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leaderboard_results.csv

@@ -1,28 +1,25 @@
-Method,sim_sparse_MF_correlation,sim_sparse_MF_pvalue,sim_sparse_CC_correlation,sim_sparse_CC_pvalue,sim_sparse_BP_correlation,sim_sparse_BP_pvalue,sim_sparse_Ave_correlation,sim_sparse_Ave_pvalue,sim_200_MF_correlation,sim_200_MF_pvalue,sim_200_CC_correlation,sim_200_CC_pvalue,sim_200_BP_correlation,sim_200_BP_pvalue,sim_200_Ave_correlation,sim_200_Ave_pvalue,sim_500_MF_correlation,sim_500_MF_pvalue,sim_500_CC_correlation,sim_500_CC_pvalue,sim_500_BP_correlation,sim_500_BP_pvalue,sim_500_Ave_correlation,sim_500_Ave_pvalue,func_MF_accuracy,func_MF_F1,func_MF_precision,func_MF_recall,func_BP_accuracy,func_BP_F1,func_BP_precision,func_BP_recall,func_CC_accuracy,func_CC_F1,func_CC_precision,func_CC_recall,func_Ave_accuracy,func_Ave_F1,func_Ave_precision,func_Ave_recall,fam_nc_f1_ave,fam_nc_accuracy_ave,fam_nc_mcc_ave,fam_uc30_f1_ave,fam_uc30_accuracy_ave,fam_uc30_mcc_ave,fam_uc50_f1_ave,fam_uc50_accuracy_ave,fam_uc50_mcc_ave,fam_mm15_f1_ave,fam_mm15_accuracy_ave,fam_mm15_mcc_ave,aff_mse_ave,aff_mae_ave,aff_corr_ave
-AAC,-0.0121,0.8508,0.0912,0.1546,0.2141,0.0007,0.0978,0.3354,,,,,,,,,,,,,,,,,0.3881,0.4097,0.4867,0.443,0.1611,0.1872,0.3225,0.1976,0.2394,0.2322,0.2829,0.2819,0.2629,0.2764,0.364,0.3075,0.6178,0.6013,0.4607,0.5459,0.5508,0.435,0.5578,0.5505,0.4354,0.5868,0.5675,0.4167,1.8478,10.5931,0.4605
-APAAC,0.1717,0.007,0.2409,0.0001,0.2736,0.0,0.2287,0.0024,,,,,,,,,,,,,,,,,0.471,0.5828,0.6744,0.5989,0.2239,0.3447,0.423,0.4093,0.2396,0.3953,0.4525,0.4603,0.3115,0.4409,0.5166,0.4895,0.4636,0.4722,0.3556,0.2315,0.2661,0.2398,0.3843,0.3888,0.2965,0.3779,0.3854,0.2879,1.7901,10.2267,0.4772
-LEARNED-VEC,0.41,0.0,0.3052,0.0,0.2987,0.0,0.338,0.0,,,,,,,,,,,,,,,,,0.5858,0.6755,0.7205,0.6822,0.3066,0.3917,0.4774,0.387,0.3162,0.4089,0.4695,0.4221,0.4029,0.492,0.5558,0.4971,0.6879,0.6754,0.5398,0.6814,0.6705,0.5323,0.6921,0.6817,0.5387,0.6564,0.6366,0.4873,1.1848,8.1308,0.7034
-PROTVEC,0.1854,0.0035,0.2058,0.0012,0.2953,0.0,0.2288,0.0016,,,,,,,,,,,,,,,,,0.5189,0.6367,0.6806,0.6692,0.2383,0.3624,0.4098,0.4215,0.2428,0.3808,0.4526,0.4208,0.3333,0.46,0.5143,0.5038,0.4383,0.4301,0.3518,0.4565,0.4486,0.3565,0.5457,0.5312,0.4064,0.5372,0.5368,0.4098,1.1341,8.0889,0.7191
-K-SEP,0.2222,0.0004,0.2944,0.0,0.2924,0.0,0.2697,0.0002,,,,,,,,,,,,,,,,,0.7068,0.809,0.848,0.8124,0.359,0.5169,0.5932,0.5497,0.3445,0.5023,0.5819,0.5385,0.4701,0.6094,0.6744,0.6335,0.7496,0.7277,0.6548,0.769,0.7695,0.6933,0.8079,0.8001,0.7068,0.7254,0.71,0.607,0.9705,7.2073,0.7613
-MUT2VEC,0.5462,0.0,0.3949,0.0,0.5799,0.0,0.507,0.0,,,,,,,,,,,,,,,,,0.4887,0.5731,0.6264,0.5738,0.3273,0.4271,0.4931,0.4205,0.3604,0.4616,0.5288,0.4561,0.3922,0.4873,0.5495,0.4835,0.5755,0.5542,0.3694,0.5786,0.5583,0.3655,0.5813,0.5618,0.3662,0.5894,0.5724,0.3617,,,
-GENE2VEC,0.1756,0.0057,0.3596,0.0,0.408,0.0,0.3144,0.0019,,,,,,,,,,,,,,,,,0.444,0.5311,0.5932,0.5266,0.3116,0.4385,0.4921,0.4214,0.374,0.5016,0.5499,0.5009,0.3765,0.4904,0.5451,0.483,0.4978,0.4668,0.2701,0.5044,0.4736,0.2709,0.4887,0.4569,0.2629,0.454,0.4135,0.2167,,,
-TCGA-EMBEDDING,0.0375,0.5578,0.5033,0.0,0.4822,0.0,0.341,0.1859,,,,,,,,,,,,,,,,,0.3026,0.3439,0.4061,0.3573,0.2366,0.3205,0.4167,0.3173,0.3416,0.4119,0.4955,0.4396,0.2936,0.3588,0.4395,0.3714,0.4831,0.4659,0.2476,0.4749,0.459,0.2444,0.4848,0.4668,0.2493,0.453,0.4342,0.1985,,,
-PFAM,0.3489,0.0,0.5107,0.0,0.4222,0.0,0.4273,0.0,,,,,,,,,,,,,,,,,0.8148,0.8644,0.9292,0.8366,0.4794,0.5572,0.6724,0.5176,0.5037,0.5806,0.7127,0.5397,0.5993,0.6674,0.7714,0.6313,0.9193,0.9233,0.875,0.9155,0.92,0.8696,0.9166,0.9204,0.8701,0.8432,0.8493,0.761,2.2579,11.6927,0.1917
-CPC-PROT,0.0605,0.3541,-0.087,0.234,0.1091,0.1043,0.0275,0.2308,,,,,,,,,,,,,,,,,0.5183,0.6545,0.7049,0.6819,0.2688,0.3955,0.5084,0.4087,0.3214,0.4352,0.5207,0.4555,0.3695,0.495,0.578,0.5153,0.7234,0.7117,0.5852,0.711,0.696,0.5716,0.7433,0.7351,0.6058,0.7159,0.7102,0.5676,0.7299,6.2609,0.8309
-ESM1B,0.3847,0.0,0.3732,0.0,0.4152,0.0,0.391,0.0,,,,,,,,,,,,,,,,,0.7657,0.8324,0.8653,0.8376,0.4152,0.5333,0.6412,0.5463,0.4682,0.6098,0.7013,0.6317,0.5497,0.6585,0.7359,0.6719,0.9336,0.9321,0.8951,0.9359,0.9339,0.8965,0.8978,0.8864,0.8423,0.9151,0.9149,0.8636,0.4828,5.0019,0.8915
-BERT-BFD,0.2919,0.0,0.4157,0.0,0.3235,0.0,0.3437,0.0,,,,,,,,,,,,,,,,,0.7667,0.8482,0.8727,0.8417,0.4867,0.6116,0.6996,0.5894,0.5062,0.6221,0.6941,0.6224,0.5865,0.6939,0.7555,0.6845,0.879,0.8748,0.8076,0.8762,0.8721,0.8046,0.8805,0.8767,0.8101,0.8561,0.8491,0.7728,0.5736,5.2118,0.874
-BERT-PFAM,0.4965,0.0,0.2218,0.0022,0.2068,0.0019,0.3084,0.0014,,,,,,,,,,,,,,,,,0.7823,0.8466,0.8594,0.8533,0.4048,0.5351,0.6125,0.5465,0.4518,0.5811,0.6603,0.5823,0.5463,0.6543,0.7107,0.6607,0.8329,0.8226,0.7505,0.8393,0.8327,0.7558,0.8223,0.8104,0.7297,0.7868,0.7716,0.68,,,
-ALBERT,0.2219,0.0006,0.3181,0.0,0.369,0.0,0.303,0.0002,,,,,,,,,,,,,,,,,0.8345,0.8854,0.9133,0.8735,0.5106,0.6255,0.7063,0.6011,0.5135,0.6355,0.7256,0.6129,0.6195,0.7155,0.7817,0.6958,0.9419,0.9414,0.9059,0.9395,0.9398,0.9026,0.9364,0.936,0.8976,0.9033,0.9038,0.8437,0.4183,4.5728,0.9071
-BLAST,0.1127,0.0776,0.0885,0.1674,0.3432,0.0,0.1815,0.0817,,,,,,,,,,,,,,,,,0.8421,0.8749,0.9219,0.8571,0.4616,0.5559,0.6807,0.502,0.4851,0.5731,0.6969,0.5298,0.5963,0.668,0.7665,0.6296,0.8899,0.8837,0.8296,0.8676,0.8537,0.7958,0.8783,0.8678,0.8101,0.7742,0.7458,0.6719,,,
-HMMER,0.1374,0.0313,0.3219,0.0,0.1577,0.0131,0.2056,0.0148,,,,,,,,,,,,,,,,,0.8579,0.8908,0.9115,0.888,0.5022,0.611,0.6448,0.6037,0.491,0.5957,0.6451,0.5868,0.6171,0.6992,0.7338,0.6928,0.8886,0.8821,0.8257,0.8786,0.8704,0.8104,0.8847,0.8775,0.8191,0.8048,0.7875,0.7075,,,
-UNIREP,0.4213,0.0,0.3248,0.0,0.4695,0.0,0.4052,0.0,,,,,,,,,,,,,,,,,0.7499,0.8232,0.8599,0.8237,0.376,0.4795,0.5962,0.4915,0.3803,0.5325,0.5883,0.5722,0.502,0.6117,0.6815,0.6291,0.7739,0.7633,0.6871,0.8253,0.8168,0.7271,0.8064,0.7961,0.7094,0.7034,0.6829,0.6069,0.7321,6.3874,0.8299
-XLNET,0.2271,0.0004,0.2549,0.0004,0.309,0.0,0.2637,0.0003,,,,,,,,,,,,,,,,,0.7114,0.8158,0.8472,0.8248,0.3729,0.4996,0.612,0.5095,0.4466,0.5878,0.6673,0.5987,0.5103,0.6344,0.7088,0.6443,0.904,0.9018,0.849,0.8677,0.8586,0.7981,0.8511,0.8368,0.7857,0.8411,0.8272,0.7531,0.6068,5.7001,0.8615
-T5,0.5664,0.0,0.3985,0.0,0.2127,0.0014,0.3925,0.0005,,,,,,,,,,,,,,,,,0.8573,0.9013,0.9224,0.8921,0.5686,0.6558,0.7127,0.6316,0.5884,0.6803,0.7561,0.6616,0.6715,0.7458,0.797,0.7284,0.941,0.9399,0.9045,0.9409,0.9396,0.9042,0.9404,0.9388,0.9036,0.9237,0.9221,0.8769,0.6035,5.462,0.8666
-SEQVEC,0.4238,0.0,0.4242,0.0,0.2436,0.0001,0.3639,0.0,,,,,,,,,,,,,,,,,0.8366,0.8857,0.9084,0.8779,0.5021,0.6003,0.647,0.5903,0.501,0.6065,0.6817,0.5918,0.6132,0.6975,0.7457,0.6867,0.915,0.913,0.863,0.9109,0.9092,0.8572,0.9102,0.908,0.8557,0.8865,0.8828,0.8175,0.5331,5.2423,0.8801
-ESM2,0.2978,0.0,0.2811,0.0001,0.4274,0.0,0.3354,0.0,,,,,,,,,,,,,,,,,0.8321,0.8743,0.8979,0.8703,0.4671,0.5987,0.6671,0.5977,0.5319,0.6472,0.7147,0.6489,0.6104,0.7067,0.7599,0.7056,0.9328,0.9308,0.8927,0.9397,0.9389,0.9033,0.93,0.9289,0.889,0.9163,0.9174,0.8676,0.4759,4.9639,0.8931
-ESM3,0.5102,0.0,0.5762,0.0,0.4227,0.0,0.5031,0.0,,,,,,,,,,,,,,,,,0.6839,0.8076,0.8416,0.8261,0.3729,0.4988,0.6074,0.5303,0.3812,0.5176,0.5913,0.5507,0.4793,0.608,0.6801,0.6357,0.8444,0.8259,0.7794,0.8906,0.8819,0.826,0.8535,0.8378,0.7926,0.851,0.833,0.7775,0.5116,5.2333,0.8888
-SaProt,0.4032,0.0,0.3691,0.0,0.2419,0.0003,0.338,0.0001,,,,,,,,,,,,,,,,,0.7678,0.831,0.8557,0.8375,0.4591,0.5752,0.6842,0.5486,0.5095,0.6016,0.686,0.6024,0.5788,0.6693,0.742,0.6629,0.8955,0.8923,0.8328,0.8904,0.8866,0.8254,0.8982,0.8971,0.8376,0.8758,0.8727,0.8044,,,
-ProstT5,0.4474,0.0,0.4156,0.0,0.0806,0.2304,0.3146,0.0768,,,,,,,,,,,,,,,,,0.8127,0.8745,0.8999,0.8733,0.545,0.6459,0.7238,0.6259,0.5417,0.6435,0.6991,0.6335,0.6331,0.7213,0.7743,0.7109,0.9317,0.9304,0.8901,0.928,0.9266,0.8844,0.9266,0.9245,0.8827,0.9098,0.9064,0.8549,0.7844,5.8314,0.8292
-tape_human_cc_embeddings,0.6262968033335666,2.3809450098674595e-26,0.7042750229409422,9.949759671910668e-35,0.6034443817052514,2.643499228007077e-24,0.6446720693265867,8.89102892735083e-25,,,,,,,,,,,,,,,,,0.6558985714285714,0.7556728571428571,0.8056014285714286,0.7481585714285715,0.4596066666666666,0.5982999999999999,0.6966700000000001,0.5842166666666667,0.5645100000000001,0.68902125,0.7482137500000001,0.67946125,0.5600050793650794,0.6809980357142856,0.7501617261904764,0.6706121626984127,0.7998797243443275,0.7937240483603916,0.6919911697821982,0.7989043958566743,0.791947472007193,0.6906668087156065,0.8003721222097535,0.7922460210949956,0.6898681337444433,0.7814408207855974,0.7717498738322244,0.6671891644093118,,,
-tape_human_bp_embeddings,0.5469837018976148,2.8621348112541442e-19,0.6846789133784649,3.419306030214691e-32,0.6168986935103876,1.293953206883564e-25,0.6161871029288224,9.540453684025638e-20,,,,,,,,,,,,,,,,,0.8130428571428572,0.87813,0.9071571428571428,0.8703842857142857,0.6123988888888889,0.72718,0.7893977777777779,0.7203233333333334,0.5630325,0.6899187500000001,0.7496887499999999,0.6841075,0.6628247486772487,0.76507625,0.8154145568783068,0.7582717063492064,0.9067629269222628,0.9045195895983068,0.8508611905155833,0.905548341124588,0.903694732664364,0.849106395307814,0.904620091487572,0.902469092667571,0.8476136627603814,0.8974276442252119,0.8953359990121719,0.8367604865953275,,,
-tape_human_mf_embeddings,0.8084498316229154,3.615332148264959e-54,0.5520261613310941,3.4731103688333775e-19,0.4488414883467357,7.504941300268128e-13,0.6031058271002484,2.501648257792831e-13,,,,,,,,,,,,,,,,,0.7405785714285714,0.8224028571428572,0.84849,0.8204500000000001,0.4976677777777777,0.6174200000000001,0.6906388888888889,0.6171388888888889,0.49320375,0.61598125,0.6789687500000001,0.61419,0.577150033068783,0.6852680357142859,0.7393658796296297,0.6839262962962964,0.9053550866435313,0.9053675928864273,0.8484790173574168,0.9009782600843634,0.9026312245967348,0.8437903487923677,0.9016047018759996,0.902639344488587,0.844619511191329,0.8902911553542989,0.8889138151401399,0.8242011269438037,,,
+Method,sim_sparse_MF_correlation,sim_sparse_CC_correlation,sim_sparse_BP_correlation,sim_sparse_Ave_correlation,sim_200_MF_correlation,sim_200_CC_correlation,sim_200_BP_correlation,sim_200_Ave_correlation,sim_500_MF_correlation,sim_500_CC_correlation,sim_500_BP_correlation,sim_500_Ave_correlation,func_MF_accuracy,func_MF_F1,func_MF_precision,func_MF_recall,func_BP_accuracy,func_BP_F1,func_BP_precision,func_BP_recall,func_CC_accuracy,func_CC_F1,func_CC_precision,func_CC_recall,func_Ave_accuracy,func_Ave_F1,func_Ave_precision,func_Ave_recall,fam_nc_f1_ave,fam_nc_accuracy_ave,fam_nc_mcc_ave,fam_uc30_f1_ave,fam_uc30_accuracy_ave,fam_uc30_mcc_ave,fam_uc50_f1_ave,fam_uc50_accuracy_ave,fam_uc50_mcc_ave,fam_mm15_f1_ave,fam_mm15_accuracy_ave,fam_mm15_mcc_ave,aff_mse_ave,aff_mae_ave,aff_corr_ave
+AAC,-0.0121,0.0912,0.2141,0.0978,,,,,,,,,0.3881,0.4097,0.4867,0.443,0.1611,0.1872,0.3225,0.1976,0.2394,0.2322,0.2829,0.2819,0.2629,0.2764,0.364,0.3075,0.6178,0.6013,0.4607,0.5459,0.5508,0.435,0.5578,0.5505,0.4354,0.5868,0.5675,0.4167,1.8478,10.5931,0.4605
+APAAC,0.1717,0.2409,0.2736,0.2287,,,,,,,,,0.471,0.5828,0.6744,0.5989,0.2239,0.3447,0.423,0.4093,0.2396,0.3953,0.4525,0.4603,0.3115,0.4409,0.5166,0.4895,0.4636,0.4722,0.3556,0.2315,0.2661,0.2398,0.3843,0.3888,0.2965,0.3779,0.3854,0.2879,1.7901,10.2267,0.4772
+LEARNED-VEC,0.41,0.3052,0.2987,0.338,,,,,,,,,0.5858,0.6755,0.7205,0.6822,0.3066,0.3917,0.4774,0.387,0.3162,0.4089,0.4695,0.4221,0.4029,0.492,0.5558,0.4971,0.6879,0.6754,0.5398,0.6814,0.6705,0.5323,0.6921,0.6817,0.5387,0.6564,0.6366,0.4873,1.1848,8.1308,0.7034
+PROTVEC,0.1854,0.2058,0.2953,0.2288,,,,,,,,,0.5189,0.6367,0.6806,0.6692,0.2383,0.3624,0.4098,0.4215,0.2428,0.3808,0.4526,0.4208,0.3333,0.46,0.5143,0.5038,0.4383,0.4301,0.3518,0.4565,0.4486,0.3565,0.5457,0.5312,0.4064,0.5372,0.5368,0.4098,1.1341,8.0889,0.7191
+K-SEP,0.2222,0.2944,0.2924,0.2697,,,,,,,,,0.7068,0.809,0.848,0.8124,0.359,0.5169,0.5932,0.5497,0.3445,0.5023,0.5819,0.5385,0.4701,0.6094,0.6744,0.6335,0.7496,0.7277,0.6548,0.769,0.7695,0.6933,0.8079,0.8001,0.7068,0.7254,0.71,0.607,0.9705,7.2073,0.7613
+MUT2VEC,0.5462,0.3949,0.5799,0.507,,,,,,,,,0.4887,0.5731,0.6264,0.5738,0.3273,0.4271,0.4931,0.4205,0.3604,0.4616,0.5288,0.4561,0.3922,0.4873,0.5495,0.4835,0.5755,0.5542,0.3694,0.5786,0.5583,0.3655,0.5813,0.5618,0.3662,0.5894,0.5724,0.3617,,,
+GENE2VEC,0.1756,0.3596,0.408,0.3144,,,,,,,,,0.444,0.5311,0.5932,0.5266,0.3116,0.4385,0.4921,0.4214,0.374,0.5016,0.5499,0.5009,0.3765,0.4904,0.5451,0.483,0.4978,0.4668,0.2701,0.5044,0.4736,0.2709,0.4887,0.4569,0.2629,0.454,0.4135,0.2167,,,
+TCGA-EMBEDDING,0.0375,0.5033,0.4822,0.341,,,,,,,,,0.3026,0.3439,0.4061,0.3573,0.2366,0.3205,0.4167,0.3173,0.3416,0.4119,0.4955,0.4396,0.2936,0.3588,0.4395,0.3714,0.4831,0.4659,0.2476,0.4749,0.459,0.2444,0.4848,0.4668,0.2493,0.453,0.4342,0.1985,,,
+PFAM,0.3489,0.5107,0.4222,0.4273,,,,,,,,,0.8148,0.8644,0.9292,0.8366,0.4794,0.5572,0.6724,0.5176,0.5037,0.5806,0.7127,0.5397,0.5993,0.6674,0.7714,0.6313,0.9193,0.9233,0.875,0.9155,0.92,0.8696,0.9166,0.9204,0.8701,0.8432,0.8493,0.761,2.2579,11.6927,0.1917
+CPC-PROT,0.0605,-0.087,0.1091,0.0275,,,,,,,,,0.5183,0.6545,0.7049,0.6819,0.2688,0.3955,0.5084,0.4087,0.3214,0.4352,0.5207,0.4555,0.3695,0.495,0.578,0.5153,0.7234,0.7117,0.5852,0.711,0.696,0.5716,0.7433,0.7351,0.6058,0.7159,0.7102,0.5676,0.7299,6.2609,0.8309
+ESM1B,0.3847,0.3732,0.4152,0.391,,,,,,,,,0.7657,0.8324,0.8653,0.8376,0.4152,0.5333,0.6412,0.5463,0.4682,0.6098,0.7013,0.6317,0.5497,0.6585,0.7359,0.6719,0.9336,0.9321,0.8951,0.9359,0.9339,0.8965,0.8978,0.8864,0.8423,0.9151,0.9149,0.8636,0.4828,5.0019,0.8915
+BERT-BFD,0.2919,0.4157,0.3235,0.3437,,,,,,,,,0.7667,0.8482,0.8727,0.8417,0.4867,0.6116,0.6996,0.5894,0.5062,0.6221,0.6941,0.6224,0.5865,0.6939,0.7555,0.6845,0.879,0.8748,0.8076,0.8762,0.8721,0.8046,0.8805,0.8767,0.8101,0.8561,0.8491,0.7728,0.5736,5.2118,0.874
+BERT-PFAM,0.4965,0.2218,0.2068,0.3084,,,,,,,,,0.7823,0.8466,0.8594,0.8533,0.4048,0.5351,0.6125,0.5465,0.4518,0.5811,0.6603,0.5823,0.5463,0.6543,0.7107,0.6607,0.8329,0.8226,0.7505,0.8393,0.8327,0.7558,0.8223,0.8104,0.7297,0.7868,0.7716,0.68,,,
+ALBERT,0.2219,0.3181,0.369,0.303,,,,,,,,,0.8345,0.8854,0.9133,0.8735,0.5106,0.6255,0.7063,0.6011,0.5135,0.6355,0.7256,0.6129,0.6195,0.7155,0.7817,0.6958,0.9419,0.9414,0.9059,0.9395,0.9398,0.9026,0.9364,0.936,0.8976,0.9033,0.9038,0.8437,0.4183,4.5728,0.9071
+BLAST,0.1127,0.0885,0.3432,0.1815,,,,,,,,,0.8421,0.8749,0.9219,0.8571,0.4616,0.5559,0.6807,0.502,0.4851,0.5731,0.6969,0.5298,0.5963,0.668,0.7665,0.6296,0.8899,0.8837,0.8296,0.8676,0.8537,0.7958,0.8783,0.8678,0.8101,0.7742,0.7458,0.6719,,,
+HMMER,0.1374,0.3219,0.1577,0.2056,,,,,,,,,0.8579,0.8908,0.9115,0.888,0.5022,0.611,0.6448,0.6037,0.491,0.5957,0.6451,0.5868,0.6171,0.6992,0.7338,0.6928,0.8886,0.8821,0.8257,0.8786,0.8704,0.8104,0.8847,0.8775,0.8191,0.8048,0.7875,0.7075,,,
+UNIREP,0.4213,0.3248,0.4695,0.4052,,,,,,,,,0.7499,0.8232,0.8599,0.8237,0.376,0.4795,0.5962,0.4915,0.3803,0.5325,0.5883,0.5722,0.502,0.6117,0.6815,0.6291,0.7739,0.7633,0.6871,0.8253,0.8168,0.7271,0.8064,0.7961,0.7094,0.7034,0.6829,0.6069,0.7321,6.3874,0.8299
+XLNET,0.2271,0.2549,0.309,0.2637,,,,,,,,,0.7114,0.8158,0.8472,0.8248,0.3729,0.4996,0.612,0.5095,0.4466,0.5878,0.6673,0.5987,0.5103,0.6344,0.7088,0.6443,0.904,0.9018,0.849,0.8677,0.8586,0.7981,0.8511,0.8368,0.7857,0.8411,0.8272,0.7531,0.6068,5.7001,0.8615
+T5,0.5664,0.3985,0.2127,0.3925,,,,,,,,,0.8573,0.9013,0.9224,0.8921,0.5686,0.6558,0.7127,0.6316,0.5884,0.6803,0.7561,0.6616,0.6715,0.7458,0.797,0.7284,0.941,0.9399,0.9045,0.9409,0.9396,0.9042,0.9404,0.9388,0.9036,0.9237,0.9221,0.8769,0.6035,5.462,0.8666
+SEQVEC,0.4238,0.4242,0.2436,0.3639,,,,,,,,,0.8366,0.8857,0.9084,0.8779,0.5021,0.6003,0.647,0.5903,0.501,0.6065,0.6817,0.5918,0.6132,0.6975,0.7457,0.6867,0.915,0.913,0.863,0.9109,0.9092,0.8572,0.9102,0.908,0.8557,0.8865,0.8828,0.8175,0.5331,5.2423,0.8801
+ESM2,0.2978,0.2811,0.4274,0.3354,,,,,,,,,0.8321,0.8743,0.8979,0.8703,0.4671,0.5987,0.6671,0.5977,0.5319,0.6472,0.7147,0.6489,0.6104,0.7067,0.7599,0.7056,0.9328,0.9308,0.8927,0.9397,0.9389,0.9033,0.93,0.9289,0.889,0.9163,0.9174,0.8676,0.4759,4.9639,0.8931
+ESM3,0.5102,0.5762,0.4227,0.5031,,,,,,,,,0.6839,0.8076,0.8416,0.8261,0.3729,0.4988,0.6074,0.5303,0.3812,0.5176,0.5913,0.5507,0.4793,0.608,0.6801,0.6357,0.8444,0.8259,0.7794,0.8906,0.8819,0.826,0.8535,0.8378,0.7926,0.851,0.833,0.7775,0.5116,5.2333,0.8888
+SaProt,0.4032,0.3691,0.2419,0.338,,,,,,,,,0.7678,0.831,0.8557,0.8375,0.4591,0.5752,0.6842,0.5486,0.5095,0.6016,0.686,0.6024,0.5788,0.6693,0.742,0.6629,0.8955,0.8923,0.8328,0.8904,0.8866,0.8254,0.8982,0.8971,0.8376,0.8758,0.8727,0.8044,,,
+ProstT5,0.4474,0.4156,0.0806,0.3146,,,,,,,,,0.8127,0.8745,0.8999,0.8733,0.545,0.6459,0.7238,0.6259,0.5417,0.6435,0.6991,0.6335,0.6331,0.7213,0.7743,0.7109,0.9317,0.9304,0.8901,0.928,0.9266,0.8844,0.9266,0.9245,0.8827,0.9098,0.9064,0.8549,0.7844,5.8314,0.8292

similarity_results.csv

@@ -1,28 +1,25 @@
-Method,sparse_MF_correlation,sparse_MF_pvalue,sparse_CC_correlation,sparse_CC_pvalue,sparse_BP_correlation,sparse_BP_pvalue,sparse_Ave_correlation,sparse_Ave_pvalue,200_MF_correlation,200_MF_pvalue,200_CC_correlation,200_CC_pvalue,200_BP_correlation,200_BP_pvalue,200_Ave_correlation,200_Ave_pvalue,500_MF_correlation,500_MF_pvalue,500_CC_correlation,500_CC_pvalue,500_BP_correlation,500_BP_pvalue,500_Ave_correlation,500_Ave_pvalue
-AAC,-0.0120530487301072,0.8508071436536463,0.0912116785938685,0.1546329908435944,0.2141018739428611,0.0007061795748057,0.0977535012688741,0.3353821046906821,,,,,,,,,,,,,,,,
-APAAC,0.1716732195001037,0.0069560423057116,0.240874262539882,0.0001405462274193,0.2735843497262189,1.2923220610249705e-05,0.2287106105887349,0.002369837251247,,,,,,,,,,,,,,,,
-LEARNED-VEC,0.4099830116701563,2.1689966436784665e-11,0.3051938408310146,1.120065867436256e-06,0.2987112063885428,1.7495423111940671e-06,0.3379626862965713,9.565432895322534e-07,,,,,,,,,,,,,,,,
-PROTVEC,0.1854412229985308,0.0035106737585576,0.2058335849333736,0.0011949062421632,0.2952566916292122,2.329746579400883e-06,0.2288438331870389,0.0015693032491,,,,,,,,,,,,,,,,
-K-SEP,0.2222351644321201,0.0004449359524399,0.2943533697632057,2.8912597759133027e-06,0.2924105791926405,2.941553534464349e-06,0.2696663711293221,0.0001502562552501,,,,,,,,,,,,,,,,
-MUT2VEC,0.5462247913812742,2.6648168646769584e-20,0.3948878923766817,8.90249286171986e-10,0.5799222876570942,1.1825607450331126e-17,0.50701165713835,2.9674976600808085e-10,,,,,,,,,,,,,,,,
-GENE2VEC,0.1756222504801268,0.0057448955732791,0.359607993537279,6.832652069339137e-09,0.407953665862896,2.5324890595081728e-11,0.3143946366267673,0.0019149674770853,,,,,,,,,,,,,,,,
-XLNET,0.2270935836252544,0.0004255217205398,0.2549405428464779,0.0003996981320453,0.3090004241910071,2.5504237823583223e-06,0.2636781835542465,0.0002759234254558,,,,,,,,,,,,,,,,
-T5,0.5663605927245389,1.6651780868008073e-21,0.3984518032670328,1.3597547816366492e-08,0.2126939158889831,0.0013983844195919,0.392502103960185,0.0004661326723799,,,,,,,,,,,,,,,,
-SEQVEC,0.4237953500744624,3.836091946107342e-12,0.4242066438730631,4.02619839196181e-12,0.2436484071644948,0.0001096113591758,0.3638834670373401,3.653712234604294e-05,,,,,,,,,,,,,,,,
-TCGA-EMBEDDING,0.0375448135213401,0.55782521975525,0.5033396964743626,6.003047049037164e-17,0.4822408636127631,8.634372908060867e-16,0.3410417912028219,0.185941739918417,,,,,,,,,,,,,,,,
-PFAM,0.3489483982233921,1.877722902620754e-08,0.510730419386372,1.114133339243178e-17,0.422215963284985,4.247926093523296e-12,0.4272982602982497,6.260492321147465e-09,,,,,,,,,,,,,,,,
-CPC-PROT,0.0604542610865414,0.3541297210052825,-0.0869798610000177,0.2340072675203556,0.1090657842339456,0.1042913765903023,0.0275133947734897,0.2308094550386468,,,,,,,,,,,,,,,,
-ESM1B,0.384697625027269,8.87075880764962e-10,0.3731936223537567,1.2308236239109248e-07,0.4151856052080267,1.0531459683186124e-10,0.3910256175296842,4.135825095622976e-08,,,,,,,,,,,,,,,,
-BERT-BFD,0.2918631086847955,4.893623100352673e-06,0.4157201514424359,2.702080353630567e-09,0.3234845992693526,7.937879082606092e-07,0.3436892864655279,1.8967043629889704e-06,,,,,,,,,,,,,,,,
-BERT-PFAM,0.4964861293154893,3.732414283758915e-16,0.2217707389039976,0.0021629150128432,0.2068266617033433,0.001903663251382,0.3083611766409434,0.0013555260880752,,,,,,,,,,,,,,,,
-ALBERT,0.2218813721583892,0.0005801073837487,0.3181002150766988,8.174677802601285e-06,0.3690126305036619,1.3363892045333629e-08,0.3029980725795833,0.0001960984751477,,,,,,,,,,,,,,,,
-BLAST,0.1127460653100103,0.0775674407393031,0.0884833522711429,0.1673988859627581,0.3431671202767732,3.1135714073061366e-08,0.1814655126193088,0.0816554526125918,,,,,,,,,,,,,,,,
-HMMER,0.1373599246282869,0.0312674758751548,0.3218542802568603,2.6085514590925364e-07,0.1577102930764373,0.0130798221788381,0.2056414993205282,0.0147825196363796,,,,,,,,,,,,,,,,
-UNIREP,0.4213327475751828,5.254792153325089e-12,0.3247590759614522,2.0048389618732375e-07,0.4695106024457135,6.036878830381285e-15,0.4052008086607828,6.682971900545196e-08,,,,,,,,,,,,,,,,
-ESM2,0.2977856665086115,3.065042702588219e-06,0.281050143088217,8.950030668598434e-05,0.4273702754644458,2.5792468349760803e-11,0.3354020283537581,3.085512506034697e-05,,,,,,,,,,,,,,,,
-ESM3,0.5102468363444927,4.10736409041891e-17,0.5762295810448107,4.115964472439376e-18,0.4227236525442803,4.440054365268544e-11,0.5030666899778612,1.4800196280763605e-11,,,,,,,,,,,,,,,,
-SaProt,0.4031774477652035,1.1194701580503788e-10,0.3690662827280969,1.7337124606608502e-07,0.2418927575878248,0.0002661196434171,0.3380454960270417,8.876437553673041e-05,,,,,,,,,,,,,,,,
-ProstT5,0.4474307637665665,4.558891379901188e-13,0.4155957269059172,2.7346299210504223e-09,0.0806352476756064,0.2304004913343529,0.3145539127826967,0.0768001646898129,,,,,,,,,,,,,,,,
-tape_human_cc_embeddings,0.6262968033335666,2.3809450098674595e-26,0.7042750229409422,9.949759671910668e-35,0.6034443817052514,2.643499228007077e-24,0.6446720693265867,8.89102892735083e-25,,,,,,,,,,,,,,,,
-tape_human_bp_embeddings,0.5469837018976148,2.8621348112541433e-19,0.6846789133784649,3.419306030214691e-32,0.6168986935103876,1.293953206883564e-25,0.6161871029288224,9.540453684025638e-20,,,,,,,,,,,,,,,,
-tape_human_mf_embeddings,0.8084498316229154,3.6153321482649593e-54,0.5520261613310941,3.4731103688333775e-19,0.44884148834673576,7.504941300268126e-13,0.6031058271002484,2.501648257792831e-13,,,,,,,,,,,,,,,,
+Method,sparse_MF_correlation,sparse_CC_correlation,sparse_BP_correlation,sparse_Ave_correlation,200_MF_correlation,200_CC_correlation,200_BP_correlation,200_Ave_correlation,500_MF_correlation,500_CC_correlation,500_BP_correlation,500_Ave_correlation
+AAC,-0.0120530487301072,0.0912116785938685,0.2141018739428611,0.0977535012688741,,,,,,,,
+APAAC,0.1716732195001037,0.240874262539882,0.2735843497262189,0.2287106105887349,,,,,,,,
+LEARNED-VEC,0.4099830116701563,0.3051938408310146,0.2987112063885428,0.3379626862965713,,,,,,,,
+PROTVEC,0.1854412229985308,0.2058335849333736,0.2952566916292122,0.2288438331870389,,,,,,,,
+K-SEP,0.2222351644321201,0.2943533697632057,0.2924105791926405,0.2696663711293221,,,,,,,,
+MUT2VEC,0.5462247913812742,0.3948878923766817,0.5799222876570942,0.50701165713835,,,,,,,,
+GENE2VEC,0.1756222504801268,0.359607993537279,0.407953665862896,0.3143946366267673,,,,,,,,
+XLNET,0.2270935836252544,0.2549405428464779,0.3090004241910071,0.2636781835542465,,,,,,,,
+T5,0.5663605927245389,0.3984518032670328,0.2126939158889831,0.392502103960185,,,,,,,,
+SEQVEC,0.4237953500744624,0.4242066438730631,0.2436484071644948,0.3638834670373401,,,,,,,,
+TCGA-EMBEDDING,0.0375448135213401,0.5033396964743626,0.4822408636127631,0.3410417912028219,,,,,,,,
+PFAM,0.3489483982233921,0.510730419386372,0.422215963284985,0.4272982602982497,,,,,,,,
+CPC-PROT,0.0604542610865414,-0.0869798610000177,0.1090657842339456,0.0275133947734897,,,,,,,,
+ESM1B,0.384697625027269,0.3731936223537567,0.4151856052080267,0.3910256175296842,,,,,,,,
+BERT-BFD,0.2918631086847955,0.4157201514424359,0.3234845992693526,0.3436892864655279,,,,,,,,
+BERT-PFAM,0.4964861293154893,0.2217707389039976,0.2068266617033433,0.3083611766409434,,,,,,,,
+ALBERT,0.2218813721583892,0.3181002150766988,0.3690126305036619,0.3029980725795833,,,,,,,,
+BLAST,0.1127460653100103,0.0884833522711429,0.3431671202767732,0.1814655126193088,,,,,,,,
+HMMER,0.1373599246282869,0.3218542802568603,0.1577102930764373,0.2056414993205282,,,,,,,,
+UNIREP,0.4213327475751828,0.3247590759614522,0.4695106024457135,0.4052008086607828,,,,,,,,
+ESM2,0.2977856665086115,0.281050143088217,0.4273702754644458,0.3354020283537581,,,,,,,,
+ESM3,0.5102468363444927,0.5762295810448107,0.4227236525442803,0.5030666899778612,,,,,,,,
+SaProt,0.4031774477652035,0.3690662827280969,0.2418927575878248,0.3380454960270417,,,,,,,,
+ProstT5,0.4474307637665665,0.4155957269059172,0.0806352476756064,0.3145539127826967,,,,,,,,