# Integration of Graph Neural Network and Neural-ODEs for Tumor Dynamic Prediction

arXiv: https://arxiv.org/abs/2310.00926 · HTML: https://mlsanity.com/paper/2310.00926/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 9 of its 27 references that are in the map.
- First posted on arXiv 2 Oct 2023.

## Builds on (most cited first, 9 of 9)

- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Neural Ordinary Differential Equations](https://mlsanity.com/paper/1806.07366/) (2018)
- [Variational Graph Auto-Encoders](https://mlsanity.com/paper/1611.07308/) (2016)
- [Strategies for Pre-training Graph Neural Networks](https://mlsanity.com/paper/1905.12265/) (2019)
- [Self-Attention Graph Pooling](https://mlsanity.com/paper/1904.08082/) (2019)
- [Mean Absolute Percentage Error for regression models](https://mlsanity.com/paper/1605.02541/) (2016)
- [Explainable Deep Learning for Tumor Dynamic Modeling and Overall Survival Prediction using Neural-ODE](https://mlsanity.com/paper/2308.01362/) (2023)
- [Hierarchical Bipartite Graph Convolution Networks](https://mlsanity.com/paper/1812.03813/) (2018)

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

- [Graph ODEs and Beyond: A Comprehensive Survey on Integrating Differential Equations with Graph Neural Networks](https://mlsanity.com/paper/2503.23167/) (2025)
- [Generative Modeling of Clinical Time Series via Latent Stochastic Differential Equations](https://mlsanity.com/paper/2511.16427/) (2025)

## Abstract (arXiv)

In anti-cancer drug development, a major scientific challenge is disentangling the complex relationships between high-dimensional genomics data from patient tumor samples, the corresponding tumor's organ of origin, the drug targets associated with given treatments and the resulting treatment response. Furthermore, to realize the aspirations of precision medicine in identifying and adjusting treatments for patients depending on the therapeutic response, there is a need for building tumor dynamic models that can integrate both longitudinal tumor size as well as multimodal, high-content data. In this work, we take a step towards enhancing personalized tumor dynamic predictions by proposing a heterogeneous graph encoder that utilizes a bipartite Graph Convolutional Neural network (GCN) combined with Neural Ordinary Differential Equations (Neural-ODEs). We applied the methodology to a large collection of patient-derived xenograft (PDX) data, spanning a wide variety of treatments (as well as their combinations) on tumors that originated from a number of different organs. We first show that the methodology is able to discover a tumor dynamic model that significantly improves upon an empirical model which is in current use. Additionally, we show that the graph encoder is able to effectively utilize multimodal data to enhance tumor predictions. Our findings indicate that the methodology holds significant promise and offers potential applications in pre-clinical settings.