Paper Citation Record · LEDGER

Towards Autonomous Mechanistic Reasoning in Virtual Cells

As of 4 August 2026, this Paper Citation Record lists 12 of 12 outbound references and 2 inbound Pith citation observations for arXiv:2604.11661.

A citation records a reference. It does not transfer a finding from one paper to another.

pith.paper-citation-record.v1
2604.11661 v3

Coverage vector

measured 12 of 12 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-07-11T11:50:26.030339Z

measured 14 of 14 standing notices

One-hop event checks from named stored sources.

Source: scholarly_work_events, retraction_status_cache, observed 2026-08-04T06:34:03.388597+00:00

measured 2 of 2 inbound itemization

Pith citing papers itemized under the disclosed page cap.

Source: paper_references, paper_reference_links, observed 2026-08-02T08:00:13.069295Z

measured 0 of 1 external citation measurements

A source-named dated measurement, never combined with another source.

Source: cited_works

Reference resolution

12 of 12 outbound references displayed

verified exact1
verified fuzzy4
unresolved6
parse uncertain0
malformed identifier0
metadata mismatch1

External citation measurements

No source-named external measurement is stored.

Outbound references

Observation 54a27e69-2d62-433b-8fd9-fa5dd021d457 · outbound

This paper cites URL https://www.biorxiv.org/content/early/2025/08/ 21/2025.08.18.670981.

Towards Autonomous Mechanistic Reasoning in Virtual Cells URL https://www.biorxiv.org/content/early/2025/08/ 21/2025.08.18.670981

Reference 1

Resolution: verified exact; doi, observed 2026-05-21T08:39:53.176727Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-04T06:34:03.388597+00:00.

Observation 541ea503-a90e-4c36-92db-7e6371a7bb1c · outbound

This paper cites DeepSeekMath: Pushing the Limits of Mathematical Reasoning in Open Language Models.

Towards Autonomous Mechanistic Reasoning in Virtual Cells DeepSeekMath: Pushing the Limits of Mathematical Reasoning in Open Language Models

Reference 2

Resolution: metadata mismatch; local_arxiv, observed 2026-05-21T08:39:53.173005Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-04T06:34:03.388597+00:00.

Observation b567c784-a809-4086-948a-8696af39964f · outbound

This paper cites an unresolved cited work.

Towards Autonomous Mechanistic Reasoning in Virtual Cells Unresolved cited work

Reference 3

Resolution: unresolved; raw_fallback, observed 2026-05-21T08:44:53.449340Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-04T06:34:03.388597+00:00.

Observation e2d324ab-76fd-446c-a181-8a68d7b00c9a · outbound

This paper cites - Explicitly mark whether each step is: - Causal (direct mechanistic or experimental evidence) - Correlative (statistical or inferred association).

Towards Autonomous Mechanistic Reasoning in Virtual Cells - Explicitly mark whether each step is: - **Causal** (direct mechanistic or experimental evidence) - **Correlative** (statistical or inferred association)

Reference 4

Resolution: verified fuzzy; raw_fallback, observed 2026-05-21T08:44:53.451856Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-04T06:34:03.388597+00:00.

Observation 2bfec725-c534-4c58-8201-c602461d29ea · outbound

This paper cites an unresolved cited work.

Towards Autonomous Mechanistic Reasoning in Virtual Cells Unresolved cited work

Reference 5

Resolution: unresolved; raw_fallback, observed 2026-05-21T08:44:53.453982Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-04T06:34:03.388597+00:00.

Observation bf3dde8d-b51a-4176-b3d6-eadb4d368b0c · outbound

This paper cites an unresolved cited work.

Towards Autonomous Mechanistic Reasoning in Virtual Cells Unresolved cited work

Reference 6

Resolution: unresolved; raw_fallback, observed 2026-05-21T08:44:53.447137Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-04T06:34:03.388597+00:00.

Observation 0cea361e-5ed6-4bb7-8d80-945f540ff76c · outbound

This paper cites an unresolved cited work.

Towards Autonomous Mechanistic Reasoning in Virtual Cells Unresolved cited work

Reference 7

Resolution: unresolved; raw_fallback, observed 2026-05-21T08:44:53.438437Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-04T06:34:03.388597+00:00.

Observation 29f960ec-a86f-45cd-bb52-241dd6dba325 · outbound

This paper cites an unresolved cited work.

Towards Autonomous Mechanistic Reasoning in Virtual Cells Unresolved cited work

Reference 8

Resolution: unresolved; raw_fallback, observed 2026-05-21T08:44:53.442228Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-04T06:34:03.388597+00:00.

Observation 19868fe9-88e9-4003-9120-375c83b127e5 · outbound

This paper cites Mechanism-of-Action Summary ( <answer>) 3.

Towards Autonomous Mechanistic Reasoning in Virtual Cells **Mechanism-of-Action Summary** ( <answer>) 3

Reference 9

Resolution: verified fuzzy; raw_fallback, observed 2026-05-21T08:44:53.433466Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-04T06:34:03.388597+00:00.

Observation 9be925c5-3165-493d-b50c-b28fb62a5b40 · outbound

This paper cites an unresolved cited work.

Towards Autonomous Mechanistic Reasoning in Virtual Cells Unresolved cited work

Reference 10

Resolution: unresolved; raw_fallback, observed 2026-05-21T08:44:53.431493Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-04T06:34:03.388597+00:00.

Observation 38812fda-38ad-407a-a752-80780e27e4eb · outbound

This paper cites The ”logical consistency” should be penalized.

Towards Autonomous Mechanistic Reasoning in Virtual Cells The ”logical consistency” should be penalized

Reference 11

Resolution: verified fuzzy; raw_fallback, observed 2026-05-21T08:44:53.440478Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-04T06:34:03.388597+00:00.

Observation ce37606e-dfb5-4437-bf90-604a4b8e208e · outbound

This paper cites Penalize missing actors/targets, unspecified directions, hand-wavy pathways, unlabeled compartments.

Towards Autonomous Mechanistic Reasoning in Virtual Cells Penalize missing actors/targets, unspecified directions, hand-wavy pathways, unlabeled compartments

Reference 12

Resolution: verified fuzzy; raw_fallback, observed 2026-05-21T08:44:53.444691Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-04T06:34:03.388597+00:00.

Pith citing papers

Observation f9b0e3d4-154c-41ee-bbe0-7df36aeccd2f · inbound

TheBioCollection: Unified Pre-Training Scale LLM Corpus for Biology cites this paper.

TheBioCollection: Unified Pre-Training Scale LLM Corpus for Biology Towards Autonomous Mechanistic Reasoning in Virtual Cells

Reference 94

Resolution: unresolved; no resolver link, observed 2026-07-13T06:39:26.167502Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 89e4f589-3af4-4d15-bab0-e924b2c2b518 · inbound

TheBioCollection: Unified Pre-Training Scale LLM Corpus for Biology cites this paper.

TheBioCollection: Unified Pre-Training Scale LLM Corpus for Biology Towards Autonomous Mechanistic Reasoning in Virtual Cells

Reference 94

Resolution: unresolved; no resolver link, observed 2026-08-02T08:00:13.069295Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.