app.py

import gradio as gr
from transformers import AutoConfig, AutoTokenizer
from bert_graph import BertForMultipleChoice
import torch
import copy
from itertools import chain

# "Comparison of mean diurnal measurements with latanoprost and timolol showed a statistical significant (P < 0.001) difference at 3, 6, and 12 months.",
# "in patients with pigmentary glaucoma, 0.005% latanoprost taken once daily was well tolerated and more effective in reducing IOP than 0.5% timolol taken twice daily."

def preprocess_function_exp(examples, tokenizer):

        # Flatten out
        pair_list = examples
        pair_len = [len(item) for item in pair_list]

        first_sentences = []
        second_sentences = []
        for line_list in pair_list:
            for line in line_list:
                sent_item = line.strip().split('\t')
                first_sentences.append(sent_item[0].strip())
                second_sentences.append(sent_item[1].strip())
        
        # Tokenize
        tokenized_examples = tokenizer(
            first_sentences,
            second_sentences,
            max_length=512,
            padding=False,
            truncation=True,
        )
        # Un-flatten
        # tokenized_inputs = {k: [v[i : i + pair_len[0]] for i in range(0, len(v), pair_len[0])] for k, v in tokenized_examples.items()}
        tokenized_inputs = {}
        for k, v in tokenized_examples.items():
            flatten_list = []
            head_idx = 0
            tail_idx = 0
            for pair_idx in pair_len:
                tail_idx = head_idx + pair_idx
                flatten_list.append(v[head_idx: tail_idx])
                head_idx = copy.copy(tail_idx)
            tokenized_inputs[k] = flatten_list

        # tokenized_inputs["pair_len"] = pair_len
        return tokenized_inputs

def DCForMultipleChoice(features, tokenizer):

        batch_size = len(features)
        argument_len = 4
        
        flattened_features = [
            [{k: v[0][i] for k, v in features.items()} for i in range(4)]
        ]
        
        flattened_features = list(chain(*flattened_features))


        batch = tokenizer.pad(
            flattened_features,
            padding=True,
            max_length=512,
            return_tensors="pt",
        )


        batch = {k: v.view(1, argument_len, -1) for k, v in batch.items()}

        return batch

def post_process_diag(predictions):
    
    num_sentences = int(len(predictions)**0.5)
    predictions_mtx = predictions.reshape(num_sentences, num_sentences)

    for i in range(num_sentences):
        for j in range(num_sentences):
            if i == j:
                predictions_mtx[i, j] = 0

    return predictions_mtx.view(-1)

def max_vote(logits1, logits2, pred1, pred2):

    pred1 = post_process_diag(pred1)
    pred2 = post_process_diag(pred2)
    pred_res = []
    confidence_res = []
    for i in range(len(logits1)):

        soft_logits1 = torch.nn.functional.softmax(logits1[i]) # [[j] for j in range(logits1.shape[1])]
        soft_logits2 = torch.nn.functional.softmax(logits2[i])

        # two class
        # torch.topk(soft_logits1, n=2)
        values_1, _ = soft_logits1.topk(k=2)
        values_2, _ = soft_logits2.topk(k=2)
        # if (values_1[0] - values_2[0]) > (values_1[1] - values_2[1]):
        #     pred_res.append(int(pred1[i].detach().cpu().numpy()))
        # else:
        #     pred_res.append(int(pred2[i].detach().cpu().numpy()))
        if (values_1[0] - values_1[1]) >= (values_2[0] - values_2[1]):
            pred_res.append(int(pred1[i].detach().cpu().numpy()))
            confidence_res.append(float((values_1[0] - values_1[1]).detach().cpu().numpy()))
        else:
            pred_res.append(int(pred2[i].detach().cpu().numpy()))
            confidence_res.append(float((values_2[0] - values_2[1]).detach().cpu().numpy()))

    return pred_res, confidence_res

def model_infer(input_a, input_b):

    config = AutoConfig.from_pretrained('michiyasunaga/BioLinkBERT-base')
    config.win_size = 13
    config.model_mode = 'bert_mtl_1d'
    config.dataset_domain = 'absRCT'
    config.voter_branch = 'dual'
    config.destroy = False

    model = BertForMultipleChoice.from_pretrained(
                'michiyasunaga/BioLinkBERT-base',
                config=config,
            )
    p_sum = torch.load('best.pth', map_location=torch.device('cpu'))
    model.load_state_dict(p_sum)
    tokenizer = AutoTokenizer.from_pretrained('michiyasunaga/BioLinkBERT-base')


    examples = [[input_a+'\t'+input_a, input_a+'\t'+input_b, input_b+'\t'+input_a, input_b+'\t'+input_b]]
    tokenized_inputs = preprocess_function_exp(examples, tokenizer)
    tokenized_inputs = DCForMultipleChoice(tokenized_inputs, tokenizer)
    outputs = model(**tokenized_inputs)
    predictions, scores = max_vote(outputs.logits[0], outputs.logits[1], outputs.logits[0].argmax(dim=-1), outputs.logits[1].argmax(dim=-1))

    prediction_a_b = predictions[1]
    prediction_b_a = predictions[2]

    label_space = {0: 'not relates', 1: 'supports', 2: 'attack'}
    label_a_b = label_space[prediction_a_b]
    label_b_a = label_space[prediction_b_a]

    return 'Head Argument {} Tail Argument'.format(label_a_b, label_b_a)


with gr.Blocks() as demo:
    #设置输入组件
    arg_1 = gr.Textbox(label="Head Argument")
    arg_2 = gr.Textbox(label="Tail Argument")

    gr.Examples([\
    "Compared with baseline measurements, both latanoprost and timolol caused a significant (P < 0.001) reduction of IOP at each hour of diurnal curve throughout the duration of therapy.",\
        "Reduction of IOP was 6.0 +/- 4.5 and 5.9 +/- 4.6 with latanoprost and 4.8 +/- 3.0 and 4.6 +/- 3.1 with timolol after 6 and 12 months, respectively.",\
        "Comparison of mean diurnal measurements with latanoprost and timolol showed a statistical significant (P < 0.001) difference at 3, 6, and 12 months.",\
        "Mean C was found to be significantly enhanced (+30%) only in the latanoprost-treated group compared with the baseline (P = 0.017).",\
        "Mean conjunctival hyperemia was graded at 0.3 in latanoprost-treated eyes and 0.2 in timolol-treated eyes.",\
        "A remarkable change in iris color was observed in both eyes of 1 of the 18 patients treated with latanoprost and none of the 18 patients who received timolol.",\
        "In the timolol group, heart rate was significantly reduced from 72 +/- 9 at baseline to 67 +/- 10 beats per minute at 12 months.",\
        "in patients with pigmentary glaucoma, 0.005% latanoprost taken once daily was well tolerated and more effective in reducing IOP than 0.5% timolol taken twice daily.",\
        "further studies may need to confirm these data on a larger sample and to evaluate the side effect of increased iris pigmentation on long-term follow-up,",\
        ], arg_1)
    gr.Examples([\
    "Compared with baseline measurements, both latanoprost and timolol caused a significant (P < 0.001) reduction of IOP at each hour of diurnal curve throughout the duration of therapy.",\
        "Reduction of IOP was 6.0 +/- 4.5 and 5.9 +/- 4.6 with latanoprost and 4.8 +/- 3.0 and 4.6 +/- 3.1 with timolol after 6 and 12 months, respectively.",\
        "Comparison of mean diurnal measurements with latanoprost and timolol showed a statistical significant (P < 0.001) difference at 3, 6, and 12 months.",\
        "Mean C was found to be significantly enhanced (+30%) only in the latanoprost-treated group compared with the baseline (P = 0.017).",\
        "Mean conjunctival hyperemia was graded at 0.3 in latanoprost-treated eyes and 0.2 in timolol-treated eyes.",\
        "A remarkable change in iris color was observed in both eyes of 1 of the 18 patients treated with latanoprost and none of the 18 patients who received timolol.",\
        "In the timolol group, heart rate was significantly reduced from 72 +/- 9 at baseline to 67 +/- 10 beats per minute at 12 months.",\
        "in patients with pigmentary glaucoma, 0.005% latanoprost taken once daily was well tolerated and more effective in reducing IOP than 0.5% timolol taken twice daily.",\
        "further studies may need to confirm these data on a larger sample and to evaluate the side effect of increased iris pigmentation on long-term follow-up,",\
        ], arg_2)
    # 设置输出组件
    output = gr.Textbox(label="Output Box")
    #设置按钮
    greet_btn = gr.Button("Run")
    #设置按钮点击事件
    greet_btn.click(fn=model_infer, inputs=[arg_1, arg_2], outputs=output)



demo.launch(share=True)