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Questions tagged [sequence-analysis]

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

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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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0answers
15 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
17 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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0answers
74 views

What exact statistical method should I use to compare two samples of targeted DNA sequencing?

I have results of targeted sequencing. It is several csv files (tables) with information about the identification number of amplicon (in two samples there are equal number of amplicons - 202) and ...
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0answers
28 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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0answers
19 views

Using autocorrelation for prediction of synthetic data series

In a stimuli prediction (seq2seq problem. X is a biosignal, y is the stimuli which the participant is exposed to during the collection of x): We have a series of biosignals we collect in a block ...
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0answers
16 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
13 views

Aggregation of sequence data

I have sequence data of students playing exercises and succeeding/failing. For example: ...
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1answer
26 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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0answers
9 views

Which length is used to compute brevity penalty when there are multiple reference sequences?

In calculating combined Bleu score, we use a Brevity Penalty parameter which is dependent on Lengths of Reference sequence and Machine Output sequence. In a case where there are multiple reference ...
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1answer
18 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
74 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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0answers
40 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
79 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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0answers
147 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
37 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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0answers
29 views

Machine Learning Classifiers: Different Lengths in Feature Matrix?

I have following data structure in a sequence database, where actions (A,B,C,D,E) were ordered as they happened in course of time. ...
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0answers
24 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
40 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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2answers
436 views

Clustering customers by their orders sequence patterns

I have dataset with clients orders. Example: ...
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0answers
129 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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0answers
5 views

grouping and categorizing differently spaced out events

I have data of client's visits to a food shelter. For each day, over 10 years, there is a 1 if the person went to the pantry and 0 if they didn't. I'm trying to group people whose pattern of use is ...
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0answers
22 views

sequence spike prediction model

There is a problem, the input can be a set of sequences, and each sequence consists of numerical values, such as . The corresponding output sequence consists of 0 or a numerical value, where only one ...
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0answers
28 views

Does MAP estimation minimize edit distance for sequence prediction?

Suppose that we have pairs of sequences ($X$, $Y$), where $Y$ is a sequence of tokens from some alphabet, and $X$ is a sequence of tokens, or real numbers, or whatever. (For example, in speech ...
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1answer
44 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
78 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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0answers
63 views

Can I use a tool like TraMineR to run a dataset of 100000 observations with an alphabet of ~200 events?

I'm doing some web analysis and I'm trying to understand if a tool like TraMineR could run a dataset that is this big. If not, what would be my options? What I'm trying to understand is: 1 - Most ...
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39 views

Is it possible to get a sort of 'correlation score' for a sequence of events resulting in a binary output?

I have command sequence data for a software application and am trying to determine how certain commands may be more or less likely to cause the application to crash. The data for each user session ...
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1answer
69 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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0answers
156 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
328 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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0answers
17 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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1answer
46 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
6k 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 ...
5
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1answer
288 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 ...
3
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1answer
1k 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
4k 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 ...
3
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1answer
217 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
553 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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0answers
37 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
82 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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1answer
85 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
86 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 ...
2
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1answer
364 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 ...
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1answer
282 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) ...
3
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1answer
2k views

How can p=1 in Fisher's exact test?

I'm comparing two datasets from DNA sequencing studies, and comparing mutation rates in genes between the two datasets, which I'm doing using a two-tailed Fisher's exact test (please correct me if I'm ...
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1answer
165 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
66 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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2answers
1k 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 ...