Negative R2 on Simple Linear Regression (with intercept)

Question

I am doing a simple Linear Regression (with intercept) which ends up presenting a negative R2, this should not be possible (cf comment 2 at the end)

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Reproducible examples of the issue:

Minimal sklearn reproducible code:

import numpy as np; print(np.__version__) # 1.23.5
import scipy; print(scipy.__version__) # 1.10.0
import sklearn as sk; print(sk.__version__) # 1.2.1
from sklearn.linear_model import LinearRegression
import pandas as pd
np.random.seed(8)
s = pd.Series(np.random.normal(10, 1, size=1_000))
l_com = np.arange(100)
df_Xy = pd.concat([s.ewm(com=com).mean() for com in l_com], axis=1)
df_Xy['y'] = s.shift(-1)
df_Xy.dropna(inplace=True)
X = df_Xy[l_com]
y_true = df_Xy.y
model = LinearRegression(fit_intercept=True) # fit_intercept=True by default anyways
model.fit(X, y_true)
print(model.score(X, y_true))
-0.15802176533843926 = NEGATIVE R2 on VM 1
-0.05854780689129546 on VM 2 (? dependent on CPU ?)

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Minimal scipy reproducible code:

import numpy as np; print(np.__version__) # 1.23.5
import scipy; print(scipy.__version__) # 1.10.0
import pandas as pd
Parameters:
(seed, N_obs, N_feat, mu_x, sigma_x, sigma_y) = (0, 100, 1000, 100, 10, 1)
Building very weird X,y arrays (High Colinearity)
np.random.seed(seed)
s = pd.Series(np.random.normal(mu_x, sigma_x, N_obs))
X_raw = np.ascontiguousarray(np.stack([s.ewm(com=com).mean() for com in np.arange(N_feat)]).T)
y_raw = np.random.normal(0, sigma_y, N_obs)
Center both arrays to zero
X_offset = X_raw.mean(axis=0)
y_offset = y_raw.mean()
X = X_raw - X_offset
y = y_raw - y_offset
OLS: Finding parameters that minimise Square Residuals:
p, ,,_ = scipy.linalg.lstsq(X, y) # <-- This is silently Failing! (resulting parameters are worst than the zero vector)
pred = np.matmul(X, p)
RSS = np.sum(np.power(y - pred, 2)) # 108.3406316733817
TSS = np.sum(np.power(y - np.mean(y), 2)) # 107.05357955882408

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• Comment 1: Yes, X matrix is computed in a very specific way (Exponential Moving averages of the target). It seems that the problem arises particularly well in this case. I'm currently trying to find an example without this "complexity".
• Comment 2: If you are a beginner/intermediate Data Scientist, please refrain from commenting something like "R2 can sometimes be negative": we are in the case of simple OLS with intercept. The Sum of Squares should be minimised, by definition.

Answer 1

Detailed explanation of the problem:

In the case of X being near-singular (high colinearity/covariance between features), different issues where coming both from scipy.linalg.lstsq() and sklearn.linear_model.LinearRegession()

Source of error 1: As @SextusEmpiricus explained, the matrix being near-singular leads to rounding errors that impact enormously the final predictions. In this sense, scipy.linalg.lstsq() is silently failing WITHOUT raising any warning or error.

Source of error 2: The matrix coming from pandas was F-contiguous. sklearn converts it to C-contiguous before calling scipy.linalg.lstsq() and then use the predict() by using a matrix multiplication right from the F-contiguous array. This lead to another layer of rounding errors. I opened another question here on Stack Overflow

Source of error 3: The first thing that LinearRegression() is doing is to center the dataframe. This goes badly in my case, I still struggle to understand why exactly.

Note: Please note that these rounding errors also depends on CPUs and hardware, which makes it even hard to achieve reproducibility.

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(Partial) Work-Around:

To work around the sklearn problems, one can:

• Ensure input matrix/array are C-contiguous
• Stop rely on LinearRegression's fit_intercept=True but instead center data manually first:

for seed in range(1000):
    np.random.seed(seed)
    s = pd.Series(np.random.normal(10, 1, size=1_000))
l_com = np.arange(100)
df_Xy = pd.concat([s.ewm(com=com).mean() for com in l_com], axis=1)
df_Xy['y'] = s.shift(-1)
df_Xy.dropna(inplace=True)

X = np.ascontiguousarray(df_Xy[l_com].values)
y = np.ascontiguousarray(df_Xy.y.values)

X_offset = X.mean(axis=0)
y_offset = y.mean()

X_centered = X - X_offset
y_centered = y - y_offset

model = LinearRegression(fit_intercept=False) # We don't rely on sklearn fit_intercept anymore
model.fit(X_centered, y_centered)
assert model.score(X_centered, y_centered) > 0 # ALL GOOD

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Moving forward / Long-term Solution:

1. I opened an issue in scipy Github to raise a Warning in scipy.linalg.lstsq when the X matrix is near-singular.

2. I opened an issue in sklearn project on Github, about inconsistency between C-cont vs F-cont arrays

Answer 2

I can reproduce it with np.random.seed(15) and dig a bit deeper. It seems a lot like a computational round-off error due to the high collinearity.

The steps I took

• I manually added a column with ones to the matrix X

  #X =  df_Xy[l_com]
  X = pd.concat([pd.DataFrame(np.repeat(1, 999)),df_Xy[l_com]], axis=1) 
  

• and used directly the function lstsq(X, y_true), for which the function LinearRegression is a wrapper, and manually compute the sum of squares

  p, res, rnk, sin = lstsq(X, y_true)
  pred = np.matmul(X, p)
  RSS = np.sum(np.power(y_true - model.predict(X=X), 2)) ## 1007.6190
  RSS2 = np.sum(np.power(y_true - pred, 2))              ## 1007.6190
  TSS = np.sum(np.power(y_true - mean(y_true), 2))       ## 995.24937
  

The R-squared is still negative.

(the above is for intercept=False interestingly, when I set it true then the result becomes even worse, but I can't yet figure out what the sourcecode does with that boolean parameter)

A reason for this behavior might be that the parameters are very large because you generated the coefficients with some exponentially weighting (I do not know enough about python to figure out easily what you are doing there, and you might provide more comments about your code) and created highly correlated features. The lstsq gives as output a very small effective rank and the coefficients are in the order of $\pm 10^{10}$.

At the moment this is as far as I can get. I find the code in python libraries difficult to decipher. The linearmodel from sklearn refers to a function lstsq from scipy/linalg and that function refers to 'gelsd', 'gelsy', 'gelss' functions from lapack which is a fortran code that is somewhere but through all the layers of wrappers and imported packages it is difficult to figure out what happens in the blackbox between input and output of linearmodel.

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The influence of the processor

print(model.score(X, y_true))
# -0.15802176533843926 = NEGATIVE R2 on VM 1
# -0.05854780689129546 on VM 2 (? dependent on CPU ?)

In the answer to this question on stack overflow it is explained that the algorithm might take slightly different steps for different CPU architectures and as a consequence there can be small differences in results for different CPUs: Is it reasonable to expect identical results for LAPACK routines on two different processor architectures?

Example: for a computer we have $(7+8) \times (1/9) \neq (7/9+8/9)$. Demonstration with R-code

options(digits=22)
(7/9) + (8/9) # 1.666666666666666518637
15/9          # 1.666666666666666740682

An algorithm might make such subtle changes in the computation to optimize the calculation speed for a processor.

In the case of a matrix inversion of a nearly singular matrix these small errors might get amplified due to the sensitivity of the computation on small differences.

(I don't have the ability to verify this with different processors, but I will check whether changing the number of cores can have a similar influence.)