Implement METRIC.NaNEuclidean

faiss/MetricType.h

@@ -33,6 +33,7 @@ enum MetricType {
     METRIC_JensenShannon,
     METRIC_Jaccard, ///< defined as: sum_i(min(a_i, b_i)) / sum_i(max(a_i, b_i))
                     ///< where a_i, b_i > 0
+    METRIC_NaNEuclidean,
 };
 
 /// all vector indices are this type

faiss/utils/extra_distances-inl.h

@@ -10,6 +10,7 @@
 
 #include <faiss/MetricType.h>
 #include <faiss/utils/distances.h>
+#include <cmath>
 #include <type_traits>
 
 namespace faiss {
@@ -130,4 +131,23 @@ inline float VectorDistance<METRIC_Jaccard>::operator()(
     return accu_num / accu_den;
 }
 
+template <>
+inline float VectorDistance<METRIC_NaNEuclidean>::operator()(
+        const float* x,
+        const float* y) const {
+    // https://scikit-learn.org/stable/modules/generated/sklearn.metrics.pairwise.nan_euclidean_distances.html
+    float accu = 0;
+    size_t present = 0;
+    for (size_t i = 0; i < d; i++) {
+        if (!std::isnan(x[i]) && !std::isnan(y[i])) {
+            float diff = x[i] - y[i];
+            accu += diff * diff;
+            present++;
+        }
+    }
+    if (present == 0) {
+        return NAN;
+    }
+    return float(d) / float(present) * accu;
+}
 } // namespace faiss

faiss/utils/extra_distances.cpp

@@ -164,6 +164,7 @@ void pairwise_extra_distances(
         HANDLE_VAR(JensenShannon);
         HANDLE_VAR(Lp);
         HANDLE_VAR(Jaccard);
+        HANDLE_VAR(NaNEuclidean);
 #undef HANDLE_VAR
         default:
             FAISS_THROW_MSG("metric type not implemented");
@@ -195,6 +196,7 @@ void knn_extra_metrics(
         HANDLE_VAR(JensenShannon);
         HANDLE_VAR(Lp);
         HANDLE_VAR(Jaccard);
+        HANDLE_VAR(NaNEuclidean);
 #undef HANDLE_VAR
         default:
             FAISS_THROW_MSG("metric type not implemented");
@@ -242,6 +244,7 @@ FlatCodesDistanceComputer* get_extra_distance_computer(
         HANDLE_VAR(JensenShannon);
         HANDLE_VAR(Lp);
         HANDLE_VAR(Jaccard);
+        HANDLE_VAR(NaNEuclidean);
 #undef HANDLE_VAR
         default:
             FAISS_THROW_MSG("metric type not implemented");

tests/test_extra_distances.py

@@ -94,6 +94,26 @@ def test_jaccard(self):
         new_dis = faiss.pairwise_distances(xq, yb, faiss.METRIC_Jaccard)
         self.assertTrue(np.allclose(ref_dis, new_dis))
 
+    def test_nan_euclidean(self):
+        xq, yb = self.make_example()
+        ref_dis = np.array([
+            [scipy.spatial.distance.sqeuclidean(x, y) for y in yb]
+            for x in xq
+        ])
+        new_dis = faiss.pairwise_distances(xq, yb, faiss.METRIC_NaNEuclidean)
+        self.assertTrue(np.allclose(ref_dis, new_dis))
+
+        x = [[3, np.nan, np.nan, 6]]
+        q = [[1, np.nan, np.nan, 5]]
+        dis = [(4 / 2 * ((3 - 1)**2 + (6 - 5)**2))]
+        new_dis = faiss.pairwise_distances(x, q, faiss.METRIC_NaNEuclidean)
+        self.assertTrue(np.allclose(new_dis, dis))
+
+        x = [[np.nan] * 4]
+        q = [[np.nan] * 4]
+        new_dis = faiss.pairwise_distances(x, q, faiss.METRIC_NaNEuclidean)
+        self.assertTrue(np.isnan(new_dis[0]))
+
 
 class TestKNN(unittest.TestCase):
     """ test that the knn search gives the same as distance matrix + argmin """