Questions tagged [sequence-analysis]

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

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33
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4answers
5k views

Is LSTM (Long Short-Term Memory) dead?

From my own experience, LSTM has a long training time, and does not improve performance significantly in many real world tasks. To make the question more specific, I want to ask when LSTM will work ...
0
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1answer
19 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 : ...
1
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1answer
30 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?
1
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1answer
382 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 ...
2
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1answer
210 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 ...
80
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14answers
26k views

What is the role of the logarithm in Shannon's entropy?

Shannon's entropy is the negative of the sum of the probabilities of each outcome multiplied by the logarithm of probabilities for each outcome. What purpose does the logarithm serve in this equation? ...
2
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1answer
170 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, ...
0
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0answers
13 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 ...
0
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0answers
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 ...
0
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1answer
507 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 ...
1
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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 ...
0
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0answers
17 views

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 ...
0
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0answers
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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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: $$F_{U_i}(x)=\sum_{n=0}^\infty \frac {2(-1)^nR^{k\alpha+n\alpha}x^{k+n}}{\Gamma(k)n!\theta^{k+n}(k+n)(k\alpha+n\alpha+2)}$$ ...
4
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1answer
30 views

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, ...
0
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0answers
20 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)...
0
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0answers
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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0answers
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 ...
0
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0answers
36 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 ...
0
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0answers
17 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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0answers
41 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 ...
1
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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 ...
8
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2answers
303 views

Identifying sequential patterns

I am working with sequence data which are long lists of malware win-api calls. I am trying to cast the problem of identifying 'malware behavior' into one of finding sequential patterns. I treat each ...
3
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0answers
116 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 ...
0
votes
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 ...
4
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0answers
508 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-...
1
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1answer
80 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 ...
2
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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 ...
1
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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 ...
1
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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 ...
2
votes
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 ...
0
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1answer
403 views

Determining the class of a new sequence using Markov chains

I want to use a Markov chain to classify a new given sequence as from model+ or model-. For that purpose first I trained two ...
2
votes
1answer
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 ...
0
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1answer
87 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 ...
3
votes
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. ...
2
votes
2answers
203 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 ...
2
votes
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 ...
2
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0answers
38 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 ...
3
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1answer
2k views

Analyzing Sankey diagrams statistically?

Sankey diagrams are helpful for visualizing multiple, interacting processes: Are there any statistical tools available that can analyze the interactions of multiple processes? I'm aware of sequence ...
1
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0answers
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 ...
0
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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 ...
2
votes
1answer
58 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 ...
1
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0answers
291 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 ...
-1
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2answers
518 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 ...
2
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1answer
55 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
231 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 ...
6
votes
1answer
407 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 ...
2
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0answers
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 ...
8
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3answers
3k views

Sequential pattern mining on single sequence

Can someone give me a hint about a good approach to find a frequent patterns in a single sequence. For example there is the single sequence ...