The use of computational models to predict response to HIV therapy for clinical cases in Romania
Bibliographic record
Abstract
INTRODUCTION: A major challenge in Romania is the optimisation of antiretroviral therapy for the many HIV-infected adults with, on average, a decade of treatment experience. The RDI has developed computational models that predict virological response to therapy but these require a genotype, which is not routinely available in Romania. Moreover the models, which were trained without any Romanian data, have proved most accurate for patients from the healthcare settings that contributed the training data. Here we develop and test a novel model that does not require a genotype, with test data from Romania. METHODS: A random forest (RF) model was developed to predict the probability of the HIV viral load (VL) being reduced to <50 copies/ml following therapy change. The input variables were baseline VL, CD4 count, treatment history and time to follow-up. The model was developed with 3188 treatment changes episodes (TCEs) from North America, Western Europe and Australia. The model's predictions for 100 independent TCEs from the RDI database were compared to those of a model trained with the same data plus genotypes and then tested using 39 TCEs from Romania in terms of the area under the ROC curve (AUC). RESULTS: When tested with the 100 independent RDI TCEs, the AUC values for the models with and without genotypes were 0.88 and 0.86 respectively. For the 39 Romanian TCEs the AUC was 0.60. However, when 14 cases with viral loads that may have been between 50 and 400 copies were removed, the AUC increased to 0.83. DISCUSSION: Despite having been trained without data from Romania, the model predicted treatment responses in treatment-experienced Romanian patients with clade F virus accurately without the need for a genotype. The results suggest that this approach might be generalisable and useful in helping design optimal salvage regimens for treatment-experienced patients in countries with limited resources where genotyping is not always available.
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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 | 0.003 | 0.011 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 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".