Graphylo: A deep learning approach for predicting regulatory DNA and RNA sites from whole-genome multiple alignments
Bibliographic record
Abstract
This study focuses on enhancing the prediction of regulatory functional sites in DNA and RNA sequences, a crucial aspect of gene regulation. Current methods, such as motif overrepresentation and machine learning, often lack specificity. To address this issue, the study leverages evolutionary information and introduces Graphylo, a deep-learning approach for predicting transcription factor binding sites in the human genome. Graphylo combines Convolutional Neural Networks for DNA sequences with Graph Convolutional Networks on phylogenetic trees, using information from placental mammals' genomes and evolutionary history. The research demonstrates that Graphylo consistently outperforms both single-species deep learning techniques and methods that incorporate inter-species conservation scores on a wide range of datasets. It achieves this by utilizing a species-based attention model for evolutionary insights and an integrated gradient approach for nucleotide-level model interpretability. This innovative approach offers a promising avenue for improving the accuracy of regulatory site prediction in genomics.
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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 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| 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".