Pith Number

pith:7RYG2CLY

pith:2025:7RYG2CLYJYD7IFSH5OFYBX3OJG

not attested not anchored not stored refs pending

HDTree: Generative Modeling of Cellular Hierarchies for Robust Lineage Inference

Changxi Chi, Chang Yu, Jingbo Zhou, Stan Z. Li, Wenzhe Li, Yongjie Xu, Zelin Zang, Zhen Lei

HDTree models cellular hierarchies in a unified latent space with a single codebook and quantized diffusion for robust lineage inference.

arxiv:2506.23287 v3 · 2025-06-29 · cs.LG · q-bio.QM

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\usepackage{pith}
\pithnumber{7RYG2CLYJYD7IFSH5OFYBX3OJG}

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Record completeness

1 Bitcoin timestamp

2 Internet Archive

3 Author claim open · sign in to claim

4 Citations open

5 Replications open

✓ Portable graph bundle live · download bundle · merged state

The bundle contains the canonical record plus signed events. A mirror can host it anywhere and recompute the same current state with the deterministic merge algorithm.

Claims

C1strongest claim

HDTree captures tree relationships within a hierarchical latent space using a unified hierarchical codebook and employs a quantized diffusion process to model continuous cell state transitions, improving stability, scalability, and biological plausibility of inferred lineages while outperforming existing methods in lineage inference accuracy, reconstruction quality, and hierarchical consistency.

C2weakest assumption

That a unified hierarchical codebook combined with quantized diffusion can accurately represent complex branching tree structures and continuous cell transitions without branch-specific modules, and that alignment with the Waddington landscape guarantees enhanced biological plausibility of the inferred lineages.

C3one line summary

HDTree introduces a hierarchical latent space with a unified codebook and quantized diffusion process to model cell state transitions and improve lineage inference accuracy and stability.

Formal links

2 machine-checked theorem links

Receipt and verification

First computed	2026-05-20T00:04:11.423391Z
Builder	pith-number-builder-2026-05-17-v1
Signature	Pith Ed25519 (`pith-v1-2026-05`) · public key
Schema	pith-number/v1.0

Canonical hash

fc706d09784e07f41647eb8b80df6e49bdfbd1a3688c4257b1a753c97a9e4588

Aliases

arxiv: 2506.23287 · arxiv_version: 2506.23287v3 · doi: 10.48550/arxiv.2506.23287 · pith_short_12: 7RYG2CLYJYD7 · pith_short_16: 7RYG2CLYJYD7IFSH · pith_short_8: 7RYG2CLY

Agent API

Resolver JSON Graph JSON Events JSON Schema Signing key

Verify this Pith Number yourself

curl -sH 'Accept: application/ld+json' https://pith.science/pith/7RYG2CLYJYD7IFSH5OFYBX3OJG \
  | jq -c '.canonical_record' \
  | python3 -c "import sys,json,hashlib; b=json.dumps(json.loads(sys.stdin.read()), sort_keys=True, separators=(',',':'), ensure_ascii=False).encode(); print(hashlib.sha256(b).hexdigest())"
# expect: fc706d09784e07f41647eb8b80df6e49bdfbd1a3688c4257b1a753c97a9e4588

Canonical record JSON

{
  "metadata": {
    "abstract_canon_sha256": "b6a5849c4fa4d98092d8ab8f9d28191d031d8892213217c977878e6925f5fe2e",
    "cross_cats_sorted": [
      "q-bio.QM"
    ],
    "license": "http://creativecommons.org/licenses/by/4.0/",
    "primary_cat": "cs.LG",
    "submitted_at": "2025-06-29T15:19:13Z",
    "title_canon_sha256": "a3c5f4ccf102cdca3de1f8898a4e8e83a4ccf48e2c1badf1506a6a61c80cc1e7"
  },
  "schema_version": "1.0",
  "source": {
    "id": "2506.23287",
    "kind": "arxiv",
    "version": 3
  }
}