Questions tagged [vectorization]

Use this tag if your code contains vectorized operations - where functions operate on whole arrays in one go. If it doesn't, but you want it to, then you should make those changes (perhaps with help from elsewhere) before presenting code for review.

Filter by
Sorted by
Tagged with
3 votes
1 answer
72 views

Calculating premium splits for policies

Looking for a better approach to write below transformation using Python. Is it possible to avoid loop and still achieve the desired output? It is too slow for 10 million rows. ...
user278818's user avatar
2 votes
1 answer
86 views

Agent based Dengue transmission simulation

I'm trying to implement the dynamics of Dengue transmission between mosquitoes and humans. I decided create two classes, one for the human population and another for the mosquitoes. Both are based on ...
Athansya's user avatar
4 votes
1 answer
181 views

Vectorized 16-bit addition in Standard C

The idea is to add a given 16-bit number N to each element of an array of 16-bit integers of arbitrary length, taking advantage of 64-bit integer types and instructions to perform the additions 4 at a ...
CPlus's user avatar
  • 928
1 vote
2 answers
144 views

Replace personal names and addresses with company ones

The problem: I am given a data frame. Somewhere in that dataframe there is 3*N number of columns that I need to modify based on a condition. The columns of interest look like this: names_1 address_1 ...
Glue's user avatar
  • 129
4 votes
1 answer
623 views

Implementation of Iterative Closest Point in C++

Here, is my implementation of Iterative Closest Point algorithm in C++. The code is written using the Eigen library. I have tried to implement an efficient coding methodology best to my knowledge ...
Aryaman Patel's user avatar
1 vote
1 answer
67 views

Make unique id based on text data column with similarity scoring

I have the following dataframe: ...
illuminato's user avatar
1 vote
1 answer
663 views

Exponentially-weighted moving mean and standard deviation of an irregularly-spaced weighted time series

The following numpy/python function computes exponentially-weighted moving mean and standard deviation of an irregularly-spaced weighted time series. I want to make it faster by getting rid of the ...
yuri kilochek's user avatar
0 votes
2 answers
57 views

Tips to Finetuning to increase the GFLOPS of a SIMD kernel

Given an Image I with dimensions as {rows, columns}, for every pixel in the image, the following needs to be computed - ...
Atharva Dubey's user avatar
3 votes
1 answer
160 views

Matlab vs C: Tensorproduct or Vec-trick (multiple times)

I am searching for a more efficient way to calculate the so called vec-trick used in Tensor algebra, see Wikipedia. Introduction: Suppose you have a matrix vector multiplication, where a matrix C ...
ConvexHull's user avatar
2 votes
0 answers
86 views

Vectorizing a working custom similarity function further using numpy

I am new to python, and even more new to vectorization. I have attempted to vectorize a custom similarity function that should return a matrix of pairwise similarities between each row in an input ...
dddxxx's user avatar
  • 121
11 votes
3 answers
2k views

My blit function for my own graphics library

Here is a blit function for a graphics library I made. I've built a small graphics library that uses an palette-indexed spritesheet to hold all of the game's sprites. The blit function copies parts of ...
coqcauderanais's user avatar
1 vote
0 answers
155 views

Computing the angle between two vectors (vectorized) for small angles and with few copies

I am implementing a function that computes the angle between two vectors when given two n-dimensional arrays and an axis along which to operate. I want to do this with as few copies as possible, and ...
FirefoxMetzger's user avatar
1 vote
1 answer
56 views

Correcting coordinates of an image with polynomial root in python

I want to optimize this for loop for correcting coordinates of an image, it takes too long which is not suited for my system. I have done some profiling, the numpy roots is taking most of the time (...
Md Mizanur Rahman's user avatar
1 vote
0 answers
136 views

Faster Tridiagonal Matrix Multiplication

I have a function that I've been trying to make faster that computes \$XA + B\$, where \$A \in \mathbb{R}^{n \times n}\$ is a tridiagonal matrix, and \$X, B \in \mathbb{R}^{m \times n}\$. In the code, ...
vlovero's user avatar
  • 101
3 votes
1 answer
154 views

Snake from the viewpoint of the snake

I wrote a little game of snake that where you can see the field in which the snake moves fixed and you can also see the "viewpoint" of the snake, which is basically calculating the positions ...
Javier Camacho's user avatar
4 votes
1 answer
54 views

optimize binary classification method for speed

I have the following code for determining TP, TN, FP and FN values for binary classification given two sparse vectors as input (using the sparse library): ...
horcle_buzz's user avatar
3 votes
0 answers
207 views

Implement vectorization instead of nested loops on dataframe

I have a dataset ('sample_data.csv') of the form below: ...
rfguy's user avatar
  • 31
4 votes
1 answer
93 views

Can this numpy code be vectorized?

I've written the following function to produce n realizations of a CIR process for a given set of parameters: ...
John Smith's user avatar
7 votes
0 answers
413 views

C# Generic high performance vectorized math operations

I'm writing a library which simplifies the usage of intrinsics in C#. It's a generic library which supports all numeric types. The goal of this library is to perform these operations at the highest ...
Gilad Freidkin's user avatar
4 votes
1 answer
151 views

Vectorized crosstabulation in Python for two arrays with two categories each

I have two Python lists, label and presence. I want to do cross-tabulation and get the count for each block out of four, such as ...
StatguyUser's user avatar
10 votes
2 answers
396 views

N-Body Optimization

I've created a serial C++ code for gravitational N-Body calculation. Because I expect to have upwards of 8-71 sparse bodies (ie, where Barnes-Hut is not necessarily practical) and running for long ...
Marius Popescu's user avatar
2 votes
0 answers
43 views

Vectorize a function that, once per row, updates multiple rows in data.table

Requirements I have a table of the different diagnoses a patient has received, with the date the diagnosis was first recorded. It so happens that in medicine, diagnoses are recorded as codes from a ...
Rumi P.'s user avatar
  • 201
1 vote
0 answers
55 views

Vectorization of Mersenne Twister? [closed]

Ahoy friends. Right now i'm selling a huge amount of HDDs and usually i used DBAN or nwipe to perform this actions. Unfortunately the PRNG Mersenne Twister is quite slow, so i get a throughput of ...
FBDIMM's user avatar
  • 11
0 votes
1 answer
481 views

Efficiently shift elements right by one in an __mm256 vector [closed]

The code below correctly shifts v256f_stats by one and puts the results into v256f_x3. This is then used to get the delta ...
IamIC's user avatar
  • 191
1 vote
0 answers
163 views

Custom Model intended to be used for Curve Fitting. Vectorization vs For Loop and jit numba capabilities

I am new to community and please pardon me if I didn't provide information as intended. This code is supposed to be creating a custom model which will be used with ...
Shankar_Dutt's user avatar
11 votes
1 answer
604 views

AVX Vectorized Multi-threaded Mandelbrot Renderer

I wrote a Mandelbrot renderer in C++ that uses AVX intrinsics to calculate 8 pixels per thread in parallel. It can compute 1080p frames with 256 max iterations in about 40 milliseconds on a 2 core 4 ...
Saad's user avatar
  • 211
2 votes
1 answer
198 views

Vectorizing equations for fsolve

I have a system of 49 equations and 49 unknowns (\$x_{1},...,x_{49}\$). All equations have the following form. \$x_{s}\sum_{r=1}^{R}\sum_{t=1}^{T}a_{s,t}b_{rs,t}=\sum_{r=1}^{R}\sum_{t=1}^{T}a_{r,t}...
Aristide Herve's user avatar
2 votes
1 answer
159 views

Vectorization, 7-bit encoding

I was curious how vectorization works and how to write suck code. To start simple I choose 7-bit encoding as my test suspect. I'm not expecting improved throughput in any way. My implementation works ...
Joni's user avatar
  • 23
6 votes
1 answer
306 views

How to make my groupby and transpose operations efficient?

I have a DataFrame of size 3,745,802 rows and 30 columns. I would like to perform certain groupby and ...
The Great's user avatar
  • 237
1 vote
0 answers
203 views

condensed nearest centroid classifier in numpy

This is my attempt to write a numpy-optimized version of a nearest centroid classifier to classify some images from the MNIST data set of handwritten digits. I am ...
Grayscale's user avatar
  • 127
4 votes
2 answers
1k views

PyTorch Vectorized Implementation for Thresholding and Computing Jaccard Index

I have been trying to optimize a code snippet which finds the optimal threshold value in a n_patch * 256 * 256 probability map to get the highest Jaccard index ...
yiping's user avatar
  • 73
4 votes
1 answer
1k views

C# System.Numerics.Vector<T> Clamp

The software that I develop uses large floating-point arrays up to the maximum size that can be allocated in C#. I have a large number of algorithms such as convolutions and filters that get executed ...
deegee's user avatar
  • 143
-2 votes
2 answers
2k views

Converting Array of `Float32` (`float`) to Array of `UINT8` (`unsigned char`) Using AVX2 [closed]

Given input array of Float32 (float) with numElements how could one efficiently convert it ...
Royi's user avatar
  • 582
0 votes
1 answer
1k views

Converting Array of `UINT8` (`unsigned char`) to Array of `Float32` (`float`) Using AVX2

Given input array of UINT8 (unsigned char) with numElements how could one efficiently ...
Royi's user avatar
  • 582
3 votes
0 answers
65 views

Optimising multiplication of matrix rows with matrix slice/page

I've recently vectorized most of the code for an optimization problem but this one still eludes me. As the procedure and not the actual values are important here, I have replaced the original matrices ...
deemel's user avatar
  • 131
1 vote
1 answer
490 views

Vectorized N-Dimensional Random Walk in Cartesian Coordinates

I have written a random-walk routine that I hope to build upon in the future. Before doing so, I was hoping to get some critique. I believe the implementation is correct. I noticed that many other ...
user avatar
3 votes
1 answer
230 views

Vectorizing matrix operation instead of for loop in circular matrices

I have a vector \$X_k\$ and a matrix \$Y_{k,j}\$, where \$k \in \{1,\dots,K\}\$ and \$j \in \{1, \dots, J\}\$. They are circular, meaning that $$\eqalign{X_{k+K} &= X_k \\ Y_{k+K,j} &= Y_{k,j} ...
Xbel's user avatar
  • 197
4 votes
1 answer
320 views

Optimizations of C Code - Bilateral Filter

I'm working on a nice approximation for the Bilateral Filter. I have a working code which runs pretty fast yet still I think much can be improved. The code (C Code,...
Royi's user avatar
  • 582
3 votes
1 answer
93 views

Generic pixel class to seamlessly alpha-blend and convert between different pixel structure layouts

Does what it says in the title. I just finished this and wanted to share with someone. Looking for possible optimizations, bugs (most of it is tested to work) or any constructive criticism. ...
user5434231's user avatar
2 votes
1 answer
6k views

Find first threshold crossing in numpy array

Given the following artificially generated data: ...
Seanny123's user avatar
  • 1,527
4 votes
2 answers
603 views

Vectorizing a complex nested for loop in R (running models on different subsets of a data set, subsetting the data differently for each loop)

This is my first time posting so hopefully I manage to get my question across in a clear and concise manner. I'm not sure this is the right place but someone on StackOverflow suggested I ask here. I ...
Tal's user avatar
  • 41
3 votes
1 answer
69 views

Determining whether a list of pathways and its genes are all included in another list

I am evaluating if a list of pathways and its genes has pathways included in another pathways. So the way I thought about it is to create a function that does just a single comparison. ...
llrs's user avatar
  • 273
1 vote
1 answer
123 views

Find the minimum value that data could have had before it was rounded

I have this function in R: ...
yoxota's user avatar
  • 21
0 votes
1 answer
78 views

1D data classification

This R code separates the values in rData. They are classified according to the class in rClass. To do that, ...
zexot's user avatar
  • 41
6 votes
2 answers
8k views

Compute a numerical derivative

Since I could not get numpy.gradient() to compute a derivative successfully, I wrote a script to compute it manually. Running the script below will output a plot of ...
user avatar
3 votes
0 answers
309 views

Merging bin-data via a bin count threshold

When performing a chi-squared test, one takes the square of the differences of the expected counts per bin and observed counts per bin, and divides these per-bin differences by the expected counts per ...
user avatar
1 vote
1 answer
93 views

vectorize 2D gradient with spatially varying bins

The following code takes in some values ssh and solves the equations for the geostrophic motion (slide 8 here). The main part of the code is the computation of the ...
shamalaia's user avatar
  • 255
1 vote
1 answer
971 views

Normalise list of N dimensional numpy arrays

I have a list of N dimensional NumPy arrays. num_vecs = 10 dims = 2 vecs = np.random.normal(size=(num_vecs, dims)) I want to normalize them, so the magnitude/...
Seanny123's user avatar
  • 1,527
6 votes
2 answers
3k views

Remove outliers from a point cloud

This function accepts a cloud of points, and returns those points that are within delta distance of the average (mean) position. ...
adrienlucca.net's user avatar
7 votes
3 answers
3k views

Converting Array of Floats to UINT8 (`char`) or UINT16 (`unsigned short`) Using SSE4

The problem is given image in 32 Bit Floating Point Format (float) how to convert it to UINT8 (char) or UNIT16 (...
Royi's user avatar
  • 582