sequenzo 0.1.24__cp311-cp311-macosx_10_9_x86_64.whl

sequenzo/big_data/clara/utils/wfcmdd.py

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+"""
+@Author  : 李欣怡
+@File    : wfcmdd.py
+@Time    : 2024/12/28 13:38
+@Desc    : 
+"""
+
+import numpy as np
+import pandas as pd
+import warnings
+
+
+def wfcmdd(diss, memb, weights=None, method="FCMdd", m=2, dnoise=None, eta=None, alpha=0.001,
+           iter_max=100, verbose=False, dlambda=None):
+    # Setting and checking argument values
+    METHODS = ["NCdd", "HNCdd", "FCMdd", "PCMdd"]
+
+    if method not in METHODS:
+        raise ValueError(f" [!] Method must be one of {METHODS}.")
+
+    # TODO:源码中没有 weights = null 时的处理
+    if weights is None:
+        weights = np.ones(len(diss), dtype=int)
+
+    # R 源码中只定义未使用
+    # pweights = weights / np.sum(weights)
+    d = np.array(diss)
+    n = d.shape[0]
+
+    if method == "NCdd":
+        if dnoise is None and dlambda is None:
+            raise ValueError(" [!] Must provide a value for dnoise or dlambda.")
+        if dlambda is not None:
+            dnoise = 1
+    elif method == "HNCdd":
+        if dnoise is None:
+            raise ValueError(" [!] Must provide a value for dnoise.")
+        m = 1
+    elif method == "PCMdd":
+        if eta is None:
+            raise ValueError(" [!] Must provide a vector of values for eta.")
+
+    # Checking the membership matrix (memb)
+    if isinstance(memb, (pd.DataFrame, np.ndarray)):  # Check if memb is matrix or dataframe-like
+        if memb.shape[0] != d.shape[1]:
+            raise ValueError(" [!] The number of rows in memb must be the same as the number of rows and columns of d.")
+        u = memb.to_numpy() if isinstance(memb, pd.DataFrame) else memb
+
+    elif isinstance(memb, list) and all(isinstance(x, (int, float)) for x in memb):
+    # else if (is.vector(memb) && is.numeric(memb))
+        u = np.zeros((n, len(memb)))
+        for k in range(len(memb)):
+            u[memb[k], k] = 1
+
+    else:
+        raise ValueError("[!] Provide a number, a vector of seeds, or membership matrix for mobile clusters.")
+
+    kMov = u.shape[1]
+    med = np.full(kMov, np.nan)
+
+    if method == "PCMdd" and len(eta) != kMov:
+        raise ValueError(" [!] Vector of reference distances (eta) must have a length equal to the number of clusters.")
+
+    if method in ["NCdd", "HNCdd"]:
+        # u <- cbind(u, vector("numeric", length = n))
+        u = np.hstack([u, np.zeros((n, 1))])
+
+    kMovNC = u.shape[1]
+    # print("kMovNC = ", kMovNC)
+    uPrev = np.zeros((n, kMovNC))
+
+    if dlambda is not None:
+        kdiv = kMov * np.sum(weights)
+
+    dist2med = np.zeros((n, kMovNC))
+    # print("dist2med = ", dist2med)
+
+    if method in ["NCdd", "HNCdd"]:
+        dist2med[:, kMovNC - 1] = dnoise
+
+    continue_flag = True
+    iter_count = 1
+    uPrev2 = 0
+    # print("u = ", u)
+    # print("d = ", d)
+    # print("med = ", med)
+    while continue_flag:
+        # Finding centers
+        for k in range(kMov):
+            # candidates < - which(apply(u[, -k, drop=FALSE], 1, max) < 1 & (!1:n % in %med[0:(k - 1)]))
+            # med[k] < - candidates[which.min((u[, k] ^ m * weights) % * % d[, candidates])]
+            # dist2med[, k] < - d[, med[k]]
+
+            u_removed_k = np.delete(u, k, axis=1)      # 去掉第 k 列
+            max_per_row = np.max(u_removed_k, axis=1)  # 每行的最大值
+
+            # 查找最大值小于 1 的行
+            candidates = np.where((max_per_row < 1) & (~np.isin(np.arange(1, len(u) + 1), med[:k])))[0]
+            # print("candidates = ", candidates)
+
+            u_k_m = u[:, k] ** m
+            # print("u_k_m = ", u_k_m)
+
+            # 按照权重与距离矩阵进行矩阵乘法
+            weighted_u_k_m = u_k_m * weights
+            # print("weighted_u_k_m =", weighted_u_k_m)
+
+            # 从 d 中选择 candidates 列
+            d_candidates = d[:, candidates]
+            # print("d_candidates =", d_candidates)
+
+            # 进行矩阵乘法
+            product = weighted_u_k_m @ d_candidates
+            # print("product = ", product)
+            # 选取最小值对应的索引
+            min_index = np.argmin(product)
+            # print("min_index = ", min_index)
+
+            med[k] = candidates[min_index]  # 更新 med[k]
+            # print("med[k] = ", med[k])
+
+            dist2med[:, k] = d[:, int(med[k])]
+            # print("dist2med[:, k] = ", dist2med[:, k])
+
+        # Updating dnoise for adaptive dnoise clustering
+        if dlambda is not None and method == "NCdd":
+            dnoise = dlambda * np.sum(dist2med[:, :-1] * weights[:, None]) / (kMov * np.sum(weights))
+            dist2med[:, kMovNC - 1] = dnoise
+
+
+        # Updating membership
+        if method == "HNCdd":
+            d2cm = np.hstack([dist2med, np.full((dist2med.shape[0], 1), dnoise)])
+            u = np.zeros_like(u)
+            minC = np.argmin(d2cm, axis=1)
+            for i in range(len(minC)):
+                u[i, minC[i]] = 1
+
+        elif method in ["FCMdd", "NCdd"]:
+            with warnings.catch_warnings():
+                warnings.simplefilter("ignore")
+                # dist2med_safe = np.where(dist2med == 0, 1e-10, dist2med)
+                # TODO : 不显示中间报错
+                u = (1 / dist2med) ** (1 / (m - 1))
+                u /= np.sum(u, axis=1, keepdims=True)
+                u[dist2med == 0] = 1
+
+        elif method == "PCMdd":
+            for k in range(kMov):
+                u[:, k] = 1 / (1 + (dist2med[:, k] / eta[k]) ** (1 / (m - 1)))
+            u[dist2med == 0] = 1
+
+        # Checking convergence
+        if iter_count > 2:
+            continue_flag = np.max(np.abs(u - uPrev)) > alpha and iter_count <= iter_max \
+                            and np.max(np.abs(u - uPrev2)) > alpha
+
+        if continue_flag:
+            uPrev2 = uPrev
+            uPrev = u
+            iter_count += 1
+            if verbose:
+                print(".", end="")
+
+    # Calculate the functional value
+    if method in ["NCdd", "FCMdd"]:
+        functional = np.sum(dist2med * (u ** m) * weights[:, None])
+    elif method == "HNCdd":
+        functional = np.sum(dist2med * (u ** m) * weights[:, None])
+    elif method == "PCMdd":
+        functional = 0
+        for k in range(kMov):
+            functional += np.sum(dist2med[:, k] * (u[:, k] ** m) * weights) + np.sum(
+                eta[k] * (1 - u[:, k]) ** m * weights)
+
+    if verbose:
+        print(f"\nIterations: {iter_count}, Functional: {functional}")
+
+    mobile_centers = med[:kMov]
+
+    return {
+        "dnoise": dnoise,
+        "memb": u,
+        "mobileCenters": mobile_centers,
+        "functional": functional
+    }
+
+
+if __name__ == "__main__":
+    diss = np.array([[0.0, 1.0, 2.0],
+                     [1.0, 0.0, 1.0],
+                     [2.0, 1.0, 0.0]])
+    diss = pd.DataFrame(diss)
+
+    memb = np.array([[0.7, 0.3],
+                     [0.2, 0.8],
+                     [0.5, 0.5]])
+
+    result = wfcmdd(diss=diss, memb=memb, method="FCMdd")
+
+    print("result['dnoise'] = ", result['dnoise'])
+    print("result['memb'] =")
+    print(result['memb'])
+    print("result['mobileCenters'] = ", result['mobileCenters'])
+    print("result['functional'] = ", result['functional'])

sequenzo/big_data/clara/visualization.py

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+"""
+@Author  : Yuqi Liang 梁彧祺
+@File    : visualization.py
+@Time    : 04/04/2025 15:21
+@Desc    :
+
+"""
+import matplotlib.pyplot as plt
+import seaborn as sns
+import numpy as np
+import pandas as pd
+
+
+def plot_scores_from_dataframe(df,
+                               k_col="k",
+                               metrics=None,
+                               norm="zscore",
+                               title="CLARA Cluster Quality Metrics",
+                               palette="Set2",
+                               line_width=2,
+                               style="whitegrid",
+                               xlabel="Number of Clusters",
+                               ylabel="Normalized Score",
+                               grid=True,
+                               save_as=None,
+                               dpi=200,
+                               figsize=(12, 8)):
+    """
+    Plot clustering metrics directly from a summary DataFrame (e.g., loaded from CSV).
+
+    :param df: DataFrame with clustering metrics. Must include a 'k' column.
+    :param k_col: Column name indicating the number of clusters.
+    :param metrics: List of metric columns to plot. If None, auto-detect numeric columns.
+    :param norm: Normalization method for plotting ('zscore', 'range', or 'none')
+    :param title: Plot title
+    :param palette: Color palette for the plot
+    :param line_width: Width of plotted lines
+    :param style: Seaborn style for the plot
+    :param xlabel: X-axis label
+    :param ylabel: Y-axis label
+    :param grid: Whether to show grid lines
+    :param save_as: File path to save the plot (optional)
+    :param dpi: DPI for saved image
+    :param figsize: Figure size in inches
+    """
+    df = df.copy()
+    df = df.sort_values(by=k_col)
+
+    if metrics is None:
+        metrics = df.select_dtypes(include=[float, int]).columns.tolist()
+        blacklist = ["Best iter", k_col] # Removed best iter as it is not part of the indicators for cluster quality evaluation
+        metrics = [m for m in metrics if m not in blacklist]
+
+    normed = {}
+    for metric in metrics:
+        values = df[metric].values.astype(float)
+        if norm == "zscore":
+            mean = np.nanmean(values)
+            std = np.nanstd(values)
+            normed[metric] = (values - mean) / std if std > 0 else values
+        elif norm == "range":
+            min_val = np.nanmin(values)
+            max_val = np.nanmax(values)
+            normed[metric] = (values - min_val) / (max_val - min_val) if max_val > min_val else values
+        else:
+            normed[metric] = values
+
+    sns.set(style=style)
+    palette_colors = sns.color_palette(palette, len(metrics))
+    plt.figure(figsize=figsize)
+
+    for idx, metric in enumerate(metrics):
+        plt.plot(df[k_col], normed[metric],
+                 label=metric,
+                 linewidth=line_width,
+                 color=palette_colors[idx])
+
+    plt.title(title, fontsize=14, fontweight="bold")
+    plt.xlabel(xlabel)
+    plt.ylabel(ylabel)
+    plt.xticks(df[k_col])
+    plt.grid(grid, linestyle="--", alpha=0.6)
+    plt.legend(title="Metric", fontsize=10)
+    plt.tight_layout()
+
+    if save_as:
+        plt.savefig(save_as, dpi=dpi)
+    plt.show()

sequenzo/clustering/KMedoids.py

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+"""
+@Author  : 李欣怡 Xinyi Li
+@File    : KMedoids.py
+@Time    : 2025/2/8 11:53
+@Desc    : 
+"""
+
+import numpy as np
+from scipy.cluster.hierarchy import cut_tree
+
+import importlib
+import sequenzo.clustering.clustering_c_code
+clustering_c_code = importlib.import_module("sequenzo.clustering.clustering_c_code")
+
+from sequenzo.clustering.utils.disscenter import disscentertrim
+
+def KMedoids(diss, k, weights=None, npass=1, initialclust=None, method='PAMonce', cluster_only=False, verbose=True):
+
+    # Lazily import the c_code module to avoid circular dependencies during installation
+    # from .__init__ import _import_c_code
+    # c_code = _import_c_code()
+
+    # Convert method to integer if it's a string
+    method_original = method
+    if isinstance(method, str):
+        method = method.lower()
+        method_map = ["kmedoids", "pam", "pamonce"]
+        if method in method_map:
+            method = method_map.index(method) + 1  # 1-based index
+
+    if not (isinstance(method, int) and method in {1, 2, 3}):
+        raise ValueError(f"[!] Unknown clustering method: {method_original}.")
+
+    if verbose:
+        method_names = ["KMedoids", "PAM", "PAMonce"]
+        method_name = method_names[method - 1]
+        print(f"[>] Starting KMedoids clustering (method: {method_name}, k={k})...")
+
+    nelements = diss.shape[0]
+    if nelements != diss.shape[1]:
+        raise ValueError(f"[!] Dissipation matrix has {nelements} elements.")
+
+    def internal_random_sample(nelements, k):
+        return np.random.choice(nelements, k, replace=False)  # 0-based 直接适用
+
+    if weights is None:
+        weights = np.ones(diss.shape[1], dtype=float)
+
+    if len(weights) != nelements:
+        raise ValueError(f"[!] 'weights' should be a vector of length {nelements}.")
+
+    if initialclust is None:
+        initialclust = internal_random_sample(nelements, k)
+    else:
+        if _validate_linkage_matrix(initialclust):
+            # initialclust = fcluster(initialclust, k, criterion='maxclust')  # 1-based 索引
+            initialclust = cut_tree(initialclust, n_clusters=k).flatten() + 1  # 1-based 索引
+        # TODO : 现在已经得到一个组了，为什么不用这个组当作 PAMonce/PAM 算法的初始化？反而利用这个组去选中心点？
+        #  初始化中心点的必要性为什么大于组？初始化中心点无论好不好，最后经过不断迭代肯定能选出较好的
+        # TODO : 就算想要从子样本扩展到全数据，入口参数的这个组也是可以的呀？
+        if len(initialclust) == nelements:
+            initialclust = disscentertrim(diss=diss, group=initialclust, medoids_index="first", weights=weights)
+
+            if len(initialclust) != k:
+                raise ValueError(f"[!] 'initialclust' should be a vector of cluster membership with k={k}.")
+
+        npass = 0
+
+    if len(initialclust) != k:
+        raise ValueError(f"[!] 'initialclust' should be a vector of medoids index of length :{k}.")
+
+    if isinstance(initialclust, list):
+        initialclust = np.asarray(initialclust)
+    if np.any((initialclust >= nelements) | (initialclust < 0)):
+        raise ValueError(f"[!] Starting medoids should be in 1:{nelements}")
+
+    if npass < 0:
+        raise ValueError("[!] 'npass' should be greater than 0")
+
+    if k < 2 or k > nelements:
+        raise ValueError(f" [!] 'k' should be in [2, {nelements}]")
+
+    if method == 1:   # KMedoid
+        memb = clustering_c_code.KMedoid(nelements,
+                                         diss.astype(np.float64),
+                                         initialclust.astype(np.int32),
+                                         npass,
+                                         weights.astype(np.float64))
+    elif method == 2:  # PAM
+        memb = clustering_c_code.PAM(nelements,
+                                     diss.astype(np.float64),
+                                     initialclust.astype(np.int32),
+                                     npass,
+                                     weights.astype(np.float64))
+    else:   # PAMonce
+        memb = clustering_c_code.PAMonce(nelements,
+                                         diss.astype(np.float64),
+                                         initialclust.astype(np.int32),
+                                         npass,
+                                         weights.astype(np.float64))
+
+    memb_matrix = memb.runclusterloop()
+
+    if verbose:
+        print("[>] Computed Successfully.")
+
+    return memb_matrix
+
+def _validate_linkage_matrix(initialclust):
+    """
+    Check that the passed matrix matches the linkage matrix type requirements
+    """
+    if not isinstance(initialclust, np.ndarray):
+        return False    # Linkage matrix must be a NumPy array
+
+    if initialclust.ndim != 2 or initialclust.shape[1] != 4:
+        return False    # Linkage matrix must be a 2D array with 4 columns
+
+    if initialclust.dtype != np.float64:
+        return False    # Linkage matrix 'Z' must contain doubles (np.float64).
+
+    return True
+
+
+if __name__ == '__main__':
+    # TODO : KMeodis 在 python3.11 里导包有 numpy 的问题
+    # TODO : sequenzo 0.1.14 里找不到 KMeodis 模块（这是 init 的问题，现已修正）
+
+    from sequenzo import *
+    import pandas as pd
+
+    # =====
+    #  CO2
+    # =====
+    # df = load_dataset('country_co2_emissions')
+    # time = list(df.columns)[1:]
+    # states = ['Very Low', 'Low', 'Middle', 'High', 'Very High']
+    # sequence_data = SequenceData(df, time=time, id_col="country", states=states)
+
+    # =========
+    # synthetic
+    # =========
+    df = pd.read_csv("/Users/xinyi/Projects/sequenzo/sequenzo/data_and_output/orignal data/not_real_detailed_data/synthetic_detailed_U5_N10000.csv")
+    _time = list(df.columns)[2:]
+    states = ["Data", "Data science", "Hardware", "Research", "Software", "Support & test", "Systems & infrastructure"]
+    df = df[['id', '1', '2', '3', '4', '5', '6', '7', '8', '9', '10']]
+    sequence_data = SequenceData(df, time=_time, id_col="id", states=states)
+
+    om = get_distance_matrix(sequence_data, method="OM", sm="TRATE", indel="auto")
+    centroid_indices = [0, 50, 100, 150, 190]
+    n_pass = 1
+
+    weights = np.ones(len(om))
+
+    # Example 1: KMedoids algorithm without specifying the center point
+    # clustering = KMedoids(diss=om,
+    #                       k=5,
+    #                       method='KMedoids',
+    #                       npass=n_pass,
+    #                       weights=weights)
+    #
+    # # Example 2: PAM algorithm with a specified center point
+    # clustering = KMedoids(diss=om,
+    #                       k=5,
+    #                       method='PAM',
+    #                       initialclust=centroid_indices,
+    #                       npass=n_pass,
+    #                       weights=weights)
+
+    # Example 3: PAMonce algorithm with default parameters
+    clustering = KMedoids(diss=om,
+                          k=5,
+                          method='PAMonce',
+                          npass=n_pass,
+                          weights=weights)
+    print(clustering)
+    uniq = np.unique(clustering)
+    print(uniq.min(), uniq.max())

sequenzo/clustering/__init__.py

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+"""
+@Author  : Yuqi Liang 梁彧祺
+@File    : __init__.py
+@Time    : 27/02/2025 09:58
+@Desc    : 
+"""
+from .hierarchical_clustering import Cluster, ClusterResults, ClusterQuality
+from .KMedoids import KMedoids
+
+
+def _import_c_code():
+    """Lazily import the c_code module to avoid circular dependencies during installation"""
+    try:
+        # Import built pybind11 extension placed under this package
+        from sequenzo.clustering import clustering_c_code
+        return clustering_c_code
+    except ImportError:
+        # If the C extension cannot be imported, return None
+        print(
+            "Warning: The C++ extension (c_code) could not be imported. Please ensure the extension module is compiled correctly.")
+        return None
+
+
+__all__ = [
+    "Cluster",
+    "ClusterResults",
+    "ClusterQuality",
+    "KMedoids",
+    # Add other functions as needed
+]