Model
GPN-MSA
DNA language model trained on a human-centred multispecies whole-genome alignment; scores a variant as the log-likelihood ratio of the alternate and reference allele.
42 evaluations · 68 results16 configurations with further results
Overview
An explanatory profile has not yet been reviewed for this record.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluations and results
42 evaluations · 68 results. Different protocols are not a single leaderboard.
Sorted by AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
| Tested configuration | Protocol and dataset | AUPRC (weighted average over chromosomes of per-chromosome AUPRC; subset 'all') | Spearman (GUANinE v1.1 test set) | AUPRC (zero-shot; BRCA1 'Both' (coding and noncoding) SNVs) | AUPRC (zero-shot; BRCA1 coding SNVs) | AUPRC (zero-shot; BRCA1 intronic SNVs) | AUPRC (zero-shot; BRCA1 noncoding SNVs) | AUPRC (zero-shot; BRCA1 splice region SNVs) | AUPRC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs) | AUPRC (zero-shot; BRCA2 coding SNVs) | AUPRC (zero-shot; BRCA2 noncoding SNVs) | AUPRC (zero-shot; ClinVar 'Both' (coding and noncoding) SNVs) | AUPRC (zero-shot; ClinVar coding SNVs, far from splice site) | AUPRC (zero-shot; ClinVar coding SNVs, highly conserved) | AUPRC (zero-shot; ClinVar coding SNVs, moderately conserved) | AUPRC (zero-shot; ClinVar coding SNVs, near splice site) | AUPRC (zero-shot; ClinVar coding SNVs, not conserved) | AUPRC (zero-shot; ClinVar coding SNVs, poorly conserved) | AUPRC (zero-shot; ClinVar coding SNVs) | AUPRC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) SNVs) | AUPRC (zero-shot; ClinVar noncoding SNVs, far from splice site) | AUPRC (zero-shot; ClinVar noncoding SNVs, highly conserved) | AUPRC (zero-shot; ClinVar noncoding SNVs, intergenic) | AUPRC (zero-shot; ClinVar noncoding SNVs, moderately conserved) | AUPRC (zero-shot; ClinVar noncoding SNVs, near splice site) | AUPRC (zero-shot; ClinVar noncoding SNVs, not conserved) | AUPRC (zero-shot; ClinVar noncoding SNVs, poorly conserved) | AUPRC (zero-shot; SpliceVarDB 'Both' (coding and noncoding) SNVs) | AUPRC (zero-shot; SpliceVarDB exonic SNVs) | AUROC (zero-shot; BRCA1 'Both' (coding and noncoding) SNVs) | AUROC (zero-shot; BRCA1 coding SNVs) | AUROC (zero-shot; BRCA1 intronic SNVs) | AUROC (zero-shot; BRCA1 noncoding SNVs) | AUROC (zero-shot; BRCA1 splice region SNVs) | AUROC (zero-shot; BRCA2 'Both' (coding and noncoding) SNVs) | AUROC (zero-shot; BRCA2 coding SNVs) | AUROC (zero-shot; BRCA2 noncoding SNVs) | AUROC (zero-shot; ClinVar 'Both' (coding and noncoding) SNVs) | AUROC (zero-shot; ClinVar coding SNVs, far from splice site) | AUROC (zero-shot; ClinVar coding SNVs, highly conserved) | AUROC (zero-shot; ClinVar coding SNVs, moderately conserved) | AUROC (zero-shot; ClinVar coding SNVs, near splice site) | AUROC (zero-shot; ClinVar coding SNVs, not conserved) | AUROC (zero-shot; ClinVar coding SNVs, poorly conserved) | AUROC (zero-shot; ClinVar coding SNVs) | AUROC (zero-shot; ClinVar low SpliceAI and Pangolin scores (both below 0.1) SNVs) | AUROC (zero-shot; ClinVar noncoding SNVs, far from splice site) | AUROC (zero-shot; ClinVar noncoding SNVs, highly conserved) | AUROC (zero-shot; ClinVar noncoding SNVs, intergenic) | AUROC (zero-shot; ClinVar noncoding SNVs, moderately conserved) | AUROC (zero-shot; ClinVar noncoding SNVs, near splice site) | AUROC (zero-shot; ClinVar noncoding SNVs, not conserved) | AUROC (zero-shot; ClinVar noncoding SNVs, poorly conserved) | AUROC (zero-shot; SpliceVarDB 'Both' (coding and noncoding) SNVs) | AUROC (zero-shot; SpliceVarDB exonic SNVs) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GPN-MSA_LLR.minus.score (TraitGym)Evaluation | TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average, TraitGym Mendelian traits, matched 9 controls | 0.694 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA.LogisticRegression.chrom (TraitGym)Evaluation | TraitGym Mendelian traits, linear-probing, AUPRC by chromosome weighted average, TraitGym Mendelian traits, matched 9 controls | 0.685 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA_absLLR.plus.score (TraitGym)Evaluation | TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average, TraitGym Mendelian traits, matched 9 controls | 0.654 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA_Embeddings.minus.inner_product (TraitGym)Evaluation | TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average, TraitGym Mendelian traits, matched 9 controls | 0.301 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA_InnerProduct.minus.score (TraitGym)Evaluation | TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average, TraitGym Mendelian traits, matched 9 controls | 0.301 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA.LogisticRegression.chrom (TraitGym)Evaluation | TraitGym Complex traits, linear-probing, AUPRC by chromosome weighted average, TraitGym Complex traits, matched 9 controls | 0.269 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA_absLLR.plus.score (TraitGym)Evaluation | TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average, TraitGym Complex traits, matched 9 controls | 0.224 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA_LLR.minus.score (TraitGym)Evaluation | TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average, TraitGym Complex traits, matched 9 controls | 0.212 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA_Embeddings.plus.cosine_distance (TraitGym)Evaluation | TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average, TraitGym Mendelian traits, matched 9 controls | 0.208 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA_Embeddings.plus.euclidean_distance (TraitGym)Evaluation | TraitGym Mendelian traits, zero-shot, AUPRC by chromosome weighted average, TraitGym Mendelian traits, matched 9 controls | 0.207 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA_Embeddings.minus.inner_product (TraitGym)Evaluation | TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average, TraitGym Complex traits, matched 9 controls | 0.177 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA_Embeddings.plus.cosine_distance (TraitGym)Evaluation | TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average, TraitGym Complex traits, matched 9 controls | 0.15 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA_Embeddings.plus.euclidean_distance (TraitGym)Evaluation | TraitGym Complex traits, zero-shot, AUPRC by chromosome weighted average, TraitGym Complex traits, matched 9 controls | 0.15 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot BRCA1 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1), BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026) | Not reported | Not reported | 0.65 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.863 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot BRCA1 coding SNVs classification (Evo 2 paper, Supplementary Data 1), BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026) | Not reported | Not reported | Not reported | 0.579 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.833 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot BRCA1 intronic SNVs classification (Evo 2 paper, Supplementary Data 1), BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | 0.097 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.653 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot BRCA1 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1), BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | 0.775 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.918 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot BRCA1 splice region SNVs classification (Evo 2 paper, Supplementary Data 1), BRCA1 saturation genome editing SNVs, Findlay et al. 2018 classes (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.832 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.891 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot BRCA2 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1), BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.57 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.838 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot BRCA2 coding SNVs classification (Evo 2 paper, Supplementary Data 1), BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.446 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.8 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot BRCA2 noncoding SNVs classification (Evo 2 paper, Supplementary Data 1), BRCA2 SNVs with functional classifications, Huang et al. 2025 (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.835 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.905 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot ClinVar 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.944 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.959 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot ClinVar coding SNVs classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.932 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.896 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot ClinVar coding SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.929 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.896 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot ClinVar coding SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.941 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.824 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot ClinVar coding SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.748 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.866 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot ClinVar coding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.962 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.896 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot ClinVar coding SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.762 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.916 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot ClinVar coding SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.708 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.882 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot ClinVar low SpliceAI and Pangolin scores (both below 0.1) SNVs classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.36 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.915 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot ClinVar noncoding SNVs, far from splice site classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.132 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.723 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot ClinVar noncoding SNVs, highly conserved classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.994 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.951 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot ClinVar noncoding SNVs, intergenic classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.87 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.884 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot ClinVar noncoding SNVs, moderately conserved classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.405 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.828 | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot ClinVar noncoding SNVs, near splice site classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.994 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.977 | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot ClinVar noncoding SNVs, not conserved classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.054 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.686 | Not reported | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot ClinVar noncoding SNVs, poorly conserved classification (Evo 2 paper, Supplementary Data 1), ClinVar October 2024 release, filtered (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.13 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.706 | Not reported | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot SpliceVarDB 'Both' (coding and noncoding) SNVs classification (Evo 2 paper, Supplementary Data 1), SpliceVarDB experimentally validated splice variants (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.846 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.79 | Not reported |
| GPN-MSA (Evo 2 paper variant effect evaluations)Evaluation | Zero-shot SpliceVarDB exonic SNVs classification (Evo 2 paper, Supplementary Data 1), SpliceVarDB experimentally validated splice variants (Brixi et al. 2026) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.548 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | 0.675 |
| GPN-MSA (evaluation mode not printed (Table 4 has no Eval. column), GUANinE v1.1)Evaluation | GUANinE v1.1 clinvar-snv, Spearman rho x100 (Table 4), GUANinE clinvar-snv test set | Not reported | 80.7 (best in column) | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (Position) (zero-shot, GUANinE v1.1)Evaluation | GUANinE v1.1 cadd-snv, Spearman rho x100 (Table 3), GUANinE cadd-snv test set | Not reported | 26.6 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
| GPN-MSA (zero-shot, GUANinE v1.1)Evaluation | GUANinE v1.1 cadd-snv, Spearman rho x100 (Table 3), GUANinE cadd-snv test set | Not reported | 29.1 | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported | Not reported |
All 68 result rows with coverage, uncertainty and sources
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Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.
Further results on linked records
16 linked records have results that are not included above, because no reviewed claim yet ties the link to this model. Each record keeps its own settings and evaluations, and its scores are on its own page.
- GPN-MSA ablation '51 mammals' (Supplementary Table 4) Configuration · configuration · 4 evaluations · 8 results
- GPN-MSA ablation '51 vertebrates' (Supplementary Table 4) Configuration · configuration · 4 evaluations · 8 results
- GPN-MSA ablation 'Default' (Supplementary Table 4) Configuration · configuration · 4 evaluations · 8 results
- GPN-MSA ablation 'Include closest primates' (Supplementary Table 4) Configuration · configuration · 4 evaluations · 8 results
- GPN-MSA ablation 'Don’t replace non-conserved' (Supplementary Table 4) Configuration · configuration · 4 evaluations · 8 results
- GPN-MSA ablation 'Don’t upweight conserved' (Supplementary Table 4) Configuration · configuration · 4 evaluations · 8 results
- GPN-MSA ablation 'Train on 100% of genome' (Supplementary Table 4) Configuration · configuration · 4 evaluations · 8 results
- GPN-MSA ablation 'Train on 50% most conserved' (Supplementary Table 4) Configuration · configuration · 4 evaluations · 8 results
- GPN-MSA ablation 'Window size = 16' (Supplementary Table 4) Configuration · configuration · 4 evaluations · 8 results
- GPN-MSA ablation 'Window size = 256' (Supplementary Table 4) Configuration · configuration · 4 evaluations · 8 results
- GPN-MSA ablation 'Window size = 32' (Supplementary Table 4) Configuration · configuration · 4 evaluations · 8 results
- GPN-MSA ablation 'Window size = 4' (Supplementary Table 4) Configuration · configuration · 4 evaluations · 8 results
- GPN-MSA ablation 'Window size = 64' (Supplementary Table 4) Configuration · configuration · 4 evaluations · 8 results
- GPN-MSA ablation 'Window size = 8' (Supplementary Table 4) Configuration · configuration · 4 evaluations · 8 results
- GPN-MSA ablation 'w/o MSA' (Supplementary Table 4) Configuration · configuration · 4 evaluations · 8 results
- GPN-MSA, main results model (bioRxiv v2) Configuration · configuration · 1 evaluation · 1 result
Use this model
How it works, versions and access
Versions and evaluated configurations
- GPN-MSA (Evo 2 paper variant effect evaluations) · configuration of
- GPN-MSA (evaluation mode not printed (Table 4 has no Eval. column), GUANinE v1.1) · configuration of
- GPN-MSA (Position) (zero-shot, GUANinE v1.1) · configuration of
- GPN-MSA (zero-shot, GUANinE v1.1) · configuration of
- GPN-MSA_absLLR.plus.score (TraitGym) · configuration of
- GPN-MSA_Embeddings.minus.inner_product (TraitGym) · configuration of
- GPN-MSA_Embeddings.plus.cosine_distance (TraitGym) · configuration of
- GPN-MSA_Embeddings.plus.euclidean_distance (TraitGym) · configuration of
- GPN-MSA_InnerProduct.minus.score (TraitGym) · configuration of
- GPN-MSA_LLR.minus.score (TraitGym) · configuration of
- GPN-MSA.LogisticRegression.chrom (TraitGym) · configuration of
Strengths, limitations and unresolved questions
Evidence
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Evidence table
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Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
3 source records and release history
- GPN-MSA: an alignment-based DNA language model for genome-wide variant effect prediction (bioRxiv v2) · Original source · bioRxiv v2, posted 2024-04-06
- songlab-cal/gpn README at commit dc5fd287 · Original source · git commit dc5fd287599f2955a79d010bca0e0f7f8178c67e (main, committed 2026-09-26)
- songlab-cal/gpn docs/models/gpn-msa.md at commit dc5fd287 · Original source · git commit dc5fd287599f2955a79d010bca0e0f7f8178c67e (main, committed 2026-09-26)
Technical metadata and extraction receipts
Stable ID: gfm-guides-20261014-gpnmsa-model-gpn-msa
- areas
- dna-genomes
- contexts
- research
- method types
- foundation_model
- reported name
- GPN-MSA
- entity level
- family
- identity scope
- Family record for the GPN-MSA model described by Benegas et al.; the published human checkpoint is songlab/gpn-msa-sapiens. Ablation and evaluation variants are configurations.
- training data
- Human reference genome with a multispecies whole-genome alignment of vertebrates (89 non-human species in the default model); prepared human training regions are published as songlab/gpn-msa-sapiens-dataset
- access
- Published checkpoint songlab/gpn-msa-sapiens on Hugging Face; inference with the gpn package ('gpn msa {vep,logits,embedding}'). The repository marks GPN-MSA as deprecated in favour of GPN-Star and no longer maintains training.
- licence
- Code: MIT (songlab-cal/gpn). Checkpoint licence not checked.
- source locator
- gpn-msa.md 'Quick start' and 'Published assets'; README model table; preprint v2 Figure 2a caption ('89 non-human species') and Methods
- missing metadata
- version: reason: inapplicable; note: Family record; versions are on configurations
Related records
- configuration of: GPN-MSA (Evo 2 paper variant effect evaluations)
- subject: maintenance_status: GPN-MSA
- configuration of: GPN-MSA ablation '51 mammals' (Supplementary Table 4)
- configuration of: GPN-MSA ablation '51 vertebrates' (Supplementary Table 4)
- configuration of: GPN-MSA ablation 'Default' (Supplementary Table 4)
- configuration of: GPN-MSA ablation 'Include closest primates' (Supplementary Table 4)
- configuration of: GPN-MSA ablation 'Don’t replace non-conserved' (Supplementary Table 4)
- configuration of: GPN-MSA ablation 'Don’t upweight conserved' (Supplementary Table 4)
- configuration of: GPN-MSA ablation 'Train on 100% of genome' (Supplementary Table 4)
- configuration of: GPN-MSA ablation 'Train on 50% most conserved' (Supplementary Table 4)
- configuration of: GPN-MSA ablation 'Window size = 16' (Supplementary Table 4)
- configuration of: GPN-MSA ablation 'Window size = 256' (Supplementary Table 4)
- configuration of: GPN-MSA ablation 'Window size = 32' (Supplementary Table 4)
- configuration of: GPN-MSA ablation 'Window size = 4' (Supplementary Table 4)
- configuration of: GPN-MSA ablation 'Window size = 64' (Supplementary Table 4)
- configuration of: GPN-MSA ablation 'Window size = 8' (Supplementary Table 4)
- configuration of: GPN-MSA ablation 'w/o MSA' (Supplementary Table 4)
- configuration of: GPN-MSA, main results model (bioRxiv v2)
- configuration of: GPN-MSA (evaluation mode not printed (Table 4 has no Eval. column), GUANinE v1.1)
- configuration of: GPN-MSA (Position) (zero-shot, GUANinE v1.1)
- configuration of: GPN-MSA (zero-shot, GUANinE v1.1)
- configuration of: GPN-MSA_absLLR.plus.score (TraitGym)
- configuration of: GPN-MSA_Embeddings.minus.inner_product (TraitGym)
- configuration of: GPN-MSA_Embeddings.plus.cosine_distance (TraitGym)
- configuration of: GPN-MSA_Embeddings.plus.euclidean_distance (TraitGym)
- configuration of: GPN-MSA_InnerProduct.minus.score (TraitGym)
- configuration of: GPN-MSA_LLR.minus.score (TraitGym)
- configuration of: GPN-MSA.LogisticRegression.chrom (TraitGym)