Questions tagged [scipy]

SciPy is a Python-based ecosystem of open-source software for mathematics, science, and engineering.

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9 views

Scipy curve_fit and method “dogbox” [on hold]

I am trying to duplicate this papers feature engineering for user activity. They take 14 days of accumulated user activity and keep the parameters (2 parameters) that fit a sigmoid to it. I would like ...
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8 views

Is Fisher Kurtosis the same as Excess Kurtosis?

The documentation for scipy.stats.describe() defines the returned kurtosis like so: ...
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17 views

Fitting data to a distribution that appears lognormal without right-hump

I will like to fit a distribution and extract its moments in Python, given Length of Stay (LOS) data in hospitals. Asking out of curiosity, suppose the plot of the data looks like: The reason why I ...
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1answer
67 views

Fitting Beta Distributions to Data

I am trying to reproduce some beta distribution parameters found in this published paper. I have two data sets, y1 and y2, that ...
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0answers
57 views

Calculating standard errors of non-OLS regressions in python and scipy [closed]

Scipy/statsmodels provides the ability to get a number of metrics from the output of an OLS regression model, a few examples of which (from statsmodels) are the following: ...
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1answer
41 views

Weighted Minkowski distance for DBSCAN

I'm trying to make clustering of image's pixels with DBSCAN, using RGB values and pixel's coordinates as features. It works well with just RGB values as features, but I want pixels with the same color,...
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71 views

Gamma Distribution CDF Intuition; Are My Parameters Correct?

I'm learning about gamma distributions and I want to make sure my reasoning is correct for an example I found here. Suppose you are fishing and you expect to get a fish once every 1/2 hour. ...
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1answer
53 views

Goodness of fit measurement in Python

I have a (pretty noisy) 1D array of data in Python that I fit a linear function to -- see plot below. The x-axis is a wavelength scale. I would like to measure the "goodness of fit" of this new line ...
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0answers
18 views

Optimizing a piecewise-linear, convex function [closed]

I want to find the matrix $U$ that minimizes the following loss function: $$ \min_U( \max_{0 \le j \le t} (\operatorname{tr}(W_jU) + b_j) + \operatorname{tr}(U^TU)) $$ The given loss function is ...
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11 views

Truncate a Hierarchical Clustering tree in order to get the cophenetic coefficient

I've gone ahead and clustered a dataset using a Euclidian Hierarchical Clustering algorithm: ...
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1answer
81 views

Chi Square Analysis Throws Error - The internally computed table of expected frequencies has a zero element at (0,)

I am trying to see the association between two variables. I used Chi-Square analysis in Scipy package in Python. Here is the crosstab result of the two variables: ...
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1answer
32 views

Difference between p-value of chi-squared calculation, and p-value in “critical value” lookup table

I am learning about chi-squared. It has two steps; a) chi-squared calculation b) critical value When I calculate chi-squared, the output includes a) chi-squared statistic (220.5) and b) a p-value (...
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1answer
29 views

least square with equality constraint and singular matrix

I have the following problem to solve: Ax = b where A is singular. To resolve this I introduce a condition Cx = d Even after this, I am not able to solve it using scipy.optimize.minimize as it ...
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115 views

How to improve Pairwise Euclidean Distance for Similarity Measure

I am trying to identify the most similar stations between two DataFrames like below: ...
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0answers
53 views

Can't understand the Beta distribution as described in this paper

I'm reading through the following paper (1). On page 2, section 2.1, there's a description of the selection of a beta distribution used: Since both the choice of s and the strategy for handling the ...
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1answer
89 views

Fixing the maximum distance within a cluster

I am trying to cluster geographical locations in such a way that all the locations inside each cluster are at max within 25 miles of each other. For this, I am using Agglomerative clustering. I am ...
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1answer
347 views

Why is computing ridge regression with a Cholesky decomposition much quicker than using SVD?

By my understanding, for a matrix with n samples and p features: Ridge regression using Cholesky decomposition takes O(p^3) time Ridge regression using SVD takes O(p^3) time Computing SVD when only ...
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0answers
49 views

Why is it much quicker to compute ridge regression than regular linear regression?

By my understanding, for a matrix with n samples and p features: Ridge regression using cholesky takes O(p^3) time Ordinary linear regression takes O(p^3) time Singular value decomposition if u, v ...
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20 views

How to stop fmin_slqsp from converging to local minimum?

I want to run linear regression with inequality constraints and non-negative coefficients. My data looks roughly like this: ...
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0answers
347 views

Proper way to plot confidence interval under normal distribution curve?

I write a small program which calculates a confidence interval for a given norm value. The output is then visualized by plotting the confidence interval and the corresponding hypothetical norm value ...
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0answers
34 views

Numerical approximation of sandwich estimator

I have found the MLE of a model using scipy.optimize.minimize with the BFGS algorithm. As is commonly done, I intend to estimate the variance from $$ Var(\theta_0) ...
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1answer
23 views
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1answer
40 views

How to estimate the leafsize of the kd-tree?

The kd-tree implementation proposed by the scipy python libray asks for the value of the leafsize parameter that is to say the maximum number of points a node can hold. It is by default set to 10. ...
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0answers
12 views

Constructing an appropriate null hypothesis?

I have a collection of 20 2D surfaces embedded in 3D. The mean curvature of each surface has been sampled. The number of samples per surface varies from ~700,000 to ~20,000,000. The choice of ...
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0answers
280 views

Calculating P-value for multivariate normal distributions?

I'm given a set of 500 ($\sigma_i, \mu_i$) that define a 500-dimensional multivariate normal distribution, where each dimension is effectively independent from all the others. Given a 500-...
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1answer
355 views

How does scipy calculate the binomial CDF so fast?

I ran scipy.stats.binom.cdf(500006, 1000000, 0.5) and it took less than a milisecond. This is crazy as binomial CDF involves summing up a bunch of binomial coefficients. What approximation algorithm ...
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1answer
150 views

How to perform batch training using L-BFGS?

I want to train a neural network for regression. The neural network is actually composed of 4 separate child neural networks, each child neural network has a layer structure of ...
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3answers
334 views

How to calculate the p-value of a test, that checked for a binary property?

16081 subjects were randomly assigned into two groups: test group: 7916 subjects control group: 8165 subjects Only the test group was exposed to something. During the test period 10 subjects of ...
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1answer
183 views

Normal distribution test ( D'Agostino and Pearson's) in Scipy - results don't make sense

I want to test if an array of numbers is approximately normally distributed. ...
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0answers
20 views

3 Layer neural network (feedforward and backpropagation) - Desired error not necessarily achieved due to precision loss

I am trying to implement a 3 layer neural network with feedforward and backpropagation. I have tested my cost function and it is working fine. My gradient function also seems ok. but when I try to ...
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1answer
29 views

Remove individual points and find slope

I am trying to delete one pair of x and y coordinates from a set of 10 data points and get the slope for the other 9 points. How do I go about this issue? Attached herewith is an image of what I am ...
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0answers
237 views

Update R2 and slope by removing outliers-python [closed]

I am using the following code to find out Linregress parameters: ...
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1answer
516 views

Statsmodels' Negative Binomial: after .fit_regularized(), how to turn PMF into PPF to get the discrete values?

I used the package statsmodels to fit a Negative Binomial to my data. This data contains ~1500 samples with 21 covariates. Since I have overdispersion in my data ...
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1answer
17 views

Can findings based on low values be considered valid?

Lets say i do have a TimeSeries with N > 300 but values like [0, 1, 2, 1, 2, 0, 2, ...] representing the visitors count of a website per day. Since there are only few visitors and each of them can be ...
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0answers
156 views

Periodogram interpretaion to get main cycles for time serie

I try to use the periodogram in order to get main cycle on my time series. My time series is a the result of measure every hour of one variable related with the atmosphere. So in one day I have 24 ...
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1answer
527 views

How to know if a parameter is statistically significant in a “curve_fit” estimation? [closed]

I use curve_fit from scipy to estimate parameter values from a specific function. ...
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1answer
124 views

nmf in scipy returns components with all zero weights

I'm trying to understand whether this behavior is a bug or a feature. Essentially, I have a dataset of ten thousand short pieces of text. I have used the CountVectorizer function to turn this into a ...
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0answers
24 views

Mode of function kstest in module scipy.stats.stats

In the function kstest in module scipy.stats.stats, there are two options for the mode, described in the help file: ...
2
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1answer
348 views

Gaussian Mixture Model

with the following code I fit a Gaussian Mixture Model to arbitrarily created data. The code is working. The only thing I encounter is that during the calculation of the multivariate_normal I ...
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1answer
628 views

Bandwidth parameters in multivariate KDE using scipy.stats.gaussian_kde

I am working on a project which involves implementing in Python two different density estimation functions over multivariate data; one using N-d histograms and the other using kernel density ...
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1answer
151 views

Scipy ttest_ind versus ks_2samp. When to use which test

From the docs ...
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1answer
190 views

Interpreting p value in SciPy Welch's T-Test [duplicate]

Can someone help me understand the meaning of the p-value of the Whelch's T Test in SciPy? test = stats.ttest_ind(x, y, equal_var=False) gives me ...
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1answer
4k views

How to Compare the Data Distribution of 2 datasets?

I'm having trouble to understand how to compare 2 sets of data by their distribution . For Example, how can I understand that column X100 has the same distribution as column Y1? Also, is there a ...
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2answers
130 views

Normality test giving confusing results

So I was transforming data for machine learning purposes and checking whether I should use the data or log-transform it. In addition to creating histograms I decided to test for normality using ...
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0answers
441 views

Tuning skopt to minimise correctly

I have a problem where I need to fit a pair of parameters in a model to best fit observed data for hundreds of instances. I need to determine these parameters to high accuracy, rather than just ...
2
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1answer
825 views

Understanding hypothesis testing (Kruskal Wallis, Mann-Whitney) when there are tied values

tldr: In Python's Scipy stats modules, the kruskal and mannwhitneyu functions will both raise an error if called with only ...
2
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0answers
90 views

Fitting two parallel lines with mutually excluding samples

I have a set of (slightly noisy) data taken from two (or more) curves, but taken either from one or the other curve. As an example, consider this code (in reality, data is noisier, especially in how ...
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2answers
396 views

Time Series: use of Box-Cox to reduce the “noise”

I am researching the best method to use with time series. FBprophet (Python) seems like a strong option. To prepare time series for Prophet I am thinking about using boxcox and inv_boxcox at the end ...
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0answers
135 views

scipy.optimize.minimize How to manage different units?

I am wondering how spicy.optimize.minimize manages different units in the searched vector. My vector is [x,y,z,yaw,pitch,roll]. The first three are translations in <...