# Interpretable graph-based models on multimodal biomedical data integration: A technical review and benchmarking

arXiv: https://arxiv.org/abs/2505.01696 · HTML: https://mlsanity.com/paper/2505.01696/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 42 of its 108 references that are in the map.
- First posted on arXiv 3 May 2025.

## Builds on (most cited first, 30 of 42)

- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [A Unified Approach to Interpreting Model Predictions](https://mlsanity.com/paper/1705.07874/) (2017)
- ["Why Should I Trust You?": Explaining the Predictions of Any Classifier](https://mlsanity.com/paper/1602.04938/) (2016)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Axiomatic Attribution for Deep Networks](https://mlsanity.com/paper/1703.01365/) (2017)
- [Deep Inside Convolutional Networks: Visualising Image Classification Models and Saliency Maps](https://mlsanity.com/paper/1312.6034/) (2013)
- [Large Language Models Encode Clinical Knowledge](https://mlsanity.com/paper/2212.13138/) (2022)
- [A Survey on Hallucination in Large Language Models: Principles, Taxonomy, Challenges, and Open Questions](https://mlsanity.com/paper/2311.05232/) (2023)
- [Learning Important Features Through Propagating Activation Differences](https://mlsanity.com/paper/1704.02685/) (2017)
- [Sanity Checks for Saliency Maps](https://mlsanity.com/paper/1810.03292/) (2018)
- [RISE: Randomized Input Sampling for Explanation of Black-box Models](https://mlsanity.com/paper/1806.07421/) (2018)
- [Galactica: A Large Language Model for Science](https://mlsanity.com/paper/2211.09085/) (2022)
- [GNNExplainer: Generating Explanations for Graph Neural Networks](https://mlsanity.com/paper/1903.03894/) (2019)
- [A Generalization of Transformer Networks to Graphs](https://mlsanity.com/paper/2012.09699/) (2020)
- [Bias and Fairness in Large Language Models: A Survey](https://mlsanity.com/paper/2309.00770/) (2023)
- [Understanding over-squashing and bottlenecks on graphs via curvature](https://mlsanity.com/paper/2111.14522/) (2021)
- [Parameterized Explainer for Graph Neural Network](https://mlsanity.com/paper/2011.04573/) (2020)
- [Explainability in Graph Neural Networks: A Taxonomic Survey](https://mlsanity.com/paper/2012.15445/) (2020)
- [Generic Attention-model Explainability for Interpreting Bi-Modal and Encoder-Decoder Transformers](https://mlsanity.com/paper/2103.15679/) (2021)
- [GatorTron: A Large Clinical Language Model to Unlock Patient Information from Unstructured Electronic Health Records](https://mlsanity.com/paper/2203.03540/) (2022)
- [Understanding the Capabilities, Limitations, and Societal Impact of Large Language Models](https://mlsanity.com/paper/2102.02503/) (2021)
- [Harnessing Explanations: LLM-to-LM Interpreter for Enhanced Text-Attributed Graph Representation Learning](https://mlsanity.com/paper/2305.19523/) (2023)
- [Towards Sparse Hierarchical Graph Classifiers](https://mlsanity.com/paper/1811.01287/) (2018)
- [LLMs for Knowledge Graph Construction and Reasoning: Recent Capabilities and Future Opportunities](https://mlsanity.com/paper/2305.13168/) (2023)
- [Evaluating Explainability for Graph Neural Networks](https://mlsanity.com/paper/2208.09339/) (2022)
- [GStarX: Explaining Graph Neural Networks with Structure-Aware Cooperative Games](https://mlsanity.com/paper/2201.12380/) (2022)
- [VQ-GNN: A Universal Framework to Scale up Graph Neural Networks using Vector Quantization](https://mlsanity.com/paper/2110.14363/) (2021)
- [From Redundancy to Relevance: Information Flow in LVLMs Across Reasoning Tasks](https://mlsanity.com/paper/2406.06579/) (2024)
- [Leveraging Medical Knowledge Graphs Into Large Language Models for Diagnosis Prediction: Design and Application Study](https://mlsanity.com/paper/2308.14321/) (2023)
- [A Survey on Spectral Graph Neural Networks](https://mlsanity.com/paper/2302.05631/) (2023)

## Abstract (arXiv)

Integrating heterogeneous biomedical data including imaging, omics, and clinical records supports accurate diagnosis and personalised care. Graph-based models fuse such non-Euclidean data by capturing spatial and relational structure, yet clinical uptake requires regulator-ready interpretability. We present the first technical survey of interpretable graph based models for multimodal biomedical data, covering 26 studies published between Jan 2019 and Sep 2024. Most target disease classification, notably cancer and rely on static graphs from simple similarity measures, while graph-native explainers are rare; post-hoc methods adapted from non-graph domains such as gradient saliency, and SHAP predominate. We group existing approaches into four interpretability families, outline trends such as graph-in-graph hierarchies, knowledge-graph edges, and dynamic topology learning, and perform a practical benchmark. Using an Alzheimer disease cohort, we compare Sensitivity Analysis, Gradient Saliency, SHAP and Graph Masking. SHAP and Sensitivity Analysis recover the broadest set of known AD pathways and Gene-Ontology terms, whereas Gradient Saliency and Graph Masking surface complementary metabolic and transport signatures. Permutation tests show all four beat random gene sets, but with distinct trade-offs: SHAP and Graph Masking offer deeper biology at higher compute cost, while Gradient Saliency and Sensitivity Analysis are quicker though coarser. We also provide a step-by-step flowchart covering graph construction, explainer choice and resource budgeting to help researchers balance transparency and performance. This review synthesises the state of interpretable graph learning for multimodal medicine, benchmarks leading techniques, and charts future directions, from advanced XAI tools to under-studied diseases, serving as a concise reference for method developers and translational scientists.