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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/AUPRC_by_chrom/3_prime_UTR_variant/GPN_final_Embeddings.plus.euclidean_distance.csv +19 -0
  2. complex_traits_matched_9/AUPRC_by_chrom/all/CADD.LogisticRegression.chrom.csv +23 -0
  3. complex_traits_matched_9/AUPRC_by_chrom/all/Caduceus_Embeddings.plus.cosine_distance.csv +23 -0
  4. complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/Borzoi.LogisticRegression.chrom.subset_from_all.csv +23 -0
  5. complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/Borzoi_L2_L2.plus.all.csv +23 -0
  6. complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/CADD.LogisticRegression.chrom.subset_from_all.csv +23 -0
  7. complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/CADD.plus.RawScore.csv +23 -0
  8. complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/Caduceus.LogisticRegression.chrom.subset_from_all.csv +23 -0
  9. complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/Caduceus_Embeddings.minus.inner_product.csv +23 -0
  10. complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/Caduceus_Embeddings.plus.euclidean_distance.csv +23 -0
  11. complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/Enformer.LogisticRegression.chrom.subset_from_all.csv +23 -0
  12. complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/Enformer_L2_L2.plus.all.csv +23 -0
  13. complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/GPN-MSA.LogisticRegression.chrom.subset_from_all.csv +23 -0
  14. complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/GPN-MSA_LLR.minus.score.csv +23 -0
  15. complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/GPN-MSA_absLLR.plus.score.csv +23 -0
  16. complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/GPN_final.LogisticRegression.chrom.subset_from_all.csv +23 -0
  17. complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/GPN_final_Embeddings.plus.euclidean_distance.csv +23 -0
  18. complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/GPN_final_LLR.minus.score.csv +23 -0
  19. complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/GPN_final_absLLR.plus.score.csv +23 -0
  20. complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/HyenaDNA.LogisticRegression.chrom.subset_from_all.csv +23 -0
  21. complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/HyenaDNA_Embeddings.minus.inner_product.csv +23 -0
  22. complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/NucleotideTransformer.LogisticRegression.chrom.subset_from_all.csv +23 -0
  23. complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/NucleotideTransformer_Embeddings.minus.inner_product.csv +23 -0
  24. complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/NucleotideTransformer_Embeddings.plus.euclidean_distance.csv +23 -0
  25. complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/Sei.LogisticRegression.chrom.subset_from_all.csv +23 -0
  26. complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/Sei.plus.seqclass_max_absdiff.csv +23 -0
  27. complex_traits_matched_9/AUPRC_by_chrom/no_eqtl_overlap/Borzoi.LogisticRegression.chrom.subset_from_all.csv +23 -0
  28. complex_traits_matched_9/AUPRC_by_chrom/no_eqtl_overlap/Borzoi_L2_L2.plus.all.csv +23 -0
  29. complex_traits_matched_9/AUPRC_by_chrom/no_eqtl_overlap/CADD+GPN-MSA+Borzoi.LogisticRegression.chrom.subset_from_all.csv +23 -0
  30. complex_traits_matched_9/AUPRC_by_chrom/no_eqtl_overlap/CADD.LogisticRegression.chrom.subset_from_all.csv +23 -0
  31. complex_traits_matched_9/AUPRC_by_chrom/no_eqtl_overlap/CADD.plus.RawScore.csv +23 -0
  32. complex_traits_matched_9/AUPRC_by_chrom/no_eqtl_overlap/GPN-MSA.LogisticRegression.chrom.subset_from_all.csv +23 -0
  33. complex_traits_matched_9/AUPRC_by_chrom/no_eqtl_overlap/GPN-MSA_absLLR.plus.score.csv +23 -0
  34. complex_traits_matched_9/AUPRC_by_chrom/non_coding_transcript_exon_variant/GPN_final.LogisticRegression.chrom.subset_from_all.csv +19 -0
  35. complex_traits_matched_9/AUPRC_by_chrom/non_coding_transcript_exon_variant/GPN_final_Embeddings.plus.euclidean_distance.csv +19 -0
  36. complex_traits_matched_9/AUPRC_by_chrom/nonexonic_AND_proximal/GPN_final.LogisticRegression.chrom.subset_from_all.csv +21 -0
  37. complex_traits_matched_9/AUPRC_by_chrom/nonexonic_AND_proximal/GPN_final_Embeddings.plus.euclidean_distance.csv +21 -0
  38. complex_traits_matched_9/AUPRC_by_chrom/pip_0.99/Borzoi.LogisticRegression.chrom.subset_from_all.csv +23 -0
  39. complex_traits_matched_9/AUPRC_by_chrom/pip_0.99/CADD+GPN-MSA+Borzoi.LogisticRegression.chrom.subset_from_all.csv +23 -0
  40. complex_traits_matched_9/AUPRC_by_chrom/pip_0.99/CADD.plus.RawScore.csv +23 -0
  41. complex_traits_matched_9/AUPRC_by_chrom/pip_0.999/Borzoi.LogisticRegression.chrom.subset_from_all.csv +23 -0
  42. complex_traits_matched_9/AUPRC_by_chrom/pip_0.999/Borzoi_L2_L2.plus.all.csv +23 -0
  43. complex_traits_matched_9/AUPRC_by_chrom/pip_0.999/CADD+GPN-MSA+Borzoi.LogisticRegression.chrom.subset_from_all.csv +23 -0
  44. complex_traits_matched_9/AUPRC_by_chrom/pip_0.999/CADD.LogisticRegression.chrom.subset_from_all.csv +23 -0
  45. complex_traits_matched_9/AUPRC_by_chrom/pip_0.999/CADD.plus.RawScore.csv +23 -0
  46. complex_traits_matched_9/AUPRC_by_chrom/pip_0.999/GPN-MSA.LogisticRegression.chrom.subset_from_all.csv +23 -0
  47. complex_traits_matched_9/AUPRC_by_chrom/pip_0.999/GPN-MSA_absLLR.plus.score.csv +23 -0
  48. complex_traits_matched_9/AUPRC_by_chrom/pleiotropy_no/Borzoi.LogisticRegression.chrom.subset_from_all.csv +23 -0
  49. complex_traits_matched_9/AUPRC_by_chrom/pleiotropy_no/Borzoi_L2_L2.plus.all.csv +23 -0
  50. complex_traits_matched_9/AUPRC_by_chrom/pleiotropy_no/CADD+GPN-MSA+Borzoi.LogisticRegression.chrom.subset_from_all.csv +23 -0
complex_traits_matched_9/AUPRC_by_chrom/3_prime_UTR_variant/GPN_final_Embeddings.plus.euclidean_distance.csv ADDED
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+ chrom,n,Model,AUPRC
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+ 12,40,GPN_final_Embeddings.plus.euclidean_distance,0.19603817235396181
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+ 14,10,GPN_final_Embeddings.plus.euclidean_distance,0.25
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+ 18,10,GPN_final_Embeddings.plus.euclidean_distance,0.14285714285714285
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+ 19,80,GPN_final_Embeddings.plus.euclidean_distance,0.13729005589028134
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+ 20,20,GPN_final_Embeddings.plus.euclidean_distance,0.14835164835164835
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+ 22,20,GPN_final_Embeddings.plus.euclidean_distance,0.15555555555555556
complex_traits_matched_9/AUPRC_by_chrom/all/CADD.LogisticRegression.chrom.csv ADDED
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+ chrom,n,Model,AUPRC
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+ 1,1000,CADD.LogisticRegression.chrom,0.2804234370631062
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+ 2,900,CADD.LogisticRegression.chrom,0.2490996879081556
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+ 22,280,CADD.LogisticRegression.chrom,0.2947758803512284
complex_traits_matched_9/AUPRC_by_chrom/all/Caduceus_Embeddings.plus.cosine_distance.csv ADDED
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+ chrom,n,Model,AUPRC
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complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/Borzoi.LogisticRegression.chrom.subset_from_all.csv ADDED
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complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/Borzoi_L2_L2.plus.all.csv ADDED
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complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/CADD.LogisticRegression.chrom.subset_from_all.csv ADDED
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complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/CADD.plus.RawScore.csv ADDED
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complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/GPN_final_LLR.minus.score.csv ADDED
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complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/GPN_final_absLLR.plus.score.csv ADDED
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complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/NucleotideTransformer.LogisticRegression.chrom.subset_from_all.csv ADDED
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1
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complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/NucleotideTransformer_Embeddings.minus.inner_product.csv ADDED
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1
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complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/NucleotideTransformer_Embeddings.plus.euclidean_distance.csv ADDED
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1
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complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/Sei.LogisticRegression.chrom.subset_from_all.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
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complex_traits_matched_9/AUPRC_by_chrom/no_cadd_overlap/Sei.plus.seqclass_max_absdiff.csv ADDED
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1
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complex_traits_matched_9/AUPRC_by_chrom/no_eqtl_overlap/Borzoi.LogisticRegression.chrom.subset_from_all.csv ADDED
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1
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complex_traits_matched_9/AUPRC_by_chrom/no_eqtl_overlap/Borzoi_L2_L2.plus.all.csv ADDED
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1
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complex_traits_matched_9/AUPRC_by_chrom/no_eqtl_overlap/CADD+GPN-MSA+Borzoi.LogisticRegression.chrom.subset_from_all.csv ADDED
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1
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complex_traits_matched_9/AUPRC_by_chrom/no_eqtl_overlap/CADD.LogisticRegression.chrom.subset_from_all.csv ADDED
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1
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complex_traits_matched_9/AUPRC_by_chrom/no_eqtl_overlap/CADD.plus.RawScore.csv ADDED
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1
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complex_traits_matched_9/AUPRC_by_chrom/no_eqtl_overlap/GPN-MSA.LogisticRegression.chrom.subset_from_all.csv ADDED
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1
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complex_traits_matched_9/AUPRC_by_chrom/no_eqtl_overlap/GPN-MSA_absLLR.plus.score.csv ADDED
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1
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complex_traits_matched_9/AUPRC_by_chrom/non_coding_transcript_exon_variant/GPN_final.LogisticRegression.chrom.subset_from_all.csv ADDED
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1
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complex_traits_matched_9/AUPRC_by_chrom/non_coding_transcript_exon_variant/GPN_final_Embeddings.plus.euclidean_distance.csv ADDED
@@ -0,0 +1,19 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
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complex_traits_matched_9/AUPRC_by_chrom/nonexonic_AND_proximal/GPN_final.LogisticRegression.chrom.subset_from_all.csv ADDED
@@ -0,0 +1,21 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
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complex_traits_matched_9/AUPRC_by_chrom/nonexonic_AND_proximal/GPN_final_Embeddings.plus.euclidean_distance.csv ADDED
@@ -0,0 +1,21 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUPRC
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complex_traits_matched_9/AUPRC_by_chrom/pip_0.99/Borzoi.LogisticRegression.chrom.subset_from_all.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUPRC
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complex_traits_matched_9/AUPRC_by_chrom/pip_0.99/CADD+GPN-MSA+Borzoi.LogisticRegression.chrom.subset_from_all.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUPRC
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complex_traits_matched_9/AUPRC_by_chrom/pip_0.99/CADD.plus.RawScore.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUPRC
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complex_traits_matched_9/AUPRC_by_chrom/pip_0.999/Borzoi.LogisticRegression.chrom.subset_from_all.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUPRC
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complex_traits_matched_9/AUPRC_by_chrom/pip_0.999/Borzoi_L2_L2.plus.all.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUPRC
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complex_traits_matched_9/AUPRC_by_chrom/pip_0.999/CADD+GPN-MSA+Borzoi.LogisticRegression.chrom.subset_from_all.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUPRC
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complex_traits_matched_9/AUPRC_by_chrom/pip_0.999/CADD.LogisticRegression.chrom.subset_from_all.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
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complex_traits_matched_9/AUPRC_by_chrom/pip_0.999/CADD.plus.RawScore.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
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complex_traits_matched_9/AUPRC_by_chrom/pip_0.999/GPN-MSA.LogisticRegression.chrom.subset_from_all.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUPRC
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complex_traits_matched_9/AUPRC_by_chrom/pip_0.999/GPN-MSA_absLLR.plus.score.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUPRC
2
+ 1,500,GPN-MSA_absLLR.plus.score,0.25032071879615736
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complex_traits_matched_9/AUPRC_by_chrom/pleiotropy_no/Borzoi.LogisticRegression.chrom.subset_from_all.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUPRC
2
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complex_traits_matched_9/AUPRC_by_chrom/pleiotropy_no/Borzoi_L2_L2.plus.all.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUPRC
2
+ 1,690,Borzoi_L2_L2.plus.all,0.21500130328730097
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complex_traits_matched_9/AUPRC_by_chrom/pleiotropy_no/CADD+GPN-MSA+Borzoi.LogisticRegression.chrom.subset_from_all.csv ADDED
@@ -0,0 +1,23 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ chrom,n,Model,AUPRC
2
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