{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/vgat-a-cancer-survival-analysis-framework","title":"VGAT: A Cancer Survival Analysis Framework Transitioning from Generative Visual Question Answering to Genomic Reconstruction","arxiv_id":"2503.19367","date":"2025-03-25","proceeding":null,"authors":["Zizhi Chen","Minghao Han","Xukun Zhang","Shuwei Ma","Tao Liu","Xing Wei","Lihua Zhang"],"abstract":"Multimodal learning combining pathology images and genomic sequences enhances cancer survival analysis but faces clinical implementation barriers due to limited access to genomic sequencing in under-resourced regions. To enable survival prediction using only whole-slide images (WSI), we propose the Visual-Genomic Answering-Guided Transformer (VGAT), a framework integrating Visual Question Answering (VQA) techniques for genomic modality reconstruction. By adapting VQA's text feature extraction approach, we derive stable genomic representations that circumvent dimensionality challenges in raw genomic data. Simultaneously, a cluster-based visual prompt module selectively enhances discriminative WSI patches, addressing noise from unfiltered image regions. Evaluated across five TCGA datasets, VGAT outperforms existing WSI-only methods, demonstrating the viability of genomic-informed inference without sequencing. This approach bridges multimodal research and clinical feasibility in resource-constrained settings. The code link is https://github.com/CZZZZZZZZZZZZZZZZZ/VGAT.","url_abs":"https://arxiv.org/abs/2503.19367v2","url_pdf":"https://arxiv.org/pdf/2503.19367v2.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"vgat-a-cancer-survival-analysis-framework","repo_url":"https://github.com/czzzzzzzzzzzzzzzzz/vgat","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"jax","reach":null}],"tasks":[{"task_slug":"generative-visual-question-answering","task_name":"Generative Visual Question Answering"},{"task_slug":"question-answering","task_name":"Question Answering"},{"task_slug":"survival-analysis","task_name":"Survival Analysis"},{"task_slug":"survival-prediction","task_name":"Survival Prediction"},{"task_slug":"visual-question-answering-1","task_name":"Visual Question Answering"},{"task_slug":"visual-question-answering","task_name":"Visual Question Answering (VQA)"},{"task_slug":"whole-slide-images","task_name":"whole slide images"}],"methods":[{"method_slug":"absolute-position-encodings","method_name":"Absolute Position Encodings"},{"method_slug":"adam","method_name":"Adam"},{"method_slug":"attention","method_name":"Attention"},{"method_slug":"bpe","method_name":"BPE"},{"method_slug":"dense-connections","method_name":"Dense Connections"},{"method_slug":"dropout","method_name":"Dropout"},{"method_slug":"label-smoothing","method_name":"Label Smoothing"},{"method_slug":"layer-normalization","method_name":"Layer Normalization"},{"method_slug":"linear-layer","method_name":"Linear Layer"},{"method_slug":"multi-head-attention","method_name":"Multi-Head Attention"},{"method_slug":"position-wise-feed-forward-layer","method_name":"Position-Wise Feed-Forward Layer"},{"method_slug":"residual-connection","method_name":"Residual Connection"},{"method_slug":"softmax","method_name":"Softmax"},{"method_slug":"transformer","method_name":"Transformer"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}