# Gene-induced Multimodal Pre-training for Image-omic Classification

arXiv: https://arxiv.org/abs/2309.02702 · HTML: https://mlsanity.com/paper/2309.02702/

## Key facts

- Cited by 9 papers in the map (data through 14 Oct 2026).
- Builds on 19 of its 23 references that are in the map.
- First posted on arXiv 6 Sep 2023.

## Builds on (most cited first, 19 of 19)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [Hierarchical Text-Conditional Image Generation with CLIP Latents](https://mlsanity.com/paper/2204.06125/) (2022)
- [Decoupled Weight Decay Regularization](https://mlsanity.com/paper/1711.05101/) (2017)
- [SimMIM: A Simple Framework for Masked Image Modeling](https://mlsanity.com/paper/2111.09886/) (2021)
- [Attention-based Deep Multiple Instance Learning](https://mlsanity.com/paper/1802.04712/) (2018)
- [Data Efficient and Weakly Supervised Computational Pathology on Whole Slide Images](https://mlsanity.com/paper/2004.09666/) (2020)
- [Self-Normalizing Neural Networks](https://mlsanity.com/paper/1706.02515/) (2017)
- [TransMIL: Transformer based Correlated Multiple Instance Learning for Whole Slide Image Classification](https://mlsanity.com/paper/2106.00908/) (2021)
- [Dual-stream Multiple Instance Learning Network for Whole Slide Image Classification with Self-supervised Contrastive Learning](https://mlsanity.com/paper/2011.08939/) (2020)
- [Nystr"omformer: A Nystr"om-Based Algorithm for Approximating Self-Attention](https://mlsanity.com/paper/2102.03902/) (2021)
- [Making the Most of Text Semantics to Improve Biomedical Vision--Language Processing](https://mlsanity.com/paper/2204.09817/) (2022)
- [Pathomic Fusion: An Integrated Framework for Fusing Histopathology and Genomic Features for Cancer Diagnosis and Prognosis](https://mlsanity.com/paper/1912.08937/) (2019)
- [Multi-Granularity Cross-modal Alignment for Generalized Medical Visual Representation Learning](https://mlsanity.com/paper/2210.06044/) (2022)
- [A Mutual Information Maximization Perspective of Language Representation Learning](https://mlsanity.com/paper/1910.08350/) (2019)
- [Generalized Radiograph Representation Learning via Cross-supervision between Images and Free-text Radiology Reports](https://mlsanity.com/paper/2111.03452/) (2021)
- [UniMiSS: Universal Medical Self-Supervised Learning via Breaking Dimensionality Barrier](https://mlsanity.com/paper/2112.09356/) (2021)
- [Toward Unpaired Multi-modal Medical Image Segmentation via Learning Structured Semantic Consistency](https://mlsanity.com/paper/2206.10571/) (2022)

## Built on by (most cited first, 9 of 9)

- [Foundation Model for Advancing Healthcare: Challenges, Opportunities, and Future Directions](https://mlsanity.com/paper/2404.03264/) (2024)
- [Transcriptomics-guided Slide Representation Learning in Computational Pathology](https://mlsanity.com/paper/2405.11618/) (2024)
- [Continual Self-supervised Learning: Towards Universal Multi-modal Medical Data Representation Learning](https://mlsanity.com/paper/2311.17597/) (2023)
- [MedUniSeg: 2D and 3D Medical Image Segmentation via a Prompt-driven Universal Model](https://mlsanity.com/paper/2410.05905/) (2024)
- [Image Distillation for Safe Data Sharing in Histopathology](https://mlsanity.com/paper/2406.13536/) (2024)
- [Genomics-guided Representation Learning for Pathologic Pan-cancer Tumor Microenvironment Subtype Prediction](https://mlsanity.com/paper/2406.06517/) (2024)
- [ModalTune: Fine-Tuning Slide-Level Foundation Models with Multi-Modal Information for Multi-task Learning in Digital Pathology](https://mlsanity.com/paper/2503.17564/) (2025)
- [Any-to-Any Learning in Computational Pathology via Triplet Multimodal Pretraining](https://mlsanity.com/paper/2505.12711/) (2025)
- [Multimodal Medical Image Classification via Synergistic Learning Pre-training](https://mlsanity.com/paper/2509.17492/) (2025)

## Abstract (arXiv)

Histology analysis of the tumor micro-environment integrated with genomic assays is the gold standard for most cancers in modern medicine. This paper proposes a Gene-induced Multimodal Pre-training (GiMP) framework, which jointly incorporates genomics and Whole Slide Images (WSIs) for classification tasks. Our work aims at dealing with the main challenges of multi-modality image-omic classification w.r.t. (1) the patient-level feature extraction difficulties from gigapixel WSIs and tens of thousands of genes, and (2) effective fusion considering high-order relevance modeling. Concretely, we first propose a group multi-head self-attention gene encoder to capture global structured features in gene expression cohorts. We design a masked patch modeling paradigm (MPM) to capture the latent pathological characteristics of different tissues. The mask strategy is randomly masking a fixed-length contiguous subsequence of patch embeddings of a WSI. Finally, we combine the classification tokens of paired modalities and propose a triplet learning module to learn high-order relevance and discriminative patient-level information.After pre-training, a simple fine-tuning can be adopted to obtain the classification results. Experimental results on the TCGA dataset show the superiority of our network architectures and our pre-training framework, achieving 99.47% in accuracy for image-omic classification. The code is publicly available at https://github.com/huangwudiduan/GIMP.