# TF-DWGNet: A Directed Weighted Graph Neural Network with Tensor Fusion for Multi-Omics Cancer Subtype Classification

arXiv: https://arxiv.org/abs/2509.16301 · HTML: https://mlsanity.com/paper/2509.16301/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 12 of its 46 references that are in the map.
- First posted on arXiv 19 Sep 2025.

## Builds on (most cited first, 12 of 12)

- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [XGBoost: A Scalable Tree Boosting System](https://mlsanity.com/paper/1603.02754/) (2016)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [A Comprehensive Survey on Graph Neural Networks](https://mlsanity.com/paper/1901.00596/) (2019)
- [Graph Neural Networks: A Review of Methods and Applications](https://mlsanity.com/paper/1812.08434/) (2018)
- [Geometric deep learning: going beyond Euclidean data](https://mlsanity.com/paper/1611.08097/) (2016)
- [Tensor Fusion Network for Multimodal Sentiment Analysis](https://mlsanity.com/paper/1707.07250/) (2017)
- [Deep Learning on Graphs: A Survey](https://mlsanity.com/paper/1812.04202/) (2018)
- [Multimodal Data Integration for Oncology in the Era of Deep Neural Networks: A Review](https://mlsanity.com/paper/2303.06471/) (2023)
- [A graph-embedded deep feedforward network for disease outcome classification and feature selection using gene expression data](https://mlsanity.com/paper/1801.06202/) (2018)

## Abstract (arXiv)

Integration and analysis of multi-omics data provide valuable insights for improving cancer subtype classification. However, such data are inherently heterogeneous, high-dimensional, and exhibit complex intra- and inter-modality dependencies. Graph neural networks (GNNs) offer a principled framework for modeling these structures, but existing approaches often rely on prior knowledge or predefined similarity networks that produce undirected or unweighted graphs and fail to capture task-specific directionality and interaction strength. Interpretability at both the modality and feature levels also remains limited. To address these challenges, we propose TF-DWGNet, a novel Graph Neural Network framework that combines tree-based Directed Weighted graph construction with Tensor Fusion for multiclass cancer subtype classification. TF-DWGNet introduces two key innovations: (i) a supervised tree-based strategy that constructs directed, weighted graphs tailored to each omics modality, and (ii) a tensor fusion mechanism that captures unimodal, bimodal, and trimodal interactions using low-rank decomposition for computational efficiency. Experiments on three real-world cancer datasets demonstrate that TF-DWGNet consistently outperforms state-of-the-art baselines across multiple metrics and statistical tests. In addition, the model provides biologically meaningful insights through modality-level contribution scores and ranked feature importance. These results highlight that TF-DWGNet is an effective and interpretable solution for multi-omics integration in cancer research.