Beyond Visualization: Building a Rigorous Benchmark for RNA Trajectory Inference

Most RNA velocity analyses rely on visual inspection of UMAP plots, but visualization alone provides no quantitative evidence of correctness. This work demonstrates the necessity of rigorous benchmarking by introducing a three-task framework that evaluates trajectory accuracy against independent methods, validates individual cell-state transitions, and assesses robustness to rare cell populations. This approach shifts RNA velocity validation from subjective visualization to objective, reproducible evaluation—critical for ensuring reliability in developmental biology inference.