{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/scrna-seq-data-clustering-by-cluster-aware","title":"scRNA-seq Data Clustering by Cluster-aware Iterative Contrastive Learning","arxiv_id":"2312.16600","date":"2023-12-27","proceeding":null,"authors":["Weikang Jiang","Jinxian Wang","Jihong Guan","Shuigeng Zhou"],"abstract":"Single-cell RNA sequencing (scRNA-seq) enables researchers to analyze gene expression at single-cell level. One important task in scRNA-seq data analysis is unsupervised clustering, which helps identify distinct cell types, laying down the foundation for other downstream analysis tasks. In this paper, we propose a novel method called Cluster-aware Iterative Contrastive Learning (CICL in short) for scRNA-seq data clustering, which utilizes an iterative representation learning and clustering framework to progressively learn the clustering structure of scRNA-seq data with a cluster-aware contrastive loss. CICL consists of a Transformer encoder, a clustering head, a projection head and a contrastive loss module. First, CICL extracts the feature vectors of the original and augmented data by the Transformer encoder. Then, it computes the clustering centroids by K-means and employs the student t-distribution to assign pseudo-labels to all cells in the clustering head. The projection-head uses a Multi-Layer Perceptron (MLP) to obtain projections of the augmented data. At last, both pseudo-labels and projections are used in the contrastive loss to guide the model training. Such a process goes iteratively so that the clustering result becomes better and better. Extensive experiments on 25 real world scRNA-seq datasets show that CICL outperforms the SOTA methods. Concretely, CICL surpasses the existing methods by from 14% to 280%, and from 5% to 133% on average in terms of performance metrics ARI and NMI respectively.","url_abs":"https://arxiv.org/abs/2312.16600v1","url_pdf":"https://arxiv.org/pdf/2312.16600v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"scrna-seq-data-clustering-by-cluster-aware","repo_url":"https://github.com/alunethy/cicl","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"clustering","task_name":"Clustering"},{"task_slug":"contrastive-learning","task_name":"Contrastive Learning"},{"task_slug":"representation-learning","task_name":"Representation Learning"}],"methods":[{"method_slug":"absolute-position-encodings","method_name":"Absolute Position Encodings"},{"method_slug":"adam","method_name":"Adam"},{"method_slug":"attention","method_name":"Attention"},{"method_slug":"bpe","method_name":"BPE"},{"method_slug":"contrastive-learning","method_name":"Contrastive Learning"},{"method_slug":"dense-connections","method_name":"Dense Connections"},{"method_slug":"dropout","method_name":"Dropout"},{"method_slug":"label-smoothing","method_name":"Label Smoothing"},{"method_slug":"layer-normalization","method_name":"Layer Normalization"},{"method_slug":"linear-layer","method_name":"Linear Layer"},{"method_slug":"multi-head-attention","method_name":"Multi-Head Attention"},{"method_slug":"position-wise-feed-forward-layer","method_name":"Position-Wise Feed-Forward Layer"},{"method_slug":"residual-connection","method_name":"Residual Connection"},{"method_slug":"softmax","method_name":"Softmax"},{"method_slug":"transformer","method_name":"Transformer"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}