Method,MF_Low_Shallow_acc uracy,MF_Low_Shallow_F1,MF_Low_Shallow_precision,MF_Low_Shallow_recall,MF_Low_Normal_acc uracy,MF_Low_Normal_F1,MF_Low_Normal_precision,MF_Low_Normal_recall,MF_Low_Specific_acc uracy,MF_Low_Specific_F1,MF_Low_Specific_precision,MF_Low_Specific_recall,MF_High_Shallow_acc uracy,MF_High_Shallow_F1,MF_High_Shallow_precision,MF_High_Shallow_recall,MF_High_Normal_acc uracy,MF_High_Normal_F1,MF_High_Normal_precision,MF_High_Normal_recall,MF_High_Specific_acc uracy,MF_High_Specific_F1,MF_High_Specific_precision,MF_High_Specific_recall,MF_Middle_Shallow_acc uracy,MF_Middle_Shallow_F1,MF_Middle_Shallow_precision,MF_Middle_Shallow_recall,MF_Middle_Normal_acc uracy,MF_Middle_Normal_F1,MF_Middle_Normal_precision,MF_Middle_Normal_recall,MF_Middle_Specific_acc uracy,MF_Middle_Specific_F1,MF_Middle_Specific_precision,MF_Middle_Specific_recall,BP_Low_Shallow_acc uracy,BP_Low_Shallow_F1,BP_Low_Shallow_precision,BP_Low_Shallow_recall,BP_Low_Normal_acc uracy,BP_Low_Normal_F1,BP_Low_Normal_precision,BP_Low_Normal_recall,BP_Low_Specific_acc uracy,BP_Low_Specific_F1,BP_Low_Specific_precision,BP_Low_Specific_recall,BP_High_Shallow_acc uracy,BP_High_Shallow_F1,BP_High_Shallow_precision,BP_High_Shallow_recall,BP_High_Normal_acc uracy,BP_High_Normal_F1,BP_High_Normal_precision,BP_High_Normal_recall,BP_High_Specific_acc uracy,BP_High_Specific_F1,BP_High_Specific_precision,BP_High_Specific_recall,BP_Middle_Shallow_acc uracy,BP_Middle_Shallow_F1,BP_Middle_Shallow_precision,BP_Middle_Shallow_recall,BP_Middle_Normal_acc uracy,BP_Middle_Normal_F1,BP_Middle_Normal_precision,BP_Middle_Normal_recall,BP_Middle_Specific_acc uracy,BP_Middle_Specific_F1,BP_Middle_Specific_precision,BP_Middle_Specific_recall,CC_Low_Shallow_acc uracy,CC_Low_Shallow_F1,CC_Low_Shallow_precision,CC_Low_Shallow_recall,CC_Low_Normal_acc uracy,CC_Low_Normal_F1,CC_Low_Normal_precision,CC_Low_Normal_recall,CC_Low_Specific_acc uracy,CC_Low_Specific_F1,CC_Low_Specific_precision,CC_Low_Specific_recall,CC_High_Shallow_acc uracy,CC_High_Shallow_F1,CC_High_Shallow_precision,CC_High_Shallow_recall,CC_High_Normal_acc uracy,CC_High_Normal_F1,CC_High_Normal_precision,CC_High_Normal_recall,CC_High_Specific_acc uracy,CC_High_Specific_F1,CC_High_Specific_precision,CC_High_Specific_recall,CC_Middle_Shallow_acc uracy,CC_Middle_Shallow_F1,CC_Middle_Shallow_precision,CC_Middle_Shallow_recall,CC_Middle_Normal_acc uracy,CC_Middle_Normal_F1,CC_Middle_Normal_precision,CC_Middle_Normal_recall,CC_Middle_Specific_acc uracy,CC_Middle_Specific_F1,CC_Middle_Specific_precision,CC_Middle_Specific_recall,Ave_Low_Shallow_acc uracy,Ave_Low_Shallow_F1,Ave_Low_Shallow_precision,Ave_Low_Shallow_recall,Ave_Low_Normal_acc uracy,Ave_Low_Normal_F1,Ave_Low_Normal_precision,Ave_Low_Normal_recall,Ave_Low_Specific_acc uracy,Ave_Low_Specific_F1,Ave_Low_Specific_precision,Ave_Low_Specific_recall,Ave_High_Shallow_acc uracy,Ave_High_Shallow_F1,Ave_High_Shallow_precision,Ave_High_Shallow_recall,Ave_High_Normal_acc uracy,Ave_High_Normal_F1,Ave_High_Normal_precision,Ave_High_Normal_recall,Ave_High_Specific_acc uracy,Ave_High_Specific_F1,Ave_High_Specific_precision,Ave_High_Specific_recall,Ave_Middle_Shallow_acc uracy,Ave_Middle_Shallow_F1,Ave_Middle_Shallow_precision,Ave_Middle_Shallow_recall,Ave_Middle_Normal_acc uracy,Ave_Middle_Normal_F1,Ave_Middle_Normal_precision,Ave_Middle_Normal_recall,Ave_Middle_Specific_acc uracy,Ave_Middle_Specific_F1,Ave_Middle_Specific_precision,Ave_Middle_Specific_recall,BP_High_Normal_accuracy,BP_High_Shallow_accuracy,BP_High_Specific_accuracy,BP_Low_Normal_accuracy,BP_Low_Shallow_accuracy,BP_Low_Specific_accuracy,BP_Middle_Normal_accuracy,BP_Middle_Shallow_accuracy,BP_Middle_Specific_accuracy,CC_High_Normal_accuracy,CC_High_Shallow_accuracy,CC_Low_Normal_accuracy,CC_Low_Shallow_accuracy,CC_Low_Specific_accuracy,CC_Middle_Normal_accuracy,CC_Middle_Shallow_accuracy,CC_Middle_Specific_accuracy,MF_High_Normal_accuracy,MF_High_Shallow_accuracy,MF_Low_Normal_accuracy,MF_Low_Shallow_accuracy,MF_Low_Specific_accuracy,MF_Middle_Normal_accuracy,MF_Middle_Shallow_accuracy,MF_Middle_Specific_accuracy
AAC,,0.34138,0.30391,0.49667,,0.55619,0.57619,0.54286,,0.20481,0.21166,0.26111,,0.26868,0.52383,0.22433,,0.8396,0.87365,0.81485,,,,,,0.37717,0.45613,0.3862,,0.37269,0.50185,0.4582,,0.31741,0.44639,0.35975,,0.17905,0.14867,0.24667,,0.05238,0.03333,0.13333,,0.2047,0.18707,0.25833,,0.07068,0.23256,0.06806,,0.02353,0.1837,0.01318,,0.33132,0.70598,0.2489,,0.28943,0.36449,0.30631,,0.3079,0.51589,0.30046,,0.22577,0.53039,0.20319,,0.19621,0.21405,0.21818,,0.10283,0.1759,0.15111,,0.07818,0.07218,0.14546,,0.47895,0.41408,0.56817,,0.37687,0.39256,0.4371,,,,,,0.14019,0.36365,0.1363,,0.3451,0.38727,0.39134,,0.13916,0.24372,0.20778,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,0.00517,0.06145,0.19704,0.13333,0.18,0.14722,0.24781,0.28025,0.1975,0.34331,0.50863,0.10667,0.21818,0.07273,0.37263,0.12571,0.16697,0.81195,0.23,0.54286,0.31667,0.26111,0.2706,0.38662,0.28512
APAAC,,0.57283,0.56204,0.65611,,0.74603,0.7131,0.80476,,0.64094,0.77639,0.61111,,0.41431,0.59164,0.45347,,0.82855,0.82134,0.85074,,,,,,0.5476,0.70004,0.51987,,0.52414,0.58006,0.53592,,0.38837,0.65098,0.35939,,0.31064,0.35444,0.36,,0.10819,0.078,0.22,,0.45563,0.50278,0.46667,,0.28031,0.35004,0.42729,,0.25509,0.41934,0.28892,,0.4761,0.5344,0.59243,,0.35915,0.50813,0.39249,,0.42333,0.58897,0.43961,,0.43351,0.47079,0.4963,,0.47603,0.45633,0.58182,,0.21377,0.23282,0.26222,,0.3564,0.41894,0.40909,,0.41989,0.64734,0.44896,,0.46312,0.49901,0.53571,,,,,,0.39135,0.47061,0.44016,,0.50018,0.4968,0.56312,,0.34141,0.39802,0.4415,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,0.15294,0.1518,0.22025,0.07333,0.19333,0.37222,0.27643,0.32583,0.24875,0.28219,0.28956,0.17333,0.14546,0.20182,0.37378,0.28102,0.16991,0.74457,0.2705,0.70476,0.41111,0.51111,0.39548,0.41097,0.31963
LEARNED-VEC,,0.6367,0.61625,0.71278,,0.7432,0.75238,0.74286,,0.60912,0.70778,0.61111,,0.5901,0.74242,0.5396,,0.83384,0.81981,0.85623,,,,,,0.6618,0.74728,0.64968,,0.67809,0.70486,0.67929,,0.65148,0.67325,0.66598,,0.41305,0.44445,0.48667,,0.18191,0.23278,0.20667,,0.61188,0.67139,0.59722,,0.18754,0.20285,0.17658,,0.21496,0.48652,0.1602,,0.54865,0.63405,0.50974,,0.44249,0.5567,0.42628,,0.44884,0.53484,0.44691,,0.4757,0.53296,0.47257,,0.34519,0.35303,0.38182,,0.34443,0.40911,0.38222,,0.20665,0.26788,0.20182,,0.5142,0.57498,0.55005,,0.47965,0.4917,0.49425,,,,,,0.51694,0.58897,0.50821,,0.50262,0.57398,0.49829,,0.36177,0.49657,0.36025,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,0.14386,0.1639,0.31852,0.14,0.32667,0.59722,0.3254,0.34934,0.39488,0.38098,0.48107,0.19333,0.29091,0.14727,0.39867,0.39248,0.24455,0.77873,0.4972,0.74286,0.58333,0.48889,0.53669,0.54977,0.50878
PROTVEC,,0.56481,0.58792,0.60611,,0.794,0.79762,0.80476,,0.66452,0.71944,0.66111,,0.58882,0.63865,0.60962,,0.83729,0.85037,0.83989,,,,,,0.62191,0.64165,0.68773,,0.53791,0.63841,0.63322,,0.48407,0.57039,0.51085,,0.15968,0.12422,0.25333,,0.18441,0.14556,0.3,,0.62246,0.60472,0.66667,,0.27615,0.35859,0.30517,,0.29803,0.40546,0.43828,,0.45489,0.60756,0.51724,,0.40241,0.48568,0.36912,,0.41673,0.48041,0.44065,,0.44714,0.47615,0.50261,,0.31974,0.40014,0.32727,,0.21127,0.27786,0.23333,,0.24969,0.29574,0.35273,,0.49097,0.64274,0.47815,,0.50247,0.60675,0.51493,,,,,,0.47768,0.53912,0.56843,,0.51563,0.54697,0.53718,,0.27872,0.31175,0.35408,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,0.13565,0.14469,0.18123,0.08,0.22,0.5,0.2411,0.2679,0.37417,0.29176,0.33926,0.17111,0.14546,0.11091,0.37527,0.31763,0.19089,0.78476,0.40704,0.71429,0.48889,0.51111,0.3552,0.488,0.40195
K-SEP,,0.72519,0.75,0.74056,,0.83944,0.82587,0.87619,,0.89985,0.93055,0.9,,0.69092,0.82714,0.6569,,0.88485,0.93669,0.84708,,,,,,0.82433,0.86234,0.82977,,0.8266,0.82425,0.86532,,0.78086,0.82715,0.78366,,0.51089,0.56,0.55333,,0.24794,0.20022,0.36667,,0.66424,0.73264,0.64722,,0.39184,0.50465,0.51184,,0.48962,0.59608,0.5533,,0.54663,0.69044,0.51104,,0.52953,0.64029,0.53074,,0.63781,0.69562,0.66185,,0.63327,0.71869,0.61091,,0.39941,0.48402,0.41818,,0.36429,0.46499,0.36667,,0.47395,0.49682,0.52,,0.52805,0.70699,0.53302,,0.58493,0.69354,0.60334,,,,,,0.61958,0.63806,0.70185,,0.5617,0.62103,0.62262,,0.48676,0.54962,0.54222,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,0.2616,0.16033,0.35111,0.12,0.29333,0.62222,0.49355,0.41862,0.51028,0.34207,0.32287,0.25555,0.36364,0.33455,0.40593,0.41437,0.3171,0.83007,0.59989,0.77619,0.61389,0.77778,0.66142,0.73415,0.66073
MUT2VEC,,0.46483,0.50954,0.48667,,0.57691,0.61198,0.65714,,0.45881,0.42174,0.53056,,0.52797,0.67262,0.44753,,0.75805,0.76301,0.75654,,,,,,0.55642,0.62383,0.53443,,0.62147,0.73958,0.57669,,0.62049,0.66925,0.60122,,0.25087,0.19733,0.36667,,0.12667,0.095,0.20667,,0.49871,0.59977,0.5,,0.48455,0.67051,0.396,,0.46374,0.64746,0.38574,,0.562,0.60817,0.52927,,0.46721,0.53327,0.43371,,0.49314,0.54953,0.48084,,0.49694,0.53695,0.48602,,0.37143,0.42424,0.34546,,0.23704,0.28667,0.23111,,0.49448,0.54011,0.52727,,0.54751,0.60828,0.58446,,0.53141,0.65729,0.52519,,,,,,0.53155,0.59572,0.51064,,0.53722,0.60817,0.51012,,0.44251,0.51008,0.41492,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,0.33293,0.33155,0.32873,0.1,0.33333,0.45278,0.37033,0.33146,0.36496,0.41587,0.5,0.23111,0.34546,0.30364,0.40465,0.39477,0.28804,0.72121,0.39729,0.55714,0.37222,0.43056,0.49578,0.41342,0.52232
GENE2VEC,,0.50382,0.55375,0.53889,,0.68548,0.65087,0.7381,,0.35766,0.54653,0.29167,,0.24096,0.44919,0.18572,,0.65908,0.67307,0.66499,,,,,,0.58835,0.60271,0.5898,,0.60329,0.62528,0.59597,,0.61038,0.64435,0.60769,,0.35333,0.38333,0.36,,0.34355,0.39333,0.32667,,0.45392,0.48519,0.44445,,0.40957,0.5472,0.35005,,0.38224,0.54224,0.31336,,0.45271,0.49027,0.44164,,0.49349,0.48935,0.50634,,0.54687,0.56703,0.54747,,0.51125,0.53092,0.50265,,0.4184,0.49515,0.38182,,0.40442,0.45333,0.38444,,0.45495,0.55545,0.44546,,0.54983,0.5782,0.59902,,0.49389,0.58938,0.5002,,,,,,0.54645,0.57488,0.53458,,0.67129,0.67167,0.68338,,0.47379,0.48082,0.47851,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,0.26279,0.29001,0.23407,0.24667,0.32667,0.35278,0.40471,0.3382,0.34841,0.39025,0.49374,0.32,0.34546,0.29455,0.5019,0.36803,0.27825,0.60124,0.16847,0.70476,0.43889,0.29167,0.46342,0.41767,0.46561
TCGA-EMBEDDING,,0.26602,0.25398,0.33611,,0.50857,0.55564,0.54762,,0.31432,0.30458,0.35278,,0.0,0.0,0.0,,0.6028,0.62251,0.61693,,,,,,0.33307,0.47984,0.32214,,0.33711,0.47471,0.32578,,0.38895,0.55784,0.35695,,0.31278,0.30889,0.4,,0.33702,0.40333,0.34667,,0.45602,0.46224,0.51111,,0.2156,0.37259,0.15993,,0.16098,0.29561,0.11299,,0.28174,0.53315,0.24303,,0.32195,0.39775,0.30766,,0.42765,0.55638,0.40043,,0.37089,0.42064,0.37348,,0.24499,0.28364,0.29091,,0.45098,0.50365,0.48889,,0.35498,0.43151,0.38364,,0.49228,0.55016,0.58617,,0.44855,0.48293,0.50406,,,,,,0.42495,0.59701,0.4081,,0.5795,0.6014,0.62607,,0.29886,0.51387,0.22928,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,0.11527,0.1524,0.17432,0.17333,0.17333,0.39445,0.30991,0.28455,0.35151,0.39349,0.51447,0.35778,0.23637,0.18364,0.53576,0.30035,0.21064,0.52032,0.0,0.51429,0.26111,0.28056,0.2736,0.25782,0.31305
PFAM,,0.79611,0.92852,0.76278,,0.87714,0.85754,0.90476,,0.88627,0.95,0.85833,,0.85595,0.94403,0.78987,,0.90977,0.91674,0.91108,,,,,,0.913,0.95168,0.888,,0.88293,0.93605,0.86236,,0.79412,0.9492,0.71537,,0.28667,0.34,0.26,,0.31202,0.34333,0.34,,0.51232,0.74944,0.48056,,0.59182,0.74692,0.49563,,0.65403,0.82793,0.54611,,0.65279,0.74558,0.58257,,0.71437,0.7574,0.71694,,0.5874,0.74518,0.56255,,0.70376,0.79565,0.67409,,0.49756,0.63636,0.43636,,0.50419,0.74889,0.40667,,0.39995,0.50182,0.35273,,0.71319,0.75918,0.7038,,0.6909,0.749,0.67532,,,,,,0.61953,0.73473,0.61386,,0.72912,0.82487,0.69435,,0.4907,0.74679,0.43481,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,0.5222,0.43592,0.41778,0.34,0.26,0.48056,0.53084,0.66738,0.65969,0.55804,0.60855,0.40667,0.43636,0.35273,0.68661,0.59797,0.38249,0.87836,0.77327,0.90476,0.68333,0.85833,0.8318,0.87777,0.71049
CPC-PROT,,0.52361,0.50333,0.59333,,0.79749,0.7723,0.86667,,0.59553,0.67242,0.58056,,0.61797,0.77352,0.58591,,0.86338,0.87945,0.85765,,,,,,0.63533,0.66886,0.67907,,0.57429,0.66673,0.59351,,0.62802,0.70234,0.69815,,0.35609,0.369,0.46,,0.11667,0.188,0.11333,,0.48917,0.56405,0.51944,,0.29418,0.51601,0.25949,,0.40203,0.57281,0.3708,,0.46849,0.65415,0.45885,,0.46389,0.51491,0.50656,,0.47183,0.60483,0.45747,,0.497,0.59226,0.53213,,0.32859,0.36167,0.33455,,0.31763,0.36741,0.32222,,0.32596,0.36377,0.34182,,0.55962,0.71439,0.55496,,0.53595,0.68722,0.52611,,,,,,0.49075,0.60274,0.54696,,0.55517,0.55563,0.61004,,0.36785,0.5126,0.40741,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,0.26613,0.19053,0.25363,0.07333,0.26667,0.36944,0.30661,0.32955,0.36365,0.39067,0.50107,0.3,0.24182,0.15455,0.44948,0.33011,0.20328,0.81313,0.48007,0.67143,0.38889,0.48333,0.40563,0.51148,0.39274
ESM1B,,0.68228,0.66889,0.72056,,0.86762,0.82659,0.93809,,0.86183,0.93611,0.82778,,0.78616,0.8777,0.77574,,0.91981,0.90026,0.94789,,,,,,0.81686,0.90021,0.80388,,0.87646,0.9423,0.84057,,0.84786,0.87056,0.84652,,0.356,0.45,0.34,,0.18571,0.26222,0.22,,0.52285,0.48464,0.59722,,0.57578,0.65506,0.62791,,0.67187,0.80767,0.6363,,0.5305,0.7126,0.51229,,0.55094,0.81284,0.52827,,0.70628,0.81752,0.71868,,0.69958,0.76869,0.73642,,0.56248,0.63051,0.57091,,0.38535,0.56691,0.36444,,0.58205,0.75614,0.58727,,0.73866,0.72588,0.80355,,0.68348,0.75501,0.70892,,,,,,0.7005,0.80327,0.74449,,0.72064,0.77008,0.72449,,0.50514,0.6022,0.54967,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,0.53659,0.39284,0.33383,0.15333,0.3,0.5,0.55089,0.41095,0.5581,0.43335,0.53247,0.27555,0.51636,0.40364,0.59787,0.5527,0.43369,0.86023,0.70955,0.77143,0.65833,0.80278,0.81408,0.72603,0.78307
BERT-BFD,,0.82337,0.8007,0.86278,,0.74698,0.73254,0.77143,,0.88395,0.95648,0.85,,0.83441,0.90541,0.78409,,0.92685,0.92839,0.92645,,,,,,0.87619,0.90152,0.86381,,0.87285,0.89893,0.86561,,0.82082,0.85757,0.80967,,0.51686,0.55667,0.54667,,0.35733,0.55778,0.32,,0.69544,0.66359,0.74167,,0.54463,0.73023,0.47292,,0.65307,0.77909,0.57944,,0.65314,0.69569,0.63654,,0.64618,0.73711,0.61252,,0.72293,0.79811,0.69873,,0.71461,0.77796,0.69624,,0.56459,0.66818,0.53636,,0.62191,0.67056,0.64667,,0.4023,0.44,0.41636,,0.71224,0.81005,0.70602,,0.66161,0.79098,0.64153,,,,,,0.72659,0.78155,0.73706,,0.71325,0.77725,0.70506,,0.57427,0.61422,0.58978,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,0.5193,0.41362,0.43409,0.24667,0.42667,0.59167,0.60503,0.52375,0.61977,0.53739,0.59329,0.51778,0.46182,0.24727,0.62506,0.64029,0.4265,0.90656,0.7608,0.5,0.75556,0.82778,0.81408,0.81183,0.75675
BERT-PFAM,,0.80089,0.805,0.81778,,0.84127,0.84643,0.84286,,0.84791,0.89325,0.85278,,0.79589,0.80244,0.80839,,0.90155,0.88749,0.9265,,,,,,0.85521,0.90337,0.83122,,0.8621,0.86062,0.8795,,0.86806,0.87652,0.86742,,0.33508,0.39333,0.33333,,0.33667,0.47778,0.3,,0.76826,0.74722,0.81389,,0.42723,0.5515,0.42617,,0.52803,0.59847,0.60503,,0.53251,0.67317,0.52944,,0.57133,0.63635,0.57993,,0.65795,0.74784,0.62934,,0.65921,0.68655,0.70106,,0.49206,0.56243,0.50182,,0.52408,0.6137,0.52,,0.49822,0.68251,0.49091,,0.62975,0.69678,0.65629,,0.61529,0.71027,0.60002,,,,,,0.68245,0.76134,0.65085,,0.68569,0.73741,0.67917,,0.52134,0.51807,0.55899,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,0.30475,0.23688,0.32782,0.22667,0.33333,0.71667,0.55968,0.43469,0.5024,0.40085,0.41117,0.47556,0.44727,0.41636,0.55263,0.55501,0.35529,0.83398,0.67471,0.84286,0.77778,0.73056,0.78591,0.78213,0.8303