Analysis of a DNA, RNA, or peptide sequence to understand its features, function, structure, or evolution.

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How to measure multichannel distances between “event” sequences?

In TraMineR, seqdistmc is used to measure multichannel distances between "state" sequences. I am wondering if there is a function to measure multichannel distances between "event" sequences.
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1answer
31 views

What is the role of log2 in Elzinga's turbulence measure?

Elzinga's turbulence measure (TraMineR User's Guide, p. 85) is the log2 of the number of "distinct subsequences that can be extracted from the distinct state sequence" multiplied by "the variance of ...
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6answers
2k views

What is the role of the logarithm in Shannon's entropy?

Shannon's entropy is the negative of the sum of the probabilities of each outcome multiplied by the logarithm of probabilities for each outcome. What purpose does the logarithm serve in this equation? ...
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1answer
36 views

Entropy of state distribution, complexity index and turbulence for sequences of varying length

I have a dataset of varying sequence lengths and want to calculate descriptive measured for it. The main cause of differing lengths is that some cases are right censored, and are dealt properly when ...
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0answers
22 views

MEMM label bias problem

I study MEMM model with application to POS tagging. The question I found that the MEMM model has one drawback - "label bias problem". More formally, The transition leaving a given state compete ...
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2answers
76 views

Should normalization completely weed out correlation?

I have two variables: ordering & length. The former measures the ordering of a sequence (i.e. all permutations of A-B-C), and the former is the length of the sequence (i.e. A-B-C has a length of ...
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1answer
37 views

Sampling from sequence data

I work with 4 sequence datasets that I want to compare. The datasets range from roughly 150 to 2000 sequences. I've been able to use TraMineR on datasets up to 1000 sequences long, but when I try to ...
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1answer
48 views

Mean and Variance of a Set of Sequences

I am trying to find the probability distribution (like mean and variance) of a set of sequences which have different length. I came into different measurement models that quantify the distance between ...
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2answers
115 views

Comparing clustering of sequences in datasets with different N?

When doing sequence analysis using a package such as TraMineR, one can calculate a clustering based on Optimal Matching (OM) distances, and then plot it as a tree. ...
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45 views

Weightining using TraMineR

I have read some posts on weighting. However, I am still unclear on the sort of weights I need to use. I am using data from the Longitudinal Survey of Australian Youth (LSAY). This survey provides ...
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2answers
122 views

Measuring entropy for event sequences?

In TraMineR the function seqient() for calculating the entropy of a sequence object is not available for event sequences (as ...
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0answers
109 views

Path Analysis from cookie data using Survival Analysis?

I have a data analysis task where I need to assign value to various advertisement exposures that lead to an online purchase. The various types of exposures are recorded in sequence but there is no ...
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1answer
112 views

How to estimate the centroid of clustered sequences?

I have run a sequence analaysis using the Optimal Matching algorithm. Afterwards, I have clustered the resulting distance matrice using the Ward algorithm and calculated silhouettes as measures of ...
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1answer
185 views

When and how to use weights for sequence analysis in social science?

Weighting in sequence analysis So far, I have scarcely found papers that address the issue of weighting for sequence analysis (using for example the optimal matching algorithm). Sequence analysis ...
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1answer
91 views

Duration weighted Optimal Matching Algorithm using R

Besides the ado provided by Brendan Halpin for Stata, is there a way to pursue an Optimal Matching using the R-package TraMineR which weights OM’s elementary ...
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1answer
240 views
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2answers
208 views

Other substitution matrices for missing value state in sequence analysis with TraMineR?

We have a question about how to deal with missing values/gaps within sequences. We like to set up our own substitution-cost matrix for the Optimal Matching process. As far as we know, TraMiner allows ...
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1answer
47 views

What is the difference between emerging and discriminative patterns?

I'm working on a way to make efficient classification on sequential patterns mining algorithms. Looking in the state-of-the-art I found that there is two type of algorithm to address this problem : ...
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2answers
119 views

Modifying the time granularity of a state sequence

I created a sequence object from my SPELL-formatted data set. The sequence length of the sequence object is 1440 (i.e., 1-min intervals for a day). Is there any easy way for TraMineR to convert the ...
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1answer
128 views

What is the relationship between substitution cost matrix and indel costs?

In TraMineR I might compute dissimilarities as such: ...
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0answers
57 views

Viterbi realignment

In the past I have trained Hidden Markov Models (HMMs) for sequence recognition with the Baum-Welch algorithm such that if there were $n$ classes, I would use training data $D_i$ for a class $i$ to ...
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4answers
1k views

Framing the negative binomial distribution for DNA sequencing

The negative binomial distribution has become a popular model for count data (specifically the expected number of sequencing reads within a given region of the genome from a given experiment) in ...
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1answer
172 views

Problems with Groups in Traminer

I'm having a problem using the group function in TraMineR. I have a data set that contains SPELL data, so multiple rows per case. I also have demographic data per case, at one row per case. I merge ...
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1answer
166 views

Optimal matching distances as percentages?

I'm using R and the library TraMineR to do sequence analysis on social science data. I have computed an optimal matching (OM) distance matrix. ...
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1answer
277 views

How to describe multi-channel sequence objects in TraMineR?

I have created a multi-channel object here: https://github.com/aronlindberg/VOSS-Sequencing-Toolkit/blob/master/creating_multichannel_object.R However, when I try to use various functions to ...