Data Denoising for Single-cell RNA sequencing

Jingshu Wang, UPENN

Friday, January 25, 2019 - 3:30pm

Single-cell RNA sequencing (scRNA-seq) measures gene expression levels in every single cell, which is a ground-breaking technology over microarrays and bulk RNA sequencing and reshapes the field of biology. Though the technology is exciting, scRNA-seq data is very noisy and often too noisy for signal detection and robust analysis. In the talk, I will discuss how we perform data denoising by learning across similar genes and borrowing information from external public datasets to improve the quality of downstream analysis.

Specifically, I will discuss how we set up the model by decomposing the randomness of scRNA-seq data into three components, the structured shared variations across genes, biological “noise” and technical noise, based on current understandings of the stochasticity in DNA transcription. I will emphasize one key challenge in each component and our contributions. I will show how we make proper assumptions on the technical noise and introduce a key feature, transfer learning, in our denoising method SAVER-X. SAVER-X uses a deep autoencoder neural network coupled with Empirical Bayes shrinkage to extract transferable gene expression features across datasets under different settings and learn from external data as prior information. I will show that SAVER-X can successfully transfer information from mouse to human cells and can guard against bias. I'll also briefly discuss our ongoing work on post-denoising inference for scRNA-seq.

Seminars generally take place in 116 Old Chemistry Building on Fridays from 3:30 - 4:30 pm. For additional information contact: or phone 919-684-8029. Sorry, but we do not have reprints available. Please feel free to contact the authors by email for follow-up information, articles, etc. Reception following seminar in 203B Old Chemistry.

Old Chemistry 116

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