Development and validation of a cuproptosis-related prognostic model for acute myeloid leukemia patients using machine learning with stacking.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38307903", "kind": "science-record", "revision": 2, "content_hash": "sha256:2702a28723b63f2fa71929c1901434c00ef5d0f0d50318168d445e9df4ae5333", "created_at": "2026-11-01T19:20:14Z", "updated_at": "2026-11-01T21:32:26Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Development and validation of a cuproptosis-related prognostic model for acute myeloid leukemia patients using machine learning with stacking.", "doi": "10.1038/s41598-024-53306-7", "pmid": "38307903", "authors": ["Xichao Wang", "Hao Sun", "Yongfei Dong", "Jie Huang", "Lu Bai", "Zaixiang Tang", "Songbai Liu", "Suning Chen"], "journal": "Scientific reports", "year": 2024, "abstract": "Our objective is to develop a prognostic model focused on cuproptosis, aimed at predicting overall survival (OS) outcomes among Acute myeloid leukemia (AML) patients. The model utilized machine learning algorithms incorporating stacking. The GSE37642 dataset was used as the training data, and the GSE12417 and TCGA-LAML cohorts were used as the validation data. Stacking was used to merge the three prediction models, subsequently using a random survival forests algorithm to refit the final model using the stacking linear predictor and clinical factors. The prediction model, featuring stacking linear predictor and clinical factors, achieved AUC values of 0.840, 0.876 and 0.892 at 1, 2 and 3 years within the GSE37642 dataset. In external validation dataset, the corresponding AUCs were 0.741, 0.754 and 0.783. The predictive performance of the model in the external dataset surpasses that of the model simply incorporates all predictors. Additionally, the final model exhibited good calibration accuracy. In conclusion, our findings indicate that the novel prediction model refines the prognostic prediction for AML patients, while the stacking strategy displays potential for model integration.", "claims": [{"id": "claim-data-access", "statement": "Raw microarray datasets of GSE37642 and GSE12417 were downloaded from GEO database. (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37642, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12417). RNA-seq data and corresponding clinical information in TCGA-LAML database were downloaded from the Genomic Data Commons Data Portal (https://portal.gdc.cancer.gov/repository). The transcriptome data and clinical information for the BeatAML cohort during this study are included in the published article (and its Supplementary Information files). (Functional genomic landscape of acute myeloid leukaemia | Nature).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38307903", "locator": "sections[25] \"Data availability\" paragraph 2", "quote": "Raw microarray datasets of GSE37642 and GSE12417 were downloaded from GEO database. (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37642, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12417). RNA-seq data and corresponding clinical information in TCGA-LAML database were downloaded from the Genomic Data Commons Data Portal (https://portal.gdc.cancer.gov/repository). The transcriptome data and clinical information for the BeatAML cohort during this study are included in the published article (and its Supplementary Information files). (Functional genomic landscape of acute myeloid leukaemia | Nature)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The prediction model, featuring stacking linear predictor and clinical factors, achieved AUC values of 0.840, 0.876 and 0.892 at 1, 2 and 3 years within the GSE37642 dataset.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38307903", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The prediction model, featuring stacking linear predictor and clinical factors, achieved AUC values of 0.840, 0.876 and 0.892 at 1, 2 and 3 years within the GSE37642 dataset."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The prediction model, featuring stacking linear predictor and clinical factors, achieved AUC values of 0.840, 0.876 and 0.892 at 1, 2 and 3 years within the GSE37642 dataset.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:38307903"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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(https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37642, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12417). RNA-seq data and corresponding clinical information in TCGA-LAML database were downloaded from the Genomic Data Commons Data Portal (https://portal.gdc.cancer.gov/repository). The transcriptome data and clinical information for the BeatAML cohort during this study are included in the published article (and its Supplementary Information files). (Functional genomic landscape of acute myeloid leukaemia | Nature).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Raw microarray datasets of GSE37642 and GSE12417 were downloaded from GEO database. (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37642, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12417). RNA-seq data and corresponding clinical information in TCGA-LAML database were downloaded from the Genomic Data Commons Data Portal (https://portal.gdc.cancer.gov/repository). The transcriptome data and clinical information for the BeatAML cohort during this study are included in the published article (and its Supplementary Information files). 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null, "platform": "570;96;97", "taxon": "Homo sapiens", "title": "Prognostic gene signature for AML", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE12417 not downloaded", "asset:data:geo:GSE12417 licence not read", "asset:data:geo:GSE37642 not downloaded", "asset:data:geo:GSE37642 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-2", "family": "correlation_analysis", "specific": "spearman", "label": "Correlation analysis", "dsl_operations": ["spearman_rho"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Spearman correlation"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["logrank_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: log_rank_test."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE37642", "GSE12417"], "resolved_accessions": ["GSE37642", "GSE12417"], "statements": ["Raw microarray datasets of GSE37642 and GSE12417 were downloaded from GEO database. (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37642, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12417). RNA-seq data and corresponding clinical information in TCGA-LAML database were downloaded from the Genomic Data Commons Data Portal (https://portal.gdc.cancer.gov/repository). The transcriptome data and clinical information for the BeatAML cohort during this study are included in the published article (and its Supplementary Information files). (Functional genomic landscape of acute myeloid leukaemia | Nature)."], "basis": "The paper names GSE37642, GSE12417 in GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["logrank_test"], "assets": ["source:pmid:38307903", "data:geo:GSE12417"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE12417"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:07:18Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 13521, "completion_tokens": 1742, "cached_tokens": 264}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:38307903", "type": "paper", "label": "pmid:38307903"}, {"id": "source:pmid:38307903", "type": "manuscript", "label": "PMID 38307903 full text"}, {"id": "data:geo:GSE12417", "type": "dataset", "label": "GEO GSE12417"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38307903", "type": "paper", "label": "pmid:38307903"}, {"id": "source:pmid:38307903", "type": "manuscript", "label": "PMID 38307903 full text"}, {"id": "data:geo:GSE12417", "type": "dataset", "label": "GEO GSE12417"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38307903", "type": "extraction", "used": ["source:pmid:38307903"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE12417", "type": "accession_resolution", "used": ["data:geo:GSE12417"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:38307903", "parent_hash": "sha256:0e99759835ad2e1e54791a665f29393d9d2d1e10b098fb399636faeecab77833", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:GSE12417 licence not read", "asset:data:geo:GSE12417 not downloaded", "asset:data:geo:GSE37642 licence not read", "asset:data:geo:GSE37642 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["logrank_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["log-rank"], "order_basis": "analysis_only", "id": "assay:1"}]}