Upload classificaiton model training statistics files

classification_models/classification_models/bert/train_stats.csv

@@ -0,0 +1,11 @@
+epoch,train_precision,train_recall,train_f1,train_loss,val_precision,val_recall,val_f1,val_loss,model_name
+0,0.9784172661870504,0.7101827676240209,0.8229954614220877,0.014274507041776904,0.92,0.575,0.7076923076923077,0.018498835089446615,bert-base-uncased
+1,0.9889807162534435,0.9373368146214099,0.9624664879356568,0.004624721559661406,0.8611111111111112,0.775,0.8157894736842106,0.02008061437229128,bert-base-uncased
+2,0.943069306930693,0.9947780678851175,0.9682337992376112,0.003600402364185868,0.7,0.875,0.7777777777777777,0.03036006969991345,bert-base-uncased
+3,1.0,1.0,1.0,0.00014941123583177185,0.7857142857142857,0.825,0.8048780487804876,0.0263319234305161,bert-base-uncased
+4,1.0,1.0,1.0,0.0002503720688442072,0.8611111111111112,0.775,0.8157894736842106,0.02472542502489761,bert-base-uncased
+5,1.0,1.0,1.0,5.175392756237112e-05,0.7555555555555555,0.85,0.7999999999999998,0.027412922202123317,bert-base-uncased
+6,1.0,1.0,1.0,3.3308245396495476e-05,0.7727272727272727,0.85,0.8095238095238095,0.029207995125903812,bert-base-uncased
+7,1.0,1.0,1.0,2.4941893463434727e-05,0.7727272727272727,0.85,0.8095238095238095,0.030616155597117712,bert-base-uncased
+8,1.0,1.0,1.0,1.9725642449676057e-05,0.7727272727272727,0.85,0.8095238095238095,0.03180020536700961,bert-base-uncased
+9,1.0,1.0,1.0,1.6138146942777896e-05,0.7727272727272727,0.85,0.8095238095238095,0.03282834709319579,bert-base-uncased

classification_models/classification_models/best/best_checkpt.txt

@@ -0,0 +1 @@
+out/classif_train_out/biomed_roberta_rct500/checkpt.pt

classification_models/classification_models/biobert/train_stats.csv

@@ -0,0 +1,11 @@
+epoch,train_precision,train_recall,train_f1,train_loss,val_precision,val_recall,val_f1,val_loss,model_name
+0,0.7239382239382239,0.97911227154047,0.832408435072142,0.01817139005912299,0.6153846153846154,1.0,0.761904761904762,0.025600876120276422,dmis-lab/biobert-v1.1
+1,0.9512820512820512,0.9686684073107049,0.9598965071151357,0.004280440020540082,0.8,0.8,0.8000000000000002,0.014763055826133152,dmis-lab/biobert-v1.1
+2,1.0,0.9686684073107049,0.9840848806366048,0.0024200166264435876,0.9310344827586207,0.675,0.7826086956521738,0.026663977433136612,dmis-lab/biobert-v1.1
+3,1.0,0.9895561357702349,0.994750656167979,0.0009970445728253857,0.9310344827586207,0.675,0.7826086956521738,0.023675157960926025,dmis-lab/biobert-v1.1
+4,0.9973958333333334,1.0,0.998696219035202,0.00024732730325334907,0.7857142857142857,0.825,0.8048780487804876,0.02356158010222299,dmis-lab/biobert-v1.1
+5,1.0,1.0,1.0,0.00010623420357309322,0.8205128205128205,0.8,0.810126582278481,0.023674944550408132,dmis-lab/biobert-v1.1
+6,1.0,1.0,1.0,5.139963606143498e-05,0.9090909090909091,0.75,0.821917808219178,0.026155920379279687,dmis-lab/biobert-v1.1
+7,1.0,1.0,1.0,3.8080539161169135e-05,0.8611111111111112,0.775,0.8157894736842106,0.026953387733127148,dmis-lab/biobert-v1.1
+8,1.0,1.0,1.0,3.008640652806465e-05,0.8378378378378378,0.775,0.8051948051948051,0.027731853440248717,dmis-lab/biobert-v1.1
+9,1.0,1.0,1.0,2.463689066397747e-05,0.8378378378378378,0.775,0.8051948051948051,0.028430018061113033,dmis-lab/biobert-v1.1

classification_models/classification_models/bioelectra/train_stats.csv

@@ -0,0 +1,11 @@
+epoch,train_precision,train_recall,train_f1,train_loss,val_precision,val_recall,val_f1,val_loss,model_name
+0,0.9528023598820059,0.8433420365535248,0.8947368421052633,0.01044820745198909,0.90625,0.725,0.8055555555555555,0.01638859953239279,kamalkraj/bioelectra-base-discriminator-pubmed
+1,0.9150485436893204,0.9843342036553525,0.9484276729559749,0.006237994696742395,0.7291666666666666,0.875,0.7954545454545454,0.020158969849910377,kamalkraj/bioelectra-base-discriminator-pubmed
+2,0.9477611940298507,0.9947780678851175,0.9707006369426752,0.0033580961518306683,0.7391304347826086,0.85,0.7906976744186046,0.02404100606042259,kamalkraj/bioelectra-base-discriminator-pubmed
+3,0.9455445544554455,0.9973890339425587,0.9707750952986023,0.0026517638641609933,0.6666666666666666,0.85,0.7472527472527473,0.03310222544197766,kamalkraj/bioelectra-base-discriminator-pubmed
+4,0.9973614775725593,0.9869451697127938,0.9921259842519685,0.0014082801262602221,0.8611111111111112,0.775,0.8157894736842106,0.022815853661898547,kamalkraj/bioelectra-base-discriminator-pubmed
+5,1.0,0.9973890339425587,0.9986928104575163,0.0005542292834646337,0.8048780487804879,0.825,0.8148148148148149,0.021040026426502743,kamalkraj/bioelectra-base-discriminator-pubmed
+6,1.0,0.9973890339425587,0.9986928104575163,0.00045303577851501153,0.8095238095238095,0.85,0.8292682926829269,0.023888022237627198,kamalkraj/bioelectra-base-discriminator-pubmed
+7,1.0,0.9973890339425587,0.9986928104575163,0.00042411089299424274,0.8095238095238095,0.85,0.8292682926829269,0.024852557845835416,kamalkraj/bioelectra-base-discriminator-pubmed
+8,1.0,0.9973890339425587,0.9986928104575163,0.00041047544624081057,0.8095238095238095,0.85,0.8292682926829269,0.025370661684739514,kamalkraj/bioelectra-base-discriminator-pubmed
+9,1.0,0.9973890339425587,0.9986928104575163,0.0004062545524324438,0.8095238095238095,0.85,0.8292682926829269,0.025555496439396305,kamalkraj/bioelectra-base-discriminator-pubmed

classification_models/classification_models/bioelectra_pmc/train_stats.csv

@@ -0,0 +1,11 @@
+epoch,train_precision,train_recall,train_f1,train_loss,val_precision,val_recall,val_f1,val_loss,model_name
+0,0.9775280898876404,0.6814621409921671,0.803076923076923,0.00987104386373051,0.9130434782608695,0.525,0.6666666666666667,0.012947645389808799,kamalkraj/bioelectra-base-discriminator-pubmed-pmc
+1,0.9644808743169399,0.9216710182767625,0.9425901201602136,0.0037882313017797245,0.7692307692307693,0.75,0.7594936708860761,0.011044292798582113,kamalkraj/bioelectra-base-discriminator-pubmed-pmc
+2,0.9867724867724867,0.9738903394255874,0.9802890932982918,0.0016966263130248486,0.8,0.8,0.8000000000000002,0.009887880499257982,kamalkraj/bioelectra-base-discriminator-pubmed-pmc
+3,0.9947368421052631,0.9869451697127938,0.9908256880733946,0.0008505548205934142,0.7804878048780488,0.8,0.7901234567901235,0.010257520109602491,kamalkraj/bioelectra-base-discriminator-pubmed-pmc
+4,1.0,0.9895561357702349,0.994750656167979,0.00042289157799489863,0.723404255319149,0.85,0.7816091954022989,0.013598124654787892,kamalkraj/bioelectra-base-discriminator-pubmed-pmc
+5,1.0,0.9895561357702349,0.994750656167979,0.0002009521190435211,0.8571428571428571,0.75,0.7999999999999999,0.01199851208512888,kamalkraj/bioelectra-base-discriminator-pubmed-pmc
+6,1.0,1.0,1.0,0.0001222710319632522,0.8048780487804879,0.825,0.8148148148148149,0.012929303091277116,kamalkraj/bioelectra-base-discriminator-pubmed-pmc
+7,1.0,1.0,1.0,9.563790452266604e-05,0.7857142857142857,0.825,0.8048780487804876,0.013420297102358356,kamalkraj/bioelectra-base-discriminator-pubmed-pmc
+8,1.0,1.0,1.0,8.425928776683043e-05,0.7857142857142857,0.825,0.8048780487804876,0.013671552047789472,kamalkraj/bioelectra-base-discriminator-pubmed-pmc
+9,1.0,1.0,1.0,8.080499151309143e-05,0.7857142857142857,0.825,0.8048780487804876,0.013759159442013915,kamalkraj/bioelectra-base-discriminator-pubmed-pmc

classification_models/classification_models/biomed_roberta/train_stats.csv

@@ -0,0 +1,11 @@
+epoch,train_precision,train_recall,train_f1,train_loss,val_precision,val_recall,val_f1,val_loss,model_name
+0,0.9324324324324325,0.9007832898172323,0.9163346613545816,0.009458284904348089,0.8157894736842105,0.775,0.7948717948717949,0.01896833876768748,allenai/biomed_roberta_base
+1,0.9425,0.9843342036553525,0.962962962962963,0.005114003262204434,0.7391304347826086,0.85,0.7906976744186046,0.02214574270278403,allenai/biomed_roberta_base
+2,0.8721461187214612,0.9973890339425587,0.930572472594397,0.007529971991952617,0.660377358490566,0.875,0.7526881720430108,0.031182770869173343,allenai/biomed_roberta_base
+3,0.9973544973544973,0.9843342036553525,0.9908015768725361,0.001354287135017738,0.8823529411764706,0.75,0.8108108108108107,0.027826228249326068,allenai/biomed_roberta_base
+4,0.9973614775725593,0.9869451697127938,0.9921259842519685,0.0005968241960891296,0.9117647058823529,0.775,0.8378378378378379,0.02560800286969053,allenai/biomed_roberta_base
+5,0.9973684210526316,0.9895561357702349,0.9934469200524246,0.0007260245411110773,0.8611111111111112,0.775,0.8157894736842106,0.02706009274350081,allenai/biomed_roberta_base
+6,0.9948051948051948,1.0,0.9973958333333334,0.0002773666454473961,0.8,0.8,0.8000000000000002,0.02885508235198381,allenai/biomed_roberta_base
+7,1.0,1.0,1.0,4.4769566775673165e-05,0.8205128205128205,0.8,0.810126582278481,0.030124010336614628,allenai/biomed_roberta_base
+8,1.0,1.0,1.0,2.552156209181686e-05,0.8205128205128205,0.8,0.810126582278481,0.031779318319050794,allenai/biomed_roberta_base
+9,1.0,1.0,1.0,2.0499527945173677e-05,0.8205128205128205,0.8,0.810126582278481,0.03267021124297314,allenai/biomed_roberta_base

classification_models/classification_models/biomed_roberta_chemprot/train_stats.csv

@@ -0,0 +1,11 @@
+epoch,train_precision,train_recall,train_f1,train_loss,val_precision,val_recall,val_f1,val_loss,model_name
+0,0.959375,0.8015665796344648,0.8733997155049786,0.011171913088553998,0.8484848484848485,0.7,0.7671232876712328,0.018006028267759946,allenai/dsp_roberta_base_dapt_biomed_tapt_chemprot_4169
+1,0.9637305699481865,0.9712793733681462,0.9674902470741222,0.003704582916028134,0.775,0.775,0.775,0.020442303480967036,allenai/dsp_roberta_base_dapt_biomed_tapt_chemprot_4169
+2,0.9597989949748744,0.9973890339425587,0.9782330345710627,0.0025039945328732918,0.72,0.9,0.7999999999999999,0.03144788168042711,allenai/dsp_roberta_base_dapt_biomed_tapt_chemprot_4169
+3,0.9895287958115183,0.9869451697127938,0.9882352941176471,0.001455927347482554,0.8333333333333334,0.75,0.7894736842105262,0.02755550272343973,allenai/dsp_roberta_base_dapt_biomed_tapt_chemprot_4169
+4,0.9695431472081218,0.9973890339425587,0.9832689832689833,0.0016717212987473636,0.7555555555555555,0.85,0.7999999999999998,0.026489118801623163,allenai/dsp_roberta_base_dapt_biomed_tapt_chemprot_4169
+5,1.0,0.9712793733681462,0.9854304635761589,0.0014181794299908464,0.90625,0.725,0.8055555555555555,0.030412140825496835,allenai/dsp_roberta_base_dapt_biomed_tapt_chemprot_4169
+6,1.0,0.9451697127937336,0.9718120805369127,0.002702542108053729,0.9333333333333333,0.7,0.8,0.03451636811768132,allenai/dsp_roberta_base_dapt_biomed_tapt_chemprot_4169
+7,1.0,0.9973890339425587,0.9986928104575163,0.00011697316976096056,0.825,0.825,0.825,0.029361976673951046,allenai/dsp_roberta_base_dapt_biomed_tapt_chemprot_4169
+8,0.9973958333333334,1.0,0.998696219035202,7.570717397341879e-05,0.7857142857142857,0.825,0.8048780487804876,0.034216466729357874,allenai/dsp_roberta_base_dapt_biomed_tapt_chemprot_4169
+9,1.0,1.0,1.0,1.4980794216353532e-05,0.8461538461538461,0.825,0.8354430379746836,0.034351127735707386,allenai/dsp_roberta_base_dapt_biomed_tapt_chemprot_4169

classification_models/classification_models/biomed_roberta_rct500/train_stats.csv

@@ -0,0 +1,11 @@
+epoch,train_precision,train_recall,train_f1,train_loss,val_precision,val_recall,val_f1,val_loss,model_name
+0,0.8911392405063291,0.9190600522193212,0.9048843187660669,0.01112631017634303,0.7441860465116279,0.8,0.7710843373493975,0.01607008360373149,allenai/dsp_roberta_base_dapt_biomed_tapt_rct_500
+1,0.8613636363636363,0.9895561357702349,0.9210206561360874,0.009340718431123793,0.6481481481481481,0.875,0.7446808510638299,0.022833876452356013,allenai/dsp_roberta_base_dapt_biomed_tapt_rct_500
+2,0.9920634920634921,0.97911227154047,0.985545335085414,0.001660655381251934,0.8421052631578947,0.8,0.8205128205128205,0.025070766710424387,allenai/dsp_roberta_base_dapt_biomed_tapt_rct_500
+3,0.9895833333333334,0.9921671018276762,0.9908735332464147,0.0011368487326580945,0.7857142857142857,0.825,0.8048780487804876,0.024920535421748675,allenai/dsp_roberta_base_dapt_biomed_tapt_rct_500
+4,0.9920844327176781,0.9817232375979112,0.9868766404199475,0.0016189292562212515,0.8888888888888888,0.8,0.8421052631578948,0.025865392525147343,allenai/dsp_roberta_base_dapt_biomed_tapt_rct_500
+5,0.9972677595628415,0.9530026109660574,0.9746328437917223,0.0027853340157098522,0.9393939393939394,0.775,0.8493150684931509,0.023250331797596044,allenai/dsp_roberta_base_dapt_biomed_tapt_rct_500
+6,0.9947916666666666,0.9973890339425587,0.9960886571056062,0.0006795547146847731,0.8292682926829268,0.85,0.8395061728395061,0.02296917518943478,allenai/dsp_roberta_base_dapt_biomed_tapt_rct_500
+7,1.0,0.9973890339425587,0.9986928104575163,0.00016438546199703822,0.85,0.85,0.85,0.02628602145339286,allenai/dsp_roberta_base_dapt_biomed_tapt_rct_500
+8,1.0,0.9973890339425587,0.9986928104575163,0.0001107595671611193,0.868421052631579,0.825,0.8461538461538461,0.028414694844955964,allenai/dsp_roberta_base_dapt_biomed_tapt_rct_500
+9,1.0,0.9973890339425587,0.9986928104575163,8.120022795234284e-05,0.868421052631579,0.825,0.8461538461538461,0.029183639874410926,allenai/dsp_roberta_base_dapt_biomed_tapt_rct_500

classification_models/classification_models/bluebert/train_stats.csv

@@ -0,0 +1,11 @@
+epoch,train_precision,train_recall,train_f1,train_loss,val_precision,val_recall,val_f1,val_loss,model_name
+0,0.9316939890710383,0.8903394255874674,0.910547396528705,0.009720431122608876,0.775,0.775,0.775,0.018403979498635297,bionlp/bluebert_pubmed_uncased_L-12_H-768_A-12
+1,0.9422110552763819,0.97911227154047,0.9603072983354674,0.004952065753798206,0.7446808510638298,0.875,0.8045977011494252,0.023243539175897273,bionlp/bluebert_pubmed_uncased_L-12_H-768_A-12
+2,0.9868766404199475,0.9817232375979112,0.9842931937172776,0.002305545422877497,0.7435897435897436,0.725,0.7341772151898733,0.02685006886556651,bionlp/bluebert_pubmed_uncased_L-12_H-768_A-12
+3,1.0,0.9712793733681462,0.9854304635761589,0.0019362409682790298,0.8285714285714286,0.725,0.7733333333333333,0.0274028305254244,bionlp/bluebert_pubmed_uncased_L-12_H-768_A-12
+4,0.9973890339425587,0.9973890339425587,0.9973890339425587,0.0005778398203690683,0.717391304347826,0.825,0.7674418604651162,0.028982650629192027,bionlp/bluebert_pubmed_uncased_L-12_H-768_A-12
+5,1.0,1.0,1.0,0.00024053492094188272,0.7333333333333333,0.825,0.776470588235294,0.03376434533710375,bionlp/bluebert_pubmed_uncased_L-12_H-768_A-12
+6,1.0,1.0,1.0,0.00013427306084040115,0.775,0.775,0.775,0.034661604544007275,bionlp/bluebert_pubmed_uncased_L-12_H-768_A-12
+7,1.0,1.0,1.0,0.00010921231882354586,0.775,0.775,0.775,0.03569693344648131,bionlp/bluebert_pubmed_uncased_L-12_H-768_A-12
+8,1.0,1.0,1.0,9.770086264477014e-05,0.775,0.775,0.775,0.036310342414328046,bionlp/bluebert_pubmed_uncased_L-12_H-768_A-12
+9,1.0,1.0,1.0,9.435002507283768e-05,0.775,0.775,0.775,0.036523135637413454,bionlp/bluebert_pubmed_uncased_L-12_H-768_A-12

classification_models/classification_models/bluebert_mimic3/train_stats.csv

@@ -0,0 +1,11 @@
+epoch,train_precision,train_recall,train_f1,train_loss,val_precision,val_recall,val_f1,val_loss,model_name
+0,0.7700892857142857,0.9007832898172323,0.8303249097472922,0.008987150152806132,0.6363636363636364,0.875,0.7368421052631579,0.011411330609951378,bionlp/bluebert_pubmed_mimic_uncased_L-12_H-768_A-12
+1,0.8894348894348895,0.9451697127937336,0.9164556962025316,0.004715619056865021,0.6875,0.825,0.75,0.011580637041127906,bionlp/bluebert_pubmed_mimic_uncased_L-12_H-768_A-12
+2,0.9833795013850416,0.9268929503916449,0.9543010752688172,0.0023050950810759438,0.8285714285714286,0.725,0.7733333333333333,0.01035606936088898,bionlp/bluebert_pubmed_mimic_uncased_L-12_H-768_A-12
+3,0.9921259842519685,0.9869451697127938,0.9895287958115184,0.0009344734671291543,0.8157894736842105,0.775,0.7948717948717949,0.01192060281645577,bionlp/bluebert_pubmed_mimic_uncased_L-12_H-768_A-12
+4,1.0,0.9947780678851175,0.9973821989528796,0.0003406010594562436,0.6888888888888889,0.775,0.7294117647058822,0.014174019015810025,bionlp/bluebert_pubmed_mimic_uncased_L-12_H-768_A-12
+5,1.0,0.9973890339425587,0.9986928104575163,0.00016091443643038484,0.775,0.775,0.775,0.016508410374323528,bionlp/bluebert_pubmed_mimic_uncased_L-12_H-768_A-12
+6,1.0,0.9973890339425587,0.9986928104575163,9.81492054787405e-05,0.7111111111111111,0.8,0.7529411764705882,0.01787827618466983,bionlp/bluebert_pubmed_mimic_uncased_L-12_H-768_A-12
+7,1.0,0.9973890339425587,0.9986928104575163,5.37390858936729e-05,0.7619047619047619,0.8,0.7804878048780488,0.018389434559540178,bionlp/bluebert_pubmed_mimic_uncased_L-12_H-768_A-12
+8,1.0,1.0,1.0,2.6995710758132737e-05,0.7804878048780488,0.8,0.7901234567901235,0.019080186040146545,bionlp/bluebert_pubmed_mimic_uncased_L-12_H-768_A-12
+9,1.0,1.0,1.0,1.873862159961704e-05,0.7692307692307693,0.75,0.7594936708860761,0.019736994175041246,bionlp/bluebert_pubmed_mimic_uncased_L-12_H-768_A-12

classification_models/classification_models/electramed/train_stats.csv

@@ -0,0 +1,11 @@
+epoch,train_precision,train_recall,train_f1,train_loss,val_precision,val_recall,val_f1,val_loss,model_name
+0,0.9182561307901907,0.8798955613577023,0.8986666666666666,0.01239368502693537,0.7631578947368421,0.725,0.7435897435897436,0.022117931231762627,giacomomiolo/electramed_base_scivocab_1M
+1,0.9282178217821783,0.97911227154047,0.9529860228716646,0.006328433326396349,0.7083333333333334,0.85,0.7727272727272727,0.019559468945148605,giacomomiolo/electramed_base_scivocab_1M
+2,0.9920844327176781,0.9817232375979112,0.9868766404199475,0.0019137250946451587,0.8285714285714286,0.725,0.7733333333333333,0.02737125280787641,giacomomiolo/electramed_base_scivocab_1M
+3,0.9973614775725593,0.9869451697127938,0.9921259842519685,0.0010245115020282279,0.8648648648648649,0.8,0.8311688311688312,0.027179485264544685,giacomomiolo/electramed_base_scivocab_1M
+4,0.9973958333333334,1.0,0.998696219035202,0.0007772715169631115,0.8421052631578947,0.8,0.8205128205128205,0.023403996475767228,giacomomiolo/electramed_base_scivocab_1M
+5,1.0,1.0,1.0,0.00018997244631183182,0.868421052631579,0.825,0.8461538461538461,0.027065005978575245,giacomomiolo/electramed_base_scivocab_1M
+6,1.0,1.0,1.0,0.0002256837288002866,0.8048780487804879,0.825,0.8148148148148149,0.02863387482931966,giacomomiolo/electramed_base_scivocab_1M
+7,1.0,1.0,1.0,0.00011905320816202906,0.8461538461538461,0.825,0.8354430379746836,0.029973150715275825,giacomomiolo/electramed_base_scivocab_1M
+8,1.0,1.0,1.0,0.00010507098332867965,0.8461538461538461,0.825,0.8354430379746836,0.030594172754248826,giacomomiolo/electramed_base_scivocab_1M
+9,1.0,1.0,1.0,0.00010099924910539091,0.8461538461538461,0.825,0.8354430379746836,0.030787097773025598,giacomomiolo/electramed_base_scivocab_1M

classification_models/classification_models/pubmedbert/train_stats.csv

@@ -0,0 +1,11 @@
+epoch,train_precision,train_recall,train_f1,train_loss,val_precision,val_recall,val_f1,val_loss,model_name
+0,0.9054726368159204,0.9503916449086162,0.9273885350318471,0.00839552013797963,0.7083333333333334,0.85,0.7727272727272727,0.015265736283746155,microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract
+1,0.9313725490196079,0.9921671018276762,0.9608091024020228,0.004351030023866887,0.72,0.9,0.7999999999999999,0.018542591236391157,microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract
+2,0.9947643979057592,0.9921671018276762,0.9934640522875817,0.0009955423226333433,0.8205128205128205,0.8,0.810126582278481,0.024405019581112894,microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract
+3,1.0,0.9608355091383812,0.9800266311584555,0.0024627792050656875,0.896551724137931,0.65,0.7536231884057972,0.029280409299616214,microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract
+4,1.0,0.9921671018276762,0.9960681520314547,0.000821842120023161,0.90625,0.725,0.8055555555555555,0.024563445849490568,microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract
+5,1.0,1.0,1.0,0.00010548271317698408,0.8292682926829268,0.85,0.8395061728395061,0.02454672244841631,microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract
+6,1.0,1.0,1.0,5.952719475804638e-05,0.8918918918918919,0.825,0.8571428571428571,0.025383336780704088,microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract
+7,1.0,1.0,1.0,4.82193034751762e-05,0.8918918918918919,0.825,0.8571428571428571,0.026037779551200017,microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract
+8,1.0,1.0,1.0,4.306133561110795e-05,0.8918918918918919,0.825,0.8571428571428571,0.02642081679835617,microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract
+9,1.0,1.0,1.0,4.150422162543674e-05,0.8918918918918919,0.825,0.8571428571428571,0.026552919484565105,microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract

classification_models/classification_models/pubmedbert_fulltext/train_stats.csv

@@ -0,0 +1,11 @@
+epoch,train_precision,train_recall,train_f1,train_loss,val_precision,val_recall,val_f1,val_loss,model_name
+0,0.8151447661469933,0.9556135770234987,0.8798076923076923,0.006913787078397118,0.6727272727272727,0.925,0.7789473684210527,0.01173496293196888,microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext
+1,0.975609756097561,0.9399477806788512,0.9574468085106382,0.0023269604963461086,0.868421052631579,0.825,0.8461538461538461,0.007677861495212939,microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext
+2,1.0,0.9921671018276762,0.9960681520314547,0.0006114699209213163,0.8536585365853658,0.875,0.8641975308641976,0.0073124838981238555,microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext
+3,0.9973890339425587,0.9973890339425587,0.9973890339425587,0.0002519216271406487,0.8,0.9,0.8470588235294118,0.009077838358451735,microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext
+4,1.0,0.9973890339425587,0.9986928104575163,0.00015439989455880919,0.8571428571428571,0.9,0.8780487804878048,0.010174539461497616,microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext
+5,1.0,0.9973890339425587,0.9986928104575163,7.890069298005837e-05,0.85,0.85,0.85,0.010329574205965366,microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext
+6,1.0,1.0,1.0,5.760939798770668e-05,0.85,0.85,0.85,0.010606441107935875,microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext
+7,1.0,1.0,1.0,4.772710740688081e-05,0.85,0.85,0.85,0.010831480271786265,microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext
+8,1.0,1.0,1.0,4.3163261537046015e-05,0.85,0.85,0.85,0.010970377743993915,microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext
+9,1.0,1.0,1.0,4.183565290465693e-05,0.85,0.85,0.85,0.011019794446117472,microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext

classification_models/classification_models/sapbert/train_stats.csv

@@ -0,0 +1,11 @@
+epoch,train_precision,train_recall,train_f1,train_loss,val_precision,val_recall,val_f1,val_loss,model_name
+0,0.9032258064516129,0.9503916449086162,0.926208651399491,0.009085559617167293,0.7608695652173914,0.875,0.813953488372093,0.014680154996473084,cambridgeltl/SapBERT-from-PubMedBERT-fulltext
+1,0.9223300970873787,0.9921671018276762,0.9559748427672956,0.005330197491086403,0.7450980392156863,0.95,0.8351648351648352,0.018500579368768248,cambridgeltl/SapBERT-from-PubMedBERT-fulltext
+2,0.9869791666666666,0.9895561357702349,0.9882659713168188,0.0014565228526770388,0.868421052631579,0.825,0.8461538461538461,0.017544608612972423,cambridgeltl/SapBERT-from-PubMedBERT-fulltext
+3,1.0,0.9373368146214099,0.967654986522911,0.003874751368766523,0.896551724137931,0.65,0.7536231884057972,0.026013132887628843,cambridgeltl/SapBERT-from-PubMedBERT-fulltext
+4,1.0,1.0,1.0,0.00020296675875236943,0.875,0.875,0.875,0.018033074280949978,cambridgeltl/SapBERT-from-PubMedBERT-fulltext
+5,1.0,1.0,1.0,8.448641662837437e-05,0.875,0.875,0.875,0.021496605871204263,cambridgeltl/SapBERT-from-PubMedBERT-fulltext
+6,1.0,1.0,1.0,5.610443015382504e-05,0.8974358974358975,0.875,0.8860759493670887,0.02243567321708707,cambridgeltl/SapBERT-from-PubMedBERT-fulltext
+7,1.0,1.0,1.0,4.216413999543657e-05,0.8974358974358975,0.875,0.8860759493670887,0.023475026533537714,cambridgeltl/SapBERT-from-PubMedBERT-fulltext
+8,1.0,1.0,1.0,3.331892964429419e-05,0.8974358974358975,0.875,0.8860759493670887,0.024344896627136115,cambridgeltl/SapBERT-from-PubMedBERT-fulltext
+9,1.0,1.0,1.0,2.721993097965e-05,0.8974358974358975,0.875,0.8860759493670887,0.02510008983513188,cambridgeltl/SapBERT-from-PubMedBERT-fulltext

classification_models/classification_models/sapbert_mean_token/train_stats.csv

@@ -0,0 +1,11 @@
+epoch,train_precision,train_recall,train_f1,train_loss,val_precision,val_recall,val_f1,val_loss,model_name
+0,0.8044943820224719,0.9347258485639687,0.8647342995169082,0.006912974002231661,0.6851851851851852,0.925,0.7872340425531915,0.009360696956421595,cambridgeltl/SapBERT-from-PubMedBERT-fulltext-mean-token
+1,0.9721448467966574,0.9112271540469974,0.9407008086253369,0.0034070002491944787,0.90625,0.725,0.8055555555555555,0.007293704264568833,cambridgeltl/SapBERT-from-PubMedBERT-fulltext-mean-token
+2,0.9973544973544973,0.9843342036553525,0.9908015768725361,0.0010259501273480337,0.9117647058823529,0.775,0.8378378378378379,0.00767672746061529,cambridgeltl/SapBERT-from-PubMedBERT-fulltext-mean-token
+3,1.0,0.9973890339425587,0.9986928104575163,0.00032081948211629433,0.8461538461538461,0.825,0.8354430379746836,0.008524248341344437,cambridgeltl/SapBERT-from-PubMedBERT-fulltext-mean-token
+4,1.0,1.0,1.0,0.00011066371854614845,0.8333333333333334,0.875,0.8536585365853658,0.010044077563585725,cambridgeltl/SapBERT-from-PubMedBERT-fulltext-mean-token
+5,1.0,1.0,1.0,6.788832001928226e-05,0.7954545454545454,0.875,0.8333333333333334,0.011806525008858374,cambridgeltl/SapBERT-from-PubMedBERT-fulltext-mean-token
+6,1.0,1.0,1.0,3.709093445744674e-05,0.8461538461538461,0.825,0.8354430379746836,0.01119547023338342,cambridgeltl/SapBERT-from-PubMedBERT-fulltext-mean-token
+7,1.0,1.0,1.0,2.8715360463120577e-05,0.8292682926829268,0.85,0.8395061728395061,0.011535523447600551,cambridgeltl/SapBERT-from-PubMedBERT-fulltext-mean-token
+8,1.0,1.0,1.0,2.327173428317874e-05,0.8292682926829268,0.85,0.8395061728395061,0.011788438888465834,cambridgeltl/SapBERT-from-PubMedBERT-fulltext-mean-token
+9,1.0,1.0,1.0,1.942019583400518e-05,0.8292682926829268,0.85,0.8395061728395061,0.01202217419192476,cambridgeltl/SapBERT-from-PubMedBERT-fulltext-mean-token

classification_models/classification_models/scibert/train_stats.csv

@@ -0,0 +1,11 @@
+epoch,train_precision,train_recall,train_f1,train_loss,val_precision,val_recall,val_f1,val_loss,model_name
+0,0.9152119700748129,0.95822454308094,0.9362244897959184,0.007909696801639712,0.7954545454545454,0.875,0.8333333333333334,0.014211524910521958,allenai/scibert_scivocab_uncased
+1,0.9180722891566265,0.9947780678851175,0.9548872180451128,0.00488481078725499,0.7,0.875,0.7777777777777777,0.019092032955315127,allenai/scibert_scivocab_uncased
+2,0.9921875,0.9947780678851175,0.9934810951760104,0.0009244462695167972,0.7608695652173914,0.875,0.813953488372093,0.023895333846152392,allenai/scibert_scivocab_uncased
+3,1.0,0.9216710182767625,0.9592391304347826,0.005162166425445645,0.9032258064516129,0.7,0.7887323943661972,0.031492474058396974,allenai/scibert_scivocab_uncased
+4,1.0,0.9373368146214099,0.967654986522911,0.002573705199167244,0.9333333333333333,0.7,0.8,0.027869759211697435,allenai/scibert_scivocab_uncased
+5,0.9871134020618557,1.0,0.993514915693904,0.0009337401260560197,0.7659574468085106,0.9,0.8275862068965516,0.03007823364727152,allenai/scibert_scivocab_uncased
+6,1.0,0.9660574412532638,0.9827357237715804,0.002005338796843401,0.8571428571428571,0.75,0.7999999999999999,0.03205650251134703,allenai/scibert_scivocab_uncased
+7,0.9921671018276762,0.9921671018276762,0.9921671018276762,0.0008296812519392951,0.7857142857142857,0.825,0.8048780487804876,0.0349798135885181,allenai/scibert_scivocab_uncased
+8,1.0,0.9973890339425587,0.9986928104575163,0.00040162273187177816,0.8421052631578947,0.8,0.8205128205128205,0.03452008556349074,allenai/scibert_scivocab_uncased
+9,0.9973544973544973,0.9843342036553525,0.9908015768725361,0.0011678959125322836,0.8857142857142857,0.775,0.8266666666666667,0.03328900252624104,allenai/scibert_scivocab_uncased