Harmonised benchmarking of foundation models for single-cell and spatial transcriptomics reveals context-dependent generalisation

arXiv:2607.17227 · q-bio.GN, q-bio.CB · Submitted 2026-07-19 · Read on arXiv

q-bio.GN, q-bio.CB

Submitted: 2026-07-19

Updated: 2026-09-17

Code: https://github.com/iced-soda/FM-benchmark

Terminology

• Embeddings — 55× in this paper · explained in 2 episodes
• Clustering — 53× in this paper · explained in 2 episodes
• Foundation Model — 47× in this paper · explained in 3 episodes
• Benchmark — 39× in this paper · explained in 2 episodes
• Foundation Models — 34× in this paper · explained in 7 episodes
• AUC — 18× in this paper · explained in 2 episodes
• Adaptation — 18× in this paper · explained in 1 episode
• Accuracy — 15× in this paper · explained in 1 episode
• Fine-Tuning — 14× in this paper · explained in 5 episodes
• Transformer — 14× in this paper · explained in 2 episodes
• Benchmarking — 9× in this paper · explained in 3 episodes
• F1 Score — 5× in this paper · explained in 3 episodes
• Adam — 4× in this paper · explained in 2 episodes
• Domain Shift — 4× in this paper · explained in 4 episodes
• Agentic AI — 3× in this paper · explained in 1 episode
• Alignment — 3× in this paper · explained in 1 episode
• Downstream Tasks — 3× in this paper · explained in 2 episodes
• Interpretability — 3× in this paper · explained in 15 episodes
• Aggregation — 2× in this paper · explained in 1 episode
• Domain Adaptation — 2× in this paper · explained in 5 episodes
• Fidelity — 2× in this paper · explained in 2 episodes
• Representation Learning — 2× in this paper · explained in 2 episodes
• Transformer Models — 2× in this paper · explained in 2 episodes
• AI Agents — 1× in this paper · explained in 2 episodes
• Abundance — 1× in this paper · explained in 1 episode
• Agentic AI Framework — 1× in this paper · explained in 1 episode
• Agentic Reasoning — 1× in this paper · explained in 1 episode
• Agentic System — 1× in this paper · explained in 2 episodes
• Calibration — 1× in this paper · explained in 7 episodes
• Catastrophic Forgetting — 1× in this paper · explained in 5 episodes
• Consistency — 1× in this paper · explained in 3 episodes
• Cosine Similarity — 1× in this paper · explained in 3 episodes
• Diffusion Model — 1× in this paper · explained in 8 episodes
• Failure Modes — 1× in this paper · explained in 3 episodes
• Foundation Models (FMs) — 1× in this paper · explained in 2 episodes
• Generative AI — 1× in this paper · explained in 2 episodes
• Human-in-the-Loop — 1× in this paper · explained in 3 episodes
• Latent Space — 1× in this paper · explained in 7 episodes
• Mouse Organogenesis Spatiotemporal Transcriptomic Atlas — 1× in this paper
• Parameter-Efficient Fine-Tuning — 1× in this paper · explained in 2 episodes
• Synthetic Data Generation — 1× in this paper · explained in 5 episodes
• Transfer Learning — 1× in this paper · explained in 10 episodes
• World Model — 1× in this paper · explained in 7 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