A sandbox for prediction and integration of DNA, RNA, and proteins in single cellsDownload PDF

Published: 11 Oct 2021, Last Modified: 23 May 2023NeurIPS 2021 Datasets and Benchmarks Track (Round 2)Readers: Everyone
Keywords: benchmarks, single-cell, computational biology, genomics
Abstract: The last decade has witnessed a technological arms race to encode the molecular states of cells into DNA libraries, turning DNA sequencers into scalable single-cell microscopes. Single-cell measurement of chromatin accessibility (DNA), gene expression (RNA), and proteins has revealed rich cellular diversity across tissues, organisms, and disease states. However, single-cell data poses a unique set of challenges. A dataset may comprise millions of cells with tens of thousands of sparse features. Identifying biologically relevant signals from the background sources of technical noise requires innovation in predictive and representational learning. Furthermore, unlike in machine vision or natural language processing, biological ground truth is limited. Here we leverage recent advances in multi-modal single-cell technologies which, by simultaneously measuring two layers of cellular processing in each cell, provide ground truth analogous to language translation. We define three key tasks to predict one modality from another and learn integrated representations of cellular state. We also generate a novel dataset of the human bone marrow specifically designed for benchmarking studies. The dataset and tasks are accessible through an open-source framework that facilitates centralized evaluation of community-submitted methods.
TL;DR: A multimodal single-cell benchmarking dataset and data integration challenge
Supplementary Material: zip
URL: https://openproblems.bio/benchmark_dataset
Contribution Process Agreement: Yes
Dataset Url: https://openproblems.bio/benchmark_dataset
License: MIT License
Author Statement: Yes
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