Table 1.
EmbedPVP variant prediction results across several ontologies with different neuro-symbolic knowledge embedding methods.
| Using the clinical phenotypes |
Using OMIM phenotypes |
||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| H@1 | H@10 | H@30 | H@50 | ROCAUC | AUPR | H@1 | H@10 | H@30 | H@50 | ROCAUC | AUPR | ||
| Genotype-based prediction tools | CADD | 116 (0.0759) | 266 (0.1741) | 467 (0.3056) | 591 (0.3868) | 0.9778 | 0.0494 | 116 (0.0759) | 266 (0.1741) | 467 (0.3056) | 591 (0.3868) | 0.9778 | 0.0494 |
| MCAP | 4 (0.0026) | 261 (0.1708) | 442 (0.2893) | 511 (0.3344) | 0.6389 | 0.0076 | 4 (0.0026) | 261 (0.1708) | 442 (0.2893) | 511 (0.3344) | 0.6389 | 0.0076 | |
| SIFT | 201 (0.1315) | 201 (0.1315) | 201 (0.1315) | 201 (0.1315) | 0.6436 | 0.0736 | 201 (0.1315) | 201 (0.1315) | 201 (0.1315) | 201 (0.1315) | 0.6436 | 0.0736 | |
| PolyPhen2 | 127 (0.0831) | 127 (0.0831) | 127 (0.0831) | 226 (0.1479) | 0.6465 | 0.0481 | 127 (0.0831) | 127 (0.0831) | 127 (0.0831) | 226 (0.1479) | 0.6465 | 0.0481 | |
| DANN | 21 (0.0137) | 263 (0.1721) | 263 (0.1721) | 263 (0.1721) | 0.8422 | 0.0115 | 21 (0.0137) | 263 (0.1721) | 263 (0.1721) | 263 (0.1721) | 0.8422 | 0.0115 | |
| MetaSVM | 20 (0.0131) | 111 (0.0726) | 318 (0.2081) | 406 (0.2657) | 0.6510 | 0.0108 | 20 (0.0131) | 111 (0.0726) | 318 (0.2081) | 406 (0.2657) | 0.6510 | 0.0108 | |
| Phenotype-based prediction tools | PHIVE | 181 (0.1185) | 325 (0.2127) | 364 (0.2382) | 380 (0.2487) | 0.8047 | 0.0709 | 346 (0.2264) | 496 (0.3246) | 518 (0.3390) | 523 (0.3423) | 0.8151 | 0.1477 |
| DeepPVP | 221 (0.1446) | 661 (0.4326) | 762 (0.4987) | 795 (0.5203) | 0.7662 | 0.1389 | 449 (0.2938) | 858 (0.5615) | 905 (0.5923) | 924 (0.6047) | 0.8041 | 0.2853 | |
| Phenix | 472 (0.3089) | 628 (0.4110) | 746 (0.4882) | 788 (0.5157) | 0.8148 | 0.2154 | 1104 (0.7225) | 1130 (0.7395) | 1153 (0.7546) | 1159 (0.7585) | 0.8206 | 0.6275 | |
| hiPHIVE | 431 (0.2821) | 653 (0.4274) | 768 (0.5026) | 809 (0.5295) | 0.8098 | 0.1982 | 868 (0.5681) | 1025 (0.6708) | 1149 (0.7520) | 1184 (0.7749) | 0.8151 | 0.4693 | |
| EmbedPVP (TransD) | GO | 307 (0.2009) | 563 (0.3685) | 726 (0.4751) | 829 (0.5425) | 0.9524 | 0.1386 | 670 (0.4385) | 894 (0.5851) | 1006 (0.6584) | 1042 (0.6819) | 0.9795 | 0.3464 |
| HP | 482 (0.3154) | 846 (0.5537) | 1007 (0.659) | 1056 (0.6911) | 0.9895 | 0.2507 | 996 (0.6518) | 1230 (0.805) | 1352 (0.8848) | 1391 (0.9103) | 0.9960 | 0.5865 | |
| MP | 396 (0.2592) | 675 (0.4418) | 868 (0.5681) | 947 (0.6198) | 0.9587 | 0.1869 | 779 (0.5098) | 922 (0.6034) | 1031 (0.6747) | 1072 (0.7016) | 0.9822 | 0.4120 | |
| UBERON | 287 (0.1878) | 509 (0.3331) | 674 (0.4411) | 800 (0.5236) | 0.9493 | 0.1278 | 699 (0.4575) | 892 (0.5838) | 995 (0.6512) | 1023 (0.6695) | 0.9775 | 0.3594 | |
| Union | 409 (0.2677) | 639 (0.4182) | 833 (0.5452) | 928 (0.6073) | 0.9581 | 0.1934 | 899 (0.5884) | 1086 (0.7107) | 1158 (0.7579) | 1245 (0.8148) | 0.9933 | 0.5087 | |
| EmbedPVP (DL2Vec) | GO | 152 (0.0995) | 382 (0.2500) | 554 (0.3626) | 614 (0.4018) | 0.9282 | 0.0659 | 491 (0.3213) | 804 (0.5262) | 944 (0.6178) | 1010 (0.6610) | 0.9787 | 0.2485 |
| HP | 362 (0.2369) | 666 (0.4359) | 787 (0.5151) | 826 (0.5406) | 0.9867 | 0.1758 | 1011 (0.6616) | 1300 (0.8508) | 1366 (0.8940) | 1384 (0.9058) | 0.9942 | 0.6168 | |
| MP | 255 (0.1669) | 491 (0.3213) | 639 (0.4182) | 701 (0.4588) | 0.9501 | 0.1128 | 639 (0.4182) | 914 (0.5982) | 1043 (0.6826) | 1106 (0.7238) | 0.9804 | 0.3386 | |
| UBERON | 174 (0.1139) | 390 (0.2552) | 498 (0.3259) | 556 (0.3639) | 0.8928 | 0.0751 | 539 (0.3527) | 801 (0.5242) | 904 (0.5916) | 940 (0.6152) | 0.9271 | 0.2713 | |
| Union | 358 (0.2343) | 636 (0.4162) | 771 (0.5046) | 824 (0.5393) | 0.9605 | 0.1673 | 950 (0.6217) | 1216 (0.7958) | 1310 (0.8573) | 1353 (0.8855) | 0.9936 | 0.5625 | |
| EmbedPVP (OWL2Vec*) | GO | 188 (0.1230) | 385 (0.2520) | 525 (0.3436) | 592 (0.3874) | 0.9190 | 0.0797 | 557 (0.3645) | 876 (0.5733) | 1011 (0.6616) | 1059 (0.6931) | 0.9780 | 0.2935 |
| HP | 409 (0.2677) | 685 (0.4483) | 783 (0.5124) | 842 (0.5510) | 0.9874 | 0.1987 | 1026 (0.6715) | 1313 (0.8593) | 1373 (0.8986) | 1391 (0.9103) | 0.9940 | 0.6304 | |
| MP | 222 (0.1453) | 470 (0.3076) | 618 (0.4045) | 677 (0.4431) | 0.9508 | 0.0992 | 665 (0.4352) | 965 (0.6315) | 1068 (0.6990) | 1116 (0.7304) | 0.9785 | 0.3582 | |
| UBERON | 158 (0.1034) | 379 (0.2480) | 474 (0.3102) | 525 (0.3436) | 0.8866 | 0.0673 | 577 (0.3776) | 800 (0.5236) | 888 (0.5812) | 937 (0.6132) | 0.9291 | 0.2937 | |
| Union | 375 (0.2454) | 650 (0.4254) | 787 (0.5151) | 835 (0.5465) | 0.9563 | 0.1774 | 959 (0.6276) | 1253 (0.8200) | 1325 (0.8671) | 1368 (0.8953) | 0.9939 | 0.5775 | |
Bold values indicate the highest scores achieved among different models.