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Unsupervised Learning from Noisy Networks with Applications to Hi-C Data

NeurIPS 2016 · Label-efficient and robust learning › Noisy labels · approach: Contrastive learning on noisy data

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Measured effects reported in the paper

What was changedWhereMeasuredEffect
Denoising the highest-resolution Hi-C map with OPT1 (single network) before clustering (ablation)Louvain clustering on Hi-C · GM12878 chr14 and chr21 simulated Hi-Ccluster agreement with ground truth (qualitative)Helped
Pooling multiple Hi-C resolutions with learned weights (OPT2) (ablation)Denoised Hi-C network · GM12878 chr14 and chr21 simulated Hi-Ccluster size / agreement with ground truth (qualitative)Helped
Adding Capture-C high-confidence links (OPT6) to multi-resolution denoising (ablation)Multi-resolution denoised Hi-C network · GM12878 chr14 and chr21 simulated Hi-Ccluster agreement with ground truth (qualitative)Helped
Increasing distance-dependent random noise on the networkLouvain baseline on highest-resolution Hi-C · Simulated Hi-C noise sweepNMIHurt
Increasing noise on the network, compared with the proposed multi-resolution denoiserProposed denoising framework · Simulated Hi-C noise sweepNMIMixed
Ratio of histone-mark covariation within vs between domains and CTCF boundary binding, proposed vs baselineProposed denoising framework · GM12878 Hi-C domainshistone covariation ratio and CTCF binding fractionHelped

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