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Graphormer model for Graph Classification (#20968)

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* [FT] First commit for graphormer architecture.

The model has no tokenizer, as it uses a collator and preprocessing function for its input management.
Architecture to be tested against original one.
The arch might need to be changed to fit the checkpoint, but a revert to the original arch will make the code less nice to read.
TODO: doc

* [FIX] removed test model

* [FIX] import error

* [FIX] black and flake

* [DOC] added paper refs

* [FIX] [DOC]

* [FIX] black

* [DOC] Updated READMEs

* [FIX] Order of imports + rm Tokenizer calls

* [FIX] Moved assert in class to prevent doc build failure

* [FIX] make fix-copies

* [Doc] update from code review

Co-authored-by: Sylvain Gugger <35901082+sgugger@users.noreply.github.com>

* [FIX] Removed Graphormer from Sequence classification model list

* [DOC] Added HF copyright to Cython file

* [DOC] Fixed comments

* [FIX] typos in class doc + removed config classes.

Todo: update doc from paper definitions

* [FIX] Removed dependency to fairseq, and replaced all asserts with Exception management

* [FIX] Homogeneized initialization of weights to pretrained constructor

* [FIX] [CP] Updated multi_hop parameter to get same results as in original implementation

* [DOC] Relevant parameter description in the configuration file

* [DOC] Updated doc and comments in main graphormer file

* [FIX] make style and quality checks

* [DOC] Fix doc format

* [FIX] [WIP] Updated part of the tests, though still a wip

* [FIX] [WIP]

* [FIX] repo consistency

* [FIX] Changed input names for more understandability

* [FIX] [BUG] updated num_classes params for propagation in the model

* simplified collator

* [FIX] Updated tests to follow new naming pattern

* [TESTS] Updated test suite along with model

* |FIX] rm tokenizer import

* [DOC] add link to graphormerdoc

* Changed section in doc from text model to graph model

* Apply suggestions from code review

Spacing, inits

Co-authored-by: Sylvain Gugger <35901082+sgugger@users.noreply.github.com>

* [DOC] Explain algos_graphormer functions

* Cython soft import protection

* Rm call to Callable in configuration graphormer

* [FIX] replaced asserts with Exceptions

* Add org to graphormer checkpoints

* Prefixed classes with Graphormer

* Management of init functions

* format

* fixes

* fix length file

* update indent

* relaunching ci

* Errors for missing cython imports

* fix style

* fix style doc

Co-authored-by: Sylvain Gugger <35901082+sgugger@users.noreply.github.com>
This commit is contained in:
Clémentine Fourrier
2023-01-19 19:05:59 +01:00
committed by GitHub
parent 758bd39e81
commit 87208a05af
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docs/source/en/_toctree.yml
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@@ -571,6 +571,11 @@
- local: model_doc/time_series_transformer
title: Time Series Transformer
title: Time series models
- isExpanded: false
sections:
- local: model_doc/graphormer
title: Graphormer
title: Graph models
title: Models
- sections:
- local: internal/modeling_utils

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@@ -113,6 +113,7 @@ The documentation is organized into five sections:
1. **[GPT-2](model_doc/gpt2)** (from OpenAI) released with the paper [Language Models are Unsupervised Multitask Learners](https://blog.openai.com/better-language-models/) by Alec Radford*, Jeffrey Wu*, Rewon Child, David Luan, Dario Amodei** and Ilya Sutskever**.
1. **[GPT-J](model_doc/gptj)** (from EleutherAI) released in the repository [kingoflolz/mesh-transformer-jax](https://github.com/kingoflolz/mesh-transformer-jax/) by Ben Wang and Aran Komatsuzaki.
1. **[GPT-Sw3](model_doc/gpt-sw3)** (from AI-Sweden) released with the paper [Lessons Learned from GPT-SW3: Building the First Large-Scale Generative Language Model for Swedish](http://www.lrec-conf.org/proceedings/lrec2022/pdf/2022.lrec-1.376.pdf) by Ariel Ekgren, Amaru Cuba Gyllensten, Evangelia Gogoulou, Alice Heiman, Severine Verlinden, Joey Öhman, Fredrik Carlsson, Magnus Sahlgren.
1. **[Graphormer](model_doc/graphormer)** (from Microsoft) released with the paper [Do Transformers Really Perform Bad for Graph Representation?](https://arxiv.org/abs/2106.05234) by Chengxuan Ying, Tianle Cai, Shengjie Luo, Shuxin Zheng, Guolin Ke, Di He, Yanming Shen, Tie-Yan Liu.
1. **[GroupViT](model_doc/groupvit)** (from UCSD, NVIDIA) released with the paper [GroupViT: Semantic Segmentation Emerges from Text Supervision](https://arxiv.org/abs/2202.11094) by Jiarui Xu, Shalini De Mello, Sifei Liu, Wonmin Byeon, Thomas Breuel, Jan Kautz, Xiaolong Wang.
1. **[Hubert](model_doc/hubert)** (from Facebook) released with the paper [HuBERT: Self-Supervised Speech Representation Learning by Masked Prediction of Hidden Units](https://arxiv.org/abs/2106.07447) by Wei-Ning Hsu, Benjamin Bolte, Yao-Hung Hubert Tsai, Kushal Lakhotia, Ruslan Salakhutdinov, Abdelrahman Mohamed.
1. **[I-BERT](model_doc/ibert)** (from Berkeley) released with the paper [I-BERT: Integer-only BERT Quantization](https://arxiv.org/abs/2101.01321) by Sehoon Kim, Amir Gholami, Zhewei Yao, Michael W. Mahoney, Kurt Keutzer.
@@ -289,6 +290,7 @@ Flax), PyTorch, and/or TensorFlow.
| GPT NeoX Japanese | ✅ | ❌ | ✅ | ❌ | ❌ |
| GPT-J | ❌ | ❌ | ✅ | ✅ | ✅ |
| GPT-Sw3 | ✅ | ✅ | ✅ | ✅ | ✅ |
| Graphormer | ❌ | ❌ | ✅ | ❌ | ❌ |
| GroupViT | ❌ | ❌ | ✅ | ✅ | ❌ |
| Hubert | ❌ | ❌ | ✅ | ✅ | ❌ |
| I-BERT | ❌ | ❌ | ✅ | ❌ | ❌ |

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<!--Copyright 2022 The HuggingFace Team and Microsoft. All rights reserved.
Licensed under the MIT License; you may not use this file except in compliance with
the License.
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
## Overview
The Graphormer model was proposed in [Do Transformers Really Perform Bad for Graph Representation?](https://arxiv.org/abs/2106.05234) by
Chengxuan Ying, Tianle Cai, Shengjie Luo, Shuxin Zheng, Guolin Ke, Di He, Yanming Shen and Tie-Yan Liu. It is a Graph Transformer model, modified to allow computations on graphs instead of text sequences by generating embeddings and features of interest during preprocessign and collation, then using a modified attention.
The abstract from the paper is the following:
*The Transformer architecture has become a dominant choice in many domains, such as natural language processing and computer vision. Yet, it has not achieved competitive performance on popular leaderboards of graph-level prediction compared to mainstream GNN variants. Therefore, it remains a mystery how Transformers could perform well for graph representation learning. In this paper, we solve this mystery by presenting Graphormer, which is built upon the standard Transformer architecture, and could attain excellent results on a broad range of graph representation learning tasks, especially on the recent OGB Large-Scale Challenge. Our key insight to utilizing Transformer in the graph is the necessity of effectively encoding the structural information of a graph into the model. To this end, we propose several simple yet effective structural encoding methods to help Graphormer better model graph-structured data. Besides, we mathematically characterize the expressive power of Graphormer and exhibit that with our ways of encoding the structural information of graphs, many popular GNN variants could be covered as the special cases of Graphormer.*
Tips:
This model will not work well on large graphs (more than 100 nodes/edges), as it will make the memory explode.
You can reduce the batch size, increase your RAM, or decrease the `UNREACHABLE_NODE_DISTANCE` parameter in algos_graphormer.pyx, but it will be hard to go above 700 nodes/edges.
This model does not use a tokenizer, but instead a special collator during training.
This model was contributed by [clefourrier](https://huggingface.co/clefourrier). The original code can be found [here](https://github.com/microsoft/Graphormer).
## GraphormerConfig
[[autodoc]] GraphormerConfig
## GraphormerModel
[[autodoc]] GraphormerModel
- forward
## GraphormerForGraphClassification
[[autodoc]] GraphormerForGraphClassification
- forward