HiCSR: a Hi-C super-resolution framework for producing highly realistic contact maps
Bibliographic record
Abstract
Abstract Motivation Hi-C data has enabled the genome-wide study of chromatin folding and architecture, and has led to important discoveries in the structure and function of chromatin conformation. Here, high resolution data plays a particularly important role as many chromatin substructures such as Topologically Associating Domains (TADs) and chromatin loops cannot be adequately studied with low resolution contact maps. However, the high sequencing costs associated with the generation of high resolution Hi-C data has become an experimental barrier. Data driven machine learning models, which allow low resolution Hi-C data to be computationally enhanced, offer a promising avenue to address this challenge. Results By carefully examining the properties of Hi-C maps and integrating various recent advances in deep learning, we developed a Hi-C Super-Resolution (HiCSR) framework capable of accurately recovering the fine details, textures, and substructures found in high resolution contact maps. This was achieved using a novel loss function tailored to the Hi-C enhancement problem which optimizes for an adversarial loss from a Generative Adversarial Network (GAN), a feature reconstruction loss derived from the latent representation of a denoising autoencoder, and a pixel-wise loss. Not only can the resulting framework generate enhanced Hi-C maps more visually similar to the original high resolution maps, it also excels on a suite of reproducibility metrics produced by members of the ENCODE Consortium compared to existing approaches, including HiCPlus, HiCNN, hicGAN and DeepHiC. Finally, we demonstrate that HiCSR is capable of enhancing Hi-C data across sequencing depth, cell types, and species, recovering biologically significant contact domain boundaries. Availability We make our implementation available for download at: https://github.com/PSI-Lab/HiCSR Contact ljlee@psi.toronto.edu Supplementary information Available Online
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".