Paper Citation Record · LEDGER

Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics

As of 9 August 2026, this Paper Citation Record lists 26 of 26 outbound references and 2 inbound Pith citation observations for arXiv:2506.22641.

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

pith.paper-citation-record.v1
2506.22641 v1

Coverage vector

measured 26 of 26 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-08-06T22:08:50.370014Z

measured 28 of 28 standing notices

One-hop event checks from named stored sources.

Source: scholarly_work_events, retraction_status_cache, observed 2026-08-09T06:31:02.800959+00:00

measured 2 of 2 inbound itemization

Pith citing papers itemized under the disclosed page cap.

Source: paper_references, paper_reference_links, observed 2026-08-02T21:54:18.379945Z

measured 0 of 1 external citation measurements

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

Source: arxiv_reference, observed 2026-07-03T09:17:48.699606Z

Reference resolution

26 of 26 outbound references displayed

verified exact0
verified fuzzy21
unresolved5
parse uncertain0
malformed identifier0
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External citation measurements

No source-named external measurement is stored.

Outbound references

Observation 431db585-02db-40f9-94e4-fecbdb72efc2 · outbound

This paper cites write newline.

Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics write newline

Reference 1

Resolution: unresolved; no resolver link, observed 2026-08-06T22:08:47.494631Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation fbf09096-d75f-43fd-8fd6-dcf22210043d · outbound

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

Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics Deep learning-based predictions of gene perturbation effects do not yet outperform simple linear methods

Reference 2

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:08:54.293029Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 20ee0bd5-6f54-4579-be9e-3389bb03f93b · outbound

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

Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics Benchmarking Transcriptomics Foundation Models for Perturbation Analysis : one PCA still rules them all

Reference 3

Resolution: unresolved; no resolver link, observed 2026-08-06T22:08:47.654138Z

Source-reported events for the cited work

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Observation d111df03-28cf-4331-9afe-5fdbb245db28 · outbound

This paper cites Z., and Szalai, B.

Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics Z., and Szalai, B

Reference 4

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:08:54.074192Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation c9354c40-6b86-47cd-99c9-a356d718a429 · outbound

This paper cites scgpt: toward building a foundation model for single-cell multi-omics using generative ai.

Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics scgpt: toward building a foundation model for single-cell multi-omics using generative ai

Reference 5

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:08:53.877623Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 28ef34b4-9ecf-4db5-b996-a5bec19c61c2 · outbound

This paper cites P., Jerby-Arnon, L., Marjanovic, N.

Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics P., Jerby-Arnon, L., Marjanovic, N

Reference 6

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:08:53.719577Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation fd9a969f-459a-476b-8e01-84504e51741b · outbound

This paper cites xtrimogene: an efficient and scalable representation learner for single-cell rna-seq data.

Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics xtrimogene: an efficient and scalable representation learner for single-cell rna-seq data

Reference 7

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:08:53.468085Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation f7fd0cd7-063d-42d2-9c12-9c49de4e8f68 · outbound

This paper cites Large-scale foundation model on single-cell transcriptomics.

Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics Large-scale foundation model on single-cell transcriptomics

Reference 8

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:08:53.230736Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 55e037cc-fa72-470c-8c21-77eec4940c84 · outbound

This paper cites scgenept: Is language all you need for modeling single-cell perturbations? bioRxiv, pp.\ 2024--10, 2024.

Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics scgenept: Is language all you need for modeling single-cell perturbations? bioRxiv, pp.\ 2024--10, 2024

Reference 9

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:08:53.044644Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 936bf756-7390-48b7-a3c7-c836e03ab4e1 · outbound

This paper cites M., Jindal, K., Solnica-Krezel, L., and Morris, S.

Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics M., Jindal, K., Solnica-Krezel, L., and Morris, S

Reference 10

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:08:52.774123Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 0115b438-990b-4c95-a7ba-c3df72bd7c5e · outbound

This paper cites Benchmarking ai models for in silico gene perturbation of cells.

Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics Benchmarking ai models for in silico gene perturbation of cells

Reference 11

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:08:52.593683Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation f5743834-d4f0-476a-8d83-92e39845cf65 · outbound

This paper cites A systematic comparison of single-cell perturbation response prediction models.

Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics A systematic comparison of single-cell perturbation response prediction models

Reference 12

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:08:52.408294Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation add3437d-7a48-4a23-94e2-b8c31cb87fec · outbound

This paper cites B., Jordan, M.

Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics B., Jordan, M

Reference 13

Resolution: unresolved; no resolver link, observed 2026-08-06T22:08:48.841377Z

Source-reported events for the cited work

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Observation 455f0cc6-dd11-43aa-a6f2-a12c1c5c8133 · outbound

This paper cites A., and Theis, F.

Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics A., and Theis, F

Reference 14

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:08:52.248726Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 9db7976c-e0b4-4739-9363-61cb3399fa3c · outbound

This paper cites L., Srivatsan, S.

Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics L., Srivatsan, S

Reference 15

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:08:52.078137Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation ba7a04f8-b553-4c1a-a4ae-40a3380a06f8 · outbound

This paper cites M., Pogson, A.

Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics M., Pogson, A

Reference 16

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:08:51.940784Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation aa7c8876-d63d-4229-81de-98858db063ea · outbound

This paper cites M., Horlbeck, M.

Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics M., Horlbeck, M

Reference 17

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:08:51.779228Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 0a51b35a-a533-4ad5-92bf-d5d323373183 · outbound

This paper cites D., Shen, C., Gross, T., Min, J., Garda, S., Yuan, B., Schumacher, L.

Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics D., Shen, C., Gross, T., Min, J., Garda, S., Yuan, B., Schumacher, L

Reference 18

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:08:51.630586Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation f9d44e03-1cf6-4aef-8ad0-627ec38d1472 · outbound

This paper cites M., Saunders, R.

Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics M., Saunders, R

Reference 19

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:08:51.458060Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 462d417b-f988-4fd2-bd31-e5b19819f5c3 · outbound

This paper cites Predicting transcriptional outcomes of novel multigene perturbations with gears.

Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics Predicting transcriptional outcomes of novel multigene perturbations with gears

Reference 20

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:08:51.288999Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 9fe33136-784b-413f-8449-3380ea193a58 · outbound

This paper cites S., Quake, S.

Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics S., Quake, S

Reference 21

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:08:51.144913Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 9143a31d-d7dd-412c-a60b-41cffbb1e2e5 · outbound

This paper cites scperb: Predict single-cell perturbation via style transfer-based variational autoencoder.

Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics scperb: Predict single-cell perturbation via style transfer-based variational autoencoder

Reference 22

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:08:50.994175Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 1243705a-9262-4e6c-909c-3c067fac29da · outbound

This paper cites V., Xiao, L., Chopra, A., Chaffin, M.

Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics V., Xiao, L., Chopra, A., Chaffin, M

Reference 23

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:08:50.856069Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 3477458b-0559-419f-a7a2-eb35818d48cf · outbound

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

Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics Perteval-scfm: Benchmarking single-cell foundation models for perturbation effect prediction

Reference 24

Resolution: unresolved; no resolver link, observed 2026-08-06T22:08:50.155586Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation aae4c80a-d27b-4224-ba11-1a4b16108579 · outbound

This paper cites A., Angerer, P., and Theis, F.

Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics A., Angerer, P., and Theis, F

Reference 25

Resolution: verified fuzzy; raw_fallback, observed 2026-08-06T22:08:50.665821Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.

Observation 5cf37302-22db-47f7-a9b9-88bbc1a36ff7 · outbound

This paper cites M., Nassar, M., Osi \'n ski, B., Eksi, R., Zhang, K., and Graepel, T.

Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics M., Nassar, M., Osi \'n ski, B., Eksi, R., Zhang, K., and Graepel, T

Reference 26

Resolution: unresolved; no resolver link, observed 2026-08-06T22:08:50.370014Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Pith citing papers

Observation df93421d-cb33-4b0e-a864-05593006b92c · inbound

Learning Adaptive Perturbation-Conditioned Contexts for Robust Transcriptional Response Prediction cites this paper.

Learning Adaptive Perturbation-Conditioned Contexts for Robust Transcriptional Response Prediction Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics

Reference 2023

Resolution: unresolved; no resolver link, observed 2026-08-02T21:54:18.379945Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 1223b22d-dfd7-4ae7-977f-29bd24dc8083 · inbound

The Metric Picks the Winner: Evaluation Choice Flips Model Rankings for Drug-Response Prediction in Unseen Chemistry cites this paper.

The Metric Picks the Winner: Evaluation Choice Flips Model Rankings for Drug-Response Prediction in Unseen Chemistry Diversity by Design: Addressing Mode Collapse Improves scRNA-seq Perturbation Modeling on Well-Calibrated Metrics

Reference 9

Resolution: verified exact; arxiv_id, observed 2026-07-03T09:17:48.701303Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-09T06:31:02.800959+00:00.