Paper Citation Record · LEDGER

No Foundations without Foundations -- Why semi-mechanistic models are essential for regulatory biology

As of 18 August 2026, this Paper Citation Record lists 19 of 19 outbound references and 2 inbound Pith citation observations for arXiv:2501.19178.

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

pith.paper-citation-record.v1
2501.19178 v1

Coverage vector

measured 19 of 19 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-08-09T21:06:19.603983Z

measured 21 of 21 standing notices

One-hop event checks from named stored sources.

Source: scholarly_work_events, retraction_status_cache, observed 2026-08-18T06:34:40.430872+00:00

measured 2 of 2 inbound itemization

Pith citing papers itemized under the disclosed page cap.

Source: paper_references, paper_reference_links, observed 2026-08-05T10:19:24.458421Z

measured 0 of 1 external citation measurements

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

Source: arxiv_reference, observed 2026-06-28T23:32:46.933363Z

Reference resolution

19 of 19 outbound references displayed

verified exact1
verified fuzzy7
unresolved10
parse uncertain0
malformed identifier0
metadata mismatch1

External citation measurements

No source-named external measurement is stored.

Outbound references

Observation 09dca3bc-3a86-45ee-8441-9967450ad3ae · outbound

This paper cites an unresolved cited work.

No Foundations without Foundations -- Why semi-mechanistic models are essential for regulatory biology Unresolved cited work

Reference 1

Resolution: unresolved; raw_fallback, observed 2026-08-09T21:06:19.943691Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 2be3d407-de80-4748-8670-6281539ee0fa · outbound

This paper cites N., Ackerman, J., Alix, E., Ando, D.

No Foundations without Foundations -- Why semi-mechanistic models are essential for regulatory biology N., Ackerman, J., Alix, E., Ando, D

Reference 3

Resolution: verified fuzzy; raw_fallback, observed 2026-08-09T21:06:20.154730Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 8f621877-bd82-403a-9ed4-613f4fab4cd7 · outbound

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

No Foundations without Foundations -- Why semi-mechanistic models are essential for regulatory biology Season combinatorial intervention predictions with Salt & Peper

Reference 4

Resolution: unresolved; no resolver link, observed 2026-08-09T21:06:19.439212Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 0b8d82a5-2f31-4717-b185-7268b20be2c3 · outbound

This paper cites Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution.

No Foundations without Foundations -- Why semi-mechanistic models are essential for regulatory biology Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution

Reference 5

Resolution: unresolved; no resolver link, observed 2026-08-09T21:06:19.445702Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 3991513d-2b2a-4fca-bf2c-817adcd41e4a · outbound

This paper cites On Neural Differential Equations.

No Foundations without Foundations -- Why semi-mechanistic models are essential for regulatory biology On Neural Differential Equations

Reference 8

Resolution: unresolved; no resolver link, observed 2026-08-09T21:06:19.462741Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation cacc33b1-b9ec-4b62-9325-4a47231b099a · outbound

This paper cites Causal modeling with stationary diffusions.

No Foundations without Foundations -- Why semi-mechanistic models are essential for regulatory biology Causal modeling with stationary diffusions

Reference 10

Resolution: verified fuzzy; raw_fallback, observed 2026-08-09T21:06:20.028068Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation e6eaa2b3-821a-4e56-9829-2bb682f87a61 · outbound

This paper cites Joint Causal Inference from Multiple Contexts.

No Foundations without Foundations -- Why semi-mechanistic models are essential for regulatory biology Joint Causal Inference from Multiple Contexts

Reference 11

Resolution: unresolved; no resolver link, observed 2026-08-09T21:06:19.508038Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation bb73a838-06e1-4866-b1b6-103c02d9cc36 · outbound

This paper cites E., Xue, A., Yazar, S., Alquicira, J., Cuomo, A., Senabouth, A., Gordon, G., Kathail, P., Ye, J., and Hewitt, A.

No Foundations without Foundations -- Why semi-mechanistic models are essential for regulatory biology E., Xue, A., Yazar, S., Alquicira, J., Cuomo, A., Senabouth, A., Gordon, G., Kathail, P., Ye, J., and Hewitt, A

Reference 13

Resolution: verified fuzzy; raw_fallback, observed 2026-08-09T21:06:19.993717Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 7456ae4a-e2b4-4d4c-aba8-b0f5287d3da2 · outbound

This paper cites M., Nassar, M., Osi´nski, B., Eksi, R., Zhang, K., and Graepel, T.

No Foundations without Foundations -- Why semi-mechanistic models are essential for regulatory biology M., Nassar, M., Osi´nski, B., Eksi, R., Zhang, K., and Graepel, T

Reference 16

Resolution: unresolved; no resolver link, observed 2026-08-09T21:06:19.588798Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation b5e6cddc-3822-4f71-aa9d-5711fde78c8e · outbound

This paper cites an unresolved cited work.

No Foundations without Foundations -- Why semi-mechanistic models are essential for regulatory biology Unresolved cited work

Reference 17

Resolution: unresolved; raw_fallback, observed 2026-08-09T21:06:19.960443Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 6b06b0a4-31ec-400e-86fa-8d3cd70517e9 · outbound

This paper cites This is repeated five times to obtain the final baseline.

No Foundations without Foundations -- Why semi-mechanistic models are essential for regulatory biology This is repeated five times to obtain the final baseline

Reference 19

Resolution: verified fuzzy; raw_fallback, observed 2026-08-09T21:06:19.927401Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation f069b129-8804-4f99-bc40-50083e170369 · outbound

This paper cites Simulation-based Benchmarking for Causal Structure Learning in Gene Perturbation Experiments.

No Foundations without Foundations -- Why semi-mechanistic models are essential for regulatory biology Simulation-based Benchmarking for Causal Structure Learning in Gene Perturbation Experiments

Reference 2005

Resolution: verified exact; local_arxiv, observed 2026-08-09T21:06:19.814139Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 99f3f34f-37cb-4a3b-9ae1-e1933d69495c · outbound

This paper cites Learning Identifiable Factorized Causal Representations of Cellular Responses.

No Foundations without Foundations -- Why semi-mechanistic models are essential for regulatory biology Learning Identifiable Factorized Causal Representations of Cellular Responses

Reference 2016

Resolution: unresolved; no resolver link, observed 2026-08-09T21:06:19.529029Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 3456d4e4-351c-4f28-8521-b2830ac5c8e7 · outbound

This paper cites Perteval-scfm: Benchmark- ing single-cell foundation models for perturbation effect prediction.

No Foundations without Foundations -- Why semi-mechanistic models are essential for regulatory biology Perteval-scfm: Benchmark- ing single-cell foundation models for perturbation effect prediction

Reference 2017

Resolution: verified fuzzy; raw_fallback, observed 2026-08-09T21:06:19.977339Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 5ad615d1-c4f6-49b0-8bcb-8747034e35dd · outbound

This paper cites PyRelationAL: a python library for active learning research and development.

No Foundations without Foundations -- Why semi-mechanistic models are essential for regulatory biology PyRelationAL: a python library for active learning research and development

Reference 2019

Resolution: unresolved; no resolver link, observed 2026-08-09T21:06:19.578107Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation d6c32b93-6c9a-4817-98cb-ff064f283b16 · outbound

This paper cites DiscoGen: Learning to Discover Gene Regulatory Networks.

No Foundations without Foundations -- Why semi-mechanistic models are essential for regulatory biology DiscoGen: Learning to Discover Gene Regulatory Networks

Reference 2020

Resolution: metadata mismatch; local_arxiv, observed 2026-08-09T21:06:19.859264Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 98142d21-6d43-4b9a-a7bb-7771fe3221cf · outbound

This paper cites Benchmarking Transcriptomics Foundation Models for Perturbation Analysis : one PCA still rules them all.

No Foundations without Foundations -- Why semi-mechanistic models are essential for regulatory biology Benchmarking Transcriptomics Foundation Models for Perturbation Analysis : one PCA still rules them all

Reference 2021

Resolution: unresolved; no resolver link, observed 2026-08-09T21:06:19.428208Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 287a90ba-223f-4301-9802-3ef692a873e7 · outbound

This paper cites Systematic reconstruction of molecular pathway signatures using scalable single-cell perturbation screens.

No Foundations without Foundations -- Why semi-mechanistic models are essential for regulatory biology Systematic reconstruction of molecular pathway signatures using scalable single-cell perturbation screens

Reference 2023

Resolution: verified fuzzy; raw_fallback, observed 2026-08-09T21:06:20.090595Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Observation 2b43867e-f276-4dfe-9c46-2185f9a20495 · outbound

This paper cites Deep learning-based predictions of gene perturbation effects do not yet outperform simple linear methods.

No Foundations without Foundations -- Why semi-mechanistic models are essential for regulatory biology Deep learning-based predictions of gene perturbation effects do not yet outperform simple linear methods

Reference 2024

Resolution: verified fuzzy; raw_fallback, observed 2026-08-09T21:06:20.193104Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.

Pith citing papers

Observation 70d15ae2-2cd9-4457-b584-332d1f1a81a4 · inbound

When three experiments are better than two: Avoiding intractable correlated aleatoric uncertainty by leveraging a novel bias--variance tradeoff cites this paper.

When three experiments are better than two: Avoiding intractable correlated aleatoric uncertainty by leveraging a novel bias--variance tradeoff No Foundations without Foundations -- Why semi-mechanistic models are essential for regulatory biology

Reference 6

Resolution: unresolved; no resolver link, observed 2026-08-05T10:19:24.458421Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation afd3d5fd-02e6-4bc8-a379-c80c0516ee36 · inbound

Chem-PerturBridge: a harmonized compendium of small molecule perturbation transcriptomic effects cites this paper.

Chem-PerturBridge: a harmonized compendium of small molecule perturbation transcriptomic effects No Foundations without Foundations -- Why semi-mechanistic models are essential for regulatory biology

Reference 45

Resolution: verified exact; arxiv_id, observed 2026-06-28T23:32:46.935143Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-18T06:34:40.430872+00:00.