Questions tagged [sequence-analysis]
Analysis of a DNA, RNA, or peptide sequence to understand its features, function, structure, or evolution.
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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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11 views
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 ...
2
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0answers
75 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
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1answer
14 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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53 views
Many-hot encoding for Hamming codes using 1D convolutional autoencoder
I am trying a simple experiment where I take 16 numbers [0 to 15] that represent the Hamming codebook, and try to reconstruct it using an autoencoder.
Instead of using a one-hot encoding scheme (16 ...
0
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1answer
29 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
45 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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0answers
49 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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0answers
25 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 ...
2
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1answer
40 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 ...
0
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1answer
26 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 ...
2
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2answers
36 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
58 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 ...
2
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0answers
30 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
29 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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13 views
Aggregation of sequence data
I have sequence data of students playing exercises and succeeding/failing. For example:
...
0
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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
30 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 ...
2
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1answer
31 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 ...
2
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2answers
143 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
173 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
188 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 ...
4
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0answers
323 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-...
2
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1answer
46 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:
<...
2
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0answers
29 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 ...
2
votes
1answer
48 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 ...
4
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2answers
778 views
Clustering customers by their orders sequence patterns
I have dataset with clients orders. Example:
...
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0answers
254 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 ...
1
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1answer
60 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:
...
2
votes
1answer
107 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
354 views
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1answer
77 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
190 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
393 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
49 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 ...
3
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1answer
8k 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
335 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
votes
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. ...
0
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2answers
5k 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 ...
4
votes
1answer
288 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.
...
4
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1answer
919 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
51 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 ...
0
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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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1answer
102 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 ...
2
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1answer
105 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
431 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
330 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) ...
2
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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 ...
