MonteCarlo | Notes for Monte Carlo and implementations of algorithms
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kandi X-RAY | MonteCarlo Summary
Notes for Monte Carlo and implementations of algorithms in Julia, R or python.
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QUESTION
I’am trying to classify bivariate point patterns into groups using spatstat. The patterns are derived from the whole slide images of lymph nodes with cancer. I’ve trained a neural network to recognize cells of three types (cancer “LP”, immune cells “bcell” and all other cells). I do not wish to analyse all other cells but use them to construct a polygonal window in the shape of the lymph node. Thus, the patterns to be analysed are immune cells and cancer cells in polygonal windows. Each pattern can have several 10k cancer cells and up to 2mio immune cells. The patterns are of the type “Small World Model” as there is no possibility of points laying outside the window.
My classification should be based on the position of the cancer cells in relation to the immune cells. E.g. most cancer cells are laying on the “islands” of immune cells but in some cases cancer cells are (seemingly) uniformly dispersed and there are only a few immune cells. In addition, the patterns are not always uniform across the node. As I’m rather new to spatial statistics I developed a simple and crude method to classify the patterns. Here in short:
- I calculated a kernel density of the immune cells with
sigma=80
because this looked “nice” for me.Den<-density(split(cells)$"bcell",sigma=80,window= cells$window)
(Should I have used e.g.sigma=bw.scott
instead?) - Then I created a tessellation image by dividing density range in 3 parts (here again, I experimented with the breaks to get some “good looking results”).
ANSWER
Answered 2021-Apr-29 at 09:21It seems you are trying to quantify the way in which the cancer cells are positioned relative to the immune cells. You could do this by something like
QUESTION
update:
My compilation command is ghc -O2 Montecarlo.hs
. My random version is random-1.1
, ghc version is 8.6.4
, and my system is macOS Big Sur 11.1 (Intel chip). The command I used to test the speed is time ./Montecarlo 10000000
, and the result it returns is real 0m17.463s, user 0m17.176s, sys 0m0.162s
.
The following is a Haskell program that uses Monte Carlo to calculate pi
. However, when the input is 10 million, the program ran for 20 seconds. The C program written in the same logic took only 0.206 seconds. Why is this, and how can I speed it up? Thank you all.
This is the Haskell version:
...ANSWER
Answered 2021-Mar-05 at 17:44It is sort of expected that on numerical applications, Haskell code tends to be say 2X to 5X slower than equivalent code written in classic imperative languages such as C/C++/Fortran. However, Haskell code being 100 times slower is very unexpected !
Sanity check: reproducing the resultUsing a somewhat oldish notebook with an Intel Celeron N2840 64 bits cpu, running Linux kernel 5.3, GLIBC 2.28, GCC 8.3, GHC 8.2.2, GHC random-1.1, we get the timings:
QUESTION
I'm trying to translate a pandas query into a SQL(ite) query. The main issue in my translation to SQL is trying to place a limit in a group.
Here is a setup (in python) of an example database.
...ANSWER
Answered 2021-Feb-24 at 16:43In any relational database all tables are unordered sets, so there is no first or last row.
So this part of your code:
QUESTION
I am using a Montecarlo simulation for predicting mpg in the mtcars data. I want to extract the coefficients of all the variables in the dataframe to compute how many times each car has lower mpg than the other car. For example how many times Toyota Corona has less predicted mpg than Datsun 710. This is my initial code using only two independent variables. I want to expand this selection to use all the variables in the data frame without manually have to include all the variables in the data frame. Is there any way I can do this?
...ANSWER
Answered 2021-Feb-06 at 01:45I haven't gone all the way through your example, but here is the nugget of how to construct a set of randomized predictor variables and matrix-multiply them by the coefficient vector to get predicted values:
Setup:
QUESTION
What I am looking for is for a method in Python or any other way to solve this, for what I know there is one method, but I couldn't find it, in context what I am doing is calculate the probability of a pair, two pairs etc to appear in a poker play using Montecarlo method, at the moment I'm using the random.sample
function to do that, but I want to use my own methods to generate random numbers that return numbers between 0-1, and I want to use Discrete Uniform Distribution in order to be sure that every number has the same probability to appear.
I apreciate any help you can give.
...ANSWER
Answered 2020-Dec-02 at 19:21If the number is a floating point number between 0 and 1 (range [0, 1)), you can do:
QUESTION
I am using the mob()
function from partykit
package and I am getting some problems when parsing the obtained model.
My main aim is to check approximately how large a sample size needs to be in order to detect the real structure of a data generating process (DGP) when breaks are present.
The code below performs a Montecarlo simulation of data with breaks and tries to identify if the break was captured by the M-fluctuation test or not.
More specifically, I want to make a count on the number of times over the total number of simulations (nreps
) that the model actually captures the DGP, conditional on a fixed sample size (N
) to get a feeling of how many data should I need to capture the real DGP.
At the end of the code, you can see the list that I get out of my simulations. The problem is that I cannot recover the information displayed on the console.
Additionally, I have some doubts about how to make the count of the "correctly identified models". For now, what I have in mind is to count as positive if the model has a break into the correct variable (z1
) at the specified region (z1>0
) with some tolerance into the break region for example if the break is at z1>0.1
or z1>-0.4
it is also valid as a positive for me. Therefore, is there any simple way of counting the models that have the stated characteristics?
I hope my example is clear enough for you to help me out. Thank you a lot in advance.
Simulate model- Ingredients to generate the DGP.
ANSWER
Answered 2020-Nov-25 at 20:09First, I would recommend to use the lmtree()
function and not vanilla mob()
. The former is faster, comes with better defaults for printing and plotting, and has more options for predictions.
Second, I recommend that you consult the vignette("partykit", package = "partykit")
which explains how party
objects are constructed and which classes and methods are involved.
Third, to determine which variable (if any) was used for splitting in the root node it is probably of interest to extract the results from all parameter instability tests. There is a dedicated sctest()
(structural change test) method for obtaining this:
QUESTION
I'm trying to do a multiprocessed version of Monte Carlo Pi calculation.
However, I always get an error that says
TypeError: map() missing 1 required positional argument: 'iterable'
I read that the error can be fixed by using starmap but it doesn't work either for some reason.
...ANSWER
Answered 2020-Nov-26 at 15:06Don't need to call partial to get map value partial rather use just pool.map
. The partial()
is used for partial function application which “freezes” some portion of a function’s arguments and/or keywords resulting in a new object with a simplified signature. But you don't have need something freeze
, if further need to use partial then you need to pass two argument to get the callable beahave. Get more about functools
QUESTION
I am searching for an equivalent function in R of the extremely convenient Stata command simulate
. The command basically allows you to declare a program
(reg_simulation
in the example below) and then invoke such a program from simulate
and store desired outputs.
Below is a Stata illustration of the usage of the simulate
program, together with my attempt to replicate it using R
.
Finally, my main question is: is this how R users will run a Montecarlo simulation? or am I missing something in terms of structure or speed bottlenecks? Thank you a lot in advance.
Stata example- Defining
reg_simulation
program.
ANSWER
Answered 2020-Nov-22 at 22:15So, following up on the comments, you want to vary your independent variables (x) and also the error term and simulate the coefficients, but you also want to catch errors if any occur. The following would do the trick:
QUESTION
I want to use MonteCarlo
function in MonteCarlo
package in R
which has one requirement among others as supply just one single function
into the MonteCarlo
package.
To run a simulation study, the user has to nest both - the generation of a sample and the calculation of the desired statistics from this sample - in a single function. This function is passed to MonteCarlo(). No additional programming is required (Vignette: The MonteCarlo Package).
Contrary to this vital condition, I have two different functions that suit my algorithm. I have used the MonteCarlo
function as provided by the correct answer in this question for a method.
I want to use a different method thus, I write the following functions (function1 and function2) for it to be passed to MonteCarlo
function as demonstrated below:
Here is the algorithm of what I want to do with R
:
- Simulate 10 time series data set from
ARIMA
model througharima.sim()
function - Split the series into overlapping sub-series of possible
2s
,3s
,4s
,5s
,6s
,7s
,8s
, and9s
. - For each size take a resample the blocks with replacement, for new series and obtain the best
ARIMA
model from the subseries from each block size throughauto.arima()
function. - Obtain for each subseries of each block sizes
RMSE
.
The below R
functions get that done.
ANSWER
Answered 2020-Oct-21 at 10:30You can put the contents of function1
into the body of function2
- including the variable assignments etc.
QUESTION
Here is the algorithm of what I want to do with R
:
- Simulate 10 time series data set from
ARIMA
model througharima.sim()
function - Split the series into sub-series of possible
2s
,3s
,4s
,5s
,6s
,7s
,8s
, and9s
. - For each size take a resample the blocks with replacement, for new series and obtain the best
ARIMA
model from the subseries from each block size throughauto.arima()
function. - Obtain for each subseries of each block sizes
RMSE
.
The below R
function get that done.
ANSWER
Answered 2020-Oct-08 at 16:37You get this error message because MonteCarlo expects bootstrap1()
to accept one parameter combination for the simulation and that it only returns one value (RMSE
) per replication. This is not the case here since the block length (lb
) is determined by the length of the simulated time series (n
) within bootstrap1
and so you will get results for n - 2
block lengths for each call.
A solution is to pass the block length as a parameter and rewrite bootstrap1()
appropriately:
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