case-against-nhst


Pre-Bayesian Comparison of Classifiers :)

Null-Hypothesis Significance Tests

A quick reintroduction


In [1]:
import numpy as np

scores_a = np.array([ 95.95,  71.4 ,  83.34,  49.99,  76.17,  86.22,  84.45,  81.87, 52.81,  75.04,  71.94,  50.12,  72.03,  60.  ,  83.69])
scores_b = np.array([ 97.88,  71.66,  82.87,  50.71,  74.17,  86.68,  85.46,  82.02, 60.08,  75.83,  74.53,  45.76,  72.65,  60.  ,  84.31])

In [2]:
sum(scores_a > scores_b), sum(scores_a == scores_b), sum(scores_b > scores_a)


Out[2]:
(3, 1, 11)

In [3]:
# Disclaimer: This is not an exemplary use of Python.
# The code is optimized for those who are not used to it.

from random import random

results = []
for match in range(1000):
    wins = 0
    for dataset in range(15):
        if random() < 0.5:
            wins += 1
    results.append(wins)

In [4]:
wins = np.bincount(results, minlength=15)
print(wins)


[  1   1   3  17  47 108 138 190 194 161  90  34  14   2   0]

In [5]:
%matplotlib inline

import matplotlib
import matplotlib.pyplot as plt

_ = plt.bar(range(15), wins)



In [6]:
sum(wins[11:])


Out[6]:
50

The logic of the test

There is around 6 % chance (60 out of 1000) that B will win 11 or more matches if the algorithms were actually same.

Since such a result is so unlikely, we reject the idea that A and B perform the same.

Testing without sweating

Compute distributions analytically.

In this case: binomial distribution.

The whole exercise above is called the sign test.

Tests that you can actually use

(but perhaps shouldn't)

A Pair of Classifiers

Wilcoxon signed-ranks test


In [7]:
import scipy.stats
scipy.stats.wilcoxon(scores_a, scores_b)


Out[7]:
WilcoxonResult(statistic=28.0, pvalue=0.12395016441234137)

Multiple classifiers

Friedman test


In [8]:
scores = np.array(
      [[  95.94595,   97.88477,   98.19664,   98.64226,   98.65337],
       [  71.39521,   71.6561 ,   73.14819,   77.2214 ,   77.26883],
       [  83.3377 ,   82.87099,   81.95057,   77.1957 ,   77.22797],
       [  49.98591,   50.70515,   51.71036,   49.49834,   49.53232],
       [  76.16673,   74.16672,   61.00001,   83.50006,   83.50006],
       [  86.21744,   86.68119,   84.88411,   86.28991,   86.40586],
       [  84.44935,   85.46383,   84.30431,   85.05801,   85.14497],
       [  81.87252,   82.02315,   80.12298,   80.21214,   80.41979],
       [  52.8114 ,   60.08016,   63.39823,   64.20668,   64.19279],
       [  75.04   ,   75.83   ,   75.65   ,   72.17   ,   72.17   ],
       [  71.93504,   74.5346 ,   73.77053,   72.31167,   72.31384],
       [  50.12499,   45.7625 ,   38.66669,   39.66248,   40.04585],
       [  72.03123,   72.64526,   72.31939,   71.50976,   71.57642],
       [  60.     ,   60.     ,   56.9375 ,   60.     ,   60.     ],
       [  83.6875 ,   84.3125 ,   85.54998,   78.57087,   79.08754],
       [  84.36091,   84.42988,   84.80345,   80.51726,   80.58623],
       [  98.31118,   98.52327,   99.05625,   99.18611,   99.17557],
       [  89.40237,   91.0858 ,   91.48102,   90.11586,   90.14524],
       [  93.33322,   93.06656,   92.06654,   93.59991,   93.59991],
       [  87.79086,   91.03252,   92.34689,   99.43702,   99.39943],
       [  87.59993,   88.43326,   91.59994,   85.79996,   85.39996],
       [  56.84723,   56.84723,   56.61866,   56.84723,   56.84723],
       [  85.09998,   86.86189,   85.57139,   76.37137,   77.24757],
       [  62.66532,   64.52785,   66.24374,   64.09357,   64.07691],
       [  74.63639,   84.63801,  100.     ,   97.80228,   97.80228],
       [  96.38929,   96.73215,   97.99556,   98.91727,   98.91727],
       [  95.76072,   99.9508 ,   99.9631 ,  100.     ,  100.     ],
       [  90.29939,   92.73304,   94.24765,   97.18137,   97.18986],
       [  92.16903,   96.91635,   96.21347,   78.59252,   80.38254],
       [  93.37478,   96.92301,   96.67273,   96.60513,   96.54662],
       [  80.41671,   79.83337,   83.16672,   73.16674,   73.66674],
       [  87.72004,   97.76273,   97.66812,   88.61625,   89.56246],
       [  75.26002,   75.70347,   74.56967,   74.32345,   74.31062],
       [  68.11142,   66.77809,   65.1114 ,   69.77806,   69.77806],
       [  47.19786,   47.87167,   47.8458 ,   41.00794,   40.94911],
       [  91.14715,   95.06921,   96.47191,   94.14284,   94.09091],
       [  85.59372,   88.36932,   88.61455,   88.9546 ,   88.9546 ],
       [  86.62217,   87.31057,   87.46307,   89.9792 ,   90.01045],
       [  93.81435,   97.81069,   97.31636,   97.841  ,   97.841  ],
       [  76.71185,   77.04996,   76.12854,   74.67613,   74.86423],
       [  92.19582,   93.30815,   94.6709 ,   92.63445,   93.03048],
       [  89.82622,   93.11031,   92.27349,   92.85163,   93.22753],
       [  79.21932,   80.90305,   81.80477,   81.05974,   81.51275],
       [  95.41686,   96.11599,   96.13167,   94.16605,   94.15662],
       [  59.03334,   59.4    ,   57.46667,   63.5    ,   63.5    ],
       [  62.06667,   67.66667,   71.79999,   77.66667,   77.5    ],
       [  46.32085,   46.72085,   43.93333,   46.78335,   46.78335],
       [  58.78783,   75.69693,   84.60603,   76.53533,   76.68688],
       [  79.968  ,   85.008  ,   84.874  ,   74.872  ,   75.522  ],
       [  64.92861,   66.7381 ,   77.90477,   60.95248,   60.95248],
       [  98.70582,   98.2058 ,   97.58814,   90.72864,   90.94432],
       [  97.19638,   97.05376,   96.36779,   95.03683,   95.28029],
       [  57.61428,   57.81658,   57.73517,   57.0753 ,   57.08878],
       [  93.98181,   94.66363,   99.6    ,   92.60908,   92.60908]])

In [9]:
scipy.stats.friedmanchisquare(scores[:, 0], scores[:, 1], scores[:, 2], scores[:, 3], scores[:, 4])


Out[9]:
FriedmanchisquareResult(statistic=20.840496657115558, pvalue=0.00034058004490788676)

In [10]:
scipy.stats.friedmanchisquare(*scores.T)


Out[10]:
FriedmanchisquareResult(statistic=20.840496657115558, pvalue=0.00034058004490788676)

Summary

Null-hypothesis significance tests are magic bullet.

  1. Formulate hypothesis.
  2. Get the data.
  3. Put it through the appropriate test.

Null-hypothesis significance tests automatize science.

Arguments against NHST

The flawed logic of NHST

  • If the null-hypothesis was true, algorithm A should have won 7 matches out of 14.

  • Algorithm A did not win 7 matches.

=> The hypothesis is false.

All trees are green; I am not green; hence, I'm not a tree.

Null-hypothesis is probabilistic:

  • If the null hypothesis is true, the number of wins is unlikely to be 11.

  • But the number of wins is 11.

=> So the null-hypothesis is unlikely to be true.

We reject the null-hypothesis (as unlikely).

  • If somebody is a US citizen, he is unlikely to be the US president.

  • But Barack Obama is the US president.

=> Barack Obama is not a US citizen.

We reject the claim that president Obama is a US citizen (as unlikely).

Birthers are right!

(Scientifically proven; p < 0.05.)

What is the p-value?

We

  1. know that the p-value is the probability of getting such data if the null hypothesis was true,
  2. pretend and act as if the p-value was the probability of the null-hypothesis.

We reject the null-hypothesis (for being too improbable, as in 2) if the observed data was improbable (as in 1).

We all know our Bayes.

$$P(H|D) = \frac{P(D|H)P(H)}{P(D)}$$

and

$$P(H|D) \ne P(D|H)$$

$P(H|D)$ depends on the prior $P(H)$.

We all

  1. know that the p-value is the probability of getting such data if the null hypothesis was true,

i.e. we know that p-value is something we don't care about.

... except that it has to be < 0.05 so we can publish.

p-values are meaningless since they represent the probability that nobody cares about.

NHST is asking for wrong interpretations

" (...) p <0.05, therefore the null-hypothesis is unlikely".

Wrong. It's not the hypothesis that's unlikely. Just the data.

" (...) p > 0.05, therefore our superfast method is no worse than the existing slow algorithm."

Wrong. You cannot prove the null. You can only reject it.

NHST is a tool and it's not the tool's fault that it's misused.

Objection. NHST is presented as a tool for researchers interested in whether their hypotheses are true or not.

If you bought a hammer because it was advertised as a tool for cutting meat, you'd send it back to Amazon.

... and write a nasty review.

Send the NHST back to ... whom?

Fisher: p-value as the evidence against the null-hypothesis.

Something weird is going on here...

Neyman & Pearson: making optimal decisions with respect to probabilities of mutually exclusive hypotheses.

Both approaches are correct.

P-values are not unlike likelihoods, which are related to probabilities.

Deciding between two hypothesis is totally not unlike decision making.

Their combination is unfortunately not.

What brought as here?

Combining the two conflicting approaches

to satisfy the wish(ful thinking) for a magic bullet for proving hypotheses.

Back to p < 0.05: Why 0.05?

0.05 is the magic $p$-value. Anything below that is success, anything above that is failure.

Nothing magic about 0.05.

No reason to print numbers related to $p < 0.05$ in bold print.

Not only is there no sacred critical value.

There is no way to reason about critical values.

P-values are meaningless.

How do you set a reasonable threshold for a meaningless value?

No, p = 0.05 doesn't mean we accept 5 % of false alternative hypotheses.

P-values are not related to probabilities of hypotheses.

NHST is revolves around the meaningless threshold (0.05) for automatizing decisions about which findings are true and which are random.

The null-hypotheses is always false

No two classifiers are exactly same (unless they are the same classifier).

Hence, we should always reject the null-hypothesis. We just need to collect enough data.

Why go through collecting all the data then, if we already know the end result?

Sorry for the spoiler, guys:

The null-hypotheses dies in Section 4.

The p-value does not distinguish between the effect size and the sample size

Arbitrarily small difference between a pair of classifiers (effect size) is statistically significant with enough data.

The p-value is the function of the effect and the sample size.

The sample size is manipulated by the researcher. Now do the math.

The p-value is intuitively understood as the indicator of the effect size.

Wrong. It is the function of effect size and sample size: same p-values do not imply same effect sizes.

Non-parametric tests make this even worse by ignoring the differences.

If one classifier consistently beats another, the difference does not matter.

Other problems

The list goes on and on.

  • NHST has problems with testing multiple hypotheses.
  • ... especially with multiple researchers performing similar experiments.
  • NHST relies on assumptions about distributions.
  • Sampling intention
  • Ignoring the data uncertainty
  • Not saying anything about the alternative hypotheses
  • ...

Abandon null-hypotheses significance tests?

Good luck with that.

Next year it will be 50 years since Meehl wrote:

Significance testing is a potent but sterile intellectual rake who leaves in his merry path a long train of ravished maidens but no viable scientific offspring.

The American Statistical Association issued a statement (quote) to steer research into a ‘post p<0.05 era.’

  1. P-values can indicate how incompatible the data are with a specified statistical model.
  2. P-values do not measure the probability that the studied hypothesis is true, or the probability that the data were produced by random chance alone.
  3. Scientific conclusions and business or policy decisions should not be based only on whether a p-value passes a specific threshold.
  4. Proper inference requires full reporting and transparency.
  5. A p-value, or statistical significance, does not measure the size of an effect or the importance of a result.
  6. By itself, a p-value does not provide a good measure of evidence regarding a model or hypothesis.

The journal of Basic and Applied Social Psychology prohibited the use the p-word in their journal.

(I believe that) NHST was useful

  • Its logic was wrong.
  • Its computation was wrong.
  • But it forced us to collect more data.
  • It forced us to sometimes concede the defeat.
  • It may have been better than nothing.
  • We didn't have the necessary computational power for the alternative, better approach.

But now we do.