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Applications of single-cell RNA sequencing in various biomedical research areas have been blooming. This new technology provides unprecedented opportunities to study disease heterogeneity at the cellular level. However, unique…

Genomics · Quantitative Biology 2021-10-26 Xinlei Mi , William Bekerman , Peter A. Sims , Peter D. Canoll , Jianhua Hu

Single-cell RNA sequencing (scRNA-seq) provides unprecedented insights into cellular heterogeneity, enabling detailed analysis of complex biological systems at single-cell resolution. However, the high dimensionality and technical noise…

Genomics · Quantitative Biology 2025-09-04 Hojjat Torabi Goudarzi , Maziyar Baran Pouyan

The attention operator is arguably the key distinguishing factor of transformer architectures, which have demonstrated state-of-the-art performance on a variety of tasks. However, transformer attention operators often impose a significant…

Machine Learning · Computer Science 2024-12-24 Ziyang Wu , Tianjiao Ding , Yifu Lu , Druv Pai , Jingyuan Zhang , Weida Wang , Yaodong Yu , Yi Ma , Benjamin D. Haeffele

Single-cell RNA sequencing (scRNA-seq) has revolutionized our ability to analyze gene expression at the resolution of individual cells, providing unprecedented insights into cellular heterogeneity and complex biological systems. This paper…

Other Quantitative Biology · Quantitative Biology 2024-06-11 Megha Patel , Nimish Magre , Himanshi Motwani , Nik Bear Brown

Multi-view attributed graph clustering is an important approach to partition multi-view data based on the attribute feature and adjacent matrices from different views. Some attempts have been made in utilizing Graph Neural Network (GNN),…

Artificial Intelligence · Computer Science 2022-11-29 Jia-Qi Lin , Man-Sheng Chen , Xi-Ran Zhu , Chang-Dong Wang , Haizhang Zhang

Graph Neural Networks (GNNs) are widely used in graph data mining tasks. Traditional GNNs follow a message passing scheme that can effectively utilize local and structural information. However, the phenomena of over-smoothing and…

Machine Learning · Computer Science 2025-04-14 Zijie Zhou , Zhaoqi Lu , Xuekai Wei , Rongqin Chen , Shenghui Zhang , Pak Lon Ip , Leong Hou U

Since the representative capacity of graph-based clustering methods is usually limited by the graph constructed on the original features, it is attractive to find whether graph neural networks (GNNs) can be applied to augment the capacity.…

Machine Learning · Computer Science 2022-12-22 Hongyuan Zhang , Jiankun Shi , Rui Zhang , Xuelong Li

Clustering holds profound significance in data mining. In recent years, graph convolutional network (GCN) has emerged as a powerful tool for deep clustering, integrating both graph structural information and node attributes. However, most…

Machine Learning · Computer Science 2024-10-29 Qiankun Li , Haobing Liu , Ruobing Jiang , Tingting Wang

Despite the success of Transformer models in vision and language tasks, they often learn knowledge from enormous data implicitly and cannot utilize structured input data directly. On the other hand, structured learning approaches such as…

Computer Vision and Pattern Recognition · Computer Science 2023-05-02 Xuehai He , Xin Eric Wang

Graph clustering aims to divide the graph into different clusters. The recently emerging deep graph clustering approaches are largely built on graph neural networks (GNN). However, GNN is designed for general graph encoding and there is a…

Machine Learning · Computer Science 2025-04-28 Zhiyuan Ning , Zaitian Wang , Ran Zhang , Ping Xu , Kunpeng Liu , Pengyang Wang , Wei Ju , Pengfei Wang , Yuanchun Zhou , Erik Cambria , Chong Chen

Automatic diagnosis has attracted increasing attention but remains challenging due to multi-step reasoning. Recent works usually address it by reinforcement learning methods. However, these methods show low efficiency and require…

Artificial Intelligence · Computer Science 2021-12-21 Junying Chen , Dongfang Li , Qingcai Chen , Wenxiu Zhou , Xin Liu

Single-Cell RNA sequencing (scRNA-seq) measurements have facilitated genome-scale transcriptomic profiling of individual cells, with the hope of deconvolving cellular dynamic changes in corresponding cell sub-populations to better…

Genomics · Quantitative Biology 2021-04-06 Seyednami Niyakan , Ehsan Hajiramezanali , Shahin Boluki , Siamak Zamani Dadaneh , Xiaoning Qian

Most recent scribble-supervised segmentation methods commonly adopt a CNN framework with an encoder-decoder architecture. Despite its multiple benefits, this framework generally can only capture small-range feature dependency for the…

Computer Vision and Pattern Recognition · Computer Science 2024-02-06 Zihan Li , Yuan Zheng , Dandan Shan , Shuzhou Yang , Qingde Li , Beizhan Wang , Yuanting Zhang , Qingqi Hong , Dinggang Shen

The Transformer architecture has shown to be a powerful tool for a wide range of tasks. It is based on the self-attention mechanism, which is an inherently computationally expensive operation with quadratic computational complexity: memory…

Machine Learning · Computer Science 2024-02-07 Adjorn van Engelenhoven , Nicola Strisciuglio , Estefanía Talavera

In the realm of Graph Neural Networks (GNNs), two exciting research directions have recently emerged: Subgraph GNNs and Graph Transformers. In this paper, we propose an architecture that integrates both approaches, dubbed Subgraphormer,…

Machine Learning · Computer Science 2024-05-29 Guy Bar-Shalom , Beatrice Bevilacqua , Haggai Maron

Transformers have demonstrated remarkable performance across diverse domains. The key component of Transformers is self-attention, which learns the relationship between any two tokens in the input sequence. Recent studies have revealed that…

Machine Learning · Computer Science 2025-05-14 Hyowon Wi , Jeongwhan Choi , Noseong Park

Understanding user intent is essential for situational and context-aware decision-making. Motivated by a real-world scenario, this work addresses intent predictions of smart device users in the vicinity of vehicles by modeling sequential…

There are various approaches to graph learning for data clustering, incorporating different spectral and structural constraints through diverse graph structures. Some methods rely on bipartite graph models, where nodes are divided into two…

Machine Learning · Computer Science 2025-05-14 Amirhossein Javaheri , Daniel P. Palomar

Capturing semantic consistency among nodes is crucial for effective graph representation learning. Existing approaches typically rely on $k$-nearest neighbors ($k$NN) or other node-level full search algorithms (FSA) to mine semantic…

Artificial Intelligence · Computer Science 2026-05-06 Genhao Tian , Taihua Xu , Shuyin Xia , Qinghua Zhang , Jie Yang , Jianjun Chen

Graphs have become increasingly popular in modeling structures and interactions in a wide variety of problems during the last decade. Graph-based clustering and semi-supervised classification techniques have shown impressive performance.…

Machine Learning · Computer Science 2020-09-01 Zhao Kang , Chong Peng , Qiang Cheng , Xinwang Liu , Xi Peng , Zenglin Xu , Ling Tian