search for: similarities

Displaying 20 results from an estimated 55222 matches for "similarities".

2004 Dec 08
2
similarity matrix conversion to dissimilarity
...ues (zero being the lowest) signify no similarity. What functions/options in R or its packages are available for making this kind of transformation of a matrix? Specifically, I am a molecular biologist. I have a set of 700+ nucleotide sequences i want to group into clusters based on sequence similarities. There is a wide range of sequences in the set, some of which are homologous to other sequences in the set. I want to use clustering to identify these groups. If the sequences were related and good be trimmed to the same length, I would do an alignment and then use phylip (or some other dista...
2004 Dec 01
1
tuning SVM's
Hi I am doing this sort of thing: POLY: > > obj = best.tune(svm, similarity ~., data = training, kernel = "polynomial") > summary(obj) Call: best.tune(svm, similarity ~ ., data = training, kernel = "polynomial") Parameters: SVM-Type: eps-regression SVM-Kernel: polynomial cost: 1 degree: 3 gamma: 0.04545455 coef.0: 0
2020 Sep 01
2
[RFC] Framework for Finding and Using Similarity at the IR Level
...xample, two sections of code could be considered similar when they contain the same instructions, but are not necessarily used in the same order. Yet, because of the way the operands are used in this different ordering, the instructions still compute the same results for the given inputs. If these similarities are recognized, it could offer improvements towards reducing code size, analyzing redundancies in a large project, or creating tools to help refactor code for a programmer. This new framework offers an interface to detect similarity at the IR level. It has an internal representation that can be a...
2004 Sep 08
8
isoMDS
...ar List: I have a question regarding an MDS procedure that I am accustomed to using. I have searched around the archives a bit and the help doc and still need a little assistance. The package isoMDS is what I need to perform the non-metric scaling, but I am working with similarity matrices, not dissimilarities. The question may end up being resolved simply. Here is a bit of substantive background. I am working on a technique where individuals organize items based on how similar they perceive the items to be. For example, assume there are 10 items. Person 1 might group items 1,2,3,4,5 in group 1 and the...
2001 Apr 10
5
Similarity matrix
I frequently use hclust on a similarity matrix. In R only a distance matrix is allowed. Is there a simple reliable transformation of a similarity matrix that will result in a distance matrix making hclust work the same as S-Plus with a similarity matrix? Venables & Ripley 3rd edition implies that a simple reversal of values will suffice. Thanks -Frank -- Frank E Harrell Jr
2009 Sep 27
1
Clustering with R - efficient processing of large sparse data sets (text data)
...es a full triangular n x n similarity matrix as input, where n = number of observations. The number of variables is 200. My data set has n = 50,000 observations (keywords), and I use ad-hoc similarity measures, not available in R, to measure keyword similarity. Here, the vast majority of the n x n similarities are equal to zero. So I am looking for a clustering procedure that would accept the following alternate input: x1, y1, s1 x2, y2, s2 ... xk, yk, sk where xi, yi are 2 keywords with similarity si > 0 (1 <= i <= k). This input would contain k = 10,000 rows, which is much smaller than n...
2008 Jun 24
5
Measuring Goodness of a Matrix
Hi all, Suppose I have 2 matrices A and B. And I want to measure how good each of this matrix is. So I intend to compare A and B with another "gold standard" matrix X. Meaning the more similar a matrix to X the better it is. What is the common way in R to measure matrix similarity (ie. A vs X, and B vs X) ? - Gundala Viswanath Jakarta - Indonesia
2012 May 26
3
How to measure level of similarity of two data frames
Hi group, I've been thinking of calculating euclidean distance between each column of a data frames that each consists of standardized numerical columns. However, I don't know if there's a way of summarizing the overall distance by some kind of metrics. If anyone know a proper way of doing so and/or a package I would greatly appreciate your suggestions. Thanks very much! Kel --
2011 Oct 07
1
R equivalent of proc varclus
Dear List What is the R package equivalent of Proc Varclus or Information Value. ANy assistance in determining R equivalents of f Oblique Component Analysis (PROC VARCLUS), Information Value (IV) and Weight Of Evidence (WOE) analysis, and business intelligence http://www.nesug.org/proceedings/nesug06/an/da23.pdf Regards, Ajay Websites- http://decisionstats.com [[alternative HTML version
2011 Dec 04
1
similarity matrix
Hello R-users, I've got a file with individuals as colums and the clusters where they occur in as rows. And I wanted a similarity matrix which tells me how many times each individual occurs with another. My eventual goal is to make Venn-diagrams from the occurence of my individuals. So I've this: cluster ind1 ind2 ind3 etc. 1 0 1 2 2 3 0 1 3
2004 Jun 10
1
question about similarities cluster using hierclust
my major is bioinformatics, and i'm trying to cluster ( agglomerate the closest pari of observations ) in R. i have already got my own similarities metric, but do not know how to clust it based on similarities instead of dissimilarities. since the help document of hierclust mentions the parameter "sim", which seems good to me, but it doesn't appear in the code of hierclust() function again? and no sample about it. so could any...
2011 Jul 12
2
apply (or similar preferred) for multiple columns
Dear all, I would like to use the apply or a similar function belonging to this family, but applying for each column (or row) but let say for each q columns. For example I would like to apply a function FUN for the first q columns of matrix X then for q+1:2*q and so on. If I do apply (X, 2, FUN) it applies for each column and not for every q columns. Is that possible with any similar function?
2008 Aug 24
2
similarity between two gene lists with varied length
Dear listers, a little off-topic: I am looking for and compare algorithms which can calculate "distance" or "similarity" between two gene lists with different lengths. Any paper, any implementation in R and any suggestion is welcome! Thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..."
2009 Oct 29
2
similarity measure for binary data
I am doing hierarchical clustering with cluster package.  I couldnot find similarity measures like matching coefficient, Jaccard coefficient and sokal and sneath. Could anyone please tell package with similarity measures for binary data? kind regards, Ms.Karunambigai M PhD Scholar Dept. of Biostatistics NIMHANS Bangalore India From cricket scores to your friends. Try the Yahoo! India
2010 Feb 25
1
taking the median across similar data
Dear All, I am analyzing the miRNA data set in which I have 817 unique probes for each they have 20 features each . I have to group the similar features and take the median across them so that I have a data with no repeats to perform invariant analysis . My data looks something similar format probename sample1 sample2 sample3 A 2.3 2.4 2.5 A
2011 Sep 13
2
help with hclust
Hello, how can I get the similarity value (i.e., the inner cluster similarity) that was used to cut a hierarchical tree at a specific height? I would appreciate your help! Best regards, Madeleine
2007 Apr 30
1
Xapian document matching
Hi, i'm wondering is there a possibility to do like ABCSok do (http://nyheter.abcsok.no/), to make "Main article" and "Same articles" collapsed to it. Like on http://news.google.com/?hl=en the same thing. "Parent" and "same article on other sites" (they do differ from each other a little bit). Maybe somebody know how to do that thing or where to read
2015 Sep 15
3
DWARF info in readobj
Hi All, I see that llvm-readobj displays information similar to GNU readelf does except DWARF data. I also see llvm-dwarfdump dumps all DWARF data in user readable format. Is there a plan for readobj to incorporate similar options? This will make readobj more feature complete for reading objects similar to readelf. If this is not the plan, will llvm-dwarfdump be a tool that regular user
2006 Feb 08
3
OpenRico LiveGrid or similar
Hi Has anyone used OpenRico''s "on-demand listbox" LiveGrid or something similar in a Rails app already? How well does it behave? I''m asking this because I need a scrollable list but the number of records in the table could be well above 5000. In the past I''ve used similar "on-demand fetchings" in desktop apps and it was a real blessing (the
2014 Apr 11
1
rsync performance on large files strongly depends on file's (dis)similarity
Hi list, I've found this post on rsync's expected performance for large files: https://lists.samba.org/archive/rsync/2007-January/017033.html I have a related but different observation to share: with files in the multi-gigabyte-range, I've noticed that rsync's runtime also depends on how much the source/destination diverge, i.e., synchronization is faster if the files are