对基于事件的标注进行新的数据json化处理——构造微调数据集

最新推荐文章于 2024-09-26 07:00:00 发布

你与民谣我与欢喜

最新推荐文章于 2024-09-26 07:00:00 发布

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文章标签： json

本文链接：https://blog.csdn.net/2201_75499442/article/details/139891245

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一、数据json化处理python脚本

具体内容与json化格式可以参考组内毛德霖同学的csdn博客

定义医学文献信息提取的输出形式：JSON与表格化模式-CSDN博客

但是我们在他的脚本上做了部分修改，修改内容具体为：由于其脚本生成的为单个文献所产生的提取结果，用来作为GPTS的训练数据，但并不支持我们已经完善的批量化的数据集，因此修改了代码的文件输入输出，能够实现对文献.txt与标注的.ann文件对的处理，具体修改见下方代码中的读取文件函数：

import json
import os

def generate_training_data_json(article, ann):
    # Extract entities from ann file
    entities = {}
    for line in ann.strip().split("\n"):
        if line.startswith("T"):
            parts = line.split("\t")
            entity_id = parts[0]
            entity_info = parts[1]
            entity_text = parts[2]
            label, start, end = entity_info.split(" ")
            entities[entity_id] = {"label": label.lower(), "start": int(start), "end": int(end), "text": entity_text}

    # Extract events from ann file
    events = {}
    for line in ann.strip().split("\n"):
        if line.startswith("E"):
            parts = line.split("\t")
            event_id = parts[0]
            event_info = parts[1]
            main_entity, *related_entities = event_info.split(" ")
            main_entity_id = main_entity.split(":")[1]
            event_data = {"main": entities[main_entity_id], "related": []}
            for related_entity in related_entities:
                if ":" in related_entity:  # Check if the related_entity contains a colon
                    label, entity_id = related_entity.split(":")
                    event_data["related"].append({"label": label.lower(), "entity": entities[entity_id]})
            events[event_id] = event_data

    # Generate fixed data
    fixed_data = {
        "total-participants": "",
        "intervention-participants": "",
        "control-participants": "",
        "age": [],
        "intervention-age": "",
        "control-age": "",
        "eligibility": "",
        "condition": [],
        "location": "",
        "ethnicity": "",
        "intervention": "",
        "control": "",
        "outcome-measure": "",
        "conclusion": ""
    }

    # Template for variable data
    variable_data_template = {
        "outcome": "",
        "iv-bin-abs": "",
        "cv-bin-abs": "",
        "iv-bin-percent": "",
        "cv-bin-percent": "",
        "iv-cont-mean": "",
        "cv-cont-mean": "",
        "iv-cont-median": "",
        "cv-cont-median": "",
        "iv-cont-sd": "",
        "cv-cont-sd": ""
    }

    variable_data_list = []

    for entity in entities.values():
        if entity["label"] in fixed_data:
            if isinstance(fixed_data[entity["label"]], list):
                fixed_data[entity["label"]].append(entity["text"])
            else:
                fixed_data[entity["label"]] = entity["text"]

    for event in events.values():
        variable_data = variable_data_template.copy()
        variable_data["outcome"] = event["main"]["text"]

        for related in event["related"]:
            variable_data[related["label"]] = related["entity"]["text"]

        variable_data_list.append(variable_data)

    # Convert lists to comma-separated strings
    for key in fixed_data:
        if isinstance(fixed_data[key], list):
            fixed_data[key] = ", ".join(fixed_data[key])

    completion = {
        "fixed_data": fixed_data,
        "variable_data": variable_data_list
    }

    # Prepare output with formatted instructions
    output_str = json.dumps(completion, ensure_ascii=False, indent=2)

    return {
        "input": f"{article.strip()}",
        "output": output_str
    }

def process_files_in_directory(directory):
    data = []
    for filename in os.listdir(directory):
        if filename.endswith(".txt"):
            txt_path = os.path.join(directory, filename)
            ann_path = txt_path.replace(".txt", ".ann")

            if os.path.exists(ann_path):
                with open(txt_path, 'r', encoding='utf-8') as txt_file:
                    article = txt_file.read()

                with open(ann_path, 'r', encoding='utf-8') as ann_file:
                    ann = ann_file.read()

                training_data = generate_training_data_json(article, ann)
                data.append({
                    "instruction": "This passage is a medical literature abstract. Extract the following data from the given medical abstract and output in the specified JSON format.         The extracted fixed fields include: -Total participants: The total number of participants in the study.         - Intervention participants: The number of participants in the intervention group.         - Control participants: The number of participants in the control group.         - Age: The age range or average age of participants.         - Intervention age: The age range or average age of participants in the intervention group.         - Control age: The age range or average age of participants in the control group.         - Eligibility: The eligibility criteria for participants.         - Condition: The medical condition or conditions being studied.         - Location: The location(s) where the study was conducted.         - Ethnicity: The ethnicity of participants.         - Intervention: The type of intervention used.         - Control: The type of control used.         - Outcome measure: The primary outcome measure(s) of the study.         - Conclusion: The conclusion of the study.         The extracted variable fields include (for each outcome event): - Outcome: The outcome event being described.         - IV Bin Abs: The absolute number or attribute value of intervention group participants corresponding to the outcome.         - CV Bin Abs: The absolute number or attribute value of control group participants corresponding to the outcome.         - IV Bin Percent: Percentage of the number of participants in the intervention group or percentage of attribute values corresponding to the outcome.         - CV Bin Percent: Percentage of the number of participants in the control group or percentage of attribute values corresponding to the outcome.         - IV Cont Mean: The mean value of the outcome measure for the intervention group.         - CV Cont Mean: The mean value of the outcome measure for the control group.         - IV Cont Median: The median value of the outcome measure for the intervention group.         - CV Cont Median: The median value of the outcome measure for the control group.         - IV Cont SD: The standard deviation of the outcome measure for the intervention group.         - CV Cont SD: The standard deviation of the outcome measure for the control group.         All fixed data fields will be wrapped in fixed_data, and all variable data fields will be wrapped in variable_data.         Fixed data fields can appear multiple times, and when they do, multiple values should be expressed in a comma-separated format.         The variable data fields are in array form, and each item in the array is found from the article, containing the description of the result (outcome) and the values of that result, making the array contain multiple outcome entries and their related values.         It is important to note that within an item in the variable_data array, the outcome serves as the primary key, and the following must be the parameters corresponding to the outcome.         Meanwhile, if an outcome in a variable_data entry does not correspond to any iv or cv type parameters, it is considered as an invalid outcome and should not appear in variable_data due to the lack of data.         Any fields starting with iv and cv should only contain numerical and unit data, without descriptive text.         The percentage can only appear in \"iv-bin-percent\" and \"cv-bin-percent\" and cannot appear in other outcome property values.         The model must only output the JSON format described below, and immediately stop output when the format output is complete, and do not output any descriptive text unrelated to the JSON format.The specific format is as follows.   {\"fixed_data\": {\"total-participants\": \"\", \"intervention-participants\": \"\", \"control-participants\": \"\", \"age\": \"\", \"intervention-age\": \"\", \"control-age\": \"\", \"eligibility\": \"\", \"condition\": \"\", \"location\": \"\", \"ethnicity\":  \"\", \"intervention\": \"\", \"control\": \"\", \"outcome-measure\": \"\", \"conclusion\": \"\"}, \"variable_data\":  [{\"outcome\": \"\", \"iv-bin-abs\": \"\", \"cv-bin-abs\":             \"\", \"iv-bin-percent\":    \"\", \"cv-bin-percent\": \"\", \"iv-cont-mean\": \"\", \"cv-cont-mean\": \"\", \"iv-cont-median\": \"\", \"cv-cont-median\": \"\", \"iv-cont-sd\": \"\", \"cv-cont-sd\": \"\"}, {\"outcome\": \"\", \"iv-bin-abs\": \"\", \"cv-bin-abs\": \"\", \"iv-bin-percent\":  \"\", \"cv-bin-percent\": \"\", \"iv-cont-mean\": \"\", \"cv-cont-mean\": \"\", \"iv-cont-median\": \"\", \"cv-cont-median\":  \"\", \"iv-cont-sd\": \"\", \"cv-cont-sd\":             \"\"}]}",
                    "input": training_data["input"],
                    "output": training_data["output"]
                })

    return data

directory_path = r"C:\Users\11746\Desktop\PubMed\NewBrat"  # 这里填写文件夹路径
training_data_list = process_files_in_directory(directory_path)

output_file = "training_data_v6.json"
with open(output_file, 'w', encoding='utf-8') as f:
    json.dump(training_data_list, f, ensure_ascii=False, indent=2)

print(f"Training data saved to {output_file}")