Questions tagged [sequence-analysis]

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

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3k 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 ...
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1answer
260 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 ...
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2answers
56 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 ...
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1answer
366 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
64 views

Is there a canonical probability distribution on an ordering/permutation

What is a good way of defining a non-uniform probability distribution on a permutation of k objects? For example, suppose the parameter was an ideal ordering, and the probability of an ordering was ...
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2answers
204 views

Using deep learning to measure the similarity between two variable length voice sequences

Usually we use DTW (Dynamic Time warpping) to measure the similarity between two variable voice sequences. However DTW is time-consuming and not easy to run in the GPU since too much control in it. I ...
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2answers
7k views

Sliding window for time series modelling

I am modelling on an univariate time series in a form as shown. Suppose the time interval in the series is daily base, namely every y was collected every day. I wanna use sliding window method to ...
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1answer
111 views

TraMineR - dont print message of seqdef

Is there a possibility to disable the initial message (1) when creating a sequence with seqdef library(TraMineR) ? (1) this ...
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1answer
63 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 ...
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1answer
462 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 ...
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2answers
47 views

Localized distance function on sequential binary data

I am trying to find a good distance function for sequential data that is all binary. For now, I am using Edit distance however I have some more domain-specific knowledge that I would like to ...
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1answer
219 views

Sequence prediction based on non-sequential inputs

I have a dataset with timestamps and event values (true or false -- these are based on sensor data which detect room occupancy). I'd like to build a model that would take a timestamp as an input and ...
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1answer
57 views

Calculating p-values for ratios of binomial variables

I have a problem that I will express in 2 ways: a math-y way and a biology way. Hopefully this will make it more clear. Math-y way: I have N observations of a pair of binomial variables, call them ...
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1answer
121 views

How to get a distance matrix using “SVRspell”?

I am trying to compute a distance matrix using the method "SVRspell" (seqdistOO function). I want to use an exponential weight of spell length equal to 2 and I want to discard matching sub-sequences ...
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1answer
584 views

what is the appropriate one-class classifier for sequenced categorical data?

Can someone suggest an algorithm for an outlier detection system? My requirements are: it supposed to be a one class classifier, where on training phase, it only fed 'normal' data however the normal ...
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1answer
125 views

What is the probability of the first positive event in an sequence of binary events where sequences have finite but random lengths?

I have a time series of observations from a longitudinal study of individual objects. These observations are seen as discrete sequences of features, one sequence per object. The sequences have ...
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1answer
125 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: ...
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1answer
175 views

Unsupervised clustering of sequence of events to subsequences

I have a big dataset of M sequences of [1 - N] events, where each event has multiple properties (start date, end date, location, ...
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1answer
53 views

Combining probabilities to find most probable window

I have a series of observations, with an associated probability that an event is occuring at timestep t, something like: [0.8, 0.8, 0.3, 0.9, 0.2] Events can ...
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39 views

What are the algorithms for fusing time series together

Assume I have multiple time series with the same length and the same range. What are the different algorithm used to fuse the time series together? what techniques would the best to combine them to ...
2
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1answer
56 views

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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37 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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1answer
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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1answer
73 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 ...
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2answers
4k views

Sequence classification via Neural Networks

What exact kind of architecture of neural networks do I need for a sequence binary/multiclass classification? The sequences can be of different length and are to be discriminated by a certain ...
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1answer
1k views

CRF equivalent in deep learning

Conditional Random Fields (CRFs) is a typical solution for a sequence labelling/segmentation problem. For example, a sequence is a string and CRFs are used to label each word as being a part of a ...
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1answer
23 views

have many error likelihoods, how to combine to get a confidence or p value?

I'm working in bioinformatics and its been a long time since I dusted on my statistics. Basically I'm working on variant calling which amounts to sequencing a large number of sequence reads and ...
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1answer
71 views

Sequence prediction: ambiguity in training set

There is a set of sequences (train set), where each element is one or multiple tags: A, B -- A -- Z -- Z, A B -- A -- Z -- D ... Given a new sequence: ...
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1answer
130 views

Can I use chi-squared test of independence to compare base compositions of human genome?

I need to prove that a given region on the genome maintains has the same base composition proportions (20% A, 15% T, 19% C, etc…) of that genome. I thought about doing Chi-squared test of independence ...
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1answer
377 views

Clarification on Number of LSTM cells per layer

When the Seq2Seq paper by Sutskever et al. refers to building an LSTM with a k-dimensional cell size, does this refer to both the feature vector size of vectors $C_t$ (cell), and $h_t$ (hidden state) ...
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1answer
189 views

How can I solve the sequence prediction problem?

Let's say I'm given a stream of characters, one at a time. Some example strings of characters that could occur might be "01234" or "hello how are". They might even be encodings of waveforms as ...
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1answer
152 views

Method to predict action based on previous sequence of actions

Given $n-1$ sequences of actions [$k_{i1}$...$k_{in}$] as training/example I want to be able to predict $k_{nn}$ in the sequence [$k_{n1}$...$k_{n(n-1)}$] where $k_{nn}$ would be the most likely ...
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1answer
550 views

What are the best packages for HMM sequence analysis?

I have a sequence of events and I want to learn discrete probabilities of transitions between them and to predict next item in a sequence. Can you point me on good papers and Python or R package for ...
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2answers
358 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 ...
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1answer
270 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 ...
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1answer
186 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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1answer
33 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
20 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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0answers
141 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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0answers
43 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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0answers
20 views

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
83 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
44 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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0answers
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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0answers
299 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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378 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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383 views
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233 views

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 ...