SemanticST: Spatially Informed Semantic Graph Learning for Clustering, Integration, and Scalable Analysis of Spatial Transcriptomics
Fuente:
arXiv
Saved in:
| Main Authors: | Zahedi, Roxana, Argha, Ahmadreza, Farbehi, Nona, Bakhshayeshi, Ivan, Ye, Youqiong, Lovell, Nigel H., Alinejad-Rokny, Hamid |
|---|---|
| Format: | Preprint |
| Published: |
2025
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
Similar Items
Transcriptomic Models for Immunotherapy Response Prediction Show Limited Cross-cohort Generalisability
by: Liang, Yuheng, et al.
Published: (2026)
by: Liang, Yuheng, et al.
Published: (2026)
How chromatin interactions shed light on interpreting non-coding genomic variants: opportunities and future direc-tions
by: Liang, Yuheng, et al.
Published: (2024)
by: Liang, Yuheng, et al.
Published: (2024)
Interpretable graph-based models on multimodal biomedical data integration: A technical review and benchmarking
by: Sadeghi, Alireza, et al.
Published: (2025)
by: Sadeghi, Alireza, et al.
Published: (2025)
CLinNET: An Interpretable and Uncertainty‐Aware Deep Learning Framework for Multi‐Modal Clinical Genomics
by: Ivan Bakhshayeshi, et al.
Published: (2026)
by: Ivan Bakhshayeshi, et al.
Published: (2026)
TransST: Transfer Learning Embedded Spatial Factor Modeling of Spatial Transcriptomics Data
by: Liu, Shuo Shuo, et al.
Published: (2025)
by: Liu, Shuo Shuo, et al.
Published: (2025)
QuST-LLM: Integrating Large Language Models for Comprehensive Spatial Transcriptomics Analysis
by: Huang, Chao Hui
Published: (2024)
by: Huang, Chao Hui
Published: (2024)
GATES: Graph Attention Network with Global Expression Fusion for Deciphering Spatial Transcriptome Architectures
by: Xiao, Xiongtao, et al.
Published: (2024)
by: Xiao, Xiongtao, et al.
Published: (2024)
Spatial Transcriptomics Iterative Hierarchical Clustering (stIHC): A Novel Method for Identifying Spatial Gene Co-Expression Modules
by: Higgins, Catherine, et al.
Published: (2025)
by: Higgins, Catherine, et al.
Published: (2025)
ST-Align: A Multimodal Foundation Model for Image-Gene Alignment in Spatial Transcriptomics
by: Lin, Yuxiang, et al.
Published: (2024)
by: Lin, Yuxiang, et al.
Published: (2024)
Benchmarking Dimensionality Reduction Techniques for Spatial Transcriptomics
by: Mahmud, Md Ishtyaq, et al.
Published: (2025)
by: Mahmud, Md Ishtyaq, et al.
Published: (2025)
HEIST: A Graph Foundation Model for Spatial Transcriptomics and Proteomics Data
by: Madhu, Hiren, et al.
Published: (2025)
by: Madhu, Hiren, et al.
Published: (2025)
Masked Graph Autoencoders with Contrastive Augmentation for Spatially Resolved Transcriptomics Data
by: Fang, Donghai, et al.
Published: (2024)
by: Fang, Donghai, et al.
Published: (2024)
Single Cells Are Spatial Tokens: Transformers for Spatial Transcriptomic Data Imputation
by: Wen, Hongzhi, et al.
Published: (2023)
by: Wen, Hongzhi, et al.
Published: (2023)
Scalable Generation of Spatial Transcriptomics from Histology Images via Whole-Slide Flow Matching
by: Huang, Tinglin, et al.
Published: (2025)
by: Huang, Tinglin, et al.
Published: (2025)
HiST: Histological Images Reconstruct Tumor Spatial Transcriptomics via MultiScale Fusion Deep Learning
by: Wei Li, et al.
Published: (2026)
by: Wei Li, et al.
Published: (2026)
Towards Unified Molecule-Enhanced Pathology Image Representation Learning via Integrating Spatial Transcriptomics
by: Han, Minghao, et al.
Published: (2024)
by: Han, Minghao, et al.
Published: (2024)
SUICA: Learning Super-high Dimensional Sparse Implicit Neural Representations for Spatial Transcriptomics
by: Zhu, Qingtian, et al.
Published: (2024)
by: Zhu, Qingtian, et al.
Published: (2024)
stMCDI: Masked Conditional Diffusion Model with Graph Neural Network for Spatial Transcriptomics Data Imputation
by: Li, Xiaoyu, et al.
Published: (2024)
by: Li, Xiaoyu, et al.
Published: (2024)
Histopathology-centered Computational Evolution of Spatial Omics: Integration, Mapping, and Foundation Models
by: Hao, Ninghui, et al.
Published: (2026)
by: Hao, Ninghui, et al.
Published: (2026)
SToFM: a Multi-scale Foundation Model for Spatial Transcriptomics
by: Zhao, Suyuan, et al.
Published: (2025)
by: Zhao, Suyuan, et al.
Published: (2025)
Multi‐Omics Evidence Based on Spatial Transcriptomics Data Reveals the Therapeutic Value of Copper Death Genes in Glioblastoma
by: Zhaoliang Xue, et al.
Published: (2026)
by: Zhaoliang Xue, et al.
Published: (2026)
Deep Learning in Single-Cell and Spatial Transcriptomics Data Analysis: Advances and Challenges from a Data Science Perspective
by: Ge, Shuang, et al.
Published: (2024)
by: Ge, Shuang, et al.
Published: (2024)
Integrative Analysis of Epigenetic, Transcriptomic, and Metabolomic Responses to Arsenic Exposure Using Coupled Matrix Factorization
by: Suthahar, Sujit Silas Armstrong, et al.
Published: (2025)
by: Suthahar, Sujit Silas Armstrong, et al.
Published: (2025)
Scalable Amortized GPLVMs for Single Cell Transcriptomics Data
by: Zhao, Sarah, et al.
Published: (2024)
by: Zhao, Sarah, et al.
Published: (2024)
Harnessing the Potential of Spatial Statistics for Spatial Omics Data with pasta
by: Emons, Martin, et al.
Published: (2024)
by: Emons, Martin, et al.
Published: (2024)
Engineering Spatial and Molecular Features from Cellular Niches to Inform Predictions of Inflammatory Bowel Disease
by: Tan, Myles Joshua Toledo, et al.
Published: (2025)
by: Tan, Myles Joshua Toledo, et al.
Published: (2025)
Multimodal Spatial Omics: From Data Acquisition to Computational Integration
by: Isik, Esra Busra, et al.
Published: (2026)
by: Isik, Esra Busra, et al.
Published: (2026)
ClusterChirp: Scalable Interactive Exploration of Omics Data with Natural Language-Guided Analysis
by: Rawal, Osho, et al.
Published: (2026)
by: Rawal, Osho, et al.
Published: (2026)
Revolutionizing Genomics with Reinforcement Learning Techniques
by: Karami, Mohsen, et al.
Published: (2023)
by: Karami, Mohsen, et al.
Published: (2023)
PRAGA: Prototype-aware Graph Adaptive Aggregation for Spatial Multi-modal Omics Analysis
by: Huang, Xinlei, et al.
Published: (2024)
by: Huang, Xinlei, et al.
Published: (2024)
ETAGE: Enhanced Test Time Adaptation with Integrated Entropy and Gradient Norms for Robust Model Performance
by: Shamsi, Afshar, et al.
Published: (2024)
by: Shamsi, Afshar, et al.
Published: (2024)
Graph Neural Networks as a Substitute for Transformers in Single-Cell Transcriptomics
by: Qi, Jiaxin, et al.
Published: (2025)
by: Qi, Jiaxin, et al.
Published: (2025)
Transcriptome signature for the identification of bevacizumab responders in ovarian cancer
by: Zolotareva, Olga, et al.
Published: (2025)
by: Zolotareva, Olga, et al.
Published: (2025)
Integrated Transcriptomic Analysis Identifies Immune Remodeling and Prognostic Signatures in Uveal Melanoma
by: Zhongmin Li, et al.
Published: (2026)
by: Zhongmin Li, et al.
Published: (2026)
A Systematic Overview of Single-Cell Transcriptomics Databases, their Use cases, and Limitations
by: Gondal, Mahnoor N., et al.
Published: (2024)
by: Gondal, Mahnoor N., et al.
Published: (2024)
Geometry-First Generative Spatial Single-Cell Reconstruction
by: Azim, Ehtesamul, et al.
Published: (2026)
by: Azim, Ehtesamul, et al.
Published: (2026)
Graph-Based Multi-Omics Integration Improves Subtype Recovery and Survival Prediction Over Classical Integration Strategies in TCGA-BRCA
by: Ahmad, Taha
Published: (2026)
by: Ahmad, Taha
Published: (2026)
TopoLa: A Universal Framework to Enhance Cell Representations for Single-cell and Spatial Omics through Topology-encoded Latent Hyperbolic Geometry
by: Zheng, Kai, et al.
Published: (2025)
by: Zheng, Kai, et al.
Published: (2025)
SPP1 + Macrophage‐Associated Prognostic Signature in Hepatocellular Carcinoma via Integrated Single‐Cell and Bulk Transcriptomic Analysis
by: Suyang Yue, et al.
Published: (2025)
by: Suyang Yue, et al.
Published: (2025)
Integrative Single‐Cell Transcriptomics and Network Pharmacology Analysis of Xiao Qing Long Tang in Pediatric Cough‐Variant Asthma
by: Mingming Cui, et al.
Published: (2026)
by: Mingming Cui, et al.
Published: (2026)
Similar Items
-
Transcriptomic Models for Immunotherapy Response Prediction Show Limited Cross-cohort Generalisability
by: Liang, Yuheng, et al.
Published: (2026) -
How chromatin interactions shed light on interpreting non-coding genomic variants: opportunities and future direc-tions
by: Liang, Yuheng, et al.
Published: (2024) -
Interpretable graph-based models on multimodal biomedical data integration: A technical review and benchmarking
by: Sadeghi, Alireza, et al.
Published: (2025) -
CLinNET: An Interpretable and Uncertainty‐Aware Deep Learning Framework for Multi‐Modal Clinical Genomics
by: Ivan Bakhshayeshi, et al.
Published: (2026) -
TransST: Transfer Learning Embedded Spatial Factor Modeling of Spatial Transcriptomics Data
by: Liu, Shuo Shuo, et al.
Published: (2025)