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new b26c3d9 [SYSTEMDS-2877] TomekLink builtin function
b26c3d9 is described below
commit b26c3d91ad7d3af791407f91a521bd344b3d0edb
Author: JustYeti32 <[email protected]>
AuthorDate: Mon Mar 1 17:36:57 2021 +0100
[SYSTEMDS-2877] TomekLink builtin function
Closes #1186
---
scripts/builtin/tomeklink.dml | 101 +++++++++++++++++++++
.../java/org/apache/sysds/common/Builtins.java | 1 +
.../functions/builtin/BuiltinTomeklinkTest.java | 92 +++++++++++++++++++
src/test/scripts/functions/builtin/tomeklink.R | 32 +++++++
src/test/scripts/functions/builtin/tomeklink.dml | 27 ++++++
5 files changed, 253 insertions(+)
diff --git a/scripts/builtin/tomeklink.dml b/scripts/builtin/tomeklink.dml
new file mode 100644
index 0000000..71b2a75
--- /dev/null
+++ b/scripts/builtin/tomeklink.dml
@@ -0,0 +1,101 @@
+#-------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements. See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership. The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied. See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+#-------------------------------------------------------------
+#
+# UNDERSAMPLING TECHNIQUE;
+# COMPUTES TOMEK LINKS AND DROPS THEM FROM DATA MATRIX AND LABEL VECTOR
+# DROPS ONLY THE MAJORITY LABEL AND CORRESPONDING POINT OF TOMEK LINKS
+#
+# INPUT PARAMETERS:
+#
---------------------------------------------------------------------------------------------
+# NAME TYPE DEFAULT MEANING
+#
---------------------------------------------------------------------------------------------
+# X MATRIX --- Data Matrix (nxm)
+# y MATRIX --- Label Matrix (nx1)
+#
---------------------------------------------------------------------------------------------
+# OUTPUT:
+# X_under - Data Matrix without Tomek links
+# y_under - Labels corresponding to undersampled data
+# drop_idx - Indices of dropped rows/labels wrt input
+
+
+###### MAIN PART ######
+
+m_tomeklink = function(Matrix[Double] X, Matrix[Double] y)
+ return (Matrix[Double] X_under, Matrix[Double] y_under, Matrix[Double]
drop_idx) {
+ majority_label = 0
+ n = nrow(X)
+ m = ncol(X)
+
+ tomek_links = get_links(X, y, majority_label)
+
+ X_under = matrix(0, rows = 0, cols = m)
+ y_under = matrix(0, rows = 0, cols = 1)
+ drop_idx = matrix(0, rows = 0, cols = 1)
+
+ for (i in 1:nrow(X)) {
+ is_link = as.scalar(tomek_links[i, 1])
+ if (is_link == 1) {
+ X_under = rbind(X_under, X[i,])
+ y_under = rbind(y_under, y[i,])
+ drop_idx = rbind(drop_idx, matrix(i, rows = 1, cols = 1))
+ }
+ }
+}
+
+###### END MAIN PART ######
+
+###### UTILS ######
+
+# nearest nb function
----------------------------------------------------------
+get_nn = function(Matrix[Double] X)
+ return (Matrix[Double] nn) {
+ nn = matrix(0, rows = nrow(X), cols = 1)
+ for (i in 1:nrow(X)) {
+ dists = rowSums((X - X[i,])^2)
+ sort_dists = order(target = dists, by = 1, decreasing = FALSE,
index.return = TRUE)
+ nn[i, 1] = as.scalar(sort_dists[2, 1]) # nearest, not self
+ }
+}
+
+# find tomek link function
----------------------------------------------------
+get_links = function(Matrix[Double] X, Matrix[Double] y, double majority_label)
+ return (Matrix[Double] tomek_links) {
+ tomek_links = matrix(0, rows = nrow(X), cols = 1)
+ nn = get_nn(X)
+
+ for (index in 1:nrow(X)) {
+ # this is a tomek link according to R: ubTomek
https://rdrr.io/cran/unbalanced/src/R/ubTomek.R
+ # other sources define it as a pair of mutual nearest neighbor
+ # where exactly one endpoint has the majority label
+
+ nn_index = as.scalar(nn[index, 1])
+ label = as.scalar(y[index, 1])
+ nn_label = as.scalar(y[nn_index, 1])
+
+ if (label != majority_label) {
+ if (nn_label == majority_label) {
+ tomek_links[nn_index, 1] = 1
+ }
+ }
+ }
+}
+
+###### END UTILS ######
diff --git a/src/main/java/org/apache/sysds/common/Builtins.java
b/src/main/java/org/apache/sysds/common/Builtins.java
index c6723f8..a0c0222 100644
--- a/src/main/java/org/apache/sysds/common/Builtins.java
+++ b/src/main/java/org/apache/sysds/common/Builtins.java
@@ -225,6 +225,7 @@ public enum Builtins {
TANH("tanh", false),
TRACE("trace", false),
TO_ONE_HOT("toOneHot", true),
+ TOMEKLINK("tomeklink", true),
TYPEOF("typeof", false),
COUNT_DISTINCT("countDistinct",false),
COUNT_DISTINCT_APPROX("countDistinctApprox",false),
diff --git
a/src/test/java/org/apache/sysds/test/functions/builtin/BuiltinTomeklinkTest.java
b/src/test/java/org/apache/sysds/test/functions/builtin/BuiltinTomeklinkTest.java
new file mode 100644
index 0000000..a251242
--- /dev/null
+++
b/src/test/java/org/apache/sysds/test/functions/builtin/BuiltinTomeklinkTest.java
@@ -0,0 +1,92 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
+package org.apache.sysds.test.functions.builtin;
+
+import org.junit.Test;
+import org.apache.sysds.common.Types.ExecMode;
+import org.apache.sysds.lops.LopProperties.ExecType;
+import org.apache.sysds.runtime.matrix.data.MatrixValue.CellIndex;
+import org.apache.sysds.test.AutomatedTestBase;
+import org.apache.sysds.test.TestConfiguration;
+import org.apache.sysds.test.TestUtils;
+
+import java.util.HashMap;
+
+public class BuiltinTomeklinkTest extends AutomatedTestBase
+{
+ private final static String TEST_NAME = "tomeklink";
+ private final static String TEST_DIR = "functions/builtin/";
+ private static final String TEST_CLASS_DIR = TEST_DIR +
BuiltinTomeklinkTest.class.getSimpleName() + "/";
+
+ private final static double eps = 1e-3;
+ private final static int rows = 53;
+ private final static int cols = 6;
+
+ @Override
+ public void setUp() {
+ addTestConfiguration(TEST_NAME,new
TestConfiguration(TEST_CLASS_DIR, TEST_NAME,new String[]{"B"}));
+ }
+
+ @Test
+ public void testTomeklinkCP() {
+ runTomeklinkTest(ExecType.CP);
+ }
+
+ @Test
+ public void testTomeklinkSP() {
+ runTomeklinkTest(ExecType.SPARK);
+ }
+
+ private void runTomeklinkTest(ExecType instType)
+ {
+ ExecMode platformOld = setExecMode(instType);
+
+ try
+ {
+ loadTestConfiguration(getTestConfiguration(TEST_NAME));
+
+ String HOME = SCRIPT_DIR + TEST_DIR;
+ fullDMLScriptName = HOME + TEST_NAME + ".dml";
+ programArgs = new String[] {"-args", input("A"),
input("B"), output("C")};
+
+ fullRScriptName = HOME + TEST_NAME + ".R";
+ rCmd = "Rscript" + " " + fullRScriptName + " " +
inputDir() + " " + expectedDir();
+
+ //generate actual dataset
+ double[][] A = getRandomMatrix(rows, cols, -1, 1, 0.7, 1);
+ writeInputMatrixWithMTD("A", A, true);
+
+ double[][] B = getRandomMatrix(rows, 1, 0, 1, 0.5, 1);
+ B = TestUtils.round(B);
+ writeInputMatrixWithMTD("B", B, true);
+
+ runTest(true, false, null, -1);
+ runRScript(true);
+
+ //compare matrices
+ HashMap<CellIndex, Double> dmlfile =
readDMLMatrixFromOutputDir("C");
+ HashMap<CellIndex, Double> rfile =
readRMatrixFromExpectedDir("C");
+ TestUtils.compareMatrices(dmlfile, rfile, eps,
"Stat-DML", "Stat-R");
+ }
+ finally {
+ rtplatform = platformOld;
+ }
+ }
+}
diff --git a/src/test/scripts/functions/builtin/tomeklink.R
b/src/test/scripts/functions/builtin/tomeklink.R
new file mode 100644
index 0000000..a051db3
--- /dev/null
+++ b/src/test/scripts/functions/builtin/tomeklink.R
@@ -0,0 +1,32 @@
+#-------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements. See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership. The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied. See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+#-------------------------------------------------------------
+
+
+args = commandArgs(TRUE)
+
+library("unbalanced")
+library("Matrix")
+
+X = as.matrix(readMM(paste(args[1], "A.mtx", sep="")))
+y = as.matrix(readMM(paste(args[1], "B.mtx", sep="")))
+
+C = sort(ubTomek(X, y, verbose=FALSE)$id.rm)
+writeMM(as(C, "CsparseMatrix"), paste(args[2], "C", sep=""))
diff --git a/src/test/scripts/functions/builtin/tomeklink.dml
b/src/test/scripts/functions/builtin/tomeklink.dml
new file mode 100644
index 0000000..8ab9145
--- /dev/null
+++ b/src/test/scripts/functions/builtin/tomeklink.dml
@@ -0,0 +1,27 @@
+#-------------------------------------------------------------
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements. See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership. The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License. You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied. See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+#-------------------------------------------------------------
+
+
+X = read($1)
+y = read($2)
+
+[X_under, y_under, drop_idx] = tomeklink(X, y)
+write(drop_idx, $3) # sorted by default
