UMAP distance is commonly over-interpreted
RESEARCH PROBLEM
How can researchers explore clusters, markers and annotations without over-interpreting a two-dimensional embedding?
Connect UMAP neighbourhoods to marker evidence, annotation provenance and the upstream choices that shaped the representation.
WHY THIS IS DIFFICULT
Automated cell labels can appear more certain than they are
Batch and QC decisions are hidden by the final figure
RESPONSIBLE APPROACH
Inspect annotated and unassigned populations
Review marker evidence for selected clusters
Treat embeddings as navigation surfaces rather than complete conclusions
RELEVANT FORNEUS RESEARCH
Working demonstration
Single-Cell AI Explorer
Interactive exploration of annotated single-cell populations, UMAP coordinates and marker-gene results.
View evidence and screenshots ↗Research projectSpatial Transcriptomics Atlas
A production-oriented research framework for spatial neighbourhoods and cell–cell communication across Visium, Xenium and MERFISH data.
View evidence and screenshots ↗INTERPRETATION BOUNDARY
- Expert biological validation remains necessary
- Upstream integration and quality control determine what can be inferred
QUESTIONS THIS PAGE ANSWERS
- interactive single-cell UMAP
- review marker gene annotations
- explore cell populations