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<!DOCTYPE html>
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<title>References | Malaria vaccine antigen identification for Plasmodium vivax</title>
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<meta name="twitter:title" content="References | Malaria vaccine antigen identification for Plasmodium vivax" />
<meta name="author" content="Renee Ti Chou" />
<meta name="date" content="2023-05-16" />
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<ul class="summary">
<li><a href="./"><i>Positive-unlabeled learning for Pv RV</i></a></li>
<li class="divider"></li>
<li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>Preface</a></li>
<li class="chapter" data-level="1" data-path="id_01_data_engineering.html"><a href="id_01_data_engineering.html"><i class="fa fa-check"></i><b>1</b> Data engineering</a>
<ul>
<li class="chapter" data-level="1.1" data-path="id_01_data_engineering.html"><a href="id_01_data_engineering.html#purf-package-installization"><i class="fa fa-check"></i><b>1.1</b> <code>purf</code> package installization</a></li>
<li class="chapter" data-level="1.2" data-path="id_01_data_engineering.html"><a href="id_01_data_engineering.html#retrieving-p.-vivax-protein-variables"><i class="fa fa-check"></i><b>1.2</b> Retrieving <em>P. vivax</em> protein variables</a>
<ul>
<li class="chapter" data-level="1.2.1" data-path="id_01_data_engineering.html"><a href="id_01_data_engineering.html#immunological-data-sets"><i class="fa fa-check"></i><b>1.2.1</b> Immunological data sets</a></li>
<li class="chapter" data-level="1.2.2" data-path="id_01_data_engineering.html"><a href="id_01_data_engineering.html#proteomic-data-sets"><i class="fa fa-check"></i><b>1.2.2</b> Proteomic data sets</a></li>
<li class="chapter" data-level="1.2.3" data-path="id_01_data_engineering.html"><a href="id_01_data_engineering.html#structural-data-sets"><i class="fa fa-check"></i><b>1.2.3</b> Structural data sets</a></li>
<li class="chapter" data-level="1.2.4" data-path="id_01_data_engineering.html"><a href="id_01_data_engineering.html#genomic-data-sets"><i class="fa fa-check"></i><b>1.2.4</b> Genomic data sets</a></li>
<li class="chapter" data-level="1.2.5" data-path="id_01_data_engineering.html"><a href="id_01_data_engineering.html#final-assembly"><i class="fa fa-check"></i><b>1.2.5</b> Final assembly</a></li>
</ul></li>
<li class="chapter" data-level="1.3" data-path="id_01_data_engineering.html"><a href="id_01_data_engineering.html#generating-ml-input"><i class="fa fa-check"></i><b>1.3</b> Generating ML input</a></li>
</ul></li>
<li class="chapter" data-level="2" data-path="id_02_model_training.html"><a href="id_02_model_training.html"><i class="fa fa-check"></i><b>2</b> Model training</a>
<ul>
<li class="chapter" data-level="2.1" data-path="id_02_model_training.html"><a href="id_02_model_training.html#hyper-parameter-tuning-for-purf"><i class="fa fa-check"></i><b>2.1</b> Hyper-parameter tuning for PURF</a>
<ul>
<li class="chapter" data-level="2.1.1" data-path="id_02_model_training.html"><a href="id_02_model_training.html#analysis"><i class="fa fa-check"></i><b>2.1.1</b> Analysis</a>
<ul>
<li class="chapter" data-level="2.1.1.1" data-path="id_02_model_training.html"><a href="id_02_model_training.html#pv-data-set"><i class="fa fa-check"></i><b>2.1.1.1</b> Pv data set</a></li>
<li class="chapter" data-level="2.1.1.2" data-path="id_02_model_training.html"><a href="id_02_model_training.html#pf-pv-combined-data-set"><i class="fa fa-check"></i><b>2.1.1.2</b> Pf + Pv combined data set</a></li>
</ul></li>
<li class="chapter" data-level="2.1.2" data-path="id_02_model_training.html"><a href="id_02_model_training.html#plotting"><i class="fa fa-check"></i><b>2.1.2</b> Plotting</a>
<ul>
<li class="chapter" data-level="2.1.2.1" data-path="id_02_model_training.html"><a href="id_02_model_training.html#pv-data-set-1"><i class="fa fa-check"></i><b>2.1.2.1</b> Pv data set</a></li>
<li class="chapter" data-level="2.1.2.2" data-path="id_02_model_training.html"><a href="id_02_model_training.html#bimodal-distribution-plot"><i class="fa fa-check"></i><b>2.1.2.2</b> Bimodal distribution plot</a></li>
<li class="chapter" data-level="2.1.2.3" data-path="id_02_model_training.html"><a href="id_02_model_training.html#known-antigen-ranking"><i class="fa fa-check"></i><b>2.1.2.3</b> Known antigen ranking</a></li>
<li class="chapter" data-level="2.1.2.4" data-path="id_02_model_training.html"><a href="id_02_model_training.html#pf-pv-combined-data-set-1"><i class="fa fa-check"></i><b>2.1.2.4</b> Pf + Pv combined data set</a></li>
<li class="chapter" data-level="2.1.2.5" data-path="id_02_model_training.html"><a href="id_02_model_training.html#bimodal-distribution-plot-1"><i class="fa fa-check"></i><b>2.1.2.5</b> Bimodal distribution plot</a></li>
<li class="chapter" data-level="2.1.2.6" data-path="id_02_model_training.html"><a href="id_02_model_training.html#known-antigen-ranking-1"><i class="fa fa-check"></i><b>2.1.2.6</b> Known antigen ranking</a></li>
</ul></li>
<li class="chapter" data-level="2.1.3" data-path="id_02_model_training.html"><a href="id_02_model_training.html#results-for-positive-level-0.5"><i class="fa fa-check"></i><b>2.1.3</b> Results for positive level = 0.5</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="3" data-path="id_03_model_evaluation.html"><a href="id_03_model_evaluation.html"><i class="fa fa-check"></i><b>3</b> Model evaluation</a>
<ul>
<li class="chapter" data-level="3.1" data-path="id_03_model_evaluation.html"><a href="id_03_model_evaluation.html#known-antigen-prediction-accuracy"><i class="fa fa-check"></i><b>3.1</b> Known antigen prediction accuracy</a>
<ul>
<li class="chapter" data-level="3.1.1" data-path="id_03_model_evaluation.html"><a href="id_03_model_evaluation.html#analysis-1"><i class="fa fa-check"></i><b>3.1.1</b> Analysis</a>
<ul>
<li class="chapter" data-level="3.1.1.1" data-path="id_03_model_evaluation.html"><a href="id_03_model_evaluation.html#pf-model-cross-species-predictions"><i class="fa fa-check"></i><b>3.1.1.1</b> Pf model cross-species predictions</a></li>
<li class="chapter" data-level="3.1.1.2" data-path="id_03_model_evaluation.html"><a href="id_03_model_evaluation.html#pv-model-cross-species-predictions"><i class="fa fa-check"></i><b>3.1.1.2</b> Pv model cross-species predictions</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="3.2" data-path="id_03_model_evaluation.html"><a href="id_03_model_evaluation.html#adversarial-controls"><i class="fa fa-check"></i><b>3.2</b> Adversarial controls</a>
<ul>
<li class="chapter" data-level="3.2.1" data-path="id_03_model_evaluation.html"><a href="id_03_model_evaluation.html#analysis-2"><i class="fa fa-check"></i><b>3.2.1</b> Analysis</a>
<ul>
<li class="chapter" data-level="3.2.1.1" data-path="id_03_model_evaluation.html"><a href="id_03_model_evaluation.html#pv-data-set-2"><i class="fa fa-check"></i><b>3.2.1.1</b> Pv data set</a></li>
<li class="chapter" data-level="3.2.1.2" data-path="id_03_model_evaluation.html"><a href="id_03_model_evaluation.html#pf-pv-combined-data-set-2"><i class="fa fa-check"></i><b>3.2.1.2</b> Pf + Pv combined data set</a></li>
</ul></li>
<li class="chapter" data-level="3.2.2" data-path="id_03_model_evaluation.html"><a href="id_03_model_evaluation.html#plotting-1"><i class="fa fa-check"></i><b>3.2.2</b> Plotting</a>
<ul>
<li class="chapter" data-level="3.2.2.1" data-path="id_03_model_evaluation.html"><a href="id_03_model_evaluation.html#mean-differences-in-scores"><i class="fa fa-check"></i><b>3.2.2.1</b> Mean differences in scores</a></li>
<li class="chapter" data-level="3.2.2.2" data-path="id_03_model_evaluation.html"><a href="id_03_model_evaluation.html#investigation-of-known-antigen-groups"><i class="fa fa-check"></i><b>3.2.2.2</b> Investigation of known antigen groups</a></li>
<li class="chapter" data-level="3.2.2.3" data-path="id_03_model_evaluation.html"><a href="id_03_model_evaluation.html#labeled-known-antigen-accuracies"><i class="fa fa-check"></i><b>3.2.2.3</b> Labeled known antigen accuracies</a></li>
</ul></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="4" data-path="id_04_model_comparisons.html"><a href="id_04_model_comparisons.html"><i class="fa fa-check"></i><b>4</b> Model comparisons</a>
<ul>
<li class="chapter" data-level="4.1" data-path="id_04_model_comparisons.html"><a href="id_04_model_comparisons.html#known-antigen-score-comparisons"><i class="fa fa-check"></i><b>4.1</b> Known antigen score comparisons</a></li>
<li class="chapter" data-level="4.2" data-path="id_04_model_comparisons.html"><a href="id_04_model_comparisons.html#known-antigen-prediction-summary"><i class="fa fa-check"></i><b>4.2</b> Known antigen prediction summary</a></li>
<li class="chapter" data-level="4.3" data-path="id_04_model_comparisons.html"><a href="id_04_model_comparisons.html#score-and-species-association"><i class="fa fa-check"></i><b>4.3</b> Score and species association</a></li>
<li class="chapter" data-level="4.4" data-path="id_04_model_comparisons.html"><a href="id_04_model_comparisons.html#unsupervised-random-forest-analysis"><i class="fa fa-check"></i><b>4.4</b> Unsupervised random forest analysis</a>
<ul>
<li class="chapter" data-level="4.4.1" data-path="id_04_model_comparisons.html"><a href="id_04_model_comparisons.html#analysis-3"><i class="fa fa-check"></i><b>4.4.1</b> Analysis</a></li>
</ul></li>
<li class="chapter" data-level="4.5" data-path="id_04_model_comparisons.html"><a href="id_04_model_comparisons.html#tree-depth-analysis"><i class="fa fa-check"></i><b>4.5</b> Tree depth analysis</a>
<ul>
<li class="chapter" data-level="4.5.1" data-path="id_04_model_comparisons.html"><a href="id_04_model_comparisons.html#analysis-4"><i class="fa fa-check"></i><b>4.5.1</b> Analysis</a></li>
<li class="chapter" data-level="4.5.2" data-path="id_04_model_comparisons.html"><a href="id_04_model_comparisons.html#plotting-2"><i class="fa fa-check"></i><b>4.5.2</b> Plotting</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="5" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html"><i class="fa fa-check"></i><b>5</b> Model interpretation</a>
<ul>
<li class="chapter" data-level="5.1" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#proximity-matrix-calculation"><i class="fa fa-check"></i><b>5.1</b> Proximity matrix calculation</a>
<ul>
<li class="chapter" data-level="5.1.1" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#analysis-5"><i class="fa fa-check"></i><b>5.1.1</b> Analysis</a>
<ul>
<li class="chapter" data-level="5.1.1.1" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#pv-data-set-3"><i class="fa fa-check"></i><b>5.1.1.1</b> Pv data set</a></li>
<li class="chapter" data-level="5.1.1.2" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#pf-pv-combined-data-set-3"><i class="fa fa-check"></i><b>5.1.1.2</b> Pf + Pv combined data set</a></li>
</ul></li>
<li class="chapter" data-level="5.1.2" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#plotting-3"><i class="fa fa-check"></i><b>5.1.2</b> Plotting</a>
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<li class="chapter" data-level="5.1.2.1" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#pf-pv-combined-data-set-4"><i class="fa fa-check"></i><b>5.1.2.1</b> Pf + Pv combined data set</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="5.2" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#clustering-of-predicted-positives"><i class="fa fa-check"></i><b>5.2</b> Clustering of predicted positives</a>
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<li class="chapter" data-level="5.2.1" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#analysis-6"><i class="fa fa-check"></i><b>5.2.1</b> Analysis</a></li>
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<li class="chapter" data-level="5.3" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#variable-importance"><i class="fa fa-check"></i><b>5.3</b> Variable importance</a>
<ul>
<li class="chapter" data-level="5.3.1" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#analysis-7"><i class="fa fa-check"></i><b>5.3.1</b> Analysis</a>
<ul>
<li class="chapter" data-level="5.3.1.1" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#pv-data-set-4"><i class="fa fa-check"></i><b>5.3.1.1</b> Pv data set</a></li>
<li class="chapter" data-level="5.3.1.2" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#pf-pv-combined-data-set-5"><i class="fa fa-check"></i><b>5.3.1.2</b> Pf + Pv combined data set</a></li>
</ul></li>
<li class="chapter" data-level="5.3.2" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#plotting-4"><i class="fa fa-check"></i><b>5.3.2</b> Plotting</a>
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<li class="chapter" data-level="5.3.2.1" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#pv-data-set-5"><i class="fa fa-check"></i><b>5.3.2.1</b> Pv data set</a></li>
<li class="chapter" data-level="5.3.2.2" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#pf-pv-combined-data-set-6"><i class="fa fa-check"></i><b>5.3.2.2</b> Pf + Pv combined data set</a></li>
</ul></li>
<li class="chapter" data-level="5.3.3" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#comparison-of-top-10-important-variables"><i class="fa fa-check"></i><b>5.3.3</b> Comparison of top 10 important variables</a>
<ul>
<li class="chapter" data-level="5.3.3.1" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#venn-diagram"><i class="fa fa-check"></i><b>5.3.3.1</b> Venn diagram</a></li>
<li class="chapter" data-level="5.3.3.2" data-path="id_05_model_interpretation.html"><a href="id_05_model_interpretation.html#top-10-variables-from-combined-model"><i class="fa fa-check"></i><b>5.3.3.2</b> Top 10 variables from combined model</a></li>
</ul></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="6" data-path="id_06_top_candidate_comparisons.html"><a href="id_06_top_candidate_comparisons.html"><i class="fa fa-check"></i><b>6</b> Top candidate comparisons</a>
<ul>
<li class="chapter" data-level="6.1" data-path="id_06_top_candidate_comparisons.html"><a href="id_06_top_candidate_comparisons.html#clustering-analysis"><i class="fa fa-check"></i><b>6.1</b> Clustering analysis</a>
<ul>
<li class="chapter" data-level="6.1.1" data-path="id_06_top_candidate_comparisons.html"><a href="id_06_top_candidate_comparisons.html#analysis-8"><i class="fa fa-check"></i><b>6.1.1</b> Analysis</a></li>
</ul></li>
<li class="chapter" data-level="6.2" data-path="id_06_top_candidate_comparisons.html"><a href="id_06_top_candidate_comparisons.html#gene-ontology-analysis"><i class="fa fa-check"></i><b>6.2</b> Gene ontology analysis</a>
<ul>
<li class="chapter" data-level="6.2.1" data-path="id_06_top_candidate_comparisons.html"><a href="id_06_top_candidate_comparisons.html#analysis-9"><i class="fa fa-check"></i><b>6.2.1</b> Analysis</a></li>
<li class="chapter" data-level="6.2.2" data-path="id_06_top_candidate_comparisons.html"><a href="id_06_top_candidate_comparisons.html#plotting-5"><i class="fa fa-check"></i><b>6.2.2</b> Plotting</a></li>
</ul></li>
<li class="chapter" data-level="6.3" data-path="id_06_top_candidate_comparisons.html"><a href="id_06_top_candidate_comparisons.html#candidate-antigen-characterization"><i class="fa fa-check"></i><b>6.3</b> Candidate antigen characterization</a>
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<li class="chapter" data-level="6.3.1" data-path="id_06_top_candidate_comparisons.html"><a href="id_06_top_candidate_comparisons.html#processing-table"><i class="fa fa-check"></i><b>6.3.1</b> Processing table</a></li>
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<li class="chapter" data-level="7" data-path="id_07_summary_of_candidates.html"><a href="id_07_summary_of_candidates.html"><i class="fa fa-check"></i><b>7</b> Summary of candidates</a></li>
<li class="chapter" data-level="" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i>References</a></li>
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<li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>
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