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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/AUPRC_by_chrom/all/Borzoi.LogisticRegression.chrom.csv +20 -0
  2. mendelian_traits_matched_9/AUPRC_by_chrom/all/CADD+Borzoi.LogisticRegression.chrom.csv +20 -0
  3. mendelian_traits_matched_9/AUPRC_by_chrom/all/CADD+GPN-MSA.LogisticRegression.chrom.csv +20 -0
  4. mendelian_traits_matched_9/AUPRC_by_chrom/all/CADD.plus.RawScore.csv +20 -0
  5. mendelian_traits_matched_9/AUPRC_by_chrom/all/Caduceus.LogisticRegression.chrom.csv +20 -0
  6. mendelian_traits_matched_9/AUPRC_by_chrom/all/Caduceus_Embeddings.minus.inner_product.csv +20 -0
  7. mendelian_traits_matched_9/AUPRC_by_chrom/all/Caduceus_Embeddings.plus.cosine_distance.csv +20 -0
  8. mendelian_traits_matched_9/AUPRC_by_chrom/all/Caduceus_Embeddings.plus.euclidean_distance.csv +20 -0
  9. mendelian_traits_matched_9/AUPRC_by_chrom/all/Caduceus_LLR.minus.score.csv +20 -0
  10. mendelian_traits_matched_9/AUPRC_by_chrom/all/Caduceus_absLLR.plus.score.csv +20 -0
  11. mendelian_traits_matched_9/AUPRC_by_chrom/all/Enformer.LogisticRegression.chrom.csv +20 -0
  12. mendelian_traits_matched_9/AUPRC_by_chrom/all/GPN-MSA.LogisticRegression.chrom.csv +20 -0
  13. mendelian_traits_matched_9/AUPRC_by_chrom/all/GPN-MSA_Embeddings.minus.inner_product.csv +20 -0
  14. mendelian_traits_matched_9/AUPRC_by_chrom/all/GPN-MSA_Embeddings.plus.cosine_distance.csv +20 -0
  15. mendelian_traits_matched_9/AUPRC_by_chrom/all/GPN-MSA_Embeddings.plus.euclidean_distance.csv +20 -0
  16. mendelian_traits_matched_9/AUPRC_by_chrom/all/GPN-MSA_InnerProduct.minus.score.csv +20 -0
  17. mendelian_traits_matched_9/AUPRC_by_chrom/all/GPN-MSA_LLR.minus.score.csv +20 -0
  18. mendelian_traits_matched_9/AUPRC_by_chrom/all/GPN-MSA_absLLR.plus.score.csv +20 -0
  19. mendelian_traits_matched_9/AUPRC_by_chrom/all/GPN_final.LogisticRegression.chrom.csv +20 -0
  20. mendelian_traits_matched_9/AUPRC_by_chrom/all/GPN_final_Embeddings.minus.inner_product.csv +20 -0
  21. mendelian_traits_matched_9/AUPRC_by_chrom/all/GPN_final_Embeddings.plus.euclidean_distance.csv +20 -0
  22. mendelian_traits_matched_9/AUPRC_by_chrom/all/GPN_final_InnerProduct.minus.score.csv +20 -0
  23. mendelian_traits_matched_9/AUPRC_by_chrom/all/GPN_final_LLR.minus.score.csv +20 -0
  24. mendelian_traits_matched_9/AUPRC_by_chrom/all/GPN_final_absLLR.plus.score.csv +20 -0
  25. mendelian_traits_matched_9/AUPRC_by_chrom/all/HyenaDNA.LogisticRegression.chrom.csv +20 -0
  26. mendelian_traits_matched_9/AUPRC_by_chrom/all/HyenaDNA_Embeddings.minus.inner_product.csv +20 -0
  27. mendelian_traits_matched_9/AUPRC_by_chrom/all/HyenaDNA_Embeddings.plus.cosine_distance.csv +20 -0
  28. mendelian_traits_matched_9/AUPRC_by_chrom/all/HyenaDNA_Embeddings.plus.euclidean_distance.csv +20 -0
  29. mendelian_traits_matched_9/AUPRC_by_chrom/all/HyenaDNA_InnerProduct.minus.score.csv +20 -0
  30. mendelian_traits_matched_9/AUPRC_by_chrom/all/HyenaDNA_LLR.minus.score.csv +20 -0
  31. mendelian_traits_matched_9/AUPRC_by_chrom/all/HyenaDNA_absLLR.plus.score.csv +20 -0
  32. mendelian_traits_matched_9/AUPRC_by_chrom/all/NucleotideTransformer.LogisticRegression.chrom.csv +20 -0
  33. mendelian_traits_matched_9/AUPRC_by_chrom/all/NucleotideTransformer_Embeddings.minus.inner_product.csv +20 -0
  34. mendelian_traits_matched_9/AUPRC_by_chrom/all/NucleotideTransformer_Embeddings.plus.euclidean_distance.csv +20 -0
  35. mendelian_traits_matched_9/AUPRC_by_chrom/all/NucleotideTransformer_InnerProduct.minus.score.csv +20 -0
  36. mendelian_traits_matched_9/AUPRC_by_chrom/all/NucleotideTransformer_LLR.minus.score.csv +20 -0
  37. mendelian_traits_matched_9/AUPRC_by_chrom/all/NucleotideTransformer_absLLR.plus.score.csv +20 -0
  38. mendelian_traits_matched_9/AUPRC_by_chrom/all/Sei.LogisticRegression.chrom.csv +20 -0
  39. mendelian_traits_matched_9/AUPRC_by_chrom/all/Sei.plus.seqclass_max_absdiff.csv +20 -0
  40. mendelian_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/Borzoi.LogisticRegression.chrom.subset_from_all.csv +20 -0
  41. mendelian_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/Borzoi_L2_L2.plus.all.csv +20 -0
  42. mendelian_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/CADD.LogisticRegression.chrom.subset_from_all.csv +20 -0
  43. mendelian_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/CADD.plus.RawScore.csv +20 -0
  44. mendelian_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/Caduceus.LogisticRegression.chrom.subset_from_all.csv +20 -0
  45. mendelian_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/Caduceus_Embeddings.minus.inner_product.csv +20 -0
  46. mendelian_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/Caduceus_Embeddings.plus.euclidean_distance.csv +20 -0
  47. mendelian_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/Enformer.LogisticRegression.chrom.subset_from_all.csv +20 -0
  48. mendelian_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/Enformer_L2_L2.plus.all.csv +20 -0
  49. mendelian_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/GPN-MSA.LogisticRegression.chrom.subset_from_all.csv +20 -0
  50. mendelian_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/GPN-MSA_LLR.minus.score.csv +20 -0
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mendelian_traits_matched_9/AUPRC_by_chrom/all/CADD+Borzoi.LogisticRegression.chrom.csv ADDED
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mendelian_traits_matched_9/AUPRC_by_chrom/all/CADD+GPN-MSA.LogisticRegression.chrom.csv ADDED
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mendelian_traits_matched_9/AUPRC_by_chrom/all/CADD.plus.RawScore.csv ADDED
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mendelian_traits_matched_9/AUPRC_by_chrom/all/Caduceus.LogisticRegression.chrom.csv ADDED
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mendelian_traits_matched_9/AUPRC_by_chrom/all/Caduceus_Embeddings.minus.inner_product.csv ADDED
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mendelian_traits_matched_9/AUPRC_by_chrom/all/Caduceus_Embeddings.plus.cosine_distance.csv ADDED
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mendelian_traits_matched_9/AUPRC_by_chrom/all/Caduceus_absLLR.plus.score.csv ADDED
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1
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mendelian_traits_matched_9/AUPRC_by_chrom/all/Enformer.LogisticRegression.chrom.csv ADDED
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mendelian_traits_matched_9/AUPRC_by_chrom/all/GPN-MSA.LogisticRegression.chrom.csv ADDED
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mendelian_traits_matched_9/AUPRC_by_chrom/all/GPN-MSA_Embeddings.minus.inner_product.csv ADDED
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mendelian_traits_matched_9/AUPRC_by_chrom/all/GPN-MSA_Embeddings.plus.cosine_distance.csv ADDED
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1
+ chrom,n,Model,AUPRC
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mendelian_traits_matched_9/AUPRC_by_chrom/all/GPN-MSA_Embeddings.plus.euclidean_distance.csv ADDED
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1
+ chrom,n,Model,AUPRC
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mendelian_traits_matched_9/AUPRC_by_chrom/all/GPN-MSA_InnerProduct.minus.score.csv ADDED
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1
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mendelian_traits_matched_9/AUPRC_by_chrom/all/GPN-MSA_LLR.minus.score.csv ADDED
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1
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mendelian_traits_matched_9/AUPRC_by_chrom/all/GPN-MSA_absLLR.plus.score.csv ADDED
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1
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mendelian_traits_matched_9/AUPRC_by_chrom/all/GPN_final.LogisticRegression.chrom.csv ADDED
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1
+ chrom,n,Model,AUPRC
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mendelian_traits_matched_9/AUPRC_by_chrom/all/GPN_final_Embeddings.minus.inner_product.csv ADDED
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1
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mendelian_traits_matched_9/AUPRC_by_chrom/all/GPN_final_Embeddings.plus.euclidean_distance.csv ADDED
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1
+ chrom,n,Model,AUPRC
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mendelian_traits_matched_9/AUPRC_by_chrom/all/GPN_final_InnerProduct.minus.score.csv ADDED
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1
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mendelian_traits_matched_9/AUPRC_by_chrom/all/GPN_final_LLR.minus.score.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUPRC
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mendelian_traits_matched_9/AUPRC_by_chrom/all/GPN_final_absLLR.plus.score.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
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mendelian_traits_matched_9/AUPRC_by_chrom/all/HyenaDNA.LogisticRegression.chrom.csv ADDED
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1
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mendelian_traits_matched_9/AUPRC_by_chrom/all/HyenaDNA_Embeddings.minus.inner_product.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
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mendelian_traits_matched_9/AUPRC_by_chrom/all/HyenaDNA_Embeddings.plus.cosine_distance.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
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mendelian_traits_matched_9/AUPRC_by_chrom/all/HyenaDNA_Embeddings.plus.euclidean_distance.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUPRC
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mendelian_traits_matched_9/AUPRC_by_chrom/all/HyenaDNA_InnerProduct.minus.score.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUPRC
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mendelian_traits_matched_9/AUPRC_by_chrom/all/HyenaDNA_LLR.minus.score.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUPRC
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mendelian_traits_matched_9/AUPRC_by_chrom/all/HyenaDNA_absLLR.plus.score.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUPRC
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mendelian_traits_matched_9/AUPRC_by_chrom/all/NucleotideTransformer.LogisticRegression.chrom.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
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+ X,500,NucleotideTransformer.LogisticRegression.chrom,0.07393262089207808
mendelian_traits_matched_9/AUPRC_by_chrom/all/NucleotideTransformer_Embeddings.minus.inner_product.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUPRC
2
+ 1,210,NucleotideTransformer_Embeddings.minus.inner_product,0.11103326051613768
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mendelian_traits_matched_9/AUPRC_by_chrom/all/NucleotideTransformer_Embeddings.plus.euclidean_distance.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUPRC
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+ 1,210,NucleotideTransformer_Embeddings.plus.euclidean_distance,0.12142875562239575
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mendelian_traits_matched_9/AUPRC_by_chrom/all/NucleotideTransformer_InnerProduct.minus.score.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUPRC
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+ 1,210,NucleotideTransformer_InnerProduct.minus.score,0.11103326051613768
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mendelian_traits_matched_9/AUPRC_by_chrom/all/NucleotideTransformer_LLR.minus.score.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUPRC
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+ 1,210,NucleotideTransformer_LLR.minus.score,0.17681945780773214
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mendelian_traits_matched_9/AUPRC_by_chrom/all/NucleotideTransformer_absLLR.plus.score.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUPRC
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+ 1,210,NucleotideTransformer_absLLR.plus.score,0.16298778622468482
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mendelian_traits_matched_9/AUPRC_by_chrom/all/Sei.LogisticRegression.chrom.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUPRC
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+ 1,210,Sei.LogisticRegression.chrom,0.2009180375683519
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mendelian_traits_matched_9/AUPRC_by_chrom/all/Sei.plus.seqclass_max_absdiff.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUPRC
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mendelian_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/Borzoi.LogisticRegression.chrom.subset_from_all.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUPRC
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mendelian_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/Borzoi_L2_L2.plus.all.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUPRC
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mendelian_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/CADD.LogisticRegression.chrom.subset_from_all.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUPRC
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mendelian_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/CADD.plus.RawScore.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUPRC
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mendelian_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/Caduceus.LogisticRegression.chrom.subset_from_all.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUPRC
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mendelian_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/Caduceus_Embeddings.minus.inner_product.csv ADDED
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1
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mendelian_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/Caduceus_Embeddings.plus.euclidean_distance.csv ADDED
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1
+ chrom,n,Model,AUPRC
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mendelian_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/Enformer.LogisticRegression.chrom.subset_from_all.csv ADDED
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1
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mendelian_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/Enformer_L2_L2.plus.all.csv ADDED
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1
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mendelian_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/GPN-MSA.LogisticRegression.chrom.subset_from_all.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUPRC
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mendelian_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/GPN-MSA_LLR.minus.score.csv ADDED
@@ -0,0 +1,20 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUPRC
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