# A Comprehensive Survey on Deep Graph Representation Learning

arXiv: https://arxiv.org/abs/2304.05055 · HTML: https://mlsanity.com/paper/2304.05055/

## Key facts

- Cited by 72 papers in the map (data through 14 Oct 2026).
- Builds on 211 of its 442 references that are in the map.
- First posted on arXiv 11 Apr 2023.

## Builds on (most cited first, 30 of 211)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [End-to-End Object Detection with Transformers](https://mlsanity.com/paper/2005.12872/) (2020)
- [Deep Unsupervised Learning using Nonequilibrium Thermodynamics](https://mlsanity.com/paper/1503.03585/) (2015)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [Generative Adversarial Networks](https://mlsanity.com/paper/2203.00667/) (2022)
- [Model-Agnostic Meta-Learning for Fast Adaptation of Deep Networks](https://mlsanity.com/paper/1703.03400/) (2017)
- [Bootstrap your own latent: A new approach to self-supervised Learning](https://mlsanity.com/paper/2006.07733/) (2020)
- [Generative Modeling by Estimating Gradients of the Data Distribution](https://mlsanity.com/paper/1907.05600/) (2019)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [Distributed Representations of Words and Phrases and their Compositionality](https://mlsanity.com/paper/1310.4546/) (2013)
- [Towards Evaluating the Robustness of Neural Networks](https://mlsanity.com/paper/1608.04644/) (2016)
- [A Comprehensive Survey on Graph Neural Networks](https://mlsanity.com/paper/1901.00596/) (2019)
- [Matching Networks for One Shot Learning](https://mlsanity.com/paper/1606.04080/) (2016)
- [Dynamic Graph CNN for Learning on Point Clouds](https://mlsanity.com/paper/1801.07829/) (2018)
- [Variational Inference with Normalizing Flows](https://mlsanity.com/paper/1505.05770/) (2015)
- [Open Graph Benchmark: Datasets for Machine Learning on Graphs](https://mlsanity.com/paper/2005.00687/) (2020)
- [Convolutional Neural Networks on Graphs with Fast Localized Spectral Filtering](https://mlsanity.com/paper/1606.09375/) (2016)
- [node2vec: Scalable Feature Learning for Networks](https://mlsanity.com/paper/1607.00653/) (2016)
- [A Survey on Bias and Fairness in Machine Learning](https://mlsanity.com/paper/1908.09635/) (2019)
- [Modeling Relational Data with Graph Convolutional Networks](https://mlsanity.com/paper/1703.06103/) (2017)
- [Graph Neural Networks: A Review of Methods and Applications](https://mlsanity.com/paper/1812.08434/) (2018)
- [DeepWalk: Online Learning of Social Representations](https://mlsanity.com/paper/1403.6652/) (2014)
- [Simplifying Graph Convolutional Networks](https://mlsanity.com/paper/1902.07153/) (2019)
- [LightGCN: Simplifying and Powering Graph Convolution Network for Recommendation](https://mlsanity.com/paper/2002.02126/) (2020)
- [Deeper Insights into Graph Convolutional Networks for Semi-Supervised Learning](https://mlsanity.com/paper/1801.07606/) (2018)
- [Weisfeiler and Leman Go Neural: Higher-order Graph Neural Networks](https://mlsanity.com/paper/1810.02244/) (2018)
- [Representation Learning on Graphs with Jumping Knowledge Networks](https://mlsanity.com/paper/1806.03536/) (2018)
- [Simple and Deep Graph Convolutional Networks](https://mlsanity.com/paper/2007.02133/) (2020)

## Built on by (most cited first, 30 of 72)

- [A Survey of Graph Neural Networks in Real world: Imbalance, Noise, Privacy and OOD Challenges](https://mlsanity.com/paper/2403.04468/) (2024)
- [CoCo: A Coupled Contrastive Framework for Unsupervised Domain Adaptive Graph Classification](https://mlsanity.com/paper/2306.04979/) (2023)
- [Semi-supervised Domain Adaptation in Graph Transfer Learning](https://mlsanity.com/paper/2309.10773/) (2023)
- [A Diffusion model for POI recommendation](https://mlsanity.com/paper/2304.07041/) (2023)
- [A Survey of Data-Efficient Graph Learning](https://mlsanity.com/paper/2402.00447/) (2024)
- [LangGFM: A Large Language Model Alone Can be a Powerful Graph Foundation Model](https://mlsanity.com/paper/2410.14961/) (2024)
- [ALEX: Towards Effective Graph Transfer Learning with Noisy Labels](https://mlsanity.com/paper/2309.14673/) (2023)
- [Unveiling Delay Effects in Traffic Forecasting: A Perspective from Spatial-Temporal Delay Differential Equations](https://mlsanity.com/paper/2402.01231/) (2024)
- [Curriculum Learning for Graph Neural Networks: Which Edges Should We Learn First](https://mlsanity.com/paper/2310.18735/) (2023)
- [Continual Learning for Smart City: A Survey](https://mlsanity.com/paper/2404.00983/) (2024)
- [Temporal Knowledge Graph Question Answering: A Survey](https://mlsanity.com/paper/2406.14191/) (2024)
- [Redundancy-Free Self-Supervised Relational Learning for Graph Clustering](https://mlsanity.com/paper/2309.04694/) (2023)
- [Hypergraph-enhanced Dual Semi-supervised Graph Classification](https://mlsanity.com/paper/2405.04773/) (2024)
- [GALA: Graph Diffusion-based Alignment with Jigsaw for Source-free Domain Adaptation](https://mlsanity.com/paper/2410.16606/) (2024)
- [RAHNet: Retrieval Augmented Hybrid Network for Long-tailed Graph Classification](https://mlsanity.com/paper/2308.02335/) (2023)
- [PGODE: Towards High-quality System Dynamics Modeling](https://mlsanity.com/paper/2311.06554/) (2023)
- [Towards Continuous Reuse of Graph Models via Holistic Memory Diversification](https://mlsanity.com/paper/2406.07413/) (2024)
- [A Comprehensive Graph Pooling Benchmark: Effectiveness, Robustness and Generalizability](https://mlsanity.com/paper/2406.09031/) (2024)
- [Rank and Align: Towards Effective Source-free Graph Domain Adaptation](https://mlsanity.com/paper/2408.12185/) (2024)
- [Order-Independence Without Fine Tuning](https://mlsanity.com/paper/2406.06581/) (2024)
- [ExGra-Med: Extended Context Graph Alignment for Medical Vision-Language Models](https://mlsanity.com/paper/2410.02615/) (2024)
- [Instance-Aware Graph Prompt Learning](https://mlsanity.com/paper/2411.17676/) (2024)
- [ScienceDB AI: An LLM-Driven Agentic Recommender System for Large-Scale Scientific Data Sharing Services](https://mlsanity.com/paper/2601.01118/) (2026)
- [Towards Long-Tailed Recognition for Graph Classification via Collaborative Experts](https://mlsanity.com/paper/2308.16609/) (2023)
- [Negative-Free Self-Supervised Gaussian Embedding of Graphs](https://mlsanity.com/paper/2411.01157/) (2024)
- [Disambiguated Node Classification with Graph Neural Networks](https://mlsanity.com/paper/2402.08824/) (2024)
- [Graph Anomaly Detection at Group Level: A Topology Pattern Enhanced Unsupervised Approach](https://mlsanity.com/paper/2308.01063/) (2023)
- [Graph AI in Medicine](https://mlsanity.com/paper/2310.13767/) (2023)
- [Incomplete Graph Learning: A Comprehensive Survey](https://mlsanity.com/paper/2502.12412/) (2025)
- [Dynamic Bundling with Large Language Models for Zero-Shot Inference on Text-Attributed Graphs](https://mlsanity.com/paper/2505.17599/) (2025)

## Abstract (arXiv)

Graph representation learning aims to effectively encode high-dimensional sparse graph-structured data into low-dimensional dense vectors, which is a fundamental task that has been widely studied in a range of fields, including machine learning and data mining. Classic graph embedding methods follow the basic idea that the embedding vectors of interconnected nodes in the graph can still maintain a relatively close distance, thereby preserving the structural information between the nodes in the graph. However, this is sub-optimal due to: (i) traditional methods have limited model capacity which limits the learning performance; (ii) existing techniques typically rely on unsupervised learning strategies and fail to couple with the latest learning paradigms; (iii) representation learning and downstream tasks are dependent on each other which should be jointly enhanced. With the remarkable success of deep learning, deep graph representation learning has shown great potential and advantages over shallow (traditional) methods, there exist a large number of deep graph representation learning techniques have been proposed in the past decade, especially graph neural networks. In this survey, we conduct a comprehensive survey on current deep graph representation learning algorithms by proposing a new taxonomy of existing state-of-the-art literature. Specifically, we systematically summarize the essential components of graph representation learning and categorize existing approaches by the ways of graph neural network architectures and the most recent advanced learning paradigms. Moreover, this survey also provides the practical and promising applications of deep graph representation learning. Last but not least, we state new perspectives and suggest challenging directions which deserve further investigations in the future.