Speed up Some Code

1 次查看（过去 30 天）
Stephen Gray
Stephen Gray 2024-5-18
评论： Voss 2024-5-19
Hi all. I'm trying to speed up the code below. It's from the SMOTE function that was wrtitten for MATLAB and works really well. The only thing is that the loops are not fast. I've looked at Parfor but that wouldn't work and I can't see how I can vectorise it either. It could be I just have to suck it up and wait but just in case, the code is :-
% This is where the magic happens ;-)
% X : Observational matrix (rows are observations, columns are variables)
% J : Synthesization vector. It has the same length as the number of
% observations (rows) in X. J determines how many times each
% observation is used as a base for synthesization.
% k : Number of nearest neighbors to consider when synthesizing.
function Xn = simpleSMOTE(X,J,k)
tic
HNSMdl = hnswSearcher(X); % To remove this, comment out this line and replace the HNSMdl below with X
[idx, ~] = knnsearch(HNSMdl,X,'k',k+1); % Find nearest neighbors (add one to the number of neighbors to find, as observations are their own nearest neighbor)
toc
Xn = nan(sum(J),size(X,2)); % Pre-allocate memory for synthesized observations
% Iterate through observations to create to synthesize new observations
for ii=1:numel(J)
P = randperm(k,J(ii))+1; % Randomize nearest neighbor pick (never pick first nearest neighbor as this is the observation itself)
for jj=1:J(ii)
x = X(idx(ii,1),:); % Observation
xk = X(idx(ii,P(jj)),:); % Nearest neighbor
Xn(sum(J(1:ii-1))+jj,:) = (xk-x)*rand+x; % Synthesize observation
end
end
end
It's from the 'for ii' bit that is slow and there are around 750000 items of 13 variables.
Steve

请先登录，再回答此问题。

采纳的回答

Voss
Voss 2024-5-18
% generate and collect all the P's first
nJ = numel(J);
P = cell(1,nJ);
for ii = 1:nJ
P{ii} = randperm(k,J(ii))+1;
end
P = [P{:}];
% then do the rest in one fell swoop
ii = repelem(1:nJ,J);
xk = X(idx(sub2ind(size(idx),ii,P)),:);
x = X(idx(ii,1),:);
Xn = (xk-x).*rand(numel(ii),1)+x;
  2 个评论
Stephen Gray
Stephen Gray 2024-5-19
Much quicker thanks! Also a good example of how to vectorise.
Steve
Voss
Voss 2024-5-19
You're welcome!

请先登录，再进行评论。

更多回答（0 个）

类别

在 Help Center 和 File Exchange 中查找有关 Nearest Neighbors 的更多信息

标签

产品


版本

R2024a

Community Treasure Hunt

Find the treasures in MATLAB Central and discover how the community can help you!

Start Hunting!

Translated by