# Know2BIO: A Comprehensive Dual-View Benchmark for Evolving Biomedical Knowledge Graphs

arXiv: https://arxiv.org/abs/2310.03221 · HTML: https://mlsanity.com/paper/2310.03221/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 23 of its 104 references that are in the map.
- First posted on arXiv 5 Oct 2023.

## Builds on (most cited first, 23 of 23)

- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [Open Graph Benchmark: Datasets for Machine Learning on Graphs](https://mlsanity.com/paper/2005.00687/) (2020)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [Embedding Entities and Relations for Learning and Inference in Knowledge Bases](https://mlsanity.com/paper/1412.6575/) (2014)
- [Complex Embeddings for Simple Link Prediction](https://mlsanity.com/paper/1606.06357/) (2016)
- [RotatE: Knowledge Graph Embedding by Relational Rotation in Complex Space](https://mlsanity.com/paper/1902.10197/) (2019)
- [Convolutional 2D Knowledge Graph Embeddings](https://mlsanity.com/paper/1707.01476/) (2017)
- [TUDataset: A collection of benchmark datasets for learning with graphs](https://mlsanity.com/paper/2007.08663/) (2020)
- [A Survey on Knowledge Graphs: Representation, Acquisition and Applications](https://mlsanity.com/paper/2002.00388/) (2020)
- [ClinicalBERT: Modeling Clinical Notes and Predicting Hospital Readmission](https://mlsanity.com/paper/1904.05342/) (2019)
- [OGB-LSC: A Large-Scale Challenge for Machine Learning on Graphs](https://mlsanity.com/paper/2103.09430/) (2021)
- [SimplE Embedding for Link Prediction in Knowledge Graphs](https://mlsanity.com/paper/1802.04868/) (2018)
- [Low-Dimensional Hyperbolic Knowledge Graph Embeddings](https://mlsanity.com/paper/2005.00545/) (2020)
- [A Novel Embedding Model for Knowledge Base Completion Based on Convolutional Neural Network](https://mlsanity.com/paper/1712.02121/) (2017)
- [Multi-relational Poincar'e Graph Embeddings](https://mlsanity.com/paper/1905.09791/) (2019)
- [CoDEx: A Comprehensive Knowledge Graph Completion Benchmark](https://mlsanity.com/paper/2009.07810/) (2020)
- [PyKEEN 1.0: A Python Library for Training and Evaluating Knowledge Graph Embeddings](https://mlsanity.com/paper/2007.14175/) (2020)
- [Universal Representation Learning of Knowledge Bases by Jointly Embedding Instances and Ontological Concepts](https://mlsanity.com/paper/2103.08115/) (2021)
- [OpenBioLink: A benchmarking framework for large-scale biomedical link prediction](https://mlsanity.com/paper/1912.04616/) (2019)
- [Benchmark and Best Practices for Biomedical Knowledge Graph Embeddings](https://mlsanity.com/paper/2006.13774/) (2020)
- [Understanding the Performance of Knowledge Graph Embeddings in Drug Discovery](https://mlsanity.com/paper/2105.10488/) (2021)
- [Dual-Geometric Space Embedding Model for Two-View Knowledge Graphs](https://mlsanity.com/paper/2209.08767/) (2022)
- [Bio-JOIE: Joint Representation Learning of Biological Knowledge Bases](https://mlsanity.com/paper/2103.04283/) (2021)

## Built on by (most cited first, 2 of 2)

- [Platform for Representation and Integration of multimodal Molecular Embeddings](https://mlsanity.com/paper/2507.07367/) (2025)
- [Drift-Aware Temporal Graph Rewiring (DATGR) for Adaptive Semantic Modeling in Biomedical Text](https://mlsanity.com/paper/2607.08490/) (2026)

## Abstract (arXiv)

Knowledge graphs (KGs) have emerged as a powerful framework for representing and integrating complex biomedical information. However, assembling KGs from diverse sources remains a significant challenge in several aspects, including entity alignment, scalability, and the need for continuous updates to keep pace with scientific advancements. Moreover, the representative power of KGs is often limited by the scarcity of multi-modal data integration. To overcome these challenges, we propose Know2BIO, a general-purpose heterogeneous KG benchmark for the biomedical domain. Know2BIO integrates data from 30 diverse sources, capturing intricate relationships across 11 biomedical categories. It currently consists of ~219,000 nodes and ~6,200,000 edges. Know2BIO is capable of user-directed automated updating to reflect the latest knowledge in biomedical science. Furthermore, Know2BIO is accompanied by multi-modal data: node features including text descriptions, protein and compound sequences and structures, enabling the utilization of emerging natural language processing methods and multi-modal data integration strategies. We evaluate KG representation models on Know2BIO, demonstrating its effectiveness as a benchmark for KG representation learning in the biomedical field. Data and source code of Know2BIO are available at https://github.com/Yijia-Xiao/Know2BIO/.