Questions tagged [sequence-analysis]

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

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14 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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42 views

Next n installment repayment prediction

I am having data from a landing company, where the data contain demographic, geographic and financial details about the customers. The problem statement is to predict the probability of customer, ...
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8 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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26 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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19 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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92 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
16 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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39 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
114 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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94 views

How to set up data to train sequence to sequence model using random forest or decision tree?

I have to predict output time series given input time series. SO I just trained random forest with one time series and I found it partially fits all remaining time series event though I didn't trained ...
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33 views

Sequence Prediction with noise / gap using markov models

I'm trying to understand if Markov models can account for a "noise event" when predicting the next item in a sequence. For instance, if i have very frequently occurring (noise) event "F", can a ...
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1answer
47 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
39 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
42 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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19 views

Shotgun sequence statistics

I trying to understand the statistics behind shotgun sequencing. Below is an excerpt from a book. Can anyone tell what does the below bold sentence mean? I did not understand the interval range and ...
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1answer
95 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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31 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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39 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
37 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
179 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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219 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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323 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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400 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
47 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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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

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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995 views

Clustering customers by their orders sequence patterns

I have dataset with clients orders. Example: ...
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307 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
64 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
120 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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373 views
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1answer
83 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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214 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
401 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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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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1answer
50 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
10k 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 ...
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1answer
371 views

predicting tree structure

This topic is actually rather hard to google for as 'tree' has been overloaded in this domain to refer to decision trees. I'd be interested in having a learning algorithm produce code, such as used ...
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1answer
2k views

Pattern identification in time series data

Imagine a set of users who always perform the same set of tasks and in the same order. Say - user A - enters the store, reads the newspaper, looks at the TV, orders coffee, eats a donut and leaves. ...
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2answers
6k 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
321 views

Predicting the observations in a POMDP with a recurrent neural network

I use neural networks for online sequence prediction. The performance of LSTM in this case, however, is not nearly as good as I expected. Maybe someone can help me understand where the problem lies. ...
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1answer
1k views

Which Algorithms can model a sequence and predict the next value of this sequence

I have a repeating sequence like the following, with occasionally random values (maybe noise): ABCDABCEDABCDABCD What could be an algorithm to model the sequence and predict a following value at a ...
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60 views

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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1answer
86 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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123 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
112 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
474 views

Why use K-medoids for sequence analysis?

In the package WeightedCluster there seems to be facilities for using K-medoids clustering (i.e. wcKMedoids()), but not the more ...