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CPPC Supplementary Note S1: implementation of methods and hyperparameter selection

Supplement 1 (media-1.pdf) of 10.64898/2026.05.21.726863v1 · Preprint

DOI: 10.64898/2026.05.21.726863 Original source

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16 evidence claims

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CPPC original submission row 2 (PPI_Weighted): facets.method_types: Facets: method types ["supervised_machine_learning"] (CPPC Supplementary Note S1, PPI_Weighted: features averaged over STRING-network neighbours, then a fitted predictor)
CPPC original submission row 3 (GWPS_K562 (H2M)): facets.method_types: Facets: method types ["supervised_machine_learning"] (CPPC Supplementary Note S1, GWPS_K562_H2M: "An MLP regressor with a single hidden layer of latent dimension 10 is then trained")
CPPC original submission row 4 (14Features): facets.method_types: Facets: method types ["supervised_machine_learning"] (CPPC Supplementary Note S1, 14Features: seven expression statistics on control and perturbed cells, then a fitted predictor)
CPPC original submission row 5 (scBERT): facets.method_types: Facets: method types ["foundation_model"] (CPPC Supplementary Note S1, scBERT: "extracts pretrained human gene embeddings from scBERT", reference 7 is titled "scBERT as a large-scale pretrained deep language model")
CPPC original submission row 6 (scVI): facets.method_types: Facets: method types ["supervised_machine_learning"] (CPPC Supplementary Note S1, scVI: gene embeddings from an LDVAE trained on the challenge data, then a fitted predictor)
CPPC original submission row 7 (Expression_Conditioned): facets.method_types: Facets: method types ["supervised_machine_learning"] (CPPC Supplementary Note S1, Expression_Conditioned: each gene represented by its expression across training conditions, then a fitted predictor)
CPPC original submission row 8 (Exon): facets.method_types: Facets: method types ["supervised_machine_learning"] (CPPC Supplementary Note S1, Exon: exon-length summary statistics, then a fitted predictor)
CPPC original submission row 9 (Gene2Vec): facets.method_types: Facets: method types ["supervised_machine_learning"] (CPPC Supplementary Note S1, Gene2Vec: pretrained gene2vec gene embeddings, then a fitted predictor)
CPPC original submission row 12 (5Features): facets.method_types: Facets: method types ["supervised_machine_learning"] (CPPC Supplementary Note S1, 5Features: expression summary statistics and cell-state marker expression, then a fitted predictor)
CPPC original submission row 16 (scETM): facets.method_types: Facets: method types ["supervised_machine_learning"] (CPPC Supplementary Note S1, scETM: gene embeddings from scETM trained on the challenge data, then a fitted predictor)
CPPC original submission row 17 (scTenifoldNet): facets.method_types: Facets: method types ["supervised_machine_learning"] (CPPC Supplementary Note S1, "Implementation of additional methods": scTenifoldNet virtual knockout, then "trains a random forest classifier" to select genes)
CPPC original submission row 18 (GO_knn): facets.method_types: Facets: method types ["conventional_pipeline"] (CPPC Supplementary Note S1, GO_knn: the weighted average of the cell state proportions of the three most similar training perturbations; main-text Methods: "does not use an explicit predictor")
CPPC original submission row 19 (LowExp): facets.method_types: Facets: method types ["conventional_pipeline"] (CPPC Supplementary Note S1, LowExp: proportions taken from the state annotations of the 5,000 training cells with the lowest expression of the gene)
CPPC original submission row 21 (interv): facets.method_types: Facets: method types ["supervised_machine_learning"] (CPPC Supplementary Note S1, Interv: LASSO cell-state classification and local LiNGAM regression)
CPPC original submission row 22 (GO-node2vec): facets.method_types: Facets: method types ["supervised_machine_learning"] (CPPC Supplementary Note S1, GO-node2vec: Node2Vec embeddings of the gene ontology, then a fitted predictor)
CPPC original submission row 24 (GeneVector): facets.method_types: Facets: method types ["supervised_machine_learning"] (CPPC Supplementary Note S1, GeneVector: pretrained GeneVector gene embeddings, then a fitted predictor)

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28 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statement	Original source and location	Review and provenance
Archive note Not archived in this batch. Source metadata	CPPC Supplementary Note S1: implementation of methods and hyperparameter selection Original source ↗ No field-specific location recorded Version: Supplement 1 (media-1.pdf) of 10.64898/2026.05.21.726863v1 Retrieved: 2026-10-12T13:55:50Z	catalogued No individual claim review recorded Audit details Field: `attributes.archive_note` Source artifact SHA-256: `80ee7ad255296a5650247f06bb1915af12adf6644c2b619417d6940e77368e9b` Hash scope: artifact_sha256 is the SHA-256 of the extracted member media-1.pdf. The archive digest describes one retrieval; a first download of the same URL was truncated and is not recorded. The licence is the article's, as printed in the Europe PMC full-text XML (PMC13228547). Archive member: media-1.pdf Inspected artifact
Archive sha256 d120cd4b0109835ca16d32cb4e909b17336ff0afc911bd81817fe7006aeaee8e Source metadata	CPPC Supplementary Note S1: implementation of methods and hyperparameter selection Original source ↗ No field-specific location recorded Version: Supplement 1 (media-1.pdf) of 10.64898/2026.05.21.726863v1 Retrieved: 2026-10-12T13:55:50Z	catalogued No individual claim review recorded Audit details Field: `attributes.archive_sha256` Source artifact SHA-256: `80ee7ad255296a5650247f06bb1915af12adf6644c2b619417d6940e77368e9b` Hash scope: artifact_sha256 is the SHA-256 of the extracted member media-1.pdf. The archive digest describes one retrieval; a first download of the same URL was truncated and is not recorded. The licence is the article's, as printed in the Europe PMC full-text XML (PMC13228547). Archive member: media-1.pdf Inspected artifact
Artifact member media-1.pdf Source metadata	CPPC Supplementary Note S1: implementation of methods and hyperparameter selection Original source ↗ No field-specific location recorded Version: Supplement 1 (media-1.pdf) of 10.64898/2026.05.21.726863v1 Retrieved: 2026-10-12T13:55:50Z	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_member` Source artifact SHA-256: `80ee7ad255296a5650247f06bb1915af12adf6644c2b619417d6940e77368e9b` Hash scope: artifact_sha256 is the SHA-256 of the extracted member media-1.pdf. The archive digest describes one retrieval; a first download of the same URL was truncated and is not recorded. The licence is the article's, as printed in the Europe PMC full-text XML (PMC13228547). Archive member: media-1.pdf Inspected artifact
Artifact SHA-256 80ee7ad255296a5650247f06bb1915af12adf6644c2b619417d6940e77368e9b Source metadata	CPPC Supplementary Note S1: implementation of methods and hyperparameter selection Original source ↗ No field-specific location recorded Version: Supplement 1 (media-1.pdf) of 10.64898/2026.05.21.726863v1 Retrieved: 2026-10-12T13:55:50Z	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_sha256` Source artifact SHA-256: `80ee7ad255296a5650247f06bb1915af12adf6644c2b619417d6940e77368e9b` Hash scope: artifact_sha256 is the SHA-256 of the extracted member media-1.pdf. The archive digest describes one retrieval; a first download of the same URL was truncated and is not recorded. The licence is the article's, as printed in the Europe PMC full-text XML (PMC13228547). Archive member: media-1.pdf Inspected artifact
Artifact url https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13228547/supplementaryFiles Source metadata	CPPC Supplementary Note S1: implementation of methods and hyperparameter selection Original source ↗ No field-specific location recorded Version: Supplement 1 (media-1.pdf) of 10.64898/2026.05.21.726863v1 Retrieved: 2026-10-12T13:55:50Z	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_url` Source artifact SHA-256: `80ee7ad255296a5650247f06bb1915af12adf6644c2b619417d6940e77368e9b` Hash scope: artifact_sha256 is the SHA-256 of the extracted member media-1.pdf. The archive digest describes one retrieval; a first download of the same URL was truncated and is not recorded. The licence is the article's, as printed in the Europe PMC full-text XML (PMC13228547). Archive member: media-1.pdf Inspected artifact
Doi 10.64898/2026.05.21.726863 Source metadata	CPPC Supplementary Note S1: implementation of methods and hyperparameter selection Original source ↗ No field-specific location recorded Version: Supplement 1 (media-1.pdf) of 10.64898/2026.05.21.726863v1 Retrieved: 2026-10-12T13:55:50Z	catalogued No individual claim review recorded Audit details Field: `attributes.doi` Source artifact SHA-256: `80ee7ad255296a5650247f06bb1915af12adf6644c2b619417d6940e77368e9b` Hash scope: artifact_sha256 is the SHA-256 of the extracted member media-1.pdf. The archive digest describes one retrieval; a first download of the same URL was truncated and is not recorded. The licence is the article's, as printed in the Europe PMC full-text XML (PMC13228547). Archive member: media-1.pdf Inspected artifact
Hash scope artifact_sha256 is the SHA-256 of the extracted member media-1.pdf. The archive digest describes one retrieval; a first download of the same URL was truncated and is not recorded. The licence is the article's, as printed in the Europe PMC full-text XML (PMC13228547). Source metadata	CPPC Supplementary Note S1: implementation of methods and hyperparameter selection Original source ↗ No field-specific location recorded Version: Supplement 1 (media-1.pdf) of 10.64898/2026.05.21.726863v1 Retrieved: 2026-10-12T13:55:50Z	catalogued No individual claim review recorded Audit details Field: `attributes.hash_scope` Source artifact SHA-256: `80ee7ad255296a5650247f06bb1915af12adf6644c2b619417d6940e77368e9b` Hash scope: artifact_sha256 is the SHA-256 of the extracted member media-1.pdf. The archive digest describes one retrieval; a first download of the same URL was truncated and is not recorded. The licence is the article's, as printed in the Europe PMC full-text XML (PMC13228547). Archive member: media-1.pdf Inspected artifact
Licence CC-BY-NC-ND-4.0 Source metadata	CPPC Supplementary Note S1: implementation of methods and hyperparameter selection Original source ↗ No field-specific location recorded Version: Supplement 1 (media-1.pdf) of 10.64898/2026.05.21.726863v1 Retrieved: 2026-10-12T13:55:50Z	catalogued No individual claim review recorded Audit details Field: `attributes.licence` Source artifact SHA-256: `80ee7ad255296a5650247f06bb1915af12adf6644c2b619417d6940e77368e9b` Hash scope: artifact_sha256 is the SHA-256 of the extracted member media-1.pdf. The archive digest describes one retrieval; a first download of the same URL was truncated and is not recorded. The licence is the article's, as printed in the Europe PMC full-text XML (PMC13228547). Archive member: media-1.pdf Inspected artifact
Media type application/pdf Source metadata	CPPC Supplementary Note S1: implementation of methods and hyperparameter selection Original source ↗ No field-specific location recorded Version: Supplement 1 (media-1.pdf) of 10.64898/2026.05.21.726863v1 Retrieved: 2026-10-12T13:55:50Z	catalogued No individual claim review recorded Audit details Field: `attributes.media_type` Source artifact SHA-256: `80ee7ad255296a5650247f06bb1915af12adf6644c2b619417d6940e77368e9b` Hash scope: artifact_sha256 is the SHA-256 of the extracted member media-1.pdf. The archive digest describes one retrieval; a first download of the same URL was truncated and is not recorded. The licence is the article's, as printed in the Europe PMC full-text XML (PMC13228547). Archive member: media-1.pdf Inspected artifact
Publication status preprint Source metadata	CPPC Supplementary Note S1: implementation of methods and hyperparameter selection Original source ↗ No field-specific location recorded Version: Supplement 1 (media-1.pdf) of 10.64898/2026.05.21.726863v1 Retrieved: 2026-10-12T13:55:50Z	catalogued No individual claim review recorded Audit details Field: `attributes.publication_status` Source artifact SHA-256: `80ee7ad255296a5650247f06bb1915af12adf6644c2b619417d6940e77368e9b` Hash scope: artifact_sha256 is the SHA-256 of the extracted member media-1.pdf. The archive digest describes one retrieval; a first download of the same URL was truncated and is not recorded. The licence is the article's, as printed in the Europe PMC full-text XML (PMC13228547). Archive member: media-1.pdf Inspected artifact

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Sources and history

Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

Supplement 1 of the Cancer Immunotherapy Data Science Challenge preprint (Zhang et al. 2026), retrieved for the 2026-10-12 method-type corrections. It describes the authors' reimplementation of the top submissions.

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Stable ID: method-type-corrections-20261012-source-cppc-note-s1

areas: single-cell
url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13228547/supplementaryFiles
artifact url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13228547/supplementaryFiles
version: Supplement 1 (media-1.pdf) of 10.64898/2026.05.21.726863v1
retrieved at: 2026-10-12T13:55:50Z
artifact member: media-1.pdf
artifact sha256: 80ee7ad255296a5650247f06bb1915af12adf6644c2b619417d6940e77368e9b
archive sha256: d120cd4b0109835ca16d32cb4e909b17336ff0afc911bd81817fe7006aeaee8e
doi: 10.64898/2026.05.21.726863
publication status: preprint
licence: CC-BY-NC-ND-4.0
media type: application/pdf
source locator: Implementation of gene features derived from top submissions; Implementation of predictors; Implementation of additional methods
retrieval method: Europe PMC supplementaryFiles ZIP; extracted member media-1.pdf; SHA-256 identifies member bytes; archive digest recorded separately
archive note: Not archived in this batch.
hash scope: artifact_sha256 is the SHA-256 of the extracted member media-1.pdf. The archive digest describes one retrieval; a first download of the same URL was truncated and is not recorded. The licence is the article's, as printed in the Europe PMC full-text XML (PMC13228547).
review: method: source-hash-verification; automated-source-review; reviewer: claude; reviewer note: Separate Claude review agent, independent of the agent that prepared the corrections; no human review claimed; date: 2026-10-12; method note: Added by this review: the corrections cite Note S1, which no source record pinned. Extracted media-1.pdf from the Europe PMC supplementary archive, hashed it, and took the licence from the article XML.; note: Independent review 2026-10-12: approved. See docs/reviews/2026-10-12-method-type-corrections.md.

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