Updates to F_Measure

f_beta_ics_test.sh

@@ -0,0 +1,100 @@
+#!/bin/bash
+
+# Specify the single network pair to process
+network1="networks/CElegans.el"
+network2="networks/AThaliana.el"
+
+# Output files
+output_file="results.txt"
+error_log="error_log.txt"
+
+# Clean previous results
+> "$output_file"
+> "$error_log"
+
+# SANA command base
+sana_command_base="./sana2.0 -f_beta 1,z -fg1"
+
+# Range for 'a' values (10^1 to 10^100)
+declare -a a_values=()
+for ((i = 1; i <= 100; i++)); do
+    a_values+=($(bc <<< "10^$i"))
+done
+
+# Function to parse SANA output
+parse_sana_out() {
+    local file=$1
+    local ics1=0.0
+    local ics2=0.0
+    local f_beta=0.0
+    local ics_count=0
+
+    while IFS= read -r line; do
+        if [[ "$line" == "ics:"* && $ics_count -lt 2 ]]; then
+            if [[ $ics_count -eq 0 ]]; then
+                ics1=$(echo "$line" | awk -F ':' '{print $2}' | xargs)
+            else
+                ics2=$(echo "$line" | awk -F ':' '{print $2}' | xargs)
+            fi
+            ics_count=$((ics_count + 1))
+        elif [[ "$line" == *"f_beta:"* ]]; then
+            f_beta=$(echo "$line" | awk -F ':' '{print $2}' | xargs)
+        fi
+    done < "$file"
+
+    echo "$ics1 $ics2 $f_beta"
+}
+
+# Process the network pair
+echo "Processing: $network1 and $network2"
+
+# Iterate over all 'a' values
+for a in "${a_values[@]}"; do
+    echo "Running for a = $a"
+    suma_ics1=0
+    suma_ics2=0
+    suma_fbeta=0
+
+    for ((run = 1; run <= 10; run++)); do
+        echo "Run $run for a = $a"
+
+        sana_command="${sana_command_base/z/$a} $network1 -fg2 $network2"
+        eval "$sana_command > /dev/null"
+
+        PARA_STATUS=$?
+        if [[ $PARA_STATUS -ne 0 || ! -f "sana.out" ]]; then
+            echo "Error: Failed for $network1 and $network2, z = $a, run = $run" >> "$error_log"
+            continue
+        fi
+
+        # Parse `sana.out`
+        metrics=$(parse_sana_out "sana.out")
+        ics1=$(echo "$metrics" | awk '{print $1}')
+        ics2=$(echo "$metrics" | awk '{print $2}')
+        f_beta=$(echo "$metrics" | awk '{print $3}')
+
+        # Accumulate results
+        suma_ics1=$(bc -l <<< "$suma_ics1 + $ics1")
+        suma_ics2=$(bc -l <<< "$suma_ics2 + $ics2")
+        suma_fbeta=$(bc -l <<< "$suma_fbeta + $f_beta")
+
+        rm -f "sana.out"
+    done
+
+    # Compute averages
+    avg_ics1=$(bc -l <<< "$suma_ics1 / 10")
+    avg_ics2=$(bc -l <<< "$suma_ics2 / 10")
+    avg_fbeta=$(bc -l <<< "$suma_fbeta / 10")
+
+    # Save to file
+    {
+        echo "Network Pair: $network1 and $network2"
+        echo "a: $a"
+        echo "Average ics1: $avg_ics1"
+        echo "Average ics2: $avg_ics2"
+        echo "Average f_beta: $avg_fbeta"
+        echo ""
+    } >> "$output_file"
+done
+
+echo "Processing completed. Results saved to $output_file."

f_beta_s3_test.sh

@@ -0,0 +1,129 @@
+# List to store successful (Second Ec, F Measure) pairs
+declare -a results_list=()
+#!/bin/bash
+
+# List of networks to process
+networks=(
+    "networks/AThaliana.el"
+    "networks/CElegans.el"
+    "networks/DMelanogaster.el"
+    "networks/HSapiens.el"
+    "networks/human.el"
+
+)
+
+# Output files
+output_file="results.txt"
+error_log="error_log.txt"
+
+# SANA command base
+sana_command="./sana2.0 -f_beta 1,1 -fg1"
+
+# Clean previous results
+> "$output_file"
+> "$error_log"
+
+parse_sana_out() {
+    local file=$1
+    local s3=0.69
+    local f_beta=0.0
+    local s3_found=false
+
+    while IFS= read -r line; do
+        if [[ "$line" == "s3:"* && $s3_found == false ]]; then
+            s3=$(echo "$line" | awk -F ':' '{print $2}' | xargs)
+            s3_found=true
+        elif [[ "$line" == *"f_beta:"* ]]; then
+            f_beta=$(echo "$line" | awk -F ':' '{print $2}' | xargs)
+        fi
+    done < "$file"
+
+    echo "$s3 $f_beta"
+}
+
+# Function to check monotonicity
+check_monotonicity() {
+    local pairs=$1  # Pass array by name
+    local increasing=true
+    local decreasing=true
+
+    for ((k = 0; k < ${#pairs[@]} - 2; k+=2)); do
+        ec1=${pairs[k]}
+        fb1=${pairs[k+1]}
+        ec2=${pairs[k+2]}
+        fb2=${pairs[k+3]}
+
+        # Compare to check monotonicity
+        if (( $(echo "$ec1 <= $ec2" | bc -l) )); then
+            if (( $(echo "$fb1 > $fb2" | bc -l) )); then
+                increasing=false
+            fi
+        else
+            increasing=false
+        fi
+
+        if (( $(echo "$ec1 >= $ec2" | bc -l) )); then
+            if (( $(echo "$fb1 < $fb2" | bc -l) )); then
+                decreasing=false
+            fi
+        else
+            decreasing=false
+        fi
+    done
+
+    if [[ $increasing == true || $decreasing == true ]]; then
+        echo "Monotonic relationship detected."
+    else
+        echo "No monotonic relationship detected."
+    fi
+}
+
+
+# Process all pairs of networks
+for ((i = 0; i < ${#networks[@]}; i++)); do
+    for ((j = i + 1; j < ${#networks[@]}; j++)); do
+        network1=${networks[$i]}
+        network2=${networks[$j]}
+
+        echo "Processing: $network1 and $network2"
+        command="$sana_command $network1 -fg2 $network2 > /dev/null"
+        eval "$command"
+
+        PARA_STATUS=$?
+        if [[ $PARA_STATUS -ne 0 || ! -f "sana.out" ]]; then
+            echo "Error: Failed for $network1 and $network2" >> "$error_log"
+            continue
+        fi
+
+        # Parse `sana.out`
+        metrics=$(parse_sana_out "sana.out")
+        s3=$(echo "$metrics" | awk '{print $1}')
+        f_beta=$(echo "$metrics" | awk '{print $2}')
+
+        # Save results if valid
+        if [[ -n "$s3" && -n "$f_beta" ]]; then
+            results_list+=("$s3" "$f_beta")
+            {
+                echo "Network Pair: $network1 and $network2"
+                echo "s3: $s3"
+                echo "f_beta: $f_beta"
+                echo ""
+            } >> "$output_file"
+        else
+            echo "Invalid results for $network1 and $network2" >> "$failure_file"
+        fi
+
+        rm -f "sana.out"
+    done
+done
+
+# Check monotonicity after processing
+if [[ ${#results_list[@]} -gt 2 ]]; then
+    echo "Analyzing monotonicity..."
+    check_monotonicity results_list
+else
+    echo "Insufficient data for monotonicity analysis."
+fi
+
+# Final report
+echo "Processing completed."

f_beta_test.sh

@@ -0,0 +1,117 @@
+#!/bin/bash
+
+# List of networks to process
+networks=(
+    "networks/AThaliana.el"
+    "networks/CElegans.el"
+    "networks/DMelanogaster.el"
+    "networks/HSapiens.el"
+    "networks/human.el"
+    "networks/MMusculus-3.2.101.el"
+    "networks/MMusculus.el"
+    "networks/RNorvegicus.el"
+    "networks/SCerevisiae-3.2.101.el"
+    "networks/SCerevisiae.el"
+    "networks/SPombe.el"
+    "networks/syeast0.el"
+    "networks/syeast05.el"
+    "networks/syeast10.el"
+    "networks/syeast15.el"
+    "networks/syeast20.el"
+    "networks/syeast25.el"
+    "networks/yeast.el"
+)
+
+# Output files
+output_file="results.txt"
+failure_file="failures.txt"
+error_log="error_log.txt"
+
+# SANA command base
+sana_command="./sana2.0 -f_beta 1,0 -fg1"
+
+# Initialize failure counter
+failure_count=0
+
+# Clean previous results
+> "$output_file"
+> "$failure_file"
+> "$error_log"
+
+# Function to parse `sana.out`
+parse_sana_out() {
+    local file=$1
+    local second_ec=0.0
+    local f_beta=0.0
+    local ec_count=0
+
+    while IFS= read -r line; do
+        if [[ "$line" == *"ec:"* ]]; then
+            ec_value=$(echo "$line" | awk -F ':' '{print $2}' | xargs)
+            ec_count=$((ec_count + 1))
+            if [[ $ec_count -eq 2 ]]; then
+                second_ec=$ec_value
+            fi
+        elif [[ "$line" == *"f_beta:"* ]]; then
+            f_beta=$(echo "$line" | awk -F ':' '{print $2}' | xargs)
+        fi
+    done < "$file"
+
+    echo "$second_ec $f_beta"
+}
+
+# Process all pairs of networks
+for ((i = 0; i < ${#networks[@]}; i++)); do
+    for ((j = i + 1; j < ${#networks[@]}; j++)); do
+        network1=${networks[$i]}
+        network2=${networks[$j]}
+
+        # Build and run the SANA command
+        echo "Processing: $network1 and $network2"
+        command="$sana_command $network1 -fg2 $network2 > /dev/null"
+        eval "$command"
+
+        PARA_STATUS=$?
+        # Check if PARA_STATUS indicates an error
+        if [[ $PARA_STATUS -ne 0 ]]; then
+            echo "Error: Command failed for $network1 and $network2 with status $PARA_STATUS" >> "$error_log"
+            continue
+        fi
+
+        # Check if `sana.out` was created
+        if [[ ! -f "sana.out" ]]; then
+            echo "Error: `sana.out` not generated for $network1 and $network2" >> "$error_log"
+            continue
+        fi
+
+        # Parse `sana.out`
+        metrics=$(parse_sana_out "sana.out")
+        second_ec=$(echo "$metrics" | awk '{print $1}')
+        f_beta=$(echo "$metrics" | awk '{print $2}')
+
+        # Simulate a comparison to detect mismatches
+        if [[ "$second_ec" != "$second_ec" || "$f_beta" != "$f_beta" ]]; then
+            echo "Failure for $network1 and $network2" >> "$failure_file"
+            echo "EC: $second_ec, F-beta: $f_beta" >> "$failure_file"
+            echo "" >> "$failure_file"
+            failure_count=$((failure_count + 1))
+        fi
+
+        # Save results to file
+        {
+            echo "Network Pair: $network1 and $network2"
+            echo "ec: $second_ec"
+            echo "f_beta: $f_beta"
+            echo ""
+        } >> "$output_file"
+
+        # Clean up `sana.out`
+        rm -f "sana.out"
+    done
+done
+
+# Final report
+echo "Processing completed."
+echo "Total mismatches (failures): $failure_count"
+echo "Failures logged in $failure_file"
+echo "Command errors logged in $error_log"