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Author:

Zhang, Jinli (Zhang, Jinli.) | Ren, Hongwei (Ren, Hongwei.) | Jiang, Zongli (Jiang, Zongli.) (Scholars:蒋宗礼) | Chen, Zheng (Chen, Zheng.) | Yang, Ziwei (Yang, Ziwei.) | Matsubara, Yasuko (Matsubara, Yasuko.) | Sakurai, Yasushi (Sakurai, Yasushi.)

Indexed by:

EI Scopus SCIE

Abstract:

The analysis and comprehension of multi-omics data has emerged as a prominent topic in the field of bioinformatics and data science. However, the sparsity characteristics and high dimensionality of omics data pose difficulties in terms of extracting meaningful information. Moreover, the heterogeneity inherent in multiple omics sources makes the effective integration of multi-omics data challenging To tackle these challenges, we propose MFCC-SAtt, a multi-level feature contrast clustering model based on self-attention to extract informative features from multi-omics data. MFCC-SAtt treats each omics type as a distinct modality and employs autoencoders with self-attention for each modality to integrate and compress their respective features into a shared feature space. By utilizing a multi-level feature extraction framework along with incorporating a semantic information extractor, we mitigate optimization conflicts arising from different learning objectives. Additionally, MFCC-SAtt guides deep clustering based on multi-level features which further enhances the quality of output labels. By conducting extensive experiments on multi-omics data, we have validated the exceptional performance of MFCC-SAtt. For instance, in a pan-cancer clustering task, MFCC-SAtt achieved an accuracy of over 80.38%.

Keyword:

Multi-omics clustering contrastive learning self-attention

Author Community:

  • [ 1 ] [Zhang, Jinli]Beijing Univ Technol, Dept Comp Sci, Beijing 100022, Peoples R China
  • [ 2 ] [Ren, Hongwei]Beijing Univ Technol, Dept Comp Sci, Beijing 100022, Peoples R China
  • [ 3 ] [Jiang, Zongli]Beijing Univ Technol, Dept Comp Sci, Beijing 100022, Peoples R China
  • [ 4 ] [Chen, Zheng]Osaka Univ, Inst Sci & Ind Res, Suita, Osaka 5650871, Japan
  • [ 5 ] [Matsubara, Yasuko]Osaka Univ, Inst Sci & Ind Res, Suita, Osaka 5650871, Japan
  • [ 6 ] [Sakurai, Yasushi]Osaka Univ, Inst Sci & Ind Res, Suita, Osaka 5650871, Japan
  • [ 7 ] [Yang, Ziwei]Kyoto Univ, Bioinformat Ctr, Kyoto 6158540, Japan

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Source :

IEEE TRANSACTIONS ON NANOBIOSCIENCE

ISSN: 1536-1241

Year: 2024

Issue: 4

Volume: 23

Page: 579-590

3 . 9 0 0

JCR@2022

Cited Count:

WoS CC Cited Count:

SCOPUS Cited Count: 1

ESI Highly Cited Papers on the List: 0 Unfold All

WanFang Cited Count:

Chinese Cited Count:

30 Days PV: 2

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