New parameter learning options

The main change here is in the parameter learning methods.  The parameters that are learned at first (i.e., if there is no evidence) are the distributions that are found directly in the data. I had to create or significantly modify several BNT files for this.

If there is evidence, the parameters are learned using a Dirichlet prior. This only required a couple of small changes to the BNW parameter learning files.

1 files changed, 150 insertions, 0 deletions

diff --git a/sourcecodes/kfold_cv.php b/sourcecodes/kfold_cv.php
new file mode 100644
index 00000000..6cae9538
--- /dev/null
+++ b/sourcecodes/kfold_cv.php
@@ -0,0 +1,150 @@
+<?php 
+include("header_new.inc");
+include("input_validate.php");
+if($_GET["My_key"]!="")
+  $keyval=valid_keyval($_GET["My_key"]);
+if($_POST["My_key"]!="")
+  $keyval=valid_keyval($_POST["My_key"]);
+?>
+
+<?php
+$varName = "";
+$varNameErr = "";
+$nm_folds="";
+
+if ($_SERVER["REQUEST_METHOD"] == "POST") {
+  $nm_folds = (int)$_POST['nm_folds'];
+  if (empty($_POST["varName"])) {
+    $varNameErr = "Entering a variable name is required";
+  } else {
+    //    $varName = test_input($_POST["varName"]);
+    $varName = valid_input($_POST["varName"]);
+    $varNameErr = "1";
+    // check if name only contains letters and whitespace
+    //    if (!preg_match("/^[\w]*$/",$varName)) {
+    //      $varNameErr = "The input string contains characters that are not allowed";
+    //    }
+  }
+}
+
+
+function test_input($data) {
+  $data = trim($data);
+  $data = stripslashes($data);
+  $data = htmlspecialchars($data);
+  return $data;
+}
+
+?>
+
+
+<!-- Site navigation menu -->
+<ul class="navbar2">
+  <li><p>Network ID:<br><?php print($keyval);?></p></li>
+</ul>
+<ul class="navbar">
+  <li><a href="javascript:void(0);"
+  NAME="Network" title="Network" onClick=window.open("layout.php?My_key=<?php print($keyval);?>","_self");>Return to network</a>
+  <li><a href="javascript:void(0);"
+  NAME="CV_predictions" title="CV_pred" onClick=window.open("cv_predictions.php?My_key=<?php print($keyval);?>","_self");>Return to validation and predictions menu</a>
+
+  <li><a href="help.php">Help</a>
+  <li><a href="home.php">Home</a>
+
+
+</ul>
+
+
+
+
+<div id="outer">
+<!-- Main content -->
+
+<?php
+  $filename1="./data/".$keyval."kfoldCV.txt";
+  $filename2="./data/".$keyval."kfoldCV_temp.txt";
+if(file_exists($filename2))
+ {?>
+<br>
+  <h2> k-fold cross-validation results are being calculated</h2>
+<br>
+<?php
+ }
+ else if(file_exists($filename1))
+ {?>
+<br>
+    <h2> <a href=<?php $d="./data/".$keyval."kfoldCV.txt"; print($d);?>>View cross-validation results</a></h2>
+<br>
+<h3>Perform k-fold cross-validation of another network variable</h3>
+<p align="justify"> 
+ Enter the name of variable and number of folds below to validate predictions of that variable.
+<br>
+</p>
+<FORM METHOD="post" ACTION="<?php echo htmlspecialchars($_SERVER["PHP_SELF"]);?>">
+  Variable name:<INPUT TYPE="text" name="varName" value="<?php echo $varName;?>" style="padding: 2px 5px; border: 2px solid; border-color: black black black black; font-family: Georgia, ..., serif; font-size: 18px; display: block; height: 30px; width: 300px;">
+<span class="error"> <?php if($varNameErr!="1") {echo $varNameErr;};?></span>
+<br>
+    Number of folds:<br><SELECT NAME="nm_folds">
+     <option value="2">2</option>
+     <option value="3">3</option>
+     <option value="4">4</option>
+     <option value="5">5</option>
+     <option value="6">6</option>
+     <option value="7">7</option>
+     <option value="8">8</option>
+     <option value="9">9</option>
+     <option value="10">10</option>
+     </select>
+     <input type='hidden' name='My_key' value='<?php print($keyval)?>'>
+     <br><br><input type="submit" name="submit" value="Submit" style="display: block; height: 30px; width:100px; font-family: Georgia, ..., serif; font-size: 16px;">
+</FORM>
+<br>
+<?php
+     } else {
+?>
+<h2>Perform k-fold cross-validation of network</h2>
+<p align="justify"> 
+  To perform cross-validation, enter the name of the variable <br>that you want to test the predictions of and the number <br>of folds that the data should be separated into below.
+<br>
+<FORM METHOD="post" ACTION="<?php echo htmlspecialchars($_SERVER["PHP_SELF"]);?>">
+  Variable Name:<INPUT TYPE="text" name="varName" value="<?php echo $varName;?>" 
+  style="padding: 2px 5px; border: 2px solid; border-color: black black black black; font-family: Georgia, ..., serif; font-size: 18px; display: block; height: 30px; width: 300px;">
+  <span class="error"> <?php if($varNameErr!="1") {echo $varNameErr;};?></span>
+  <br>
+     Number of folds:<br><SELECT NAME="nm_folds">
+     <option value="2">2</option>
+     <option value="3">3</option>
+     <option value="4">4</option>
+     <option value="5">5</option>
+     <option value="6">6</option>
+     <option value="7">7</option>
+     <option value="8">8</option>
+     <option value="9">9</option>
+     <option value="10">10</option>
+     </select>
+     <input type='hidden' name='My_key' value='<?php print($keyval)?>'>
+     <br><br><input type="submit" name="submit" value="Submit" style="display: block; height: 30px; width:100px; font-family: Georgia, ..., serif; font-size: 16px;">
+</FORM>
+</p>
+<br>
+
+<?php
+}
+
+if($nm_folds!="")
+{
+  $command = './run_kfold '.$keyval.' '.$varName.' '.$nm_folds;
+  $output = shell_exec("$command > /dev/null 2 > /dev/null &");
+  $pred_link='cv_predictions.php?My_key='.$keyval;
+  sleep(1);
+  echo "<br>";
+  echo "Calculation submitted";
+  echo "<br>";
+  echo "<a href=$pred_link>Click to return to cross-validation and predictions menu</a>";
+}
+?>
+
+</div>
+</body>
+
+