{"paper":{"title":"Uncovering smooth structures in single-cell data with PCS-guided neighbor embeddings","license":"http://creativecommons.org/licenses/by-nc-sa/4.0/","headline":"","cross_cats":["cs.LG","q-bio.GN","stat.AP"],"primary_cat":"stat.ML","authors_text":"Bin Yu, Jingyuan Hu, Rong Ma, Xi Li","submitted_at":"2025-06-27T13:45:55Z","abstract_excerpt":"Single-cell sequencing is revolutionizing biology by enabling detailed investigations of cell-state transitions. Many biological processes unfold along continuous trajectories, yet it remains challenging to extract smooth, low-dimensional representations from inherently noisy, high-dimensional single-cell data. Neighbor embedding (NE) algorithms, such as t-SNE and UMAP, are widely used to embed high-dimensional single-cell data into low dimensions. But they often introduce undesirable distortions, resulting in misleading interpretations. Existing evaluation methods for NE algorithms primarily "},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2506.22228","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2506.22228/integrity.json","findings":[],"available":true,"detectors_run":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938"},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"}