Evidence map›Paper›PMID 39546597›Full record

ArticleScience advances2024

Generative adversarial networks accurately reconstruct pan-cancer histology from pathologic, genomic, and radiographic latent features.

Frederick M Howard, Hanna M Hieromnimon, Siddhi Ramesh, James Dolezal, Sara Kochanny, Qianchen Zhang, Brad Feiger, Joseph Peterson, Cheng Fan, Charles M Perou and 5 more

Abstract read
In one paragraph

Article in Science advances, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
17citing papers in PubMed, 2 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

17 citing papers in PubMed, 2 syntheses or guidelines pooled it.

  1. Pooled it
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  4. Artificial intelligence virtual bone organoids (AIVBOs).Journal of orthopaedic translation · 2026
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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

15 authors.

Frederick M HowardDepartment of Medicine, University of Chicago, Chicago, IL, USA.ORCID 0000-0002-6039-1141
Hanna M HieromnimonDepartment of Medicine, University of Chicago, Chicago, IL, USA.ORCID 0000-0001-8727-5290
Siddhi RameshDepartment of Medicine, University of Chicago, Chicago, IL, USA.
James DolezalGeisinger Cancer Institute, Danville, PA, USA.ORCID 0000-0002-6788-7203
Sara KochannyDepartment of Medicine, University of Chicago, Chicago, IL, USA.ORCID 0000-0003-3755-1175
Qianchen ZhangDepartment of Medicine, University of Chicago, Chicago, IL, USA.
Brad FeigerSimBioSys, Chicago, IL, USA.
Joseph PetersonSimBioSys, Chicago, IL, USA.ORCID 0000-0003-0989-5288
Cheng FanLineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.ORCID 0000-0002-4658-959X
Charles M PerouLineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.ORCID 0000-0001-9827-2247
Jasmine VickeryDepartment of Pathology, University of Pennsylvania Health System, Pennsylvania, PA, USA.ORCID 0009-0008-6946-8847
Megan SullivanDepartment of Pathology, NorthShore University HealthSystem, Evanston, IL, USA.ORCID 0009-0005-0687-6841
Kimberly ColeDepartment of Pathology, University of Chicago, Chicago, IL, USA.
Galina KhramtsovaDepartment of Pathology, University of Chicago, Chicago, IL, USA.ORCID 0000-0001-9625-1549
Alexander T PearsonDepartment of Medicine, University of Chicago, Chicago, IL, USA.ORCID 0000-0003-2801-7456

Funding

Tissue Procurement & PathologyP50CA058223 · NCI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI CHARLES M PEROU · 1992 to 2026
$59.3M
UNC-CH CENTER FOR ENVIRONMENTAL HEALTH &SUSCEPTIBILITYP30ES010126 · NIEHS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Stephanie Engel · 2001 to 2026
$36.3M
The Funding Mechanism of the Pilot TrialR01CA276652 · NCI · UNIVERSITY OF CHICAGO · PI Hiroyuki Abe, Gregory S. Karczmar · 2023 to 2026
$5.0M
Integrating Clinical, Pathologic, and Immune Features to Predict Breast Cancer Recurrence and Chemotherapy BenefitK08CA283261 · NCI · UNIVERSITY OF CHICAGO · PI Frederick Matthew Howard · 2023 to 2026
$806k
Deep learning for oral premalignancy evaluationR56DE030958 · NIDCR · UNIVERSITY OF CHICAGO · PI PEARSON, ALEXANDER THOMAS · 2021 to 2021
$331k
NCI NIH HHS K08 CA283261NCI NIH HHS P50 CA058223NCI NIH HHS R01 CA276652NIDCR NIH HHS R56 DE030958NIEHS NIH HHS P30 ES010126
6 · The paper itself

Abstract

Artificial intelligence models have been increasingly used in the analysis of tumor histology to perform tasks ranging from routine classification to identification of molecular features. These approaches distill cancer histologic images into high-level features, which are used in predictions, but understanding the biologic meaning of such features remains challenging. We present and validate a custom generative adversarial network-HistoXGAN-capable of reconstructing representative histology using feature vectors produced by common feature extractors. We evaluate HistoXGAN across 29 cancer subtypes and demonstrate that reconstructed images retain information regarding tumor grade, histologic subtype, and gene expression patterns. We leverage HistoXGAN to illustrate the underlying histologic features for deep learning models for actionable mutations, identify model reliance on histologic batch effect in predictions, and demonstrate accurate reconstruction of tumor histology from radiographic imaging for a "virtual biopsy."

Indexed as

GenomicsNeoplasmsAlgorithmsDeep LearningHumansImage Processing, Computer-AssistedNeural Networks, Computer

Identifiers

PMID39546597
PMCPMC11567005

What OpenQuestion holds

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LicenceCC BY-NC
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.