Robust statistics and Trimean

from scipy.stats import skewnorm
import numpy as np
import matplotlib.pyplot as plt

Let’s generate some data that might be something we find in the real world.

skew_magnitude = -6
arr = skewnorm.rvs(skew_magnitude, loc=0, scale=1000, size=100000)

(The skew is a third-order moment.)

plt.hist(arr, bins=100, density=True)
plt.show()

Let’s get a very common measure of central tendency:

np.mean(arr)

-789.5809069979605

The mean overstates the central tendency because of the skew.

The mean is defined as

\[\bar{x} = \frac{1}{n} \sum_{i=1}^n x_i\]

and treats all numbers equally. No matter how big or small.

One can “fix” this by looking at “robust” statistics that are often rank based. Rank based means that we sort the data and then base our statistics on the rank of the data. In this way, they are no longer sensitive to outliers.

def interquartile_range(arr):
    q1 = np.percentile(arr, 25)
    q3 = np.percentile(arr, 75)
    return q3 - q1

print("Median", np.percentile(arr, 50))
print("Interquartile Range", interquartile_range(arr))
print("Mean", arr.mean())
print("Standard Deviation", arr.std())

Median -679.7024551978025
Interquartile Range 834.2816858677052
Mean -789.5809069979605
Standard Deviation 614.9363837309692

A very nice measure of centrality is the so-called trimean.

“An advantage of the trimean as a measure of the center (of a distribution) is that it combines the median’s emphasis on center values with the midhinge’s attention to the extremes.”

— Herbert F. Weisberg, Central Tendency and Variability

It is defined as

\[ \text{trimean} = \frac{Q_1 + 2Q_2 + Q_3}{4} \]

where \(Q_1\) is the first quartile, \(Q_2\) is the median, and \(Q_3\) is the third quartile.

def trimean(arr):
    q1 = np.percentile(arr, 25)
    q3 = np.percentile(arr, 75)
    median = np.percentile(arr, 50)
    return (q1 + 2*median + q3)/4

print("Trimean", trimean(arr))

Trimean -708.4430042323374

Guo, Jeff, and Philippe Schwaller. 2024. “It Takes Two to Tango: Directly Optimizing for Constrained Synthesizability in Generative Molecular Design.” arXiv. https://doi.org/10.48550/ARXIV.2410.11527.

Landrum, Gregory A., Jessica Braun, Paul Katzberger, Marc T. Lehner, and Sereina Riniker. 2024. “Lwreg: A Lightweight System for Chemical Registration and Data Storage.” Journal of Chemical Information and Modeling 64 (16): 6247–52. https://doi.org/10.1021/acs.jcim.4c01133.

Orsi, Markus, and Jean-Louis Reymond. 2024. “One Chiral Fingerprint to Find Them All.” Journal of Cheminformatics 16 (1): 53.