Refining sequence-to-expression modelling with chromatin accessibility
Bibliographic record
Abstract
MOTIVATION: Sequence-to-expression models typically do not consider chromatin accessibility, a major factor limiting gene regulation. We hypothesized that supplying accessibility as an input feature would allow a sequence-to-expression model to focus on important open regions of the genome. RESULTS: We found that the performance of such an augmented model was significantly better than that of sequence-only or accessibility-only models with similar architectures. Specifically, its ability to predict the expression of highly variable genes and gene expression in other cell types improved, and higher attribution scores in the input DNA sequences of the augmented model conformed to accessibility, enabling the learning of cell type-specific sequence patterns. Additionally, we show that fine-tuning a pre-trained sequence-only model with both sequence and accessibility can boost performance further and highlight the importance of sequencing depth in sequence-to-expression prediction. AVAILABILITY AND IMPLEMENTATION: Source code is available on GitHub at https://github.com/lapohosorsolya/accessible_seq2exp.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.003 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.002 |
| Insufficient payload (model declined to judge) | 0.002 | 0.001 |
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 source (direct Gemma or distilled Codex), 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".