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Questions tagged [data-analysis]

Data Analysis is the process of evaluating data using analytical and logical reasoning to examine each component of the data provided.

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20
votes
2answers
2k views

Algorithms for a many-to-many generalized assignment problem

I can't seem to find any literature on algorithms which can be used to solve a many-to-many generalized assignment problem (GAP), i.e. models where not only can more tasks be assigned to one agent, ...
16
votes
2answers
1k views

Best practice for storing hierarchical simulation data

TL,DR What is the accepted best practice in scientific computing circles for storing large quantities of hierarchically structured data? For example, SQL does not play nicely with large sparse ...
11
votes
4answers
13k views

Fastest PCA algorithm for high-dimensional data

I would like to perform a PCA on a dataset composed of approximately 40 000 samples, each sample displaying about 10 000 features. Using Matlab princomp function consistently takes over half an hour ...
11
votes
2answers
11k views

Pandas limitations and its alternatives in Python

I read somewhere that Pandas was first developed for the financial world, at least not especially for natural sciences (physics, biology and so on), so is there any similar data analysis Python ...
10
votes
2answers
134 views

Matching Similar Items from a Set

I'm trying to match items. Given a set of $n$ items I can rank on a scale from 0 to 100 of how similar they are to one another. For instance, if item $n_1$ is milk and item $n_2$ is also milk, then ...
9
votes
1answer
5k views

What is the difference between Computational Science and Data Science? [closed]

Background: My PhD was in 'Computational Science'. My dissertation was on the analysis of X-Ray Diffraction Data and analysis of thermally perturbed nuclei in the overall dynamic analysis of the ...
8
votes
4answers
632 views

Should I use a database to handle large amounts of results?

Background: I am currently running a large amount parameter variation experiments. They are being run in Python 2.6+, using numpy. These experiments are going to take about 2 weeks to run. Roughly I ...
6
votes
1answer
1k views

Fit my data to Lissajous curve in Matlab

I'm acquiring data which looks like this: Theoretically it should be possible to fit it with a Lissajous curve, which is typically defined in the following way: $x = A \sin(a t + \delta)$, and $y = ...
6
votes
1answer
360 views

Is resampling more accurate than block average for statistical analysis of data?

I'm working in laboratories where molecular dynamics data are almost always analysed usign block average as stated in the famous Allen and Tildesley book. We divide the datas in blocks of size $M$ on ...
5
votes
1answer
295 views

Iterative Cunnigham correction in Millikans oil-drop experiment

I tried to write an analysis program in python for the Millikan experiment based on a paper from Jones "The Millikan oil‐drop experiment: Making it worthwhile" However, I cannot reproduce the ...
5
votes
2answers
303 views

Dimensionality reduction of the domain of f(x)

I'm wondering if there is something analogous to a PCA for data sets where there is a dependent variable. (Though I am interested in any method of dimensionality reduction, PCA is just an example.) ...
5
votes
1answer
286 views

Recommendation for a python book for data processing

I've been doing FORTRAN programming for 10 years and I've started using python for a few years now, mostly for data processing. I've been lucky enough to work with people that are knowledgeable ...
4
votes
1answer
2k views

Is there a relationship between the covariance matrix and the partial derivative?

Suppose that there are $N$ pieces of data, each of which contains $M$ parameter values such that $N >> M$. If we put this information into matrix form ($N$ rows, $M$ columns) and then compute ...
3
votes
1answer
153 views

Monte Carlo Simulation - Random Number Motivation

For Monte Carlo simulations, or any other numerical methods that rely heavily on the quality of the pseudo-random numbers generated (i.e even/desired distribution on a certain domain) for that matter, ...
3
votes
1answer
89 views

GPGPU/FPGA programming for Combinatorial Analysis

Recently, I have taken an interest in performing combinatorial analysis for the game of 21 (blackjack) and attempted to use my AMD APU to try and thread the program via the 4 cores on the chip. ...
3
votes
1answer
722 views

How to do local FFT on huge 3D vector data cell mesh and visualize it spatially?

Simulation type: I'm running a simulation with the OOMMF micromagnetics package http://math.nist.gov/oommf/ where are magnet is represented by a mesh of 3 million cells, it gets excited by a ...
3
votes
1answer
917 views

Similarity of two CSV files (or more?)

A CSV file is characterized by a header, describing the n datarows to come. The header is a text string separated by a separator. A CSV header might look like (C1) ...
3
votes
1answer
422 views

what is the best theory/model to use for prediction in multivariate data?

I use software for pollutant propagation on rivers that takes as input a set of parameters ($p_1,p_2,\ldots,p_n$) and creates an output file which is basically a matrix where on each row the ...
3
votes
2answers
66 views

Parameter Fitting: Need measure of data 'support' for a parameter solution

I am estimating parameters on a dataset that would, for the most part, result in a weakly constrained solution. The dataset however also contains a few more data points that make the solution well-...
3
votes
1answer
178 views

similarity/distance measurement between two ranked sequence

Is there an efficient way to measure similarity/distance between two sequences of ranked numbers/letters. The two sequences are of different length, and only have some elements in common? For example,...
3
votes
0answers
117 views

Spatio-temopral wavelet analysis

Am quite new to wavelet analysis and would like some help. I am performing a spatio-temporal analysis of monthly gridded rainfall data. With PCA, I can reduce the dimension of the rainfall data into a ...
3
votes
1answer
127 views

Calculation of Multivariate Coherence

I trying to detecting whether a data set of time series has a global change in frequencies. Calculating the average (or median) pairwise coherence, I feel, misses the point because I am trying to get ...
2
votes
2answers
324 views

Extracting time scales information from empirical cumulative distribution function

I have a stochastic process (a Markov chain actually) that has two absorbing states. I am using a difference equation to calculate the first passage time to either of the absorbing states. There are ...
2
votes
2answers
86 views

Estimate (non-)drift in noisy data

I have a time series representing the result of a complex calculation (physical simulation). Due to round-off errors and approximation errors, there will be some "noise" on the data series. In some ...
2
votes
1answer
152 views

Which statistical method should I use for comparing machine run-time of two algorithms?

I am comparing the run-time of two algorithm by solving different instance of the problems. Sample of my data: ...
2
votes
3answers
400 views

R/C/C++ library for N-dimensional arrays

I'm looking for a library that is either in R or easily wrappable with R, that can do the following things: construct and subset N-dimensional arrays perform operations such as ...
2
votes
1answer
113 views

How to check experimental data against a theoretical curve? (Python)

I am trying to check the agreement of a dataset against a theoretical curve, specifically a bandstop filter in an RLC circuit. I have generated a function which describes the curve we expect from the ...
2
votes
3answers
236 views

Clustering with points lying along different 3D planes

I have a bunch of data points in 3D that lie along a few planes. What would be the best approaches to estimate the normals of these planes? Edit: There are roughly equal number of points lying along ...
2
votes
1answer
41 views

Simple Path to Route Algorithm

I'm currently conducting research into subway paths, but stand in front of a problem, with no programming knowledge and an extremely short time-limit. Probably the question I am asking is trivial, ...
2
votes
1answer
115 views

How to extract connected components from persistence diagram?

From the given point cloud (Fig. 1), I use Scipy-TDA to extract persistence diagram (Fig. 2). What I'm interested in is to extract 3 circles. For example, I'd like to know 3 center points and labels ...
2
votes
0answers
825 views

Computing the structure factor from positions and radial distribution function [closed]

I'm currently analysing some spatial point patterns that come from some fluid dynamics simulations and I'm having some difficulty computing the structure factor, $S(\pmb{k})$, from both the positions ...
2
votes
0answers
31 views

Identifying the time window at which a meteorological factor influences tree growth the most

This is a problem I am encountering in a research project. I have thought of a naive approach to solve it which relies on many assumptions, is not guaranteed to work, and would be tedious and ...
2
votes
0answers
58 views

Error in treating non-uniformly spaced data as uniform

In discussing smoothing filters, Numerical Recipes p. 772 says ... irregularly sampled data, where the values $f_i$ are not uniformly spaced ... one can simply pretend that the data points are ...
2
votes
0answers
1k views

Can post-processing use topoSet and createPatch without screwing up the results?

I would like to use patchAverage to obtain the average pressure on an object that consists of multiple patches (due to different boundary conditions), however ...
1
vote
2answers
3k views

Python implementation for Frechet Distance

I am working on a trajectory analysis project using python and its data science related libraries. I am planning to implement Frechet Distance algorithm for trajectory analysis, each trajectory has ...
1
vote
1answer
462 views

FFT (Numerical Recipes in FORTRAN 77)

I am trying to use the subroutine twofft which in turn uses subroutine four1 in the book(Numerical Recipes in Fortran) to ...
1
vote
1answer
62 views

library for arithmetic operations on unstructured xyz

I've got several sets of xyz-data where x,y are coordinates and z is a 'value'. I want to be able to do simple arithmetic operations on these data. The x,y locations are not necessarily the same in ...
1
vote
1answer
69 views

Best way of storing numerical data in a compact manner, while leaving it accessible for tools like GnuPlot?

My simulation, written in C++, generates a large amount (roughly ~500) of text files for each set of parameters I try to simulate, with four columns of ~5k double values in each file. Furthermore, to ...
1
vote
1answer
63 views

Is there a better way to do run time analysis than this?

I currently have 2 different functions with options to vectorise them: acc_rej_sine(max_iter, algorithm=None) and ...
1
vote
1answer
76 views

Finite difference for Lighthill source term

I have experimental data containing horizontal and vertical components of speed and I need to evaluate this: $$ \frac{\partial^2}{\partial x_i \partial x_j}\left(v_iv_j\right) $$ Denoting $U$ as ...
1
vote
1answer
101 views

classification machinery needed

Consider a set of 7D vectors. Each vector belongs to one of four classes. After mapping to 3D with PCA and coloring each point according its class the dataset looks like as shown below: For the ...
1
vote
1answer
84 views

Line scan in a 2D histogram

So I have a 2D histogram, in the third dimention are the counts. What I want to achieve is by choosing two random position, make a plot of a 1D histogram along the line that passes through the two ...
1
vote
1answer
38 views

Adding data with different abscissas

This question may be better suited for an Astronomy Stack Exchange site, but I figured I'd ask here. Say I have measurements of something as a function of radius for a number of objects. Here's an ...
1
vote
1answer
72 views

Extract clusters from a graph of absolute-distance edge

I don't know if I have formulated this problem right: I have tons of items and the distances between each pair of them. Feeding this data into some visualization tool, I am able to create a nice ...
1
vote
1answer
324 views

Clustering data based on the radius of a sphere

I have a data-set that has four columns [X Y Z C]. I would like to find all the C values that are in a given sphere centered at [X, Y, Z] with a radius r. What is the best approach to address this ...
1
vote
0answers
85 views

Eigenfaces Algorithm

This might be a silly quesntion but recently I've been trying to program the eigenface algorithm using PCA, so I arranged the face vectors vertically in a matrix X such as: X = [x1,x2,x3,...,xn]; In ...
1
vote
0answers
25 views

Validating a Markov chain and Bagging to find overall model

let´s say I estimated a Markov chain by splitting my data into traning and test data, and estimating the transition matrix for the traning data yields $$ P= \begin{bmatrix} p11 & p12 &...
1
vote
0answers
106 views

Implementing Frechet Distance on pandas data frame [duplicate]

I am working on a trajectory analysis project using python and its data science related libraries. I am planning to implement Frechet Distance algorithm for trajectory analysis, each trajectory has ...
1
vote
0answers
30 views

Use custom defined metric(not matrix) in Javaplex

I'm about to get started trying to use Javaplex for the first time for some application in topological data analysis (TDA) and I want to use a custom defined metric. From looking over the documents, I ...
1
vote
0answers
44 views

Manipulating/Extracting Data and Developing Methods - Language Choice [closed]

As a general programming enthusiast and aspiring Bioinformatician student I have an intermediate understanding of computing (languages) as well as Java, and to a lesser extent C++. Having knowledge in ...