def load_data(self, path: RichPath, folds_to_load: Optional[Set[DataFold]] = None) -> None:
"""Load the data from disk."""
logger.info(f"Starting to load data from {path}.")
# If we haven't defined what folds to load, load all:
if folds_to_load is None:
folds_to_load = {DataFold.TRAIN, DataFold.VALIDATION, DataFold.TEST}
if DataFold.TRAIN in folds_to_load:
data_file = path.join("train.jsonl.gz")
self.vocab_source = self._build_vocab(
dataset = [datapoint["graph"]["node_features"] for datapoint in data_file.read_by_file_suffix()],
vocab_size=self.max_vocab_size
)
self.vocab_target = self._build_vocab(
dataset = [datapoint["Target"] for datapoint in data_file.read_by_file_suffix()],
vocab_size=self.max_vocab_size
)
self._loaded_data[DataFold.TRAIN] = self.__load_data(data_file)
logger.debug("Done loading training data.")
if DataFold.VALIDATION in folds_to_load:
self._loaded_data[DataFold.VALIDATION] = self.__load_data(path.join("valid.jsonl.gz"))
logger.debug("Done loading validation data.")
if DataFold.TEST in folds_to_load:
self._loaded_data[DataFold.TEST] = self.__load_data(path.join("test.jsonl.gz"))
logger.debug("Done loading test data.")
def load_data(self,
path: RichPath,
folds_to_load: Optional[Set[DataFold]] = None) -> None:
"""Load the data from disk."""
logger.info(f"Starting to load data from {path}.")
if self.metadata == {}:
metadata_path = path.join("metadata.pkl.gz")
if metadata_path.exists():
logger.info(f"Loading metadata from {metadata_path}")
self._metadata = metadata_path.read_by_file_suffix()
else:
logger.warning(
"Using metadata passed to constructor, not metadata stored with data."
)
# If we haven't defined what folds to load, load all:
if folds_to_load is None:
folds_to_load = {
DataFold.TRAIN, DataFold.VALIDATION, DataFold.TEST
}
if DataFold.TRAIN in folds_to_load:
self._loaded_data[DataFold.TRAIN] = self.__load_data(
path.join("train.jsonl.gz"))
logger.debug("Done loading training data.")
if DataFold.VALIDATION in folds_to_load:
self._loaded_data[DataFold.VALIDATION] = self.__load_data(
path.join("valid.jsonl.gz"))
logger.debug("Done loading validation data.")
if DataFold.TEST in folds_to_load:
self._loaded_data[DataFold.TEST] = self.__load_data(
path.join("test.jsonl.gz"))
logger.debug("Done loading test data.")
def load_data(self, path: RichPath) -> None:
# Note that as __load_data produces a generator, we explicitly force loading
# (and caching) here:
self._loaded_data[DataFold.TRAIN] = \
list(self.__load_data(path.join("graphs-train"), DataFold.TRAIN))
self._loaded_data[DataFold.VALIDATION] = \
list(self.__load_data(path.join("graphs-valid"), DataFold.VALIDATION))
def load_data(self,
path: RichPath,
folds_to_load: Optional[Set[DataFold]] = None) -> None:
"""Load the data from disk."""
logger.info(f"Starting to load data from {path}.")
self.load_metadata(path)
# If we haven't defined what folds to load, load all:
if folds_to_load is None:
folds_to_load = {
DataFold.TRAIN, DataFold.VALIDATION, DataFold.TEST
}
if DataFold.TRAIN in folds_to_load:
self._loaded_data[DataFold.TRAIN] = self.__load_data(
path.join("train.jsonl.gz"))
logger.debug("Done loading training data.")
if DataFold.VALIDATION in folds_to_load:
self._loaded_data[DataFold.VALIDATION] = self.__load_data(
path.join("valid.jsonl.gz"))
logger.debug("Done loading validation data.")
if DataFold.TEST in folds_to_load:
self._loaded_data[DataFold.TEST] = self.__load_data(
path.join("test.jsonl.gz"))
logger.debug("Done loading test data.")
def __load_data(self, data_dir: RichPath,
data_fold: DataFold) -> List[GraphSample]:
if data_fold == None:
data_fold = "train"
if data_fold == DataFold.TRAIN:
data_name = "train"
elif data_fold == DataFold.VALIDATION:
data_name = "valid"
elif data_fold == DataFold.TEST:
data_name = "test"
else:
raise ValueError("Unknown data fold '%s'" % str(data_fold))
print(" Loading DEOBFUSCATION %s data from %s." %
(data_name, data_dir))
if data_dir.join("%s-saved.pkl.gz" % data_name).is_file():
read_data = data_dir.join("%s-saved.pkl.gz" %
data_name).read_by_file_suffix()
return read_data["all_graphs"], read_data["properties"]
all_untensorised = data_dir.join("%s.pkl.gz" %
data_name).read_by_file_suffix()
graphs = all_untensorised["graphs"]
properties = dict()
properties["all_user_nodes"] = all_untensorised["name_to_id_mapping"]
properties["user_defined_nodes_number"] = all_untensorised[
"total_user_defined_nodes"]
properties["edge_mapping"] = all_untensorised["edge_name_to_id"]
properties["__num_labels"] = len(properties["all_user_nodes"])
properties["__num_edge_types"] = len(properties["edge_mapping"])
properties["__num_types"] = len(all_untensorised["type_to_id"])
all_graphs = []
for i in tqdm(range(len(graphs))):
old_graph = graphs[i]
if (old_graph["user_defined_nodes_number"] > 0):
all_graphs.append(
self.create_graph_sample(
old_graph, properties["__num_edge_types"],
len(properties["all_user_nodes"])))
print_graph_number = 2500
print([
all_untensorised["ids_to_names"][x]
for x in all_graphs[print_graph_number].labels
], all_graphs[print_graph_number].nodes_mask)
print(all_graphs[print_graph_number])
to_save = dict()
to_save["all_graphs"] = all_graphs
to_save["properties"] = properties
data_dir.join("%s-saved.pkl.gz" %
data_name).save_as_compressed_file(to_save)
print("Saved modified data to %s-saved.pkl.gz" % data_name)
return all_graphs, properties
def df_to_jsonl(df: pd.DataFrame,
RichPath_obj: RichPath,
i: int,
basefilename='codedata') -> str:
dest_filename = f'{basefilename}_{str(i).zfill(5)}.jsonl.gz'
RichPath_obj.join(dest_filename).save_as_compressed_file(
df.to_dict(orient='records'))
return str(RichPath_obj.join(dest_filename))
def run_train(model_class: Type[Model],
train_data_path: RichPath,
valid_data_path: RichPath,
save_folder: str,
hyperparameters: Dict[str, Any],
run_name: Optional[str]=None,
quiet: bool=False) \
-> RichPath:
train_data_chunk_paths = train_data_path.get_filtered_files_in_dir('chunk_*')
valid_data_chunk_paths = valid_data_path.get_filtered_files_in_dir('valid_chunk_*')
model = model_class(hyperparameters, run_name=run_name, model_save_dir=save_folder, log_save_dir=save_folder)
if os.path.exists(model.model_save_path):
model = model_restore_helper.restore(RichPath.create(model.model_save_path), is_train=True)
model.train_log("Resuming training run %s of model %s with following hypers:\n%s" % (hyperparameters['run_id'],
model.__class__.__name__,
json.dumps(
hyperparameters)))
resume = True
else:
model.load_existing_metadata(train_data_path.join('metadata.pkl.gz'))
model.make_model(is_train=True)
model.train_log("Starting training run %s of model %s with following hypers:\n%s" % (hyperparameters['run_id'],
model.__class__.__name__,
json.dumps(hyperparameters)))
resume = False
model_path = model.train(train_data_chunk_paths, valid_data_chunk_paths, quiet=quiet, resume=resume)
return model_path
def __load_data(self, data_dir: RichPath, data_fold: DataFold):
if data_fold == DataFold.TRAIN:
data_name = "train"
elif data_fold == DataFold.VALIDATION:
data_name = "valid"
elif data_fold == DataFold.TEST:
data_name = "test"
else:
raise ValueError("Unknown data fold '%s'" % str(data_fold))
print(" Loading observer %s data from %s." % (data_name, data_dir))
graph_pickle_data = data_dir.join("%s_data_collection.pickle" %
data_name).read_by_file_suffix()
graph_id_to_edges: Dict[int, List[Tuple[int, int]]] = {}
graph_id_to_features: Dict[int, List[np.ndarray]] = {}
graph_id_to_targets: Dict[int, List[np.ndarray]] = {}
#graph_id_to_node_offset: Dict[int, int] = {}
for graph_id, graph in enumerate(
graph_pickle_data, 1
): #graph_pickle_data is a list of dictionary. graph_id start at 1
graph_id_to_features[graph_id] = []
graph_id_to_targets[graph_id] = []
graph_id_to_edges[graph_id] = []
for node_dict in graph['graph']['nodes']:
graph_id_to_features[graph_id].append(
np.array(list(node_dict.values())))
for target_dict in graph['actions'].values():
graph_id_to_targets[graph_id].append(
np.array(list(target_dict.values())))
#convert source, target node from id to position of nodes in the list
for edge_dict in graph['graph']['links']:
src_node, tgt_node = edge_dict['source'], edge_dict['target']
graph_id_to_edges[graph_id].append((src_node, tgt_node))
final_graphs = []
for graph_id in graph_id_to_edges.keys():
num_nodes = len(graph_id_to_features[graph_id])
adjacency_lists, type_to_node_to_num_inedges = process_adjacency_lists(
adjacency_lists=[graph_id_to_edges[graph_id]],
num_nodes=num_nodes,
add_self_loop_edges=self.params["add_self_loop_edges"],
tied_fwd_bkwd_edge_types=self._tied_fwd_bkwd_edge_types,
)
final_graphs.append(
TFAgentsGraphSample(
adjacency_lists=adjacency_lists,
type_to_node_to_num_inedges=type_to_node_to_num_inedges,
node_features=np.array(graph_id_to_features[graph_id]),
node_targets=np.array(graph_id_to_targets[graph_id]),
))
return final_graphs
def load_data(self,
path: RichPath,
folds_to_load: Optional[Set[DataFold]] = None) -> None:
# 如果没有定义加载数据属于哪个集，那么需要同时加载训练集、验证集和测试集
if folds_to_load is None:
folds_to_load = {
DataFold.TRAIN, DataFold.VALIDATION, DataFold.TEST
}
if DataFold.TRAIN in folds_to_load:
self._loaded_data[DataFold.TRAIN] = self.__load_data(
path.join("train_token.json"))
if DataFold.VALIDATION in folds_to_load:
self._loaded_data[DataFold.VALIDATION] = self.__load_data(
path.join("validate_token.json"))
if DataFold.TEST in folds_to_load:
self._loaded_data[DataFold.TEST] = self.__load_data(
path.join("test_token.json"))
def load_metadata(self, path: RichPath) -> None:
"""Load the metadata for a dataset (such as vocabularies, names of properties, ...)
from a path on disk.
Note: Implementors needing to act on metadata information before loading any actual data
should override this method.
"""
if self.metadata == {}:
metadata_path = path.join("metadata.pkl.gz")
if metadata_path.exists():
logger.info(f"Loading metadata from {metadata_path}")
self._metadata = metadata_path.read_by_file_suffix()
else:
logger.warning("Using metadata passed to constructor, not metadata stored with data.")
def split_many_files(input_dir: RichPath, output_dir: RichPath,
train_ratio: float, valid_ratio: float, test_ratio: float,
test_only_projects: Set[str]) -> None:
output_paths = {} # type: Dict[str, RichPath]
for split_name in ['train', 'valid', 'test', 'test-only']:
graph_dir_name_for_split_type = input_dir.basename() + '-' + split_name
graph_dir_for_split_type = output_dir.join(
graph_dir_name_for_split_type)
output_paths[split_name] = graph_dir_for_split_type
graph_dir_for_split_type.make_as_dir()
pool = Pool()
pool.starmap(split_file,
[(f, output_paths, train_ratio, valid_ratio, test_ratio,
test_only_projects)
for f in input_dir.get_filtered_files_in_dir('*')])
return None
def __load_data(self, data_dir: RichPath,
data_fold: DataFold) -> List[GraphSample]:
if data_fold == DataFold.TRAIN:
data_name = "train"
elif data_fold == DataFold.VALIDATION:
data_name = "valid"
elif data_fold == DataFold.TEST:
data_name = "test"
else:
raise ValueError("Unknown data fold '%s'" % str(data_fold))
print(" Loading PPI %s data from %s." % (data_name, data_dir))
graph_json_data = data_dir.join("%s_graph.json" %
data_name).read_by_file_suffix()
node_to_features = data_dir.join("%s_feats.npy" %
data_name).read_by_file_suffix()
node_to_labels = data_dir.join("%s_labels.npy" %
data_name).read_by_file_suffix()
node_to_graph_id = data_dir.join("%s_graph_id.npy" %
data_name).read_by_file_suffix()
self.__initial_node_feature_size = node_to_features.shape[-1]
self.__num_labels = node_to_labels.shape[-1]
# We read in all the data in two steps:
# (1) Read features, labels and insert self-loop edges (edge type 0).
# Implicitly, this gives us the number of nodes per graph.
# (2) Read all edges, and shift them so that each graph starts with node 0.
fwd_edge_type = 0
self.__num_edge_types = 1
if self.params['add_self_loop_edges']:
self_loop_edge_type = self.__num_edge_types
self.__num_edge_types += 1
if not self.params['tie_fwd_bkwd_edges']:
bkwd_edge_type = self.__num_edge_types
self.__num_edge_types += 1
graph_id_to_graph_data = {} # type: Dict[int, GraphSample]
graph_id_to_node_offset = {}
num_total_nodes = node_to_features.shape[0]
for node_id in range(num_total_nodes):
graph_id = node_to_graph_id[node_id]
# In case we are entering a new graph, note its ID, so that we can normalise everything to start at 0
if graph_id not in graph_id_to_graph_data:
graph_id_to_graph_data[graph_id] = \
GraphSample(adjacency_lists=[[] for _ in range(self.__num_edge_types)],
type_to_node_to_num_incoming_edges=[[] for _ in range(self.__num_edge_types)],
node_features=[],
node_labels=[])
graph_id_to_node_offset[graph_id] = node_id
cur_graph_data = graph_id_to_graph_data[graph_id]
cur_graph_data.node_features.append(node_to_features[node_id])
cur_graph_data.node_labels.append(node_to_labels[node_id])
shifted_node_id = node_id - graph_id_to_node_offset[graph_id]
if self.params['add_self_loop_edges']:
cur_graph_data.adjacency_lists[self_loop_edge_type].append(
(shifted_node_id, shifted_node_id))
cur_graph_data.type_to_node_to_num_incoming_edges[
self_loop_edge_type].append(1)
# Prepare reading of the edges by setting counters to 0:
for graph_data in graph_id_to_graph_data.values():
num_graph_nodes = len(graph_data.node_features)
graph_data.type_to_node_to_num_incoming_edges[
fwd_edge_type] = np.zeros([num_graph_nodes], np.int32)
if not self.params['tie_fwd_bkwd_edges']:
graph_data.type_to_node_to_num_incoming_edges[
bkwd_edge_type] = np.zeros([num_graph_nodes], np.int32)
for edge_info in graph_json_data['links']:
src_node, tgt_node = edge_info['source'], edge_info['target']
# First, shift node IDs so that each graph starts at node 0:
graph_id = node_to_graph_id[src_node]
graph_node_offset = graph_id_to_node_offset[graph_id]
src_node, tgt_node = src_node - graph_node_offset, tgt_node - graph_node_offset
cur_graph_data = graph_id_to_graph_data[graph_id]
cur_graph_data.adjacency_lists[fwd_edge_type].append(
(src_node, tgt_node))
cur_graph_data.type_to_node_to_num_incoming_edges[fwd_edge_type][
tgt_node] += 1
if not self.params['tie_fwd_bkwd_edges']:
cur_graph_data.adjacency_lists[bkwd_edge_type].append(
(tgt_node, src_node))
cur_graph_data.type_to_node_to_num_incoming_edges[
bkwd_edge_type][src_node] += 1
final_graphs = []
for graph_data in graph_id_to_graph_data.values():
# numpy-ize:
adj_lists = []
for edge_type_idx in range(self.__num_edge_types):
adj_lists.append(
np.array(graph_data.adjacency_lists[edge_type_idx]))
final_graphs.append(
GraphSample(adjacency_lists=adj_lists,
type_to_node_to_num_incoming_edges=np.array(
graph_data.type_to_node_to_num_incoming_edges),
node_features=np.array(graph_data.node_features),
node_labels=np.array(graph_data.node_labels)))
return final_graphs
def load_eval_data_from_path(self, path: RichPath) -> Iterable[Any]:
if path.path == self.default_data_path():
path = path.join("graphs-test")
return iter(self.__load_data(path, DataFold.TEST))
def tensorise_data_in_dir(self,
input_data_dir: RichPath,
output_dir: RichPath,
for_test: bool,
max_num_files: Optional[int]=None,
add_raw_data: bool=False,
return_num_original_samples: bool = False) \
-> Union[List[RichPath], Tuple[List[RichPath], int]]:
"""
Tensorises data in directory by sample-by-sample, generating "chunk" files of
lists of tensorised samples that are then consumed in the split_data_into_minibatches
pipeline to construct minibatches.
Args:
input_data_dir: Where to load the raw data from (should come from the extraction pipeline)
output_dir: Where to store the data to.
for_test: Flag indicating if the data is to be used for testing (which required additional tensorisation steps)
max_num_files: Maximal number of files to load data from.
add_raw_data: Flag indicating that the original data should be added to the tensorised data.
return_num_original_samples: Flag indicating that the return value should contain the
number of samples we tried to load, including those that we discarded (e.g., because
they were too big)
Return:
List of paths to the generated chunk files, or tuple of that list and the number
of samples loaded (iff return_num_original_samples was set)
"""
data_files = get_data_files_from_directory(input_data_dir,
max_num_files)
tensorisation_argument_tuples = []
chunk_paths = []
for (partition_idx, raw_graph_file_partition) in enumerate(
partition_files_by_size(data_files, 40 * 1024 * 1024)):
target_file = output_dir.join("chunk_%04i.pkl.gz" %
(partition_idx, ))
tensorisation_argument_tuples.append(
(raw_graph_file_partition, target_file))
chunk_paths.append(target_file)
parsing_result_data = {"num_all_samples": 0, "num_used_samples": 0}
data_file_parser_fn = make_data_file_parser(type(self),
self.hyperparameters,
self.metadata,
for_test=for_test,
add_raw_data=add_raw_data)
def received_result_callback(result):
(num_all_samples, num_used_samples) = result
parsing_result_data['num_all_samples'] += num_all_samples
parsing_result_data['num_used_samples'] += num_used_samples
def finished_callback():
pass
run_jobs_in_parallel(tensorisation_argument_tuples,
data_file_parser_fn, received_result_callback,
finished_callback)
# Store the metadata we used for this as well, so that we can re-use the results:
metadata_path = output_dir.join("metadata.pkl.gz")
metadata_path.save_as_compressed_file({
"hyperparameters":
self.hyperparameters,
"metadata":
self.__metadata,
"num_used_samples":
parsing_result_data['num_used_samples'],
"num_all_samples":
parsing_result_data['num_all_samples']
})
self.train_log(
"Tensorised %i (%i before filtering) samples from '%s' into '%s'."
% (parsing_result_data['num_used_samples'],
parsing_result_data['num_all_samples'], input_data_dir,
output_dir))
if return_num_original_samples:
return chunk_paths, parsing_result_data['num_all_samples']
return chunk_paths
def load_eval_data_from_path(self, path: RichPath) -> Iterable[Any]:
if path.path == self.default_data_path():
path = path.join("test.jsonl.gz")
return self.__load_data(path)
def load_data(self, path: RichPath) -> None:
self._loaded_data[DataFold.TRAIN] = self.__load_data(
path.join("train.jsonl.gz"))
self._loaded_data[DataFold.VALIDATION] = self.__load_data(
path.join("valid.jsonl.gz"))
def __load_data(self, data_dir: RichPath,
data_fold: DataFold) -> List[PPIGraphSample]:
"""
ppi数据集包括4类文件，分别是
XXX_feats.npy
XXX_graph.json
XXX_graph_id.npy
XXX_labels.npy
read_by_file_suffix() : 读取 npy、json、pkl、jsonl等类型的文件
"""
if data_fold == DataFold.TRAIN:
data_name = "train"
elif data_fold == DataFold.VALIDATION:
data_name = "valid"
elif data_fold == DataFold.TEST:
data_name = "test"
else:
raise ValueError("Unknown data fold '%s'" % str(data_fold))
print(" Loading PPI %s data from %s." % (data_name, data_dir))
graph_json_data = data_dir.join("%s_graph.json" %
data_name).read_by_file_suffix()
node_to_features = data_dir.join("%s_feats.npy" %
data_name).read_by_file_suffix()
node_to_labels = data_dir.join("%s_labels.npy" %
data_name).read_by_file_suffix()
node_to_graph_id = data_dir.join("%s_graph_id.npy" %
data_name).read_by_file_suffix()
# We read in all the data in two steps:
# (1) Read features and labels. Implicitly, this gives us the number of nodes per graph.
# 每个节点的特征是50维，每个节点的label是121个
# (2) Read all edges, and shift them so that each graph starts with node 0.
# 提取每个节点的边、特征、标签和节点
graph_id_to_edges: Dict[int, List[Tuple[int, int]]] = {}
graph_id_to_features: Dict[int, List[np.ndarray]] = {}
graph_id_to_labels: Dict[int, List[np.ndarray]] = {}
graph_id_to_node_offset: Dict[int, int] = {}
num_total_nodes = node_to_features.shape[0]
for node_id in range(num_total_nodes):
graph_id = node_to_graph_id[node_id]
# In case we are entering a new graph, note its ID, so that we can normalise everything to start at 0
if graph_id not in graph_id_to_edges:
graph_id_to_edges[graph_id] = []
graph_id_to_features[graph_id] = []
graph_id_to_labels[graph_id] = []
graph_id_to_node_offset[graph_id] = node_id
graph_id_to_features[graph_id].append(node_to_features[node_id])
graph_id_to_labels[graph_id].append(node_to_labels[node_id])
for edge_info in graph_json_data["links"]:
src_node, tgt_node = edge_info["source"], edge_info["target"]
# First, shift node IDs so that each graph starts at node 0:
graph_id = node_to_graph_id[src_node]
graph_node_offset = graph_id_to_node_offset[graph_id]
src_node, tgt_node = src_node - graph_node_offset, tgt_node - graph_node_offset
graph_id_to_edges[graph_id].append((src_node, tgt_node))
final_graphs = []
for graph_id in graph_id_to_edges.keys():
num_nodes = len(graph_id_to_features[graph_id])
adjacency_lists, type_to_node_to_num_inedges = process_adjacency_lists(
adjacency_lists=[graph_id_to_edges[graph_id]],
num_nodes=num_nodes,
add_self_loop_edges=self.params["add_self_loop_edges"],
tied_fwd_bkwd_edge_types=self._tied_fwd_bkwd_edge_types,
)
final_graphs.append(
PPIGraphSample(
adjacency_lists=adjacency_lists,
type_to_node_to_num_inedges=type_to_node_to_num_inedges,
node_features=np.array(graph_id_to_features[graph_id]),
node_labels=np.array(graph_id_to_labels[graph_id]),
))
return final_graphs
def load_data(cls, data_dir: RichPath,
data_fold: str) -> List[PPIGraphSample]:
print(" Loading PPI %s data from %s." % (data_fold, data_dir))
graph_json_data = data_dir.join("%s_graph.json" %
data_fold).read_by_file_suffix()
node_to_features = data_dir.join("%s_feats.npy" %
data_fold).read_by_file_suffix()
node_to_labels = data_dir.join("%s_labels.npy" %
data_fold).read_by_file_suffix()
node_to_graph_id = data_dir.join("%s_graph_id.npy" %
data_fold).read_by_file_suffix()
# We read in all the data in two steps:
# (1) Read features, labels. Implicitly, this gives us the number of nodes per graph.
# (2) Read all edges, and shift them so that each graph starts with node 0.
fwd_edge_type = 0
graph_id_to_graph_data: Dict[int, PPIGraphSample] = {}
graph_id_to_node_offset: Dict[int, int] = {}
num_total_nodes = node_to_features.shape[0]
for node_id in range(num_total_nodes):
graph_id = node_to_graph_id[node_id]
# In case we are entering a new graph, note its ID, so that we can normalise everything to start at 0
if graph_id not in graph_id_to_graph_data:
graph_id_to_graph_data[graph_id] = PPIGraphSample(
adjacency_lists=[[]],
node_features=[],
node_labels=[],
)
graph_id_to_node_offset[graph_id] = node_id
cur_graph_data = graph_id_to_graph_data[graph_id]
cur_graph_data.node_features.append(node_to_features[node_id])
cur_graph_data.node_labels.append(node_to_labels[node_id])
for edge_info in graph_json_data["links"]:
src_node, tgt_node = edge_info["source"], edge_info["target"]
# First, shift node IDs so that each graph starts at node 0:
graph_id = node_to_graph_id[src_node]
graph_node_offset = graph_id_to_node_offset[graph_id]
src_node, tgt_node = src_node - graph_node_offset, tgt_node - graph_node_offset
cur_graph_data = graph_id_to_graph_data[graph_id]
cur_graph_data.adjacency_lists[fwd_edge_type].append(
(src_node, tgt_node))
final_graphs = []
for graph_data in graph_id_to_graph_data.values():
# numpy-ize:
adj_lists = [
np.array(graph_data.adjacency_lists[fwd_edge_type],
dtype=np.int32)
]
final_graphs.append(
PPIGraphSample(
adjacency_lists=adj_lists,
node_features=np.array(graph_data.node_features,
dtype=np.float32),
node_labels=np.array(graph_data.node_labels,
dtype=np.bool),
))
return final_graphs
def _write_data(out_dir: RichPath, window_idx: int, chunk_size: int, data_window: List[Any]):
np.random.shuffle(data_window)
for chunk_idx, data_chunk in enumerate(chunked(data_window, chunk_size)):
out_file = out_dir.join('chunk_%i-%i.jsonl.gz' % (window_idx, chunk_idx))
out_file.save_as_compressed_file(data_chunk)
