Exemplo n.º 1
0
Arquivo: mica.py Projeto: DiNAi/misvm
    def fit(self, bags, y):
        """
        @param bags : a sequence of n bags; each bag is an m-by-k array-like
                      object containing m instances with k features
        @param y : an array-like object of length n containing -1/+1 labels
        """
        self._bags = map(np.asmatrix, bags)
        bs = BagSplitter(self._bags,
                         np.asmatrix(y).reshape((-1, 1)))
        self._X = bs.instances
        Ln = bs.L_n
        Lp = bs.L_p
        Xp = bs.X_p
        m = Ln + Xp
        if self.scale_C:
            C = self.C / float(len(self._bags))
        else:
            C = self.C

        K = kernel_by_name(self.kernel, gamma=self.gamma, p=self.p)(self._X, self._X)
        new_classes = np.matrix(np.vstack([-np.ones((Ln, 1)),
                                           np.ones((Xp, 1))]))
        self._y = new_classes
        D = spdiag(new_classes)
        setup = list(self._setup_svm(new_classes, new_classes, C))[1:]
        setup[0] = np.matrix([0])
        qp = IterativeQP(*setup)

        c = cvxmat(np.hstack([np.zeros(Lp + 1),
                              np.ones(Xp + Ln)]))
        b = cvxmat(np.ones((Xp, 1)))
        A = spz(Xp, Lp + 1 + Xp + Ln)
        for row, (i, j) in enumerate(slices(bs.pos_groups)):
            A[row, i:j] = 1.0

        bottom_left = sparse(t([[-spI(Lp), spz(Lp)],
                                [spz(m, Lp), spz(m)]]))
        bottom_right = sparse([spz(Lp, m), -spI(m)])
        inst_cons = sparse(t([[spz(Xp, Lp), -spo(Xp)],
                              [spz(Ln, Lp), spo(Ln)]]))
        G = sparse(t([[inst_cons, -spI(m)],
                      [bottom_left, bottom_right]]))
        h = cvxmat(np.vstack([-np.ones((Xp, 1)),
                              np.zeros((Ln + Lp + m, 1))]))

        def to_V(upsilon):
            bot = np.zeros((Xp, Lp))
            for row, (i, j) in enumerate(slices(bs.pos_groups)):
                bot[row, i:j] = upsilon.flat[i:j]
            return sp.bmat([[sp.eye(Ln, Ln), None],
                            [None, sp.coo_matrix(bot)]])

        class MICACCCP(CCCP):

            def bailout(cself, alphas, upsilon, svm):
                return svm

            def iterate(cself, alphas, upsilon, svm):
                V = to_V(upsilon)
                cself.mention('Update QP...')
                qp.update_H(D * V * K * V.T * D)
                cself.mention('Solve QP...')
                alphas, obj = qp.solve(self.verbose)
                svm = MICA(kernel=self.kernel, gamma=self.gamma, p=self.p,
                           verbose=self.verbose, sv_cutoff=self.sv_cutoff)
                svm._X = self._X
                svm._y = self._y
                svm._V = V
                svm._alphas = alphas
                svm._objective = obj
                svm._compute_separator(K)
                svm._K = K

                cself.mention('Update LP...')
                for row, (i, j) in enumerate(slices(bs.pos_groups)):
                    G[row, i:j] = cvxmat(-svm._dotprods[Ln + i: Ln + j].T)
                h[Xp: Xp + Ln] = cvxmat(-(1 + svm._dotprods[:Ln]))

                cself.mention('Solve LP...')
                sol, _ = linprog(c, G, h, A, b, verbose=self.verbose)
                new_upsilon = sol[:Lp]

                if cself.check_tolerance(np.linalg.norm(upsilon - new_upsilon)):
                    return None, svm

                return {'alphas': alphas, 'upsilon': new_upsilon, 'svm': svm}, None

        best_obj = float('inf')
        best_svm = None
        for rr in range(self.restarts + 1):
            if rr == 0:
                if self.verbose:
                    print 'Non-random start...'
                upsilon0 = np.matrix(np.vstack([np.ones((size, 1)) / float(size)
                                                for size in bs.pos_groups]))
            else:
                if self.verbose:
                    print 'Random restart %d of %d...' % (rr, self.restarts)
                upsilon0 = np.matrix(np.vstack([rand_convex(size).T
                                                for size in bs.pos_groups]))
            cccp = MICACCCP(verbose=self.verbose, alphas=None, upsilon=upsilon0,
                            svm=None, max_iters=self.max_iters)
            svm = cccp.solve()
            if svm is not None:
                obj = float(svm._objective)
                if obj < best_obj:
                    best_svm = svm
                    best_obj = obj

        if best_svm is not None:
            self._V = best_svm._V
            self._alphas = best_svm._alphas
            self._objective = best_svm._objective
            self._compute_separator(best_svm._K)
            self._bag_predictions = self.predict(self._bags)
Exemplo n.º 2
0
Arquivo: misvm.py Projeto: DiNAi/misvm
    def fit(self, bags, y):
        """
        @param bags : a sequence of n bags; each bag is an m-by-k array-like
                      object containing m instances with k features
        @param y : an array-like object of length n containing -1/+1 labels
        """
        def transform(mx):
            """
            Transform into np.matrix if array/list
            ignore scipy.sparse matrix
            """
            if issparse(mx):
                return mx.todense()
            return np.asmatrix(mx)

        self._bags = [transform(bag) for bag in bags]
        y = np.asmatrix(y).reshape((-1, 1))

        bs = BagSplitter(self._bags, y)
        best_obj = float('inf')
        best_svm = None
        for rr in range(self.restarts + 1):
            if rr == 0:
                if self.verbose:
                    print 'Non-random start...'
                pos_bag_avgs = np.vstack([np.average(bag, axis=0) for bag in bs.pos_bags])
            else:
                if self.verbose:
                    print 'Random restart %d of %d...' % (rr, self.restarts)
                pos_bag_avgs = np.vstack([rand_convex(len(bag)) * bag for bag in bs.pos_bags])

            intial_instances = np.vstack([bs.neg_instances, pos_bag_avgs])
            classes = np.vstack([-np.ones((bs.L_n, 1)),
                                 np.ones((bs.X_p, 1))])

            # Setup SVM and QP
            if self.scale_C:
                C = self.C / float(len(intial_instances))
            else:
                C = self.C
            setup = self._setup_svm(intial_instances, classes, C)
            K = setup[0]
            qp = IterativeQP(*setup[1:])

            # Fix Gx <= h
            neg_cons = spzeros(bs.X_n, bs.L_n)
            for b, (l, u) in enumerate(slices(bs.neg_groups)):
                neg_cons[b, l:u] = 1.0
            pos_cons = speye(bs.X_p)
            bot_left = spzeros(bs.X_p, bs.L_n)
            top_right = spzeros(bs.X_n, bs.X_p)
            half_cons = sparse([[neg_cons, bot_left],
                                [top_right, pos_cons]])
            qp.G = sparse([-speye(bs.X_p + bs.L_n), half_cons])
            qp.h = cvxmat(np.vstack([np.zeros((bs.X_p + bs.L_n, 1)),
                                     C * np.ones((bs.X_p + bs.X_n, 1))]))

            # Precompute kernel for all positive instances
            kernel = kernel_by_name(self.kernel, gamma=self.gamma, p=self.p)
            K_all = kernel(bs.instances, bs.instances)

            neg_selectors = np.array(range(bs.L_n))

            class MISVMCCCP(CCCP):

                def bailout(cself, svm, selectors, instances, K):
                    return svm

                def iterate(cself, svm, selectors, instances, K):
                    cself.mention('Training SVM...')
                    alphas, obj = qp.solve(cself.verbose)

                    # Construct SVM from solution
                    svm = SVM(kernel=self.kernel, gamma=self.gamma, p=self.p,
                              verbose=self.verbose, sv_cutoff=self.sv_cutoff)
                    svm._X = instances
                    svm._y = classes
                    svm._alphas = alphas
                    svm._objective = obj
                    svm._compute_separator(K)
                    svm._K = K

                    cself.mention('Recomputing classes...')
                    p_confs = svm.predict(bs.pos_instances)
                    pos_selectors = bs.L_n + np.array([l + np.argmax(p_confs[l:u])
                                                       for l, u in slices(bs.pos_groups)])
                    new_selectors = np.hstack([neg_selectors, pos_selectors])

                    if selectors is None:
                        sel_diff = len(new_selectors)
                    else:
                        sel_diff = np.nonzero(new_selectors - selectors)[0].size

                    cself.mention('Selector differences: %d' % sel_diff)
                    if sel_diff == 0:
                        return None, svm
                    elif sel_diff > 5:
                        # Clear results to avoid a
                        # bad starting point in
                        # the next iteration
                        qp.clear_results()

                    cself.mention('Updating QP...')
                    indices = (new_selectors,)
                    K = K_all[indices].T[indices].T
                    D = spdiag(classes)
                    qp.update_H(D * K * D)
                    return {'svm': svm, 'selectors': new_selectors,
                            'instances': bs.instances[indices], 'K': K}, None

            cccp = MISVMCCCP(verbose=self.verbose, svm=None, selectors=None,
                             instances=intial_instances, K=K, max_iters=self.max_iters)
            svm = cccp.solve()
            if svm is not None:
                obj = float(svm._objective)
                if obj < best_obj:
                    best_svm = svm
                    best_obj = obj

        if best_svm is not None:
            self._X = best_svm._X
            self._y = best_svm._y
            self._alphas = best_svm._alphas
            self._objective = best_svm._objective
            self._compute_separator(best_svm._K)
Exemplo n.º 3
0
    def fit(self, bags, y):
        """
        @param bags : a sequence of n bags; each bag is an m-by-k array-like
                      object containing m instances with k features
        @param y : an array-like object of length n containing -1/+1 labels
        """
        def transform(mx):
            """
            Transform into np.matrix if array/list
            ignore scipy.sparse matrix
            """
            if issparse(mx):
                return mx.todense()
            return np.asmatrix(mx)

        self._bags = [transform(bag) for bag in bags]
        y = np.asmatrix(y).reshape((-1, 1))

        bs = BagSplitter(self._bags, y)
        best_obj = float('inf')
        best_svm = None
        for rr in range(self.restarts + 1):
            if rr == 0:
                if self.verbose:
                    print('Non-random start...')
                pos_bag_avgs = np.vstack([np.average(bag, axis=0) for bag in bs.pos_bags])
            else:
                if self.verbose:
                    print('Random restart %d of %d...' % (rr, self.restarts))
                pos_bag_avgs = np.vstack([rand_convex(len(bag)) * bag for bag in bs.pos_bags])

            intial_instances = np.vstack([bs.neg_instances, pos_bag_avgs])
            classes = np.vstack([-np.ones((bs.L_n, 1)),
                                 np.ones((bs.X_p, 1))])

            # Setup SVM and QP
            if self.scale_C:
                C = self.C / float(len(intial_instances))
            else:
                C = self.C
            setup = self._setup_svm(intial_instances, classes, C)
            K = setup[0]
            qp = IterativeQP(*setup[1:])

            # Fix Gx <= h
            neg_cons = spzeros(bs.X_n, bs.L_n)
            for b, (l, u) in enumerate(slices(bs.neg_groups)):
                neg_cons[b, l:u] = 1.0
            pos_cons = speye(bs.X_p)
            bot_left = spzeros(bs.X_p, bs.L_n)
            top_right = spzeros(bs.X_n, bs.X_p)
            half_cons = sparse([[neg_cons, bot_left],
                                [top_right, pos_cons]])
            qp.G = sparse([-speye(bs.X_p + bs.L_n), half_cons])
            qp.h = cvxmat(np.vstack([np.zeros((bs.X_p + bs.L_n, 1)),
                                     C * np.ones((bs.X_p + bs.X_n, 1))]))

            # Precompute kernel for all positive instances
            kernel = kernel_by_name(self.kernel, gamma=self.gamma, p=self.p)
            K_all = kernel(bs.instances, bs.instances)

            neg_selectors = np.array(range(bs.L_n))

            class MISVMCCCP(CCCP):

                def bailout(cself, svm, selectors, instances, K):
                    return svm

                def iterate(cself, svm, selectors, instances, K):
                    cself.mention('Training SVM...')
                    alphas, obj = qp.solve(cself.verbose)

                    # Construct SVM from solution
                    svm = SVM(kernel=self.kernel, gamma=self.gamma, p=self.p,
                              verbose=self.verbose, sv_cutoff=self.sv_cutoff)
                    svm._X = instances
                    svm._y = classes
                    svm._alphas = alphas
                    svm._objective = obj
                    svm._compute_separator(K)
                    svm._K = K

                    cself.mention('Recomputing classes...')
                    p_confs = svm.predict(bs.pos_instances)
                    pos_selectors = bs.L_n + np.array([l + np.argmax(p_confs[l:u])
                                                       for l, u in slices(bs.pos_groups)])
                    new_selectors = np.hstack([neg_selectors, pos_selectors])

                    if selectors is None:
                        sel_diff = len(new_selectors)
                    else:
                        sel_diff = np.nonzero(new_selectors - selectors)[0].size

                    cself.mention('Selector differences: %d' % sel_diff)
                    if sel_diff == 0:
                        return None, svm
                    elif sel_diff > 5:
                        # Clear results to avoid a
                        # bad starting point in
                        # the next iteration
                        qp.clear_results()

                    cself.mention('Updating QP...')
                    indices = (new_selectors,)
                    K = K_all[indices].T[indices].T
                    D = spdiag(classes)
                    qp.update_H(D * K * D)
                    return {'svm': svm, 'selectors': new_selectors,
                            'instances': bs.instances[indices], 'K': K}, None

            cccp = MISVMCCCP(verbose=self.verbose, svm=None, selectors=None,
                             instances=intial_instances, K=K, max_iters=self.max_iters)
            svm = cccp.solve()
            if svm is not None:
                obj = float(svm._objective)
                if obj < best_obj:
                    best_svm = svm
                    best_obj = obj

        if best_svm is not None:
            self._X = best_svm._X
            self._y = best_svm._y
            self._alphas = best_svm._alphas
            self._objective = best_svm._objective
            self._compute_separator(best_svm._K)
Exemplo n.º 4
0
    def fit(self, bags, y):
        """
        @param bags : a sequence of n bags; each bag is an m-by-k array-like
                      object containing m instances with k features
        @param y : an array-like object of length n containing -1/+1 labels
        """
        self._bags = map(np.asmatrix, bags)
        bs = BagSplitter(self._bags, np.asmatrix(y).reshape((-1, 1)))
        self._X = bs.instances
        Ln = bs.L_n
        Lp = bs.L_p
        Xp = bs.X_p
        m = Ln + Xp
        if self.scale_C:
            C = self.C / float(len(self._bags))
        else:
            C = self.C

        K = kernel_by_name(self.kernel, gamma=self.gamma, p=self.p)(self._X,
                                                                    self._X)
        new_classes = np.matrix(
            np.vstack([-np.ones((Ln, 1)), np.ones((Xp, 1))]))
        self._y = new_classes
        D = spdiag(new_classes)
        setup = list(self._setup_svm(new_classes, new_classes, C))[1:]
        setup[0] = np.matrix([0])
        qp = IterativeQP(*setup)

        c = cvxmat(np.hstack([np.zeros(Lp + 1), np.ones(Xp + Ln)]))
        b = cvxmat(np.ones((Xp, 1)))
        A = spz(Xp, Lp + 1 + Xp + Ln)
        for row, (i, j) in enumerate(slices(bs.pos_groups)):
            A[row, i:j] = 1.0

        bottom_left = sparse(t([[-spI(Lp), spz(Lp)], [spz(m, Lp), spz(m)]]))
        bottom_right = sparse([spz(Lp, m), -spI(m)])
        inst_cons = sparse(t([[spz(Xp, Lp), -spo(Xp)], [spz(Ln, Lp),
                                                        spo(Ln)]]))
        G = sparse(t([[inst_cons, -spI(m)], [bottom_left, bottom_right]]))
        h = cvxmat(np.vstack([-np.ones((Xp, 1)), np.zeros((Ln + Lp + m, 1))]))

        def to_V(upsilon):
            bot = np.zeros((Xp, Lp))
            for row, (i, j) in enumerate(slices(bs.pos_groups)):
                bot[row, i:j] = upsilon.flat[i:j]
            return sp.bmat([[sp.eye(Ln, Ln), None], [None,
                                                     sp.coo_matrix(bot)]])

        class MICACCCP(CCCP):
            def bailout(cself, alphas, upsilon, svm):
                return svm

            def iterate(cself, alphas, upsilon, svm):
                V = to_V(upsilon)
                cself.mention('Update QP...')
                qp.update_H(D * V * K * V.T * D)
                cself.mention('Solve QP...')
                alphas, obj = qp.solve(self.verbose)
                svm = MICA(kernel=self.kernel,
                           gamma=self.gamma,
                           p=self.p,
                           verbose=self.verbose,
                           sv_cutoff=self.sv_cutoff)
                svm._X = self._X
                svm._y = self._y
                svm._V = V
                svm._alphas = alphas
                svm._objective = obj
                svm._compute_separator(K)
                svm._K = K

                cself.mention('Update LP...')
                for row, (i, j) in enumerate(slices(bs.pos_groups)):
                    G[row, i:j] = cvxmat(-svm._dotprods[Ln + i:Ln + j].T)
                h[Xp:Xp + Ln] = cvxmat(-(1 + svm._dotprods[:Ln]))

                cself.mention('Solve LP...')
                sol, _ = linprog(c, G, h, A, b, verbose=self.verbose)
                new_upsilon = sol[:Lp]

                if cself.check_tolerance(np.linalg.norm(upsilon -
                                                        new_upsilon)):
                    return None, svm

                return {
                    'alphas': alphas,
                    'upsilon': new_upsilon,
                    'svm': svm
                }, None

        best_obj = float('inf')
        best_svm = None
        for rr in range(self.restarts + 1):
            if rr == 0:
                if self.verbose:
                    print 'Non-random start...'
                upsilon0 = np.matrix(
                    np.vstack([
                        np.ones((size, 1)) / float(size)
                        for size in bs.pos_groups
                    ]))
            else:
                if self.verbose:
                    print 'Random restart %d of %d...' % (rr, self.restarts)
                upsilon0 = np.matrix(
                    np.vstack([rand_convex(size).T for size in bs.pos_groups]))
            cccp = MICACCCP(verbose=self.verbose,
                            alphas=None,
                            upsilon=upsilon0,
                            svm=None,
                            max_iters=self.max_iters)
            svm = cccp.solve()
            if svm is not None:
                obj = float(svm._objective)
                if obj < best_obj:
                    best_svm = svm
                    best_obj = obj

        if best_svm is not None:
            self._V = best_svm._V
            self._alphas = best_svm._alphas
            self._objective = best_svm._objective
            self._compute_separator(best_svm._K)
            self._bag_predictions = self.predict(self._bags)