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

learn more… | top users | synonyms

0
votes
0answers
14 views

simple temporal classification with LSTM

I'm working on a sequence labeling for specific type of data using LSTM network. However at the moment i'm trying the algorithm with some toy data. I've written the matlab code to implement the ...
2
votes
1answer
13 views

How the total pseudo R2 is calculated with the “dissmfac” function in TraMineR?

I am using the discrepancy analysis in TraMineR. I performed univariate analysis with "dissassoc" to measure the effect of each variable. Then, I did a multi-factors analysis using "dissmfac" to ...
0
votes
0answers
18 views

Clustering and differentially expressed genes in RNAseq

I have performed differential analysis with DESeq2, edgeR and voom-limma. My goal was to evaluate each methods on my data. Now I would like to perform clustering with the genes found differentially ...
2
votes
1answer
21 views

Optimal matching distances

If I have two sequences: 1: A-B-C-D 1: X-A-B-C-D and I do: library(TraMineR) seqdist(sequence1, sequence2, method = "OM") ...
0
votes
0answers
21 views

How to build a model that maps strings to lists of strings?

I have a mapping from strings to rows in a data table. Each strings maps to exactly one row in a table but the opposite is not generally true (one row can be "bound" to different strings. For example ...
9
votes
2answers
78 views

How to prove cooperation from behavioural sequences

Situation: Two birds (male and female) protect their eggs in nest against an intruder. Each bird can use either attack or threat for protection, and be either present or absent. There is a pattern ...
0
votes
0answers
6 views

Representing pairs of proteins as feature vectors

I am attempting to predict whether two proteins will interact or not (binary classification task - pair of proteins as input and 1 or 0 for output indicating interaction). I have thousands of positive ...
0
votes
0answers
32 views

What is the optimal observation sequence length to train HMM?

I want to train HMM based on 11000 files each has a long sequence, this huge number to train, training time is too much, how I will choose the t = observation length to train HMM?
0
votes
0answers
16 views

Analysis of classification result

Assume you observed a system for 24 hours and collected data points each minute (each data points contain some host information like cpu_usage,... All elements are numeric). Also, there is a trained ...
1
vote
0answers
13 views

Sequence analysis with multiple sequences

I would like to recognize different states in a sequence of multiple vectors. To make it little more clear, here is an example: I have 2 (or more) vectors in a sequence: head position(HP) and eye ...
1
vote
1answer
24 views

Length-dependent indel costs in OMA algorithm?

I re-read this article after a long time (this time paying attention to the fine print) and noticed that they use indel costs that depend on sequence length in their OMA. They argue that it is done to ...
3
votes
1answer
487 views

Using Keras LSTM RNN for variable length sequence prediction

I have a set of sequences. Each sequence is the form $\{(s_1,l_1),(s_2,l_2) \ldots\}$ where $s_i$'s are real valued numbers and $l_i$s are labels from a fixed alphabet. It is important to note that ...
0
votes
1answer
23 views

How to calculate a blosum matrix with X% identity?

Calculating a blosum matrix is easy and many explanations online exist. However, given a set of sequences and asked to get X% identity I am unsure of. Say they said 80% identity with the following ...
0
votes
0answers
64 views

Distinguish long and short term fluctuations in time series

I have a sequence of events $(e_1,e_2,\dotsc,e_n)$, and each event $(e_i)$ is described by two features $(t_i,F1,F2)$, where $t_i$ is the time of capturing the event. The events $(e_i)$ are captured ...
0
votes
1answer
15 views

Method for inferring tree structure from messy sequence data

I have data about case events in criminal cases. These data are in the form of sequence like ...
3
votes
0answers
58 views

Analyzing Sankey diagrams statistically?

Sankey diagrams are helpful for visualizing multiple, interacting processes: Are there any statistical tools available that can analyze the interactions of multiple processes? I'm aware of sequence ...
0
votes
0answers
25 views

Mining sequential associations using entropy measures

Assume I have a sequence that looks like this: A-A-A-B-A-A-C-A-A-B-C Let's say I want to predict to use the sequences of letter that occur between one letter and ...
0
votes
0answers
96 views

RNNLIB: How to get CTC output label sequence locations?

I'm using Alex's RNNLIB (http://sourceforge.net/projects/rnnl/) with CTC output on one of my projects. I am up to the step that I have successfully trained a network with 3 hidden layers (with an ...
0
votes
0answers
38 views

Calculating the significance of lift

The lift (in data mining, especially for sequential association rules), is calculated as: "by dividing the confidence by the unconditional probability of the consequent" ...
3
votes
2answers
46 views

Position-dependent substitution cost matrix for sequence alignment

Many sequence alignment algorithms and those which measure similarity between sequences require specification of a cost matrix defined on the sequence alphabet. However, the cost incurred does not ...
0
votes
0answers
20 views

How do I calculate the inter-rater agreement for sequence alignments?

I am having this task of aligning one sequence of sentences to another sequence of sentences. Let's say we have sequence 1 and sequence 2 as an example of the task: Sequence 1:  A B C D E  F ...
0
votes
0answers
25 views

Sequential pattern mining on mutiple sequences

Can someone give me a hint about a good approach to find a frequent patterns in a multiple sequences. Each sequences is a combination of 7 characters M,E,N,S,U,R,G. The length of each sequences is ...
0
votes
0answers
16 views

Domain of sequence information

The larger project is to build an SVM model using protein sequence information as input. From the sequence [C,E,D,T....] I generate sequence based variables. For example, mass is represented by ...
4
votes
2answers
451 views

similarity measure between two different ordered sequences

I know we can quantify the similarity between two sequences with the same length and same elements by rank order correlation. But how to measure similarity between two sequences of different length, ...
1
vote
2answers
141 views

Comparing mutation frequency between a case and a pool of controls

I"m working in genomics and trying to come up with the appropriate statistical test for my question. To call mutations in a tumor's DNA, we use sequencing that samples from the total population of ...
0
votes
0answers
22 views

Help Simple Conditional Counts Example

Let's say we have a sequence $S$ \begin{align} t \quad 0 \quad 1 \quad 2 \quad 3 \quad 4 \\ S_t \quad 1 \quad 1 \quad 0 \quad 0 \quad 1 \end{align} And we want to predict $S_{t+1}$ by selecting ...
0
votes
0answers
119 views

Market Basket Analysis

I am learning "Market Basket Analysis" and I need a clarification about Advantages and Disadvantages or Pro's and Con's of the "Market Basket Analysis". And some cases where actually this "Market ...
0
votes
1answer
293 views

what is “target delay” in the context of RNN/LSTM?

I'm currently reading a paper on sequence-to-sequence classification (speech-to-text) and it is stated that "there are ways to introduce future context, such as adding a delay between the ...
5
votes
2answers
617 views

Sequential pattern mining on single sequence

Can someone give me a hint about a good approach to find a frequent patterns in a single sequence. For example there is the single sequence ...
1
vote
3answers
87 views

Central limit theorem for sum of differences

I have a quick question. If we have a sequence of i.i.d random variables, $X_1,X_2,X_3,\ldots,X_n$. Then, we make sequence below: $$ S=X_1-X_2+X_3-X_4+\ldots+X_n $$ Does central limit theorem work in ...
3
votes
2answers
71 views

How to interpret p-values in output of seqecmpgroup()?

The seqecmpgroup() function returns a table that, among other things, include p-values for each identified subsequence. How should these be interpreted? I can see ...
2
votes
1answer
139 views

How to do centroid clustering of sequences?

I want to cluster sequences using centroids. In the hclust package it is noted that "Method "centroid" is typically meant to be used with squared Euclidean ...
1
vote
0answers
116 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
249 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
317 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
44 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
67 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 ...
4
votes
1answer
303 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
123 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
112 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
96 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: ...
5
votes
1answer
279 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
85 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 ...
3
votes
1answer
110 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
94 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 ...
38
votes
9answers
7k 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? ...
2
votes
1answer
398 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 ...
4
votes
2answers
472 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
87 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 ...
3
votes
1answer
335 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 ...