Paper Citation Record · LEDGER

StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction

As of 4 August 2026, this Paper Citation Record lists 28 of 28 outbound references and 2 inbound Pith citation observations for arXiv:2605.16104.

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

pith.paper-citation-record.v1
2605.16104 v1

Coverage vector

measured 28 of 28 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-05-19T17:07:13.090295Z

measured 30 of 30 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 2 of 2 inbound itemization

Pith citing papers itemized under the disclosed page cap.

Source: paper_references, paper_reference_links, observed 2026-07-12T10:51:47.238632Z

measured 0 of 1 external citation measurements

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

Source: pith, observed 2026-07-01T12:35:44.097506Z

Reference resolution

28 of 28 outbound references displayed

verified exact5
verified fuzzy22
unresolved0
parse uncertain0
malformed identifier1
metadata mismatch0

External citation measurements

No source-named external measurement is stored.

Outbound references

Observation 46046052-aaff-4fce-8d69-7bbee2e831b2 · outbound

This paper cites How to build the virtual cell with artificial intelligence: Priorities and opportunities.Cell, 187(25):7045–7063.

StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction How to build the virtual cell with artificial intelligence: Priorities and opportunities.Cell, 187(25):7045–7063

Reference 1

Resolution: verified fuzzy; raw_fallback, observed 2026-05-19T17:13:09.645556Z

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 664939a2-326c-4e7a-b6d1-e05ff76f7d25 · outbound

This paper cites Digital twins in oncology: where we are and where we hope to go.BMJ oncology, 4(1):e000893.

StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction Digital twins in oncology: where we are and where we hope to go.BMJ oncology, 4(1):e000893

Reference 2

Resolution: verified fuzzy; raw_fallback, observed 2026-05-19T17:13:09.650974Z

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 3a7c0f78-7b2a-49b6-9d22-496c2dc843ac · outbound

This paper cites Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines.Nature Methods, 22(8):1657–1661.

StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines.Nature Methods, 22(8):1657–1661

Reference 3

Resolution: verified fuzzy; raw_fallback, observed 2026-05-19T17:13:09.648012Z

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 30228340-3dbf-476a-b21f-97d38630375d · outbound

This paper cites A next generation connectivity map: L1000 platform and the first 1,000,000 profiles.

StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction A next generation connectivity map: L1000 platform and the first 1,000,000 profiles

Reference 4

Resolution: verified fuzzy; raw_fallback, observed 2026-05-19T17:13:09.627770Z

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 d2b58a1d-0e33-4c20-85e1-d8948e399890 · outbound

This paper cites A pre-trained large generative model for translating single-cell transcriptomes to proteomes.Nature Biomedical Engineering, pages 1–20.

StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction A pre-trained large generative model for translating single-cell transcriptomes to proteomes.Nature Biomedical Engineering, pages 1–20

Reference 5

Resolution: verified fuzzy; raw_fallback, observed 2026-05-19T17:13:09.643652Z

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 ff640afa-a85d-4cbc-8c67-c214d4e9ff2e · outbound

This paper cites sclinguist: A pre-trained hyena-based foundation model for cross-modality translation in single-cell multi-omics.bioRxiv, pages 2025–09.

StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction sclinguist: A pre-trained hyena-based foundation model for cross-modality translation in single-cell multi-omics.bioRxiv, pages 2025–09

Reference 6

Resolution: verified fuzzy; raw_fallback, observed 2026-05-19T17:13:09.639471Z

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 8b6aac98-c10d-434f-926b-3bbbdd8d7a0c · outbound

This paper cites A Closer Look at Multimodal Representation Collapse.

StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction A Closer Look at Multimodal Representation Collapse

Reference 7

Resolution: verified exact; arxiv_id, observed 2026-05-19T17:07:41.501815Z

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 64089996-e979-4d6c-94a0-e605384892cc · outbound

This paper cites Factorized contrastive learning: Going beyond multi-view redundancy.Advances in Neural Information Processing Systems, 36:32971–32998.

StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction Factorized contrastive learning: Going beyond multi-view redundancy.Advances in Neural Information Processing Systems, 36:32971–32998

Reference 8

Resolution: verified fuzzy; raw_fallback, observed 2026-05-19T17:13:09.639262Z

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 e778b015-119e-4ca9-82c4-2a18f4717a60 · outbound

This paper cites Alexander Wolf, and Fabian J.

StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction Alexander Wolf, and Fabian J

Reference 9

Resolution: verified fuzzy; raw_fallback, observed 2026-05-19T17:13:09.652716Z

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 4d28c8e6-9246-42ce-8eb5-63dfa881c354 · outbound

This paper cites Predicting transcriptional responses to novel chemical perturbations using deep generative model for drug discovery.Nature Communications, 15(1):9256.

StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction Predicting transcriptional responses to novel chemical perturbations using deep generative model for drug discovery.Nature Communications, 15(1):9256

Reference 10

Resolution: verified fuzzy; raw_fallback, observed 2026-05-19T17:13:09.625890Z

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 74ecdc34-56ef-422a-bdb4-ead0cf82a379 · outbound

This paper cites Predicting cellular responses to novel drug perturbations at a single-cell resolution.

StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction Predicting cellular responses to novel drug perturbations at a single-cell resolution

Reference 11

Resolution: verified fuzzy; raw_fallback, observed 2026-05-19T17:13:09.647331Z

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 2148a01b-6cb3-4d11-a8d3-e4005a429846 · outbound

This paper cites Predicting drug responses of unseen cell types through transfer learning with foundation models.

StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction Predicting drug responses of unseen cell types through transfer learning with foundation models

Reference 12

Resolution: verified fuzzy; raw_fallback, observed 2026-05-19T17:13:09.649172Z

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 ee939236-329e-410a-ad32-d0a09a67ff13 · outbound

This paper cites Benchmarking algorithms for generalizable single-cell perturbation response prediction.Nature Methods, 23:451 – 464.

StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction Benchmarking algorithms for generalizable single-cell perturbation response prediction.Nature Methods, 23:451 – 464

Reference 13

Resolution: verified fuzzy; raw_fallback, observed 2026-05-19T17:13:09.644122Z

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 4ade5d4f-fb60-4e5d-9258-99f32dd5290a · outbound

This paper cites Conditional out-of-distribution generation for unpaired data using transfer vae.

StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction Conditional out-of-distribution generation for unpaired data using transfer vae

Reference 14

Resolution: verified fuzzy; raw_fallback, observed 2026-05-19T17:13:09.614215Z

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 ad625d84-211d-4948-b899-d367e8fdd1a3 · outbound

This paper cites A cell atlas foundation model for scalable search of similar human cells.Nature, 638(8052):1085–1094.

StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction A cell atlas foundation model for scalable search of similar human cells.Nature, 638(8052):1085–1094

Reference 15

Resolution: verified fuzzy; raw_fallback, observed 2026-05-19T17:13:09.611484Z

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 f533df28-cb0d-471e-bc53-906b347ce9df · outbound

This paper cites Adduri et al.

StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction Adduri et al

Reference 16

Resolution: verified fuzzy; raw_fallback, observed 2026-05-19T17:13:09.609584Z

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 f2d237c8-11d8-44ef-8238-73bbe57be8e9 · outbound

This paper cites A pre-trained large generative model for translating single-cell transcriptomes to proteomes.

StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction A pre-trained large generative model for translating single-cell transcriptomes to proteomes

Reference 17

Resolution: verified fuzzy; raw_fallback, observed 2026-05-19T17:13:09.607785Z

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 05b178f8-01ae-4a7b-a955-b5cc12ff47ca · outbound

This paper cites Predicting cellular responses to complex perturbations in high-throughput screens.

StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction Predicting cellular responses to complex perturbations in high-throughput screens

Reference 18

Resolution: verified fuzzy; raw_fallback, observed 2026-05-19T17:13:09.604117Z

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 b788ef02-9282-44ac-ba26-863537668fcb · outbound

This paper cites CellFlow enables generative single-cell phenotype modeling with flow matching.bioRxiv.

StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction CellFlow enables generative single-cell phenotype modeling with flow matching.bioRxiv

Reference 19

Resolution: verified fuzzy; raw_fallback, observed 2026-05-19T17:13:09.619411Z

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 eb3ad90f-ffb1-4d1b-a8a2-842037123331 · outbound

This paper cites Perturbdiff: Functional diffusion for single-cell perturbation modeling.

StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction Perturbdiff: Functional diffusion for single-cell perturbation modeling

Reference 20

Resolution: verified exact; arxiv_id, observed 2026-05-19T17:07:41.513659Z

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 2d7f4f96-1f87-4137-aa15-324f7709a6b9 · outbound

This paper cites scdfm: Distributional flow matching model for robust single-cell perturbation prediction.

StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction scdfm: Distributional flow matching model for robust single-cell perturbation prediction

Reference 21

Resolution: verified exact; arxiv_id, observed 2026-05-19T17:07:41.510586Z

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 6a31b347-1588-443f-80a3-7bfa652ab5a8 · outbound

This paper cites Uni-mol: A universal 3d molecular representation learning framework.

StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction Uni-mol: A universal 3d molecular representation learning framework

Reference 22

Resolution: verified fuzzy; raw_fallback, observed 2026-05-19T17:13:09.649866Z

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 242bb037-887b-412a-9246-b0ec8f74362b · outbound

This paper cites Denoising Diffusion Implicit Models.

StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction Denoising Diffusion Implicit Models

Reference 23

Resolution: verified exact; local_arxiv, observed 2026-05-19T17:07:41.504407Z

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 d95b27bb-d9c6-4bf6-918b-d0ae9e14c3fe · outbound

This paper cites The cardiac glycoside convallatoxin inhibits the growth of colorectal cancer cells in a p53-independent manner.Molecular genetics and metabolism reports, 13:42–45.

StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction The cardiac glycoside convallatoxin inhibits the growth of colorectal cancer cells in a p53-independent manner.Molecular genetics and metabolism reports, 13:42–45

Reference 24

Resolution: verified fuzzy; raw_fallback, observed 2026-05-19T17:13:09.651763Z

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 8d44ec4a-04bf-44e6-a784-bbfd00661b4e · outbound

This paper cites Chemistry and anticancer activity of cardiac glycosides: A review.Chemical Biology & Drug Design, 100(3):364–375.

StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction Chemistry and anticancer activity of cardiac glycosides: A review.Chemical Biology & Drug Design, 100(3):364–375

Reference 25

Resolution: verified fuzzy; raw_fallback, observed 2026-05-19T17:13:09.615322Z

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 3cd3fde6-8947-4db8-b7e8-5c8e177e86ed · outbound

This paper cites Corum: the comprehensive resource of mammalian protein complexes—2019.Nucleic acids research, 47(D1):D559–D563.

StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction Corum: the comprehensive resource of mammalian protein complexes—2019.Nucleic acids research, 47(D1):D559–D563

Reference 26

Resolution: verified fuzzy; raw_fallback, observed 2026-05-19T17:13:09.631286Z

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 cae5721b-ab1d-4b60-887d-0b720410cb3c · outbound

This paper cites Progressive Distillation for Fast Sampling of Diffusion Models.

StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction Progressive Distillation for Fast Sampling of Diffusion Models

Reference 27

Resolution: verified exact; local_arxiv, observed 2026-05-19T17:07:41.507645Z

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 1d958d7c-51b0-4433-b844-f62128c67b8b · outbound

This paper cites Common- DEGs.

StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction Common- DEGs

Reference 28

Resolution: malformed identifier; raw_fallback, observed 2026-05-19T17:13:09.637517Z

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.

Pith citing papers

Observation 90de2080-b732-4401-a657-761c6208f189 · inbound

Modeling Cell-Cycle-Aware Single-Cell Drug Perturbation Responses cites this paper.

Modeling Cell-Cycle-Aware Single-Cell Drug Perturbation Responses StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction

Reference 16

Resolution: verified exact; local_arxiv, observed 2026-07-01T12:35:44.098935Z

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 3aaea291-39e9-46b5-bfab-cebd21354030 · inbound

Modeling Cell-Cycle-Aware Single-Cell Drug Perturbation Responses cites this paper.

Modeling Cell-Cycle-Aware Single-Cell Drug Perturbation Responses StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction

Reference 19

Resolution: unresolved; no resolver link, observed 2026-07-12T10:51:47.238632Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.