用机器学习方法从症状预测疾

Myth丶恋晨 2022-05-16 09:11 114阅读 0赞

# 一、编程环境 #

Win10  
Python3.6  
Jupyter Notebook  
Graphviz （简介和安装请参考[https://www.jianshu.com/p/b559dc689b7f][https_www.jianshu.com_p_b559dc689b7f]）

# 二、数据源 #

[http://people.dbmi.columbia.edu/~friedma/Projects/DiseaseSymptomKB/index.html][http_people.dbmi.columbia.edu_friedma_Projects_DiseaseSymptomKB_index.html]  
把这个网址里的数据拷贝到csv文件中，并命名为dataset\_uncleaned.csv

# 三、清洗数据 #

1 将疾病和对应的多个症状放到字典里，key为疾病，value为多个症状。  
注意，有些疾病和症状包含了特殊符号’^’，需要先处理成’\_’再切割。

import csv
    from collections import defaultdict
    
    disease_list = []
    
    def return_list(disease):
        disease_list = []
        match = disease.replace('^','_').split('_')
        ctr = 1
        for group in match:
            if ctr%2==0:
                disease_list.append(group)
            ctr = ctr + 1
    
        return disease_list
    
    with open("Scraped-Data/dataset_uncleaned.csv") as csvfile:
        reader = csv.reader(csvfile)
        disease=""
        weight = 0
        disease_list = []
        dict_wt = {}
        dict_=defaultdict(list)
        for row in reader:
    
            if row[0]!="\xc2\xa0" and row[0]!="":
                disease = row[0]
                disease_list = return_list(disease)
                weight = row[1]
    
            if row[2]!="\xc2\xa0" and row[2]!="":
                symptom_list = return_list(row[2])
    
                for d in disease_list:
                    for s in symptom_list:
                        dict_[d].append(s)
                    dict_wt[d] = weight
    
        print (dict_)

2 将疾病-症状-样本数写到dataset\_clean.csv中，注意，每个疾病对应着一个样本数和多个症状。

with open("Scraped-Data/dataset_clean.csv","w") as csvfile:
        writer = csv.writer(csvfile)
        for key,values in dict_.items():
            for v in values:
                #key = str.encode(key)
                key = str.encode(key).decode('utf-8')
                #.strip()
                #v = v.encode('utf-8').strip()
                #v = str.encode(v)
                writer.writerow([key,v,dict_wt[key]])

注意，此时看到的csv中，每行数据下面有一行空行，这个先不用处理，下面的步骤会处理。

3 给数据表dataset\_clean.csv中的每列数据加上列标题

columns = ['Source','Target','Weight']
    data = pd.read_csv("Scraped-Data/dataset_clean.csv",names=columns, encoding ="ISO-8859-1")
    data.head()
    data.to_csv("Scraped-Data/dataset_clean.csv",index=False)

此时，每行下面的空行消失了。

4 标注数据并存到nodetable.csv中  
数据分为三列，第一列ID是疾病名称或症状名称；第二列Label是疾病名称或症状名称，与ID完全一样；第三标属性标明了这个ID或Label是病症或症状。

slist = []
    dlist = []
    with open("Scraped-Data/nodetable.csv","w") as csvfile:
        writer = csv.writer(csvfile)
    
        for key,values in dict_.items():
            for v in values:
                if v not in slist:
                    writer.writerow([v,v,"symptom"])
                    slist.append(v)
            if key not in dlist:
                writer.writerow([key,key,"disease"])
                dlist.append(key)
    
    nt_columns = ['Id','Label','Attribute']
    nt_data = pd.read_csv("Scraped-Data/nodetable.csv",names=nt_columns, encoding ="ISO-8859-1",)
    nt_data.head()
    nt_data.to_csv("Scraped-Data/nodetable.csv",index=False)

# 四、分析清洗好的数据 #

data = pd.read_csv("Scraped-Data/dataset_clean.csv", encoding ="ISO-8859-1")
    len(data['Source'].unique()) len(data['Target'].unique()) df = pd.DataFrame(data) df_1 = pd.get_dummies(df.Target) df_1 df df_s = df['Source'] df_pivoted = pd.concat([df_s,df_1], axis=1) df_pivoted.drop_duplicates(keep='first',inplace=True) df_pivoted len(df_pivoted) cols = df_pivoted.columns print(cols) df_pivoted = df_pivoted.groupby('Source').sum() df_pivoted = df_pivoted.reset_index() df_pivoted len(df_pivoted) df_pivoted.to_csv("Scraped-Data/df_pivoted.csv")

这此代码主要是分析数据，比如疾病有多少种，症状有多少种。每种疾病对应的症状标记为1，没对应上的症状标记为0，将这些数据合并后存到df\_pivoted.csv中。

# 五、用朴素贝叶斯来训练模型 #

x = df_pivoted[cols]
    y = df_pivoted['Source']
    import pandas as pd
    import seaborn as sns
    import matplotlib.pyplot as plt
    %matplotlib inline
    from sklearn.naive_bayes import MultinomialNB
    from sklearn.cross_validation import train_test_split
    x_train, x_test, y_train, y_test = train_test_split(x, y, test_size=0.33, random_state=42)
    mnb = MultinomialNB()
    mnb = mnb.fit(x_train, y_train)
    mnb.score(x_test, y_test)

得分为0，意味着没有预测能力。  
这是因为，对于149条数据（对应着149种疾病），被预测的那1/3的疾病是没有见过的，所以算法没有办法对没见过的疾病进行预测。

改为用全部的数据进行训练，并用全部的数据进行预测

mnb_tot = MultinomialNB()
    mnb_tot = mnb_tot.fit(x, y)
    mnb_tot.score(x, y)

得分率为0.8993288590604027

打印出预测不准确的疾病

disease_pred = mnb_tot.predict(x)
    disease_real = y.values
    for i in range(0, len(disease_real)):
        if disease_pred[i]!=disease_real[i]:
            print ('Pred: {0} Actual:{1}'.format(disease_pred[i].ljust(30), disease_real[i]))

运行结果：

Pred: HIV Actual:acquiredÂ immuno-deficiency syndrome
    Pred: biliary calculus Actual:cholelithiasis
    Pred: coronary arteriosclerosis Actual:coronary heart disease
    Pred: depression mental Actual:depressive disorder
    Pred: HIV Actual:hiv infections
    Pred: carcinoma breast Actual:malignant neoplasm of breast
    Pred: carcinoma of lung Actual:malignant neoplasm of lung
    Pred: carcinoma prostate Actual:malignant neoplasm of prostate
    Pred: carcinoma colon Actual:malignant tumor of colon
    Pred: candidiasis Actual:oralcandidiasis
    Pred: effusion pericardial Actual:pericardial effusion body substance
    Pred: malignant neoplasms Actual:primary malignant neoplasm
    Pred: sepsis (invertebrate) Actual:septicemia
    Pred: sepsis (invertebrate) Actual:systemic infection
    Pred: tonic-clonic epilepsy Actual:tonic-clonic seizures

# 六、用决策树来训练模型 #

from sklearn.tree import DecisionTreeClassifier, export_graphviz
    dt = DecisionTreeClassifier()
    clf_dt=dt.fit(x,y)
    print ("Acurracy: ", clf_dt.score(x,y))

得到的分数为0.8993288590604027，这与上面用朴素贝叶斯算法得到的结果一样。

下面要可视化决策树的节点分布  
1 生成tree.dot

from sklearn import tree 
    from sklearn.tree import export_graphviz
    
    export_graphviz(dt, 
                    out_file='DOT-files/tree.dot', 
                    feature_names=cols)

在工程目录下的DOT-files目录下，可以看到生成了tree.dot文件。

打开cmd终端，进入到tree.dot所在的目录，即DOT-files/中，执行

dot -Tpng tree.dot -o ..\tree.png

会得到tree.png  
但是如果tree.dot太大的话，有可能报内存不够的错误：  
dot: failure to create cairo surface: out of memory  
2 在jupyter notebook中显示tree.png

from IPython.display import Image
    Image(filename='tree.png')

程序来源于[https://github.com/Aniruddha-Tapas/Predicting-Diseases-From-Symptoms][https_github.com_Aniruddha-Tapas_Predicting-Diseases-From-Symptoms]  
笔者在这里只是学习、分析、记录，版权属于原作者。

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[https_www.jianshu.com_p_b559dc689b7f]: https://www.jianshu.com/p/b559dc689b7f
[http_people.dbmi.columbia.edu_friedma_Projects_DiseaseSymptomKB_index.html]: http://people.dbmi.columbia.edu/~friedma/Projects/DiseaseSymptomKB/index.html
[https_github.com_Aniruddha-Tapas_Predicting-Diseases-From-Symptoms]: https://github.com/Aniruddha-Tapas/Predicting-Diseases-From-Symptoms
[QQ_.png]: /images/20220516/91b912f8ef0e4a3883b2bbefd65ea18c.png