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,,,