csv +2 -0
  47. complex_traits_matched_9/AUROC_by_chrom_weighted_average/all/CADD.LogisticRegression.chrom.csv +2 -0
  48. complex_traits_matched_9/AUROC_by_chrom_weighted_average/all/CADD.plus.RawScore.csv +2 -0
  49. complex_traits_matched_9/AUROC_by_chrom_weighted_average/all/Caduceus.LogisticRegression.chrom.csv +2 -0
  50. complex_traits_matched_9/AUROC_by_chrom_weighted_average/all/Caduceus_Embeddings.minus.inner_product.csv +2 -0
complex_traits_matched_9/AUROC_by_chrom/all/Borzoi.LogisticRegression.chrom.csv ADDED
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complex_traits_matched_9/AUROC_by_chrom/all/Borzoi_L2_L2.plus.all.csv ADDED
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complex_traits_matched_9/AUROC_by_chrom/all/CADD+Borzoi.LogisticRegression.chrom.csv ADDED
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complex_traits_matched_9/AUROC_by_chrom/all/Caduceus_Embeddings.minus.inner_product.csv ADDED
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complex_traits_matched_9/AUROC_by_chrom/all/Caduceus_Embeddings.plus.cosine_distance.csv ADDED
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complex_traits_matched_9/AUROC_by_chrom/all/Caduceus_Embeddings.plus.euclidean_distance.csv ADDED
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complex_traits_matched_9/AUROC_by_chrom/all/Caduceus_LLR.minus.score.csv ADDED
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complex_traits_matched_9/AUROC_by_chrom/all/Caduceus_absLLR.plus.score.csv ADDED
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+ chrom,n,Model,AUROC
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complex_traits_matched_9/AUROC_by_chrom/all/Enformer.LogisticRegression.chrom.csv ADDED
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1
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complex_traits_matched_9/AUROC_by_chrom/all/Enformer_L2_L2.plus.all.csv ADDED
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complex_traits_matched_9/AUROC_by_chrom/all/GPN-MSA+Borzoi.LogisticRegression.chrom.csv ADDED
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complex_traits_matched_9/AUROC_by_chrom/all/GPN-MSA_Embeddings.minus.inner_product.csv ADDED
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complex_traits_matched_9/AUROC_by_chrom/all/GPN-MSA_Embeddings.plus.cosine_distance.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
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complex_traits_matched_9/AUROC_by_chrom/all/GPN-MSA_Embeddings.plus.euclidean_distance.csv ADDED
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1
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complex_traits_matched_9/AUROC_by_chrom/all/GPN-MSA_LLR.minus.score.csv ADDED
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1
+ chrom,n,Model,AUROC
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complex_traits_matched_9/AUROC_by_chrom/all/GPN-MSA_absLLR.plus.score.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
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complex_traits_matched_9/AUROC_by_chrom/all/GPN_final.LogisticRegression.chrom.csv ADDED
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1
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complex_traits_matched_9/AUROC_by_chrom/all/GPN_final_Embeddings.minus.inner_product.csv ADDED
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1
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complex_traits_matched_9/AUROC_by_chrom/all/GPN_final_Embeddings.plus.cosine_distance.csv ADDED
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1
+ chrom,n,Model,AUROC
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complex_traits_matched_9/AUROC_by_chrom/all/GPN_final_Embeddings.plus.euclidean_distance.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
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complex_traits_matched_9/AUROC_by_chrom/all/GPN_final_LLR.minus.score.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUROC
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complex_traits_matched_9/AUROC_by_chrom/all/GPN_final_absLLR.plus.score.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUROC
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complex_traits_matched_9/AUROC_by_chrom/all/HyenaDNA.LogisticRegression.chrom.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUROC
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complex_traits_matched_9/AUROC_by_chrom/all/HyenaDNA_Embeddings.minus.inner_product.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
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complex_traits_matched_9/AUROC_by_chrom/all/HyenaDNA_Embeddings.plus.cosine_distance.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
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complex_traits_matched_9/AUROC_by_chrom/all/HyenaDNA_Embeddings.plus.euclidean_distance.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
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complex_traits_matched_9/AUROC_by_chrom/all/HyenaDNA_LLR.minus.score.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUROC
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complex_traits_matched_9/AUROC_by_chrom/all/HyenaDNA_absLLR.plus.score.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUROC
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complex_traits_matched_9/AUROC_by_chrom/all/NucleotideTransformer.LogisticRegression.chrom.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
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complex_traits_matched_9/AUROC_by_chrom/all/NucleotideTransformer_Embeddings.minus.inner_product.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
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complex_traits_matched_9/AUROC_by_chrom/all/NucleotideTransformer_Embeddings.plus.cosine_distance.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
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complex_traits_matched_9/AUROC_by_chrom/all/NucleotideTransformer_Embeddings.plus.euclidean_distance.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
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complex_traits_matched_9/AUROC_by_chrom/all/NucleotideTransformer_LLR.minus.score.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUROC
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+ 3,650,NucleotideTransformer_LLR.minus.score,0.4876002629848784
5
+ 4,400,NucleotideTransformer_LLR.minus.score,0.4552777777777778
6
+ 5,510,NucleotideTransformer_LLR.minus.score,0.5018582596437268
7
+ 6,780,NucleotideTransformer_LLR.minus.score,0.517203594126671
8
+ 7,540,NucleotideTransformer_LLR.minus.score,0.3922039323273891
9
+ 8,460,NucleotideTransformer_LLR.minus.score,0.38384793110691035
10
+ 9,440,NucleotideTransformer_LLR.minus.score,0.45867768595041325
11
+ 10,510,NucleotideTransformer_LLR.minus.score,0.46456491093169294
12
+ 11,680,NucleotideTransformer_LLR.minus.score,0.5165801614763552
13
+ 12,590,NucleotideTransformer_LLR.minus.score,0.5369465989977337
14
+ 13,200,NucleotideTransformer_LLR.minus.score,0.41
15
+ 14,380,NucleotideTransformer_LLR.minus.score,0.481763619575254
16
+ 15,390,NucleotideTransformer_LLR.minus.score,0.5107020235225364
17
+ 16,590,NucleotideTransformer_LLR.minus.score,0.4434230265887835
18
+ 17,560,NucleotideTransformer_LLR.minus.score,0.49447278911564624
19
+ 18,290,NucleotideTransformer_LLR.minus.score,0.41075439291848326
20
+ 19,580,NucleotideTransformer_LLR.minus.score,0.48705245078610115
21
+ 20,530,NucleotideTransformer_LLR.minus.score,0.508089078754796
22
+ 21,140,NucleotideTransformer_LLR.minus.score,0.5487528344671202
23
+ 22,280,NucleotideTransformer_LLR.minus.score,0.5625000000000001
complex_traits_matched_9/AUROC_by_chrom/all/NucleotideTransformer_absLLR.plus.score.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUROC
2
+ 1,1000,NucleotideTransformer_absLLR.plus.score,0.46863333333333335
3
+ 2,900,NucleotideTransformer_absLLR.plus.score,0.46794238683127576
4
+ 3,650,NucleotideTransformer_absLLR.plus.score,0.46608809993425376
5
+ 4,400,NucleotideTransformer_absLLR.plus.score,0.4857638888888889
6
+ 5,510,NucleotideTransformer_absLLR.plus.score,0.42218804733222265
7
+ 6,780,NucleotideTransformer_absLLR.plus.score,0.44185112133830085
8
+ 7,540,NucleotideTransformer_absLLR.plus.score,0.509564090839811
9
+ 8,460,NucleotideTransformer_absLLR.plus.score,0.44770006301197224
10
+ 9,440,NucleotideTransformer_absLLR.plus.score,0.42412764003673104
11
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12
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13
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14
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15
+ 14,380,NucleotideTransformer_absLLR.plus.score,0.5065404739919974
16
+ 15,390,NucleotideTransformer_absLLR.plus.score,0.3558331507049456
17
+ 16,590,NucleotideTransformer_absLLR.plus.score,0.4865460116824667
18
+ 17,560,NucleotideTransformer_absLLR.plus.score,0.5065901360544218
19
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20
+ 19,580,NucleotideTransformer_absLLR.plus.score,0.5177037917822698
21
+ 20,530,NucleotideTransformer_absLLR.plus.score,0.4270400696174993
22
+ 21,140,NucleotideTransformer_absLLR.plus.score,0.42176870748299317
23
+ 22,280,NucleotideTransformer_absLLR.plus.score,0.528061224489796
complex_traits_matched_9/AUROC_by_chrom/all/Sei.LogisticRegression.chrom.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUROC
2
+ 1,1000,Sei.LogisticRegression.chrom,0.5585444444444445
3
+ 2,900,Sei.LogisticRegression.chrom,0.6113305898491084
4
+ 3,650,Sei.LogisticRegression.chrom,0.5719658119658121
5
+ 4,400,Sei.LogisticRegression.chrom,0.5467361111111111
6
+ 5,510,Sei.LogisticRegression.chrom,0.5606817890554914
7
+ 6,780,Sei.LogisticRegression.chrom,0.6078420629702681
8
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9
+ 8,460,Sei.LogisticRegression.chrom,0.6168346985927327
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11
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13
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14
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15
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16
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17
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18
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19
+ 18,290,Sei.LogisticRegression.chrom,0.6739331483683445
20
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21
+ 20,530,Sei.LogisticRegression.chrom,0.5269570032830979
22
+ 21,140,Sei.LogisticRegression.chrom,0.6354875283446713
23
+ 22,280,Sei.LogisticRegression.chrom,0.6067176870748299
complex_traits_matched_9/AUROC_by_chrom/all/Sei.plus.seqclass_max_absdiff.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUROC
2
+ 1,1000,Sei.plus.seqclass_max_absdiff,0.6051555555555556
3
+ 2,900,Sei.plus.seqclass_max_absdiff,0.5945816186556927
4
+ 3,650,Sei.plus.seqclass_max_absdiff,0.5818540433925048
5
+ 4,400,Sei.plus.seqclass_max_absdiff,0.5626388888888889
6
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7
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8
+ 7,540,Sei.plus.seqclass_max_absdiff,0.6644566377076665
9
+ 8,460,Sei.plus.seqclass_max_absdiff,0.6198277672757824
10
+ 9,440,Sei.plus.seqclass_max_absdiff,0.6524908172635445
11
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12
+ 11,680,Sei.plus.seqclass_max_absdiff,0.6418685121107266
13
+ 12,590,Sei.plus.seqclass_max_absdiff,0.6352580676050943
14
+ 13,200,Sei.plus.seqclass_max_absdiff,0.6494444444444445
15
+ 14,380,Sei.plus.seqclass_max_absdiff,0.6423514927670052
16
+ 15,390,Sei.plus.seqclass_max_absdiff,0.621082621082621
17
+ 16,590,Sei.plus.seqclass_max_absdiff,0.6142551629480673
18
+ 17,560,Sei.plus.seqclass_max_absdiff,0.5228528911564627
19
+ 18,290,Sei.plus.seqclass_max_absdiff,0.6958647113224996
20
+ 19,580,Sei.plus.seqclass_max_absdiff,0.5769916765755053
21
+ 20,530,Sei.plus.seqclass_max_absdiff,0.5483564732407737
22
+ 21,140,Sei.plus.seqclass_max_absdiff,0.604875283446712
23
+ 22,280,Sei.plus.seqclass_max_absdiff,0.6461167800453514
complex_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,0.6861624983961824,0.009593431157750161
complex_traits_matched_9/AUROC_by_chrom_weighted_average/all/Borzoi_L2_L2.plus.all.csv ADDED
@@ -0,0 +1,2 @@
 
 
 
1
+ model,metric,score,se
2
+ Borzoi_L2_L2.plus.all,AUROC,0.645880928239982,0.008231606575369437
complex_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,0.7226995279168825,0.010224592694300134
complex_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,0.6976000941721767,0.010087737626696949
complex_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,0.6958667741245484,0.009657502013736632
complex_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,0.6155839016156137,0.009337989689475558
complex_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,0.5829148475724354,0.010898684546777792
complex_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,0.49232748217222705,0.014326535148337637