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

Terminology

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