Paper Citation Record · LEDGER

Knowledge Graphs and Reasoning LLMs for Finding Simple Yet Effective Transcriptomic Perturbation Predictors

As of 4 August 2026, this Paper Citation Record lists 24 of 24 outbound references and 0 inbound Pith citation observations for arXiv:2606.08816.

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

pith.paper-citation-record.v1
2606.08816 v1

Coverage vector

measured 24 of 24 reference resolution

Typed states for the displayed outbound observations.

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

measured 24 of 24 standing notices

One-hop event checks from named stored sources.

Source: scholarly_work_events, retraction_status_cache, observed 2026-08-03T06:30:56.289259+00:00

measured 0 of 0 inbound itemization

Pith citing papers itemized under the disclosed page cap.

Source: paper_references, paper_reference_links

measured 0 of 1 external citation measurements

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

Source: cited_works

Reference resolution

24 of 24 outbound references displayed

verified exact14
verified fuzzy0
unresolved6
parse uncertain0
malformed identifier0
metadata mismatch4

External citation measurements

No source-named external measurement is stored.

Outbound references

Observation 6e375d62-d0d9-4067-875e-f6223f0fbd5c · outbound

This paper cites Nature Methods , volume=.

Knowledge Graphs and Reasoning LLMs for Finding Simple Yet Effective Transcriptomic Perturbation Predictors Nature Methods , volume=

Reference 1

Resolution: metadata mismatch; doi, observed 2026-06-27T18:41:08.306149Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-03T06:30:56.289259+00:00.

Observation 21b4960d-4a9a-4d44-95f0-1c3d7a848f8f · outbound

This paper cites an unresolved cited work.

Knowledge Graphs and Reasoning LLMs for Finding Simple Yet Effective Transcriptomic Perturbation Predictors Unresolved cited work

Reference 2

Resolution: unresolved; no resolver link, observed 2026-06-27T18:31:59.962779Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 1c477123-16bf-4ba4-a40b-f5ad33e0b6b7 · outbound

This paper cites Stark, Gabriele Gut, Jacobo Sarabia del Castillo, Mitch Levesque, Kjong- Van Lehmann, Lucas Pelkmans, Andreas Krause, and Gunnar R ¨atsch.

Knowledge Graphs and Reasoning LLMs for Finding Simple Yet Effective Transcriptomic Perturbation Predictors Stark, Gabriele Gut, Jacobo Sarabia del Castillo, Mitch Levesque, Kjong- Van Lehmann, Lucas Pelkmans, Andreas Krause, and Gunnar R ¨atsch

Reference 3

Resolution: metadata mismatch; doi, observed 2026-06-27T18:41:08.294161Z

Source-reported events for the cited work

correction dated 2023-10-30. Source: crossref record 10.1038/s41592-023-02073-w->10.1038/s41592-023-01969-x:correction, observed 2026-07-11T02:55:58.631449+00:00. This notice travels one citation hop only.

Observation c568f3f9-b63a-4a8b-a0ea-fdeb68c2730a · outbound

This paper cites Cell , author =.

Knowledge Graphs and Reasoning LLMs for Finding Simple Yet Effective Transcriptomic Perturbation Predictors Cell , author =

Reference 4

Resolution: verified exact; doi, observed 2026-06-27T18:41:08.301742Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-03T06:30:56.289259+00:00.

Observation 41b97b36-efcc-4398-8ab4-e45526a65e63 · outbound

This paper cites doi: 10.1101/2023.10.

Knowledge Graphs and Reasoning LLMs for Finding Simple Yet Effective Transcriptomic Perturbation Predictors doi: 10.1101/2023.10

Reference 5

Resolution: verified exact; doi, observed 2026-06-27T18:41:08.307715Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-03T06:30:56.289259+00:00.

Observation b3cac8df-1f48-498b-8478-39a7a9226a58 · outbound

This paper cites Buenrostro, Nir Yosef, Carolina Caldas, Rui Sun, and Bing He.

Knowledge Graphs and Reasoning LLMs for Finding Simple Yet Effective Transcriptomic Perturbation Predictors Buenrostro, Nir Yosef, Carolina Caldas, Rui Sun, and Bing He

Reference 6

Resolution: metadata mismatch; doi, observed 2026-06-27T18:41:08.296287Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-03T06:30:56.289259+00:00.

Observation be743b1c-b2d0-47c9-b5fc-9b8ba83f4511 · outbound

This paper cites Season combinatorial intervention predictions with Salt & Peper.

Knowledge Graphs and Reasoning LLMs for Finding Simple Yet Effective Transcriptomic Perturbation Predictors Season combinatorial intervention predictions with Salt & Peper

Reference 7

Resolution: verified exact; arxiv_id, observed 2026-07-02T22:57:26.507595Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-03T06:30:56.289259+00:00.

Observation 01308e61-e42e-4d40-b5d2-f21831f93138 · outbound

This paper cites an unresolved cited work.

Knowledge Graphs and Reasoning LLMs for Finding Simple Yet Effective Transcriptomic Perturbation Predictors Unresolved cited work

Reference 8

Resolution: unresolved; no resolver link, observed 2026-06-27T18:31:59.962779Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 5dfc69e2-3122-4c2f-817a-18fd900944a6 · outbound

This paper cites Korbak, E.

Knowledge Graphs and Reasoning LLMs for Finding Simple Yet Effective Transcriptomic Perturbation Predictors Korbak, E

Reference 9

Resolution: unresolved; no resolver link, observed 2026-06-27T18:31:59.962779Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 1265e076-80d8-4ca6-acc9-3ae6888c3899 · outbound

This paper cites Levine, S.

Knowledge Graphs and Reasoning LLMs for Finding Simple Yet Effective Transcriptomic Perturbation Predictors Levine, S

Reference 10

Resolution: unresolved; no resolver link, observed 2026-06-27T18:31:59.962779Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation b61ae19e-2409-4693-b19a-57970707f8e1 · outbound

This paper cites an unresolved cited work.

Knowledge Graphs and Reasoning LLMs for Finding Simple Yet Effective Transcriptomic Perturbation Predictors Unresolved cited work

Reference 11

Resolution: verified exact; arxiv_id, observed 2026-07-02T22:57:26.519300Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-03T06:30:56.289259+00:00.

Observation 72ad2825-d945-411c-b1d0-3b768a53c4fc · outbound

This paper cites Alexander Wolf, and Fabian J.

Knowledge Graphs and Reasoning LLMs for Finding Simple Yet Effective Transcriptomic Perturbation Predictors Alexander Wolf, and Fabian J

Reference 12

Resolution: verified exact; doi, observed 2026-06-27T18:41:08.300053Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-03T06:30:56.289259+00:00.

Observation 21868888-cafb-4cbe-a45d-354bd3638c6b · outbound

This paper cites Ibarra, Sanjay R.

Knowledge Graphs and Reasoning LLMs for Finding Simple Yet Effective Transcriptomic Perturbation Predictors Ibarra, Sanjay R

Reference 13

Resolution: verified exact; doi, observed 2026-06-27T18:41:08.298162Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-03T06:30:56.289259+00:00.

Observation 79a462b3-b344-46bf-8af7-ced70a43e9a6 · outbound

This paper cites Virtual Cells: Predict, Explain, Discover.

Knowledge Graphs and Reasoning LLMs for Finding Simple Yet Effective Transcriptomic Perturbation Predictors Virtual Cells: Predict, Explain, Discover

Reference 14

Resolution: verified exact; arxiv_id, observed 2026-07-02T22:57:26.518195Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-03T06:30:56.289259+00:00.

Observation 48a2ea8d-0c63-46b8-bbe8-230b21e4d405 · outbound

This paper cites Proximal Policy Optimization Algorithms.

Knowledge Graphs and Reasoning LLMs for Finding Simple Yet Effective Transcriptomic Perturbation Predictors Proximal Policy Optimization Algorithms

Reference 15

Resolution: metadata mismatch; local_arxiv, observed 2026-06-27T18:41:08.304441Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-03T06:30:56.289259+00:00.

Observation 7918b674-79df-4569-b9cf-380416247fc2 · outbound

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

Knowledge Graphs and Reasoning LLMs for Finding Simple Yet Effective Transcriptomic Perturbation Predictors DeepSeekMath: Pushing the Limits of Mathematical Reasoning in Open Language Models

Reference 16

Resolution: verified exact; local_arxiv, observed 2026-07-02T22:57:26.512913Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-03T06:30:56.289259+00:00.

Observation b0c11de3-8f91-44a8-a262-8b9f51834372 · outbound

This paper cites Szklarczyk, R.

Knowledge Graphs and Reasoning LLMs for Finding Simple Yet Effective Transcriptomic Perturbation Predictors Szklarczyk, R

Reference 17

Resolution: unresolved; no resolver link, observed 2026-06-27T18:31:59.962779Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 0f90b67f-08eb-4513-88a1-0e31b5fc5305 · outbound

This paper cites Cellforge: Agentic design of virtual cell models.

Knowledge Graphs and Reasoning LLMs for Finding Simple Yet Effective Transcriptomic Perturbation Predictors Cellforge: Agentic design of virtual cell models

Reference 18

Resolution: verified exact; arxiv_id, observed 2026-07-02T22:57:26.515597Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-03T06:30:56.289259+00:00.

Observation d2c267b5-b10e-4a06-b89f-b26b5fecdb9a · outbound

This paper cites TxPert: Leveraging Biochemical Relationships for Out-of-Distribution Transcriptomic Perturbation Prediction.

Knowledge Graphs and Reasoning LLMs for Finding Simple Yet Effective Transcriptomic Perturbation Predictors TxPert: Leveraging Biochemical Relationships for Out-of-Distribution Transcriptomic Perturbation Prediction

Reference 19

Resolution: verified exact; arxiv_id, observed 2026-07-02T22:57:26.520743Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-03T06:30:56.289259+00:00.

Observation 6a0a2aa2-9ae8-4fed-9a32-92ebc069d5fb · outbound

This paper cites Contextualizing biological perturbation experiments through language.

Knowledge Graphs and Reasoning LLMs for Finding Simple Yet Effective Transcriptomic Perturbation Predictors Contextualizing biological perturbation experiments through language

Reference 20

Resolution: verified exact; arxiv_id, observed 2026-07-02T22:57:26.529907Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-03T06:30:56.289259+00:00.

Observation bcb6881d-e0a7-47c9-89c3-27be700c7efe · outbound

This paper cites Perturbench: Benchmarking machine learning models for cellular perturbation analysis.arXiv preprint arXiv:2408.10609.

Knowledge Graphs and Reasoning LLMs for Finding Simple Yet Effective Transcriptomic Perturbation Predictors Perturbench: Benchmarking machine learning models for cellular perturbation analysis.arXiv preprint arXiv:2408.10609

Reference 21

Resolution: verified exact; arxiv_id, observed 2026-07-02T22:57:26.536612Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-03T06:30:56.289259+00:00.

Observation 9c540719-056f-44b9-a67e-e100b4bed684 · outbound

This paper cites Group Sequence Policy Optimization.

Knowledge Graphs and Reasoning LLMs for Finding Simple Yet Effective Transcriptomic Perturbation Predictors Group Sequence Policy Optimization

Reference 22

Resolution: verified exact; local_arxiv, observed 2026-07-02T22:57:26.533996Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-03T06:30:56.289259+00:00.

Observation 0dad800d-5b8d-44d4-be49-51c02e5353a1 · outbound

This paper cites Automated Discovery of Pairwise Interactions from Unstructured Data.

Knowledge Graphs and Reasoning LLMs for Finding Simple Yet Effective Transcriptomic Perturbation Predictors Automated Discovery of Pairwise Interactions from Unstructured Data

Reference 23

Resolution: verified exact; arxiv_id, observed 2026-07-02T22:57:26.525162Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-03T06:30:56.289259+00:00.

Observation cf12126b-507c-4bc2-9841-d9ec29c3261b · outbound

This paper cites All Training Genes.

Knowledge Graphs and Reasoning LLMs for Finding Simple Yet Effective Transcriptomic Perturbation Predictors All Training Genes

Reference 24

Resolution: unresolved; no resolver link, observed 2026-06-27T18:31:59.962779Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Pith citing papers

No inbound Pith citation observations are available.