Questions tagged [sequence-analysis]

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

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540 views

traditional state-space models and LSTMs

I am trying to understand the nature of LSTMs in relation to intuitions from traditional state-space models (e.g., Kalman filtering). The code below aims to simulate a simple univariate linear state-...
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134 views

Which distance metric to use to cluster categorical sequences (clickstreams or clickpaths)?

For my research, I want to cluster website visitors based on their clickstreams to understand different information behavior patterns (i.e., customer/visitor journeys). The data can be characterized ...
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Dealing with the order of features (sequences)?

Assume we have following sequence database that is subsequently converted with one-hot encoding: 1 2 3 4 0 A B C D 1 B A D NA 2 A D C NA One-hot encoded: <...
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38 views

Selection of differentially expressed genes

I don't have any statistical background. Have some questions. I see in some research papers they select differentially expressed genes based on fold change and p.value. And in some other papers I ...
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52 views

Testing pdist() for statistical significance

Using pdist() in the PST package, two probabilistic suffix trees (PSTs) can be compared to each other. The function will output ...
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18 views

What are the classifiers that can be used for sequence data?

I've been going through the classifiers like Naive Bayes, Decision Tree etc. I've a sequence data like so ...
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20 views

Training two Hidden markov models vs two state Hidden Markov models

I have a scenario where I have log of events followed by some kind of special event (e.g Failure etc). I have two kind of sequences (events, that are observations, can be common in both sequence), ...
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1answer
45 views

Sequences comparison metrics

I know about Edit distance, Longest Common Subsequence and their normalized versions to measure the similarity between sequences But do we have any similarity measures other than the above ones?
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1answer
23 views

How is conditioning on a variable different than specifying nested random effects

How is conditioning on a variable similar to or different from using a mixed effect model? I am a biologist. I'm analyzing my data. I have body sites nested within individuals. We're interested in ...
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144 views

On the convergence of infinite sum of a hypergeometric function resulted from a nested sum

I am interested in finding the CDF of the sum $U=\sum_{i=0}^N U_i$ where: $$F_{U_i}(x)=\sum_{n=0}^\infty \frac {2(-1)^nR^{k\alpha+n\alpha}x^{k+n}}{\Gamma(k)n!\theta^{k+n}(k+n)(k\alpha+n\alpha+2)}$$ ...
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34 views

Analyse set of Sequences of varying length with PCA?

Task description I have a dataset with strings indicating the sequence of the screens a user visit when making a purchase on an app. A string could be: "1,2,1,2,3,3,4,5,6,7,3,2,5,6". Another string ...
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48 views

Likelihood Matrix from a Random Forest?

I'm going through the supporting material of a paper (https://science.sciencemag.org/content/360/6384/81) , trying to reproduce their results (see below, note that HVG=highly variable gene). The data ...
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Ideas for determining the optimal sequence of calls and emails to maximize the probability of a sales lead converting to a sale?

I have a large data set of sales leads that are in the form of a lead_id, a sequence of binary integers that denote the order of emails and phone calls made to a sales lead, and the binary outcome of ...
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1answer
104 views

Handling missing data in Sequence Analysis (TraMineR) within the observation window

I´m using sequence analysis. I have a question about how to deal with missing data within the observation window. The starting point of the analysis is when respondents leave secondary school (t0). I ...
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1answer
46 views

How to understand “multimodal” RNNs for image captioning?

This paper Deep Visual-Semantic Alignments for Generating Image Descriptions on image captioning proposed a Multimodal Recurrent Neural Network architecture. From my understanding, the multimodal RNN ...
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47 views

Probability of Finding Two Matching Subsequences in a Sequence

I'm currently studying DNA sequencing and am trying to find a formula which gives the probability that a subsequence of length $k$ appears twice in a sequence of $L$ bases (characters); this is pretty ...
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312 views

Is Length Normalization used in each step of Beam Search?

In Andrew Ng's lesson on refining Beam Search, it seems that Length Normalization is used ONLY AFTER LAST STEP of Beam Search, that is, when the B most probable sequences have been generated. My ...
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390 views

Generate sequence of random autocorrelated numbers

Back in the university I was working on a program that generates a sequence of random autocorrelated numbers. Autocorrelated meaning that each next value is close to the previous one and depends on it ...
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Conditional combinations and permutations to identify sequences and patterns in R

I want to identify repeated behavioural patterns in a trader's account. The trader will typically transfer funds into his account denominated in a particular asset, buy and sell different assets, then ...
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37 views

Issues in comparing clustering of different population

I often hear that comparing clustering computed on different population is mathematically incorrect. However, I never found any references about it. Imagine I am working on a dataset such as ...
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15 views

How to classify the combination of two string values should be the same independent or order

I have data for Airline flights that include both origin and destination (airports). So for example, I have one flight that goes from Chicago to New York: ORD-JFK; and a flight from New York to ...
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77 views

Sequence mining with sparse events

I am struggling in finding a good prediction model for the following dataset I have collected. I have sampled a four parameters (say A, B, C, D) which are a normalised values between 0 and 1 among a ...
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139 views

Categorization of variables based on selection process response

EDIT: Following a discussion on Meta, I will try to clarify this question more, hopefully giving more context which should help solve some of the issues. I have 12 observations for several hundred ...
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28 views

Combining probabilities with different amount of evidence in sequence learning

Let us think of a simple case of sequence prediction. Based on 20 observed items, b was observed 16 times, c 3 times, and d only 1 time. The sequence is as follows: ...
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170 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 ...
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45 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 ...
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1answer
389 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 ...
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525 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 N(\...
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204 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 ...
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8 views

Strength of the association between different modalities of the same variable over time

I wanted to ask for help concerning a problem that I am currently working on and for which I have not yet been able to find a reasonable solution. I am a beginner in statistics and data analytics and ...
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14 views

Sequences classification: Instances generation for training\test set

I have problem modeling issues. Basically, I have a (binary) classification problem for sequences, in which: I need to predict the state of an object at a time i+1, given the info till time i I have ...
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12 views

Training and testing transformer model from scratch

As you know, transformers are one of the strongest model in the field of NLP and machine translation. I know there are many resources, but I still could not find a good tutorial teaching how to use ...
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19 views

Predicting sequence element based on the previous M and the following N elements

I have an array of sequences of equal length, each sequence contains 300 numbers (M=300). Each element in a sequence is a number from 1 to 9: ...
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14 views

Graphs to sequences

I would like to apply network metrics to sequence analysis. The approach is described in this paper https://link.springer.com/chapter/10.1007/978-3-319-95420-2_7 However I don't know how to translate ...
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4 views

Deep learning framework for sequence to numeric model

I have a very large dataset consisting of 10 base pairs of DNA (dictionary = A, C, G, T) and a numeric outcome which is a count between 0 and 10. E.g. GCTAGCATGA -> 2 GTAGAGTCGA -> 1 What is the ...
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23 views

Predicting the Winner of a sequence of numbers

I have various series of numbers of different lengths (ranging from 4 to 10) such as the example below: [1.5, 5.0, 6.0, 6.0, 8.0] [1.4, 6.0, 7.5, 9.0, 50.0, 100.0, 200.0] For each one of them I ...
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21 views

Adding binary variable to sequence predicting y?

I would like to predict the relationship between two independent variables and a dependent one (model1): x1 + x2 = y Now, x1 is a sequence of vectors (a document composed of a sequence-of-sentences)...
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9 views

Deep learning technique for finding sub pattern

I have a list of strings each with thier target output value. The output in each case is a sub string of the input Eg ABCFHDF-> FHD HJLKSOK-> JLK GSJKOPS-> JKO My question is what area of sequence ...
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How to perform feature extraction(PseAAC)?

I am working on K-Post Translational Modification of protein. I have gone thorugh a lot of papers. But there is no detailed view of how to extract feature like PseAAC. Any python code /package is ...
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19 views

Optimal matching analysis for proportional data

I have a dataset constructed from twitter data consisting of users, and their proportional activity in an issue. The data is currently stored as a dictionary of dictionary: Current format: ...
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38 views

Predicting the loan default probability for next t intervals by predictSurvProb()

I have a loan dataset that contains details of customers for different loan types. Every category of loan have different tenure(starting from 6Months to 60Months) We are defining "Good" or "Bad" to a ...
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18 views

Testing whether a sequence of runs obeys a given distribution

Let $p ∼ B(α,β)$ and $X ∼ Bin(n,p)$. Given a sequence $x \in X$, how would I calculate the probability that x is indeed obeying the given distribution as opposed to some other distribution?
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Is there any sequence dissimilarity measure that has an intuitive interpretation like the dissimilarity index has?

I want to know how much the sequences in my sample differ from a given ideal-typical sequence. Is there any intuitive way of interpreting the dissimilarity measures for sequences? If it would be the ...
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88 views

Is using “Normal Approximation to binomial distribution” to test mutation enrichment in genomic region correct?

We are analyzing cancer patient mutation data. We defined set of region on the human genome as binding events, (for the ones who is interested in to the subject, it is a transcription factor binding ...
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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 ...
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65 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 ...