Questions tagged [algorithms]

A description of the specific steps needed to solve a particular problem in an unambiguous way, expressed in an abstract form.

Filter by
Sorted by
Tagged with
1
vote
0answers
34 views

Surface mesh from labeled 3D points

I'm trying to figure out how to create a surface mesh from a set of labeled 3D points. The 3D object could be something like part of a cave system or asteroid where there would be parts of the surface ...
1
vote
0answers
22 views

Combining many probabilities, modifying, seeking general formula

CONTEXT I need to combine the probability of occurrence of many thousands of events for millions of individuals (trees) in an agent-based/individual-based simulation model developed in NetLogo (agent-...
2
votes
1answer
36 views

Question regarding the energy computation of the Ising-Spin Model

In most of the Monte-Carlo-Algorithms I studied, I found, at the place where they compute the energy, always a line of code, where they divided by four. For example, this code-snippet is taken from ...
1
vote
1answer
74 views

Machine Learning for Optimization

I have a function which takes 100+ coefficients and outputs $x$. I wish to optimise $x$. Running the simulation 50 000 times will take around 15 minutes, however, this happens in parallel - and the ...
1
vote
0answers
49 views

Assume $AX = C$. How to determine which entry of $BX - D$ is non-negative?

Let $A,B$ be $n \times n$ matrices and $C,D$ be $n \times 1$ matrices. Moreover, all entries of $A,B,C,D$ are non-negative. Assume that there is a unique matrix $X$ that solves $AX = C$. My goal is ...
0
votes
2answers
63 views

Best way to find biggest & smallest number in a random list?

Given a list of some length, containing random numbers. What method would need the least amount of checks to find the largest & smallest number in the list? My best guess is: (list_length)/2 ...
-1
votes
1answer
25 views

An almost surly fine-time game of coin toss where you win with probability $p$

Given a fair coin and a number $p\in(0,1)$. How do you design a game that finishes in a finite number of tosses with a probability of $1$? And further, with the probability $p$ you win the game. I ...
0
votes
0answers
35 views

What constraints, if any, are there on constructible patterns in Conway's Game of Life?

Conway's Game of Life is Turing-complete. Interesting demos of this: A clock Tetris I note that Turing-completeness doesn't require that any specifically encoded state be reachable, does it? ...
1
vote
1answer
47 views

Newman algorithm yielding different result to what is given in his paper

Summary I am trying to implement Newman's algorithm for community detection, outlined in this paper. I am testing my implementation against one of the datasets used in that paper to benchmark the ...
1
vote
2answers
92 views

Using MILP to place a set of primers along a genome

Define variables $p_i,u_i\in\{0,1\}^G$, for $i=1,\ldots,8$ and $G=30000$. Let $v$ be a constant vector also in $\{0,1\}^G$, with approximately 25% of its entries equal to $1$ (randomly located). Let ...
1
vote
0answers
25 views

Unable to achieve semi-linear running time in computation of continuant

I am trying to compute the continuant of a list of numbers $a_0, a_1,...,a_n$, defined by the recursion relation: $K_{n+1} = a_{n+1} K_n + K_{n-1}$ and $K_0 = 1$ (see Wikipedia). I am trying to use ...
0
votes
0answers
16 views

Boundary conditions for triangular lattice in comsol

I am trying to simulate an infinite 2D triangular lattice in Comsol but I am confused that how should I use periodic floquet boundary conditions on the unit-cell. A unit cell that I am using is given ...
3
votes
1answer
85 views

Can you compare integer part of two fractions without division?

Suppose we need to compare $\left \lfloor{a / b}\right \rfloor $ and $\left \lfloor{c / d}\right \rfloor $ . One way would of course be to calculate $a/b$ and $c/d$ by division. Is their a faster way?
5
votes
2answers
141 views

Fast algorithm for computing the similarity between two arrays

Suppose there are two arrays (They have the same length), I want to give a quantitative description about the similarity between them. I define a formula like this, which means we can shuffle them ...
5
votes
1answer
55 views

Is there an efficient algorithm for calculation of continued fraction expansion from decimal digits?

Suppose to calculate the continued fraction expansion of $\pi$, the common-sense algorithm would be to take the decimal part, perform inversion, which will give the next term as integer part, and the ...
7
votes
1answer
117 views

Numerically stable and fast sum of last K elements in sequence

Suppose I have a long, possibly infinite, sequence $x := [x_1, x_2, ...]$, and I want to use it to compute another sequence $y:=[y_1, y_2, ...]$ where each element is the sum of the last K elements of ...
5
votes
0answers
73 views

Efficient way to find eigenvalues of complex symmetric matrix with real off-diagonal elements

My goal is to find all eigenvalues (and eigenvectors) in a given range of magnitudes of a complex symmetric matrix with real off-diagonal elements (only diagonal elements are complex). Currently I'm ...
2
votes
0answers
24 views

Alternatives to breadth-first-search in 3D grid cluster detection?

I've got a question about a good way to find the quickest algorithm for my problem: problem: I've got a 3D cubical grid containing voxels that are either 1 or 0. It is stored as a flattened array. If ...
2
votes
0answers
40 views

Evaluating integral $F(r_2) = \frac{1}{r_2^n} \int_0^{r_2} r_1^n f(r_1)\ \mathrm{d}r_1$ without growing instability

I have the following expression to be numerically integrated in a vector-based library (e.g. numpy, MATLAB, etc), $$ F(r_2) = \frac{1}{r_2^n} \int_0^{r_2} r_1^n f(r_1)\ \mathrm{d}r_1, $$ where $n$ is ...
1
vote
0answers
18 views

SHREC 2010 Descriptors

I will appreciate if I may find someone how can clarify for me the part regarding the quality of feature descriptor, shown in the figure below: and this screenshot is from the article: SHREC All my ...
3
votes
1answer
67 views

Evaluate 3D Shape Descriptor

I'm trying to create my own 3d shape descriptor, the idea is that how I may evaluate how much my descriptor is well and good? What I checked is that they evaluate descriptors through shape matching, ...
3
votes
0answers
65 views

Computation of Troullier-Martins pseudowavefunctions

The computation of Troullier-Martins pseudowavefunctions has been described in [1]. The pseudowavefunction $R^{\textrm{PP}}_l$ is defined by $$ R^{\textrm{PP}}_l(r) = \left\{ \begin{array}{ll} R^{\...
10
votes
3answers
339 views

Should benchmarkings be done at all? What is the point?

I am reading a paper which compares algorithm A versus algorithm B. It shows that algorithm A is faster than algorithm B via benchmarking that shows the CPU time. What is the point of this? Any ...
1
vote
0answers
67 views

How to approach geographic data interpolation by distance?

let's say I have a set of geographic locations (lat, lng) resulting from a query. Those locations have some kind of internal ranking, my set is sorted by this number in a descending order. Now I'm ...
3
votes
1answer
76 views

Calculate Transformation Matrix between two sensors

My question is if I can calculate the transformation matrix between two sensors. Each sensor provides a $4\times 4$ matrix for every timestep recorded. The sensors are moving and have some noise in ...
0
votes
0answers
59 views

What is Voronoi particle tracking?

I've been trying to track this down, but google is giving paywall papers that don't appear to be directly related to computational science, or simply don't explain the source algorithm. There's an ...
5
votes
1answer
239 views

Understanding butcher tableau when it comes to implicit methods

I've been learning about butcher tables and am having some difficulty understanding how to translate them when it comes to implicit methods. Specifically, I'm looking at backwards Euler: \begin{array}...
2
votes
0answers
157 views

What exactly is the cause(s) of blow-up for too-large step size in a method like RK4?

I have been working on creating a few home-made numerical methods, and I am using them to visualize text-book problems from my Strogatz dynamics textbook. It feels like a good way to learn numerical ...
1
vote
0answers
58 views

Hybrid Ellpack-Itpack (ELL) + COO Sparse Matrix Representation decomposition threshold

Hybrid ELL-COO sparse matrix representation can be done as in the picture, I was looking intensively, however I couldn't find out what is the threshold of decomposing the original matrix into ELL part ...
3
votes
1answer
83 views

Efficient computation of leading eigenvector of a matrix product of the form $ADA^T$, where $D$ is diagonal

Let $A=[A_1|\ldots|A_m] \in \mathbb R^{n \times m}$ with $n \gg m \gg 1$ and $D=\text{diag}(d_1,\ldots,d_m)$ where $d_1,\ldots,d_m > 0$, and consider the $n\times n$ positive-definite matrix $X=\...
0
votes
0answers
31 views

solving electron motion in undulator by Boris method

I am trying to use Boris scheme to solve the electron trajectory in undulator. The undulator field I used is: $$B_x = b_0\sin(2\pi \tfrac{z}{\lambda_u})$$ where $b_0 = \dfrac{2\pi c_{0}K}{q m_{e} \...
1
vote
1answer
124 views

Weighted moving variance

i have a time-series and, in analogy with exponentially weighted moving average, i would like to compute the exponentially weighted moving standard deviation or variance in an efficient, numerically ...
0
votes
1answer
63 views

Dealing neighbor list in NVT Monte Carlo (MC) simulation

I'm making a NVT Monte Carlo (MC) simulation code with only short range interaction. I found many MC tutorial codes (usually Lennard-Jones system) in online. However, most of them are doing energy ...
4
votes
2answers
132 views

Efficient algorithm to decide if a graph is a cactus?

A cactus is a connected graph in which every edge belongs to at most one simple cycle. How should one modify the Depth First Search algorithm to obtain an efficient algorithm that determines if a ...
4
votes
1answer
195 views

Fast algorithm for computing cofactor matrix

I wonder if there is a fast algorithm, say ($\mathcal O(n^3)$) for computing the cofactor matrix (or conjugate matrix) of an $N\times N$ square matrix. And yes, one could first compute its determinant ...
1
vote
1answer
35 views

How is the D value being updated at simple RRT algorithm?

I am studying the following lecture (image) regarding 5 iterations of the simple RRT algorithm. I am trying to understand how each value is being updated regarding each iteration. I have figured out ...
0
votes
0answers
33 views

A preconditioner for self-consistent iteration

I tried to derive a preconditioner for self-consistent iteration similar to section IX in arXiv:0804.2583. For simplicity, consider here only one orbital (one or two electrons) systems. Suppose that ...
0
votes
1answer
230 views

Chip testing problem

An engineer has n supposedly identical integrated-circuit chips that in principle are capable of testing each other. The engineer test jig accommodates two chips at a time. When the jig is loaded, ...
4
votes
1answer
46 views

Single-variable multimodal derivative-free optimization (for a well-behaved function)

Are there well-established approaches to single-variable multimodal optimization? Given $f:\mathbb{R}\rightarrow\mathbb{R}$ that: has several local minima within a given range of interest $[a,b]$ is ...
3
votes
1answer
111 views

How to justify using available code (in different language) for comparing algorithms

I have proposed an algorithm for a scheduling problem in a submitting paper. In the revision, the reviewer asked us to compare with another algorithm from the literature. Our algorithm is in MATLAB, ...
3
votes
1answer
95 views

How to find a pair of divisors as close as possible to each other?

For a given integer $n\in\mathbb{N}^*$, I want to find a pair $(x,y)\in{\mathbb{N}^*}^2$ such that $x*y=n$ and $|y-x|$ is as small as possible. A naive algorithm I found is : ...
2
votes
0answers
47 views

Cover a polygon with least amount of parallelograms [closed]

I am solving the task that is as follows: Input: a polygon. Can be any kind of polygon without self intersections. Can be a non-convex and with holes inside. Goal: to cover it with 2 (at least) or ...
0
votes
1answer
134 views

Finding a shortest path in a graph

If each edge of a graph $G$ is unweighted or has equal weights, then the shortest path between two nodes in that graph is the path that contains the fewest number of edges. Such a path can be obtained ...
2
votes
3answers
166 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 ...
1
vote
0answers
44 views

How to numerically calculate the transition dipole integral in periodic systems?

Now I have wave functions $\psi_a$ and $\psi_b$ of two states in Gaussian CUBE format. I'd like to evaluate the transition dipole moment integral $\pmb\mu$ between these two states. As my simulation ...
0
votes
1answer
76 views

Stability of PDEs

I am currently trying to solve some PDEs with FiPy. At page 56, the manual mentions (https://www.ctcms.nist.gov/fipy/download/fipy-3.0.pdf). The largest stable timestep that can be taken for this ...
0
votes
1answer
76 views

Python sequence cluster exercise

I am working through an exercise in my textbook and implementing the code in Python to practice dynamic programming. I feel like I am right on the edge of figuring it out, but after many hours, I come ...
1
vote
0answers
35 views

Number of $S_n$-orbits in $P^k(\{1,\dots,n\})$

This is a particular case of a question I asked on Mathematics Stackexchange, question which got no answer so far. Let $n$ and $k$ be integers with $n\ge1$, $k\ge0$, and let $a(n,k)$ be the number of ...
2
votes
0answers
28 views

Piecewise-linear Continuations vs Marching Squares/Cubes

It seems that both piecewise-linear continuation and marching squares are methods to produce iso-contours of a scalar function given the function's values on a grid. It seems that piecwise-linear ...
0
votes
1answer
21 views

Binary tree for 2 elements [closed]

I want to understand Binary Search for 2 element list made of 1,2. I draw a tree as below. Is it correct? If I want to search for an element 2, it will make 2 comparisons. If I want to search for ...

1
2 3 4 5
10