import numpy as np import gradio as gr from transformers import AutoTokenizer,AutoModelForSequenceClassification from transformers import set_seed from torch.utils.data import Dataset,DataLoader import torch import torch.nn as nn import numpy as np import warnings warnings.filterwarnings('ignore') set_seed(4) device = "cpu" model_checkpoint = "facebook/esm2_t6_8M_UR50D" tokenizer = AutoTokenizer.from_pretrained(model_checkpoint) def AMP(file): test_sequences = file class MyDataset(Dataset): def __init__(self,dict_data) -> None: super(MyDataset,self).__init__() self.data=dict_data def __getitem__(self, index): return self.data['text'][index] def __len__(self): return len(self.data['text']) def collate_fn(batch): max_len = 30 pt_batch=tokenizer([b[0] for b in batch], max_length=max_len, padding="max_length",truncation=True, return_tensors='pt') return {'input_ids':pt_batch['input_ids'], 'attention_mask':pt_batch['attention_mask']} test_dict = {"text":test_sequences} test_data=MyDataset(test_dict) test_dataloader=DataLoader(test_data,batch_size=len(test_sequences), collate_fn=collate_fn) class MyModel(nn.Module): def __init__(self): super().__init__() self.bert = AutoModelForSequenceClassification.from_pretrained(model_checkpoint,num_labels=320) self.bn1 = nn.BatchNorm1d(256) self.bn2 = nn.BatchNorm1d(128) self.bn3 = nn.BatchNorm1d(64) self.relu = nn.ReLU() self.fc1 = nn.Linear(320,256) self.fc2 = nn.Linear(256,128) self.fc3 = nn.Linear(128,64) self.output_layer = nn.Linear(64,2) self.dropout = nn.Dropout(0) def forward(self,x): with torch.no_grad(): bert_output = self.bert(input_ids=x['input_ids'].to(device),attention_mask=x['attention_mask'].to(device)) output_feature = self.dropout(bert_output["logits"]) output_feature = self.relu(self.bn1(self.fc1(output_feature))) output_feature = self.relu(self.bn2(self.fc2(output_feature))) output_feature = self.relu(self.bn3(self.fc3(output_feature))) output_feature = self.output_layer(output_feature) return torch.softmax(output_feature,dim=1) model = MyModel() model.load_state_dict(torch.load("best_model.pth")) model = model.to(device) model.eval() out = [] out_probability = [] with torch.no_grad(): for index, batch in enumerate(test_dataloader): batchs = {k: v for k, v in batch.items()} predict = model(batchs) # tsne_plot(output_feature,batchs) out_probability.extend(np.max(np.array(predict.cpu()),axis=1).tolist()) # out_probability.extend(np.array(predict.cpu())[:, -1].tolist()) test_argmax = np.argmax(predict.cpu(), axis=1).tolist() out.extend(test_argmax) return out, out_probability iface = gr.Interface(fn=AMP, inputs="text"(label="input sequence"), outputs= ["text"(label="class"), "text"(label="probability")]) iface.launch()