update thesis

Author: AldisiRana

content/methods.tex

@@ -137,12 +137,8 @@ \section{Binary Classification}
 
 A logistic regression model was used for binary classification to predict edges between a given pair of nodes.
 The logistic regression is one of the most popular statistical models used for binary classification because it is simple, easy to interpret, and proven to perform well in many classification and prediction tasks.
-The results of the classifier are interpreted using two measures, $p$-value and minus log probability.
-The $p$-value is the probability that the null hypothesis is true.
-In this case, it is that a given edge does not exist between two nodes in the graph.
-The \ac{MLP} is also reported to enable easier interpretation.
-Generally, a $p$-value of less than 0.05, corresponding to an \ac{MLP} of greater than 1.3, is considered to be significant.
-It is worth mentioning that in this thesis, the $p$-value is mainly for ranking purposes, and multiple hypothesis testing correction was not employed.
+The results of the classifier were ranked using log odds ratio (LOR). The lower LOR is, the higher is the probability of the prediction to be true.
+
 
 \section{Evaluation Metrics}\label{evaluation_section}
 

content/results.tex

@@ -122,7 +122,7 @@ \section{Interpretation of Model Predictions}
 The predictions were created by querying the name or identifier of a certain entity.
 Furthermore, the type of entities to be predicted could also be specified.
 Three types of relations could be predicted using the model: drug-phenotype, drug-target, and target-phenotype.
-For each relation predicted, the $p$-value and \ac{MLP} value were calculated and used for ranking.
+For each relation predicted, the LOR was calculated and used for ranking.
 Since methods for drug-target associations, or drug target identification, are well developed, those association results were omitted from the interpretations.
 To validate the new predictions of the model, positive controls were also presented for drug-phenotype associations.
 
@@ -135,29 +135,29 @@ \subsection{Predicting the Phenotypes for a Drug}
 
 \begin{table}[!ht]
     \centering
-    \begin{tabular}{|l|l|l|r|r|}
+    \begin{tabular}{|l|l|l|r|}
         \hline
-        \textbf{Namespace} & \textbf{Identifier} & \textbf{Name} & \textbf{$p$-value} & \textbf{MLP} \\
+        \textbf{Namespace} & \textbf{Identifier} & \textbf{Name} & \textbf{LOR} \\
         \hline
-        umls & C0006384 & Bundle branch block & 0.000 & 3.475 \\
+        umls & C0006384 & Bundle branch block & 0.000 \\
         \hline
-        umls & C0575090 & Balance disorder & 0.000 & 3.539 \\
+        umls & C0575090 & Balance disorder & 0.000 \\
         \hline
-        umls & C0878544 & Cardiomyopathy & 0.001 & 2.918 \\
+        umls & C0878544 & Cardiomyopathy & 0.001 \\
         \hline
-        umls & C0233794 & Memory impairment & 0.001 & 2.870 \\
+        umls & C0233794 & Memory impairment & 0.001\\
         \hline
-        umls & C0004239 & Atrial flutter & 0.001 & 3.297 \\
+        umls & C0004239 & Atrial flutter & 0.001 \\
         \hline
-        umls & C0160390 & Liver injury & 0.001 & 3.175 \\
+        umls & C0160390 & Liver injury & 0.001 \\
         \hline
-        umls & C0020676 & Hypothyroidism & 0.001 & 2.911 \\
+        umls & C0020676 & Hypothyroidism & 0.001\\
         \hline
-        umls & C0002884 & Hypochromic anaemia & 0.001 & 3.059 \\
+        umls & C0002884 & Hypochromic anaemia & 0.001 \\
         \hline
-        umls & C0034069 & Pulmonary fibrosis & 0.001 & 2.901 \\
+        umls & C0034069 & Pulmonary fibrosis & 0.001\\
         \hline
-        umls & C0233477 & Dysphoria & 0.001 & 3.066 \\
+        umls & C0233477 & Dysphoria & 0.001 \\
         \hline
     \end{tabular}
     \captionsetup{justification=centering}
@@ -185,17 +185,17 @@ \subsection{Predicting the Phenotypes for a Drug}
 
 \begin{table}[!ht]
     \centering
-    \begin{tabular}{|l|l|l|r|r|}
+    \begin{tabular}{|l|l|l|r|}
         \hline
-        \textbf{Namespace} & \textbf{Identifier} & \textbf{Name} & \textbf{$p$-value} & \textbf{MLP} \\
+        \textbf{Namespace} & \textbf{Identifier} & \textbf{Name} & \textbf{LOR} \\
         \hline
-        umls & C1320474 & Nuchal rigidity & 0.0 & 3.318 \\
+        umls & C1320474 & Nuchal rigidity & 0.0 \\
         \hline
-        umls & C0002453 & Amenorrhoea & 0.0 & 3.619 \\
+        umls & C0002453 & Amenorrhoea & 0.0  \\
         \hline
-        umls & C0011168 & Dysphagia & 0.0 & 3.408 \\
+        umls & C0011168 & Dysphagia & 0.0  \\
         \hline
-        umls & C0033117 & Priapism & 0.0 & 3.515 \\
+        umls & C0033117 & Priapism & 0.0 \\
         \hline
     \end{tabular}
     \captionsetup{justification=centering}
@@ -215,29 +215,29 @@ \subsection{Predicting the Drugs for a Phenotype}
 
 \begin{table}[!hb]
     \centering
-    \begin{tabular}{|l|l|l|r|r|}
+    \begin{tabular}{|l|l|l|r|}
         \hline
-        \textbf{Namespace} & \textbf{Identifier} & \textbf{Name} & \textbf{$p$-value} & \textbf{MLP} \\
+        \textbf{Namespace} & \textbf{Identifier} & \textbf{Name} & \textbf{LOR} \\
         \hline
-        pubchem.compound & 146570 & Escitalopram & 0.000 & 3.315 \\
+        pubchem.compound & 146570 & Escitalopram & 0.000 \\
         \hline
-        pubchem.compound & 5002 & Quetiapine & 0.001 & 2.883 \\
+        pubchem.compound & 5002 & Quetiapine & 0.001 \\
         \hline
-        pubchem.compound & 5486971 & Pregabalin & 0.001 & 3.111 \\
+        pubchem.compound & 5486971 & Pregabalin & 0.001 \\
         \hline
-        pubchem.compound & 68617 & Sertraline & 0.002 & 2.763 \\
+        pubchem.compound & 68617 & Sertraline & 0.002 \\
         \hline
-        pubchem.compound & 5719 & Zaleplon & 0.002 & 2.807 \\
+        pubchem.compound & 5719 & Zaleplon & 0.002  \\
         \hline
-        pubchem.compound & 60853 & Ziprasidone HCL & 0.002 & 2.613 \\
+        pubchem.compound & 60853 & Ziprasidone HCL & 0.002 \\
         \hline
-        pubchem.compound & 3345 & Fentanyl & 0.002 & 2.630 \\
+        pubchem.compound & 3345 & Fentanyl & 0.002  \\
         \hline
-        pubchem.compound & 5210 & Sibutramine & 0.002 & 2.613 \\
+        pubchem.compound & 5210 & Sibutramine & 0.002 \\
         \hline
-        pubchem.compound & 44602 & Arbaclofen & 0.003 & 2.554 \\
+        pubchem.compound & 44602 & Arbaclofen & 0.003 \\
         \hline
-        pubchem.compound & 154101 & Dexmethylphenidate & 0.003 & 2.475 \\
+        pubchem.compound & 154101 & Dexmethylphenidate & 0.003 \\
         \hline
     \end{tabular}
     \captionsetup{justification=centering}
@@ -285,17 +285,17 @@ \subsection{Predicting the Drugs for a Phenotype}
 
 \begin{table}[!ht]
     \centering
-    \begin{tabular}{|l|l|l|r|r|}
+    \begin{tabular}{|l|l|l|r|}
         \hline
-        \textbf{Namespace} & \textbf{Identifier} & \textbf{Name} & \textbf{$p$-value} & \textbf{MLP} \\
+        \textbf{Namespace} & \textbf{Identifier} & \textbf{Name} & \textbf{LOR} \\
         \hline
-        pubchem.compound & 26757 & Selegiline & 0.001 & 2.831 \\
+        pubchem.compound & 26757 & Selegiline & 0.001  \\
         \hline
-        pubchem.compound & 60795 & Aripiprazole & 0.001 & 2.856 \\
+        pubchem.compound & 60795 & Aripiprazole & 0.001 \\
         \hline
-        pubchem.compound & 5095 & Ropinirole & 0.001 & 2.997 \\
+        pubchem.compound & 5095 & Ropinirole & 0.001 \\
         \hline
-        pubchem.compound & 2801 & Clomipramine & 0.002 & 2.823 \\
+        pubchem.compound & 2801 & Clomipramine & 0.002 \\
         \hline
     \end{tabular}
     \captionsetup{justification=centering}
@@ -311,29 +311,29 @@ \subsection{Predicting the Phenotypes for a Target}
 
 \begin{table}[!ht]
     \centering
-    \begin{tabular}{ |l|l|l|r|r| }
+    \begin{tabular}{ |l|l|l|r| }
         \hline
-        \textbf{Namespace} & \textbf{Identifier} & \textbf{Name} & \textbf{$p$-value} & \textbf{MLP} \\
+        \textbf{Namespace} & \textbf{Identifier} & \textbf{Name} & \textbf{LOR}  \\
         \hline
-        umls & C0013384 & Dyskinesia & 0.009 & 2.070 \\
+        umls & C0013384 & Dyskinesia & 0.009  \\
         \hline
-        umls & C0015371 & Extrapyramidal disorder & 0.013 & 1.889 \\
+        umls & C0015371 & Extrapyramidal disorder & 0.013  \\
         \hline
-        umls & C0026837 & Muscle rigidity & 0.015 & 1.811 \\
+        umls & C0026837 & Muscle rigidity & 0.015  \\
         \hline
-        umls & C0234133 & Extrapyramidal symptoms & 0.022 & 1.649 \\
+        umls & C0234133 & Extrapyramidal symptoms & 0.022  \\
         \hline
-        umls & C0026961 & Mydriasis & 0.023 & 1.639 \\
+        umls & C0026961 & Mydriasis & 0.023  \\
         \hline
-        umls & C0013144 & Drowsiness & 0.025 & 1.605 \\
+        umls & C0013144 & Drowsiness & 0.025  \\
         \hline
-        umls & C0085631 & Agitation & 0.025 & 1.597 \\
+        umls & C0085631 & Agitation & 0.025  \\
         \hline
-        umls & C0686347 & Tardive dyskinesia & 0.038 & 1.419 \\
+        umls & C0686347 & Tardive dyskinesia & 0.038  \\
         \hline
-        umls & C0242422 & Parkinsonism & 0.044 & 1.356 \\
+        umls & C0242422 & Parkinsonism & 0.044  \\
         \hline
-        umls & C0235063 & Respiratory depression & 0.053 & 1.273 \\
+        umls & C0235063 & Respiratory depression & 0.053 \\
         \hline
     \end{tabular}
     \captionsetup{justification=centering}