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Unsupervised Learning from Noisy Networks with Applications to Hi-C Data
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Measured effects reported in the paper
| What was changed | Where | Measured | Effect |
|---|---|---|---|
| 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-C | cluster 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-C | cluster 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-C | cluster agreement with ground truth (qualitative) | Helped |
| Increasing distance-dependent random noise on the network | Louvain baseline on highest-resolution Hi-C · Simulated Hi-C noise sweep | NMI | Hurt |
| Increasing noise on the network, compared with the proposed multi-resolution denoiser | Proposed denoising framework · Simulated Hi-C noise sweep | NMI | Mixed |
| Ratio of histone-mark covariation within vs between domains and CTCF boundary binding, proposed vs baseline | Proposed denoising framework · GM12878 Hi-C domains | histone covariation ratio and CTCF binding fraction | Helped |
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