Questions tagged [sequence-analysis]

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

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how to extract the probable subsequence per state with hmm

With both the original sequence and hidden state matrice available, how can I extract the most probable subsequence per state. Many thanks.
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R seqHMM: find optimal number of hidden states [closed]

Is there any good way to determine the optimal numbers of hidden states in a hidden markov model when it is unknown? Would be nice if it is possible to refer esp. to the seqHMM package in R. Many ...
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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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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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330 views

How To Solve A Sequence Question [closed]

I'm taking a course on R on edx, but I have been stocked here for days. Please Which integer values are between the maximum and minimum heights? For example, if the minimum height is 10.2 and the ...
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1answer
19 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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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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138 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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1answer
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Can LSTMs classify multivariate time sequences?

I've been learning about LSTMs and I commonly see them applied to the same type of task. For example, given a 1D list of values, predict which class they belong to. Or, given 8 values from 8 sensors, ...
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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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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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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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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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35 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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13 views

Binary Sequence Prediction Model with Time dependant features

I got a very long sequence of binary items (0 or 1). Each item is associated to a timestamp. For example : ...
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37 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
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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Models for interdependent finite sequences?

I have a large set S of pairs of (short) sequences (, )_i where the first sequence of each pair comes from sequence set A and the second sequence of each pair comes from the sequence set B. Sequences ...
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114 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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1answer
21 views

ATGC sequence of gene expression data [closed]

I am not a pro in genetics so please excuse my non-technical language. I need dataset which contains the gene expression as well as the associated ATGC sequence with each gene expression value. For ...
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1answer
71 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
166 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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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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2answers
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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
192 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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37 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 ...
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45 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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1answer
27 views

Estimation of partitioning error in next-generation sequencing experiments

[Edited: explanation of the partitioning error] I would like to estimate how the initial number of molecules (or the level of gene expression) affects reproducibility between technical replicates of ...
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1answer
57 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
201 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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286 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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2answers
487 views

How to stretch a time series to any length, n, without padding? [duplicate]

What algorithms are most suitable if I want to strect a time series to a certain length, n. I dont want to just pad the time series with values at the beginning or end, I want the pattern of the data ...
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490 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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1answer
51 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
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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Clustering customers by their orders sequence patterns

I have dataset with clients orders. Example: ...
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367 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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1answer
70 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
142 views

TraMineR: predicting class membership of new sequences

Question summary This question pertains to analyzing dissimilarities between discrete state sequences (e.g., using TraMineR), more specifically to classifying new, ...
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383 views
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1answer
92 views

Occurrence of at least 1 HT and HH in sequences of 4 coin flips not equally likely

I was reading this interesting article on hot hands and streaks in sports. The article revolves around the 16 possible sequences of 4 coin flips (H = heads, T = tails): ...
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230 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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1answer
425 views

Recurrent Neural Network model with more than one input

I know RNNs (with LSTMs or GRUs) are now one of the most promising options for modelling sequential data, when ordering of the data matters. However, sometimes there are also some categorical ...
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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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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
11k views

Optimum number of epochs and neurons for an LSTM network

I wanted to know if there's a way to select an optimum number of epochs and neurons to forecast a certain time series using LSTM, the motive being automation of the forecasting problem, i.e. the ...