Data-Driven Soft Labeling Scales DNA Read Classification to Whole-Body Cell-Type Deconvolution

arXiv:2607.04987 · cs.LG, q-bio.GN, q-bio.QM · Submitted 2026-07-06 · Read on arXiv

cs.LG, q-bio.GN, q-bio.QM

Submitted: 2026-07-06

Updated: 2026-09-29

Code: https://github.com/CompEpigen/methylbert

License: http://creativecommons.org/licenses/by-sa/4.0/

The gist: Revised following peer review.

Terminology

• Calibration — 39× in this paper · explained in 7 episodes
• Aggregation — 9× in this paper · explained in 1 episode
• alpha — 8× in this paper · explained in 1 episode
• Generalization — 6× in this paper · explained in 13 episodes
• Transformer — 6× in this paper · explained in 2 episodes
• Core — 5× in this paper · explained in 2 episodes
• Feature Selection — 5× in this paper · explained in 4 episodes
• Accuracy — 4× in this paper · explained in 1 episode
• Adam — 4× in this paper · explained in 2 episodes
• Regularization — 4× in this paper · explained in 3 episodes
• Alignment — 3× in this paper · explained in 1 episode
• Benchmark — 3× in this paper · explained in 2 episodes
• Fine-Tuning — 3× in this paper · explained in 5 episodes
• Maximum Likelihood Estimation — 3× in this paper
• Adaptation — 2× in this paper · explained in 1 episode
• Multi-Layer Perceptron — 2× in this paper
• Non-Negative Least Squares — 2× in this paper
• Ontology — 2× in this paper · explained in 2 episodes
• Probability Simplex Least Squares — 2× in this paper
• Whole Genome Bisulfite Sequencing — 2× in this paper
• AdamW Optimizer — 1× in this paper · explained in 1 episode
• Attention Mechanism — 1× in this paper · explained in 3 episodes
• Bayesian Framework — 1× in this paper · explained in 3 episodes
• Benchmarking — 1× in this paper · explained in 4 episodes
• Consistency — 1× in this paper · explained in 3 episodes
• Cross-Attention Mechanism — 1× in this paper · explained in 2 episodes
• Embeddings — 1× in this paper · explained in 2 episodes
• Entropy-weighted Cross Entropy — 1× in this paper
• Fidelity — 1× in this paper · explained in 2 episodes
• Gene Expression Omnibus — 1× in this paper
• Interpretability — 1× in this paper · explained in 15 episodes
• Reduced Representation Bisulfite Sequencing — 1× in this paper
• Robustness — 1× in this paper · explained in 5 episodes
• Single-layer Wide Network — 1× in this paper

Abstract

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