graphkit-learn/gklearn/tests/test_graph_kernels.py

"""Tests of graph kernels.
"""

import pytest
import multiprocessing
import numpy as np

##############################################################################

def test_list_graph_kernels():
	"""
	"""
	from gklearn.kernels import GRAPH_KERNELS, list_of_graph_kernels
	assert list_of_graph_kernels() == [i for i in GRAPH_KERNELS]


##############################################################################

def chooseDataset(ds_name):
	"""Choose dataset according to name.
	"""
	from gklearn.utils import Dataset

	dataset = Dataset()

	# no node labels (and no edge labels).
	if ds_name == 'Alkane':
		dataset.load_predefined_dataset(ds_name)
		dataset.trim_dataset(edge_required=False)
		irrelevant_labels = {'node_attrs': ['x', 'y', 'z'], 'edge_labels': ['bond_stereo']}
		dataset.remove_labels(**irrelevant_labels)
		dataset.cut_graphs(range(1, 10))
	# node symbolic labels.
	elif ds_name == 'Acyclic':
		dataset.load_predefined_dataset(ds_name)
		dataset.trim_dataset(edge_required=False)
		irrelevant_labels = {'node_attrs': ['x', 'y', 'z'], 'edge_labels': ['bond_stereo']}
		dataset.remove_labels(**irrelevant_labels)
	# node non-symbolic labels.
	elif ds_name == 'Letter-med':
		dataset.load_predefined_dataset(ds_name)
		dataset.trim_dataset(edge_required=False)
	# node symbolic and non-symbolic labels (and edge symbolic labels).
	elif ds_name == 'AIDS':
		dataset.load_predefined_dataset(ds_name)
		dataset.trim_dataset(edge_required=False)
	# edge non-symbolic labels (no node labels).
	elif ds_name == 'Fingerprint_edge':
		dataset.load_predefined_dataset('Fingerprint')
		dataset.trim_dataset(edge_required=True)
		irrelevant_labels = {'edge_attrs': ['orient', 'angle']}
		dataset.remove_labels(**irrelevant_labels)
	# edge non-symbolic labels (and node non-symbolic labels).
	elif ds_name == 'Fingerprint':
		dataset.load_predefined_dataset(ds_name)
		dataset.trim_dataset(edge_required=True)
	# edge symbolic and non-symbolic labels (and node symbolic and non-symbolic labels).
	elif ds_name == 'Cuneiform':
		dataset.load_predefined_dataset(ds_name)
		dataset.trim_dataset(edge_required=True)

	dataset.cut_graphs(range(0, 3))

	return dataset


def assert_equality(compute_fun, **kwargs):
	"""Check if outputs are the same using different methods to compute.

	Parameters
	----------
	compute_fun : function
		The function to compute the kernel, with the same key word arguments as
		kwargs.
	**kwargs : dict
		The key word arguments over the grid of which the kernel results are
		compared.

	Returns
	-------
	None.
	"""
	from sklearn.model_selection import ParameterGrid
	param_grid = ParameterGrid(kwargs)

	result_lists = [[], [], []]
	for params in list(param_grid):
		results = compute_fun(**params)
		for rs, lst in zip(results, result_lists):
			lst.append(rs)
	for lst in result_lists:
		for i in range(len(lst[:-1])):
			assert np.array_equal(lst[i], lst[i + 1])


@pytest.mark.parametrize('ds_name', ['Alkane', 'AIDS'])
@pytest.mark.parametrize('weight,compute_method', [(0.01, 'geo'), (1, 'exp')])
# @pytest.mark.parametrize('parallel', ['imap_unordered', None])
def test_CommonWalk(ds_name, weight, compute_method):
	"""Test common walk kernel.
	"""
	def compute(parallel=None):
		from gklearn.kernels import CommonWalk
		import networkx as nx

		dataset = chooseDataset(ds_name)
		dataset.load_graphs([g for g in dataset.graphs if nx.number_of_nodes(g) > 1])

		try:
			graph_kernel = CommonWalk(node_labels=dataset.node_labels,
						edge_labels=dataset.edge_labels,
						ds_infos=dataset.get_dataset_infos(keys=['directed']),
						weight=weight,
						compute_method=compute_method)
			gram_matrix, run_time = graph_kernel.compute(dataset.graphs,
				parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)
			kernel_list, run_time = graph_kernel.compute(dataset.graphs[0], dataset.graphs[1:],
				parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)
			kernel, run_time = graph_kernel.compute(dataset.graphs[0], dataset.graphs[1],
				parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)

		except Exception as exception:
			assert False, exception
		else:
			return gram_matrix, kernel_list, kernel

	assert_equality(compute, parallel=['imap_unordered', None])


@pytest.mark.parametrize('ds_name', ['Alkane', 'AIDS'])
@pytest.mark.parametrize('remove_totters', [False]) #[True, False])
# @pytest.mark.parametrize('parallel', ['imap_unordered', None])
def test_Marginalized(ds_name, remove_totters):
	"""Test marginalized kernel.
	"""
	def compute(parallel=None):
		from gklearn.kernels import Marginalized

		dataset = chooseDataset(ds_name)

		try:
			graph_kernel = Marginalized(node_labels=dataset.node_labels,
						edge_labels=dataset.edge_labels,
						ds_infos=dataset.get_dataset_infos(keys=['directed']),
						p_quit=0.5,
						n_iteration=2,
						remove_totters=remove_totters)
			gram_matrix, run_time = graph_kernel.compute(dataset.graphs,
				parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)
			kernel_list, run_time = graph_kernel.compute(dataset.graphs[0], dataset.graphs[1:],
				parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)
			kernel, run_time = graph_kernel.compute(dataset.graphs[0], dataset.graphs[1],
				parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)

		except Exception as exception:
			assert False, exception
		else:
			return gram_matrix, kernel_list, kernel

	assert_equality(compute, parallel=['imap_unordered', None])


@pytest.mark.parametrize('ds_name', ['Acyclic'])
# @pytest.mark.parametrize('parallel', ['imap_unordered', None])
def test_SylvesterEquation(ds_name):
	"""Test sylvester equation kernel.
	"""
	def compute(parallel=None):
		from gklearn.kernels import SylvesterEquation

		dataset = chooseDataset(ds_name)

		try:
			graph_kernel = SylvesterEquation(
								ds_infos=dataset.get_dataset_infos(keys=['directed']),
								weight=1e-3,
								p=None,
								q=None,
								edge_weight=None)
			gram_matrix, run_time = graph_kernel.compute(dataset.graphs,
				parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)
			kernel_list, run_time = graph_kernel.compute(dataset.graphs[0], dataset.graphs[1:],
				parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)
			kernel, run_time = graph_kernel.compute(dataset.graphs[0], dataset.graphs[1],
				parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)

		except Exception as exception:
			assert False, exception
		else:
			return gram_matrix, kernel_list, kernel

	assert_equality(compute, parallel=['imap_unordered', None])


@pytest.mark.parametrize('ds_name', ['Acyclic', 'AIDS'])
# @pytest.mark.parametrize('parallel', ['imap_unordered', None])
def test_ConjugateGradient(ds_name):
	"""Test conjugate gradient kernel.
	"""
	def compute(parallel=None):
		from gklearn.kernels import ConjugateGradient
		from gklearn.utils.kernels import deltakernel, gaussiankernel, kernelproduct
		import functools

		dataset = chooseDataset(ds_name)

		mixkernel = functools.partial(kernelproduct, deltakernel, gaussiankernel)
		sub_kernels = {'symb': deltakernel, 'nsymb': gaussiankernel, 'mix': mixkernel}

		try:
			graph_kernel = ConjugateGradient(
								node_labels=dataset.node_labels,
								node_attrs=dataset.node_attrs,
								edge_labels=dataset.edge_labels,
								edge_attrs=dataset.edge_attrs,
								ds_infos=dataset.get_dataset_infos(keys=['directed']),
								weight=1e-3,
								p=None,
								q=None,
								edge_weight=None,
								node_kernels=sub_kernels,
								edge_kernels=sub_kernels)
			gram_matrix, run_time = graph_kernel.compute(dataset.graphs,
				parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)
			kernel_list, run_time = graph_kernel.compute(dataset.graphs[0], dataset.graphs[1:],
				parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)
			kernel, run_time = graph_kernel.compute(dataset.graphs[0], dataset.graphs[1],
				parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)

		except Exception as exception:
			assert False, exception
		else:
			return gram_matrix, kernel_list, kernel

	assert_equality(compute, parallel=['imap_unordered', None])


@pytest.mark.parametrize('ds_name', ['Acyclic', 'AIDS'])
# @pytest.mark.parametrize('parallel', ['imap_unordered', None])
def test_FixedPoint(ds_name):
	"""Test fixed point kernel.
	"""
	def compute(parallel=None):
		from gklearn.kernels import FixedPoint
		from gklearn.utils.kernels import deltakernel, gaussiankernel, kernelproduct
		import functools

		dataset = chooseDataset(ds_name)

		mixkernel = functools.partial(kernelproduct, deltakernel, gaussiankernel)
		sub_kernels = {'symb': deltakernel, 'nsymb': gaussiankernel, 'mix': mixkernel}

		try:
			graph_kernel = FixedPoint(
								node_labels=dataset.node_labels,
								node_attrs=dataset.node_attrs,
								edge_labels=dataset.edge_labels,
								edge_attrs=dataset.edge_attrs,
								ds_infos=dataset.get_dataset_infos(keys=['directed']),
								weight=1e-3,
								p=None,
								q=None,
								edge_weight=None,
								node_kernels=sub_kernels,
								edge_kernels=sub_kernels)
			gram_matrix, run_time = graph_kernel.compute(dataset.graphs,
				parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)
			kernel_list, run_time = graph_kernel.compute(dataset.graphs[0], dataset.graphs[1:],
				parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)
			kernel, run_time = graph_kernel.compute(dataset.graphs[0], dataset.graphs[1],
				parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)

		except Exception as exception:
			assert False, exception
		else:
			return gram_matrix, kernel_list, kernel

	assert_equality(compute, parallel=['imap_unordered', None])


@pytest.mark.parametrize('ds_name', ['Acyclic'])
@pytest.mark.parametrize('sub_kernel', ['exp', 'geo'])
# @pytest.mark.parametrize('parallel', ['imap_unordered', None])
def test_SpectralDecomposition(ds_name, sub_kernel):
	"""Test spectral decomposition kernel.
	"""
	def compute(parallel=None):
		from gklearn.kernels import SpectralDecomposition

		dataset = chooseDataset(ds_name)

		try:
			graph_kernel = SpectralDecomposition(
								ds_infos=dataset.get_dataset_infos(keys=['directed']),
								weight=1e-3,
								p=None,
								q=None,
								edge_weight=None,
								sub_kernel=sub_kernel)
			gram_matrix, run_time = graph_kernel.compute(dataset.graphs,
				parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)
			kernel_list, run_time = graph_kernel.compute(dataset.graphs[0], dataset.graphs[1:],
				parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)
			kernel, run_time = graph_kernel.compute(dataset.graphs[0], dataset.graphs[1],
				parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)

		except Exception as exception:
			assert False, exception
		else:
			return gram_matrix, kernel_list, kernel

	assert_equality(compute, parallel=['imap_unordered', None])


# @pytest.mark.parametrize(
#		'compute_method,ds_name,sub_kernel',
#		[
#			('sylvester', 'Alkane', None),
#			('conjugate', 'Alkane', None),
#			('conjugate', 'AIDS', None),
#			('fp', 'Alkane', None),
#			('fp', 'AIDS', None),
#			('spectral', 'Alkane', 'exp'),
#			('spectral', 'Alkane', 'geo'),
#		]
# )
# @pytest.mark.parametrize('parallel', ['imap_unordered', None])
# def test_RandomWalk(ds_name, compute_method, sub_kernel, parallel):
#	"""Test random walk kernel.
#	"""
#	from gklearn.kernels import RandomWalk
#	from gklearn.utils.kernels import deltakernel, gaussiankernel, kernelproduct
#	import functools
#
#	dataset = chooseDataset(ds_name)

#	mixkernel = functools.partial(kernelproduct, deltakernel, gaussiankernel)
#	sub_kernels = {'symb': deltakernel, 'nsymb': gaussiankernel, 'mix': mixkernel}
# #	try:
#	graph_kernel = RandomWalk(node_labels=dataset.node_labels,
#						node_attrs=dataset.node_attrs,
#						edge_labels=dataset.edge_labels,
#						edge_attrs=dataset.edge_attrs,
#						ds_infos=dataset.get_dataset_infos(keys=['directed']),
#						compute_method=compute_method,
#						weight=1e-3,
#						p=None,
#						q=None,
#						edge_weight=None,
#						node_kernels=sub_kernels,
#						edge_kernels=sub_kernels,
#						sub_kernel=sub_kernel)
#	gram_matrix, run_time = graph_kernel.compute(dataset.graphs,
#		parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)
#	kernel_list, run_time = graph_kernel.compute(dataset.graphs[0], dataset.graphs[1:],
#		parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)
#	kernel, run_time = graph_kernel.compute(dataset.graphs[0], dataset.graphs[1],
#		parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)

#	except Exception as exception:
#		assert False, exception


@pytest.mark.parametrize('ds_name', ['Alkane', 'Acyclic', 'Letter-med', 'AIDS', 'Fingerprint'])
# @pytest.mark.parametrize('parallel', ['imap_unordered', None])
def test_ShortestPath(ds_name):
	"""Test shortest path kernel.
	"""
	def compute(parallel=None, fcsp=None):
		from gklearn.kernels import ShortestPath
		from gklearn.utils.kernels import deltakernel, gaussiankernel, kernelproduct
		import functools

		dataset = chooseDataset(ds_name)

		mixkernel = functools.partial(kernelproduct, deltakernel, gaussiankernel)
		sub_kernels = {'symb': deltakernel, 'nsymb': gaussiankernel, 'mix': mixkernel}
		try:
			graph_kernel = ShortestPath(node_labels=dataset.node_labels,
						node_attrs=dataset.node_attrs,
						ds_infos=dataset.get_dataset_infos(keys=['directed']),
						fcsp=fcsp,
						node_kernels=sub_kernels)
			gram_matrix, run_time = graph_kernel.compute(dataset.graphs,
				parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)
			kernel_list, run_time = graph_kernel.compute(dataset.graphs[0], dataset.graphs[1:],
				parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)
			kernel, run_time = graph_kernel.compute(dataset.graphs[0], dataset.graphs[1],
				parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)

		except Exception as exception:
			assert False, exception
		else:
			return gram_matrix, kernel_list, kernel

	assert_equality(compute, parallel=['imap_unordered', None], fcsp=[True, False])


#@pytest.mark.parametrize('ds_name', ['Alkane', 'Acyclic', 'Letter-med', 'AIDS', 'Fingerprint'])
@pytest.mark.parametrize('ds_name', ['Alkane', 'Acyclic', 'Letter-med', 'AIDS', 'Fingerprint', 'Fingerprint_edge', 'Cuneiform'])
# @pytest.mark.parametrize('parallel', ['imap_unordered', None])
def test_StructuralSP(ds_name):
	"""Test structural shortest path kernel.
	"""
	def compute(parallel=None, fcsp=None):
		from gklearn.kernels import StructuralSP
		from gklearn.utils.kernels import deltakernel, gaussiankernel, kernelproduct
		import functools

		dataset = chooseDataset(ds_name)

		mixkernel = functools.partial(kernelproduct, deltakernel, gaussiankernel)
		sub_kernels = {'symb': deltakernel, 'nsymb': gaussiankernel, 'mix': mixkernel}
		try:
			graph_kernel = StructuralSP(node_labels=dataset.node_labels,
						 edge_labels=dataset.edge_labels,
						 node_attrs=dataset.node_attrs,
						 edge_attrs=dataset.edge_attrs,
						 ds_infos=dataset.get_dataset_infos(keys=['directed']),
						 fcsp=fcsp,
						 node_kernels=sub_kernels,
						 edge_kernels=sub_kernels)
			gram_matrix, run_time = graph_kernel.compute(dataset.graphs,
	 			parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)
			kernel_list, run_time = graph_kernel.compute(dataset.graphs[0], dataset.graphs[1:],
	 			parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)
			kernel, run_time = graph_kernel.compute(dataset.graphs[0], dataset.graphs[1],
	 			parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)

		except Exception as exception:
			assert False, exception
		else:
			return gram_matrix, kernel_list, kernel

	assert_equality(compute, parallel=['imap_unordered', None], fcsp=[True, False])


@pytest.mark.parametrize('ds_name', ['Alkane', 'AIDS'])
# @pytest.mark.parametrize('parallel', ['imap_unordered', None])
#@pytest.mark.parametrize('k_func', ['MinMax', 'tanimoto', None])
@pytest.mark.parametrize('k_func', ['MinMax', 'tanimoto'])
# @pytest.mark.parametrize('compute_method', ['trie', 'naive'])
def test_PathUpToH(ds_name, k_func):
	"""Test path kernel up to length $h$.
	"""
	def compute(parallel=None, compute_method=None):
		from gklearn.kernels import PathUpToH

		dataset = chooseDataset(ds_name)

		try:
			graph_kernel = PathUpToH(node_labels=dataset.node_labels,
						 edge_labels=dataset.edge_labels,
						 ds_infos=dataset.get_dataset_infos(keys=['directed']),
						 depth=2, k_func=k_func, compute_method=compute_method)
			gram_matrix, run_time = graph_kernel.compute(dataset.graphs,
				parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)
			kernel_list, run_time = graph_kernel.compute(dataset.graphs[0], dataset.graphs[1:],
				parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)
			kernel, run_time = graph_kernel.compute(dataset.graphs[0], dataset.graphs[1],
				parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)
		except Exception as exception:
			assert False, exception
		else:
			return gram_matrix, kernel_list, kernel

	assert_equality(compute, parallel=['imap_unordered', None],
				 compute_method=['trie', 'naive'])


@pytest.mark.parametrize('ds_name', ['Alkane', 'AIDS'])
# @pytest.mark.parametrize('parallel', ['imap_unordered', None])
def test_Treelet(ds_name):
	"""Test treelet kernel.
	"""
	def compute(parallel=None):
		from gklearn.kernels import Treelet
		from gklearn.utils.kernels import polynomialkernel
		import functools

		dataset = chooseDataset(ds_name)

		pkernel = functools.partial(polynomialkernel, d=2, c=1e5)
		try:
			graph_kernel = Treelet(node_labels=dataset.node_labels,
						 edge_labels=dataset.edge_labels,
						 ds_infos=dataset.get_dataset_infos(keys=['directed']),
						 sub_kernel=pkernel)
			gram_matrix, run_time = graph_kernel.compute(dataset.graphs,
				parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)
			kernel_list, run_time = graph_kernel.compute(dataset.graphs[0], dataset.graphs[1:],
				parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)
			kernel, run_time = graph_kernel.compute(dataset.graphs[0], dataset.graphs[1],
				parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)
		except Exception as exception:
			assert False, exception
		else:
			return gram_matrix, kernel_list, kernel

	assert_equality(compute, parallel=['imap_unordered', None])


@pytest.mark.parametrize('ds_name', ['Acyclic'])
#@pytest.mark.parametrize('base_kernel', ['subtree', 'sp', 'edge'])
# @pytest.mark.parametrize('base_kernel', ['subtree'])
# @pytest.mark.parametrize('parallel', ['imap_unordered', None])
def test_WLSubtree(ds_name):
	"""Test Weisfeiler-Lehman subtree kernel.
	"""
	def compute(parallel=None):
		from gklearn.kernels import WLSubtree

		dataset = chooseDataset(ds_name)

		try:
			graph_kernel = WLSubtree(node_labels=dataset.node_labels,
						 edge_labels=dataset.edge_labels,
						 ds_infos=dataset.get_dataset_infos(keys=['directed']),
						 height=2)
			gram_matrix, run_time = graph_kernel.compute(dataset.graphs,
				parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)
			kernel_list, run_time = graph_kernel.compute(dataset.graphs[0], dataset.graphs[1:],
				parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)
			kernel, run_time = graph_kernel.compute(dataset.graphs[0], dataset.graphs[1],
				parallel=parallel, n_jobs=multiprocessing.cpu_count(), verbose=True)
		except Exception as exception:
			assert False, exception
		else:
			return gram_matrix, kernel_list, kernel

	assert_equality(compute, parallel=['imap_unordered', None])


if __name__ == "__main__":
 	test_list_graph_kernels()
#	test_spkernel('Alkane', 'imap_unordered')
 	# test_ShortestPath('Alkane')
# 	test_StructuralSP('Fingerprint_edge', 'imap_unordered')
# 	test_StructuralSP('Alkane', None)
# 	test_StructuralSP('Cuneiform', None)
# 	test_WLSubtree('Acyclic', 'imap_unordered')
#	test_RandomWalk('Acyclic', 'sylvester', None, 'imap_unordered')
#	test_RandomWalk('Acyclic', 'conjugate', None, 'imap_unordered')
#	test_RandomWalk('Acyclic', 'fp', None, None)
#	test_RandomWalk('Acyclic', 'spectral', 'exp', 'imap_unordered')
# 	test_CommonWalk('Alkane', 0.01, 'geo')
# 	test_ShortestPath('Acyclic')