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Questions tagged [cooccurrence]

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Co-occurrence matrix factorization ALS

Let's say I have an item-item co-occurrence matrix that I want to factorize. I'll thus only have item factors. Is it possible to learn the factors using ALS ? I can't see how given that we'd have to ...
Koowah's user avatar
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1 answer
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How to compute Mutual Information

I am absolutely new to MI (and just really bad at it too!) and was wondering if someone could explain to me how to resolve this question. "Say word A occurs once per 1'000 words (i.e, Freq. (A)=0,...
Ella's user avatar
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2 votes
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1k views

Accuracy of PMI (Pointwise Mutual Information) calculation from co-occurrence matrix

Background When calculate PMI or PPMI from a co-occurrence matrix (COM), it sums each row (co-occurrences) of the COM e.g. 2 for pineapple as in the formula in the snapshot. For this question, it is ...
mon's user avatar
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1 vote
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Best way to visualize which few data points out of many occur together frequently

Problem statement I am trying to construct a model that predicts stock price volatility on a given day based on data points represented as strings that may or may not be present on that day. My ...
Way Spurr-Chen's user avatar
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1 answer
60 views

Measure like relative frequency that also weights the total [closed]

Background I see a lot of publications mentioning relative frequencies to indicate the presence of certain genes in a specific area. For example: ...
KingBoomie's user avatar
5 votes
1 answer
995 views

Fisher exact test for mutation co-occurence

I've a dataset of 492 samples, for each sample I've information regarding if gene X has a germline mutation and a somatic mutation. I would like to test co-occurence of germline and somatic mutation ...
Nicolas Rosewick's user avatar
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191 views

Comparing species correlations between species in two habitats

I have two community data sets (samples as rows, species as columns, populated with abundance). This data comes from two habitats/sites, with differing numbers of samples at each site. What I want ...
Cody K's user avatar
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1 vote
2 answers
1k views

Entropy or co-occurrence matrix to compute the randomness of gray scale images?

I have an algorithm that outputs gray scale images (not normalized). These images often contain a lot of random noise and sometimes also contain spatial structures. I would like to have some kind of ...
Gilfoyle's user avatar
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1 vote
1 answer
786 views

Correlation Test for Non-Mutually-Exclusive Categorical Data

I have a table of 288 rows and 4 columns where each row corresponds to a tumour sample, and each column is a gene. All of the values are 0 or 1, to indicate whether there's a mutation in a particular ...
JSneathThompson's user avatar
0 votes
1 answer
155 views

Why the two conditional entropy are not comparable?

I am learning the basics of text mining. For finding the syntagmatic relations in the text like the word "technology" occurs whenever the word "information" occurs i.e co-occurrence of words "...
Sanjeev's user avatar
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6 votes
1 answer
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"Normalising" join probability of n events, by taking n-th root

I have a group of events which I guess you could call a compound events. Each event is something like: $$A=A_1\cap A_2\cap...\cap A_{n_a}$$ I am estimating the probability of the over all event by ...
Frames Catherine White's user avatar
3 votes
0 answers
460 views

Cross Co-occurrence between two corpora

I've looked around for a solution to this problem specifically in nltk, quite a bit but couldn't find much help either on SO or elsewhere. My problem is as follows: I have a set of aligned pairs of ...
user1669710's user avatar