PopPert: Population-level Joint-Distribution Modeling for Single-Cell Perturbation Prediction

arXiv:2609.01357 · q-bio.GN, cs.AI · Submitted 2026-09-01 · Read on arXiv

q-bio.GN, cs.AI

Submitted: 2026-09-01

Updated: 2026-09-01

Code: https://github.com/whd1125/PopPert

Terminology

• Copula — 23× in this paper · explained in 2 episodes
• AUC — 14× in this paper · explained in 2 episodes
• Ablation — 9× in this paper · explained in 1 episode
• Benchmark — 9× in this paper · explained in 2 episodes
• Alignment — 5× in this paper · explained in 1 episode
• Transformer — 5× in this paper · explained in 2 episodes
• Distribution Matching — 4× in this paper · explained in 2 episodes
• Flow Matching — 4× in this paper · explained in 8 episodes
• Loss Function — 4× in this paper · explained in 2 episodes
• Ablation study — 2× in this paper · explained in 1 episode
• Accuracy — 2× in this paper · explained in 1 episode
• Aggregation — 2× in this paper · explained in 1 episode
• Embeddings — 2× in this paper · explained in 2 episodes
• Generalization — 2× in this paper · explained in 13 episodes
• Latent Space — 2× in this paper · explained in 7 episodes
• Agentic AI — 1× in this paper · explained in 1 episode
• Core — 1× in this paper · explained in 2 episodes
• Diffusion Model — 1× in this paper · explained in 8 episodes
• Fidelity — 1× in this paper · explained in 2 episodes
• Flow Matching Model — 1× in this paper · explained in 2 episodes
• Foundation Model — 1× in this paper · explained in 3 episodes
• Generative AI — 1× in this paper · explained in 2 episodes
• Mode Collapse — 1× in this paper · explained in 2 episodes
• Optimal Transport — 1× in this paper · explained in 5 episodes
• Transformer Architecture — 1× in this paper · explained in 2 episodes

Sources

• Doloris: Dual Conditional Diffusion Implicit Bridges with Sparsity Masking Strategy for Unpaired Single-Cell Perturbation Estimation
• Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics
• Modeling Gene Expression Distributional Shifts for Unseen Genetic Perturbations

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• WTKO-CNN: Deep Learning Reveals Sequence Motifs Distinguishing Wild-Type and Knockout ATAC-seq Peaks
• Stable-Shift: Biologically Structured Prediction of Transcriptional Responses to Unseen Gene Perturbations