sequenzo 0.1.31__cp310-cp310-macosx_10_9_x86_64.whl

sequenzo/clustering/src/KMedoid.cpp

@@ -0,0 +1,263 @@
+#include <pybind11/pybind11.h>
+#include <pybind11/numpy.h>
+#include <vector>
+#include <iostream>
+#ifdef _OPENMP
+#include <omp.h>
+#endif
+#include <random>
+#include <cfloat>
+#include <climits>
+#include <cmath>
+
+using namespace std;
+namespace py = pybind11;
+
+class KMedoid {
+protected:
+    int nelements;        // Number of elements (data points)
+    int nclusters;        // Number of clusters (medoids)
+    int npass;            // Maximum number of iterations
+
+    vector<int> tclusterid;        // Temporary cluster assignment for each element
+    vector<int> saved;             // Saved cluster assignments to check for convergence
+    vector<int> clusterMembership; // Cluster membership indices (flattened 2D: nclusters x nelements)
+    vector<int> clusterSize;       // Size of each cluster
+
+    py::array_t<double> diss;      // Distance matrix (2D numpy array)
+    py::array_t<int> centroids;    // Medoid indices (1D numpy array)
+    py::array_t<double> weights;   // Weights of elements (1D numpy array)
+
+public:
+    // Constructor initializes members and allocates necessary storage
+    KMedoid(int nelements, py::array_t<double> diss,
+            py::array_t<int> centroids, int npass,
+            py::array_t<double> weights)
+        : nelements(nelements),
+          diss(diss),
+          centroids(centroids),
+          npass(npass),
+          weights(weights),
+          nclusters(static_cast<int>(centroids.size())) {
+        // 注释掉信息性打印，避免在并行环境（如 CLARA）中降低性能
+        // py::print("[>] Starting KMedoids...");
+
+        tclusterid.resize(nelements);
+        saved.resize(nelements);
+        clusterMembership.resize(nelements * nclusters);
+        clusterSize.resize(nclusters);
+        fill(clusterSize.begin(), clusterSize.end(), 0);
+    }
+
+    // Initialize medoids using a k-means++ style seeding method for better starting points
+    void init_medoids() {
+        auto ptr_diss = diss.unchecked<2>();
+        auto ptr_centroids = centroids.mutable_unchecked<1>();
+        auto ptr_weights = weights.unchecked<1>();
+
+        vector<int> selected;                             // Indices of selected medoids
+        vector<double> min_dists(nelements, DBL_MAX);     // Minimum distance to selected medoids
+
+        mt19937 rng(random_device{}()); // 3. Random number generator initialization (non-deterministic seed)
+        uniform_int_distribution<> dist(0, nelements - 1);
+
+        // Randomly choose the first medoid
+        int first = dist(rng);
+        selected.push_back(first);
+        ptr_centroids[0] = first;
+
+        for (int k = 1; k < nclusters; ++k) {
+            int last = selected.back();
+
+            // Update min_dists using only the last selected medoid
+            for (int i = 0; i < nelements; ++i) {
+                double d = ptr_diss(i, last);
+                if (d < min_dists[i]) min_dists[i] = d;
+            }
+
+            // Compute weighted total distance
+            double total_weight = 0.0;
+            for (int i = 0; i < nelements; ++i) {
+                total_weight += min_dists[i] * ptr_weights[i];
+            }
+
+            // Handle degenerate case
+            if (total_weight <= 1e-10) {
+                int fallback = dist(rng);
+                selected.push_back(fallback);
+                ptr_centroids[k] = fallback;
+                continue;
+            }
+
+            // Select next medoid using weighted probability
+            uniform_real_distribution<double> rdist(0, total_weight);
+            double r = rdist(rng), accumulator = 0.0;
+            int next = -1;
+
+            for (int i = 0; i < nelements; ++i) {
+                accumulator += min_dists[i] * ptr_weights[i];
+                if (accumulator >= r) {
+                    next = i;
+                    break;
+                }
+            }
+
+            if (next == -1) next = dist(rng);  // fallback again just in case
+            selected.push_back(next);
+            ptr_centroids[k] = next;
+        }
+    }
+
+
+    // Update medoids by selecting the element minimizing the sum of weighted distances to all other elements in the cluster
+    void getclustermedoids() {
+        auto ptr_weights = weights.unchecked<1>();
+        auto ptr_diss = diss.unchecked<2>();
+        auto ptr_centroids = centroids.mutable_unchecked<1>();
+
+        #pragma omp parallel for schedule(dynamic)
+        for (int k = 0; k < nclusters; ++k) {
+            int size = clusterSize[k];
+            double best = DBL_MAX;
+            int bestID = 0;
+
+            // Iterate over all members of cluster k to find the best medoid
+            for (int i = 0; i < size; ++i) {
+                int ii = clusterMembership[k * nelements + i];
+                double current = 0;
+
+                // Sum weighted distances from candidate medoid ii to all other members
+                for (int j = 0; j < size; ++j) {
+                    if (i == j) continue;
+                    int jj = clusterMembership[k * nelements + j];
+                    current += ptr_weights[jj] * ptr_diss(ii, jj);
+                    if (current >= best) break;  // Early stop if worse than current best
+                }
+
+                if (current < best) {
+                    best = current;
+                    bestID = ii;
+                }
+            }
+
+            ptr_centroids[k] = bestID;  // Assign best medoid for cluster k
+        }
+    }
+
+    // Main loop to run the clustering process until convergence or max iterations
+    py::array_t<int> runclusterloop() {
+        auto ptr_weights = weights.unchecked<1>();
+        auto ptr_diss = diss.unchecked<2>();
+        auto ptr_centroids = centroids.mutable_unchecked<1>();
+
+        double total = DBL_MAX;
+        int counter = 0;
+        int period = 10;  // Frequency to save cluster assignments for convergence checking
+
+        while (counter <= npass) {
+            PyErr_CheckSignals();  // Allow Python interruption
+
+            double prev = total;
+            total = 0;
+
+            if (counter > 0) getclustermedoids();
+
+            // Periodically save cluster assignment to check for convergence
+            if (counter % period == 0) {
+                for (int i = 0; i < nelements; ++i)
+                    saved[i] = tclusterid[i];
+
+                if (period < INT_MAX / 2) period *= 2;  // Exponentially increase period
+            }
+
+            counter++;
+
+            vector<vector<int>> localMembers(nclusters);
+
+            // Parallel assignment of elements to closest medoid
+            #pragma omp parallel
+            {
+                vector<vector<int>> threadLocal(nclusters);
+
+                #pragma omp for reduction(+:total) schedule(static)
+                for (int i = 0; i < nelements; ++i) {
+                    double dist = DBL_MAX;
+                    int assign = 0;
+
+                    // Find nearest medoid
+                    for (int k = 0; k < nclusters; ++k) {
+                        int j = ptr_centroids[k];
+                        double tdistance = ptr_diss(i, j);
+
+                        if (tdistance < dist) {
+                            dist = tdistance;
+                            assign = k;
+                        }
+                    }
+
+                    tclusterid[i] = assign;
+                    threadLocal[assign].push_back(i);
+                    total += ptr_weights[i] * dist;
+                }
+
+                // Merge thread local cluster memberships into shared vector safely
+                #pragma omp critical
+                {
+                    for (int k = 0; k < nclusters; ++k) {
+                        localMembers[k].insert(
+                            localMembers[k].end(),
+                            threadLocal[k].begin(),
+                            threadLocal[k].end()
+                        );
+                    }
+                }
+            }
+
+            // Update cluster membership and sizes
+            for (int k = 0; k < nclusters; ++k) {
+                clusterSize[k] = static_cast<int>(localMembers[k].size());
+
+                // If a cluster is empty, reinitialize medoids and restart
+                if (clusterSize[k] == 0) {
+                    init_medoids();
+                    counter = 0;
+                    break;
+                }
+
+                for (int i = 0; i < clusterSize[k]; ++i) {
+                    clusterMembership[k * nelements + i] = localMembers[k][i];
+                }
+            }
+
+            // Convergence check based on total cost change
+            if (abs(total - prev) < 1e-6) break;
+
+            // Check if cluster assignments are unchanged from last saved
+            bool same = true;
+            for (int i = 0; i < nelements; ++i) {
+                if (saved[i] != tclusterid[i]) {
+                    same = false;
+                    break;
+                }
+            }
+
+            if (same) break;
+        }
+
+        return getResultArray();
+    }
+
+    // Construct and return the final array of medoid assignments for each element
+    py::array_t<int> getResultArray() const {
+        py::array_t<int> result(nelements);
+        auto results = result.mutable_unchecked<1>();
+        auto centroid = centroids.unchecked<1>();
+
+        #pragma omp parallel for schedule(static)
+        for (int i = 0; i < nelements; ++i) {
+            results(i) = centroid(tclusterid[i]);
+        }
+
+        return result;
+    }
+};

sequenzo/clustering/src/PAM.cpp

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+#include <pybind11/pybind11.h>
+#include <pybind11/numpy.h>
+#include <vector>
+#include <iostream>
+#ifdef _OPENMP
+#include <omp.h>
+#endif
+#include <cfloat>
+#include <climits>
+#include <cmath>
+#define WEIGHTED_CLUST_TOL -1e-10
+using namespace std;
+namespace py = pybind11;
+
+class PAM {
+public:
+    // Constructor: Initializes the PAM algorithm with required parameters.
+    PAM(int nelements, py::array_t<double> diss,
+        py::array_t<int> centroids, int npass, py::array_t<double> weights) {
+        // 注释掉信息性打印，避免在并行环境（如 CLARA）中降低性能
+        // py::print("[>] Starting Partitioning Around Medoids (PAM)...");
+
+        try {
+            this->nelements = nelements;
+            this->centroids = centroids;
+            this->npass = npass;
+            this->weights = weights;
+            this->diss = diss;
+            this->maxdist = 0.0;
+            this->nclusters = static_cast<int>(centroids.size()); // Number of clusters
+            this->tclusterid.resize(nelements); // Initialize cluster id vector
+            this->computeMaxDist(); // Compute the maximum distance for use later
+
+            // Initialize dysma and dysmb with maxdist
+            dysma.resize(nelements, maxdist);
+            dysmb.resize(nelements, maxdist);
+        } catch (const exception &e) {
+            py::print("Error: ", e.what()); // Error handling
+        }
+    }
+
+    // Computes the maximum distance between any two elements in the distance matrix.
+    void computeMaxDist() {
+        auto ptr_diss = diss.unchecked<2>();
+
+        // The manual array collects the thread maxima
+        int nthreads = 1;
+        #ifdef _OPENMP
+        #pragma omp parallel
+        {
+            #pragma omp single
+            nthreads = omp_get_num_threads();
+        }
+        #endif
+
+        std::vector<double> thread_max(nthreads, 0.0);
+
+        #ifdef _OPENMP
+        #pragma omp parallel
+        {
+            int tid = omp_get_thread_num();
+        #else
+        {
+            int tid = 0;
+        #endif
+            double local = 0.0;
+
+            #ifdef _OPENMP
+            #pragma omp for schedule(static)
+            #endif
+            for (int i = 0; i < nelements; ++i) {
+                for (int j = i + 1; j < nelements; ++j) {
+                    double val = ptr_diss(i, j);
+                    if (val > local) local = val;
+                }
+            }
+
+            thread_max[tid] = local;
+        }
+
+        // Final reduction (serial, fast)
+        double max_val = 0.0;
+        for (double val : thread_max) {
+            if (val > max_val) max_val = val;
+        }
+
+        maxdist = 1.1 * max_val + 1.0;
+    }
+
+
+    // Runs the PAM clustering loop, repeatedly updating centroids and assigning elements to clusters.
+    py::array_t<int> runclusterloop() {
+        auto ptr_weights = weights.unchecked<1>(); // Access to the weights
+        auto ptr_diss = diss.unchecked<2>(); // Access to the distance matrix
+        auto ptr_centroids = centroids.mutable_unchecked<1>(); // Access to the centroids
+
+        double dzsky;
+        int ipass = 0;
+        int hbest = -1;
+        int nbest = -1;
+        int k, icluster, h;
+        double total = -1.0;
+        int nclusters = static_cast<int>(centroids.size());
+
+        do {
+            // Parallel loop to update dysma and dysmb based on current centroids
+            #pragma omp parallel for schedule(static)
+            for (int i = 0; i < nelements; i++) {
+                dysmb[i] = maxdist;
+                dysma[i] = maxdist;
+
+                // Update dysma and dysmb values based on the distance to centroids
+                for (int k = 0; k < nclusters; k++) {
+                    int icluster = ptr_centroids(k);
+                    double dist = ptr_diss(i, icluster);
+
+                    if (dysma[i] > dist) {
+                        dysmb[i] = dysma[i];
+                        dysma[i] = dist;
+                        tclusterid[i] = k; // Assign element to the current cluster
+                    } else if (dysmb[i] > dist) {
+                        dysmb[i] = dist;
+                    }
+                }
+            }
+
+            // If total hasn't been calculated yet, calculate it
+            if (total < 0) {
+                total = 0;
+
+                // Parallel loop to calculate the total weighted distance
+                #pragma omp parallel for reduction(+:total) schedule(static)
+                for (int i = 0; i < nelements; i++) {
+                    total += ptr_weights[i] * dysma[i];
+                }
+            }
+
+            dzsky = 1; // Initialize dzsky to 1 for the change cost comparison
+
+            // Parallel loop to compute the cost of switching elements' medoids
+            #pragma omp parallel for schedule(dynamic)
+            for (int h = 0; h < nelements; h++) {
+                bool is_current_medoid = false;
+                for (int k = 0; k < nclusters; k++) {
+                    if (h == ptr_centroids[k]) {
+                        is_current_medoid = true;
+                        break;
+                    }
+                }
+
+                if (is_current_medoid) // Skip if the element is already a medoid
+                    continue;
+
+                double local_dzsky = dzsky;
+                int local_hbest = -1;
+                int local_nbest = -1;
+
+                // Evaluate the change cost for switching each element with a new medoid
+                for (int k = 0; k < nclusters; k++) {
+                    int i = ptr_centroids[k];
+                    double dz = 0.0;
+
+                    for (int j = 0; j < nelements; j++) {
+                        if (ptr_diss(i, j) == dysma[j]) {
+                            double small = (dysmb[j] > ptr_diss(h, j)) ? ptr_diss(h, j) : dysmb[j];
+                            dz += ptr_weights[j] * (-dysma[j] + small); // Update change cost
+                        } else if (ptr_diss(h, j) < dysma[j]) {
+                            dz += ptr_weights[j] * (-dysma[j] + ptr_diss(h, j));
+                        }
+                    }
+
+                    // Keep track of the best change
+                    if (dz < local_dzsky) {
+                        local_dzsky = dz;
+                        local_hbest = h;
+                        local_nbest = i;
+                    }
+                }
+
+                // Critical section to update dzsky with the best change
+                #pragma omp critical
+                {
+                    if (local_dzsky < dzsky) {
+                        dzsky = local_dzsky;
+                        hbest = local_hbest;
+                        nbest = local_nbest;
+                    }
+                }
+            }
+
+            // If there was an improvement in the total cost, update the centroids
+            if (dzsky < 0) {
+                for (k = 0; k < nclusters; k++) {
+                    if (ptr_centroids[k] == nbest) {
+                        ptr_centroids[k] = hbest; // Swap the medoids
+                    }
+                }
+
+                total += dzsky; // Update the total cost
+            }
+
+            ipass++; // Increment pass count
+            if (ipass >= npass) {
+                break; // Break if max passes reached
+            }
+        } while (dzsky < 0); // Repeat until no improvement
+
+        return getResultArray(); // Return the final cluster assignments
+    }
+
+    // Returns an array of cluster assignments for each element
+    py::array_t<int> getResultArray() const {
+        py::array_t<int> result(nelements);
+        auto results = result.mutable_unchecked<1>();
+        auto centroid = centroids.unchecked<1>();
+
+        #pragma omp parallel for schedule(static)
+        for (int i = 0; i < nelements; ++i) {
+            results(i) = centroid(tclusterid[i]);
+        }
+
+        return result;
+    }
+
+
+protected:
+    int nelements;               // Number of elements to cluster
+    py::array_t<double> diss;    // Distance matrix
+    py::array_t<int> centroids;  // Initial centroids
+    int npass;                   // Number of passes for the algorithm
+    py::array_t<double> weights; // Element weights
+    vector<int> tclusterid;      // Cluster IDs for each element
+    vector<double> dysmb;        // Temporary variable for distances
+    int nclusters;               // Number of clusters
+    double maxdist;              // Maximum distance value
+    vector<double> dysma;        // Temporary variable for distances
+};