From ccca86fef9dcdb20f488761cf968b08906444ab3 Mon Sep 17 00:00:00 2001 From: chaoyi-wu <18706207256@163.com> Date: Sun, 13 Aug 2023 11:19:53 +0800 Subject: [PATCH] upload --- Quick_demo/MedKEBERT/config.json | 27 + Quick_demo/MedKEBERT/special_tokens_map.json | 7 + Quick_demo/MedKEBERT/tokenizer.json | 29045 +++++++++++++++++ Quick_demo/MedKEBERT/tokenizer_config.json | 15 + Quick_demo/MedKEBERT/vocab.txt | 28895 ++++++++++++++++ Quick_demo/Model/RadFM/my_embedding_layer.py | 80 +- src/Model/RadFM/my_embedding_layer.py | 10 +- 7 files changed, 58039 insertions(+), 40 deletions(-) create mode 100644 Quick_demo/MedKEBERT/config.json create mode 100644 Quick_demo/MedKEBERT/special_tokens_map.json create mode 100644 Quick_demo/MedKEBERT/tokenizer.json create mode 100644 Quick_demo/MedKEBERT/tokenizer_config.json create mode 100644 Quick_demo/MedKEBERT/vocab.txt diff --git a/Quick_demo/MedKEBERT/config.json b/Quick_demo/MedKEBERT/config.json new file mode 100644 index 0000000..82962cc --- /dev/null +++ b/Quick_demo/MedKEBERT/config.json @@ -0,0 +1,27 @@ +{ + "_name_or_path": "xmcmic/Med-KEBERT", + "architectures": [ + "BertModel" + ], + "attention_probs_dropout_prob": 0.1, + "classifier_dropout": null, + "gradient_checkpointing": false, + "hidden_act": "gelu", + "hidden_dropout_prob": 0.1, + "hidden_size": 768, + "initializer_range": 0.02, + "intermediate_size": 3072, + "layer_norm_eps": 1e-12, + "max_position_embeddings": 512, + "model_type": "bert", + "num_attention_heads": 12, + "num_hidden_layers": 12, + "output_hidden_states": true, + "pad_token_id": 0, + "position_embedding_type": "absolute", + "torch_dtype": "float32", + "transformers_version": "4.24.0", + "type_vocab_size": 2, + "use_cache": true, + "vocab_size": 30522 +} diff --git a/Quick_demo/MedKEBERT/special_tokens_map.json b/Quick_demo/MedKEBERT/special_tokens_map.json new file mode 100644 index 0000000..a8b3208 --- /dev/null +++ b/Quick_demo/MedKEBERT/special_tokens_map.json @@ -0,0 +1,7 @@ +{ + "cls_token": "[CLS]", + "mask_token": "[MASK]", + "pad_token": "[PAD]", + "sep_token": "[SEP]", + "unk_token": "[UNK]" +} diff --git a/Quick_demo/MedKEBERT/tokenizer.json b/Quick_demo/MedKEBERT/tokenizer.json new file mode 100644 index 0000000..1fee4cd --- /dev/null +++ b/Quick_demo/MedKEBERT/tokenizer.json @@ -0,0 +1,29045 @@ +{ + "version": "1.0", + "truncation": null, + "padding": null, + "added_tokens": [ + { + "id": 0, + "content": "[PAD]", + "single_word": false, + "lstrip": false, + "rstrip": false, + "normalized": false, + "special": true + }, + { + "id": 1, + "content": "[UNK]", + "single_word": false, + "lstrip": false, + "rstrip": false, + "normalized": false, + "special": true + }, + { + "id": 2, + "content": "[CLS]", + "single_word": false, + "lstrip": false, + "rstrip": false, + "normalized": false, + "special": true + }, + { + "id": 3, + "content": "[SEP]", + "single_word": false, + "lstrip": false, + "rstrip": false, + "normalized": false, + "special": true + }, + { + 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b/Quick_demo/MedKEBERT/tokenizer_config.json new file mode 100644 index 0000000..f4db0bf --- /dev/null +++ b/Quick_demo/MedKEBERT/tokenizer_config.json @@ -0,0 +1,15 @@ +{ + "cls_token": "[CLS]", + "do_basic_tokenize": true, + "do_lower_case": true, + "mask_token": "[MASK]", + "name_or_path": "xmcmic/Med-KEBERT", + "never_split": null, + "pad_token": "[PAD]", + "sep_token": "[SEP]", + "special_tokens_map_file": null, + "strip_accents": null, + "tokenize_chinese_chars": true, + "tokenizer_class": "BertTokenizer", + "unk_token": "[UNK]" +} diff --git a/Quick_demo/MedKEBERT/vocab.txt b/Quick_demo/MedKEBERT/vocab.txt new file mode 100644 index 0000000..9d65c84 --- /dev/null +++ b/Quick_demo/MedKEBERT/vocab.txt @@ -0,0 +1,28895 @@ +[PAD] +[UNK] +[CLS] +[SEP] +[MASK] +! +# +$ +% +& +' +( +) +* ++ +, +- +. +/ +0 +1 +2 +3 +4 +5 +6 +7 +8 +9 +: +; +< += +> +? +@ +[ +\ +] +^ +_ +` +a +b +c +d +e +f +g +h +i +j +k +l +m +n +o +p +q +r +s +t +u +v +w +x +y +z +{ +| +} +~ +¡ +¢ +£ +¤ +¥ +¦ +§ +¨ +© 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+saponin +mould +spawning +dpc +pentyl +##enk +chur +ensembles +neuroleptics +##osfamide +absor +##v6 +octahedral +##answ +pulmon +356 +opacification +##adders +##aglobulin +tourniquet +enema +ferred +forget +nonverbal +iva +352 +meticulous +abscisic +burkholderia +gii +influent +##pots +botan +348 +dihydrox +micrometast +digitized +rs22 +lips +pfo +igd +visitors +cd11c +lights +emf +##engine +ethm +chlorpyr +cisterna +##opyranoside +autoradiographic +perchlorate +synonym +##ercise +stereochemistry +##wall +dyslexia +excursion +tesla +autophosphorylation +##ipin +upar +resurf +sterilized +granulomatosis +µmol +eicosapentaenoic +##castle +##ecretion +structuring +##phys +bulbar +ketoac +sydney +mnc +extramedullary +rhu +tropism +hypophosph +clarifying +judgement +jord +puzz +diplopia +deoxynucleotidyl +lympho +##alogy +##6c +clothing +tph diff --git a/Quick_demo/Model/RadFM/my_embedding_layer.py b/Quick_demo/Model/RadFM/my_embedding_layer.py index 0c1b9b2..47a3667 100644 --- a/Quick_demo/Model/RadFM/my_embedding_layer.py +++ b/Quick_demo/Model/RadFM/my_embedding_layer.py @@ -12,7 +12,7 @@ from torch.utils.checkpoint import checkpoint from torch.autograd import Variable import random -from transformers import AutoTokenizer, AutoModel +from transformers import AutoTokenizer, AutoModel, AutoConfig, BertModel class MyEmbedding(nn.Module): def __init__(self, num_embeddings=32000, embedding_dim=5120, perceiver_num=32,vis_dim = 768, patch_size=32, frame_patch_size = 4 ,seg_channel = 256): @@ -26,10 +26,16 @@ def __init__(self, num_embeddings=32000, embedding_dim=5120, perceiver_num=32,vi self.frame_patch_size = frame_patch_size self.seg_channel = seg_channel - self.bert_tokenizer = AutoTokenizer.from_pretrained("/gpfs/home/cs/leijiayu/wuchaoyi/multi_modal/src/MedKEBERT") - self.bert_model = AutoModel.from_pretrained("/gpfs/home/cs/leijiayu/wuchaoyi/multi_modal/src/MedKEBERT") + ## The bert model is useless for generation. Load it just for keeping model the same with the pre-train checkpoint. + self.bert_tokenizer = AutoTokenizer.from_pretrained("./MedKEBERT") + self.bert_model = BertModel(AutoConfig.from_pretrained("./MedKEBERT/")) self.bert_projection_fc = nn.Linear(768,vis_dim) + ## the MedKEBERT can be downloaded from https://huggingface.co/xmcmic/Med-KEBERT/tree/main ## + # self.bert_tokenizer = AutoTokenizer.from_pretrained("xmcmic/Med-KEBERT") + # self.bert_model = AutoModel.from_pretrained("xmcmic/Med-KEBERT") + # self.bert_projection_fc = nn.Linear(768,vis_dim) + self.vision_encoder = ViT( image_size = 512, # image size frames = 512, # max number of frames @@ -80,44 +86,44 @@ def forward(self, text_input, vision_x, key_words_query = None): vision_x = rearrange(vision_x, "(b s F) v d -> b s F v d", b=B, s=S,F=1) loss_matching = None - if key_words_query != None: - # key_words_query list[list[str]] B, words, each word matches corresponding vision_x embedding - query_words = [item for sublist in key_words_query for item in sublist] - query_words = list(set(query_words)) - if len(query_words)>16: - random.shuffle(query_words) - query_words = query_words[0:16] - if query_words != []: - contrastive_labels = torch.zeros(B,len(query_words)) #B Q - for i,sublist in enumerate(key_words_query): - for j,item in enumerate(query_words): - if item in sublist: - contrastive_labels[i,j] = 1 - contrastive_labels = contrastive_labels.to(vision_x.dtype).to(vision_x.device) + # if key_words_query != None: + # # key_words_query list[list[str]] B, words, each word matches corresponding vision_x embedding + # query_words = [item for sublist in key_words_query for item in sublist] + # query_words = list(set(query_words)) + # if len(query_words)>16: + # random.shuffle(query_words) + # query_words = query_words[0:16] + # if query_words != []: + # contrastive_labels = torch.zeros(B,len(query_words)) #B Q + # for i,sublist in enumerate(key_words_query): + # for j,item in enumerate(query_words): + # if item in sublist: + # contrastive_labels[i,j] = 1 + # contrastive_labels = contrastive_labels.to(vision_x.dtype).to(vision_x.device) - with torch.no_grad(): - query_words_embedding = self.bert_tokenizer(query_words, padding='max_length', truncation=True, max_length=256,return_tensors="pt") - query_words_embedding = self.bert_model(input_ids = query_words_embedding['input_ids'].to(vision_x.device),attention_mask = query_words_embedding['attention_mask'].to(vision_x.device))['last_hidden_state'][:,0,:].to(vision_x.dtype).to(vision_x.device) # Q,D - query_words_embedding = self.bert_projection_fc(query_words_embedding) - query_words_embedding = query_words_embedding.unsqueeze(0).repeat(B,1,1) # B,Q,D - _,N,_ = query_words_embedding.shape + # with torch.no_grad(): + # query_words_embedding = self.bert_tokenizer(query_words, padding='max_length', truncation=True, max_length=256,return_tensors="pt") + # query_words_embedding = self.bert_model(input_ids = query_words_embedding['input_ids'].to(vision_x.device),attention_mask = query_words_embedding['attention_mask'].to(vision_x.device))['last_hidden_state'][:,0,:].to(vision_x.dtype).to(vision_x.device) # Q,D + # query_words_embedding = self.bert_projection_fc(query_words_embedding) + # query_words_embedding = query_words_embedding.unsqueeze(0).repeat(B,1,1) # B,Q,D + # _,N,_ = query_words_embedding.shape - image_embedding = vision_x.mean(dim=1) # B V D average pooling 去除掉多模态。 - image_embedding = rearrange(image_embedding, "b F v d -> b (F v) d") - pos_embedding = rearrange(pos_embedding, "(b s) v d -> b s v d", b=B, s=S)[:,0,:,:] + # image_embedding = vision_x.mean(dim=1) # B V D average pooling 去除掉多模态。 + # image_embedding = rearrange(image_embedding, "b F v d -> b (F v) d") + # pos_embedding = rearrange(pos_embedding, "(b s) v d -> b s v d", b=B, s=S)[:,0,:,:] - image_embedding = image_embedding.transpose(0,1) # (H/P W/P D/P) B D - pos_embedding = pos_embedding.transpose(0,1) # (H/P W/P D/P) B D - query_words_embedding = query_words_embedding.transpose(0,1) # N B D + # image_embedding = image_embedding.transpose(0,1) # (H/P W/P D/P) B D + # pos_embedding = pos_embedding.transpose(0,1) # (H/P W/P D/P) B D + # query_words_embedding = query_words_embedding.transpose(0,1) # N B D - oo_embedding,_ = self.transformer_decoder(query_words_embedding, image_embedding, pos = pos_embedding) - oo_embedding = oo_embedding.transpose(0,1) # B Q D - oo_embedding = rearrange(oo_embedding, 'b n d -> (b n) d') - oo_embedding = self.transformer_decoder_mlp(oo_embedding) - oo_embedding = self.cls_head(oo_embedding).mean(dim = -1) - oo_embedding = rearrange(oo_embedding, '(b n) -> b n', b=B, n=N) # B Q - # oo_embedding = rearrange(oo_embedding, 'b n d -> b (n d)') # B Q - loss_matching = F.binary_cross_entropy_with_logits(oo_embedding, contrastive_labels) + # oo_embedding,_ = self.transformer_decoder(query_words_embedding, image_embedding, pos = pos_embedding) + # oo_embedding = oo_embedding.transpose(0,1) # B Q D + # oo_embedding = rearrange(oo_embedding, 'b n d -> (b n) d') + # oo_embedding = self.transformer_decoder_mlp(oo_embedding) + # oo_embedding = self.cls_head(oo_embedding).mean(dim = -1) + # oo_embedding = rearrange(oo_embedding, '(b n) -> b n', b=B, n=N) # B Q + # # oo_embedding = rearrange(oo_embedding, 'b n d -> b (n d)') # B Q + # loss_matching = F.binary_cross_entropy_with_logits(oo_embedding, contrastive_labels) vision_x = self.perceiver(vision_x) # reshapes to (b, S, n, d) #vision_x = checkpoint(self.perceiver,vision_x) diff --git a/src/Model/RadFM/my_embedding_layer.py b/src/Model/RadFM/my_embedding_layer.py index 0c1b9b2..ab39a78 100644 --- a/src/Model/RadFM/my_embedding_layer.py +++ b/src/Model/RadFM/my_embedding_layer.py @@ -25,9 +25,10 @@ def __init__(self, num_embeddings=32000, embedding_dim=5120, perceiver_num=32,vi self.patch_size = patch_size self.frame_patch_size = frame_patch_size self.seg_channel = seg_channel - - self.bert_tokenizer = AutoTokenizer.from_pretrained("/gpfs/home/cs/leijiayu/wuchaoyi/multi_modal/src/MedKEBERT") - self.bert_model = AutoModel.from_pretrained("/gpfs/home/cs/leijiayu/wuchaoyi/multi_modal/src/MedKEBERT") + + ## the MedKEBERT can be downloaded from https://huggingface.co/xmcmic/Med-KEBERT/tree/main ## + self.bert_tokenizer = AutoTokenizer.from_pretrained("xmcmic/Med-KEBERT") + self.bert_model = AutoModel.from_pretrained("xmcmic/Med-KEBERT") self.bert_projection_fc = nn.Linear(768,vis_dim) self.vision_encoder = ViT( @@ -80,7 +81,10 @@ def forward(self, text_input, vision_x, key_words_query = None): vision_x = rearrange(vision_x, "(b s F) v d -> b s F v d", b=B, s=S,F=1) loss_matching = None + if key_words_query != None: + ## we do not use the following parts in final version. + ## You can quota the following codes and if so the bert models will be useless. # key_words_query list[list[str]] B, words, each word matches corresponding vision_x embedding query_words = [item for sublist in key_words_query for item in sublist] query_words = list(set(query_words))