Add Mahalanobis distance and update Normal.LogProb

distmv/normal.go

@@ -11,6 +11,7 @@ import (
 
 	"github.com/gonum/floats"
 	"github.com/gonum/matrix/mat64"
+	"github.com/gonum/stat"
 	"github.com/gonum/stat/distuv"
 )
 
@@ -183,17 +184,9 @@ func (n *Normal) LogProb(x []float64) float64 {
 	if len(x) != dim {
 		panic(badSizeMismatch)
 	}
-	// Compute the normalization constant
 	c := -0.5*float64(dim)*logTwoPi - n.logSqrtDet
-
+	dst := stat.Mahalanobis(mat64.NewVector(dim, x), mat64.NewVector(dim, n.mu), &n.chol)
-	// Compute (x-mu)'Sigma^-1 (x-mu)
+	return c - 0.5*dst*dst
-	xMinusMu := make([]float64, dim)
-	floats.SubTo(xMinusMu, x, n.mu)
-	d := mat64.NewVector(dim, xMinusMu)
-	tmp := make([]float64, dim)
-	tmpVec := mat64.NewVector(dim, tmp)
-	tmpVec.SolveCholeskyVec(&n.chol, d)
-	return c - 0.5*floats.Dot(tmp, xMinusMu)
 }
 
 // MarginalNormal returns the marginal distribution of the given input variables.

statmat.go

@@ -128,3 +128,20 @@ func corrToCov(c *mat64.SymDense, sigma []float64) {
 		}
 	}
 }
+
+// Mahalanobis computes the Mahalanobis distance
+//  D = sqrt((x-y)^T * Σ^-1 * (x-y))
+// between the vectors x and y given the cholesky decomposition of Σ.
+// Mahalanobis returns NaN if the linear solve fails.
+//
+// See https://en.wikipedia.org/wiki/Mahalanobis_distance for more information.
+func Mahalanobis(x, y *mat64.Vector, chol *mat64.Cholesky) float64 {
+	var diff mat64.Vector
+	diff.SubVec(x, y)
+	var tmp mat64.Vector
+	err := tmp.SolveCholeskyVec(chol, &diff)
+	if err != nil {
+		return math.NaN()
+	}
+	return math.Sqrt(mat64.Dot(&tmp, &diff))
+}

statmat_test.go

@@ -262,6 +262,36 @@ func TestCorrCov(t *testing.T) {
 	}
 }
 
+func TestMahalanobis(t *testing.T) {
+	// Comparison with scipy.
+	for cas, test := range []struct {
+		x, y  *mat64.Vector
+		Sigma *mat64.SymDense
+		ans   float64
+	}{
+		{
+			x: mat64.NewVector(3, []float64{1, 2, 3}),
+			y: mat64.NewVector(3, []float64{0.8, 1.1, -1}),
+			Sigma: mat64.NewSymDense(3,
+				[]float64{
+					0.8, 0.3, 0.1,
+					0.3, 0.7, -0.1,
+					0.1, -0.1, 7}),
+			ans: 1.9251757377680914,
+		},
+	} {
+		var chol mat64.Cholesky
+		ok := chol.Factorize(test.Sigma)
+		if !ok {
+			panic("bad test")
+		}
+		ans := Mahalanobis(test.x, test.y, &chol)
+		if math.Abs(ans-test.ans) > 1e-14 {
+			t.Errorf("Cas %d: got %v, want %v", cas, ans, test.ans)
+		}
+	}
+}
+
 // benchmarks
 
 func randMat(r, c int) mat64.Matrix {