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configuration_graphormer.py
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configuration_graphormer.py
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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__)
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.
activation_dropout (`float`, *optional*, defaults to 0.1):
The dropout probability for the activation of the linear transformer layer.
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,
activation_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.activation_dropout = activation_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,
)