Subcellularly Resolved Single-Cell Embedding Learning with Transcriptomic data, Protein Structure and Localization Information

arXiv:2609.02344 · q-bio.GN, cs.AI · Submitted 2026-09-02 · Read on arXiv

q-bio.GN, cs.AI

Submitted: 2026-09-02

Updated: 2026-09-02

Comments: 20 pages, 4 figures, and 1 tables

Code: https://github.com/ZHOUZHEN2002/RNA

License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/

Terminology

• Embeddings — 37× in this paper · explained in 2 episodes
• Representation Learning — 15× in this paper · explained in 2 episodes
• Transformer — 15× in this paper · explained in 2 episodes
• Accuracy — 10× in this paper · explained in 1 episode
• Abundance — 8× in this paper · explained in 1 episode
• Foundation Model — 8× in this paper · explained in 3 episodes
• Alignment — 6× in this paper · explained in 1 episode
• F1 Score — 6× in this paper · explained in 3 episodes
• Attention Mechanism — 5× in this paper · explained in 2 episodes
• Benchmark — 4× in this paper · explained in 2 episodes
• Consistency — 4× in this paper · explained in 3 episodes
• Foundation Models — 4× in this paper · explained in 7 episodes
• Multimodal Fusion — 4× in this paper · explained in 3 episodes
• Cross-Attention Mechanism — 3× in this paper · explained in 2 episodes
• Generative AI — 3× in this paper · explained in 2 episodes
• Ablation — 2× in this paper · explained in 1 episode
• Downstream Tasks — 2× in this paper · explained in 2 episodes
• Generalization — 2× in this paper · explained in 13 episodes
• Latent Representation — 2× in this paper · explained in 2 episodes
• Latent Space — 2× in this paper · explained in 7 episodes
• Transformer Architecture — 2× in this paper · explained in 2 episodes
• Adam — 1× in this paper · explained in 2 episodes
• Benchmarking — 1× in this paper · explained in 3 episodes
• Clustering — 1× in this paper · explained in 2 episodes
• Fidelity — 1× in this paper · explained in 2 episodes
• Interpretability — 1× in this paper · explained in 15 episodes
• Latent Representations — 1× in this paper · explained in 3 episodes
• Loss Function — 1× in this paper · explained in 2 episodes
• Multimodal Learning — 1× in this paper · explained in 2 episodes
• Objective Function — 1× in this paper · explained in 2 episodes
• Robustness — 1× in this paper · explained in 5 episodes
• Transfer Learning — 1× in this paper · explained in 10 episodes
• Transferability — 1× in this paper · explained in 4 episodes
• Unified Framework — 1× in this paper · explained in 5 episodes

Related papers

• WTKO-CNN: Deep Learning Reveals Sequence Motifs Distinguishing Wild-Type and Knockout ATAC-seq Peaks
• Robust Machine Learning for Regulatory Sequence Modeling under Biological and Technical Distribution Shifts
• Stable-Shift: Biologically Structured Prediction of Transcriptional Responses to Unseen Gene Perturbations