CoreMS 4.0.0__py3-none-any.whl

corems/molecular_id/calc/math_distance.py

@@ -0,0 +1,1637 @@
+import warnings
+
+import numpy as np
+import scipy.stats
+
+""" Collection of spectral similarity methods.
+
+Based on  Yuanyue Li code at https://github.com/YuanyueLi/SpectralEntropy/blob/master/spectral_entropy/math_distance.py 
+and paper: Li, Y., Kind, T., Folz, J. et al. Spectral entropy outperforms MS/MS dot product similarity for small-molecule compound identification. Nat Methods 18, 1524–1531 (2021). https://doi.org/10.1038/s41592-021-01331-z
+"""
+
+
+def entropy_distance(v, y):
+    """Calculate entropy distance between two vectors
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Entropy distance between v and y
+
+    """
+    merged = v + y
+    entropy_increase = (
+        2 * scipy.stats.entropy(merged)
+        - scipy.stats.entropy(v)
+        - scipy.stats.entropy(y)
+    )
+    return entropy_increase
+
+
+def _weight_intensity_for_entropy(x):
+    """Weight intensity for entropy
+
+    Parameters
+    ----------
+    x : array_like
+        Vector
+
+    Returns
+    -------
+    array_like
+        Weighted vector
+    """
+    if sum(x) > 0:
+        WEIGHT_START = 0.25
+        WEIGHT_SLOPE = 0.5
+
+        entropy_x = scipy.stats.entropy(x)
+        weight = WEIGHT_START + WEIGHT_SLOPE * entropy_x
+        x = np.power(x, weight)
+        x = x / sum(x)
+        return x
+
+
+def weighted_entropy_distance(v, y):
+    """Calculate weighted entropy distance between two vectors
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Weighted entropy distance between v and y
+    """
+    v = _weight_intensity_for_entropy(v)
+    y = _weight_intensity_for_entropy(y)
+
+    merged = v + y
+    entropy_increase = (
+        2 * scipy.stats.entropy(merged)
+        - scipy.stats.entropy(v)
+        - scipy.stats.entropy(y)
+    )
+    return entropy_increase
+
+
+def chebyshev_distance(v, y):
+    r"""Chebyshev distance
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Chebyshev distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        \underset{i}{\max}{(|v_{i}\ -\ y_{i}|)}
+    """
+    return np.max(np.abs(v - y))
+
+
+def squared_euclidean_distance(v, y):
+    r"""Squared Euclidean distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Squared Euclidean distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        \sum(v_{i}-y_{i})^2
+    """
+    return np.sum(np.power(v - y, 2))
+
+
+def fidelity_similarity(v, y):
+    r"""Fidelity similarity:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Fidelity similarity between v and y
+    Notes
+    -----
+    .. math::
+
+        \sum\sqrt{v_{i}y_{i}}
+    """
+    return np.sum(np.sqrt(v * y))
+
+
+def matusita_distance(v, y):
+    r"""Matusita distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Matusita distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        \sqrt{\sum(\sqrt{v_{i}}-\sqrt{y_{i}})^2}
+    """
+    return np.sqrt(np.sum(np.power(np.sqrt(v) - np.sqrt(y), 2)))
+
+
+def squared_chord_distance(v, y):
+    r"""Squared-chord distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Squared-chord distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        \sum(\sqrt{v_{i}}-\sqrt{y_{i}})^2
+    """
+    return np.sum(np.power(np.sqrt(v) - np.sqrt(y), 2))
+
+
+def bhattacharya_1_distance(v, y):
+    r"""Bhattacharya 1 distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Bhattacharya 1 distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        (\arccos{(\sum\sqrt{v_{i}y_{i}})})^2
+    """
+    s = np.sum(np.sqrt(v * y))
+    # TODO:Fix this!
+    if s > 1:
+        if s > 1 + 1e-6:
+            warnings.warn(
+                "Error in calculating Bhattacharya 1 distance, got arccos {}".format(s)
+            )
+        s = 1
+    return np.power(np.arccos(s), 2)
+
+
+def bhattacharya_2_distance(v, y):
+    r"""Bhattacharya 2 distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Bhattacharya 2 distance between v and y
+    Notes
+    -----
+    .. math::
+
+        -\ln{(\sum\sqrt{v_{i}y_{i}})}
+    """
+    s = np.sum(np.sqrt(v * y))
+    if s == 0:
+        return np.inf
+    else:
+        return -np.log(s)
+
+
+def harmonic_mean_similarity(v, y):
+    r"""Harmonic mean similarity:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Harmonic mean similarity between v and y
+
+    Notes
+    -----
+    .. math::
+
+        #1-2\sum(\frac{v_{i}y_{i}}{v_{i}+y_{i}})
+        2\sum(\frac{v_{i}y_{i}}{v_{i}+y_{i}})
+    """
+    # return 1 - 2 * np.sum(v * y / (v + y))
+    return 2 * np.sum(v * y / (v + y))
+
+
+# def pearson_chi_squared_distance(v, y):
+#    r"""
+#    Pearson χ2 distance:
+#
+#    .. math::
+#
+#        \sum\frac{(v_{i}-y_{i})^2}{y_{i}}
+#    """
+#    return np.sum(np.power(v - y, 2) / y)
+
+
+# def neyman_chi_squared_distance(v, y):
+#    r"""
+#    Neyman χ2 distance:
+#
+#    .. math::
+#
+#        \sum\frac{(v_{i}-y_{i})^2}{v_{i}}
+#    """
+#    return np.sum(np.power(v - y, 2) / v)
+
+
+# def probabilistic_symmetric_chi_squared_distance(v, y):
+#    r"""
+#    Probabilistic symmetric χ2 distance:
+#
+#    .. math::
+#
+#        \frac{1}{2} \times \sum\frac{(v_{i}-y_{i}\ )^2}{v_{i}+y_{i}\ }
+#    """
+#    return 1 / 2 * np.sum(np.power(v - y, 2) / (v + y))
+
+
+# def topsoe_distance(v, y):
+#    r"""
+#    Topsøe distance:
+#
+#    .. math::
+#
+#        \sum{(v_{i}ln\frac{v_{i}}{Z_i}+y_{i}ln\frac{y_{i}}{Z_i}),\ \ \ Z_i=\frac{1}{2}(v_{i}+y_{i})}
+#    """
+#    z = 1 / 2 * (v + y)
+#    z[z == 0] = 1
+#    vz = v / z
+#    yz = y / z
+#    vz[v == 0] = 1
+#    yz[y == 0] = 1
+#    return np.sum(v * np.log(vz) + y * np.log(yz))
+
+
+def chernoff_distance(v, y):
+    r"""Chernoff distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Chernoff distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        \max{(-ln\sum(v_{i}^ty_{i}^{1-t})^{1-t})},\ t=0.1,\ 0\le\ t<1
+    """
+    t = 0.1
+    return np.max(-np.log(np.sum(np.power(np.power(v, t) * np.power(y, 1 - t), 1 - t))))
+
+
+def ruzicka_distance(v, y):
+    r"""Ruzicka distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Ruzicka distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        \frac{\sum{|v_{i}-y_{i}|}}{\sum{\max(v_{i},y_{i})}}
+    """
+    dist = np.sum(np.abs(v - y)) / np.sum(np.maximum(v, y))
+    return dist
+
+
+def roberts_distance(v, y):
+    r"""Roberts distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Roberts distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        1-\sum\frac{(v_{i}+y_{i})\frac{\min{(v_{i},y_{i})}}{\max{(v_{i},y_{i})}}}{\sum(v_{i}+y_{i})}
+    """
+    return 1 - np.sum((v + y) * np.minimum(v, y) / np.maximum(v, y) / np.sum(v + y))
+
+
+def intersection_distance(v, y):
+    r"""Intersection distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Intersection distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        1-\frac{\sum\min{(v_{i},y_{i})}}{\min(\sum{v_{i},\sum{y_{i})}}}
+    """
+    return 1 - np.sum(np.minimum(v, y)) / min(np.sum(v), np.sum(y))
+
+
+def motyka_distance(v, y):
+    r"""Motyka distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Motyka distance between v and y
+    Notes
+    -----
+    .. math::
+
+        -\frac{\sum\min{(y_{i},v_{i})}}{\sum(y_{i}+v_{i})}
+    """
+    dist = np.sum(np.minimum(v, y)) / np.sum(v + y)
+    return dist
+
+
+def canberra_distance(v, y):
+    r"""Canberra distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Canberra distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        #\sum\frac{|v_{i}-y_{i}|}{|v_{i}|+|y_{i}|}
+        \sum_{i}\frac{|y_{i} - v_{i}|}{y_{i} + v_{i}}
+    """
+    # return np.sum(np.abs(v - y) / (np.abs(v) + np.abs(y)))
+    return np.sum(np.abs(y - v) / (y + v))
+
+
+def canberra_metric(v, y):
+    r"""Canberra Metric
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Canberra metric between v and y
+    Notes
+    -----
+    .. math::
+
+        \frac{1}{\sum_{i}I(v_{i}\neq 0)}\sum_{i}\frac{|y_{i}-v_{i}|}{(y_{i}+v_{i})}
+    """
+
+    return (1 / np.sum(v > 0)) * np.sum(np.abs(y - v) / (y + v))
+
+
+def kulczynski_1_distance(v, y):
+    r"""Kulczynski 1 distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Kulczynski 1 distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        \frac{\sum{|v_i}-y_i|}{\sum m\ i\ n\ (v_i,y_i)}
+    """
+    return np.sum(np.abs(y - v)) / np.sum(np.minimum(y, v))
+
+
+def baroni_urbani_buser_distance(v, y):
+    r"""Baroni-Urbani-Buser distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Baroni-Urbani-Buser distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        1-\frac{\sum\min{(v_i,y_i)}+\sqrt{\sum\min{(v_i,y_i)}\sum(\max{(v)}-\max{(v_i,y_i)})}}{\sum{\max{(v_i,y_i)}+\sqrt{\sum{\min{(v_i,y_i)}\sum(\max{(v)}-\max{(v_i,y_i)})}}}}
+    """
+    if np.max(v) < np.max(y):
+        v, y = y, v
+    d1 = np.sqrt(np.sum(np.minimum(v, y) * np.sum(max(v) - np.maximum(v, y))))
+    return 1 - (np.sum(np.minimum(v, y)) + d1) / (np.sum(np.maximum(v, y)) + d1)
+
+
+def penrose_size_distance(v, y):
+    r"""Penrose size distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Penrose size distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        \sqrt N\sum{|y_i-v_i|}
+    """
+    n = np.sum(v > 0)
+    return np.sqrt(n) * np.sum(np.abs(y - v))
+
+
+def mean_character_distance(v, y):
+    r"""
+    Mean character distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Mean character distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        \frac{1}{N}\sum{|y_i-v_i|}
+    """
+    n = np.sum(v > 0)
+    return 1 / n * np.sum(np.abs(y - v))
+
+
+def lorentzian_distance(v, y):
+    r"""
+    Lorentzian distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Lorentzian distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        \sum{\ln(1+|v_i-y_i|)}
+    """
+    return np.sum(np.log(1 + np.abs(y - v)))
+
+
+def penrose_shape_distance(v, y):
+    r"""
+    Penrose shape distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Penrose shape distance between v and y
+    Notes
+    -----
+    .. math::
+
+        \sqrt{\sum((v_i-\bar{v})-(y_i-\bar{y}))^2}
+    """
+    v_avg = np.mean(v)
+    y_avg = np.mean(y)
+    return np.sqrt(np.sum(np.power((y - y_avg) - (v - v_avg), 2)))
+
+
+def clark_distance(v, y):
+    r"""
+    Clark distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Clark distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        #(\frac{1}{N}\sum(\frac{v_i-y_i}{|v_i|+|y_i|})^2)^\frac{1}{2}
+        \sqrt{\sum(\frac{|v_i-y_i|}{v_i+y_i})^2}
+    """
+    # n = np.sum(v > 0)
+    # return np.sqrt(1 / n * np.sum(np.power((v - y) / (np.abs(v) + np.abs(y)), 2)))
+    return np.sqrt(np.sum(np.power(np.abs(y - v) / (y + v), 2)))
+
+
+def hellinger_distance(v, y):
+    r"""
+    Hellinger distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Hellinger distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        #\sqrt{2\sum(\sqrt{\frac{v_i}{\bar{v}}}-\sqrt{\frac{y_i}{\bar{y}}})^2}
+        \sqrt{2\sum(\sqrt{v_i}-\sqrt{y_i})^2}
+    """
+    # v_avg = np.mean(v)
+    # y_avg = np.mean(y)
+    # return np.sqrt(2 * np.sum(np.power(np.sqrt(v / v_avg) - np.sqrt(y / y_avg), 2)))
+    return np.sqrt(2 * np.sum(np.power(np.sqrt(y) - np.sqrt(v), 2)))
+
+
+def whittaker_index_of_association_distance(v, y):
+    r"""
+    Whittaker index of association distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Whittaker index of association distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        \frac{1}{2}\sum|\frac{v_i}{\bar{v}}-\frac{y_i}{\bar{y}}|
+    """
+    v_avg = np.mean(v)
+    y_avg = np.mean(y)
+    return 1 / 2 * np.sum(np.abs(v / v_avg - y / y_avg))
+
+
+# def symmetric_chi_squared_distance(v, y):
+#    r"""
+#    Symmetric χ2 distance:
+#
+#    .. math::
+#
+#        \sqrt{\sum{\frac{\bar{v}+\bar{y}}{N(\bar{v}+\bar{y})^2}\frac{(v_i\bar{y}-y_i\bar{v})^2}{v_i+y_i}\ }}
+#    """
+#    v_avg = np.mean(v)
+#    y_avg = np.mean(y)
+#    n = np.sum(v > 0)
+#
+#    d1 = (v_avg + y_avg) / (n * np.power(v_avg + y_avg, 2))
+#    return np.sqrt(d1 * np.sum(np.power(v * y_avg - y * v_avg, 2) / (v + y)))
+
+
+def similarity_index_distance(v, y):
+    r"""
+    Similarity Index Distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Similarity Index Distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        \sqrt{\frac{\sum\{\frac{v_i-y_i}{y_i}\}^2}{N}}
+    """
+    n = np.sum(v > 0)
+    return np.sqrt(1 / n * np.sum(np.power((v - y) / y, 2)))
+
+
+def improved_similarity_distance(v, y):
+    r"""
+    Improved Similarity Index:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Improved Similarity Index between v and y
+
+    Notes
+    -----
+    .. math::
+
+        \sqrt{\frac{1}{N}\sum\{\frac{y_i-v_i}{y_i+v_i}\}^2}
+    """
+    n = np.sum(v > 0)
+    return np.sqrt(1 / n * np.sum(np.power((y - v) / (y + v), 2)))
+
+
+def absolute_value_distance(v, y):
+    r"""
+    Absolute Value Distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Absolute Value Distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        \frac { \sum(|y_i-v_i|)}{\sum v_i}
+
+    """
+    dist = np.sum(np.abs(y - v)) / np.sum(v)
+    return dist
+
+
+def spectral_contrast_angle_distance(v, y):
+    r"""
+    Spectral Contrast Angle:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Spectral Contrast Angle between v and y
+
+    Notes
+    -----
+    .. math::
+
+        1 - \frac{\sum{y_iv_i}}{\sqrt{\sum y_i^2\sum v_i^2}}
+        \arccos(\frac{\sum_{P}y_{p}^* v_{p}^*}{\sqrt{\sum_{P}y_{p}^{*2} \sum_{P}v_{p}^{*2}}})
+    """
+    # return 1 - np.sum(y * v) / \
+    #       np.sqrt(np.sum(np.power(y, 2)) * np.sum(np.power(v, 2)))
+
+    return np.arccos(
+        np.sum(y * v) / (np.sqrt(np.sum(np.power(y, 2)) * np.sum(np.power(v, 2))))
+    )
+
+
+def wave_hedges_distance(v, y):
+    r"""
+    Wave Hedges distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Wave Hedges distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        \sum\frac{|v_i-y_i|}{\max{(v_i,y_i)}}
+    """
+    return np.sum(np.abs(v - y) / np.maximum(v, y))
+
+
+def dice_similarity(v, y):
+    r"""
+    Dice similarity:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Dice similarity between v and y
+
+    Notes
+    -----
+    .. math::
+
+        \frac{\sum(v_i-y_i)^2}{\sum v_i^2+\sum y_i^2}
+        \frac{2 * \sum_{i}v_{i}y_{i}}{\sum_{i}y_{i}^2 + \sum_{i}v_{i}^2}
+    """
+    return 2 * np.sum(v * y) / (np.sum(np.power(v, 2)) + np.sum(np.power(y, 2)))
+
+
+def inner_product_distance(v, y):
+    r"""
+    Inner Product distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Inner product distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        1-\sum{v_iy_i}
+    """
+    return 1 - np.sum(v * y)
+
+
+def divergence_distance(v, y):
+    r"""
+    Divergence distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Divergence distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        2\sum\frac{(v_i-y_i)^2}{(v_i+y_i)^2}
+    """
+    return 2 * np.sum((np.power(v - y, 2)) / np.power(v + y, 2))
+
+
+def _chi_squared_distance(v, y):
+    r"""
+    Additive symmetric χ2 distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Additive symmetric χ2 distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        \sum\frac{(v_i-y_i)^2(v_i+y_i)}{v_iy_i}
+    """
+    dist = np.sum(np.power(v - y, 2) * (v + y) / (v * y))
+    return dist
+
+
+def jensen_difference_distance(v, y):
+    r"""
+    Jensen difference:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Jensen difference distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        \sum[\frac{1}{2}(v_i\ln{v_i}+y_i\ln{y_i})-(\frac{v_i+y_i}{2})\ln{(\frac{v_i+y_i}{2})}]
+    """
+    y_v_avg = (y + v) / 2
+    return np.sum(1 / 2 * (y * np.log(y) + v * np.log(v)) - y_v_avg * np.log(y_v_avg))
+
+
+def kumar_johnson_distance(v, y):
+    r"""
+    Kumar-Johnson distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Kumar Johnson distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        \sum\frac{(v_i^2-y_i^2)^2}{2(v_iy_i)^\frac{3}{2}}
+    """
+    return np.sum(
+        np.power(np.power(v, 2) - np.power(y, 2), 2) / (2 * np.power(v * y, 3 / 2))
+    )
+
+
+def avg_l_distance(v, y):
+    r"""
+    Avg (L1, L∞) distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Average L distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        \frac{1}{2}(\sum|v_i-y_i|+\underset{i}{\max}{|v_i-y_i|})
+    """
+    return 1 / 2 * (np.sum(np.abs(v - y)) + max(np.abs(v - y)))
+
+
+def vicis_wave_hadges_distance(v, y):
+    r"""
+    Vicis-Wave Hadges distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Vicis Wave Hadges distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        \sum\frac{|v_i-y_i|}{\min{(v_i,\ y_i)}}
+    """
+    return np.sum(np.abs(v - y) / np.minimum(v, y))
+
+
+def vicis_symmetric_chi_squared_1_distance(v, y):
+    r"""
+    Vicis-Symmetric χ2 1 distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Vici Symmetric χ2 1 distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        \sum\frac{(v_i-y_i)^2}{\min{(v_i,y_i)^2}}
+    """
+    return np.sum(np.power(v - y, 2) / np.power(np.minimum(v, y), 2))
+
+
+def vicis_symmetric_chi_squared_2_distance(v, y):
+    r"""
+    Vicis-Symmetric χ2 2 distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Vicis Symmetric χ2 2 distance between v and y
+
+    Notes
+    -----
+
+    .. math::
+
+        \sum\frac{(v_i-y_i)^2}{\min{(v_i,y_i)}}
+    """
+    return np.sum(np.power(v - y, 2) / np.minimum(v, y))
+
+
+def vicis_symmetric_chi_squared_3_distance(v, y):
+    r"""
+    Vicis-Symmetric χ2 3 distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Vici Symmetric χ2 3 distance between v and y
+
+    Notes
+    -----
+
+    .. math::
+
+        \sum\frac{(v_i-y_i)^2}{\max{(v_i,y_i)}}
+    """
+    return np.sum(np.power(v - y, 2) / np.maximum(v, y))
+
+
+def max_symmetric_chi_squared_distance(v, y):
+    r"""
+    Max-Symmetric χ2 distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Max-Symmetric χ2 distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        \max{(\sum\frac{(v_i-y_i)^2}{v_i},\sum\frac{(v_i-y_i)^2}{y_i})}
+    """
+    return max(np.sum(np.power(v - y, 2) / v), np.sum(np.power(v - y, 2) / y))
+
+
+def min_symmetric_chi_squared_distance(v, y):
+    r"""
+    Min-Symmetric χ2 distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Min-Symmetric χ2 distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        \min{(\sum\frac{(v_i-y_i)^2}{v_i},\sum\frac{(v_i-y_i)^2}{y_i})}
+    """
+    return min(np.sum(np.power(v - y, 2) / v), np.sum(np.power(v - y, 2) / y))
+
+
+def additive_sym_chi_sq(v, y):
+    r"""
+    Additive Symmetric χ2 distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Additive Symmetric χ2 distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        \sum_{i}\frac{(y_{i} - v_{i})^2(y_{i}+v_{i})}{y_{i}v_{i}}
+    """
+    return np.sum((np.power(y - v, 2) * (y + v)) / (y * v))
+
+
+def bhattacharya_distance(v, y):
+    r"""
+    Bhattacharya Distance:
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Bhattcharya distance between v and y
+
+    Notes
+    -----
+    .. math::
+
+        -ln(\sum_{i}\sqrt{y_{i}v_{i}})
+    """
+    return -1 * np.log(np.sum(np.sqrt(y * v)))
+
+
+def generalized_ochiai_index(v, y):
+    r"""
+    Generalized Ochiai Index
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Generalized Ochiai Index between v and y
+
+    Notes
+    -----
+    .. math::
+
+        1 - \frac{\sum_{i}min(y_{i}, v_{i})}{\sqrt{\sum_{i}y_{i} \sum_{i}v_{i}}}
+    """
+
+    ind = np.sum(np.minimum(y, v)) / np.sqrt(np.sum(y) * np.sum(v))
+    return 1 - ind
+
+
+def gower_distance(v, y):
+    r"""
+    Gower Distance
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Gower distance between v and y
+
+    Notes
+    -----
+
+    .. math::
+
+        \frac{1}{N}\sum_{i}|y_{i} - v_{i}|
+    """
+
+    n = np.sum(y > 0)
+    return (1 / n) * np.sum(np.abs(y - v))
+
+
+def impr_sqrt_cosine_sim(v, y):
+    r"""
+    Improved Square Root Cosine Similarity
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Improved Square Root Cosine Similarity between v and y
+
+    Notes
+    -----
+    .. math::
+
+        \frac{\sum_{i}\sqrt{y_{i}v_{i}}}{\sum_{i}\sqrt{y_{i}}\sum_{i}\sqrt{v_{i}}}
+    """
+
+    return np.sum(np.sqrt(y * v)) / (np.sum(np.sqrt(y)) * np.sum(np.sqrt(v)))
+
+
+def intersection_sim(v, y):
+    r"""
+    Intersection Similarity
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Intersection Similarity between v and y
+
+    Notes
+    -----
+    .. math::
+
+        \sum_{i}min(y_{i}, v_{i})
+    """
+
+    return np.sum(np.minimum(y, v))
+
+
+def j_divergence(v, y):
+    r"""
+    J Divergence
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        J Divergence between v and y
+
+    Notes
+    -----
+    .. math::
+
+        \sum_{i}(y_{i} - v_{i}) ln(\frac{y_{i}}{v_{i}})
+    """
+
+    return np.sum((v - y) * np.log(v / y))
+
+
+def jensen_shannon_index(v, y):
+    r"""
+    Jensen-Shannon Index
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Jensen Shannon Index between v and y
+
+    Notes
+    -----
+    .. math::
+
+        \frac{1}{2}[\sum_{i}y_{i}ln(\frac{2y_{i}}{y_{i} + v_{i}}) + \sum_{i}v_{i}ln(\frac{2v_{i}}{y_{i}+v_{i}})]
+    """
+
+    return (1 / 2) * (
+        np.sum(y * np.log(2 * y / (y + v))) + np.sum(v * np.log(2 * v / (y + v)))
+    )
+
+
+def k_divergence(v, y):
+    r"""
+    K-Divergence
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        K-Divergence between v and y
+
+    Notes
+    -----
+    .. math::
+
+        \sum_{i}y_{i}ln(\frac{2y_{i}}{y_{i} + v_{i}})
+    """
+
+    return np.sum(v * np.log((2 * v) / (y + v)))
+
+
+def topsoe_distance(v, y):
+    r"""Topsoe distance
+
+    Parameters
+    ----------
+    v : array_like
+        Vector 1
+    y : array_like
+        Vector 2
+
+    Returns
+    -------
+    float
+        Topsoe distance between v and y
+
+    Notes
+    -----
+    """
+    # [Chae] commented out the previous one; please review
+    # v[v==0] = 1 #added by amt
+    # y[y==0] = 1 #added by amt
+    return np.sum((y * np.log((2 * y) / (y + v))) + (v * np.log((2 * v) / (y + v))))
+
+
+def probabilistic_symmetric_chi_squared_distance(v, y):
+    r"""Fixed
+    "I commented out the previous one; please review"
+    """
+    return 2 * np.sum(np.sum(np.power(y - v, 2) / (y + v)))
+
+
+def VW6(v, y):
+    r"""
+    "appears to be the same as max_symmetric_chi_squared_distance"
+    """
+    return min(np.sum(np.power(y - v, 2) / y), np.sum(np.power(y - v, 2) / v))
+
+
+def VW5(v, y):
+    r"""
+    "appears to be the same as max_symmetric_chi_squared_distance"
+    """
+    return max(np.sum(np.power(y - v, 2) / y), np.sum(np.power(y - v, 2) / v))
+
+
+def VW4(v, y):
+    r"""
+    "Tecnically the Symmetric chi2 eq63"
+    """
+    return np.sum(np.power(y - v, 2) / np.maximum(y, v))
+
+
+def VW3(v, y):
+    r"""
+    "New"
+    """
+    return np.sum(np.power(y - v, 2) / np.minimum(y, v))
+
+
+def VW2(v, y):
+    r"""
+    "New"
+    """
+    return np.sum(np.power(y - v, 2) / np.power(np.minimum(y, v), 2))
+
+
+def VW1(v, y):
+    r"""
+    "New"
+    """
+    return np.sum(np.abs(y - v) / np.minimum(y, v))
+
+
+def taneja_divergence(v, y):
+    r"""
+    "New"
+    """
+    return np.sum(((y + v) / 2) * np.log((y + v) / (2 * np.sqrt(y * v))))
+
+
+def symmetric_chi_squared_distance(v, y):
+    r"""
+    "New"
+    """
+    return np.sum(np.power(y - v, 2) / (y * v))
+
+
+def squared_chi_squared_distance(v, y):
+    r"""
+    "New"
+    """
+    return np.sum(np.power(y - v, 2) / (y + v))
+
+
+def square_root_cosine_correlation(v, y):
+    r"""
+    "New"
+    """
+    return np.sum(np.sqrt(y * v)) / (np.sum(y) * np.sum(v))
+
+
+def sorensen_distance(v, y):
+    r"""
+    "New"
+    """
+    return np.sum(np.abs(y - v)) / (np.sum(y + v))
+
+
+def Pearson_chi_squared_distance(v, y):
+    r"""
+    "New"
+    """
+    return np.sum(np.power(y - v, 2) / v)
+
+
+def Neyman_chi_squared_distance(v, y):
+    r"""
+    "New"
+    """
+    return np.sum(np.power(y - v, 2) / y)
+
+
+def Minokowski_3(v, y):
+    r"""
+    "New"
+    """
+    return np.power(np.sum(np.power(np.abs(y - v), 3)), 1 / 3)
+
+
+def Minokowski_4(v, y):
+    r"""
+    "New"
+    """
+    return np.power(np.sum(np.power(np.abs(y - v), 4)), 1 / 4)
+
+
+def kumarjohnson_divergence(v, y):
+    r"""
+    "New"
+    """
+    return np.sum(
+        np.power(np.power(y, 2) + np.power(v, 2), 2) / (2 * np.power(y * v, 3 / 2))
+    )
+
+
+def kumarhassebrook_similarity(v, y):
+    r"""
+    "New"
+    """
+    return np.sum(y * v) / (
+        np.sum(np.power(y, 2)) + np.sum(np.power(v, 2)) - np.sum(y * v)
+    )
+
+
+def kullbackleibler_divergence(v, y):
+    r"""
+    "New"
+    """
+    return np.sum(v * np.log(v / y))
+
+
+def soergel_distance(v, y):
+    r"""
+    "New"
+    """
+    return np.sum(np.abs(y - v)) / np.sum(np.maximum(y, v))