--- a
+++ b/build_dataset.sh
@@ -0,0 +1,159 @@
+#!/bin/bash
+
+# Capture the start time
+start_time=$(date +%s)
+
+# Read username and password (for PhysioNet)
+read -p "Username: " USERNAME
+read -s -p "Password: " PASSWORD
+
+# Define directories and file names
+MIMIC_CXR="https://physionet.org/files/mimic-cxr-jpg/2.0.0"
+CHEST_IMAGENOME_BASE="https://physionet.org/files/chest-imagenome/1.0.0"
+CHEST_IMAGENOME_SILVER="${CHEST_IMAGENOME_BASE}/silver_dataset"
+CHEST_IMAGENOME_GOLD="$CHEST_IMAGENOME_BASE/gold_dataset"
+CHEST_IMAGENOME_UTILS="$CHEST_IMAGENOME_BASE/utils/scene_postprocessing"
+CHEST_IMAGENOME_SEMANTICS="$CHEST_IMAGENOME_BASE/semantics"
+MIMIC_IV="https://physionet.org/files/mimiciv/2.2"
+
+# Define wget parameters for readability
+WGET_PARAMS="-r -N -c -np --user $USERNAME --password $PASSWORD"
+
+# Helper function to download and extract files
+download_and_extract() {
+    local file_url=$1
+    local destination_dir=$2
+    local file_name=$(basename "$file_url")
+
+    # Download the file
+    wget $WGET_PARAMS "$file_url"
+
+    # Extract if it's a zip file
+    if [[ "$file_name" == *.zip ]]; then
+        unzip -o "$destination_dir/$file_name" -d "$destination_dir" # -o: overwrite
+    fi
+
+    # Extract if it's a gzip file
+    if [[ "$file_name" == *.gz ]]; then
+        gzip -d "$destination_dir/$file_name"
+    fi
+}
+
+# Download MIMIC-CXR metadata
+download_and_extract "$MIMIC_CXR/mimic-cxr-2.0.0-metadata.csv.gz" "physionet.org/files/mimic-cxr-jpg/2.0.0"
+
+# Download Chest Imagenome files
+download_and_extract "$CHEST_IMAGENOME_SILVER/scene_graph.zip" "physionet.org/files/chest-imagenome/1.0.0/silver_dataset"
+download_and_extract "$CHEST_IMAGENOME_GOLD/gold_attributes_relations_500pts_500studies1st.txt" "physionet.org/files/chest-imagenome/1.0.0/gold_dataset"
+download_and_extract "$CHEST_IMAGENOME_GOLD/gold_bbox_coordinate_annotations_1000images.csv" "physionet.org/files/chest-imagenome/1.0.0/gold_dataset"
+download_and_extract "$CHEST_IMAGENOME_UTILS/scenegraph_postprocessing.py" "physionet.org/files/chest-imagenome/1.0.0/utils/scene_postprocessing"
+download_and_extract "$CHEST_IMAGENOME_SEMANTICS/attribute_relations_v1.txt" "physionet.org/files/chest-imagenome/1.0.0/semantics"
+download_and_extract "$CHEST_IMAGENOME_SEMANTICS/label_to_UMLS_mapping.json" "physionet.org/files/chest-imagenome/1.0.0/semantics"
+download_and_extract "$CHEST_IMAGENOME_SEMANTICS/objects_extracted_from_reports_v1.txt" "physionet.org/files/chest-imagenome/1.0.0/semantics"
+
+# Download MIMIC-IV hosp modules
+download_and_extract "$MIMIC_IV/hosp/admissions.csv.gz" "physionet.org/files/mimiciv/2.2/hosp"
+download_and_extract "$MIMIC_IV/hosp/diagnoses_icd.csv.gz" "physionet.org/files/mimiciv/2.2/hosp"
+download_and_extract "$MIMIC_IV/hosp/d_icd_diagnoses.csv.gz" "physionet.org/files/mimiciv/2.2/hosp"
+download_and_extract "$MIMIC_IV/hosp/d_icd_procedures.csv.gz" "physionet.org/files/mimiciv/2.2/hosp"
+download_and_extract "$MIMIC_IV/hosp/d_labitems.csv.gz" "physionet.org/files/mimiciv/2.2/hosp"
+download_and_extract "$MIMIC_IV/hosp/labevents.csv.gz" "physionet.org/files/mimiciv/2.2/hosp"
+download_and_extract "$MIMIC_IV/hosp/microbiologyevents.csv.gz" "physionet.org/files/mimiciv/2.2/hosp"
+download_and_extract "$MIMIC_IV/hosp/patients.csv.gz" "physionet.org/files/mimiciv/2.2/hosp"
+download_and_extract "$MIMIC_IV/hosp/prescriptions.csv.gz" "physionet.org/files/mimiciv/2.2/hosp"
+download_and_extract "$MIMIC_IV/hosp/procedures_icd.csv.gz" "physionet.org/files/mimiciv/2.2/hosp"
+download_and_extract "$MIMIC_IV/hosp/transfers.csv.gz" "physionet.org/files/mimiciv/2.2/hosp"
+
+# Download MIMIC-IV icu modules
+download_and_extract "$MIMIC_IV/icu/chartevents.csv.gz" "physionet.org/files/mimiciv/2.2/icu"
+download_and_extract "$MIMIC_IV/icu/d_items.csv.gz" "physionet.org/files/mimiciv/2.2/icu"
+download_and_extract "$MIMIC_IV/icu/icustays.csv.gz" "physionet.org/files/mimiciv/2.2/icu"
+download_and_extract "$MIMIC_IV/icu/inputevents.csv.gz" "physionet.org/files/mimiciv/2.2/icu"
+download_and_extract "$MIMIC_IV/icu/outputevents.csv.gz" "physionet.org/files/mimiciv/2.2/icu"
+
+# Save currentdirectory
+orig_dir=$(pwd)
+
+# Change directory and run python script
+if [ ! -f "physionet.org/files/chest-imagenome/1.0.0/silver_dataset/scene_tabular/attribute_relations_tabular.txt" ] || [ ! -f "physionet.org/files/chest-imagenome/1.0.0/silver_dataset/scene_tabular/bbox_objects_tabular.txt" ]; then
+    cd "physionet.org/files/chest-imagenome/1.0.0/utils/scene_postprocessing"
+
+    echo '{
+        "SCENE_DIR": "../../silver_dataset/scene_graph",
+        "OUTPUT_DIR": "../../silver_dataset/scene_tabular",
+        "OUTPUT_TYPE": ["attributes", "objects"],
+        "RDF_LEVEL": "study_id",
+        "RESOURCE": "../../semantics/label_to_UMLS_mapping.json",
+        "AGGREGATION": "last",
+        "INCLUDE_SECTIONS": "all"
+    }' > scenegraph_postprocessing_settings.json
+    python scenegraph_postprocessing.py
+    echo "Done with scene postprocessing"
+fi
+
+# Return to the original directory
+cd "$orig_dir"
+
+# Preprocessing and generate dataset
+SAVE_DIR="dataset_builder/preprocessed_data/"
+PREPROCESS_SCRIPTS=("preprocess_cohort.py" "preprocess_label.py")
+SPLITS=("train" "valid" "test")
+
+mkdir -p "$SAVE_DIR"
+
+for split in "${SPLITS[@]}"; do
+    if [ ! -f "${SAVE_DIR}/${split}_dataset.csv" ]; then
+        for script in "${PREPROCESS_SCRIPTS[@]}"; do
+            python "dataset_builder/${script}" \
+                --mimic_cxr_jpg_dir "physionet.org/files/mimic-cxr-jpg/2.0.0/" \
+                --chest_imagenome_dir "physionet.org/files/chest-imagenome/1.0.0/" \
+                --save_dir "$SAVE_DIR"
+        done
+    fi
+done
+
+# DB preprocessing code
+declare -A splits=( ["test"]=400 ["train"]=800 )  # Array of splits and their corresponding number of patients
+
+for split in "${!splits[@]}"; do
+    num_patient=${splits[$split]}
+    
+    echo "Processing $split split with $num_patient patients..."
+    
+    python dataset_builder/preprocess_db.py \
+    --split "$split" \
+    --mimic_iv_dir "physionet.org/files/mimiciv/2.2/" \
+    --mimic_cxr_jpg_dir "physionet.org/files/mimic-cxr-jpg/2.0.0/" \
+    --chest_imagenome_dir "physionet.org/files/chest-imagenome/1.0.0/" \
+    --db_name mimic_iv_cxr \
+    --out_dir "./database" \
+    --deid \
+    --timeshift \
+    --current_time "2105-12-31 23:59:00" \
+    --start_year 2100 \
+    --time_span 5 \
+    --cur_patient_ratio 0.1 \
+    --num_patient $num_patient
+done
+
+echo "Database preprocessing complete."
+
+# Answer generation code
+for split in "${SPLITS[@]}"; do
+    python dataset_builder/generate_answer.py \
+        --mimic_iv_dir "physionet.org/files/mimiciv/2.2/" \
+        --mimic_cxr_jpg_dir "physionet.org/files/mimic-cxr-jpg/2.0.0/" \
+        --chest_imagenome_dir "physionet.org/files/chest-imagenome/1.0.0/" \
+        --json_file_path "dataset/mimic_iv_cxr/_${split}.json" \
+        --db_file_path "database/mimic_iv_cxr/${split}/mimic_iv_cxr.db" \
+        --output_path "dataset/mimic_iv_cxr/${split}.json"
+done
+
+# Capture the end time
+end_time=$(date +%s)
+
+# Calculate the runtime
+runtime=$((end_time - start_time))
+
+# Display the runtime
+echo "Script runtime: $runtime seconds"
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