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added_tokens.json

@@ -0,0 +1,3078 @@
+{
+  "<boi>": 35074,
+  "<bom>": 35071,
+  "<bop>": 35066,
+  "<eoi>": 35073,
+  "<eom>": 35067,
+  "<eop>": 35063,
+  "<extra_id_0>": 32099,
+  "<extra_id_10>": 32089,
+  "<extra_id_11>": 32088,
+  "<extra_id_12>": 32087,
+  "<extra_id_13>": 32086,
+  "<extra_id_14>": 32085,
+  "<extra_id_15>": 32084,
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+  "<extra_id_17>": 32082,
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+  "<extra_id_19>": 32080,
+  "<extra_id_1>": 32098,
+  "<extra_id_20>": 32079,
+  "<extra_id_21>": 32078,
+  "<extra_id_22>": 32077,
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+  "<extra_id_25>": 32074,
+  "<extra_id_26>": 32073,
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+  "<extra_id_29>": 32070,
+  "<extra_id_2>": 32097,
+  "<extra_id_30>": 32069,
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+  "<extra_id_77>": 32022,
+  "<extra_id_78>": 32021,
+  "<extra_id_79>": 32020,
+  "<extra_id_7>": 32092,
+  "<extra_id_80>": 32019,
+  "<extra_id_81>": 32018,
+  "<extra_id_82>": 32017,
+  "<extra_id_83>": 32016,
+  "<extra_id_84>": 32015,
+  "<extra_id_85>": 32014,
+  "<extra_id_86>": 32013,
+  "<extra_id_87>": 32012,
+  "<extra_id_88>": 32011,
+  "<extra_id_89>": 32010,
+  "<extra_id_8>": 32091,
+  "<extra_id_90>": 32009,
+  "<extra_id_91>": 32008,
+  "<extra_id_92>": 32007,
+  "<extra_id_93>": 32006,
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+  "<extra_id_95>": 32004,
+  "<extra_id_96>": 32003,
+  "<extra_id_97>": 32002,
+  "<extra_id_98>": 32001,
+  "<extra_id_99>": 32000,
+  "<extra_id_9>": 32090,
+  "<p>A": 32100,
+  "<p>C": 32101,
+  "<p>D": 32102,
+  "<p>E": 32103,
+  "<p>F": 32104,
+  "<p>G": 32105,
+  "<p>H": 32106,
+  "<p>I": 32107,
+  "<p>K": 32108,
+  "<p>L": 32109,
+  "<p>M": 32110,
+  "<p>N": 32111,
+  "<p>P": 32112,
+  "<p>Q": 32113,
+  "<p>R": 32114,
+  "<p>S": 32115,
+  "<p>T": 32116,
+  "<p>V": 32117,
+  "<p>W": 32118,
+  "<p>Y": 32119,
+  "DESCRIPTION": 35068,
+  "FUNCTION": 35070,
+  "IUPAC": 35075,
+  "MOLECULE NAME": 35072,
+  "PROTEIN FAMILIES": 35064,
+  "PROTEIN NAME": 35069,
+  "SUBCELLULAR LOCATION": 35065,
+  "[#11C-1]": 34809,
+  "[#11CH1]": 34772,
+  "[#11C]": 32177,
+  "[#121Sb]": 32200,
+  "[#12CH1]": 32522,
+  "[#13C-1]": 33245,
+  "[#13CH1]": 34692,
+  "[#13C]": 32874,
+  "[#13N]": 33007,
+  "[#14C-1]": 33877,
+  "[#14CH1]": 33622,
+  "[#14C]": 33992,
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+  "[#15N]": 33321,
+  "[#15O+1]": 33445,
+  "[#16O+1]": 32376,
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+  "[#17CH1]": 33689,
+  "[#17O+1]": 32807,
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+  "[#18CH1]": 32989,
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+  "[#34S+1]": 34627,
+  "[#99Tc]": 34132,
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+  "[#B-1]": 34157,
+  "[#B]": 32885,
+  "[#Bi]": 34031,
+  "[#Br]": 32978,
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+  "[#C+1]": 34373,
+  "[#C-1]": 33359,
+  "[#CH0]": 34822,
+  "[#C]": 33286,
+  "[#Ce]": 32187,
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+  "[#Co]": 34500,
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+  "[#Er]": 33139,
+  "[#Eu]": 34994,
+  "[#Fe+1]": 33529,
+  "[#Fe]": 34940,
+  "[#Ga]": 32802,
+  "[#Gd]": 34981,
+  "[#GeH1]": 32379,
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+  "[#Hf+1]": 34664,
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+  "[#I]": 34345,
+  "[#In]": 32530,
+  "[#Ir+1]": 33205,
+  "[#La]": 33210,
+  "[#Lu]": 34656,
+  "[#Mn]": 34331,
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+  "[#O+1]": 33152,
+  "[#Os+2]": 34541,
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+  "[#P+1]": 34616,
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+  "[#PH1+1]": 32369,
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+  "[#S+1]": 34020,
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+  "[#Si+1]": 32691,
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+  "[#Te]": 34199,
+  "[#Th]": 32473,
+  "[#Ti+1]": 34902,
+  "[#Ti]": 32502,
+  "[#Tl]": 33651,
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+  "[#U]": 33074,
+  "[#V+1]": 33201,
+  "[#V]": 34948,
+  "[#W+1]": 33000,
+  "[#W-1]": 33041,
+  "[#WH1]": 34629,
+  "[#W]": 33692,
+  "[#Y]": 32526,
+  "[#Yb]": 32197,
+  "[#Zr+1]": 34779,
+  "[#Zr]": 33477,
+  "[-/Ring2]": 32375,
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+  "[/-Ring1]": 33996,
+  "[/-Ring2]": 34249,
+  "[/-Ring3]": 34910,
+  "[/11CH3]": 33784,
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+  "[/123I]": 32695,
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+  "[/125I]": 33662,
+  "[/125Te]": 34688,
+  "[/127I]": 32781,
+  "[/12C]": 33102,
+  "[/131I]": 32284,
+  "[/13C@@H1]": 33670,
+  "[/13C@H1]": 32173,
+  "[/13CH1-1]": 32459,
+  "[/13CH1]": 33213,
+  "[/13CH2]": 33621,
+  "[/13CH3]": 34829,
+  "[/13C]": 34580,
+  "[/14C@H1]": 33046,
+  "[/14CH1]": 33386,
+  "[/14CH2-1]": 33560,
+  "[/14CH2]": 33978,
+  "[/14CH3]": 33921,
+  "[/14C]": 34451,
+  "[/14NH1]": 34240,
+  "[/15N+1]": 33131,
+  "[/15NH1]": 34064,
+  "[/15NH2]": 34372,
+  "[/15N]": 32880,
+  "[/18C]": 34037,
+  "[/18F]": 33068,
+  "[/18OH1]": 34195,
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+  "[/19F]": 34133,
+  "[/2H]": 34318,
+  "[/32P]": 33358,
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+  "[/35Cl]": 34875,
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+  "[/37Cl]": 33627,
+  "[/3H]": 34783,
+  "[/76Br]": 33035,
+  "[/79Br]": 32485,
+  "[/80Br]": 32605,
+  "[/9C]": 32413,
+  "[/Al+1]": 32753,
+  "[/Al+2]": 32626,
+  "[/Al-1]": 32186,
+  "[/AlH1+1]": 33019,
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+  "[/At]": 34543,
+  "[/B+1]": 34865,
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+  "[/Br-1]": 32617,
+  "[/Br]": 34260,
+  "[/C+1]": 34102,
+  "[/C-1]": 32436,
+  "[/C@@H1]": 33873,
+  "[/C@@]": 33142,
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+  "[/C@]": 33220,
+  "[/CH0]": 34182,
+  "[/CH1+1]": 33539,
+  "[/CH1-1]": 33165,
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+  "[/CH2]": 34322,
+  "[/C]": 32853,
+  "[/Cl+1]": 33228,
+  "[/Cl-1]": 33990,
+  "[/ClH1+1]": 33496,
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+  "[/F]": 34505,
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+  "[/GeH3]": 33484,
+  "[/Ge]": 32524,
+  "[/H]": 34913,
+  "[/Hg+1]": 32520,
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+  "[/Hg]": 32210,
+  "[/I+1]": 33395,
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+  "[/N+1]": 33216,
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+  "[/N@+1]": 32945,
+  "[/N@@+1]": 34090,
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+  "[/NH1-1]": 33958,
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+  "[/S@@]": 34016,
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+  "[120Sn]": 34140,
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+  "[120Xe]": 32508,
+  "[121I-1]": 33013,
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+  "[\\W]": 33184
+}

config.json

@@ -0,0 +1,50 @@
+{
+  "_name_or_path": "QizhiPei/biot5-plus-base",
+  "architectures": [
+    "T5ForSequenceClassification"
+  ],
+  "classifier_dropout": 0.05,
+  "cls_num_heads": 4,
+  "d_ff": 2048,
+  "d_kv": 64,
+  "d_model": 768,
+  "decoder_start_token_id": 0,
+  "dense_act_fn": "gelu_new",
+  "dropout_rate": 0.05,
+  "eos_token_id": 1,
+  "feed_forward_proj": "gated-gelu",
+  "focal_gamma": 2.0,
+  "id2label": {
+    "0": "non-PMT/vPvM",
+    "1": "PMT/vPvM"
+  },
+  "initializer_factor": 1.0,
+  "is_encoder_decoder": true,
+  "is_gated_act": true,
+  "label2id": {
+    "PMT/vPvM": 1,
+    "non-PMT/vPvM": 0
+  },
+  "layer_norm_epsilon": 1e-06,
+  "loss_function": "cross_entropy",
+  "model_type": "t5",
+  "num_decoder_layers": 12,
+  "num_heads": 12,
+  "num_layers": 12,
+  "output_past": true,
+  "pad_token_id": 0,
+  "problem_type": "single_label_classification",
+  "relative_attention_max_distance": 128,
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