计算方法实验6：对鸢尾花数据集进行主成分分析(PCA)并可视化

任务

iris数据集包含150条数据，从iris.txt读取，每条数据有4个属性值和一个标签（标签取值为0，1，2）。要求对这150个4维数据进行PCA，可视化展示这些数据在前两个主方向上的分布，其中不同标签的数据需用不同的颜色或形状加以区分。

算法

m个n维数据向量去中心化后（各向量的每个维度减去这个维度在所有向量上均值），按列排列构成矩阵${\mathbf{X}}_{n\times m}$，计算协方差矩阵${\mathbf{Var}}_{n\times n}=\frac{1}{m}\mathbf{X}{\mathbf{X}}^{\mathbf{T}}$的特征值，选取最大两个特征值对应的特征向量构成矩阵${\mathbf{P}}_{2\times n}$，则${\mathbf{Y}}_{2\times m}=\mathbf{PX}$即PCA后的结果，也就是把四维数据压缩为二维，每个数据对应二维平面上的一个点。
对PCA的详解，可以参考这篇文章；关于PCA与奇异值分解的联系，可以参考这篇文章；关于如何用C++求矩阵特征值（Jacobi方法）和特征向量及对矩阵进行奇异值分解，可以参考这篇文章。

代码

C++实现PCA

#include<bits/stdc++.h>
using namespace std;

// 读取鸢尾花数据集到一个二维数组中
vector<vector<long double>> readIrisData(const string& filename);

// 读取第五列的值到一个向量中
vector<long double> readfifthValue(const string& filename);

// 从矩阵 A 非对角元中选择最大的元素，并返回其位置
pair<int, int> chooseMax(vector<vector<long double>> A);

// 计算矩阵 A 的转置
vector<vector<long double>> calAT(vector<vector<long double>> A);

// 计算矩阵 A 和其转置的乘积
vector<vector<long double>> calAAT(vector<vector<long double>> A);

// 计算矩阵Q^T * A * Q的每个元素，使用给定的参数 p, q, t, c, d
long double calculateElement(const vector<vector<long double>> A, int i, int j, long double p, long double q, long double t, long double c, long double d);

// 计算矩阵 Q^T * A * Q
vector<vector<long double>> calQTAQ(vector<vector<long double>> A);

// 判断Jacobi迭代方法是否满足结束条件
int judgeEnd(vector<vector<long double>> A);

// 计算矩阵 A 的特征值
vector<long double> calEigenValue(vector<vector<long double>> A);

// 对矩阵 A 进行列主元化成上三角
vector<vector<long double>> Column_Elimination(vector<vector<long double>> A);

// 求解系数矩阵为上三角矩阵A的线性方程组
vector<long double> SolveUpperTriangle(vector<vector<long double>> A, vector<long double> b);

// 解系数矩阵为上三角矩阵 A 的线性方程组，且A全为0的行数为 cnt
vector<vector<long double>> solve(vector<vector<long double>> A, int cnt);

// 计算矩阵 A 的特征向量，使用给定的特征值
vector<vector<long double>> calEigenVector(vector<vector<long double>> A, vector<long double> eigenValue);

// 计算 Sigma 矩阵，使用给定的特征值 x 和矩阵的行数 n1 和列数 n2
vector<vector<long double>> calSigma(vector<long double> x,int n1, int n2);

// 计算向量 x 的欧几里得范数
long double EuclideanNorm(vector<long double> x);

// 对矩阵 A 进行归一化
vector<vector<long double>> Normalization(vector<vector<long double>> A);

// 计算矩阵 A 和 B 的乘积
vector<vector<long double>> multiplyMatrices(const vector<vector<long double>> A, const vector<vector<long double>> B);

int main()
{
    vector<vector<long double>> X = calAT(readIrisData("iris.txt"));
    int n1 = X.size();
    int n2 = X[0].size();
    vector<vector<long double>> tempX(n1, vector<long double>(n2));
    long double sum = 0;
    for(int i = 0; i < n1; i++)
    {
        long double sum = 0;
        for(int j = 0; j < n2; j++)
            sum += X[i][j];
        long double avg = sum / n2;
        for(int j = 0; j < n2; j++)
            tempX[i][j] = X[i][j] - avg;
    }
    vector<vector<long double>> tempXT = calAT(tempX);
    vector<vector<long double>> tempXXT = multiplyMatrices(tempX, tempXT);
    vector<vector<long double>> Var(n1, vector<long double>(n1));
    for(int i = 0; i < n1; i++)
        for(int j = 0; j < n1; j++)
            Var[i][j] = tempXXT[i][j] / n2;
    vector<long double> x =calEigenValue(Var);
    sort(x.begin(), x.end());
    reverse(x.begin(), x.end());
    cout<<"特征值："<<endl;
    for(int i = 0; i < n1; i++)
        cout << x[i] << " ";
    cout << endl;
    vector<long double> x1;
    x1.reserve(x.size());
    unique_copy(x.begin(), x.end(), back_inserter(x1));
    vector<vector<long double>> EigenVector = Normalization(calEigenVector(Var, x1));
    vector<vector<long double>> P(EigenVector.begin(), next(EigenVector.begin(), 2));
    cout << "P: " << endl;
    for(int i = 0; i < 2; i++)
    {
        for(int j = 0; j < n1; j++)
            cout << P[i][j] << " ";
        cout << endl;
    }
    
    vector<vector<long double>> Y = multiplyMatrices(P, X);
    cout << "Y: " << endl;
    for(int i = 0; i < 2; i++)
    {
        for(int j = 0; j < n2; j++)
            cout << Y[i][j] << " ";
        cout << endl;
    }
    return 0;
}

// 读取鸢尾花数据集到一个二维数组中
vector<vector<long double>> readIrisData(const string& filename) {
    ifstream file(filename);
    vector<vector<long double>> X;
    string line;

    while (getline(file, line)) {
        stringstream ss(line);
        vector<long double> row;
        string value;
        int counter = 0;
        while (getline(ss, value, ',') && counter < 4) {
            row.push_back(stod(value));
            counter++;
        }
        X.push_back(row);
    }
    return X;
}

// 读取第五列的值到一个向量中
vector<long double> readfifthValue(const string& filename) {
    ifstream file(filename);
    vector<long double> fifthValues;
    string line;

    while (getline(file, line)) {
        stringstream ss(line);
        string value;
        int counter = 0;
        while (getline(ss, value, ',') && counter < 4) {
            counter++;
        }
        if (counter == 4) { 
            long double fifthValue = stold(value);
            fifthValues.push_back(fifthValue);
        }
    }
    return fifthValues;
}

// 找到矩阵 A 中非对角元中绝对值最大的元素，并返回其位置
pair<int, int> chooseMax(vector<vector<long double>> A)
{
    long double max = 0;
    pair<int, int> maxPos;
    int n = A.size();
    for(int i = 0; i < n; i++)
        for(int j = 0; j < n; j++)
            if(i != j && fabsl(A[i][j]) > max)
            {
                max = fabsl(A[i][j]);
                maxPos = make_pair(i, j);
            }
    return maxPos;
}

// 计算矩阵 A 的转置
vector<vector<long double>> calAT(vector<vector<long double>> A)
{
    int n1 = A.size();
    int n2 = A[0].size();
    vector<vector<long double>> AT(n2, vector<long double>(n1));
    for(int i = 0; i < n1; i++)
        for(int j = 0; j < n2; j++)
            AT[j][i] = A[i][j];
    return AT;
}

// 计算两个矩阵的乘积
vector<vector<long double>> multiplyMatrices(const vector<vector<long double>> A, const vector<vector<long double>> B) {
    int n1 = A.size();
    int n2 = B[0].size();
    int n3 = A[0].size();
    vector<vector<long double>> result(n1, vector<long double>(n2, 0.0));

    for(int i = 0; i < n1; i++) {
        for(int j = 0; j < n2; j++) {
            for(int k = 0; k < n3; k++) {
                result[i][j] += A[i][k] * B[k][j];
            }
        }
    }
    return result;
}

// 计算矩阵Q^T * A * Q的每个元素，使用给定的参数 p, q, t, c, d
long double calculateElement(const vector<vector<long double>> A, int i, int j, long double p, long double q, long double t, long double c, long double d) {
    if (i == p && j == p)
        return A[p][p] - t * A[p][q];
    else if (i == q && j == q)
        return A[q][q] + t * A[p][q];
    else if ((i == p && j == q) || (i == q && j == p))
        return 0;
    else if (i != q && i != p && (j == p || j == q))
        return (j == p ? c : d) * A[p][i] - (j == p ? d : (-c)) * A[q][i];
    else if ((i == p || i == q) && j != q && j != p)
        return (i == p ? c : d) * A[p][j] - (i == p ? d : (-c)) * A[q][j];
    else
        return A[i][j];
}

// 计算矩阵 Q^T * A * Q
vector<vector<long double>> calQTAQ(vector<vector<long double>> A)
{
    int n = A.size();
    pair<int, int> maxPos = chooseMax(A);
    int row = maxPos.first;
    int col = maxPos.second;
    
    long double s = (A[col][col] - A[row][row]) / (2 * A[row][col]);
    long double t = 0;
    if(s == 0)
        t = 1;
    else if(abs(-s + sqrt(1 + s * s)) <= abs(-s - sqrt(1 + s * s)))
        t = -s + sqrt(1 + s * s);
    else
        t = -s - sqrt(1 + s * s);

    long double c = 1 / sqrt(1 + t * t);
    long double d = t * c;

    vector<vector<long double>> QTAQ(n, vector<long double>(n));
    for(int i = 0; i < n; i++)
        for(int j = 0; j < n; j++)
            QTAQ[i][j] = calculateElement(A, i, j, row, col, t, c, d);
    return QTAQ;
}

// 判断Jacobi迭代方法是否满足结束条件
int judgeEnd(vector<vector<long double>> A)
{
    int i, j;
    int n = A.size();
    for(i = 0; i < n; i++)
        for(j = 0; j < n; j++)
            if(i != j && fabsl(A[i][j]) >= 1e-6)
                return 0;
    if(i == n && j == n) 
        return 1;
}

// 计算矩阵 A 的特征值
vector<long double> calEigenValue(vector<vector<long double>> A)
{
    int n = A.size();
    vector<long double> eigenValue(n);
    vector<vector<long double>> QTAQ= calQTAQ(A);
    int i, j;
    while(!judgeEnd(QTAQ))
        QTAQ = calQTAQ(QTAQ);
    for(i = 0; i < n; i++)
        eigenValue[i] =QTAQ[i][i];
    return eigenValue;
}

// 对矩阵 A 进行列主元化成上三角
vector<vector<long double>> Column_Elimination(vector<vector<long double>> A)
{
    int n = A.size();
    vector<vector<long double>> Temp(n, vector<long double>(n));
    for(int i = 0; i < n; i++)
        for(int j = 0; j < n; j++)
            Temp[i][j] = A[i][j];
    for(int col = 0; col < n; col++)
    {
        long double maxnum = abs(Temp[col][col]);
        int maxrow = col;
        for(int row = col + 1; row < n; row++)
        {
            if(abs(Temp[row][col]) > maxnum)
            {
                maxnum = abs(Temp[row][col]);
                maxrow = row;
            }
        }
        swap(Temp[col], Temp[maxrow]);
        for(int row = col + 1; row < n; row++)
        {
            long double res = Temp[row][col] / Temp[col][col];
            for(int loc = col; loc < n; loc++)
                Temp[row][loc] -= Temp[col][loc] * res; 
        }
    }
    return Temp;
}

// 求解系数矩阵为上三角矩阵A的线性方程组
vector<long double> SolveUpperTriangle(vector<vector<long double>> A, vector<long double> b)
{
    int n = A.size();
    vector<long double> x(n);
    vector<vector<long double>> Temp(n, vector<long double>(n+1));
    for(int i = 0; i < n; i++)
        for(int j = 0; j < n; j++)
            Temp[i][j] = A[i][j];
    for(int i = 0; i < n; i++)
        Temp[i][n] = b[i];
    for(int row = n-1; row >= 0; row--)
    {
        for(int col = row + 1; col < n; col++)
        {
            Temp[row][n] -= Temp[col][n] * Temp[row][col] / Temp[col][col];
            Temp[row][col] = 0;
        }
        Temp[row][n] /= Temp[row][row];
        Temp[row][row] = 1;
    }
    for(int i = 0; i < n; i++)
        x[i] = Temp[i][n];
    return x;
}

// 解系数矩阵为上三角矩阵 A 的线性方程组，且A全为0的行数为 cnt
vector<vector<long double>> solve(vector<vector<long double>> A, int cnt)
{
    int n = A.size();
    vector<vector<long double>> x(cnt, vector<long double>(n));
    vector<vector<long double>> Temp(n-cnt, vector<long double>(n-cnt));
    vector<long double> Tempb(n-cnt);
    for(int i = 0; i < cnt; i++)
    {
        for(int j = n - 1; j >= n - cnt; j--)
        {
            if(j >= n - i)
                x[i][j] = 0;
            else
                x[i][j] = 1;
        }
    }
    for(int i = 0; i < n - cnt; i++)
        for(int j = 0; j < n - cnt; j++)
            Temp[i][j] = A[i][j];
    for(int i = 0; i < cnt; i++)
    {
        for(int j = n - cnt - 1; j >=  0; j--)
        {
            Tempb[j] = 0;
            for(int k = 0; k < cnt; k++)
                Tempb[j] -= A[j][n- cnt + k] * x[i][n- cnt + k];
        }
        vector<long double> res = SolveUpperTriangle(Temp, Tempb);
        for(int j = 0; j < n - cnt; j++)
            x[i][j] = res[j];
    }
    return x;
}

// 使用给定的特征值计算矩阵 A 的特征向量
vector<vector<long double>> calEigenVector(vector<vector<long double>> A, vector<long double> eigenValue)
{
    int n = A.size();
    int num = 0;
    vector<vector<long double>> x(n, vector<long double>(n));
    vector<vector<long double>> tempMartix(n, vector<long double>(n));
    vector<vector<long double>> eigenVector(n, vector<long double>(n));
    for(int k = 0; k < n; k++)
    {
        for(int i = 0; i < n; i++)
            for(int j = 0; j < n; j++)
                i == j ? tempMartix[i][j] = A[i][j] - eigenValue[k] : tempMartix[i][j] = A[i][j];

        vector<vector<long double>> B = Column_Elimination(tempMartix);
        int cnt = 0;//记录消元后全为0的行数
        for(int i = 0; i < n; i++)
        {
            for(int j = 0; j < n; j++)
            {
                if(fabsl(B[i][j]) > 1e-7)
                    break;
                else if(j == n - 1)
                    cnt++;
            }
        }
        vector<vector<long double>> result = solve(B, cnt);
        for(int i = 0; i < cnt; i++)
            copy(result[i].begin(), result[i].end(), x[num + i].begin());
        num += cnt;
    }
    return x;
}

// 使用给定的特征值 x 和矩阵的行数 n1 和列数 n2，计算 Sigma 矩阵
vector<vector<long double>> calSigma(vector<long double> x, int n1, int n2)
{
    vector<vector<long double>> Sigma(n1, vector<long double>(n2));
    for(int i = 0; i < min(n1, n2); i++)
        Sigma[i][i] = sqrt(x[i]);
    return Sigma;
}

// 计算向量 x 的欧几里得范数
long double EuclideanNorm(vector<long double> x)
{
    long double norm = 0;
    for(int i = 0; i < x.size(); i++)
        norm += x[i] * x[i];
    return sqrt(norm);
}

// 对矩阵 A 进行归一化
vector<vector<long double>> Normalization(vector<vector<long double>> A)
{
    int rows = A.size();
    for(int i = 0; i < rows; i++)
    {
        long double norm = EuclideanNorm(A[i]);
        int cols = A[i].size();
        for(int j = 0; j < cols; j++)
            A[i][j] /= norm;
    }
    return A;
}

计算结果

python实现PCA并将结果可视化

import numpy as np
from scipy.linalg import eigh
import matplotlib.pyplot as plt

def readIrisData(filename):
    data = np.genfromtxt(filename, delimiter=',', dtype='float', encoding=None)
    return data[:, :4].T, data[:, 4]

X, labels = readIrisData("iris.txt")

Var = np.cov(X)
x, EigenVector = eigh(Var)
x = sorted(x, reverse=True)

P = EigenVector[:, -2:].T
P = P[::-1]#反转P的行顺序
Y = np.dot(P, X)

plt.figure()
label_set = set(labels)
colors = ['r', 'g', 'b']
shapes = ['o', 's', '^']

for i, label in enumerate(label_set):#enumerate函数返回每个标签及其索引
    x = [Y[0, j] for j in range(Y.shape[1]) if labels[j] == label]
    y = [Y[1, j] for j in range(Y.shape[1]) if labels[j] == label]
    plt.scatter(x, y, color=colors[i], marker=shapes[i], label=int(label))

plt.legend()#添加图例
plt.show()

可视化结果