def __init__(self,
entity_counts,
sparsity=0.5,
embedding_dims=2,
tucker=False,
batch_dim=True):
self.n_student = entity_counts[0]
self.n_course = entity_counts[1]
self.n_professor = entity_counts[2]
self.sparsity = sparsity
self.embedding_dims = embedding_dims
self.tucker = tucker
# Wether to include a batch dimension
self.batch_dim = batch_dim
ent_students = Entity(0, self.n_student)
ent_courses = Entity(1, self.n_course)
ent_professors = Entity(2, self.n_professor)
entities = [ent_students, ent_courses, ent_professors]
relations = []
relations.append(Relation(0, [ent_students, ent_courses], 1))
relations.append(Relation(1, [ent_students, ent_professors], 1))
relations.append(Relation(2, [ent_professors, ent_courses], 1))
relations.append(Relation(3, [ent_courses, ent_courses], 1))
relations.append(Relation(4, [ent_courses, ent_courses], 1))
self.schema = DataSchema(entities, relations)
self.embedding_dims = embedding_dims
np.random.seed(0)
self.embeddings = self.make_embeddings(self.embedding_dims)
self.data = self.make_data(self.tucker)
self.observed = self.make_observed(self.sparsity)
def get_node_classification_data(self):
entities = self.schema.entities
self.schema_out = DataSchema([entities[TARGET_NODE_TYPE]], [
Relation(0,
[entities[TARGET_NODE_TYPE], entities[TARGET_NODE_TYPE]],
is_set=True)
])
target_indices = []
targets = []
with open(LABEL_FILE_STR, 'r') as label_file:
lines = label_file.readlines()
for line in lines:
node_id, node_name, node_type, node_label = line.rstrip(
).split('\t')
node_type = int(node_type)
node_id = self.node_id_to_idx[node_type][int(node_id)]
node_label = int(node_label)
target_indices.append(node_id)
targets.append(node_label)
self.target_indices = torch.LongTensor(target_indices)
self.targets = torch.LongTensor(targets)
self.n_outputs = self.schema.entities[TARGET_NODE_TYPE].n_instances
self.data_target = SparseMatrixData(self.schema_out)
def __init__(self, n_student, n_course, n_professor):
self.n_student = n_student
self.n_course = n_course
self.n_professor = n_professor
ent_students = Entity(0, self.n_student)
ent_courses = Entity(1, self.n_course)
ent_professors = Entity(2, self.n_professor)
entities = [ent_students, ent_courses, ent_professors]
#TODO: Fix student self-relation to have two channels
relations = []
#Takes
relations.append(Relation(0, [ent_students, ent_courses], 1))
#Reference
relations.append(Relation(1, [ent_students, ent_professors], 1))
#Teaches
relations.append(Relation(2, [ent_professors, ent_courses], 1))
#Prereq
relations.append(Relation(3, [ent_courses, ent_courses], 1))
#Student
relations.append(Relation(4, [ent_students], 1))
#Course
relations.append(Relation(5, [ent_courses], 1))
#Professor
relations.append(Relation(6, [ent_professors], 1))
# pick n dimensions
# Draw from n-dimensional normal dist to get encodings for each entity
self.schema = DataSchema(entities, relations)
self.embeddings = None
def __init__(self, schema, dims):
super(EntityPooling, self).__init__()
self.schema = schema
self.dims = dims
self.out_shape = [e.n_instances for e in self.schema.entities]
# Make a "schema" for the encodings
enc_relations = {
i: Relation(i, [self.schema.entities[i]])
for i in range(len(self.schema.entities))
}
self.enc_schema = DataSchema(self.schema.entities, enc_relations)
def __init__(self,
schema,
input_dim=1,
output_dim=1,
entities=None,
pool_op='mean'):
'''
input_dim: either a rel_id: dimension dict, or an integer for all relations
output_dim: either a rel_id: dimension dict, or an integer for all relations
'''
if entities == None:
entities = schema.entities
enc_relations = {
entity.id: Relation(entity.id, [entity, entity], is_set=True)
for entity in entities
}
encodings_schema = DataSchema(entities, enc_relations)
super().__init__(schema,
input_dim,
output_dim,
schema_out=encodings_schema,
pool_op=pool_op)
def __init__(self,
schema,
input_dim=1,
output_dim=1,
entities=None,
pool_op='mean'):
'''
schema: schema to broadcast to
input_dim: either a rel_id: dimension dict, or an integer for all relations
output_dim: either a rel_id: dimension dict, or an integer for all relations
entities: if specified, these are the input entities for the encodings
'''
if entities == None:
entities = schema.entities
enc_relations = {
entity.id: Relation(entity.id, [entity, entity], is_set=True)
for entity in entities
}
encodings_schema = DataSchema(entities, enc_relations)
super().__init__(encodings_schema,
input_dim,
output_dim,
schema_out=schema,
pool_op=pool_op)
def __init__(self, entity_counts, sparsity=0.5, n_channels=1):
self.n_student = entity_counts[0]
self.n_course = entity_counts[1]
self.n_professor = entity_counts[2]
# Upper estimate of sparsity
self.sparsity = sparsity
ent_students = Entity(0, self.n_student)
ent_courses = Entity(1, self.n_course)
ent_professors = Entity(2, self.n_professor)
entities = [ent_students, ent_courses, ent_professors]
relations = []
relations.append(Relation(0, [ent_students, ent_courses], 1))
relations.append(Relation(1, [ent_students, ent_professors], 1))
relations.append(Relation(2, [ent_professors, ent_courses], 1))
relations.append(
Relation(3, [ent_students, ent_professors, ent_courses], 1))
relations.append(Relation(4, [ent_courses, ent_courses], 1))
relations.append(Relation(5, [ent_students], 1))
#relations.append(Relation(6, [ent_students, ent_students, ent_students, ent_courses], 1))
self.schema = DataSchema(entities, relations)
self.observed = self.make_observed(self.sparsity, n_channels)
args = get_hyperparams(argv)
print(args)
set_seed(args.seed)
dataloader = PubMedData(args.node_labels)
schema = dataloader.schema
data = dataloader.data.to(device)
indices_identity, indices_transpose = data.calculate_indices()
embedding_entity = schema.entities[TARGET_NODE_TYPE]
input_channels = {
rel.id: data[rel.id].n_channels
for rel in schema.relations
}
embedding_schema = DataSchema(
schema.entities,
Relation(0, [embedding_entity, embedding_entity], is_set=True))
n_instances = embedding_entity.n_instances
data_embedding = SparseMatrixData(embedding_schema)
data_embedding[0] = SparseMatrix(
indices=torch.arange(n_instances, dtype=torch.int64).repeat(2, 1),
values=torch.zeros([n_instances, args.embedding_dim]),
shape=(n_instances, n_instances, args.embedding_dim),
is_set=True)
data_embedding.to(device)
target_schema = DataSchema(schema.entities,
schema.relations[TARGET_REL_ID])
target_node_idx_to_id = dataloader.target_node_idx_to_id
#%%
net = SparseMatrixAutoEncoder(schema,
input_channels,
layers=args.layers,
def __init__(self):
self.target_relation = 'advisedBy'
data_raw = {
rel_name: {key: list()
for key in schema_dict[rel_name].keys()}
for rel_name in schema_dict.keys()
}
for relation_name in relation_names:
with open(csv_file_str.format(relation_name)) as file:
reader = csv.reader(file)
keys = schema_dict[relation_name].keys()
for cols in reader:
for key, col in zip(keys, cols):
data_raw[relation_name][key].append(col)
ent_person = Entity(0, len(data_raw['person']['p_id']))
ent_course = Entity(1, len(data_raw['course']['course_id']))
entities = [ent_person, ent_course]
rel_person_matrix = Relation(0, [ent_person, ent_person], is_set=True)
rel_person = Relation(0, [ent_person])
rel_course_matrix = Relation(1, [ent_course, ent_course], is_set=True)
rel_course = Relation(1, [ent_course])
rel_advisedBy = Relation(2, [ent_person, ent_person])
rel_taughtBy = Relation(3, [ent_course, ent_person])
relations_matrix = [
rel_person_matrix, rel_course_matrix, rel_advisedBy, rel_taughtBy
]
relations = [rel_person, rel_course, rel_taughtBy]
self.target_rel_id = 2
self.schema = DataSchema(entities, relations)
schema_matrix = DataSchema(entities, relations_matrix)
matrix_data = SparseMatrixData(schema_matrix)
ent_id_to_idx_dict = {
'person': self.id_to_idx(data_raw['person']['p_id']),
'course': self.id_to_idx(data_raw['course']['course_id'])
}
for relation in relations_matrix:
relation_name = relation_names[relation.id]
print(relation_name)
if relation.is_set:
data_matrix = self.set_relation_to_matrix(
relation, schema_dict[relation_name],
data_raw[relation_name])
else:
if relation_name == 'advisedBy':
ent_n_id_str = 'p_id'
ent_m_id_str = 'p_id_dummy'
elif relation_name == 'taughtBy':
ent_n_id_str = 'course_id'
ent_m_id_str = 'p_id'
data_matrix = self.binary_relation_to_matrix(
relation, schema_dict[relation_name],
data_raw[relation_name], ent_id_to_idx_dict, ent_n_id_str,
ent_m_id_str)
matrix_data[relation.id] = data_matrix
rel_out = Relation(2, [ent_person, ent_person])
self.schema_out = DataSchema([ent_person], [rel_out])
self.output_dim = 1
data = Data(self.schema)
for rel_matrix in schema_matrix.relations:
for rel in self.schema.relations:
if rel_matrix.id == rel.id:
data_matrix = matrix_data[rel_matrix.id]
if rel_matrix.is_set:
dense_data = torch.diagonal(data_matrix.to_dense(), 0,
1, 2).unsqueeze(0)
else:
dense_data = data_matrix.to_dense().unsqueeze(0)
data[rel.id] = dense_data
self.data = data
self.target = matrix_data[self.target_rel_id].to_dense().squeeze()
features = sp.csr_matrix(features, dtype=np.float32)
rowsum = np.array(features.sum(1))
r_inv = np.power(rowsum, -1).flatten()
r_inv[np.isinf(r_inv)] = 0.
r_mat_inv = sp.diags(r_inv)
features = r_mat_inv.dot(features)
return torch.Tensor(features.todense())
ent_movie = Entity(0, raw_data['movie_feature'].shape[0])
ent_actor = Entity(1, raw_data['movie_actor'].shape[1])
ent_director = Entity(2, raw_data['movie_director'].shape[1])
ent_keyword = Entity(3, raw_data['movie_keyword'].shape[1])
entities = [ent_movie, ent_actor, ent_director, ent_keyword]
relations = []
rel_movie_actor = Relation(0, [ent_movie, ent_actor])
rel_movie_director = Relation(1, [ent_movie, ent_director])
rel_movie_keyword = Relation(2, [ent_movie, ent_keyword])
rel_movie_feature = Relation(3, [ent_movie, ent_movie], is_set=True)
relations = [rel_movie_actor, rel_movie_director, rel_movie_keyword, rel_movie_feature]
schema = DataSchema(entities, relations)
schema_out = DataSchema([ent_movie], [Relation(0, [ent_movie, ent_movie], is_set=True)])
data = SparseMatrixData(schema)
for rel_i, rel_name in enumerate(relation_names):
if rel_name == 'movie_feature':
values = preprocess_features(raw_data[rel_name])
data[rel_i] = SparseMatrix.from_embed_diag(values)
else:
data[rel_i] = SparseMatrix.from_scipy_sparse(raw_data[rel_name])
#print("X_out: ", X_out)
expected_shape = [batch_size] + [out_dim] + relation_j.get_shape()
print("Out shape: ", list(X_out.shape))
print("Expected shape: ", expected_shape)
assert(list(X_out.shape) == expected_shape)
#%%
if __name__ == '__main__':
#Example
##Ri = {n1, n2, n3}
#Rj = {m1, m2}
X = torch.tensor(np.arange(12, dtype=np.float32)).view(1, 1, 2,2,3)
# Entity index : number instances mapping
entities = [Entity(0, 3), Entity(1, 2), Entity(2, 5)]
relation_i = Relation(0, [entities[1], entities[1], entities[0]])
relation_j = Relation(1, [entities[0], entities[1]])
test_layer_single_block(X, entities, relation_i, relation_j, 1, 7, 1)
# %%
# Example 2
#Ri = {n1, n2}
#Rj = {m1, m2, m3}
X = torch.tensor(np.arange(16, dtype=np.float32)).view(1, 1,4,4)
entities = [Entity(0, 3), Entity(1, 2), Entity(2, 4)]
relation_i = Relation(0, [entities[2], entities[2]])
relation_j = Relation(1, [entities[0], entities[1], entities[1]])
test_layer_single_block(X, entities, relation_i, relation_j, 1, 3, 1)
def load_data_flat(prefix,
use_node_attrs=True,
use_edge_data=True,
node_val='one'):
'''
Load data into one matrix with all relations, reproducing Maron 2019
The first [# relation types] channels are adjacency matrices,
while the next [sum of feature dimensions per entity type] channels have
node attributes on the relevant segment of their diagonals if use_node_attrs=True.
If node features aren't included, then ndoe_val is used instead.
'''
dl = data_loader(DATA_FILE_DIR + prefix)
total_n_nodes = dl.nodes['total']
entities = [Entity(0, total_n_nodes)]
relations = {0: Relation(0, [entities[0], entities[0]])}
schema = DataSchema(entities, relations)
# Sparse Matrix containing all data
data_full = sum(dl.links['data'].values()).tocoo()
data_diag = scipy.sparse.coo_matrix(
(np.ones(total_n_nodes),
(np.arange(total_n_nodes), np.arange(total_n_nodes))),
(total_n_nodes, total_n_nodes))
data_full += data_diag
data_full = SparseMatrix.from_scipy_sparse(data_full.tocoo()).zero_()
data_out = SparseMatrix.from_other_sparse_matrix(data_full, 0)
# Load up all edge data
for rel_id in sorted(dl.links['data'].keys()):
data_matrix = dl.links['data'][rel_id]
data_rel = SparseMatrix.from_scipy_sparse(data_matrix.tocoo())
if not use_edge_data:
# Use only adjacency information
data_rel.values = torch.ones(data_rel.values.shape)
data_rel_full = SparseMatrix.from_other_sparse_matrix(data_full,
1) + data_rel
data_out.values = torch.cat([data_out.values, data_rel_full.values], 1)
data_out.n_channels += 1
if use_node_attrs:
for ent_id, attr_matrix in dl.nodes['attr'].items():
start_i = dl.nodes['shift'][ent_id]
n_instances = dl.nodes['count'][ent_id]
if attr_matrix is None:
if node_val == 'zero':
attr_matrix = np.zeros((n_instances, 1))
elif node_val == 'rand':
attr_matrix = np.random.randn(n_instances, 1)
else:
attr_matrix = np.ones((n_instances, 1))
n_channels = attr_matrix.shape[1]
indices = torch.arange(start_i,
start_i + n_instances).unsqueeze(0).repeat(
2, 1)
data_rel = SparseMatrix(
indices=indices,
values=torch.FloatTensor(attr_matrix),
shape=np.array([total_n_nodes, total_n_nodes, n_channels]),
is_set=True)
data_rel_full = SparseMatrix.from_other_sparse_matrix(
data_full, n_channels) + data_rel
data_out.values = torch.cat(
[data_out.values, data_rel_full.values], 1)
data_out.n_channels += n_channels
data = SparseMatrixData(schema)
data[0] = data_out
return schema,\
data, \
dl
def load_data():
paper_names = []
classes = []
word_names = ['word'+str(i+1) for i in range(1433)]
with open(csv_file_str.format('paper')) as paperfile:
reader = csv.reader(paperfile)
for paper_name, class_name in reader:
paper_names.append(paper_name)
classes.append(class_name)
class_names = list(np.unique(classes))
class_name_to_idx = {class_name : i for i, class_name in enumerate(class_names)}
paper_name_to_idx = {paper_name: i for i, paper_name in enumerate(paper_names)}
paper = np.array([[paper_name_to_idx[paper_name] for paper_name in paper_names],
[class_name_to_idx[class_name] for class_name in classes]])
cites = []
with open(csv_file_str.format('cites')) as citesfile:
reader = csv.reader(citesfile)
for citer, citee in reader:
cites.append([paper_name_to_idx[citer], paper_name_to_idx[citee]])
cites = np.array(cites).T
content = []
def word_to_idx(word):
'''
words all formatted like: "word1328"
'''
return int(word[4:]) - 1
with open(csv_file_str.format('content')) as contentfile:
reader = csv.reader(contentfile)
for paper_name, word_name in reader:
content.append([paper_name_to_idx[paper_name],
word_to_idx(word_name)])
content = np.array(content).T
n_papers = len(paper_names)
n_classes = len(class_names)
n_words = len(word_names)
ent_papers = Entity(0, n_papers)
ent_classes = Entity(1, n_classes)
ent_words = Entity(2, n_words)
entities = [ent_papers, ent_classes, ent_words]
rel_paper = Relation(0, [ent_papers, ent_classes])
rel_cites = Relation(1, [ent_papers, ent_papers])
rel_content = Relation(2, [ent_papers, ent_words])
relations = [rel_paper, rel_cites, rel_content]
schema = DataSchema(entities, relations)
class_targets = torch.LongTensor(paper[1])
paper_matrix = torch.zeros(n_papers, n_classes)
paper_matrix[paper] = 1
cites_matrix = torch.zeros(n_papers, n_papers)
cites_matrix[cites] = 1
content_matrix = torch.zeros(n_papers, n_words)
content_matrix[content] = 1
data = Data(schema)
data[0] = paper_matrix.unsqueeze(0).unsqueeze(0)
data[1] = cites_matrix.unsqueeze(0).unsqueeze(0)
data[2] = content_matrix.unsqueeze(0).unsqueeze(0)
return data, schema, class_targets
def load_data(prefix,
use_node_attrs=True,
use_edge_data=True,
use_other_edges=True,
node_val='one'):
dl = data_loader(DATA_FILE_DIR + prefix)
all_entities = [
Entity(entity_id, n_instances)
for entity_id, n_instances in sorted(dl.nodes['count'].items())
]
relations = {}
test_types = dl.test_types
if use_other_edges:
for rel_id, (entity_i, entity_j) in sorted(dl.links['meta'].items()):
relations[rel_id] = Relation(
rel_id, [all_entities[entity_i], all_entities[entity_j]])
else:
for rel_id in test_types:
entity_i, entity_j = dl.links['meta'][rel_id]
relations[rel_id] = Relation(
rel_id, [all_entities[entity_i], all_entities[entity_j]])
if use_other_edges:
entities = all_entities
else:
entities = list(np.unique(relations[test_types[0]].entities))
max_relation = max(relations) + 1
if use_node_attrs:
# Create fake relations to represent node attributes
for entity in entities:
rel_id = max_relation + entity.id
relations[rel_id] = Relation(rel_id, [entity, entity], is_set=True)
schema = DataSchema(entities, relations)
data = SparseMatrixData(schema)
for rel_id, data_matrix in dl.links['data'].items():
if use_other_edges or rel_id in test_types:
# Get subset belonging to entities in relation
relation = relations[rel_id]
start_i = dl.nodes['shift'][relation.entities[0].id]
end_i = start_i + dl.nodes['count'][relation.entities[0].id]
start_j = dl.nodes['shift'][relation.entities[1].id]
end_j = start_j + dl.nodes['count'][relation.entities[1].id]
rel_matrix = data_matrix[start_i:end_i, start_j:end_j]
data[rel_id] = SparseMatrix.from_scipy_sparse(rel_matrix.tocoo())
if not use_edge_data:
# Use only adjacency information
data[rel_id].values = torch.ones(data[rel_id].values.shape)
if use_node_attrs:
for ent in entities:
ent_id = ent.id
attr_matrix = dl.nodes['attr'][ent_id]
n_instances = dl.nodes['count'][ent_id]
if attr_matrix is None:
if node_val == 'zero':
attr_matrix = np.zeros((n_instances, 1))
elif node_val == 'rand':
attr_matrix = np.random.randn(n_instances, 1)
else:
attr_matrix = np.ones((n_instances, 1))
n_channels = attr_matrix.shape[1]
rel_id = ent_id + max_relation
indices = torch.arange(n_instances).unsqueeze(0).repeat(2, 1)
data[rel_id] = SparseMatrix(
indices=indices,
values=torch.FloatTensor(attr_matrix),
shape=np.array([n_instances, n_instances, n_channels]),
is_set=True)
return schema,\
data, \
dl
def load_data(prefix='DBLP',
use_node_attrs=True,
use_edge_data=True,
feats_type=0):
dl = data_loader(DATA_FILE_DIR + prefix)
# Create Schema
entities = [
Entity(entity_id, n_instances)
for entity_id, n_instances in sorted(dl.nodes['count'].items())
]
relations = {
rel_id: Relation(rel_id, [entities[entity_i], entities[entity_j]])
for rel_id, (entity_i, entity_j) in sorted(dl.links['meta'].items())
}
num_relations = len(relations)
if use_node_attrs:
# Create fake relations to represent node attributes
for entity in entities:
rel_id = num_relations + entity.id
relations[rel_id] = Relation(rel_id, [entity, entity], is_set=True)
schema = DataSchema(entities, relations)
# Collect data
data = SparseMatrixData(schema)
for rel_id, data_matrix in dl.links['data'].items():
# Get subset belonging to entities in relation
start_i = dl.nodes['shift'][relations[rel_id].entities[0].id]
end_i = start_i + dl.nodes['count'][relations[rel_id].entities[0].id]
start_j = dl.nodes['shift'][relations[rel_id].entities[1].id]
end_j = start_j + dl.nodes['count'][relations[rel_id].entities[1].id]
rel_matrix = data_matrix[start_i:end_i, start_j:end_j]
data[rel_id] = SparseMatrix.from_scipy_sparse(rel_matrix.tocoo())
if not use_edge_data:
# Use only adjacency information
data[rel_id].values = torch.ones(data[rel_id].values.shape)
target_entity = 0
if use_node_attrs:
for ent_id, attr_matrix in dl.nodes['attr'].items():
if attr_matrix is None:
# Attribute for each node is a single 1
attr_matrix = np.ones(dl.nodes['count'][ent_id])[:, None]
n_channels = attr_matrix.shape[1]
rel_id = ent_id + num_relations
n_instances = dl.nodes['count'][ent_id]
indices = torch.arange(n_instances).unsqueeze(0).repeat(2, 1)
data[rel_id] = SparseMatrix(
indices=indices,
values=torch.FloatTensor(attr_matrix),
shape=np.array([n_instances, n_instances, n_channels]),
is_set=True)
n_outputs = dl.nodes['count'][target_entity]
n_output_classes = dl.labels_train['num_classes']
schema_out = DataSchema([entities[target_entity]], [
Relation(0, [entities[target_entity], entities[target_entity]],
is_set=True)
])
data_target = SparseMatrixData(schema_out)
data_target[0] = SparseMatrix(
indices=torch.arange(n_outputs, dtype=torch.int64).repeat(2, 1),
values=torch.zeros([n_outputs, n_output_classes]),
shape=(n_outputs, n_outputs, n_output_classes),
is_set=True)
labels = np.zeros((dl.nodes['count'][0], dl.labels_train['num_classes']),
dtype=int)
val_ratio = 0.2
train_idx = np.nonzero(dl.labels_train['mask'])[0]
np.random.shuffle(train_idx)
split = int(train_idx.shape[0] * val_ratio)
val_idx = train_idx[:split]
train_idx = train_idx[split:]
train_idx = np.sort(train_idx)
val_idx = np.sort(val_idx)
test_idx = np.nonzero(dl.labels_test['mask'])[0]
labels[train_idx] = dl.labels_train['data'][train_idx]
labels[val_idx] = dl.labels_train['data'][val_idx]
if prefix != 'IMDB':
labels = labels.argmax(axis=1)
train_val_test_idx = {}
train_val_test_idx['train_idx'] = train_idx
train_val_test_idx['val_idx'] = val_idx
train_val_test_idx['test_idx'] = test_idx
return schema,\
schema_out, \
data, \
data_target, \
labels,\
train_val_test_idx,\
dl
def __init__(self):
data_raw = {
rel_name: {key: list()
for key in schema_dict[rel_name].keys()}
for rel_name in schema_dict.keys()
}
for relation_name in relation_names:
with open(csv_file_str.format(relation_name)) as file:
reader = csv.reader(file)
keys = schema_dict[relation_name].keys()
for cols in reader:
for key, col in zip(keys, cols):
data_raw[relation_name][key].append(col)
ent_person = Entity(0, len(data_raw['person']['p_id']))
ent_course = Entity(1, len(data_raw['course']['course_id']))
entities = [ent_person, ent_course]
rel_person = Relation(0, [ent_person, ent_person], is_set=True)
rel_course = Relation(1, [ent_course, ent_course], is_set=True)
rel_advisedBy = Relation(2, [ent_person, ent_person])
rel_taughtBy = Relation(3, [ent_course, ent_person])
relations = [rel_person, rel_course, rel_advisedBy, rel_taughtBy]
self.schema = DataSchema(entities, relations)
self.data = SparseMatrixData(self.schema)
ent_id_to_idx_dict = {
'person': self.id_to_idx(data_raw['person']['p_id']),
'course': self.id_to_idx(data_raw['course']['course_id'])
}
for relation in relations:
relation_name = relation_names[relation.id]
print(relation_name)
if relation.is_set:
data_matrix = self.set_relation_to_matrix(
relation, schema_dict[relation_name],
data_raw[relation_name])
else:
if relation_name == 'advisedBy':
ent_n_id_str = 'p_id'
ent_m_id_str = 'p_id_dummy'
elif relation_name == 'taughtBy':
ent_n_id_str = 'course_id'
ent_m_id_str = 'p_id'
data_matrix = self.binary_relation_to_matrix(
relation, schema_dict[relation_name],
data_raw[relation_name], ent_id_to_idx_dict, ent_n_id_str,
ent_m_id_str)
self.data[relation.id] = data_matrix
self.target = self.get_targets(
data_raw[self.TARGET_RELATION][self.TARGET_KEY],
schema_dict[self.TARGET_RELATION][self.TARGET_KEY])
self.target_rel_id = 0
rel_out = Relation(self.target_rel_id, [ent_person, ent_person],
is_set=True)
self.schema_out = DataSchema([ent_person], [rel_out])
self.data_target = Data(self.schema_out)
n_output_classes = len(
np.unique(data_raw[self.TARGET_RELATION][self.TARGET_KEY]))
self.output_dim = n_output_classes
n_person = ent_person.n_instances
self.data_target[self.target_rel_id] = SparseMatrix(
indices=torch.arange(n_person, dtype=torch.int64).repeat(2, 1),
values=torch.zeros([n_person, n_output_classes]),
shape=(n_person, n_person, n_output_classes))
def __init__(self, use_node_attrs=True):
entities = [
Entity(entity_id, n_instances)
for entity_id, n_instances in ENTITY_N_INSTANCES.items()
]
relations = [
Relation(rel_id, [entities[entity_i], entities[entity_j]])
for rel_id, (entity_i, entity_j) in RELATION_IDX.items()
]
if use_node_attrs:
for entity_id in ENTITY_N_INSTANCES.keys():
rel = Relation(10 + entity_id,
[entities[entity_id], entities[entity_id]],
is_set=True)
relations.append(rel)
self.schema = DataSchema(entities, relations)
self.node_id_to_idx = {ent_i: {} for ent_i in range(len(entities))}
with open(NODE_FILE_STR, 'r') as node_file:
lines = node_file.readlines()
node_counter = {ent_i: 0 for ent_i in range(len(entities))}
for line in lines:
node_id, node_name, node_type, values = line.rstrip().split(
'\t')
node_id = int(node_id)
node_type = int(node_type)
node_idx = node_counter[node_type]
self.node_id_to_idx[node_type][node_id] = node_idx
node_counter[node_type] += 1
target_node_id_to_idx = self.node_id_to_idx[TARGET_NODE_TYPE]
self.target_node_idx_to_id = {
idx: id
for id, idx in target_node_id_to_idx.items()
}
raw_data_indices = {rel_id: [] for rel_id in range(len(relations))}
raw_data_values = {rel_id: [] for rel_id in range(len(relations))}
if use_node_attrs:
with open(NODE_FILE_STR, 'r') as node_file:
lines = node_file.readlines()
for line in lines:
node_id, node_name, node_type, values = line.rstrip(
).split('\t')
node_type = int(node_type)
node_id = self.node_id_to_idx[node_type][int(node_id)]
values = list(map(float, values.split(',')))
raw_data_indices[10 + node_type].append([node_id, node_id])
raw_data_values[10 + node_type].append(values)
with open(LINK_FILE_STR, 'r') as link_file:
lines = link_file.readlines()
for line in lines:
node_i, node_j, rel_num, val = line.rstrip().split('\t')
rel_num = int(rel_num)
node_i_type, node_j_type = RELATION_IDX[rel_num]
node_i = self.node_id_to_idx[node_i_type][int(node_i)]
node_j = self.node_id_to_idx[node_j_type][int(node_j)]
val = float(val)
raw_data_indices[rel_num].append([node_i, node_j])
raw_data_values[rel_num].append([val])
self.data = SparseMatrixData(self.schema)
for rel in relations:
indices = torch.LongTensor(raw_data_indices[rel.id]).T
values = torch.Tensor(raw_data_values[rel.id])
n = rel.entities[0].n_instances
m = rel.entities[1].n_instances
n_channels = values.shape[1]
data_matrix = SparseMatrix(indices=indices,
values=values,
shape=np.array([n, m, n_channels]),
is_set=rel.is_set)
del raw_data_indices[rel.id]
del raw_data_values[rel.id]
self.data[rel.id] = data_matrix
n_content = 2 * int(0.2 * n_papers * n_words)
content = np.stack([
np.random.randint(0, n_papers, (n_content)),
np.random.randint(0, n_words, (n_content))
])
content = np.unique(cites, axis=1)
content_matrix = SparseMatrix(indices=torch.LongTensor(content),
values=value_dist.sample(
(content.shape[1], 1)),
shape=(n_papers, n_words, 1)).coalesce()
ent_papers = Entity(0, n_papers)
#ent_classes = Entity(1, n_classes)
ent_words = Entity(1, n_words)
rel_paper = Relation(0, [ent_papers, ent_papers], is_set=True)
rel_cites = Relation(0, [ent_papers, ent_papers])
rel_content = Relation(1, [ent_papers, ent_words])
schema = DataSchema([ent_papers, ent_words], [rel_cites, rel_content])
schema_out = DataSchema([ent_papers], [rel_paper])
targets = torch.LongTensor(paper[1])
data = SparseMatrixData(schema)
data[0] = cites_matrix
data[1] = content_matrix
indices_identity, indices_transpose = data.calculate_indices()
data_target = Data(schema_out)
data_target[0] = SparseMatrix(indices=torch.arange(
n_papers, dtype=torch.int64).repeat(2, 1),
def load_data():
paper_names = []
classes = []
word_names = ['word' + str(i + 1) for i in range(1433)]
with open(csv_file_str.format('paper')) as paperfile:
reader = csv.reader(paperfile)
for paper_name, class_name in reader:
paper_names.append(paper_name)
classes.append(class_name)
class_names = list(np.unique(classes))
class_name_to_idx = {
class_name: i
for i, class_name in enumerate(class_names)
}
paper_name_to_idx = {
paper_name: i
for i, paper_name in enumerate(paper_names)
}
paper = np.array(
[[paper_name_to_idx[paper_name] for paper_name in paper_names],
[class_name_to_idx[class_name] for class_name in classes]])
cites = []
with open(csv_file_str.format('cites')) as citesfile:
reader = csv.reader(citesfile)
for citer, citee in reader:
cites.append([paper_name_to_idx[citer], paper_name_to_idx[citee]])
cites = np.array(cites).T
content = []
def word_to_idx(word):
'''
words all formatted like: "word1328"
'''
return int(word[4:]) - 1
with open(csv_file_str.format('content')) as contentfile:
reader = csv.reader(contentfile)
for paper_name, word_name in reader:
content.append(
[paper_name_to_idx[paper_name],
word_to_idx(word_name)])
content = np.array(content).T
n_papers = len(paper_names)
n_classes = len(class_names)
n_words = len(word_names)
ent_papers = Entity(0, n_papers)
ent_classes = Entity(1, n_classes)
ent_words = Entity(2, n_words)
entities = [ent_papers, ent_classes, ent_words]
rel_paper = Relation(0, [ent_papers, ent_classes])
rel_cites = Relation(1, [ent_papers, ent_papers])
rel_content = Relation(2, [ent_papers, ent_words])
relations = [rel_paper, rel_cites, rel_content]
schema = DataSchema(entities, relations)
# For each paper, get a random negative sample
random_class_offset = np.random.randint(1, n_classes, (n_papers, ))
paper_neg = np.stack(
(paper[0], (paper[1] + random_class_offset) % n_classes))
paper_matrix = SparseTensor(
indices=torch.LongTensor(np.concatenate((paper, paper_neg), axis=1)),
values=torch.cat((torch.ones(
1, paper.shape[1]), torch.zeros(1, paper_neg.shape[1])), 1),
shape=np.array([n_papers, n_classes])).coalesce()
class_targets = torch.LongTensor(paper[1])
# Randomly fill in values and coalesce to remove duplicates
cites_neg = np.random.randint(0, n_papers, cites.shape)
cites_matrix = SparseTensor(
indices=torch.LongTensor(np.concatenate((cites, cites_neg), axis=1)),
values=torch.cat((torch.ones(
1, cites.shape[1]), torch.zeros(1, cites_neg.shape[1])), 1),
shape=np.array([n_papers, n_papers])).coalesce()
# For each paper, randomly fill in values and coalesce to remove duplicates
content_neg = np.stack(
(np.random.randint(0, n_papers, (content.shape[1], )),
np.random.randint(0, n_words, (content.shape[1], ))))
content_matrix = SparseTensor(
indices=torch.LongTensor(np.concatenate((content, content_neg),
axis=1)),
values=torch.cat((torch.ones(
1, content.shape[1]), torch.zeros(1, content_neg.shape[1])), 1),
shape=np.array([n_papers, n_words])).coalesce()
paper_dense_indices = np.array([
np.tile(range(n_papers), n_classes),
np.repeat(range(n_classes), n_papers)
])
paper_dense_values = torch.zeros(paper_dense_indices.shape[1])
for paper_i, class_name in enumerate(classes):
class_i = class_name_to_idx[class_name]
paper_dense_values[paper_i * n_classes + class_i] = 1
paper_dense_matrix = SparseTensor(
indices=torch.LongTensor(paper_dense_indices),
values=torch.Tensor(paper_dense_values).unsqueeze(0),
shape=np.array([n_papers, n_classes]))
data = SparseTensorData(schema)
data[0] = paper_dense_matrix
data[1] = cites_matrix
data[2] = content_matrix
return data, schema, class_targets
def load_data_flat(prefix,
use_node_attrs=True,
use_edge_data=True,
node_val='zero',
feats_type=0):
'''
Load data into one matrix with all relations, reproducing Maron 2019
The first [# relation types] channels are adjacency matrices,
while the next [sum of feature dimensions per entity type] channels have
node attributes on the relevant segment of their diagonals if use_node_attrs=True.
If node features aren't included, then ndoe_val is used instead.
'''
dl = data_loader(DATA_FILE_DIR + prefix)
total_n_nodes = dl.nodes['total']
entities = [Entity(0, total_n_nodes)]
relations = {0: Relation(0, [entities[0], entities[0]])}
schema = DataSchema(entities, relations)
# Sparse Matrix containing all data
data_full = sum(dl.links['data'].values()).tocoo()
data_diag = scipy.sparse.coo_matrix(
(np.ones(total_n_nodes),
(np.arange(total_n_nodes), np.arange(total_n_nodes))),
(total_n_nodes, total_n_nodes))
data_full += data_diag
data_full = SparseMatrix.from_scipy_sparse(data_full.tocoo()).zero_()
data_out = SparseMatrix.from_other_sparse_matrix(data_full, 0)
# Load up all edge data
for rel_id in sorted(dl.links['data'].keys()):
data_matrix = dl.links['data'][rel_id]
data_rel = SparseMatrix.from_scipy_sparse(data_matrix.tocoo())
if not use_edge_data:
# Use only adjacency information
data_rel.values = torch.ones(data_rel.values.shape)
data_rel_full = SparseMatrix.from_other_sparse_matrix(data_full,
1) + data_rel
data_out.values = torch.cat([data_out.values, data_rel_full.values], 1)
data_out.n_channels += 1
target_entity = 0
if use_node_attrs:
for ent_id, attr_matrix in dl.nodes['attr'].items():
start_i = dl.nodes['shift'][ent_id]
n_instances = dl.nodes['count'][ent_id]
if attr_matrix is None:
if node_val == 'zero':
attr_matrix = np.zeros((n_instances, 1))
elif node_val == 'rand':
attr_matrix = np.random.randn(n_instances, 1)
else:
attr_matrix = np.ones((n_instances, 1))
if feats_type == 1 and ent_id != target_entity:
# To keep same behaviour as non-LGNN model, use 10 dimensions
attr_matrix = np.zeros((n_instances, 10))
n_channels = attr_matrix.shape[1]
indices = torch.arange(start_i,
start_i + n_instances).unsqueeze(0).repeat(
2, 1)
data_rel = SparseMatrix(
indices=indices,
values=torch.FloatTensor(attr_matrix),
shape=np.array([total_n_nodes, total_n_nodes, n_channels]),
is_set=True)
data_rel_full = SparseMatrix.from_other_sparse_matrix(
data_full, n_channels) + data_rel
data_out.values = torch.cat(
[data_out.values, data_rel_full.values], 1)
data_out.n_channels += n_channels
data = SparseMatrixData(schema)
data[0] = data_out
n_outputs = total_n_nodes
n_output_classes = dl.labels_train['num_classes']
schema_out = DataSchema([entities[target_entity]], [
Relation(0, [entities[target_entity], entities[target_entity]],
is_set=True)
])
data_target = SparseMatrixData(schema_out)
data_target[0] = SparseMatrix(
indices=torch.arange(n_outputs, dtype=torch.int64).repeat(2, 1),
values=torch.zeros([n_outputs, n_output_classes]),
shape=(n_outputs, n_outputs, n_output_classes),
is_set=True)
labels = np.zeros((dl.nodes['count'][0], dl.labels_train['num_classes']),
dtype=int)
val_ratio = 0.2
train_idx = np.nonzero(dl.labels_train['mask'])[0]
np.random.shuffle(train_idx)
split = int(train_idx.shape[0] * val_ratio)
val_idx = train_idx[:split]
train_idx = train_idx[split:]
train_idx = np.sort(train_idx)
val_idx = np.sort(val_idx)
test_idx = np.nonzero(dl.labels_test['mask'])[0]
labels[train_idx] = dl.labels_train['data'][train_idx]
labels[val_idx] = dl.labels_train['data'][val_idx]
if prefix != 'IMDB':
labels = labels.argmax(axis=1)
train_val_test_idx = {}
train_val_test_idx['train_idx'] = train_idx
train_val_test_idx['val_idx'] = val_idx
train_val_test_idx['test_idx'] = test_idx
return schema,\
schema_out, \
data, \
data_target, \
labels,\
train_val_test_idx,\
dl