Questions tagged [jaccard-similarity]
Jaccard similarity (or jaccard coefficient) is a similarity function for computing the similarity between two sets
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Jaccard Index for Binary Data in R using dist function
I have a presence/absence table of 0s and 1s and I would like to cluster this data. I want to create a pairwise matrix using R's dist function which has a binary ...
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1answer
35 views
jaccard distance if one samples is a subset
I have a very basic question but I cannot find an answer (especially for a clustering situation). I am trying to do hierarchical clustering of samples using jaccard distances. One sample contains ...
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1answer
33 views
Addressing “Unbalanced Features” or Feature Taxonomy for Nearest Neighbor / Similarity Calculations
The main question is how to address an imbalance in representation of feature "sets" when calculating similarity. I'll motivate with an example scenario:
Suppose we have objects described by a binary ...
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0answers
52 views
Jaccard Similarity in R Input Prep [closed]
Could I get assistance generating dynamic comparison vectors to use in the Jaccard function in R? For instance, if I have two sets:
"a" "b" "c"
and
"b" "c" "f"
the union vector would be a,b,c,f ...
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0answers
41 views
Downsampling features: how to select the most optimal features to recapitulate clustering [closed]
I've performed single cell analysis in which each gene represents a feature to cluster upon; there are about 20,000 genes expressed across all the cells in the dataset. I use the top 1500 or so ...
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62 views
Interpretation of Overlapping p-value = 0 and Odss ratio = Inf
I would like to conduct an enrichment analysis between two lists using GeneOverlap package in R. I am comparing gene IDs from each list, and there is no NAs in there.
This is the code I'm using:
<...
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172 views
Jaccard distance for sets of different sizes
Is the Jaccard distance still a metric if applied to sets of different sizes? Or does it require the input sets are of the same length?
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78 views
Jaccard Similarity for matrices
I want to use the jaccard similarity to measure the quality of my binary segmentation. I found a function in the library sklearn.metrics called jaccard_similarity_score and I found in another forum ...
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72 views
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3answers
1k views
Can I use Manhattan distance on binary data for hierarchical clustering?
I understand that classically Jaccard and Hamming work best with binary data, but is there anything specifically wrong with using a Manhattan distance instead with the complete linkage function?
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0answers
209 views
Estimate Jaccard similarity based on a sample
The Jaccard similarity of two sets, $A$ and $B$, is defined as: $Jaccard(A,B)=\frac{A\cap{B}}{A\cup{B}}$.
Say that I only have a sample of $P\%$ of each of the sets: $A'$ and $B'$. What would be a ...
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194 views
Measure similar to Jaccard index but comparing more than two groups at a time
I am interested in looking at the amount of sharing between several samples (each represented as a vector of character strings), and to do pairwise comparisions, I have been using Jaccard indices. Is ...
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1answer
2k views
Calculating Jaccard similarity in R: all duo combinations for multiple groups and creating a matrix or cluster plotting with the index [closed]
I have been trying to compute Jaccard similarity index for all possible duo combinations for 7 communities and to create a matrix, or preferably Cluster plotting with the similarity index.
There are ...
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0answers
251 views
How do I calculate the Jaccard distance for normal distributions?
I'm trying to replicate the results in this paper. I'm stuck at this part: specifically,
calculate Jaccard intersection of pdata1 & pdata2
Is there some neat ...
4
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1answer
774 views
What is the significance of the Jaccard similarity score?
I understand how to calculate the jaccard similarity , but never quite understood the logic behind why are we calculating it. How does it show the similarity between two sets? What relation exactly ...
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0answers
45 views
Correlation of continuous-time series
I have two continuous time series of discrete events. The data from them are timestamps of occurences, e.g.
...
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1answer
33 views
Measuring simmilarity of observations (non numeric)
I have a dataset of format :
day,measurement1,measurement2
1,a,b
1,a,c
1,f,s
2,a,b
2,a,c
2,f,g
3,a,d
3,a,q
3,f,s
In this example day1 is more similar with day2 ...
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0answers
115 views
Calculating Similarity between two multiset
I need to find similarity between two multiset. For example,
$$A = \{a, a, b, c, d\}$$
$$B = \{a, b, b, d\}$$
I know that I can use Jaccard Index but it gives same weight for each element. As ...
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0answers
269 views
Dummy data clustering: OK to apply Euclidian distance hierarchical clustering on Jaccard similarity matrix?
I created dummy variables (binary data) from categorical variables where I want to partition N subjects into multiple classes by some clustering method. I created a Jaccard similarity index matrix for ...
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0answers
31 views
Similarity between bar plots (counts of categories)?
What are the best ways to compare (calculate similarity) between two bar plots? For example:
...
6
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3answers
2k views
Similarity measures for more than 2 variables
If I have two binary variables, I can determine the similarity of these variables quite easily with different similarity measures, e.g. with the Jaccard similarity measure:
$J = \frac{M_{11}}{M_{01} +...
1
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1answer
345 views
Interpretation of Jaccard similarity for binary networks
Given two undirected networks with the same amount of nodes defined by $A_{ij}^1$ and $A_{ij}^2$, we take the unique unordered pairs $(i, j)$. After sorting them, we then have two binary vectors $\vec{...
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0answers
32 views
How to statistically validate that one clustering technique is more effective than other on Binary data
Problem statement - Idea is to cluster students based on their assessment pattern and score.
Data = I have a data set that contains Binary data of students answers(Correct/incorrect) which i have ...
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1answer
44 views
How to form clusters when features are sets of string objects
I am building a movie recommender. But unlike common recommender from movielens data, features of my movies are sets like actor list, genre list, list of producers and writers etc.
I know I can use ...
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2answers
206 views
Detecting misclassified data points using distance matrix
I have a data set of around 65,000 items from a public database that have each been assigned to one of around 1,800 classes, but unfortunately I am aware that quite a few are misclassified. My goals ...
4
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1answer
2k views
Jaccard similarity coefficient vs. Point-wise mutual information coefficient
Can you explain the difference between the Jaccard similarity coefficient and the pointwise mutual information (PMI) measure? It would be great if you could add a few examples.
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2answers
4k views
Accuracy vs Jaccard for multiclass problem
TL;DR For a multiclass problem, is Jaccard score the same as accuracy?
Update March 29, 2019
The wrong implementation in scikit-learn is now fixed with pull request #13151. Hooray!
P.S. The lesson ...
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0answers
135 views
Threshold value for nodes similarity
I am working on an algorithm for community detection on complex systems, where those systems are modeled as graphs. To form community i need to find similarity between nodes.
I am using Jaccard ...
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0answers
326 views
Jaccard coefficient (0011 and 1100 most similar?)
I try to compare different binary objects, lets say:
...
1
vote
1answer
439 views
How to compare a Ranked List?
I have 50 products. For each product, I identify 3 related products (1 top related, 2 (partially related, least related)) using similarity measures. I want to compare the ranked list generated by my ...
0
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2answers
522 views
Jaccard similarity of sets with approximate element matching
Consider two sets like this:
A = {'hello', 'world'} and B = {'Hello', 'helo', 'goodbye'}.
I want to measure the similarity between these two sets. There are two levels to this problem:
Comparing ...
2
votes
1answer
1k views
NMDS from Jaccard and Bray-Curtis identical. Is that a bad thing?
The dataset is ecological (species abundance), where I am calculating distances between 51 sampling sites, based on abundances of 3200 species. The species abundance values go up to 2700, and the rest ...
2
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1answer
5k views
Jaccard distance vs Levenshtein distance for fuzzy matching
My data is similar to the following data, but far bigger and more complex.
Apple
Banana
Those fruits
Tomato
Cocumber
These vegetables
I would like to get the ...
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1answer
5k views
What are the difference between Dice, Jaccard, and overlap coefficients? [closed]
I come across three different statistical measures to compare two sets, in particular to segmentation on images (e.g., comparing the similarity between the ground truth and the segmented result).
...
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1answer
34 views
I want to find similarity for 20 organisms on 25 parameters? How to do this ? Any software is available for this? [closed]
How to find similarity for 20 organisms on 25 parameters? How to do this ? Any software available for this?
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0answers
215 views
Find similarity score between multiple items based on tags assigned to them
I am working for a client who is in e-commerce. They have thousands of offerings and each has its own set of tags. Now, they want to find similar designs dynamically based on the item selected by the ...
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0answers
267 views
Statistical Interpretation of Average Pairwise Similarity
I have assembled binary vectors (0/1 for all elements and equal weight and arranged in time order) that have been separated into different cohorts where a unique event of interest occurs. I have ...
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0answers
102 views
Similarity measures and document length
I have an application where I need to measure the similarity between the (TF-IDF?) representation of two documents: $\mathbf{a}$ and $\mathbf{b}$ while still taking the document length into account.
...
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0answers
158 views
Numerical Similarity Measures for Dirty Data
I need to compare two datasets to see if they are "similar" in terms of numerical similarity between given columns. The problem is, however, that I do not know the characteristics of the 2nd dataset. ...
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2answers
1k views
Significance Test for Jaccard Distance
I am looking for a significance test for the Jaccard Distance (JD).
As an example, I have two datasets as follows:
Baseline: $\left| A\bigcap B \right|=57;\ \left| A\bigcup B \right|=275\quad \...
2
votes
1answer
314 views
Is the Jaccard Index a function of the number of elements in a list?
I am trying to understand a research result. Imagine 10 different psychological questionnaires 1,2,3,...10 of different length (i.e. number of questions) that are all supposedly measuring the same ...
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0answers
409 views
Approach to find similarity between two different types of matrices
I'm using the movielens dataset to give recommendations to a user based on genre of the movies.
I have two matrices, one contains the genre the user likes. We are considering user3 for now
I also ...
0
votes
1answer
86 views
How to soften or mitigate vector similarity measure?
I would like to evaluate a similarity between two objects X and Y by comparing a neighbourhood in which they're located.
I construct two sets of nine concentric and equidistant circles with centers ...
1
vote
1answer
324 views
Selecting the number of hashes for minhash? Working with extremely sparse data and want more collisions
I'm attempting to use minhash to generate clusters and similarities, and I am primarily using ideas from these resources.
http://www2007.org/papers/paper570.pdf
https://chrisjmccormick.wordpress.com/...
2
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0answers
872 views
Similarity between sets with different size
is there a distance measure like jaccard for sets with different sizes?
For example A=['a','b','c'] and B=['a','d']
I would like to include the total intersection as well as the order.
The ...
0
votes
1answer
815 views
confusion matrix and Jaccard index computation in O(n) for cluster comparison
My problem:
I have two clustering (or partitions) of a set of numbers $\{1,...,n\}$, each with $k$ cluster (or subsets), that i have to compare and, to do that, i'd like to try some different indexes ...
1
vote
1answer
793 views
Apriori versus Jaccard Coeff for recommender-system
I developed a market basket program for a retailer. I used the pymining library association rules function. I assume this uses the Apriori algorithm. I got 340,000 rules for an input of 17,000 ...
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5answers
19k views
Jaccard similarity in R
I want to compare 2 vectors of length 43; they have values of 0 (not present) and 1 (present). I will refer to $M_{1,1}$ as situations in which both 1 are present, and $M_{1,0}$ and $M_{0,1}$ to ...
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0answers
674 views
should I count repeated items in jaccard similarity?
I have two lists: A and B where Size(A) = 4 and size(B) = 10. I would like to find the Jaccard similarity between these two lists.
Suppose A = {Tom, George, John, Jennifer} and B={Tom, Jessica, ...
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0answers
843 views
Cosine similarity between two types of user profiles
I have a movie dataset containing preference (ratings) of users on movies and also attributes of movies (genre, cast, director). I created two types of profiles for users based on the movie attributes ...
