Tolerance for termination is ignored in scipy optimize minimize - python-3.x

I have a simple optimization problem that, with some specific data, makes scipy.optimize.minimize ignore the tol argument. From the documentation, tol determines the "tolerance for termination", that is, the maximum error accepted for the objective function, in my understanding (am I wrong?). However in the next working example, when tol is set to 0.1 for example, or other small numbers, the optimizations finishes with a "Optimization terminated successfully" message even when the objective function > tol. Is this a bug in Scipy's method or am I misunderstanding something here?
The optimization problem: I need to make a linear combination of var1 and var2, which are two time series, scaling them by parameters Btd and Bta. I need that the mean of the linear combination approximates to a target value Target, a scalar. So I simply minimize the absolute difference between np.mean(Btd*var1 + Bta*var2) and Target. The constraints are that the scaling coefficients must be >0 and that the ratio of means np.mean(Btd*var1)/np.mean(Bta*var2) should approximate to the function gi/(1-gi), where gi is a scalar in the interval [0,1].
Reproducible code:
import numpy as np
import scipy.optimize as opt
# The data that exactly reproduce the error:
time = np.arange(1979,2011)
var2=np.array([ 88.95705521, 74.5398773 , 72.08588957, 65.64417178,
50. , 72.39263804, 77.3006135 , 72.08588957,
64.41717791, 96.62576687, 69.93865031, 84.96932515,
86.50306748, 82.20858896, 80.98159509, 73.00613497,
66.25766871, 67.48466258, 79.75460123, 65.64417178,
70.24539877, 84.66257669, 76.3803681 , 83.74233129,
83.74233129, 78.2208589 , 88.03680982, 87.73006135,
100. , 71.16564417, 73.6196319 , 85.58282209])
var1=np.array([300. , 420.89552239, 333.58208955, 355.97014925,
376.11940299, 510.44776119, 420.89552239, 434.32835821,
333.58208955, 394.02985075, 523.88059701, 411.94029851,
353.73134328, 434.32835821, 355.97014925, 398.50746269,
476.86567164, 371.64179104, 445.52238806, 544.02985075,
416.41791045, 427.6119403 , 541.79104478, 579.85074627,
429.85074627, 414.17910448, 420.89552239, 528.35820896,
577.6119403 , 490.29850746, 600. , 454.47761194])
X=np.transpose([var1, var2])
# Global parameters
Target = 3.0
gi = 0.7
# This model is a simple linear combination of the two time series.
def MyModel(modelparams, X, gi):
Bta, Btd = modelparams
Eta = Bta*X[:,0]
Etd = Btd*X[:,1]
Etot = Eta + Etd
return Etot, Eta, Etd
# Objective function
def Obj(modelparams):
Bta, Bdt = modelparams
Etot, Eta, Etd = MyModel([Bta, Bdt], X, gi)
return abs(np.mean(Etot)-Target)
# Ratio constraint
def Ratio(modelparams):
import numpy as np
Bta, Btd = modelparams
Etot, Eta, Etd = MyModel([Bta, Btd], X, gi)
A = np.mean(Etd)/np.mean(Eta)
B = gi/(1-gi)
# The epsilon comes in to loosen a bit only this constraint
epsilon = 0.1
return -abs(abs(A-B)-epsilon)
# This is my solution to make the parameters different from zero.
# The ineq-type constraint makes them >=0.
def TDPos(modelparams):
Bta, Btd = modelparams
return Btd - 10**(-5)
def TAPos(modelparams):
Bta, Btd = modelparams
return Bta - 10**(-5)
constraints=[{'type': 'ineq', 'fun': Ratio},
{'type': 'ineq', 'fun': TDPos},
{'type': 'ineq', 'fun': TAPos}]
# Bounds or Model Parameters
bounds=((0, None), (0, None))
# Minimize
modelparams0=[Target/np.nanmean(var1), Target/np.nanmean(var2)]
result = opt.minimize(Obj, modelparams0,
tol=0.1,
method='SLSQP',
options={'maxiter': 40000 }, #,'ftol': 0.1},
bounds=bounds,
constraints=constraints)
print(result)
Prints out:
fun: 3.0
jac: array([439.92537314, 77.31019938])
message: 'Optimization terminated successfully.'
nfev: 20
nit: 4
njev: 4
status: 0
success: True
x: array([0., 0.])
My problem:
fun: 3.0 > tol: 0.1
which is not desired.
TL;DR: scipy.optimize.minimize ignores the stop argument tol. Why?
EDIT: Moreover, the optimal solution [0, 0] ignores two of the ineq constraints, designed to make this couple of parameters > 10**(-5). Is this part of the same problem?

Related

Python: Fitting a piecewise polynomial

I am trying to fit a piecewise polynomial function
Code:
import numpy as np
import scipy
from scipy.interpolate import UnivariateSpline, splrep
from scipy.optimize import curve_fit
from matplotlib import pyplot as plt
def piecewise_func(x, X, Y):
"""
cond_l: condition list
func_l: function list
"""
spl = UnivariateSpline(X, Y, k=3, s=0.5)
tck = (spl._data[8], spl._data[9], 3) # tck = (knots, coefficients, degree)
p = scipy.interpolate.PPoly.from_spline(tck)
cond_l = []
func_l = []
for idx, i in enumerate(range(3, len(spl.get_knots()) + 3 - 1)):
cond_l.append([(x >= p.x[i] & x < p.x[i + 1])])
func_l.append([lambda x: p.c[3, i] + p.c[2, i] * x + p.c[1, i] * x ** 2 + p.c[0, i] * x ** 3])
return np.piecewise(x, cond_l, func_l)
if __name__ == '__main__':
xdata = [0.28190937, 0.63429607, 0.91620544, 1.68793236, 2.32350115, 2.95215219, 4.5,
4.78103382, 7.2, 7.53430054, 8.03627018, 9., 9.86212529, 11.25951191, 11.62658532, 11.65598578, 13.90295926]
ydata = [0.36273168, 0.81614628, 1.17887796, 1.4475374, 5.52692706, 2.17548169, 3.55313396, 3.80326533, 7.75556311, 8.30176616, 10.72117182, 11.2499386,
11.72296513, 11.02146624, 14.51260631, 20.59365525, 21.77847853]
spl = UnivariateSpline(xdata, ydata, k=3, s=1)
plt.plot(xdata, ydata, '*')
plt.plot(xdata, spl(xdata))
plt.show()
p, e = curve_fit(piecewise_func, xdata, ydata)
# x_plot = np.linspace(0., 0.15, len(x))
# plt.plot(x, y, "+")
# plt.plot(x, (piecewise_func(x_plot, *p)), 'C3-', lw=3)
I tried the UnivariateSpline function to interpolate, I see the following result
However, I don't want the polynomial curve to pass through all data points. I tried varying the smoothing factor but I am not able to obtain something like the one below.
Expected output:
I'm trying curve fitting (Use UnivariateSpline to fit data tightly) to get the expected output and I have the following issues.
piecewise_func in the code posted returns the piecewise polynomial.
Passing this to curve_fit(piecewise_func, xdata, ydata) returns an error
Error:
res = leastsq(func, p0, Dfun=jac, full_output=1, **kwargs)
ValueError: diff requires input that is at least one dimensional
I am not sure what is wrong.
Suggestions on how to get the expected fit will be
of great help.
I would recommend having a closer look at the parameter s in the UnivariateSpline documentation:
s : float or None, optional
Positive smoothing factor used to choose the number of knots. Number of knots will be increased until the smoothing condition is satisfied:
sum((w[i] * (y[i]-spl(x[i])))**2, axis=0) <= s
If s is None, s = len(w) which should be a good value if 1/w[i] is an estimate of the standard deviation of y[i]. If 0, spline will interpolate through all data points. Default is None.
Since you do not set w, this is just a complicated way of saying that s is the least squares error that you allow, i.e., squared errors summed over all the data points. Your value of 1 does not lead to interpolation but it is quite tight compared to what you want to achieve.
Taking
spl = UnivariateSpline(xdata, ydata, k=3, s=10)
you get the following:
Yet closer to your goal is s=100:
So my recommendation is to play around with s and if that proves insufficient, to ask a new question describing what you need more precisely. I haven't had a proper look at the problem with piecewise_func.

How to solve non linear optimization problem with scipy

I need to solve a non linear optimization problem in Python. I found out that scipy solves optimization problems, however I don't know what I am doing wrong since with some example input it can't find the correct solution that I have in NEOS server solver Knitro AMPL.
My problem is that, given a set of points it must find the biggest ellipse inscribed that at max touches those points and the points are never included inside of it.
Theory
Formulating the optimization problem, I have a and b the semiaxis, phi the rotation, xc and yc the coordinates of the centre and points the list of points with each element in the form of [x, y] -> [0, 1] indices.
On paper the problem and the constraints are these, a, b, phi, xc, yc are real, the points are integers:
NEOS
The files I used in NEOS are these:
mod
dat
run
With successful results (complete):
xc = 143.012
yc = 262.634
a = 181.489
b = 140.429
phi = 1.43575
Python
So, my python code is this, it is my first time using scipy for optimization, so I don't exclude errors of understanding how it works from the documentation.
from typing import List
import numpy as np
from scipy.optimize import *
def ellipse_calc(
points: List[List[int]],
verbose: bool = False
):
centre = [0, 0]
for i in range(len(points)):
centre[0] += points[i][0]
centre[1] += points[i][1]
centre[0] /= len(points)
centre[1] /= len(points)
if verbose:
print(f'centre: {centre[0]:.2f}, {centre[1]:.2f}')
max_x = max([p[0] for p in points])
max_y = max([p[1] for p in points])
min_x = min([p[0] for p in points])
min_y = min([p[1] for p in points])
initial_axis = 0.25 * (max_x - min_x + max_y - min_y)
if verbose:
print(initial_axis)
constraints = [
NonlinearConstraint(lambda x: x[0], 1, np.inf),
NonlinearConstraint(lambda x: x[1], 1, np.inf),
NonlinearConstraint(lambda x: x[2], 0, np.inf),
]
for i in range(len(points)):
constraints += [NonlinearConstraint(
lambda x:
(points[i][0] - x[3]) ** 2 * (np.cos(x[2]) ** 2 / x[0]**2 + np.sin(x[2]) ** 2 / x[1]**2) +
(points[i][1] - x[4]) ** 2 * (np.sin(x[2]) ** 2 / x[0]**2 + np.cos(x[2]) ** 2 / x[1]**2) +
2 * (points[i][0] - x[3]) * (points[i][1] - x[4]) *
np.cos(x[2]) * np.sin(x[2]) * (1 / x[1]**2 - 1 / x[0]**2), 1, np.inf)]
result = minimize(
lambda x: -np.pi * x[0] * x[1],
[initial_axis, initial_axis, 0, centre[0], centre[1]],
constraints=constraints
)
print(result)
if __name__ == '__main__':
points = [[50,44],[91,44],[161,44],[177,44],[44,88],[189,88],[239,88],[259,88],[2,132],[250,132],[2,176],[329,176],[2,220],[289,220],[2,264],[288,264],[2,308],[277,308],[2,352],[285,352],[2,396],[25,396],[35,396],[231,396],[284,396],[298,396],[36,440],[76,440],[106,440],[173,440]]
ellipse_calc(points, True)
This try, that has the same data I tried on NEOS gives as output the following:
fun: -8.992626773255127e+40
jac: array([-5.68832805e+20, -4.96651566e+20, -0.00000000e+00, -0.00000000e+00,
-0.00000000e+00])
message: 'Inequality constraints incompatible'
nfev: 54
nit: 10
njev: 9
status: 4
success: False
x: array([ 1.58089104e+20, 1.81065104e+20, -1.24564497e+15, -1.55647883e+10,
-2.76654483e+10])
Does anyone know what I am doing wrong and how to fix it? Also, I don't really know if it is possible to solve this problem with scipy, in that case I am looking for a free library to solve it or even to alternative methods of finding that ellipse equation
This isn't a complete answer, but it should help you to get started. Here are two hints:
Pass simple box constraints on the variables as boundaries, not as constraints. That is, use
bounds = [(1, None), (1, None), (0, None), (None, None), (None, None)]
and pass it to minimize via the bounds parameter.
You need to be really careful when defining constraints through lambda expressions inside a loop, see here. You need to capture the loop variable i by lambda x, i=i: your_fun. Otherwise, each of your constraints uses i=29 and thus evaluates the last point. This can easily be observed by evaluating all constraints for a specific value.
Then you should at least get a feasible solution with an objective value of 79384. Note also that you can shorten your code significantly by using numpy functions instead of loops.

Curve fitting with known coefficients in Python

I tried using Numpy, Scipy and Scikitlearn, but couldn't find what I need in any of them, basically I need to fit a curve to a dataset, but restricting some of the coefficients to known values, I found how to do it in MATLAB, using fittype, but couldn't do it in python.
In my case I have a dataset of X and Y and I need to find the best fitting curve, I know it's a polynomial of second degree (ax^2 + bx + c) and I know it's values of b and c, so I just needed it to find the value of a.
The solution I found in MATLAB was https://www.mathworks.com/matlabcentral/answers/216688-constraining-polyfit-with-known-coefficients which is the same problem as mine, but with the difference that their polynomial was of degree 5th, how could I do something similar in python?
To add some info: I need to fit a curve to a dataset, so things like scipy.optimize.curve_fit that expects a function won't work (at least as far as I tried).
The tools you have available usually expect functions only inputting their parameters (a being the only unknown in your case), or inputting their parameters and some data (a, x, and y in your case).
Scipy's curve-fit handles that use-case just fine, so long as we hand it a function that it understands. It expects x first and all your parameters as the remaining arguments:
from scipy.optimize import curve_fit
import numpy as np
b = 0
c = 0
def f(x, a):
return c+x*(b+x*a)
x = np.linspace(-5, 5)
y = x**2
# params == [1.]
params, _ = curve_fit(f, x, y)
Alternatively you can reach for your favorite minimization routine. The difference here is that you manually construct the error function so that it only inputs the parameters you care about, and then you don't need to provide that data to scipy.
from scipy.optimize import minimize
import numpy as np
b = 0
c = 0
x = np.linspace(-5, 5)
y = x**2
def error(a):
prediction = c+x*(b+x*a)
return np.linalg.norm(prediction-y)/len(prediction)**.5
result = minimize(error, np.array([42.]))
assert result.success
# params == [1.]
params = result.x
I don't think scipy has a partially applied polynomial fit function built-in, but you could use either of the above ideas to easily build one yourself if you do that kind of thing a lot.
from scipy.optimize import curve_fit
import numpy as np
def polyfit(coefs, x, y):
# build a mapping from null coefficient locations to locations in the function
# coefficients we're passing to curve_fit
#
# idx[j]==i means that unknown_coefs[i] belongs in coefs[j]
_tmp = [i for i,c in enumerate(coefs) if c is None]
idx = {j:i for i,j in enumerate(_tmp)}
def f(x, *unknown_coefs):
# create the entire polynomial's coefficients by filling in the unknown
# values in the right places, using the aforementioned mapping
p = [(unknown_coefs[idx[i]] if c is None else c) for i,c in enumerate(coefs)]
return np.polyval(p, x)
# we're passing an initial value just so that scipy knows how many parameters
# to use
params, _ = curve_fit(f, x, y, np.zeros((sum(c is None for c in coefs),)))
# return all the polynomial's coefficients, not just the few we just discovered
return np.array([(params[idx[i]] if c is None else c) for i,c in enumerate(coefs)])
x = np.linspace(-5, 5)
y = x**2
# (unknown)x^2 + 1x + 0
# params == [1, 0, 0.]
params = fit([None, 0, 0], x, y)
Similar features exist in nearly every mainstream scientific library; you just might need to reshape your problem a bit to frame it in terms of the available primitives.

Numba jit and Scipy

I have found a few posts on the subject here, but most of them did not have a useful answer.
I have a 3D NumPy dataset [images number, x, y] in which the probability that the pixel belongs to a class is stored as a float (0-1). I would like to correct the wrong segmented pixels (with high performance).
The probabilities are part of a movie in which objects are moving from right to left and possibly back again. The basic idea is that I fit the pixels with a Gaussian function or comparable function and look at around 15-30 images ( [i-15 : i+15 ,x, y] ). It is very probable that if the previous 5 pixels and the following 5 pixels are classified in this class, this pixel also belongs to this class.
To illustrate my problem I add a sample code, the results were calculated without the usage of numba:
from scipy.optimize import curve_fit
from scipy import exp
import numpy as np
from numba import jit
#jit
def fit(size_of_array, outputAI, correct_output):
x = range(size_of_array[0])
for i in range(size_of_array[1]):
for k in range(size_of_array[2]):
args, cov = curve_fit(gaus, x, outputAI[:, i, k])
correct_output[2, i, k] = gaus(2, *args)
return correct_output
#jit
def gaus(x, a, x0, sigma):
return a*exp(-(x-x0)**2/(2*sigma**2))
if __name__ == '__main__':
# output_AI = [imageNr, x, y] example 5, 2, 2
# At position [2][1][1] is the error, the pixels before and after were classified to the class but not this pixel.
# The objects do not move in such a speed, so the probability should be corrected.
outputAI = np.array([[[0.1, 0], [0, 0]], [[0.8, 0.3], [0, 0.2]], [[1, 0.1], [0, 0.2]],
[[0.1, 0.3], [0, 0.2]], [[0.8, 0.3], [0, 0.2]]])
correct_output = np.zeros(outputAI.shape)
# I correct now in this example only all pixels in image 3, in the code a loop runs over the whole 3D array and
# corrects every image and every pixel separately
size_of_array = outputAI.shape
correct_output = fit(size_of_array, outputAI, correct_output)
# numba error: Compilation is falling back to object mode WITH looplifting enabled because Function "fit" failed
# type inference due to: Untyped global name 'curve_fit': cannot determine Numba type of <class 'function'>
print(correct_output[2])
# [[9.88432346e-01 2.10068763e-01]
# [6.02428922e-20 2.07921125e-01]]
# The wrong pixel at position [0][0] was corrected from 0.2 to almost 1, the others are still not assigned
# to the class.
Unfortunately numba does NOT work. I always get the following error:
Compilation is falling back to object mode WITH looplifting enabled because Function "fit" failed type inference due to: Untyped global name 'curve_fit': cannot determine Numba type of <class 'function'>
** ------------------------------------------------------------------------**
Update 04.08.2020
Currently I have this solution for my problem in mind. But I am open for further suggestions.
from scipy.optimize import curve_fit
from scipy import exp
import numpy as np
import time
def fit_without_scipy(input):
x = range(input.size)
x0 = outputAI[i].argmax()
a = input.max()
var = (input - input.mean())**2
return a * np.exp(-(x - x0) ** 2 / (2 * var.mean()))
def fit(input):
x = range(len(input))
try:
args, cov = curve_fit(gaus, x, outputAI[i])
return gaus(x, *args)
except:
return input
def gaus(x, a, x0, sigma):
return a * exp(-(x - x0) ** 2 / (2 * sigma ** 2))
if __name__ == '__main__':
nr = 31
N = 100000
x = np.linspace(0, 30, nr)
outputAI = np.zeros((N, nr))
correct_output = outputAI.copy()
correct_output_numba = outputAI.copy()
perfekt_result = outputAI.copy()
for i in range(N):
perfekt_result[i] = gaus(x, np.random.random(), np.random.randint(-N, 2*N), np.random.random() * np.random.randint(0, 100))
outputAI[i] = perfekt_result[i] + np.random.normal(0, 0.5, nr)
start = time.time()
for i in range(N):
correct_output[i] = fit(outputAI[i])
print("Time with scipy: " + str(time.time() - start))
start = time.time()
for i in range(N):
correct_output_numba[i] = fit_without_scipy(outputAI[i])
print("Time without scipy: " + str(time.time() - start))
for i in range(N):
correct_output[i] = abs(correct_output[i] - perfekt_result[i])
correct_output_numba[i] = abs(correct_output_numba[i] - perfekt_result[i])
print("Mean deviation with scipy: " + str(correct_output.mean()))
print("Mean deviation without scipy: " + str(correct_output_numba.mean()))
Output [with nr = 31 and N = 100000]:
Time with scipy: 193.27853846549988 secs
Time without scipy: 2.782526969909668 secs
Mean deviation with scipy: 0.03508043754489116
Mean deviation without scipy: 0.0419951370808896
In the next step I would try to speed up the code even more with numba. Currently this does not work because of the argmax function.
Curve_fit eventually calls into either least_squares (pure python) or leastsq (C extension). You have three options:
figure out how to make numba-jitted code talk to a C extension which powers leastsq
extract relevant parts of least_squares and numba.jit them
implement the LowLevelCallable support for least_squares or minimize.
None of these is easy. OTOH all of these would be interesting to a wider audience if successful.

How to avoid NaN in numpy implementation of logistic regression?

EDIT: I already made significant progress. My current question is written after my last edit below and can be answered without the context.
I currently follow Andrew Ng's Machine Learning Course on Coursera and tried to implement logistic regression today.
Notation:
X is a (m x n)-matrix with vectors of input variables as rows (m training samples of n-1 variables, the entries of the first column are equal to 1 everywhere to represent a constant).
y is the corresponding vector of expected output samples (column vector with m entries equal to 0 or 1)
theta is the vector of model coefficients (row vector with n entries)
For an input row vector x the model will predict the probability sigmoid(x * theta.T) for a positive outcome.
This is my Python3/numpy implementation:
import numpy as np
def sigmoid(x):
return 1 / (1 + np.exp(-x))
vec_sigmoid = np.vectorize(sigmoid)
def logistic_cost(X, y, theta):
summands = np.multiply(y, np.log(vec_sigmoid(X*theta.T))) + np.multiply(1 - y, np.log(1 - vec_sigmoid(X*theta.T)))
return - np.sum(summands) / len(y)
def gradient_descent(X, y, learning_rate, num_iterations):
num_parameters = X.shape[1] # dim theta
theta = np.matrix([0.0 for i in range(num_parameters)]) # init theta
cost = [0.0 for i in range(num_iterations)]
for it in range(num_iterations):
error = np.repeat(vec_sigmoid(X * theta.T) - y, num_parameters, axis=1)
error_derivative = np.sum(np.multiply(error, X), axis=0)
theta = theta - (learning_rate / len(y)) * error_derivative
cost[it] = logistic_cost(X, y, theta)
return theta, cost
This implementation seems to work fine, but I encountered a problem when calculating the logistic-cost. At some point the gradient descent algorithm converges to a pretty good fitting theta and the following happens:
For some input row X_i with expected outcome 1 X * theta.T will become positive with a good margin (for example 23.207). This will lead to sigmoid(X_i * theta) to become exactly 1.0000 (this is because of lost precision I think). This is a good prediction (since the expected outcome is equal to 1), but this breaks the calculation of the logistic cost, since np.log(1 - vec_sigmoid(X*theta.T)) will evaluate to NaN. This shouldn't be a problem, since the term is multiplied with 1 - y = 0, but once a value of NaN occurs, the whole calculation is broken (0 * NaN = NaN).
How should I handle this in the vectorized implementation, since np.multiply(1 - y, np.log(1 - vec_sigmoid(X*theta.T))) is calculated in every row of X (not only where y = 0)?
Example input:
X = np.matrix([[1. , 0. , 0. ],
[1. , 1. , 0. ],
[1. , 0. , 1. ],
[1. , 0.5, 0.3],
[1. , 1. , 0.2]])
y = np.matrix([[0],
[1],
[1],
[0],
[1]])
Then theta, _ = gradient_descent(X, y, 10000, 10000) (yes, in this case we can set the learning rate this large) will set theta as:
theta = np.matrix([[-3000.04008972, 3499.97995514, 4099.98797308]])
This will lead to vec_sigmoid(X * theta.T) to be the really good prediction of:
np.matrix([[0.00000000e+00], # 0
[1.00000000e+00], # 1
[1.00000000e+00], # 1
[1.95334953e-09], # nearly zero
[1.00000000e+00]]) # 1
but logistic_cost(X, y, theta) evaluates to NaN.
EDIT:
I came up with the following solution. I just replaced the logistic_cost function with:
def new_logistic_cost(X, y, theta):
term1 = vec_sigmoid(X*theta.T)
term1[y == 0] = 1
term2 = 1 - vec_sigmoid(X*theta.T)
term2[y == 1] = 1
summands = np.multiply(y, np.log(term1)) + np.multiply(1 - y, np.log(term2))
return - np.sum(summands) / len(y)
By using the mask I just calculate log(1) at the places at which the result will be multiplied with zero anyway. Now log(0) will only happen in wrong implementations of gradient descent.
Open questions: How can I make this solution more clean? Is it possible to achieve a similar effect in a cleaner way?
If you don't mind using SciPy, you could import expit and xlog1py from scipy.special:
from scipy.special import expit, xlog1py
and replace the expression
np.multiply(1 - y, np.log(1 - vec_sigmoid(X*theta.T)))
with
xlog1py(1 - y, -expit(X*theta.T))
I know it is an old question but I ran into the same problem, and maybe it can help others in the future, I actually solved it by implementing normalization on the data before appending X0.
def normalize_data(X):
mean = np.mean(X, axis=0)
std = np.std(X, axis=0)
return (X-mean) / std
After this all worked well!

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