--- a
+++ b/graph_algorithm/CrossValidation.java
@@ -0,0 +1,138 @@
+package GraphAlgorithm;
+
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import network.CommGeneticsLoader;
+import network.DisGraph;
+import network.SparseVector;
+import util.DCNOMIMUMLSIDmap;
+
+/**
+ * Implements leave one out cross validation to test the performance of disease genetics prediction
+ * @author zhengc
+ *
+ */
+public class CrossValidation {
+
+	private Map<String, Integer> generank = new HashMap<>();
+	
+	/**
+	 * Initiate and create a cross validation object 
+	 * @param cgg CommGeneticsGraph
+	 * @param dis query disease
+	 * @param genelist omim genes for query disease
+	 * @throws IOException
+	 */
+	public CrossValidation(DisGraph cgg, String dis, List<String> genelist) throws IOException {
+		String dis_id = null;
+		if (DCNOMIMUMLSIDmap.dcnnameidmap.containsKey(dis)) {
+			dis_id = DCNOMIMUMLSIDmap.dcnnameidmap.get(dis);
+		} else {
+			System.out.println("No such disease in this network!");
+		}
+		
+		List<String> dislist = new ArrayList<>();
+		dislist.add(dis);
+		SparseVector seed = RandomWalk.createSeedVector(dislist);
+		int dis_idx = CommGeneticsLoader.entry_index.get(dis_id);
+		
+		int count = 1;
+		for (String gene : genelist) {
+			System.out.println(count + " of " +  genelist.size());
+			if (CommGeneticsLoader.entry_index.containsKey(gene)) {
+				int gene_idx = CommGeneticsLoader.entry_index.get(gene);
+				cgg.removeEdge(dis_idx, gene_idx);
+				RandomWalk rw = new RandomWalk(cgg, seed, 0.2);
+				Map<String, Integer> result = rw.getRWRank();
+				int rank = result.get(gene);
+				generank.put(gene, rank);
+				count++;
+			}
+		}
+	}
+	
+	/**
+	 * Get disease OMIM gene ranking from leave one out cross validation 
+	 * @return disease OMIM gene ranking map
+	 */
+	public Map<String, Integer> getCV() {
+		return generank;
+	}
+	
+	/** 
+	 * Write leave one out cross validation to a file
+	 * @param cv disease OMIM gene ranking map
+	 * @param cvfile a file to be written
+	 * @throws IOException
+	 */
+	public static void saveCV(Map<String, Integer> cv, String cvfile) throws IOException {
+		BufferedWriter bw = new BufferedWriter(new FileWriter(new File(cvfile)));
+		bw.write("Gene" + ","  + "Rank" + "," + "Percentage" +  "\n");
+		for (String gene : cv.keySet()) {
+//			System.out.println(sortedgenemap.get(s));
+			int rank = cv.get(gene);
+			double perc = rank / CommGeneticsLoader.num_gene * 100;
+			bw.write(gene + "," + rank + "," + perc + "\n");
+		}
+		bw.close();
+	}
+	
+	public static void main(String[] args) throws IOException {
+		
+		System.out.println("Building network...");
+		
+		String dcnmapfile = "/Users/zhengc/workspace/FARES/data/FARES/map/term_umls_id_diso";
+		String omimmapfile = "/Users/zhengc/workspace/FARES/data/OMIM/map/OMIM_umls_id_diso";
+		util.DCNOMIMUMLSIDmap.createDCNIdNameMap(dcnmapfile);
+		util.DCNOMIMUMLSIDmap.createOMIMIdNameMap(omimmapfile);
+		
+		String DCN_dis = "dementia";
+		String OMIM_pat = "alzheimer";
+		
+		DCNOMIMUMLSIDmap domim = new DCNOMIMUMLSIDmap(DCN_dis, OMIM_pat);
+		Map<String, List<String>> dcn_omim = domim.getDCNOMIMUMLSIDmap();
+		
+		/*
+		 * Build the bipartite network
+		 */
+		String commnetfile = "/Users/zhengc/Projects/AD_comorbidity/data/fares_comm_net_conf_ISMB_final_public.txt";
+		String dmnfile = "/Users/zhengc/Projects/AD_comorbidity/data/dmn_dm.txt";
+		String ppifile = "/Users/zhengc/Projects/AD_comorbidity/data/gene_gene_string_cut.txt";
+		String disgenefile = "/Users/zhengc/workspace/FARES/data/OMIM/mapped_OMIM/OMIM_disease_gene_umls_id_diso";
+		DisGraph cgg = null;
+		try {
+//			cgg = CommGeneticsLoader.createCommGeneticsGraph(commnetfile, dmnfile, ppifile, disgenefile, dcn_omim);
+			cgg = CommGeneticsLoader.createCommGeneticsGraph(commnetfile, ppifile, disgenefile, dcn_omim);
+		} catch (IOException e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+		}
+		
+		System.out.println("Done!");
+		
+		/*
+		 * Cross validation
+		 */
+		System.out.println("Starting crossvalidate...");
+		
+		String genelistfile = "/Users/zhengc/Projects/AD_comorbidity/data/AD_omim_genes.txt";
+		List<String> genelist = util.FileToList.createListFromfile(genelistfile);
+		
+		CrossValidation cv = new CrossValidation(cgg, DCN_dis, genelist);
+		Map<String, Integer> generank = cv.getCV();
+		
+		for (String gene : generank.keySet()) {
+			System.out.println(gene + ": " + generank.get(gene));
+		}
+		
+		String cv_result_file = "/Users/zhengc/Projects/AD_comorbidity/results/evaluation/cv_result.csv";
+		saveCV(generank, cv_result_file);
+
+	}
+}