# BALI: Enhancing Biomedical Language Representations through Knowledge Graph and Language Model Alignment

arXiv: https://arxiv.org/abs/2509.07588 · HTML: https://mlsanity.com/paper/2509.07588/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 49 of its 91 references that are in the map.
- First posted on arXiv 9 Sep 2025.

## Builds on (most cited first, 30 of 49)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [LLaMA: Open and Efficient Foundation Language Models](https://mlsanity.com/paper/2302.13971/) (2023)
- [Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks](https://mlsanity.com/paper/2005.11401/) (2020)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Representation Learning with Contrastive Predictive Coding](https://mlsanity.com/paper/1807.03748/) (2018)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [Fast Graph Representation Learning with PyTorch Geometric](https://mlsanity.com/paper/1903.02428/) (2019)
- [SciBERT: A Pretrained Language Model for Scientific Text](https://mlsanity.com/paper/1903.10676/) (2019)
- [What Disease does this Patient Have? A Large-scale Open Domain Question Answering Dataset from Medical Exams](https://mlsanity.com/paper/2009.13081/) (2020)
- [ZeRO: Memory Optimizations Toward Training Trillion Parameter Models](https://mlsanity.com/paper/1910.02054/) (2019)
- [PubMedQA: A Dataset for Biomedical Research Question Answering](https://mlsanity.com/paper/1909.06146/) (2019)
- [Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing](https://mlsanity.com/paper/2007.15779/) (2020)
- [Publicly Available Clinical BERT Embeddings](https://mlsanity.com/paper/1904.03323/) (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)
- [REPLUG: Retrieval-Augmented Black-Box Language Models](https://mlsanity.com/paper/2301.12652/) (2023)
- [Capabilities of GPT-4 on Medical Challenge Problems](https://mlsanity.com/paper/2303.13375/) (2023)
- [ERNIE: Enhanced Language Representation with Informative Entities](https://mlsanity.com/paper/1905.07129/) (2019)
- [QA-GNN: Reasoning with Language Models and Knowledge Graphs for Question Answering](https://mlsanity.com/paper/2104.06378/) (2021)
- [Multi-Similarity Loss with General Pair Weighting for Deep Metric Learning](https://mlsanity.com/paper/1904.06627/) (2019)
- [KEPLER: A Unified Model for Knowledge Embedding and Pre-trained Language Representation](https://mlsanity.com/paper/1911.06136/) (2019)
- [K-BERT: Enabling Language Representation with Knowledge Graph](https://mlsanity.com/paper/1909.07606/) (2019)
- [Generating Images with Multimodal Language Models](https://mlsanity.com/paper/2305.17216/) (2023)
- [Self-Alignment Pretraining for Biomedical Entity Representations](https://mlsanity.com/paper/2010.11784/) (2020)
- [SimplE Embedding for Link Prediction in Knowledge Graphs](https://mlsanity.com/paper/1802.04868/) (2018)
- [GreaseLM: Graph REASoning Enhanced Language Models for Question Answering](https://mlsanity.com/paper/2201.08860/) (2022)
- [Deep Bidirectional Language-Knowledge Graph Pretraining](https://mlsanity.com/paper/2210.09338/) (2022)
- [Can Language Models be Biomedical Knowledge Bases?](https://mlsanity.com/paper/2109.07154/) (2021)

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

- [A Hybrid Knowledge-Grounded Framework for Safety and Traceability in Prescription Verification](https://mlsanity.com/paper/2603.10891/) (2026)
- [Aligning Biomedical Texts and Knowledge Graphs: A Systematic Comparison of Lightweight Alignment Strategies](https://mlsanity.com/paper/2608.23214/) (2026)

## Abstract (arXiv)

In recent years, there has been substantial progress in using pretrained Language Models (LMs) on a range of tasks aimed at improving the understanding of biomedical texts. Nonetheless, existing biomedical LLMs show limited comprehension of complex, domain-specific concept structures and the factual information encoded in biomedical Knowledge Graphs (KGs). In this work, we propose BALI (Biomedical Knowledge Graph and Language Model Alignment), a novel joint LM and KG pre-training method that augments an LM with external knowledge by the simultaneous learning of a dedicated KG encoder and aligning the representations of both the LM and the graph. For a given textual sequence, we link biomedical concept mentions to the Unified Medical Language System (UMLS) KG and utilize local KG subgraphs as cross-modal positive samples for these mentions. Our empirical findings indicate that implementing our method on several leading biomedical LMs, such as PubMedBERT and BioLinkBERT, improves their performance on a range of language understanding tasks and the quality of entity representations, even with minimal pre-training on a small alignment dataset sourced from PubMed scientific abstracts.