DWNN-RLS: regularized least squares method for predicting circRNA-disease associations
Why this work is in the frame
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Bibliographic record
Abstract
BACKGROUND: Many evidences have demonstrated that circRNAs (circular RNA) play important roles in controlling gene expression of human, mouse and nematode. More importantly, circRNAs are also involved in many diseases through fine tuning of post-transcriptional gene expression by sequestering the miRNAs which associate with diseases. Therefore, identifying the circRNA-disease associations is very appealing to comprehensively understand the mechanism, treatment and diagnose of diseases, yet challenging. As the complex mechanism between circRNAs and diseases, wet-lab experiments are expensive and time-consuming to discover novel circRNA-disease associations. Therefore, it is of dire need to employ the computational methods to discover novel circRNA-disease associations. RESULT: In this study, we develop a method (DWNN-RLS) to predict circRNA-disease associations based on Regularized Least Squares of Kronecker product kernel. The similarity of circRNAs is computed from the Gaussian Interaction Profile(GIP) based on known circRNA-disease associations. In addition, the similarity of diseases is integrated by the mean of GIP similarity and sematic similarity which is computed by the direct acyclic graph (DAG) representation of diseases. The kernels of circRNA-disease pairs are constructed from the Kronecker product of the kernels of circRNAs and diseases. DWNN (decreasing weight k-nearest neighbor) method is adopted to calculate the initial relational score for new circRNAs and diseases. The Kronecker product kernel based regularised least squares approach is used to predict new circRNA-disease associations. We adopt 5-fold cross validation (5CV), 10-fold cross validation (10CV) and leave one out cross validation (LOOCV) to assess the prediction performance of our method, and compare it with other six competing methods (RLS-avg, RLS-Kron, NetLapRLS, KATZ, NBI, WP). CONLUSION: The experiment results show that DWNN-RLS reaches the AUC values of 0.8854, 0.9205 and 0.9701 in 5CV, 10CV and LOOCV, respectively, which illustrates that DWNN-RLS is superior to the competing methods RLS-avg, RLS-Kron, NetLapRLS, KATZ, NBI, WP. In addition, case studies also show that DWNN-RLS is an effective method to predict new circRNA-disease associations.
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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 | 0.001 | 0.003 |
| 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 it