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RCA2: a scalable supervised clustering algorithm that reduces batch effects in scRNA-seq data.

ABSTRACT: The transcriptomic diversity of cell types in the human body can be analysed in unprecedented detail using single cell (SC) technologies. Unsupervised clustering of SC transcriptomes, which is the default technique for defining cell types, is prone to group cells by technical, rather than biological, variation. Compared to de-novo (unsupervised) clustering, we demonstrate using multiple benchmarks that supervised clustering, which uses reference transcriptomes as a guide, is robust to batch effects and data quality artifacts. Here, we present RCA2, the first algorithm to combine reference projection (batch effect robustness) with graph-based clustering (scalability). In addition, RCA2 provides a user-friendly framework incorporating multiple commonly used downstream analysis modules. RCA2 also provides new reference panels for human and mouse and supports generation of custom panels. Furthermore, RCA2 facilitates cell type-specific QC, which is essential for accurate clustering of data from heterogeneous tissues. We demonstrate the advantages of RCA2 on SC data from human bone marrow, healthy PBMCs and PBMCs from COVID-19 patients. Scalable supervised clustering methods such as RCA2 will facilitate unified analysis of cohort-scale SC datasets.

SUBMITTER: Schmidt F

PROVIDER: S-EPMC8344557 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundSingle-cell RNA sequencing (scRNA-seq) has emerged has a main strategy to study transcriptional activity at the cellular level. Clustering analysis is routinely performed on scRNA-seq data to explore, recognize or discover underlying cell identities. The high dimensionality of scRNA-seq data and its significant sparsity accentuated by frequent dropout events, introducing false zero count observations, make the clustering analysis computationally challenging. Even though multiple scRNA-seq clustering techniques have been proposed, there is no consensus on the best performing approach. On a parallel research track, self-supervised contrastive learning recently achieved state-of-the-art results on images clustering and, subsequently, image classification.ResultsWe propose contrastive-sc, a new unsupervised learning method for scRNA-seq data that perform cell clustering. The method consists of two consecutive phases: first, an artificial neural network learns an embedding for each cell through a representation training phase. The embedding is then clustered in the second phase with a general clustering algorithm (i.e. KMeans or Leiden community detection). The proposed representation training phase is a new adaptation of the self-supervised contrastive learning framework, initially proposed for image processing, to scRNA-seq data. contrastive-sc has been compared with ten state-of-the-art techniques. A broad experimental study has been conducted on both simulated and real-world datasets, assessing multiple external and internal clustering performance metrics (i.e. ARI, NMI, Silhouette, Calinski scores). Our experimental analysis shows that constastive-sc compares favorably with state-of-the-art methods on both simulated and real-world datasets.ConclusionOn average, our method identifies well-defined clusters in close agreement with ground truth annotations. Our method is computationally efficient, being fast to train and having a limited memory footprint. contrastive-sc maintains good performance when only a fraction of input cells is provided and is robust to changes in hyperparameters or network architecture. The decoupling between the creation of the embedding and the clustering phase allows the flexibility to choose a suitable clustering algorithm (i.e. KMeans when the number of expected clusters is known, Leiden otherwise) or to integrate the embedding with other existing techniques.

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RCA2: a scalable supervised clustering algorithm that reduces batch effects in scRNA-seq data.

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