Predicting a biological response of molecules from their chemical properties using diverse and optimized ensembles of stochastic gradient boosting machine
Bibliographic record
Abstract
The development of a new drug largely depends on trial and error. It typically involves synthesizing thousands of compounds that finally becomes a drug. This process is extremely expensive and slow. Therefore, the ability to accurately predict the biological activity of molecules, and understand the rationale behind those predictions would be of great value to the pharmaceutical industry. Gradient Boosting Machines (GBMs) are powerful ensemble learning techniques that have been successfully applied to several low-dimensional applications. Despite their high accuracy, GBMs suffer from major drawbacks such as high memory-consumption. In this paper, using real, high-dimensional (i.e. 1776 predictors) molecules dataset, we demonstrate that by using different feature selection/reduction techniques, the computations costs for building and tuning GBMs can be substantially reduced at a slight drop in prediction accuracy. In addition, by fusing the decisions made by the ensembles using two fusion techniques, namely a majority vote and an optimized feedforward neural network, we obtain a better prediction accuracy than the individual accuracy of all ensembles.
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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 | 0.002 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.001 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| 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 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".