graphkit-learn/gklearn/tests/test_graphkernels.py

"""Tests of graph kernels.
"""

import pytest
import multiprocessing


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

    # no node labels (and no edge labels).
    if ds_name == 'Alkane':
        ds_file = 'datasets/Alkane/dataset.ds'
        ds_y = 'datasets/Alkane/dataset_boiling_point_names.txt'
        Gn, y = loadDataset(ds_file, filename_y=ds_y)
        for G in Gn:
            for node in G.nodes:
                del G.nodes[node]['attributes']
    # node symbolic labels.
    elif ds_name == 'Acyclic':
        ds_file = 'datasets/acyclic/dataset_bps.ds'
        Gn, y = loadDataset(ds_file)
        for G in Gn:
            for node in G.nodes:
                del G.nodes[node]['attributes']
    # node non-symbolic labels.
    elif ds_name == 'Letter-med':
        ds_file = 'datasets/Letter-med/Letter-med_A.txt'
        Gn, y = loadDataset(ds_file)
    # node symbolic and non-symbolic labels (and edge symbolic labels).
    elif ds_name == 'AIDS':
        ds_file = 'datasets/AIDS/AIDS_A.txt'
        Gn, y = loadDataset(ds_file)
    
    # edge non-symbolic labels (no node labels).
    elif ds_name == 'Fingerprint_edge':
        import networkx as nx
        ds_file = 'datasets/Fingerprint/Fingerprint_A.txt'
        Gn, y = loadDataset(ds_file)
        Gn = [(idx, G) for idx, G in enumerate(Gn) if nx.number_of_edges(G) != 0]
        idx = [G[0] for G in Gn]
        Gn = [G[1] for G in Gn]
        y = [y[i] for i in idx]
        for G in Gn:
            G.graph['node_attrs'] = []
            for node in G.nodes:
                del G.nodes[node]['attributes']
                del G.nodes[node]['x']
                del G.nodes[node]['y']
    # edge non-symbolic labels (and node non-symbolic labels).
    elif ds_name == 'Fingerprint':
        import networkx as nx
        ds_file = 'datasets/Fingerprint/Fingerprint_A.txt'
        Gn, y = loadDataset(ds_file)
        Gn = [(idx, G) for idx, G in enumerate(Gn) if nx.number_of_edges(G) != 0]
        idx = [G[0] for G in Gn]
        Gn = [G[1] for G in Gn]
        y = [y[i] for i in idx]
    # edge symbolic and non-symbolic labels (and node symbolic and non-symbolic labels).
    elif ds_name == 'Cuneiform':
        import networkx as nx
        ds_file = 'datasets/Cuneiform/Cuneiform_A.txt'
        Gn, y = loadDataset(ds_file)
    
    Gn = Gn[0:3]
    y = y[0:3]
    
    return Gn, y


@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_commonwalkkernel(ds_name, weight, compute_method):
    """Test common walk kernel.
    """
    from gklearn.kernels.commonWalkKernel import commonwalkkernel
    
    Gn, y = chooseDataset(ds_name)

    try:
        Kmatrix, run_time, idx = commonwalkkernel(Gn, 
                                             node_label='atom', 
                                             edge_label='bond_type',
                                             weight=weight,
                                             compute_method=compute_method,
#                                             parallel=parallel,
                                             n_jobs=multiprocessing.cpu_count(), 
                                             verbose=True)
    except Exception as exception:
        assert False, exception
        
        
@pytest.mark.parametrize('ds_name', ['Alkane', 'AIDS'])
@pytest.mark.parametrize('remove_totters', [True, False])
#@pytest.mark.parametrize('parallel', ['imap_unordered', None])
def test_marginalizedkernel(ds_name, remove_totters):
    """Test marginalized kernel.
    """
    from gklearn.kernels.marginalizedKernel import marginalizedkernel
    
    Gn, y = chooseDataset(ds_name)

    try:
        Kmatrix, run_time = marginalizedkernel(Gn, 
                                               node_label='atom', 
                                               edge_label='bond_type',
                                               p_quit=0.5,
                                               n_iteration=2,
                                               remove_totters=remove_totters,
#                                               parallel=parallel,
                                               n_jobs=multiprocessing.cpu_count(), 
                                               verbose=True)
    except Exception as exception:
        assert False, exception
        
        
@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_randomwalkkernel(ds_name, compute_method, sub_kernel):
    """Test random walk kernel kernel.
    """
    from gklearn.kernels.randomWalkKernel import randomwalkkernel
    from gklearn.utils.kernels import deltakernel, gaussiankernel, kernelproduct
    import functools
    
    Gn, y = chooseDataset(ds_name)

    mixkernel = functools.partial(kernelproduct, deltakernel, gaussiankernel)
    sub_kernels = [{'symb': deltakernel, 'nsymb': gaussiankernel, 'mix': mixkernel}]
    try:
        Kmatrix, run_time, idx = randomwalkkernel(Gn,
                                                  compute_method=compute_method,
                                                  weight=1e-3,
                                                  p=None,
                                                  q=None,
                                                  edge_weight=None,
                                                  node_kernels=sub_kernels,
                                                  edge_kernels=sub_kernels,
                                                  node_label='atom', 
                                                  edge_label='bond_type',
                                                  sub_kernel=sub_kernel,
#                                                  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])
@pytest.mark.parametrize('parallel', ['imap_unordered'])
def test_spkernel(ds_name, parallel):
    """Test shortest path kernel.
    """
    from gklearn.kernels.spKernel import spkernel
    from gklearn.utils.kernels import deltakernel, gaussiankernel, kernelproduct
    import functools
    
    Gn, y = chooseDataset(ds_name)
    
    mixkernel = functools.partial(kernelproduct, deltakernel, gaussiankernel)
    sub_kernels = {'symb': deltakernel, 'nsymb': gaussiankernel, 'mix': mixkernel}
    try:
        Kmatrix, run_time, idx = spkernel(Gn, node_label='atom', 
            node_kernels=sub_kernels,
            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('ds_name', ['Alkane', 'Acyclic', 'Letter-med', 'AIDS', 'Fingerprint', 'Fingerprint_edge', 'Cuneiform'])
@pytest.mark.parametrize('parallel', ['imap_unordered', None])
def test_structuralspkernel(ds_name, parallel):
    """Test structural shortest path kernel.
    """
    from gklearn.kernels.structuralspKernel import structuralspkernel
    from gklearn.utils.kernels import deltakernel, gaussiankernel, kernelproduct
    import functools
    
    Gn, y = chooseDataset(ds_name)
    
    mixkernel = functools.partial(kernelproduct, deltakernel, gaussiankernel)
    sub_kernels = {'symb': deltakernel, 'nsymb': gaussiankernel, 'mix': mixkernel}
    try:
        Kmatrix, run_time = structuralspkernel(Gn, node_label='atom', 
                      edge_label='bond_type', node_kernels=sub_kernels,
                      edge_kernels=sub_kernels,
                      parallel=parallel, n_jobs=multiprocessing.cpu_count(), 
                      verbose=True)
    except Exception as exception:
        assert False, exception


@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_untilhpathkernel(ds_name, parallel, k_func, compute_method):
    """Test path kernel up to length $h$.
    """
    from gklearn.kernels.untilHPathKernel import untilhpathkernel
    
    Gn, y = chooseDataset(ds_name)
    
    try:
        Kmatrix, run_time = untilhpathkernel(Gn, node_label='atom', 
                          edge_label='bond_type',
                          depth=2, k_func=k_func, compute_method=compute_method,
                          parallel=parallel, 
                          n_jobs=multiprocessing.cpu_count(), verbose=True)
    except Exception as exception:
        assert False, exception
    
    
@pytest.mark.parametrize('ds_name', ['Alkane', 'AIDS'])
@pytest.mark.parametrize('parallel', ['imap_unordered', None])
def test_treeletkernel(ds_name, parallel):
    """Test treelet kernel.
    """
    from gklearn.kernels.treeletKernel import treeletkernel
    from gklearn.utils.kernels import polynomialkernel
    import functools
    
    Gn, y = chooseDataset(ds_name)

    pkernel = functools.partial(polynomialkernel, d=2, c=1e5)    
    try:
        Kmatrix, run_time = treeletkernel(Gn, 
                                          sub_kernel=pkernel,
                                          node_label='atom', 
                                          edge_label='bond_type',
                                          parallel=parallel,
                                          n_jobs=multiprocessing.cpu_count(), 
                                          verbose=True)
    except Exception as exception:
        assert False, exception
        
        
@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_weisfeilerlehmankernel(ds_name, parallel, base_kernel):
    """Test Weisfeiler-Lehman kernel.
    """
    from gklearn.kernels.weisfeilerLehmanKernel import weisfeilerlehmankernel
    
    Gn, y = chooseDataset(ds_name)

    try:
        Kmatrix, run_time = weisfeilerlehmankernel(Gn, 
                                                   node_label='atom', 
                                                   edge_label='bond_type',
                                                   height=2,
                                                   base_kernel=base_kernel,
                                                   parallel=parallel,
                                                   n_jobs=multiprocessing.cpu_count(), 
                                                   verbose=True)
    except Exception as exception:
        assert False, exception
        

if __name__ == "__main__":
#    test_spkernel('Alkane', 'imap_unordered')
    test_structuralspkernel('Fingerprint_edge', 'imap_unordered')