Evidence map›Paper›PMID 40166226›Full record

ArticlebioRxiv : the preprint server for biology2025

Thuong Nguyen, Vandana Panwar, Vipul Jamale, Averi Perny, Cecilia Dusek, Qi Cai, Payal Kapur, Gaudenz Danuser, Satwik Rajaram

Abstract readPreprint
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Thuong NguyenLyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA.ORCID 0000-0003-3466-5337
Vandana PanwarDepartment of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Vipul JamaleLyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Averi PernyLyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Cecilia DusekDepartment of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Qi CaiDepartment of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Payal KapurDepartment of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Gaudenz DanuserLyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA.ORCID 0000-0001-8583-2014
Satwik RajaramLyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA.

Funding

University of Texas Southwestern Medical Center SPORE in Kidney CancerP50CA196516 · NCI · UT SOUTHWESTERN MEDICAL CENTER · PI Payal Kapur, Payal Kapur · 2016 to 2026
$24.7M
Functional causality in regulating cell morphogenesisR35GM136428 · NIGMS · UT SOUTHWESTERN MEDICAL CENTER · PI DANUSER, GAUDENZ · 2020 to 2024
$4.1M
NCI NIH HHS P50 CA196516NIGMS NIH HHS R35 GM136428
6 · The paper itself

Abstract

Deep learning (DL) has excelled in tissue image classification, presenting opportunities to discover biological behaviors escaping visual inspection. However, the methods to produce fine-grained insights from spatially scattered information do not exist. Here, we introduce Delta-Marches, a framework for mechanistic interpretability that leverages generative models to produce high-fidelity images from semantic latent representations. By identifying directions in this space corresponding to class transitions, we simulate controlled morphological changes between classes. Comparing each image to its class-shifted counterpart enables a secondary model to nominate features most affected by the shift. This approach overcomes sample-to-sample variability and yields idealized, interpretable transformations at subcellular resolution. We prototype the approach in the context of histopathological grading of clear cell renal cell carcinoma. Delta-Marches generate synthetic grade transitions indistinguishable from real images and autonomously pinpoints nuclear enlargement and increased nucleolar count in tumor cells as key properties of higher grades - features identifiable only through the method's subcellular precision. In addition to these features mirroring clinical criteria, it also reveals reduced vasculature, a pattern reported in multiple studies but absent from standard grading rubrics. These results indicate Delta-March's potential to convert complex and spatially-distributed features into rules for image classification.

Identifiers

PMID40166226
PMCPMC11956981

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.