Evidence map›Paper›PMID 40914154›Full record

ArticleCell reports methods2025

SuperGLUE facilitates an explainable training framework for multi-modal data analysis.

Tianyu Liu, Jia Zhao, Hongyu Zhao

Abstract read
In one paragraph

Article in Cell reports methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Review
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

3 authors.

Tianyu LiuInterdepartmental Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT 06511, USA; Department of Biostatistics, Yale University, New Haven, CT 06511, USA.
Jia ZhaoDepartment of Biostatistics, Yale University, New Haven, CT 06511, USA.
Hongyu ZhaoInterdepartmental Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT 06511, USA; Department of Biostatistics, Yale University, New Haven, CT 06511, USA. Electronic address: hongyu.zhao@yale.edu.

Funding

Laboratory, Data Analysis, and Coordinating Center (LDACC) for the Developmental Human Genotype-Tissue Expression ProjectU24HG012108 · NHGRI · YALE UNIVERSITY · PI GERSTEIN, MARK BENDER, HUTTNER, ANITA JULIANE · 2021 to 2025
$8.7M
Computational and Statistical Methods to determine variant effect across cell types and development stagesU01HG013840 · NHGRI · YALE UNIVERSITY · PI GERSTEIN, MARK BENDER, ZHAO, HONGYU · 2024 to 2024
$1.9M
NHGRI NIH HHS U01 HG013840NHGRI NIH HHS U24 HG012108
6 · The paper itself

Abstract

Single-cell multi-modal data integration has been an area of active research in recent years. However, it is difficult to unify the integration process of different omics in a pipeline and evaluate the contributions of data integration. In this article, we revisit the definition and contributions of multi-modal data integration and propose a strong and scalable method based on probabilistic deep learning with an explainable framework powered by statistical modeling to extract meaningful information after data integration. Our proposed method is capable of integrating different types of omics and sensing data. It offers an approach to discovering important relationships among biological features or cell states. We demonstrate that our method outperforms other baseline models in preserving both local and global structures and perform a comprehensive analysis for mining structural relationships in complex biological systems, including inference of gene regulatory networks, extraction of significant biological linkages, and analysis of differentially regulatory relationships.

Indexed as

Computational BiologyData AnalysisDeep LearningSingle-Cell AnalysisAlgorithmsGene Regulatory NetworksHumansCP: Computational biologyCP: Systems biologyembeddingsgene regulatory network inferencemulti-omics data analysisperturbation analysissingle-cell sequencing

Identifiers

PMID40914154
PMCPMC12539260

What OpenQuestion holds

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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.