Dataset Information

Knowledge-based classification of fine-grained immune cell types in single-cell RNA-Seq data.

ABSTRACT: Single-cell RNA sequencing (scRNA-Seq) is an emerging strategy for characterizing immune cell populations. Compared to flow or mass cytometry, scRNA-Seq could potentially identify cell types and activation states that lack precise cell surface markers. However, scRNA-Seq is currently limited due to the need to manually classify each immune cell from its transcriptional profile. While recently developed algorithms accurately annotate coarse cell types (e.g. T cells versus macrophages), making fine distinctions (e.g. CD8+ effector memory T cells) remains a difficult challenge. To address this, we developed a machine learning classifier called ImmClassifier that leverages a hierarchical ontology of cell type. We demonstrate that its predictions are highly concordant with flow-based markers from CITE-seq and outperforms other tools (+15% recall, +14% precision) in distinguishing fine-grained cell types with comparable performance on coarse ones. Thus, ImmClassifier can be used to explore more deeply the heterogeneity of the immune system in scRNA-Seq experiments.

SUBMITTER: Liu X

PROVIDER: S-EPMC8536868 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature

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Publications

Knowledge-based classification of fine-grained immune cell types in single-cell RNA-Seq data.

Liu Xuan X Gosline Sara J C SJC Pflieger Lance T LT Wallet Pierre P Iyer Archana A Guinney Justin J Bild Andrea H AH Chang Jeffrey T JT

Briefings in bioinformatics 20210901 5

Single-cell RNA sequencing (scRNA-Seq) is an emerging strategy for characterizing immune cell populations. Compared to flow or mass cytometry, scRNA-Seq could potentially identify cell types and activation states that lack precise cell surface markers. However, scRNA-Seq is currently limited due to the need to manually classify each immune cell from its transcriptional profile. While recently developed algorithms accurately annotate coarse cell types (e.g. T cells versus macrophages), making fin ...[more]

PMID: 33681983

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Project description:ObjectiveFine-grained classification of historical traditional villages plays a crucial role in guiding the future development and construction of urban and rural areas. This study aims to propose a new dataset for fine-grained classification of traditional villages and to propose an efficient progressive attention network for the problem of low accuracy and efficiency of fine-grained traditional historical village classification.Methods and resultsFirstly, in order to further study the long-standing problem of fine-grained classification of traditional villages, a new fine-grained classification dataset of traditional villages containing 4,400 images, referred to as PVCD, is proposed by crawling and hand-arranging. Secondly, a new Progressive Attention Module, abbreviated as PAM, is also proposed. PAM engages in attentional modeling of prominent spatial features within the spatial dimension, subsequently applying attentional modeling to channel features beneath the identified salient spatial features. This process involves salient spatial feature attention modeling of prominent channel features within the dimension to extract discriminative information for fine-grained classification, thereby enhancing the performance of classifying traditional villages with precision. Finally, a new knowledge distillation strategy of softened alignment distillation, or SAD for short, is proposed, which simply and efficiently transfers the knowledge of softened category probability distributions through. Notably, based on the above proposed PAM, the lightweight EPANet-Student and the heavyweight EPANet-Teacher are proposed. In addition, the heavyweight EPANet-Teacher transfers the knowledge of fine-grained categorization of traditional villages to the lightweight EPANet-Student through the proposed SAD, abbreviated as EPANet-KD. The experimental results show that the proposed EPANet-Teacher achieves state-of-the-art performance with an accuracy of 67.27%, and the proposed EPANet-KD achieves comparable performance to the proposed EPANet-Teacher with 3.32M parameters and 0.42G computation.ConclusionThe proposed EPANet-KD maintains a good balance of accuracy and efficiency in the fine-grained classification of traditional villages, considerably promoting the research on the fine-grained classification of traditional villages. In addition, it facilitates the digital preservation and development of traditional villages. All datasets, codes and benchmarking results are publicly available for the promotion of this research area. https://github.com/Jack13026212687/EPANet-KD.

Dataset Information

Knowledge-based classification of fine-grained immune cell types in single-cell RNA-Seq data.

Publications

Knowledge-based classification of fine-grained immune cell types in single-cell RNA-Seq data.

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