Create collating_graphormer.pyx

collating_graphormer.pyx

@@ -0,0 +1,134 @@
+# Copyright (c) Microsoft Corporation and HuggingFace
+# Licensed under the MIT License.
+
+from typing import Any, Dict, List, Mapping
+
+import numpy as np
+import torch
+
+from ...utils import is_cython_available, requires_backends
+
+
+if is_cython_available():
+    import pyximport
+
+    pyximport.install(setup_args={"include_dirs": np.get_include()})
+    from . import algos_graphormer  # noqa E402
+
+
+def convert_to_single_emb(x, offset: int = 512):
+    feature_num = x.shape[1] if len(x.shape) > 1 else 1
+    feature_offset = 1 + np.arange(0, feature_num * offset, offset, dtype=np.int64)
+    x = x + feature_offset
+    return x
+
+
+def preprocess_item(item, keep_features=True):
+    requires_backends(preprocess_item, ["cython"])
+
+    if keep_features and "edge_attr" in item.keys():  # edge_attr
+        edge_attr = np.asarray(item["edge_attr"], dtype=np.int64)
+    else:
+        edge_attr = np.ones((len(item["edge_index"][0]), 1), dtype=np.int64)  # same embedding for all
+
+    if keep_features and "node_feat" in item.keys():  # input_nodes
+        node_feature = np.asarray(item["node_feat"], dtype=np.int64)
+    else:
+        node_feature = np.ones((item["num_nodes"], 1), dtype=np.int64)  # same embedding for all
+
+    edge_index = np.asarray(item["edge_index"], dtype=np.int64)
+
+    input_nodes = convert_to_single_emb(node_feature) + 1
+    num_nodes = item["num_nodes"]
+
+    if len(edge_attr.shape) == 1:
+        edge_attr = edge_attr[:, None]
+    attn_edge_type = np.zeros([num_nodes, num_nodes, edge_attr.shape[-1]], dtype=np.int64)
+    attn_edge_type[edge_index[0], edge_index[1]] = convert_to_single_emb(edge_attr) + 1
+
+    # node adj matrix [num_nodes, num_nodes] bool
+    adj = np.zeros([num_nodes, num_nodes], dtype=bool)
+    adj[edge_index[0], edge_index[1]] = True
+
+    shortest_path_result, path = algos_graphormer.floyd_warshall(adj)
+    max_dist = np.amax(shortest_path_result)
+
+    input_edges = algos_graphormer.gen_edge_input(max_dist, path, attn_edge_type)
+    attn_bias = np.zeros([num_nodes + 1, num_nodes + 1], dtype=np.single)  # with graph token
+
+    # combine
+    item["input_nodes"] = input_nodes + 1  # we shift all indices by one for padding
+    item["attn_bias"] = attn_bias
+    item["attn_edge_type"] = attn_edge_type
+    item["spatial_pos"] = shortest_path_result.astype(np.int64) + 1  # we shift all indices by one for padding
+    item["in_degree"] = np.sum(adj, axis=1).reshape(-1) + 1  # we shift all indices by one for padding
+    item["out_degree"] = item["in_degree"]  # for undirected graph
+    item["input_edges"] = input_edges + 1  # we shift all indices by one for padding
+    if "labels" not in item:
+        item["labels"] = item["y"]
+
+    return item
+
+
+class GraphormerDataCollator:
+    def __init__(self, spatial_pos_max=20, on_the_fly_processing=False):
+        if not is_cython_available():
+            raise ImportError("Graphormer preprocessing needs Cython (pyximport)")
+
+        self.spatial_pos_max = spatial_pos_max
+        self.on_the_fly_processing = on_the_fly_processing
+
+    def __call__(self, features: List[dict]) -> Dict[str, Any]:
+        if self.on_the_fly_processing:
+            features = [preprocess_item(i) for i in features]
+
+        if not isinstance(features[0], Mapping):
+            features = [vars(f) for f in features]
+        batch = {}
+
+        max_node_num = max(len(i["input_nodes"]) for i in features)
+        node_feat_size = len(features[0]["input_nodes"][0])
+        edge_feat_size = len(features[0]["attn_edge_type"][0][0])
+        max_dist = max(len(i["input_edges"][0][0]) for i in features)
+        edge_input_size = len(features[0]["input_edges"][0][0][0])
+        batch_size = len(features)
+
+        batch["attn_bias"] = torch.zeros(batch_size, max_node_num + 1, max_node_num + 1, dtype=torch.float)
+        batch["attn_edge_type"] = torch.zeros(batch_size, max_node_num, max_node_num, edge_feat_size, dtype=torch.long)
+        batch["spatial_pos"] = torch.zeros(batch_size, max_node_num, max_node_num, dtype=torch.long)
+        batch["in_degree"] = torch.zeros(batch_size, max_node_num, dtype=torch.long)
+        batch["input_nodes"] = torch.zeros(batch_size, max_node_num, node_feat_size, dtype=torch.long)
+        batch["input_edges"] = torch.zeros(
+            batch_size, max_node_num, max_node_num, max_dist, edge_input_size, dtype=torch.long
+        )
+
+        for ix, f in enumerate(features):
+            for k in ["attn_bias", "attn_edge_type", "spatial_pos", "in_degree", "input_nodes", "input_edges"]:
+                f[k] = torch.tensor(f[k])
+
+            if len(f["attn_bias"][1:, 1:][f["spatial_pos"] >= self.spatial_pos_max]) > 0:
+                f["attn_bias"][1:, 1:][f["spatial_pos"] >= self.spatial_pos_max] = float("-inf")
+
+            batch["attn_bias"][ix, : f["attn_bias"].shape[0], : f["attn_bias"].shape[1]] = f["attn_bias"]
+            batch["attn_edge_type"][ix, : f["attn_edge_type"].shape[0], : f["attn_edge_type"].shape[1], :] = f[
+                "attn_edge_type"
+            ]
+            batch["spatial_pos"][ix, : f["spatial_pos"].shape[0], : f["spatial_pos"].shape[1]] = f["spatial_pos"]
+            batch["in_degree"][ix, : f["in_degree"].shape[0]] = f["in_degree"]
+            batch["input_nodes"][ix, : f["input_nodes"].shape[0], :] = f["input_nodes"]
+            batch["input_edges"][
+                ix, : f["input_edges"].shape[0], : f["input_edges"].shape[1], : f["input_edges"].shape[2], :
+            ] = f["input_edges"]
+
+        batch["out_degree"] = batch["in_degree"]
+
+        sample = features[0]["labels"]
+        if len(sample) == 1:  # one task
+            if isinstance(sample[0], float):  # regression
+                batch["labels"] = torch.from_numpy(np.concatenate([i["labels"] for i in features]))
+            else:  # binary classification
+                batch["labels"] = torch.from_numpy(np.concatenate([i["labels"] for i in features]))
+        else:  # multi task classification, left to float to keep the NaNs
+            batch["labels"] = torch.from_numpy(np.stack([i["labels"] for i in features], axis=0))
+
+        return batch