Create configuration_graphormer.pyx

configuration_graphormer.pyx

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+# coding=utf-8
+# Copyright 2022 Microsoft, clefourrier and The HuggingFace Inc. team. All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+""" Graphormer model configuration"""
+
+from ...configuration_utils import PretrainedConfig
+from ...utils import logging
+
+
+logger = logging.get_logger(__name__)
+
+GRAPHORMER_PRETRAINED_CONFIG_ARCHIVE_MAP = {
+    # pcqm4mv1 now deprecated
+    "graphormer-base": "https://huggingface.co/clefourrier/graphormer-base-pcqm4mv2/resolve/main/config.json",
+    # See all Graphormer models at https://huggingface.co/models?filter=graphormer
+}
+
+
+class GraphormerConfig(PretrainedConfig):
+    r"""
+    This is the configuration class to store the configuration of a [`~GraphormerModel`]. It is used to instantiate an
+    Graphormer model according to the specified arguments, defining the model architecture. Instantiating a
+    configuration with the defaults will yield a similar configuration to that of the Graphormer
+    [graphormer-base-pcqm4mv1](https://huggingface.co/graphormer-base-pcqm4mv1) architecture.
+
+    Configuration objects inherit from [`PretrainedConfig`] and can be used to control the model outputs. Read the
+    documentation from [`PretrainedConfig`] for more information.
+
+
+    Args:
+        num_classes (`int`, *optional*, defaults to 1):
+            Number of target classes or labels, set to n for binary classification of n tasks.
+        num_atoms (`int`, *optional*, defaults to 512*9):
+            Number of node types in the graphs.
+        num_edges (`int`, *optional*, defaults to 512*3):
+            Number of edges types in the graph.
+        num_in_degree (`int`, *optional*, defaults to 512):
+            Number of in degrees types in the input graphs.
+        num_out_degree (`int`, *optional*, defaults to 512):
+            Number of out degrees types in the input graphs.
+        num_edge_dis (`int`, *optional*, defaults to 128):
+            Number of edge dis in the input graphs.
+        multi_hop_max_dist (`int`, *optional*, defaults to 20):
+            Maximum distance of multi hop edges between two nodes.
+        spatial_pos_max (`int`, *optional*, defaults to 1024):
+            Maximum distance between nodes in the graph attention bias matrices, used during preprocessing and
+            collation.
+        edge_type (`str`, *optional*, defaults to multihop):
+            Type of edge relation chosen.
+        max_nodes (`int`, *optional*, defaults to 512):
+            Maximum number of nodes which can be parsed for the input graphs.
+        share_input_output_embed (`bool`, *optional*, defaults to `False`):
+            Shares the embedding layer between encoder and decoder - careful, True is not implemented.
+        num_layers (`int`, *optional*, defaults to 12):
+            Number of layers.
+        embedding_dim (`int`, *optional*, defaults to 768):
+            Dimension of the embedding layer in encoder.
+        ffn_embedding_dim (`int`, *optional*, defaults to 768):
+            Dimension of the "intermediate" (often named feed-forward) layer in encoder.
+        num_attention_heads (`int`, *optional*, defaults to 32):
+            Number of attention heads in the encoder.
+        self_attention (`bool`, *optional*, defaults to `True`):
+            Model is self attentive (False not implemented).
+        activation_function (`str` or `function`, *optional*, defaults to `"gelu"`):
+            The non-linear activation function (function or string) in the encoder and pooler. If string, `"gelu"`,
+            `"relu"`, `"silu"` and `"gelu_new"` are supported.
+        dropout (`float`, *optional*, defaults to 0.1):
+            The dropout probability for all fully connected layers in the embeddings, encoder, and pooler.
+        attention_dropout (`float`, *optional*, defaults to 0.1):
+            The dropout probability for the attention weights.
+        layerdrop (`float`, *optional*, defaults to 0.0):
+            The LayerDrop probability for the encoder. See the [LayerDrop paper](see https://arxiv.org/abs/1909.11556)
+            for more details.
+        bias (`bool`, *optional*, defaults to `True`):
+            Uses bias in the attention module - unsupported at the moment.
+        embed_scale(`float`, *optional*, defaults to None):
+            Scaling factor for the node embeddings.
+        num_trans_layers_to_freeze (`int`, *optional*, defaults to 0):
+            Number of transformer layers to freeze.
+        encoder_normalize_before (`bool`, *optional*, defaults to `False`):
+            Normalize features before encoding the graph.
+        pre_layernorm (`bool`, *optional*, defaults to `False`):
+            Apply layernorm before self attention and the feed forward network. Without this, post layernorm will be
+            used.
+        apply_graphormer_init (`bool`, *optional*, defaults to `False`):
+            Apply a custom graphormer initialisation to the model before training.
+        freeze_embeddings (`bool`, *optional*, defaults to `False`):
+            Freeze the embedding layer, or train it along the model.
+        encoder_normalize_before (`bool`, *optional*, defaults to `False`):
+            Apply the layer norm before each encoder block.
+        q_noise (`float`, *optional*, defaults to 0.0):
+            Amount of quantization noise (see "Training with Quantization Noise for Extreme Model Compression"). (For
+            more detail, see fairseq's documentation on quant_noise).
+        qn_block_size (`int`, *optional*, defaults to 8):
+            Size of the blocks for subsequent quantization with iPQ (see q_noise).
+        kdim (`int`, *optional*, defaults to None):
+            Dimension of the key in the attention, if different from the other values.
+        vdim (`int`, *optional*, defaults to None):
+            Dimension of the value in the attention, if different from the other values.
+        use_cache (`bool`, *optional*, defaults to `True`):
+            Whether or not the model should return the last key/values attentions (not used by all models).
+        traceable (`bool`, *optional*, defaults to `False`):
+            Changes return value of the encoder's inner_state to stacked tensors.
+
+        Example:
+            ```python
+            >>> from transformers import GraphormerForGraphClassification, GraphormerConfig
+
+            >>> # Initializing a Graphormer graphormer-base-pcqm4mv2 style configuration
+            >>> configuration = GraphormerConfig()
+
+            >>> # Initializing a model from the graphormer-base-pcqm4mv1 style configuration
+            >>> model = GraphormerForGraphClassification(configuration)
+
+            >>> # Accessing the model configuration
+            >>> configuration = model.config
+            ```
+    """
+    model_type = "graphormer"
+    keys_to_ignore_at_inference = ["past_key_values"]
+
+    def __init__(
+        self,
+        num_classes: int = 1,
+        num_atoms: int = 512 * 9,
+        num_edges: int = 512 * 3,
+        num_in_degree: int = 512,
+        num_out_degree: int = 512,
+        num_spatial: int = 512,
+        num_edge_dis: int = 128,
+        multi_hop_max_dist: int = 5,  # sometimes is 20
+        spatial_pos_max: int = 1024,
+        edge_type: str = "multi_hop",
+        max_nodes: int = 512,
+        share_input_output_embed: bool = False,
+        num_hidden_layers: int = 12,
+        embedding_dim: int = 768,
+        ffn_embedding_dim: int = 768,
+        num_attention_heads: int = 32,
+        dropout: float = 0.1,
+        attention_dropout: float = 0.1,
+        layerdrop: float = 0.0,
+        encoder_normalize_before: bool = False,
+        pre_layernorm: bool = False,
+        apply_graphormer_init: bool = False,
+        activation_fn: str = "gelu",
+        embed_scale: float = None,
+        freeze_embeddings: bool = False,
+        num_trans_layers_to_freeze: int = 0,
+        traceable: bool = False,
+        q_noise: float = 0.0,
+        qn_block_size: int = 8,
+        kdim: int = None,
+        vdim: int = None,
+        bias: bool = True,
+        self_attention: bool = True,
+        pad_token_id=0,
+        bos_token_id=1,
+        eos_token_id=2,
+        **kwargs,
+    ):
+        self.num_classes = num_classes
+        self.num_atoms = num_atoms
+        self.num_in_degree = num_in_degree
+        self.num_out_degree = num_out_degree
+        self.num_edges = num_edges
+        self.num_spatial = num_spatial
+        self.num_edge_dis = num_edge_dis
+        self.edge_type = edge_type
+        self.multi_hop_max_dist = multi_hop_max_dist
+        self.spatial_pos_max = spatial_pos_max
+        self.max_nodes = max_nodes
+        self.num_hidden_layers = num_hidden_layers
+        self.embedding_dim = embedding_dim
+        self.hidden_size = embedding_dim
+        self.ffn_embedding_dim = ffn_embedding_dim
+        self.num_attention_heads = num_attention_heads
+        self.dropout = dropout
+        self.attention_dropout = attention_dropout
+        self.layerdrop = layerdrop
+        self.encoder_normalize_before = encoder_normalize_before
+        self.pre_layernorm = pre_layernorm
+        self.apply_graphormer_init = apply_graphormer_init
+        self.activation_fn = activation_fn
+        self.embed_scale = embed_scale
+        self.freeze_embeddings = freeze_embeddings
+        self.num_trans_layers_to_freeze = num_trans_layers_to_freeze
+        self.share_input_output_embed = share_input_output_embed
+        self.traceable = traceable
+        self.q_noise = q_noise
+        self.qn_block_size = qn_block_size
+
+        # These parameters are here for future extensions
+        # atm, the model only supports self attention
+        self.kdim = kdim
+        self.vdim = vdim
+        self.self_attention = self_attention
+        self.bias = bias
+
+        super().__init__(
+            pad_token_id=pad_token_id,
+            bos_token_id=bos_token_id,
+            eos_token_id=eos_token_id,
+            **kwargs,
+        )