Awesome

This is the official implementation of the following paper:

GLBench: A Comprehensive Benchmark for Graphs with Large Language Models [Paper]

Yuhan Li, Peisong Wang, Xiao Zhu, Aochuan Chen, Haiyun Jiang, Deng Cai, Victor Wai Kin Chan, Jia Li

Environment Setup

Before you begin, ensure that you have Anaconda or Miniconda installed on your system. This guide assumes that you have a CUDA-enabled GPU. After create your conda environment (we recommend python==3.10), please run

pip install -r requirements.txt

to install python packages.

Datasets

All datasets in GLBench are available in this link. Please place them in the datasets folder.

Benchmarking

Supervised

Classical(GNN)

Benchmark the Classical GNNs (grid-search hyperparameters)

cd models/gnn
bash models/gnn/run.sh

LLM

Benchmark the LLMs in supervised settings (Sent-BERT, BERT, RoBERTa)

cd models/llm/llm_supervised
bash roberta_search.sh

Benchmark the LLMs in zero-shot settings (gpt-4o, gpt-3.5-turbo,llama3-70b,deepseek-chat)

cd models/llm/llm_zeroshot
python inference.py --model gpt-4o --data cora

Enhancer

• GIANT

Due to some package conflicts or version limitations, we recommend using docker to run GIANT. The docker file is in

models/enhancer/giant-xrt/dockerfile

After starting the Docker container, run

cd models/enhancer/giant-xrt/
bash run_all.sh

• TAPE

cd models/enhancer/TAPE/
bash run.sh

• OFA

cd models/enhancer/OneForAll/
bash run.sh

• ENGINE

Predictor

• InstructGLM
• GraphText

Due to some package conflicts or version limitations, we recommend using docker to run GraphText. The docker file is in

models/predictor/GraphText/dockerfile

After starting the Docker container, run

cd models/predictor/GraphText
bash run.sh

• GraphAdapter

cd models/predictor/GraphAdapter
bash run.sh

• LLaGA

Aignment

• GLEM

cd models/alignment/GLEM
bash run.sh

• Patton

bash run_pretrain.sh
bash nc_class_train.sh
bash nc_class_test.sh

We also provide seperate scripts for different datasets.

• Zero-shot

LLM

Benchmark the LLMs(LLaMA3, GPT-3.5-turbo, GPT-4o, DeepSeek-chat)

cd models/llm

You can use your own API key for OpenAI.

Enhancer

• OFA

cd models/enhancer/OneForAll/
bash run_zeroshot.sh

• ZeroG

cd models/enhancer/ZeroG/
bash run.sh

Predictor

• GraphGPT

cd models/predictor/GraphGPT
bash ./scripts/eval_script/graphgpt_eval.sh

FYI: our other works

Acknowledgement

We are appreciated to all authors of works we cite for their solid work and clear code organization! The orginal version of the GraphLLM methods are listed as follows:

Alignment:

GLEM:

• (2022.10) [ICLR' 2023] Learning on Large-scale Text-attributed Graphs via Variational Inference [Paper | Code]

Patton:

• (2023.05) [ACL' 2023] PATTON : Language Model Pretraining on Text-Rich Networks [Paper | Code]

Enhancer:

ENGINE:

• (2024.01) [IJCAI' 2024] Efficient Tuning and Inference for Large Language Models on Textual Graphs [Paper]

GIANT:

• (2022.03) [ICLR' 2022] Node Feature Extraction by Self-Supervised Multi-scale Neighborhood Prediction [Paper | Code]

OFA:

• (2023.09) [ICLR' 2024] One for All: Towards Training One Graph Model for All Classification Tasks [Paper | Code]

TAPE:

• (2023.05) [ICLR' 2024] Harnessing Explanations: LLM-to-LM Interpreter for Enhanced Text-Attributed Graph Representation Learning [Paper | Code]

ZeroG:

• (2024.02) [KDD' 2024] ZeroG: Investigating Cross-dataset Zero-shot Transferability in Graphs [Paper] | Code]

Predictor:

GraphAdapter:

• (2024.02) [WWW' 2024] Can GNN be Good Adapter for LLMs? [Paper]

GraphGPT:

• (2023.10) [SIGIR' 2024] GraphGPT: Graph Instruction Tuning for Large Language Models [Paper | Code]

GraphText:

• (2023.10) [Arxiv' 2023] GraphText: Graph Reasoning in Text Space [Paper] | Code]

InstructGLM:

• (2023.08) [Arxiv' 2023] Natural Language is All a Graph Needs [Paper | Code]

LLaGA:

• (2024.02) [Arxiv' 2024] LLaGA: Large Language and Graph Assistant [Paper | Code]

Code Base Structure

$CODE_DIR
    ├── datasets
    └── models
        ├── alignment
        │   ├── GLEM
        │   └── Patton
        ├── enhancer
        │   ├── ENGINE
        │   ├── giant-xrt
        │   ├── OneForAll
        │   ├── TAPE
        │   └── ZeroG
        ├── gnn
        ├── llm
        │   ├── deepseek-chat
        │   ├── gpt-3.5-turbo
        │   ├── gpt-4o
        │   └── llama3-70b
        └── predictor
           ├── GraphAdapter
           ├── GraphGPT
           ├── GraphText
           ├── InstructGLM
           └── LLaGA