Predicting drug–drug interactions by graph convolutional network with multi-kernel
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Bibliographic record
Abstract
Drug repositioning is proposed to find novel usages for existing drugs. Among many types of drug repositioning approaches, predicting drug-drug interactions (DDIs) helps explore the pharmacological functions of drugs and achieves potential drugs for novel treatments. A number of models have been applied to predict DDIs. The DDI network, which is constructed from the known DDIs, is a common part in many of the existing methods. However, the functions of DDIs are different, and thus integrating them in a single DDI graph may overlook some useful information. We propose a graph convolutional network with multi-kernel (GCNMK) to predict potential DDIs. GCNMK adopts two DDI graph kernels for the graph convolutional layers, namely, increased DDI graph consisting of 'increase'-related DDIs and decreased DDI graph consisting of 'decrease'-related DDIs. The learned drug features are fed into a block with three fully connected layers for the DDI prediction. We compare various types of drug features, whereas the target feature of drugs outperforms all other types of features and their concatenated features. In comparison with three different DDI prediction methods, our proposed GCNMK achieves the best performance in terms of area under receiver operating characteristic curve and area under precision-recall curve. In case studies, we identify the top 20 potential DDIs from all unknown DDIs, and the top 10 potential DDIs from the unknown DDIs among breast, colorectal and lung neoplasms-related drugs. Most of them have evidence to support the existence of their interactions. fangxiang.wu@usask.ca.
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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 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.001 |
| 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