def test_mlgk_kernel_range_check():
MarginalizedGraphKernel(
node_kernel=KroneckerDelta(1e-7),
edge_kernel=TensorProduct(attribute=SquareExponential(1.0)))
MarginalizedGraphKernel(
node_kernel=TensorProduct(feature=KroneckerDelta(0.5)),
edge_kernel=TensorProduct(attribute=SquareExponential(1.0)))
with pytest.warns(DeprecationWarning):
MarginalizedGraphKernel(
node_kernel=KroneckerDelta(0),
edge_kernel=TensorProduct(attribute=SquareExponential(1.0)))
with pytest.warns(DeprecationWarning):
MarginalizedGraphKernel(
node_kernel=TensorProduct(feature=KroneckerDelta(0.5)) + 1,
edge_kernel=SquareExponential(1.0))
with pytest.warns(DeprecationWarning):
MarginalizedGraphKernel(
node_kernel=TensorProduct(feature=KroneckerDelta(0.5)),
edge_kernel=TensorProduct(attribute=SquareExponential(1.0)) + 1)
with pytest.warns(DeprecationWarning):
MarginalizedGraphKernel(
node_kernel=KroneckerDelta(0.5) * 2,
edge_kernel=TensorProduct(attribute=SquareExponential(1.0)))
with pytest.warns(DeprecationWarning):
MarginalizedGraphKernel(
node_kernel=TensorProduct(feature=KroneckerDelta(0.5)),
edge_kernel=TensorProduct(attribute=SquareExponential(1.0)) * 2)
def _makekernel(self, **kwargs):
self.kernel = MarginalizedGraphKernel(
TensorProduct(element=KroneckerDelta(self.element_prior)),
TensorProduct(length=SquareExponential(self.edge_length_scale)),
q=self.stopping_probability,
p=self.starting_probability,
**kwargs)
def test_mlgk_on_permuted_graph():
g = Graph.from_ase(molecule('C6H6'))
for _ in range(10):
h = g.permute(np.random.permutation(len(g.nodes)))
kernel = MarginalizedGraphKernel(
TensorProduct(element=KroneckerDelta(0.5)),
TensorProduct(length=SquareExponential(0.1)))
assert (kernel([g], [h]).item() == pytest.approx(kernel([g]).item()))
def _combine_microk(rule: Literal['Tensorproduct', 'Additive',
'Additive_p'], microk_dict: Dict):
if rule == 'Tensorproduct':
return TensorProduct(**microk_dict)
elif rule == 'Additive':
return Normalize(Additive(**microk_dict))
elif rule == 'Additive_p':
return Additive_p(**microk_dict)
else:
raise RuntimeError(f'Unknown type: {rule}')
def test_maximin_basic():
metric = MaxiMin(node_kernel=TensorProduct(element=KroneckerDelta(0.5)),
edge_kernel=TensorProduct(length=SquareExponential(0.1)),
q=0.01)
distance = metric(G)
assert distance.shape == (len(G), len(G))
assert np.allclose(distance.diagonal(), 0, atol=1e-3)
assert np.all(distance >= 0)
assert np.allclose(distance, distance.T, rtol=1e-14, atol=1e-14)
distance = metric(G, G)
assert distance.shape == (len(G), len(G))
assert np.allclose(distance.diagonal(), 0, atol=1e-3)
assert np.all(distance >= 0)
assert np.allclose(distance, distance.T, rtol=1e-4, atol=1e-4)
distance = metric(G, H)
assert distance.shape == (len(G), len(H))
assert np.all(distance >= 0)
def test_mlgk_fixed_hyperparameters():
g = nx.Graph()
g.add_node(0, feature=0)
g.add_node(1, feature=1)
g.add_node(2, feature=0)
g.add_edge(0, 1, attribute=1.0)
g.add_edge(0, 2, attribute=2.0)
G = [Graph.from_networkx(g)]
knodeV = TensorProduct(feature=KroneckerDelta(0.5))
knodeF = TensorProduct(feature=KroneckerDelta(0.5, h_bounds='fixed'))
kedgeV = TensorProduct(attribute=SquareExponential(1.0))
kedgeF = TensorProduct(
attribute=SquareExponential(1.0, length_scale_bounds='fixed'))
kernelVV = MarginalizedGraphKernel(knodeV, kedgeV)
kernelVF = MarginalizedGraphKernel(knodeV, kedgeF)
kernelFV = MarginalizedGraphKernel(knodeF, kedgeV)
kernelFF = MarginalizedGraphKernel(knodeF, kedgeF)
assert (len(kernelVV.theta) == len(kernelVF.theta) + 1)
assert (len(kernelVV.theta) == len(kernelFV.theta) + 1)
assert (len(kernelVV.theta) == len(kernelFF.theta) + 2)
assert (len(kernelVV.bounds) == len(kernelVF.bounds) + 1)
assert (len(kernelVV.bounds) == len(kernelFV.bounds) + 1)
assert (len(kernelVV.bounds) == len(kernelFF.bounds) + 2)
Rvv, dRvv = kernelVV(G, eval_gradient=True)
Rvf, dRvf = kernelVF(G, eval_gradient=True)
Rfv, dRfv = kernelFV(G, eval_gradient=True)
Rff, dRff = kernelFF(G, eval_gradient=True)
assert (Rvv == pytest.approx(Rvf))
assert (Rvv == pytest.approx(Rfv))
assert (Rvv == pytest.approx(Rff))
assert (dRvv.shape[2] == dRvf.shape[2] + 1)
assert (dRvv.shape[2] == dRfv.shape[2] + 1)
assert (dRvv.shape[2] == dRff.shape[2] + 2)
assert (dRvv[:, :, kernelVF.active_theta_mask] == pytest.approx(dRvf))
assert (dRvv[:, :, kernelFV.active_theta_mask] == pytest.approx(dRfv))
assert (dRvv[:, :, kernelFF.active_theta_mask] == pytest.approx(dRff))
def __init__(self,
use_charge=False,
adjacency='default',
q=0.01,
element_delta=0.2,
bond_eps=0.02,
charge_eps=0.2):
self.use_charge = use_charge
if adjacency == 'default':
self.adjacency = AtomicAdjacency(shape='tent2', zoom=0.75)
else:
self.adjacency = adjacency
self.q = q
if use_charge:
self.node_kernel = TensorProduct(
element=KroneckerDelta(element_delta),
charge=SquareExponential(charge_eps),
)
else:
self.node_kernel = TensorProduct(
element=KroneckerDelta(element_delta))
self.edge_kernel = TensorProduct(length=SquareExponential(bond_eps))
def test_mlgk_large():
g = nx.Graph()
n = 24
for i, row in enumerate(np.random.randint(0, 2, (n, n))):
g.add_node(i, type=0)
for j, pred in enumerate(row[:i]):
if pred:
g.add_edge(i, j, weight=1)
dfg = Graph.from_networkx(g, weight='weight')
q = 0.5
node_kernel = TensorProduct(type=KroneckerDelta(1.0))
edge_kernel = Constant(1.0)
mlgk = MarginalizedGraphKernel(node_kernel, edge_kernel, q=q)
dot = mlgk([dfg])
gold = MLGK(dfg, node_kernel, edge_kernel, q, q)
assert (dot.shape == (1, 1))
assert (dot.item() == pytest.approx(gold))
def test_mlgk_dtype():
g = nx.Graph()
n = 8
for i, row in enumerate(np.random.randint(0, 2, (n, n))):
g.add_node(i, type=0)
for j, pred in enumerate(row[:i]):
if pred:
g.add_edge(i, j, weight=1)
dfg = Graph.from_networkx(g, weight='weight')
q = 0.5
node_kernel = TensorProduct(type=KroneckerDelta(1.0))
edge_kernel = Constant(1.0)
for dtype in [np.float, np.float32, np.float64]:
mlgk = MarginalizedGraphKernel(node_kernel,
edge_kernel,
q=q,
dtype=dtype)
assert (mlgk([dfg]).dtype == dtype)
assert (mlgk.diag([dfg]).dtype == dtype)
g1 = nx.Graph()
g1.add_node(0, category=(1, 2), symbol=1)
g1.add_node(1, category=(2, ), symbol=2)
g1.add_edge(0, 1, w=1.0, spectra=[0.5, 0.2])
g2 = nx.Graph()
g2.add_node(0, category=(1, 3), symbol=1)
g2.add_node(1, category=(2, 3, 5), symbol=2)
g2.add_node(2, category=(1, ), symbol=1)
g2.add_edge(0, 1, w=2.0, spectra=[0.1, 0.9, 1.5])
g2.add_edge(0, 2, w=0.5, spectra=[0.4])
g2.add_edge(1, 2, w=0.5, spectra=[0.3, 0.6])
# Define node and edge base kernels using the R-convolution framework
# Reference: Haussler, David. Convolution kernels on discrete structures. 1999.
knode = TensorProduct(symbol=KroneckerDelta(0.5),
category=Convolution(KroneckerDelta(0.5)))
kedge = TensorProduct(spectra=Convolution(SquareExponential(0.3)))
# compose the marginalized graph kernel and compute pairwise similarity
mlgk = MarginalizedGraphKernel(knode, kedge, q=0.05)
R = mlgk([Graph.from_networkx(g, weight='w') for g in [g1, g2]])
# normalize the similarity matrix
d = np.diag(R)**-0.5
K = np.diag(d).dot(R).dot(np.diag(d))
print(K)
g2.add_edge(0, 1)
g2.add_edge(1, 2)
# {1.0, 1} -- {2.0, 1}
# \ /
# {1.0, 2}
g3 = nx.Graph()
g3.add_node(0, radius=1.0, category=1)
g3.add_node(1, radius=2.0, category=1)
g3.add_node(2, radius=1.0, category=2)
g3.add_edge(0, 1)
g3.add_edge(0, 2)
g3.add_edge(1, 2)
# define node and edge kernelets
knode = TensorProduct(radius=SquareExponential(0.5),
category=KroneckerDelta(0.5))
kedge = Constant(1.0)
# compose the marginalized graph kernel and compute pairwise similarity
mlgk = MarginalizedGraphKernel(knode, kedge, q=0.05)
R = mlgk([Graph.from_networkx(g) for g in [g1, g2, g3]])
# normalize the similarity matrix
d = np.diag(R)**-0.5
K = np.diag(d).dot(R).dot(np.diag(d))
print(K)
def __call__(self, graphs, diags, node_kernel, edge_kernel, p, q, eps,
ftol, gtol, jobs, starts, gramian, active, gradient, nX, nY,
nJ, traits, timer):
''' transfer graphs and starting probabilities to GPU '''
timer.tic('transferring graphs to GPU')
og_last = None
graphs_d = umempty(len(graphs), dtype=OctileGraph.dtype)
for i, g in enumerate(graphs):
og, ogstate = self._register_graph(g)
if i > 0:
self._assert_homogeneous(og_last, og)
og_last = og
graphs_d[i] = ogstate
weighted = og_last.weighted
node_t = og_last.node_t
edge_t = og_last.edge_t
timer.toc('transferring graphs to GPU')
''' allocate global job counter '''
timer.tic('allocate global job counter')
i_job_global = umzeros(1, np.uint32)
timer.toc('allocate global job counter')
''' code generation '''
timer.tic('code generation')
if weighted:
edge_kernel = TensorProduct(weight=Product(),
label=edge_kernel)
use_theta_grid = traits.eval_gradient is True
node_kernel_src = self.gencode_kernel(node_kernel, 'node_kernel')
edge_kernel_src = self.gencode_kernel(edge_kernel, 'edge_kernel')
p_start_src = self.gencode_probability(p, 'p_start')
with self.template.context(traits=traits) as template:
self.source = template.render(
node_kernel=node_kernel_src,
edge_kernel=edge_kernel_src,
p_start=p_start_src,
node_t=decltype(node_t),
edge_t=decltype(edge_t)
)
timer.toc('code generation')
''' JIT '''
timer.tic('JIT')
kernel = self.module.get_function('graph_maximin_distance')
timer.toc('JIT')
''' calculate launch configuration '''
timer.tic('calculating launch configuration')
launch_block_count = (self.device.MULTIPROCESSOR_COUNT
* self.block_per_sm)
shmem_bytes_per_warp = self.module.get_global(
'shmem_bytes_per_warp'
)[1]
shmem_bytes_per_block = (shmem_bytes_per_warp * self.block_size
// self.device.WARP_SIZE)
max_graph_size = np.max([len(g.nodes) for g in graphs])
scratch_pcg = self.allocate_pcg_scratch(
launch_block_count, max_graph_size
)
''' copy micro kernel parameters to GPU '''
for name, uker in [('node_kernel', node_kernel),
('edge_kernel', edge_kernel)]:
states = np.array(
self.pack_state(uker, diff_grid=use_theta_grid, diff_eps=eps),
dtype=uker.dtype
)
p_uker, _ = self.module.get_global(name)
cuda.memcpy_htod(p_uker, states[:1])
if use_theta_grid:
p_diff_grid, _ = self.module.get_global(f'{name}_diff_grid')
p_flat_theta, _ = self.module.get_global(f'{name}_flat_theta')
cuda.memcpy_htod(p_diff_grid, states[1:])
cuda.memcpy_htod(
p_flat_theta,
np.fromiter(flatten(uker.theta), dtype=np.float32)
)
p_p_start, _ = self.module.get_global('p_start')
cuda.memcpy_htod(
p_p_start, np.array([p.state], dtype=p.dtype)
)
timer.toc('calculating launch configuration')
''' GPU kernel execution '''
timer.tic('GPU kernel execution')
kernel(
graphs_d,
diags,
scratch_pcg,
jobs,
starts,
gramian,
active,
gradient if gradient is not None else np.uintp(0),
i_job_global,
np.uint32(len(jobs)),
np.uint32(nX),
np.uint32(nY),
np.uint32(nJ),
np.float32(q),
np.float32(q), # placeholder for q0
np.float32(eps),
np.float32(ftol),
np.float32(gtol),
grid=(launch_block_count, 1, 1),
block=(self.block_size, 1, 1),
shared=shmem_bytes_per_block,
)
self.ctx.synchronize()
timer.toc('GPU kernel execution')
from graphdot import Graph
from graphdot.kernel.marginalized import MarginalizedGraphKernel
from graphdot.kernel.fix import Normalization
from graphdot.microkernel import (TensorProduct, DotProduct, Constant)
# The 'category' attribute on the nodes could have variable lengths.
# So does the 'spectra' attributes on the edges.
g1 = nx.Graph()
g1.add_node(0, soap=[0.5, 1.5, 2.5, 0.5])
g1.add_node(1, soap=[0.5, 1.5, 2.5, 0.5])
g1.add_edge(0, 1, w=1.0)
g2 = nx.Graph()
g2.add_node(0, soap=[0.5, 1.5, 2.5, 3.5])
g2.add_node(1, soap=[1.5, 1.5, 0.5, 3.5])
g2.add_node(2, soap=[0.5, 2.5, 2.5, 0.5])
g2.add_edge(0, 1, w=2.0)
g2.add_edge(0, 2, w=0.5)
g2.add_edge(1, 2, w=0.5)
# compose the marginalized graph kernel and compute pairwise similarity
mlgk = Normalization(
MarginalizedGraphKernel(
node_kernel=TensorProduct(soap=DotProduct().normalized),
edge_kernel=Constant(1),
q=0.05))
G = [Graph.from_networkx(g, weight='w') for g in [g1, g2]]
print(f'Whole-graph similarity\n{mlgk(G)}')
print(f'Nodal similarity\n{mlgk(G, nodal=True)}')
from graphdot.kernel.fix import Normalization
from graphdot.metric.maximin import MaxiMin
from ase.build import molecule
np.set_printoptions(linewidth=999, precision=4, suppress=True)
molecules = [
molecule('CH4'),
molecule('NH3'),
molecule('CH3OH'),
molecule('H2O'),
]
graphs = [Graph.from_ase(m) for m in molecules]
metric = MaxiMin(node_kernel=TensorProduct(element=KroneckerDelta(0.5)),
edge_kernel=TensorProduct(length=SquareExponential(0.1)),
q=0.01)
kernel = Normalization(
MarginalizedGraphKernel(
node_kernel=TensorProduct(element=KroneckerDelta(0.5)),
edge_kernel=TensorProduct(length=SquareExponential(0.1)),
q=0.01))
def check_hausdorff(X, Y=None):
# GPU direct computation
D = metric(X, Y)
# Manual approach
K = kernel(X, Y, nodal=True)
d = np.sqrt(np.maximum(0, 2 - 2 * K))
'CC', # ethane
'CCO', # acetic acid
'CCN', # ethylamine
'C=C', # ethene
'CC=C', # propene
'CC=CC', # 2-n-butene
]
# convert to molecular graphs
# nodes(atoms) has 'aromatic', 'charge', 'element', 'hcount' attributes
# edges(bonds) has the 'order' attribute
graphs = [Graph.from_smiles(smi) for smi in smiles_list]
# define node and edge kernelets
knode = TensorProduct(aromatic=KroneckerDelta(0.8),
charge=SquareExponential(1.0),
element=KroneckerDelta(0.5),
hcount=SquareExponential(1.0))
kedge = TensorProduct(order=KroneckerDelta(0.5))
# compose the marginalized graph kernel and compute pairwise similarity
kernel = MarginalizedGraphKernel(knode, kedge, q=0.05)
R = kernel(graphs)
# normalize the similarity matrix and then print
d = np.diag(R)**-0.5
K = np.diag(d).dot(R).dot(np.diag(d))
print(pd.DataFrame(K, columns=smiles_list, index=smiles_list))
Graph.from_networkx(unlabeled_graph2)
]),
'knode':
Constant(1.0),
'kedge':
Constant(1.0),
'q': [0.01, 0.05, 0.1, 0.5]
},
'labeled': {
'graphs':
Graph.unify_datatype([
Graph.from_networkx(labeled_graph1),
Graph.from_networkx(labeled_graph2)
]),
'knode':
TensorProduct(hybridization=KroneckerDelta(0.3),
charge=SquareExponential(1.) + 0.01).normalized,
'kedge':
Additive(order=KroneckerDelta(0.3),
length=SquareExponential(0.05)).normalized,
'q': [0.01, 0.05, 0.1, 0.5]
},
'weighted': {
'graphs':
Graph.unify_datatype([
Graph.from_networkx(weighted_graph1, weight='w'),
Graph.from_networkx(weighted_graph2, weight='w')
]),
'knode':
Additive(hybridization=KroneckerDelta(0.3),
charge=SquareExponential(1.0)).normalized,
'kedge':