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

learn more… | top users | synonyms

1
vote
1answer
37 views

Correctness of a proof for Hodges' estimator

We know the following is Hodges' estimator: $$ \delta_n = \begin{cases} \bar{X}_n & |X_n| \geq n^{-1/4} \\ a\bar{X}_n & |X_n| < n^{-1/4} \\ \end{cases} $$ where $X_1, ..., X_n \sim ...
3
votes
2answers
58 views

Mining patterns in continuous sequence

I have data in form of $N$ sequences $s_j=(t_i, e_i)_{i\in\{1,\ldots,n_j\}}$ with $n_j$ data-points each, where $t_i$ is a time-stamp and $e_i$ is a categorial event, say $e_i\in\{A,B,C,D\}$. The $N$ ...
1
vote
1answer
43 views

Comparing two sequence objects?

Using TraMineR, is it possible to compare two sequence objects to calculate the discrepancy between them? By this I mean not comparing two sequences but two sets of ...
2
votes
2answers
35 views

Can a 1st Order Model capture information that a 2nd Order model can't?

Let's say we have some sequence $y_1 \ldots y_n$. By definition, a 2nd order Markov model can capture more information from the sequence than a first or zeroth order Markov model. What I'm interested ...
0
votes
1answer
29 views

Determining the class of a new sequence using Markov chains

I want to use a Markov chain to classify a new given sequence as from model+ or model-. For that purpose first I trained two ...
0
votes
0answers
12 views

Normalize sequence lengths

I'm implementing a Markov Chain Model for web site access sequences. Some sequences are very lengthy and some are very short containing a single transition. Lengthy sequences generate a very low ...
0
votes
0answers
4 views

what is the meaning of the Samples in NER?

I would like to know in NER (Named Entity Recognition ) problem , which concept should be considered as samples? each token as a sample? or each sentence ? or each Named Entity should be considered ...
2
votes
1answer
106 views

Visualize process data

I have a dataset of order processing with 8 million rows with following columns: HistoryId - Identity column of the records ...
2
votes
1answer
46 views

Predicting on data consisting of many independent short time series?

I have a dataset which contains many (hundreds) of short (3-30 obs) timeseries of different lengths. Each series is currently represented as a number indicating how long it took to the next event. To ...
1
vote
0answers
65 views

modeling changing items in market basket analysis

I'm performing a "dynamic" market basket analysis where a customer transaction is traced from the beginning (here it has an initial basket of product) to the finalized purchase (where there is the ...
2
votes
1answer
79 views

Finding all largest sequences

What would be a good / efficient algorithm or approach to find all the largest sequences within a list of chains with varying lengths? For instance these chains: ...
4
votes
1answer
100 views

Statistical test to assess differences between two sequencing methods

To asses differences between two DNA sequencing methods (454 and MiSeq) I have made artificial mixtures of different bacteria in the lab (mock communities). An Example might be (numbers are ...
1
vote
1answer
51 views

Hypergeometric test

I have compared 1370 genes which are obtained from ChIP-sequencing analysis and 652 genes which are differentially regulated genes obtained by analyzing affymetrix 430.2.0 mouse array. When I ...
2
votes
1answer
58 views

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.
1
vote
1answer
48 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 ...
22
votes
6answers
3k 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? ...
1
vote
1answer
121 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 ...
0
votes
0answers
259 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 ...
4
votes
2answers
160 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 ...
3
votes
1answer
52 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 ...
2
votes
1answer
115 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 ...
3
votes
2answers
191 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. ...
3
votes
1answer
50 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 ...
3
votes
2answers
170 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 ...
3
votes
1answer
207 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 ...
6
votes
1answer
245 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 ...
2
votes
1answer
129 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 ...
2
votes
1answer
287 views
6
votes
2answers
243 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 ...
3
votes
1answer
55 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 : ...
4
votes
2answers
140 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 ...
4
votes
1answer
165 views

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

In TraMineR I might compute dissimilarities as such: ...
1
vote
0answers
70 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 ...
13
votes
4answers
2k 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 ...
5
votes
1answer
235 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 ...
2
votes
1answer
204 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. ...
4
votes
1answer
365 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 ...