INSCT

Integrating millions of single cells using batch-aware triplet neural networks. INtegration of millions of Single Cells using batch-aware Triplet networks. insct is a deep learning algorithm which calculates an integrated embedding for scRNA-seq data. With insct, you can:. a, INSCT learns a data representation, which integrates cells across batches. The goal of the network is to minimize the distance between Anchor and Positive while maximizing the distance between Anchor and Negative. Anchor and Positive pairs consist of transcriptionally similar cells from different batches. The Negative is a transcriptomically dissimilar cell sampled from the same batch as the Anchor. b, Principal components of three data points corresponding to Anchor, Positive and Negative are fed into three identical neural networks, which share weights. The triplet loss function is used to train the network weights and the two-dimensional embedding layer activations represent the integrated embedding.