scikit-survival 0.26.0__cp314-cp314-win_amd64.whl

sksurv/svm/survival_svm.py

@@ -0,0 +1,1236 @@
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+from abc import ABCMeta, abstractmethod
+from numbers import Integral, Real
+import warnings
+
+import numexpr
+import numpy as np
+from scipy.optimize import minimize
+from sklearn.base import BaseEstimator
+from sklearn.exceptions import ConvergenceWarning
+from sklearn.metrics.pairwise import PAIRWISE_KERNEL_FUNCTIONS, pairwise_kernels
+from sklearn.utils._param_validation import Interval, StrOptions
+from sklearn.utils.extmath import safe_sparse_dot, squared_norm
+from sklearn.utils.validation import (
+    check_array,
+    check_consistent_length,
+    check_is_fitted,
+    check_random_state,
+    check_X_y,
+    validate_data,
+)
+
+from ..base import SurvivalAnalysisMixin
+from ..bintrees import AVLTree, RBTree
+from ..exceptions import NoComparablePairException
+from ..util import check_array_survival
+from ._prsvm import survival_constraints_simple, survival_constraints_with_support_vectors
+
+
+class Counter(metaclass=ABCMeta):
+    @abstractmethod
+    def __init__(self, x, y, status, time=None):
+        self.x, self.y = check_X_y(x, y)
+
+        assert np.issubdtype(y.dtype, np.integer), f"y vector must have integer type, but was {y.dtype}"
+        assert y.min() == 0, "minimum element of y vector must be 0"
+
+        if time is None:
+            self.status = check_array(status, dtype=bool, ensure_2d=False)
+            check_consistent_length(self.x, self.status)
+        else:
+            self.status = check_array(status, dtype=bool, ensure_2d=False)
+            self.time = check_array(time, ensure_2d=False)
+            check_consistent_length(self.x, self.status, self.time)
+
+        self.eps = np.finfo(self.x.dtype).eps
+
+    def update_sort_order(self, w):
+        xw = np.dot(self.x, w)
+        order = xw.argsort(kind="mergesort")
+        self.xw = xw[order]
+        self.order = order
+        return xw
+
+    @abstractmethod
+    def calculate(self, v):
+        """Return l_plus, xv_plus, l_minus, xv_minus"""
+
+
+class OrderStatisticTreeSurvivalCounter(Counter):
+    """Counting method used by :class:`LargeScaleOptimizer` for survival analysis.
+
+    Parameters
+    ----------
+    x : array, shape = (n_samples, n_features)
+        Feature matrix
+
+    y : array of int, shape = (n_samples,)
+        Unique ranks of samples, starting with 0.
+
+    status : array of bool, shape = (n_samples,)
+        Event indicator of samples.
+
+    tree_class : type
+        The class to use as an order statistic tree, either
+        :class:`sksurv.bintrees.AVLTree` or :class:`sksurv.bintrees.RBTree`.
+
+    time : array, shape = (n_samples,)
+        Survival times.
+    """
+
+    def __init__(self, x, y, status, tree_class, time=None):
+        super().__init__(x, y, status, time)
+        self._tree_class = tree_class
+
+    def calculate(self, v):
+        # only self.xw is sorted, for everything else use self.order
+        # the order of return values is with respect to original order of samples, NOT self.order
+        xv = np.dot(self.x, v)
+
+        od = self.order
+
+        n_samples = self.x.shape[0]
+        l_plus = np.zeros(n_samples, dtype=int)
+        l_minus = np.zeros(n_samples, dtype=int)
+        xv_plus = np.zeros(n_samples, dtype=float)
+        xv_minus = np.zeros(n_samples, dtype=float)
+
+        j = 0
+        tree = self._tree_class(n_samples)
+        for i in range(n_samples):
+            while j < n_samples and 1 - self.xw[j] + self.xw[i] > 0:
+                tree.insert(self.y[od[j]], xv[od[j]])
+                j += 1
+
+            # larger (root of t, y[od[i]])
+            count, vec_sum = tree.count_larger_with_event(self.y[od[i]], self.status[od[i]])
+            l_plus[od[i]] = count
+            xv_plus[od[i]] = vec_sum
+
+        tree = self._tree_class(n_samples)
+        j = n_samples - 1
+        for i in range(j, -1, -1):
+            while j >= 0 and 1 - self.xw[i] + self.xw[j] > 0:
+                if self.status[od[j]]:
+                    tree.insert(self.y[od[j]], xv[od[j]])
+                j -= 1
+
+            # smaller (root of T, y[od[i]])
+            count, vec_sum = tree.count_smaller(self.y[od[i]])
+            l_minus[od[i]] = count
+            xv_minus[od[i]] = vec_sum
+
+        return l_plus, xv_plus, l_minus, xv_minus
+
+
+class SurvivalCounter(Counter):
+    def __init__(self, x, y, status, n_relevance_levels, time=None):
+        super().__init__(x, y, status, time)
+        self.n_relevance_levels = n_relevance_levels
+
+    def _count_values(self):
+        """Return dict mapping relevance level to sample index"""
+        indices = {yi: [i] for i, yi in enumerate(self.y) if self.status[i]}
+
+        return indices
+
+    def calculate(self, v):
+        n_samples = self.x.shape[0]
+        l_plus = np.zeros(n_samples, dtype=int)
+        l_minus = np.zeros(n_samples, dtype=int)
+        xv_plus = np.zeros(n_samples, dtype=float)
+        xv_minus = np.zeros(n_samples, dtype=float)
+        indices = self._count_values()
+
+        od = self.order
+
+        for relevance in range(self.n_relevance_levels):
+            j = 0
+            count_plus = 0
+            # relevance levels are unique, therefore count can only be 1 or 0
+            count_minus = 1 if relevance in indices else 0
+            xv_count_plus = 0
+            xv_count_minus = np.dot(self.x.take(indices.get(relevance, []), axis=0), v).sum()
+
+            for i in range(n_samples):
+                if self.y[od[i]] != relevance or not self.status[od[i]]:
+                    continue
+
+                while j < n_samples and 1 - self.xw[j] + self.xw[i] > 0:
+                    if self.y[od[j]] > relevance:
+                        count_plus += 1
+                        xv_count_plus += np.dot(self.x[od[j], :], v)
+                        l_minus[od[j]] += count_minus
+                        xv_minus[od[j]] += xv_count_minus
+
+                    j += 1
+
+                l_plus[od[i]] = count_plus
+                xv_plus[od[i]] += xv_count_plus
+                count_minus -= 1
+                xv_count_minus -= np.dot(self.x.take(od[i], axis=0), v)
+
+        return l_plus, xv_plus, l_minus, xv_minus
+
+
+class RankSVMOptimizer(metaclass=ABCMeta):
+    """Abstract base class for all optimizers"""
+
+    def __init__(self, alpha, rank_ratio, timeit=False):
+        self.alpha = alpha
+        self.rank_ratio = rank_ratio
+        self.timeit = timeit
+
+        self._last_w = None
+        # cache gradient computations
+        self._last_gradient_w = None
+        self._last_gradient = None
+
+    @abstractmethod
+    def _objective_func(self, w):
+        """Evaluate objective function at w"""
+
+    @abstractmethod
+    def _update_constraints(self, w):
+        """Update constraints"""
+
+    @abstractmethod
+    def _gradient_func(self, w):
+        """Evaluate gradient at w"""
+
+    @abstractmethod
+    def _hessian_func(self, w, s):
+        """Evaluate Hessian at w"""
+
+    @property
+    @abstractmethod
+    def n_coefficients(self):
+        """Return number of coefficients (includes intercept)"""
+
+    def _update_constraints_if_necessary(self, w):
+        needs_update = (w != self._last_w).any()
+        if needs_update:
+            self._update_constraints(w)
+            self._last_w = w.copy()
+        return needs_update
+
+    def _do_objective_func(self, w):
+        self._update_constraints_if_necessary(w)
+        return self._objective_func(w)
+
+    def _do_gradient_func(self, w):
+        if self._last_gradient_w is not None and (w == self._last_gradient_w).all():
+            return self._last_gradient
+
+        self._update_constraints_if_necessary(w)
+        self._last_gradient_w = w.copy()
+        self._last_gradient = self._gradient_func(w)
+        return self._last_gradient
+
+    def _init_coefficients(self):
+        w = np.zeros(self.n_coefficients)
+        self._update_constraints(w)
+        self._last_w = w.copy()
+        return w
+
+    def run(self, **kwargs):
+        w = self._init_coefficients()
+
+        timings = None
+        if self.timeit:
+            import timeit
+
+            def _inner():
+                return minimize(
+                    self._do_objective_func,
+                    w,
+                    method="newton-cg",
+                    jac=self._do_gradient_func,
+                    hessp=self._hessian_func,
+                    **kwargs,
+                )
+
+            timer = timeit.Timer(_inner)
+            timings = timer.repeat(self.timeit, number=1)
+
+        opt_result = minimize(
+            self._do_objective_func,
+            w,
+            method="newton-cg",
+            jac=self._do_gradient_func,
+            hessp=self._hessian_func,
+            **kwargs,
+        )
+        opt_result["timings"] = timings
+
+        return opt_result
+
+
+class SimpleOptimizer(RankSVMOptimizer):
+    """Simple optimizer, which explicitly constructs matrix of all pairs of samples"""
+
+    def __init__(self, x, y, alpha, rank_ratio, timeit=False):
+        super().__init__(alpha, rank_ratio, timeit)
+        self.data_x = x
+        self.constraints = survival_constraints_simple(np.asarray(y, dtype=np.uint8))
+
+        if self.constraints.shape[0] == 0:
+            raise NoComparablePairException("Data has no comparable pairs, cannot fit model.")
+
+        self.L = np.ones(self.constraints.shape[0])
+
+    @property
+    def n_coefficients(self):
+        return self.data_x.shape[1]
+
+    def _objective_func(self, w):
+        val = 0.5 * squared_norm(w) + 0.5 * self.alpha * squared_norm(self.L)
+        return val
+
+    def _update_constraints(self, w):
+        self.xw = np.dot(self.data_x, w)
+        self.L = 1 - self.constraints.dot(self.xw)
+        np.maximum(0, self.L, out=self.L)
+        support_vectors = np.nonzero(self.L > 0)[0]
+        self.Asv = self.constraints[support_vectors, :]
+
+    def _gradient_func(self, w):
+        # sum over columns without running into overflow problems
+        col_sum = self.Asv.sum(axis=0, dtype=int)
+        v = col_sum.A.squeeze()
+
+        z = np.dot(self.data_x.T, (self.Asv.T.dot(self.Asv.dot(self.xw)) - v))
+        return w + self.alpha * z
+
+    def _hessian_func(self, w, s):
+        z = self.alpha * self.Asv.dot(np.dot(self.data_x, s))
+        return s + np.dot(safe_sparse_dot(z.T, self.Asv), self.data_x).T
+
+
+class PRSVMOptimizer(RankSVMOptimizer):
+    """PRSVM optimizer that after each iteration of Newton's method
+    constructs matrix of support vector pairs"""
+
+    def __init__(self, x, y, alpha, rank_ratio, timeit=False):
+        super().__init__(alpha, rank_ratio, timeit)
+        self.data_x = x
+        self.data_y = np.asarray(y, dtype=np.uint8)
+        self._constraints = lambda w: survival_constraints_with_support_vectors(self.data_y, w)
+
+        Aw = self._constraints(np.zeros(x.shape[1]))
+        if Aw.shape[0] == 0:
+            raise NoComparablePairException("Data has no comparable pairs, cannot fit model.")
+
+    @property
+    def n_coefficients(self):
+        return self.data_x.shape[1]
+
+    def _objective_func(self, w):
+        z = self.Aw.shape[0] + squared_norm(self.AXw) - 2.0 * self.AXw.sum()
+        val = 0.5 * squared_norm(w) + 0.5 * self.alpha * z
+        return val
+
+    def _update_constraints(self, w):
+        xw = np.dot(self.data_x, w)
+        self.Aw = self._constraints(xw)
+        self.AXw = self.Aw.dot(xw)
+
+    def _gradient_func(self, w):
+        # sum over columns without running into overflow problems
+        col_sum = self.Aw.sum(axis=0, dtype=int)
+        v = col_sum.A.squeeze()
+        z = np.dot(self.data_x.T, self.Aw.T.dot(self.AXw) - v)
+        return w + self.alpha * z
+
+    def _hessian_func(self, w, s):
+        v = self.Aw.dot(np.dot(self.data_x, s))
+        z = self.alpha * np.dot(self.data_x.T, self.Aw.T.dot(v))
+        return s + z
+
+
+class LargeScaleOptimizer(RankSVMOptimizer):
+    """Optimizer that does not explicitly create matrix of constraints
+
+    Parameters
+    ----------
+    alpha : float
+        Regularization parameter.
+
+    rank_ratio : float
+        Trade-off between regression and ranking objectives.
+
+    fit_intercept : bool
+        Whether to fit an intercept. Only used if regression objective
+        is optimized (rank_ratio < 1.0).
+
+    counter : :class:`OrderStatisticTreeSurvivalCounter` or :class:`SurvivalCounter`
+        An instance of a :class:`Counter` subclass used for counting comparable pairs.
+
+    References
+    ----------
+    Lee, C.-P., & Lin, C.-J. (2014). Supplement Materials for "Large-scale linear RankSVM". Neural Computation, 26(4),
+        781–817. doi:10.1162/NECO_a_00571
+    """
+
+    def __init__(self, alpha, rank_ratio, fit_intercept, counter, timeit=False):
+        super().__init__(alpha, rank_ratio, timeit)
+
+        self._counter = counter
+        self._regr_penalty = (1.0 - rank_ratio) * alpha
+        self._rank_penalty = rank_ratio * alpha
+        self._has_time = hasattr(self._counter, "time") and self._regr_penalty > 0
+        self._fit_intercept = fit_intercept if self._has_time else False
+
+    @property
+    def n_coefficients(self):
+        n = self._counter.x.shape[1]
+        if self._fit_intercept:
+            n += 1
+        return n
+
+    def _init_coefficients(self):
+        w = super()._init_coefficients()
+        n = w.shape[0]
+        if self._fit_intercept:
+            w[0] = self._counter.time.mean()
+            n -= 1
+
+        l_plus, _, l_minus, _ = self._counter.calculate(np.zeros(n))
+        if np.all(l_plus == 0) and np.all(l_minus == 0):
+            raise NoComparablePairException("Data has no comparable pairs, cannot fit model.")
+
+        return w
+
+    def _split_coefficents(self, w):
+        """Split into intercept/bias and feature-specific coefficients"""
+        if self._fit_intercept:
+            bias = w[0]
+            wf = w[1:]
+        else:
+            bias = 0.0
+            wf = w
+        return bias, wf
+
+    def _objective_func(self, w):
+        bias, wf = self._split_coefficents(w)
+
+        l_plus, xv_plus, l_minus, xv_minus = self._counter.calculate(wf)  # pylint: disable=unused-variable
+
+        xw = self._xw
+        val = 0.5 * squared_norm(wf)
+        if self._has_time:
+            val += (
+                0.5 * self._regr_penalty * squared_norm(self.y_compressed - bias - xw.compress(self.regr_mask, axis=0))
+            )
+
+        val += (
+            0.5
+            * self._rank_penalty
+            * numexpr.evaluate(
+                "sum(xw * ((l_plus + l_minus) * xw - xv_plus - xv_minus - 2 * (l_minus - l_plus)) + l_minus)"
+            )
+        )
+
+        return val
+
+    def _update_constraints(self, w):
+        bias, wf = self._split_coefficents(w)
+
+        self._xw = self._counter.update_sort_order(wf)
+
+        if self._has_time:
+            pred_time = self._counter.time - self._xw - bias
+            self.regr_mask = (pred_time > 0) | self._counter.status
+            self.y_compressed = self._counter.time.compress(self.regr_mask, axis=0)
+
+    def _gradient_func(self, w):
+        bias, wf = self._split_coefficents(w)
+
+        l_plus, xv_plus, l_minus, xv_minus = self._counter.calculate(wf)  # pylint: disable=unused-variable
+        x = self._counter.x
+
+        xw = self._xw  # pylint: disable=unused-variable; # noqa: F841
+        z = numexpr.evaluate("(l_plus + l_minus) * xw - xv_plus - xv_minus - l_minus + l_plus")
+
+        grad = wf + self._rank_penalty * np.dot(x.T, z)
+        if self._has_time:
+            xc = x.compress(self.regr_mask, axis=0)
+            xcs = np.dot(xc, wf)
+            grad += self._regr_penalty * (np.dot(xc.T, xcs) + xc.sum(axis=0) * bias - np.dot(xc.T, self.y_compressed))
+
+            # intercept
+            if self._fit_intercept:
+                grad_intercept = self._regr_penalty * (xcs.sum() + xc.shape[0] * bias - self.y_compressed.sum())
+                grad = np.r_[grad_intercept, grad]
+
+        return grad
+
+    def _hessian_func(self, w, s):
+        s_bias, s_feat = self._split_coefficents(s)
+
+        l_plus, xv_plus, l_minus, xv_minus = self._counter.calculate(s_feat)  # pylint: disable=unused-variable
+        x = self._counter.x
+
+        xs = np.dot(x, s_feat)  # pylint: disable=unused-variable
+        xs = numexpr.evaluate("(l_plus + l_minus) * xs - xv_plus - xv_minus")
+
+        hessp = s_feat + self._rank_penalty * np.dot(x.T, xs)
+        if self._has_time:
+            xc = x.compress(self.regr_mask, axis=0)
+            hessp += self._regr_penalty * np.dot(xc.T, np.dot(xc, s_feat))
+
+            # intercept
+            if self._fit_intercept:
+                xsum = xc.sum(axis=0)
+                hessp += self._regr_penalty * xsum * s_bias
+                hessp_intercept = self._regr_penalty * xc.shape[0] * s_bias + self._regr_penalty * np.dot(xsum, s_feat)
+                hessp = np.r_[hessp_intercept, hessp]
+
+        return hessp
+
+
+class NonlinearLargeScaleOptimizer(RankSVMOptimizer):
+    """Optimizer that does not explicitly create matrix of constraints
+
+    Parameters
+    ----------
+    alpha : float
+        Regularization parameter.
+
+    rank_ratio : float
+        Trade-off between regression and ranking objectives.
+
+    counter : :class:`OrderStatisticTreeSurvivalCounter` or :class:`SurvivalCounter`
+        An instance of a :class:`Counter` subclass used for counting comparable pairs.
+
+    References
+    ----------
+    Lee, C.-P., & Lin, C.-J. (2014). Supplement Materials for "Large-scale linear RankSVM". Neural Computation, 26(4),
+        781–817. doi:10.1162/NECO_a_00571
+    """
+
+    def __init__(self, alpha, rank_ratio, fit_intercept, counter, timeit=False):
+        super().__init__(alpha, rank_ratio, timeit)
+
+        self._counter = counter
+        self._fit_intercept = fit_intercept
+        self._rank_penalty = rank_ratio * alpha
+        self._regr_penalty = (1.0 - rank_ratio) * alpha
+        self._has_time = hasattr(self._counter, "time") and self._regr_penalty > 0
+        self._fit_intercept = fit_intercept if self._has_time else False
+
+    @property
+    def n_coefficients(self):
+        n = self._counter.x.shape[0]
+        if self._fit_intercept:
+            n += 1
+        return n
+
+    def _init_coefficients(self):
+        w = super()._init_coefficients()
+        n = w.shape[0]
+        if self._fit_intercept:
+            w[0] = self._counter.time.mean()
+            n -= 1
+
+        l_plus, _, l_minus, _ = self._counter.calculate(np.zeros(n))
+        if np.all(l_plus == 0) and np.all(l_minus == 0):
+            raise NoComparablePairException("Data has no comparable pairs, cannot fit model.")
+
+        return w
+
+    def _split_coefficents(self, w):
+        """Split into intercept/bias and feature-specific coefficients"""
+        if self._fit_intercept:
+            bias = w[0]
+            wf = w[1:]
+        else:
+            bias = 0.0
+            wf = w
+        return bias, wf
+
+    def _update_constraints(self, beta_bias):
+        bias, beta = self._split_coefficents(beta_bias)
+
+        self._Kw = self._counter.update_sort_order(beta)
+
+        if self._has_time:
+            pred_time = self._counter.time - self._Kw - bias
+            self.regr_mask = (pred_time > 0) | self._counter.status
+            self.y_compressed = self._counter.time.compress(self.regr_mask, axis=0)
+
+    def _objective_func(self, beta_bias):
+        bias, beta = self._split_coefficents(beta_bias)
+
+        Kw = self._Kw
+
+        val = 0.5 * np.dot(beta, Kw)
+        if self._has_time:
+            val += (
+                0.5 * self._regr_penalty * squared_norm(self.y_compressed - bias - Kw.compress(self.regr_mask, axis=0))
+            )
+
+        l_plus, xv_plus, l_minus, xv_minus = self._counter.calculate(beta)  # pylint: disable=unused-variable
+        val += (
+            0.5
+            * self._rank_penalty
+            * numexpr.evaluate(
+                "sum(Kw * ((l_plus + l_minus) * Kw - xv_plus - xv_minus - 2 * (l_minus - l_plus)) + l_minus)"
+            )
+        )
+
+        return val
+
+    def _gradient_func(self, beta_bias):
+        bias, beta = self._split_coefficents(beta_bias)
+
+        K = self._counter.x
+        Kw = self._Kw
+
+        l_plus, xv_plus, l_minus, xv_minus = self._counter.calculate(beta)  # pylint: disable=unused-variable
+        z = numexpr.evaluate("(l_plus + l_minus) * Kw - xv_plus - xv_minus - l_minus + l_plus")
+
+        gradient = Kw + self._rank_penalty * np.dot(K, z)
+        if self._has_time:
+            K_comp = K.compress(self.regr_mask, axis=0)
+            K_comp_beta = np.dot(K_comp, beta)
+            gradient += self._regr_penalty * (
+                np.dot(K_comp.T, K_comp_beta) + K_comp.sum(axis=0) * bias - np.dot(K_comp.T, self.y_compressed)
+            )
+
+            # intercept
+            if self._fit_intercept:
+                grad_intercept = self._regr_penalty * (
+                    K_comp_beta.sum() + K_comp.shape[0] * bias - self.y_compressed.sum()
+                )
+                gradient = np.r_[grad_intercept, gradient]
+
+        return gradient
+
+    def _hessian_func(self, _beta, s):
+        s_bias, s_feat = self._split_coefficents(s)
+
+        K = self._counter.x
+        Ks = np.dot(K, s_feat)
+
+        l_plus, xv_plus, l_minus, xv_minus = self._counter.calculate(s_feat)  # pylint: disable=unused-variable
+        xs = numexpr.evaluate("(l_plus + l_minus) * Ks - xv_plus - xv_minus")
+
+        hessian = Ks + self._rank_penalty * np.dot(K, xs)
+        if self._has_time:
+            K_comp = K.compress(self.regr_mask, axis=0)
+            hessian += self._regr_penalty * np.dot(K_comp.T, np.dot(K_comp, s_feat))
+
+            # intercept
+            if self._fit_intercept:
+                xsum = K_comp.sum(axis=0)
+                hessian += self._regr_penalty * xsum * s_bias
+                hessian_intercept = self._regr_penalty * K_comp.shape[0] * s_bias + self._regr_penalty * np.dot(
+                    xsum, s_feat
+                )
+                hessian = np.r_[hessian_intercept, hessian]
+
+        return hessian
+
+
+class BaseSurvivalSVM(BaseEstimator, metaclass=ABCMeta):
+    _parameter_constraints = {
+        "alpha": [Interval(Real, 0.0, None, closed="neither")],
+        "rank_ratio": [Interval(Real, 0.0, 1.0, closed="both")],
+        "fit_intercept": ["boolean"],
+        "max_iter": [Interval(Integral, 1, None, closed="left")],
+        "verbose": ["verbose"],
+        "tol": [Interval(Real, 0.0, None, closed="neither"), None],
+        "random_state": ["random_state"],
+        "timeit": [Interval(Integral, 1, None, closed="left"), "boolean"],
+    }
+
+    @abstractmethod
+    def __init__(
+        self,
+        alpha=1,
+        rank_ratio=1.0,
+        fit_intercept=False,
+        max_iter=20,
+        verbose=False,
+        tol=None,
+        optimizer=None,
+        random_state=None,
+        timeit=False,
+    ):
+        self.alpha = alpha
+        self.rank_ratio = rank_ratio
+        self.fit_intercept = fit_intercept
+        self.max_iter = max_iter
+        self.verbose = verbose
+        self.tol = tol
+        self.optimizer = optimizer
+        self.random_state = random_state
+        self.timeit = timeit
+
+        self.coef_ = None
+        self.optimizer_result_ = None
+
+    def _create_optimizer(self, X, y, status):
+        """Samples are ordered by relevance"""
+        if self.optimizer is None:
+            self.optimizer = "avltree"
+
+        times, ranks = y
+
+        if self.optimizer == "simple":
+            optimizer = SimpleOptimizer(X, status, self.alpha, self.rank_ratio, timeit=self.timeit)
+        elif self.optimizer == "PRSVM":
+            optimizer = PRSVMOptimizer(X, status, self.alpha, self.rank_ratio, timeit=self.timeit)
+        elif self.optimizer == "direct-count":
+            optimizer = LargeScaleOptimizer(
+                self.alpha,
+                self.rank_ratio,
+                self.fit_intercept,
+                SurvivalCounter(X, ranks, status, len(ranks), times),
+                timeit=self.timeit,
+            )
+        elif self.optimizer == "rbtree":
+            optimizer = LargeScaleOptimizer(
+                self.alpha,
+                self.rank_ratio,
+                self.fit_intercept,
+                OrderStatisticTreeSurvivalCounter(X, ranks, status, RBTree, times),
+                timeit=self.timeit,
+            )
+        elif self.optimizer == "avltree":
+            optimizer = LargeScaleOptimizer(
+                self.alpha,
+                self.rank_ratio,
+                self.fit_intercept,
+                OrderStatisticTreeSurvivalCounter(X, ranks, status, AVLTree, times),
+                timeit=self.timeit,
+            )
+
+        return optimizer
+
+    @property
+    def _predict_risk_score(self):
+        return self.rank_ratio == 1
+
+    @abstractmethod
+    def _fit(self, X, time, event, samples_order):
+        """Create and run optimizer"""
+
+    @abstractmethod
+    def predict(self, X):
+        """Predict risk scores or transformed survival times.
+
+        If the model has been fit only considering the ranking objective
+        (``rank_ratio = 1``), predictions are risk scores (i.e. higher values
+        indicate an increased risk of experiencing an event). The scores
+        have no unit and are only meaningful to rank samples by their risk
+        of experiencing an event.
+
+        If the regression objective has been used (``rank_ratio < 1``),
+        predictions are transformed survival times.
+        Lower scores indicate shorter survival, higher scores longer survival.
+
+        Parameters
+        ----------
+        X : array-like, shape = (n_samples, n_features)
+            The input samples.
+
+        Returns
+        -------
+        y : ndarray, shape = (n_samples,), dtype=float
+            Risk scores (if ``rank_ratio = 1``), or transformed survival times
+            (if ``rank_ratio < 1``).
+        """
+
+    def _validate_for_fit(self, X):
+        return validate_data(self, X, ensure_min_samples=2)
+
+    def fit(self, X, y):
+        """Build a survival support vector machine model from training data.
+
+        Parameters
+        ----------
+        X : array-like, shape = (n_samples, n_features)
+            Data matrix.
+
+        y : structured array, shape = (n_samples,)
+            A structured array with two fields. The first field is a boolean
+            where ``True`` indicates an event and ``False`` indicates right-censoring.
+            The second field is a float with the time of event or time of censoring.
+
+        Returns
+        -------
+        self
+        """
+        X = self._validate_for_fit(X)
+        event, time = check_array_survival(X, y, allow_time_zero=False)
+
+        self._validate_params()
+
+        if self.fit_intercept and self.rank_ratio == 1.0:
+            raise ValueError("fit_intercept=True is only meaningful if rank_ratio < 1.0")
+
+        if self.rank_ratio < 1.0:
+            if self.optimizer in {"simple", "PRSVM"}:
+                raise ValueError(f"optimizer {self.optimizer!r} does not implement regression objective")
+
+            # log-transform time
+            time = np.log(time)
+            assert np.isfinite(time).all()
+
+        random_state = check_random_state(self.random_state)
+        samples_order = BaseSurvivalSVM._argsort_and_resolve_ties(time, random_state)
+
+        opt_result = self._fit(X, time, event, samples_order)
+        coef = opt_result.x
+        if self.fit_intercept:
+            self.coef_ = coef[1:]
+            self.intercept_ = coef[0]
+        else:
+            self.coef_ = coef
+
+        if not opt_result.success:
+            warnings.warn(
+                ("Optimization did not converge: " + opt_result.message), category=ConvergenceWarning, stacklevel=2
+            )
+        self.optimizer_result_ = opt_result
+
+        return self
+
+    @property
+    def n_iter_(self):
+        return self.optimizer_result_.nit
+
+    @staticmethod
+    def _argsort_and_resolve_ties(time, random_state):
+        """Like np.argsort, but resolves ties uniformly at random"""
+        n_samples = len(time)
+        order = np.argsort(time, kind="mergesort")
+
+        i = 0
+        while i < n_samples - 1:
+            inext = i + 1
+            while inext < n_samples and time[order[i]] == time[order[inext]]:
+                inext += 1
+
+            if i + 1 != inext:
+                # resolve ties randomly
+                random_state.shuffle(order[i:inext])
+            i = inext
+        return order
+
+
+class FastSurvivalSVM(BaseSurvivalSVM, SurvivalAnalysisMixin):
+    r"""Implements an efficient linear Support Vector Machine for survival analysis,
+    capable of optimizing both ranking and regression objectives.
+
+    Training data consists of *n* triplets :math:`(\mathbf{x}_i, y_i, \delta_i)`,
+    where :math:`\mathbf{x}_i` is a *d*-dimensional feature vector, :math:`y_i > 0`
+    the survival time or time of censoring, and :math:`\delta_i \in \{0,1\}`
+    the binary event indicator. Using the training data, the objective is to
+    minimize the following function:
+
+    .. math::
+
+         \arg \min_{\mathbf{w}, b} \frac{1}{2} \mathbf{w}^\top \mathbf{w}
+         + \frac{\alpha}{2} \left[ r \sum_{i,j \in \mathcal{P}}
+         \max(0, 1 - (\mathbf{w}^\top \mathbf{x}_i - \mathbf{w}^\top \mathbf{x}_j))^2
+         + (1 - r) \sum_{i=0}^n \left( \zeta_{\mathbf{w}, b} (y_i, x_i, \delta_i)
+         \right)^2 \right]
+
+        \zeta_{\mathbf{w},b} (y_i, \mathbf{x}_i, \delta_i) =
+        \begin{cases}
+        \max(0, y_i - \mathbf{w}^\top \mathbf{x}_i - b) \quad \text{if $\delta_i = 0$,} \\
+        y_i - \mathbf{w}^\top \mathbf{x}_i - b \quad \text{if $\delta_i = 1$,} \\
+        \end{cases}
+
+        \mathcal{P} = \{ (i, j) \mid y_i > y_j \land \delta_j = 1 \}_{i,j=1,\dots,n}
+
+    The hyper-parameter :math:`\alpha > 0` determines the amount of regularization
+    to apply: a smaller value increases the amount of regularization and a
+    higher value reduces the amount of regularization. The hyper-parameter
+    :math:`r \in [0; 1]` determines the trade-off between the ranking objective
+    and the regression objective. If :math:`r = 1` it reduces to the ranking
+    objective, and if :math:`r = 0` to the regression objective. If the regression
+    objective is used, survival/censoring times are log-transformed and thus cannot be
+    zero or negative.
+
+    See the :ref:`User Guide </user_guide/survival-svm.ipynb>` and [1]_ for further description.
+
+    Parameters
+    ----------
+    alpha : float, default: 1
+        Weight of penalizing the squared hinge loss in the objective function. Must be greater than 0.
+
+    rank_ratio : float, optional, default: 1.0
+        Mixing parameter between regression and ranking objectives, with ``0 <= rank_ratio <= 1``.
+        If ``rank_ratio = 1``, only ranking is performed. If ``rank_ratio = 0``, only regression
+        is performed. A ``rank_ratio`` less than 1.0 (i.e., including a regression objective) is
+        only supported if the ``optimizer`` is 'avltree', 'rbtree', or 'direct-count'.
+
+    fit_intercept : bool, optional, default: False
+        Whether to calculate an intercept for the regression model. If set to ``False``, no intercept
+        will be calculated. This parameter has no effect if ``rank_ratio = 1``, i.e., only ranking is performed.
+
+    max_iter : int, optional, default: 20
+        Maximum number of iterations to perform in Newton optimization.
+
+    verbose : bool, optional, default: False
+        If ``True``, print messages during optimization.
+
+    tol : float or None, optional, default: None
+        Tolerance for termination. If ``None``, the solver's default tolerance is used.
+        See :func:`scipy.optimize.minimize`.
+
+    optimizer : {'avltree', 'direct-count', 'PRSVM', 'rbtree', 'simple'}, optional, default: 'avltree'
+        Specifies which optimizer to use.
+
+    random_state : int, :class:`numpy.random.RandomState` instance, or None, optional, default: None
+        Used to resolve ties in survival times. Pass an int for reproducible output across
+        multiple :meth:`fit` calls.
+
+    timeit : bool, int, or None, optional, default: False
+        If ``True`` or a non-zero integer, the time taken for optimization is measured.
+        If an integer is provided, the optimization is repeated that many times.
+        Results can be accessed from the ``optimizer_result_`` attribute.
+
+    Attributes
+    ----------
+    coef_ : ndarray, shape = (n_features,), dtype = float
+        Coefficients of the features in the decision function.
+
+    optimizer_result_ : :class:`scipy.optimize.OptimizeResult`
+        Stats returned by the optimizer. See :class:`scipy.optimize.OptimizeResult`.
+
+    n_features_in_ : int
+        Number of features seen during ``fit``.
+
+    feature_names_in_ : ndarray, shape = (`n_features_in_`,), dtype = object
+        Names of features seen during ``fit``. Defined only when `X`
+        has feature names that are all strings.
+
+    n_iter_ : int
+        Number of iterations run by the optimization routine to fit the model.
+
+    See also
+    --------
+    FastKernelSurvivalSVM
+        Fast implementation for arbitrary kernel functions.
+
+    References
+    ----------
+    .. [1] Pölsterl, S., Navab, N., and Katouzian, A.,
+           "Fast Training of Support Vector Machines for Survival Analysis",
+           Machine Learning and Knowledge Discovery in Databases: European Conference,
+           ECML PKDD 2015, Porto, Portugal,
+           Lecture Notes in Computer Science, vol. 9285, pp. 243-259 (2015)
+    """
+
+    _parameter_constraints = {
+        **BaseSurvivalSVM._parameter_constraints,
+        "optimizer": [StrOptions({"simple", "PRSVM", "direct-count", "rbtree", "avltree"}), None],
+    }
+
+    def __init__(
+        self,
+        alpha=1,
+        *,
+        rank_ratio=1.0,
+        fit_intercept=False,
+        max_iter=20,
+        verbose=False,
+        tol=None,
+        optimizer=None,
+        random_state=None,
+        timeit=False,
+    ):
+        super().__init__(
+            alpha=alpha,
+            rank_ratio=rank_ratio,
+            fit_intercept=fit_intercept,
+            max_iter=max_iter,
+            verbose=verbose,
+            tol=tol,
+            optimizer=optimizer,
+            random_state=random_state,
+            timeit=timeit,
+        )
+
+    def _fit(self, X, time, event, samples_order):
+        data_y = (time[samples_order], np.arange(len(samples_order)))
+        status = event[samples_order]
+
+        optimizer = self._create_optimizer(X[samples_order], data_y, status)
+        opt_result = optimizer.run(tol=self.tol, options={"maxiter": self.max_iter, "disp": self.verbose})
+        return opt_result
+
+    def predict(self, X):
+        check_is_fitted(self, "coef_")
+        X = validate_data(self, X, reset=False)
+
+        val = np.dot(X, self.coef_)
+        if hasattr(self, "intercept_"):
+            val += self.intercept_
+
+        # Order by increasing survival time if objective is pure ranking
+        if self.rank_ratio == 1:
+            val *= -1
+        else:
+            # model was fitted on log(time), transform to original scale
+            val = np.exp(val)
+
+        return val
+
+
+class FastKernelSurvivalSVM(BaseSurvivalSVM, SurvivalAnalysisMixin):
+    """Implements an efficient kernel Support Vector Machine for survival analysis.
+
+    The model extends :class:`FastSurvivalSVM` to non-linear relationships through kernel functions.
+
+    See the :ref:`User Guide </user_guide/survival-svm.ipynb>` and [1]_ for further description.
+
+    Parameters
+    ----------
+    alpha : float, default: 1
+        Weight of penalizing the squared hinge loss in the objective function. Must be greater than 0.
+
+    rank_ratio : float, optional, default: 1.0
+        Mixing parameter between regression and ranking objectives, with ``0 <= rank_ratio <= 1``.
+        If ``rank_ratio = 1``, only ranking is performed. If ``rank_ratio = 0``, only regression
+        is performed. A ``rank_ratio`` less than 1.0 (i.e., including a regression objective) is
+        only supported if the ``optimizer`` is 'avltree', 'PRSVM', or 'rbtree'.
+
+    fit_intercept : bool, optional, default: False
+        Whether to calculate an intercept for the regression model. If set to ``False``, no intercept
+        will be calculated. This parameter has no effect if ``rank_ratio = 1``, i.e., only ranking is performed.
+
+    kernel : str or callable, default: 'rbf'
+        Kernel mapping used internally. This parameter is directly passed to
+        :func:`sklearn.metrics.pairwise.pairwise_kernels`.
+        If `kernel` is a string, it must be one of the metrics
+        in `pairwise.PAIRWISE_KERNEL_FUNCTIONS` or "precomputed".
+        If `kernel` is "precomputed", X is assumed to be a kernel matrix.
+        Alternatively, if `kernel` is a callable function, it is called on
+        each pair of instances (rows) and the resulting value recorded. The
+        callable should take two rows from X as input and return the
+        corresponding kernel value as a single number. This means that
+        callables from :mod:`sklearn.metrics.pairwise` are not allowed, as
+        they operate on matrices, not single samples. Use the string
+        identifying the kernel instead.
+
+    gamma : float, optional, default: None
+        Gamma parameter for the RBF, laplacian, polynomial, exponential chi2
+        and sigmoid kernels. Interpretation of the default value is left to
+        the kernel; see the documentation for :mod:`sklearn.metrics.pairwise`.
+        Ignored by other kernels.
+
+    degree : int, optional, default: 3
+        Degree of the polynomial kernel. Ignored by other kernels.
+
+    coef0 : float, optional, default: 1
+        Zero coefficient for polynomial and sigmoid kernels.
+        Ignored by other kernels.
+
+    kernel_params : dict or None, optional, default: None
+        Additional parameters (keyword arguments) for kernel function passed
+        as callable object.
+
+    max_iter : int, optional, default: 20
+        Maximum number of iterations to perform in Newton optimization
+
+    verbose : bool, optional, default: False
+        If ``True``, print messages during optimization.
+
+    tol : float or None, optional, default: None
+        Tolerance for termination. If ``None``, the solver's default tolerance is used.
+        See :func:`scipy.optimize.minimize`.
+
+    optimizer : {'avltree', 'rbtree'}, optional, default: 'rbtree'
+        Specifies which optimizer to use..
+
+    random_state : int, :class:`numpy.random.RandomState` instance, or None, optional, default: None
+        Used to resolve ties in survival times. Pass an int for reproducible output across
+        multiple :meth:`fit` calls.
+
+    timeit : bool, int, or None, optional, default: False
+        If ``True`` or a non-zero integer, the time taken for optimization is measured.
+        If an integer is provided, the optimization is repeated that many times.
+        Results can be accessed from the ``optimizer_result_`` attribute.
+
+    Attributes
+    ----------
+    coef_ : ndarray, shape = (n_samples,), dtype = float
+        Weights assigned to the samples in training data to represent
+        the decision function in kernel space.
+
+    fit_X_ : ndarray, shape = (n_samples, `n_features_in_`), dtype = float
+        Training data used for fitting. Used to compute the kernel matrix for prediction.
+
+    optimizer_result_ : :class:`scipy.optimize.OptimizeResult`
+        Stats returned by the optimizer. See :class:`scipy.optimize.OptimizeResult`.
+
+    n_features_in_ : int
+        Number of features seen during ``fit``.
+
+    feature_names_in_ : ndarray, shape = (`n_features_in_`,), dtype = object
+        Names of features seen during ``fit``. Defined only when `X`
+        has feature names that are all strings.
+
+    n_iter_ : int
+        Number of iterations run by the optimization routine to fit the model.
+
+    See also
+    --------
+    FastSurvivalSVM
+        Fast implementation for linear kernel.
+
+    References
+    ----------
+    .. [1] Pölsterl, S., Navab, N., and Katouzian, A.,
+           *An Efficient Training Algorithm for Kernel Survival Support Vector Machines*
+           4th Workshop on Machine Learning in Life Sciences,
+           23 September 2016, Riva del Garda, Italy. arXiv:1611.07054
+    """
+
+    _parameter_constraints = {
+        **FastSurvivalSVM._parameter_constraints,
+        "kernel": [
+            StrOptions(set(PAIRWISE_KERNEL_FUNCTIONS.keys()) | {"precomputed"}),
+            callable,
+        ],
+        "gamma": [Interval(Real, 0.0, None, closed="left"), None],
+        "degree": [Interval(Integral, 0, None, closed="left")],
+        "coef0": [Interval(Real, None, None, closed="neither")],
+        "kernel_params": [dict, None],
+        "optimizer": [StrOptions({"rbtree", "avltree"}), None],
+    }
+
+    def __init__(
+        self,
+        alpha=1,
+        *,
+        rank_ratio=1.0,
+        fit_intercept=False,
+        kernel="rbf",
+        gamma=None,
+        degree=3,
+        coef0=1,
+        kernel_params=None,
+        max_iter=20,
+        verbose=False,
+        tol=None,
+        optimizer=None,
+        random_state=None,
+        timeit=False,
+    ):
+        super().__init__(
+            alpha=alpha,
+            rank_ratio=rank_ratio,
+            fit_intercept=fit_intercept,
+            max_iter=max_iter,
+            verbose=verbose,
+            tol=tol,
+            optimizer=optimizer,
+            random_state=random_state,
+            timeit=timeit,
+        )
+        self.kernel = kernel
+        self.gamma = gamma
+        self.degree = degree
+        self.coef0 = coef0
+        self.kernel_params = kernel_params
+
+    def __sklearn_tags__(self):
+        # tell sklearn.utils.metaestimators._safe_split function that we expect kernel matrix
+        tags = super().__sklearn_tags__()
+        tags.input_tags.pairwise = self.kernel == "precomputed"
+        return tags
+
+    def _get_kernel(self, X, Y=None):
+        if callable(self.kernel):
+            params = self.kernel_params or {}
+        else:
+            params = {"gamma": self.gamma, "degree": self.degree, "coef0": self.coef0}
+        return pairwise_kernels(X, Y, metric=self.kernel, filter_params=True, **params)
+
+    def _create_optimizer(self, kernel_mat, y, status):
+        if self.optimizer is None:
+            self.optimizer = "rbtree"
+
+        times, ranks = y
+
+        if self.optimizer == "rbtree":
+            optimizer = NonlinearLargeScaleOptimizer(
+                self.alpha,
+                self.rank_ratio,
+                self.fit_intercept,
+                OrderStatisticTreeSurvivalCounter(kernel_mat, ranks, status, RBTree, times),
+                timeit=self.timeit,
+            )
+        elif self.optimizer == "avltree":
+            optimizer = NonlinearLargeScaleOptimizer(
+                self.alpha,
+                self.rank_ratio,
+                self.fit_intercept,
+                OrderStatisticTreeSurvivalCounter(kernel_mat, ranks, status, AVLTree, times),
+                timeit=self.timeit,
+            )
+
+        return optimizer
+
+    def _validate_for_fit(self, X):
+        if self.kernel != "precomputed":
+            return super()._validate_for_fit(X)
+        return X
+
+    def _fit(self, X, time, event, samples_order):
+        # don't reorder X here, because it might be a precomputed kernel matrix
+        kernel_mat = self._get_kernel(X)
+        if (np.abs(kernel_mat.T - kernel_mat) > 1e-12).any():
+            raise ValueError("kernel matrix is not symmetric")
+
+        data_y = (time[samples_order], np.arange(len(samples_order)))
+        status = event[samples_order]
+
+        optimizer = self._create_optimizer(kernel_mat[np.ix_(samples_order, samples_order)], data_y, status)
+        opt_result = optimizer.run(tol=self.tol, options={"maxiter": self.max_iter, "disp": self.verbose})
+
+        # reorder coefficients according to order in original training data,
+        # i.e., reverse ordering according to samples_order
+        self.fit_X_ = X
+        if self.fit_intercept:
+            opt_result.x[samples_order + 1] = opt_result.x[1:].copy()
+        else:
+            opt_result.x[samples_order] = opt_result.x.copy()
+
+        return opt_result
+
+    def predict(self, X):
+        X = validate_data(self, X, reset=False)
+        kernel_mat = self._get_kernel(X, self.fit_X_)
+
+        val = np.dot(kernel_mat, self.coef_)
+        if hasattr(self, "intercept_"):
+            val += self.intercept_
+
+        # Order by increasing survival time if objective is pure ranking
+        if self.rank_ratio == 1:
+            val *= -1
+        else:
+            # model was fitted on log(time), transform to original scale
+            val = np.exp(val)
+
+        return val