Evidence map›Paper›PMID 39705362›Full record

ArticleScience advances2024

Quantifying interpretation reproducibility in Vision Transformer models with TAVAC.

Yue Zhao, Dylan Agyemang, Yang Liu, Matt Mahoney, Sheng Li

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 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Article
  2. Non-targeted metabolomics can identify disease-specific characteristics of ischemic stroke.Metabolomics : Official journal of the Metabolomic Society · 2025
    Article
  3. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

5 authors.

Yue ZhaoThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID 0000-0002-8764-505X
Dylan AgyemangDepartment of Mathematics and Statistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.ORCID 0009-0009-4725-663X
Yang LiuThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID 0000-0003-4433-1066
Matt MahoneyThe Jackson Laboratory for Mouse Genetics, Bar Harbor, ME, USA.ORCID 0000-0003-1425-5939
Sheng LiThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID 0000-0002-9543-6274

Funding

The Jackson Laboratory Senescence Tissue Mapping Center (JAX-Sen TMC) - Data Analysis CoreU54AG079753 · NIA · JACKSON LABORATORY · PI ROSENTHAL, NADIA A · 2022 to 2025
$11.0M
An Integrative Computational Framework for DNA Hydroxymethylation Data Mining and InterpretationR35GM133562 · NIGMS · JACKSON LABORATORY · PI LI, SHENG · 2019 to 2023
$2.4M
Multi-omic phenotyping of human transcriptional regulatorsU01HG013175 · NHGRI · JACKSON LABORATORY · PI Brian S White · 2023 to 2026
$2.2M
The impact of reduction of cellular senescence on age-related epigenetic heterogeneityU01CA271830 · NCI · UNIVERSITY OF SOUTHERN CALIFORNIA · PI DEGREGORI, JAMES V, LI, SHENG · 2021 to 2025
$1.9M
Integrating high-throughput histology with systems genetics through causal graphical modelsR01GM141309 · NIGMS · JACKSON LABORATORY · PI MAHONEY, JOHN MATTHEW · 2022 to 2025
$1.5M
Summer Undergraduate Research Fellowship in the Molecular Biology and Genomics of Human CancerR25CA233420 · NCI · JACKSON LABORATORY · PI Jeffrey Hsu-Min Chuang, Sarah Wojiski · 2019 to 2026
$866k
3D Genome Reorganization and Epigenome Dynamics of Clonal HematopoiesisR56AG071766 · NIA · JACKSON LABORATORY · PI LI, SHENG, OGURO, HIDEYUKI · 2022 to 2022
$343k
NCI NIH HHS R25 CA233420NCI NIH HHS U01 CA271830NHGRI NIH HHS U01 HG013175NIA NIH HHS R56 AG071766NIA NIH HHS U54 AG079753NIGMS NIH HHS R01 GM141309NIGMS NIH HHS R35 GM133562
6 · The paper itself

Abstract

Deep learning algorithms can extract meaningful diagnostic features from biomedical images, promising improved patient care in digital pathology. Vision Transformer (ViT) models capture long-range spatial relationships and offer robust prediction power and better interpretability for image classification tasks than convolutional neural network models. However, limited annotated biomedical imaging datasets can cause ViT models to overfit, leading to false predictions due to random noise. To address this, we introduce Training Attention and Validation Attention Consistency (TAVAC), a metric for evaluating ViT model overfitting and quantifying interpretation reproducibility. By comparing high-attention regions between training and testing, we tested TAVAC on four public image classification datasets and two independent breast cancer histological image datasets. Overfitted models showed significantly lower TAVAC scores. TAVAC also distinguishes off-target from on-target attentions and measures interpretation generalization at a fine-grained cellular level. Beyond diagnostics, TAVAC enhances interpretative reproducibility in basic research, revealing critical spatial patterns and cellular structures of biomedical and other general nonbiomedical images.

Indexed as

Deep LearningAlgorithmsBreast NeoplasmsFemaleHumansImage Interpretation, Computer-AssistedImage Processing, Computer-AssistedNeural Networks, ComputerReproducibility of Results

Identifiers

PMID39705362
PMCPMC11661421

What OpenQuestion holds

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LicenceCC BY-NC
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Registered trials

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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.