Single cell RNA sequencing (scRNA-Seq) is being widely used in biomedical research and generated enormous volume and diversity of data. The raw data contain multiple types of noise and technical artifacts, which need thorough cleaning. Existing denoising and imputation methods largely focus on a single type of noise (i.e., dropouts) and have strong distribution assumptions which greatly limit their performance and application. Here we design and develop the AutoClass model, integrating two deep neural network components, an autoencoder, and a classifier, as to maximize both noise removal and signal retention. AutoClass is distribution agnostic as it makes no assumption on specific data distributions, hence can effectively clean a wide range of noise and artifacts. AutoClass outperforms the state-of-art methods in multiple types of scRNA-Seq data analyses, including data recovery, differential expression analysis, clustering analysis, and batch effect removal. Importantly, AutoClass is robust on key hyperparameter settings including bottleneck layer size, pre-clustering number and classifier weight. We have made AutoClass open source at: https://github.com/datapplab/AutoClass . Single cell RNA sequencing (scRNA-Seq) is widely used in biomedical research. Here the authors develop a novel AI model-AutoClass, which effectively cleans a wide range of noise and artifacts in scRNA-Seq data and improves downstream analyses.

Just as asking a single person about their health will provide tailored, personalized information impossible to glean from a large poll, an individual cell's genome or transcriptome can provide much more information about their place in living systems than sequencing a whole batch of cells. But until recent years, the technology didn't exist to get that high resolution genomic data--and until today, there wasn't a reliable way to ensure the high quality and usefulness of that data. Researchers from the University of North Carolina at Charlotte, led by Dr. Weijun Luo and Dr. Cory Brouwer, have developed an artificial intelligence algorithm to "clean" noisy single-cell RNA sequencing (scRNA-Seq) data. The study, "A Universal Deep Neural Network for In-Depth Cleaning of Single-Cell RNA-Seq Data," was published in Nature Communications on April 7, 2022. From identifying the specific genes associated with sickle cell anemia and breast cancer to creating the mRNA vaccines in the ongoing COVID-19 pandemic, scientists have been searching genomes to unlock the secrets of life since the Human Genome Project of the 1990s.

Get up and running with Transformers! Start using the pipeline() for rapid inference, and quickly load a pretrained model and tokenizer with an AutoClass to solve your text, vision or audio task. All code examples presented in the documentation have a toggle on the top left for PyTorch and TensorFlow. If not, the code is expected to work for both backends without any change. For more details about the pipeline() and associated tasks, refer to the documentation here.

In Proceedings of the Fifth International Conference on Machine Learning, pages 54-64, Ann Arbor, Michigan.

This paper describes a Bayesian technique for unsupervised classification of data and its computer implementation, AutoClass. Given real valued or discrete data, AutoClass determines the most probable number of classes present in the data, the most probable descriptions of those classes, and each object's probability of membership in each class. The program performs as well as or better than other automatic classification systems when run on the same data and contains no ad hoc similarity measures or stopping criteria. AutoClass has been applied to several databases in which it has discovered classes representing previously unsuspected phenomena.