scientific-computing – Tarik Billa

sigmoidal regression with scipy, numpy, python, etc

January 5, 2024 by Tarik

Using scipy.optimize.leastsq: import numpy as np import matplotlib.pyplot as plt import scipy.optimize def sigmoid(p,x): x0,y0,c,k=p y = c / (1 + np.exp(-k*(x-x0))) + y0 return y def residuals(p,x,y): return y – sigmoid(p,x) def resize(arr,lower=0.0,upper=1.0): arr=arr.copy() if lower>upper: lower,upper=upper,lower arr -= arr.min() arr *= (upper-lower)/arr.max() arr += lower return arr # raw data x = np.array([821,576,473,377,326],dtype=”float”) … Read more

Open source alternative to MATLAB’s fmincon function? [closed]

August 29, 2023 by Tarik

Is your problem convex? Linear? Non-linear? I agree that SciPy.optimize will probably do the job, but fmincon is a sort of bazooka for solving optimization problems, and you’ll be better off if you can confine it to one of the categories below (in increasing level of difficulty to solve efficiently) Linear Program (LP) Quadratic Program … Read more

Numerically stable softmax

August 11, 2023 by Tarik

The softmax exp(x)/sum(exp(x)) is actually numerically well-behaved. It has only positive terms, so we needn’t worry about loss of significance, and the denominator is at least as large as the numerator, so the result is guaranteed to fall between 0 and 1. The only accident that might happen is over- or under-flow in the exponentials. … Read more

How to test scientific software?

August 10, 2023 by Tarik

I am also in academia and I have written quantum mechanical simulation programs to be executed on our cluster. I made the same observation regarding testing or even version control. I was even worse: in my case I am using a C++ library for my simulations and the code I got from others was pure … Read more

The reading list for scientific programmer [closed]

May 10, 2023 by Tarik

At some stage you’re going to need floating point arithmetic. It’s hard to do it well, less hard to do it competently, and easy to do it badly. This paper is a must read: What Every Computer Scientist Should Know About Floating-Point Arithmetic

multithreaded blas in python/numpy

May 5, 2023 by Tarik

I already posted this in another thread but I think it fits better in this one: UPDATE (30.07.2014): I re-run the the benchmark on our new HPC. Both the hardware as well as the software stack changed from the setup in the original answer. I put the results in a google spreadsheet (contains also the … Read more

Is the order of a Python dictionary guaranteed over iterations?

March 23, 2023 by Tarik

Yes, the same order is guaranteed if it is not modified. See the docs here. Edit: Regarding if changing the value (but not adding/removing a key) will affect the order, this is what the comments in the C-source says: /* CAUTION: PyDict_SetItem() must guarantee that it won’t resize the * dictionary if it’s merely replacing … Read more

Plotting with C# [closed]

March 10, 2023 by Tarik

There is OxyPlot which I recommend. It has packages for WPF, Metro, Silverlight, Windows Forms, Avalonia UI, XWT. Besides graphics it can export to SVG, PDF, Open XML, etc. And it even supports Mono and Xamarin for Android and iOS. It is actively developed too. There is also a new (at least for me) open … Read more

Principal components analysis using pandas dataframe

March 7, 2023 by Tarik

Most sklearn objects work with pandas dataframes just fine, would something like this work for you? import pandas as pd import numpy as np from sklearn.decomposition import PCA df = pd.DataFrame(data=np.random.normal(0, 1, (20, 10))) pca = PCA(n_components=5) pca.fit(df) You can access the components themselves with pca.components_

True or false output based on a probability

February 22, 2023 by Tarik

import random def decision(probability): return random.random() < probability