Python theano.sparse() Examples

def test_sparse_shared_memory():
    # Note : There are no inplace ops on sparse matrix yet. If one is
    # someday implemented, we could test it here.
    a = random_lil((3, 4), 'float32', 3).tocsr()
    m1 = random_lil((4, 4), 'float32', 3).tocsr()
    m2 = random_lil((4, 4), 'float32', 3).tocsr()
    x = SparseType('csr', dtype='float32')()
    y = SparseType('csr', dtype='float32')()

    sdot = theano.sparse.structured_dot
    z = sdot(x * 3, m1) + sdot(y * 2, m2)

    f = theano.function([theano.In(x, mutable=True),
                         theano.In(y, mutable=True)], z, mode='FAST_RUN')

    def f_(x, y, m1=m1, m2=m2):
        return ((x * 3) * m1) + ((y * 2) * m2)

    assert SparseType.may_share_memory(a, a)  # This is trivial
    result = f(a, a)
    result_ = f_(a, a)
    assert (result_.todense() == result.todense()).all() 

def test_GetItem2Lists(self):

        a, A = sparse_random_inputs('csr', (4, 5))
        b, B = sparse_random_inputs('csc', (4, 5))
        y = a[0][[0, 0, 1, 3], [0, 1, 2, 4]]
        z = b[0][[0, 0, 1, 3], [0, 1, 2, 4]]

        fa = theano.function([a[0]], y)
        fb = theano.function([b[0]], z)

        t_geta = fa(A[0])
        t_getb = fb(B[0])

        s_geta = numpy.asarray(scipy.sparse.csr_matrix(A[0])[[0, 0, 1, 3], [0, 1, 2, 4]])
        s_getb = numpy.asarray(scipy.sparse.csc_matrix(B[0])[[0, 0, 1, 3], [0, 1, 2, 4]])

        utt.assert_allclose(t_geta, s_geta)
        utt.assert_allclose(t_getb, s_getb) 

def test_local_csm_grad_c():
    raise SkipTest("Opt disabled as it don't support unsorted indices")
    if not theano.config.cxx:
        raise SkipTest("G++ not available, so we need to skip this test.")
    data = tensor.vector()
    indices, indptr, shape = (tensor.ivector(), tensor.ivector(),
                              tensor.ivector())
    mode = theano.compile.mode.get_default_mode()

    if theano.config.mode == 'FAST_COMPILE':
        mode = theano.compile.Mode(linker='c|py', optimizer='fast_compile')

    mode = mode.including("specialize", "local_csm_grad_c")
    for CS, cast in [(sparse.CSC, sp.csc_matrix), (sparse.CSR, sp.csr_matrix)]:
        cost = tensor.sum(sparse.DenseFromSparse()(CS(data, indices, indptr, shape)))
        f = theano.function(
            [data, indices, indptr, shape],
            tensor.grad(cost, data),
            mode=mode)
        assert not any(isinstance(node.op, sparse.CSMGrad) for node
                       in f.maker.fgraph.toposort())
        v = cast(random_lil((10, 40),
                            config.floatX, 3))
        f(v.data, v.indices, v.indptr, v.shape) 

def local_structured_dot(node):
    if node.op == sparse._structured_dot:
        a, b = node.inputs
        if a.type.format == 'csc':
            a_val, a_ind, a_ptr, a_shape = csm_properties(a)
            a_nsparse = a_shape[0]
            return [sd_csc(a_val, a_ind, a_ptr, a_nsparse, b)]
        if a.type.format == 'csr':
            a_val, a_ind, a_ptr, a_shape = csm_properties(a)
            return [sd_csr(a_val, a_ind, a_ptr, b)]
    return False


# Commented out because
# a) it is only slightly faster than scipy these days, and sometimes a little
# slower, and
# b) the resulting graphs make it very difficult for an op to do size checking
# on the matrices involved.  dimension mismatches are hard to detect sensibly.
# register_specialize(local_structured_dot) 

def make_node(self, x, y):
        x, y = sparse.as_sparse_variable(x), tensor.as_tensor_variable(y)
        out_dtype = scalar.upcast(x.type.dtype, y.type.dtype)
        if self.inplace:
            assert out_dtype == y.dtype

        indices, indptr, data = csm_indices(x), csm_indptr(x), csm_data(x)
        # We either use CSC or CSR depending on the format of input
        assert self.format == x.type.format
        # The magic number two here arises because L{scipy.sparse}
        # objects must be matrices (have dimension 2)
        assert y.type.ndim == 2
        out = tensor.TensorType(dtype=out_dtype,
                                broadcastable=y.type.broadcastable)()
        return gof.Apply(self,
                         [data, indices, indptr, y],
                         [out]) 

def test_op(self):
        for format in sparse.sparse_formats:
            for out_f in sparse.sparse_formats:
                for dtype in sparse.all_dtypes:
                    blocks = self.mat[format]

                    f = theano.function(
                        self.x[format],
                        self.op_class(
                            format=out_f, dtype=dtype)(*self.x[format]),
                        allow_input_downcast=True)

                    tested = f(*blocks)
                    expected = self.expected_f(blocks,
                                               format=out_f,
                                               dtype=dtype)

                    utt.assert_allclose(expected.toarray(), tested.toarray())
                    assert tested.format == expected.format
                    assert tested.dtype == expected.dtype 

def test_grad(self):
        for format in sparse.sparse_formats:
            for i_dtype in sparse.float_dtypes:
                for o_dtype in tensor.float_dtypes:
                    if o_dtype == 'float16':
                        # Don't test float16 output.
                        continue
                    _, data = sparse_random_inputs(
                        format,
                        shape=(4, 7),
                        out_dtype=i_dtype)

                    eps = None
                    if o_dtype == 'float32':
                        eps = 1e-2

                    verify_grad_sparse(Cast(o_dtype), data, eps=eps) 

def test_local_csm_properties_csm():
    data = tensor.vector()
    indices, indptr, shape = (tensor.ivector(), tensor.ivector(),
                              tensor.ivector())
    mode = theano.compile.mode.get_default_mode()
    mode = mode.including("specialize", "local_csm_properties_csm")
    for CS, cast in [(sparse.CSC, sp.csc_matrix),
                     (sparse.CSR, sp.csr_matrix)]:
        f = theano.function([data, indices, indptr, shape],
                            sparse.csm_properties(
                                CS(data, indices, indptr, shape)),
                            mode=mode)
        assert not any(
            isinstance(node.op, (sparse.CSM, sparse.CSMProperties))
            for node in f.maker.fgraph.toposort())
        v = cast(random_lil((10, 40),
                            config.floatX, 3))
        f(v.data, v.indices, v.indptr, v.shape) 

def test_local_mul_s_d():
    if not theano.config.cxx:
        raise SkipTest("G++ not available, so we need to skip this test.")
    mode = theano.compile.mode.get_default_mode()
    mode = mode.including("specialize", "local_mul_s_d")

    for sp_format in sparse.sparse_formats:
        inputs = [getattr(theano.sparse, sp_format + '_matrix')(),
                  tensor.matrix()]

        f = theano.function(inputs,
                            sparse.mul_s_d(*inputs),
                            mode=mode)

        assert not any(isinstance(node.op, sparse.MulSD) for node
                       in f.maker.fgraph.toposort()) 

def test_local_mul_s_v():
    if not theano.config.cxx:
        raise SkipTest("G++ not available, so we need to skip this test.")
    mode = theano.compile.mode.get_default_mode()
    mode = mode.including("specialize", "local_mul_s_v")

    for sp_format in ['csr']:  # Not implemented for other format
        inputs = [getattr(theano.sparse, sp_format + '_matrix')(),
                  tensor.vector()]

        f = theano.function(inputs,
                            sparse.mul_s_v(*inputs),
                            mode=mode)

        assert not any(isinstance(node.op, sparse.MulSV) for node
                       in f.maker.fgraph.toposort()) 

def test_local_sampling_dot_csr():
    if not theano.config.cxx:
        raise SkipTest("G++ not available, so we need to skip this test.")
    mode = theano.compile.mode.get_default_mode()
    mode = mode.including("specialize", "local_sampling_dot_csr")

    for sp_format in ['csr']:  # Not implemented for other format
        inputs = [tensor.matrix(),
                  tensor.matrix(),
                  getattr(theano.sparse, sp_format + '_matrix')()]

        f = theano.function(inputs,
                            sparse.sampling_dot(*inputs),
                            mode=mode)

        if theano.config.blas.ldflags:
            assert not any(isinstance(node.op, sparse.SamplingDot) for node
                       in f.maker.fgraph.toposort())
        else:
            # SamplingDotCSR's C implementation needs blas, so it should not
            # be inserted
            assert not any(isinstance(node.op, sparse.opt.SamplingDotCSR) for node
                       in f.maker.fgraph.toposort()) 

def test_infer_shape(self):
        mat = (numpy.arange(12) + 1).reshape((4, 3))
        mat[0, 1] = mat[1, 0] = mat[2, 2] = 0

        x_csc = theano.sparse.csc_matrix(dtype=theano.config.floatX)
        mat_csc = sp.csc_matrix(mat, dtype=theano.config.floatX)
        self._compile_and_check([x_csc],
                                [Remove0()(x_csc)],
                                [mat_csc],
                                self.op_class)

        x_csr = theano.sparse.csr_matrix(dtype=theano.config.floatX)
        mat_csr = sp.csr_matrix(mat, dtype=theano.config.floatX)
        self._compile_and_check([x_csr],
                                [Remove0()(x_csr)],
                                [mat_csr],
                                self.op_class) 

def test_op(self):
        for format in sparse.sparse_formats:
            for shape in zip(range(5, 9), range(3, 7)[::-1]):
                variable, data = sparse_random_inputs(format, shape=shape)

                data[0][0, 0] = data[0][1, 1] = 0

                f = theano.function(variable, self.op(*variable))
                tested = f(*data)
                expected = data[0]
                expected.eliminate_zeros()

                assert all(tested.data == expected.data)
                assert not all(tested.data == 0)

                tested = tested.toarray()
                expected = expected.toarray()
                utt.assert_allclose(expected, tested) 

def test_equality_case(self):
        """
        Test assuring normal behaviour when values
        in the matrices are equal
        """

        scipy_ver = [int(n) for n in scipy.__version__.split('.')[:2]]

        if (bool(scipy_ver < [0, 13])):
            raise SkipTest("comparison operators need newer release of scipy")

        x = sparse.csc_matrix()
        y = theano.tensor.matrix()

        m1 = sp.csc_matrix((2, 2), dtype=theano.config.floatX)
        m2 = numpy.asarray([[0, 0], [0, 0]], dtype=theano.config.floatX)

        for func in self.testsDic:

            op = func(y, x)
            f = theano.function([y, x], op)

            self.assertTrue(numpy.array_equal(f(m2, m1),
                                              self.testsDic[func](m2, m1))) 

def test_op(self):
        for format in sparse.sparse_formats:
            for axis in self.possible_axis:
                variable, data = sparse_random_inputs(format,
                                                      shape=(10, 10))

                z = theano.sparse.sp_sum(variable[0], axis=axis)
                if axis is None:
                    assert z.type.broadcastable == ()
                else:
                    assert z.type.broadcastable == (False, )

                f = theano.function(variable, self.op(variable[0], axis=axis))
                tested = f(*data)
                expected = data[0].todense().sum(axis).ravel()
                utt.assert_allclose(expected, tested) 

def test_csm_unsorted(self):
        """
        Test support for gradients of unsorted inputs.
        """
        sp_types = {'csc': sp.csc_matrix,
                    'csr': sp.csr_matrix}

        for format in ['csr', 'csc', ]:
            for dtype in ['float32', 'float64']:
                x = tensor.tensor(dtype=dtype, broadcastable=(False,))
                y = tensor.ivector()
                z = tensor.ivector()
                s = tensor.ivector()
                # Sparse advanced indexing produces unsorted sparse matrices
                a = sparse_random_inputs(format, (4, 3), out_dtype=dtype,
                                         unsorted_indices=True)[1][0]
                # Make sure it's unsorted
                assert not a.has_sorted_indices
                def my_op(x):
                    y = tensor.constant(a.indices)
                    z = tensor.constant(a.indptr)
                    s = tensor.constant(a.shape)
                    return tensor.sum(
                        dense_from_sparse(CSM(format)(x, y, z, s) * a))
                verify_grad_sparse(my_op, [a.data]) 

def test_dot_sparse_sparse(self):
        # test dot for 2 input sparse matrix
        sparse_dtype = 'float64'
        sp_mat = {'csc': sp.csc_matrix,
                  'csr': sp.csr_matrix,
                  'bsr': sp.csr_matrix}

        for sparse_format_a in ['csc', 'csr', 'bsr']:
            for sparse_format_b in ['csc', 'csr', 'bsr']:
                a = SparseType(sparse_format_a, dtype=sparse_dtype)()
                b = SparseType(sparse_format_b, dtype=sparse_dtype)()
                d = theano.dot(a, b)
                f = theano.function([a, b], theano.Out(d, borrow=True))
                topo = f.maker.fgraph.toposort()
                for M, N, K, nnz in [(4, 3, 2, 3),
                                     (40, 30, 20, 3),
                                     (40, 30, 20, 30),
                                     (400, 3000, 200, 6000),
                                 ]:
                    a_val = sp_mat[sparse_format_a](
                        random_lil((M, N), sparse_dtype, nnz))
                    b_val = sp_mat[sparse_format_b](
                        random_lil((N, K), sparse_dtype, nnz))
                    f(a_val, b_val) 

def test_csr_dense(self):
        x = theano.sparse.csr_matrix('x')
        y = theano.tensor.matrix('y')
        v = theano.tensor.vector('v')

        for (x, y, x_v, y_v) in [(x, y, self.x_csr, self.y),
                                 (x, v, self.x_csr, self.v_100),
                                 (v, x, self.v_10, self.x_csr)]:
            f_a = theano.function([x, y], theano.sparse.dot(x, y))
            f_b = lambda x, y: x * y

            utt.assert_allclose(f_a(x_v, y_v), f_b(x_v, y_v))

            # Test infer_shape
            self._compile_and_check([x, y], [theano.sparse.dot(x, y)],
                                    [x_v, y_v],
                                    (Dot, Usmm, UsmmCscDense)) 

def test_csc_dense(self):
        x = theano.sparse.csc_matrix('x')
        y = theano.tensor.matrix('y')
        v = theano.tensor.vector('v')

        for (x, y, x_v, y_v) in [(x, y, self.x_csc, self.y),
                                 (x, v, self.x_csc, self.v_100),
                                 (v, x, self.v_10, self.x_csc)]:

            f_a = theano.function([x, y], theano.sparse.dot(x, y))
            f_b = lambda x, y: x * y

            utt.assert_allclose(f_a(x_v, y_v), f_b(x_v, y_v))

            # Test infer_shape
            self._compile_and_check([x, y], [theano.sparse.dot(x, y)],
                                    [x_v, y_v],
                                    (Dot, Usmm, UsmmCscDense)) 

def test_GetItemList(self):

        a, A = sparse_random_inputs('csr', (4, 5))
        b, B = sparse_random_inputs('csc', (4, 5))
        y = a[0][[0, 1, 2, 3, 1]]
        z = b[0][[0, 1, 2, 3, 1]]

        fa = theano.function([a[0]], y)
        fb = theano.function([b[0]], z)

        t_geta = fa(A[0]).todense()
        t_getb = fb(B[0]).todense()

        s_geta = scipy.sparse.csr_matrix(A[0])[[0, 1, 2, 3, 1]].todense()
        s_getb = scipy.sparse.csc_matrix(B[0])[[0, 1, 2, 3, 1]].todense()

        utt.assert_allclose(t_geta, s_geta)
        utt.assert_allclose(t_getb, s_getb) 

def placeholder(shape=None, ndim=None, dtype=None, sparse=False, name=None):
    '''Instantiate an input data placeholder variable.
    '''
    if dtype is None:
        dtype = floatx()
    if shape is None and ndim is None:
        raise ValueError('Specify either a shape or ndim value.')
    if shape is not None:
        ndim = len(shape)
    else:
        shape = tuple([None for _ in range(ndim)])

    broadcast = (False,) * ndim
    if sparse:
        _assert_sparse_module()
        x = th_sparse_module.csr_matrix(name=name, dtype=dtype)
    else:
        x = T.TensorType(dtype, broadcast)(name)
    x._keras_shape = shape
    x._uses_learning_phase = False
    return x 

def test_int32_dtype(self):
        # Reported on the theano-user mailing-list:
        # https://groups.google.com/d/msg/theano-users/MT9ui8LtTsY/rwatwEF9zWAJ
        size = 9
        intX = 'int32'

        C = tensor.matrix('C', dtype=intX)
        I = tensor.matrix('I', dtype=intX)

        fI = I.flatten()
        data = tensor.ones_like(fI)
        indptr = tensor.arange(data.shape[0] + 1, dtype='int32')

        m1 = sparse.CSR(data, fI, indptr, (8, size))
        m2 = sparse.dot(m1, C)
        y = m2.reshape(shape=(2, 4, 9), ndim=3)

        f = theano.function(inputs=[I, C], outputs=y)
        i = numpy.asarray([[4, 3, 7, 7], [2, 8, 4, 5]], dtype=intX)
        a = numpy.asarray(numpy.random.randint(0, 100, (size, size)),
                          dtype=intX)
        f(i, a) 

def _assert_sparse_module():
    if not th_sparse_module:
        raise ImportError("Failed to import theano.sparse\n"
                          "You probably need to pip install nose-parameterized") 

def test_grad(self):
        for format in sparse.sparse_formats:
            variable, data = sparse_random_inputs(format, shape=(8, 10))
            variable.append(tensor.vector())
            data.append(numpy.random.random(10).astype(config.floatX))

            verify_grad_sparse(self.op, data, structured=True) 

def setUp(self):
        super(ColScaleCSCTester, self).setUp()
        self.op = sparse.col_scale 

def test_grad(self):
        for format in sparse.sparse_formats:
            variable, data = sparse_random_inputs(format, shape=(8, 10))
            variable.append(tensor.vector())
            data.append(numpy.random.random(8).astype(config.floatX))

            verify_grad_sparse(self.op, data, structured=True) 

def setUp(self):
        super(SpSumTester, self).setUp()
        self.op_class = sparse.SpSum
        self.op = sparse.sp_sum 

def _format_info(nb):
    x = {}
    mat = {}

    for format in sparse.sparse_formats:
        variable = getattr(theano.sparse, format + '_matrix')
        spa = getattr(sp, format + '_matrix')

        x[format] = [variable() for t in range(nb)]
        mat[format] = [spa(random_lil((3, 4), theano.config.floatX, 8))
                       for t in range(nb)]
    return x, mat 

def setUp(self):
        super(AddSSDataTester, self).setUp()
        self.op_class = AddSSData

        for format in sparse.sparse_formats:
            variable = getattr(theano.sparse, format + '_matrix')

            rand = numpy.array(
                numpy.random.random_integers(3, size=(3, 4)) - 1,
                dtype=theano.config.floatX)
            constant = as_sparse_format(rand, format)

            self.x[format] = [variable() for t in range(2)]
            self.a[format] = [constant for t in range(2)] 

def test_grad(self):
        for format in sparse.sparse_formats:
            for out_f in sparse.sparse_formats:
                for dtype in sparse.float_dtypes:
                    verify_grad_sparse(
                        self.op_class(format=out_f, dtype=dtype),
                        self.mat[format],
                        structured=False,
                        eps=1e-2,
                        )