# Tagged Questions

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

30 views

### Method to predict action based on previous sequence of actions

Given $n-1$ sequences of actions [$k_{i1}$...$k_{in}$] as training/example I want to be able to predict $k_{nn}$ in the sequence [$k_{n1}$...$k_{n(n-1)}$] where $k_{nn}$ would be the most likely ...
73 views

### How do I statistically rephrase this question

I am analyzing a dataset containing observations from n number of attempts by players in a game. If I am building a regression model to predict the outcome of each attempt given 1 or more descriptors ...
46 views

### pattern recognition for sequence data

There are a lot of data sequences, I am trying to find pairs of sequences that are similar with other. Trivially, we can define some distance measure, and compare each pair of sequence in terms of ...
25 views

### what is the appropriate one-class classifier for sequenced categorical data?

Can someone suggest an algorithm for an outlier detection system? My requirements are: it supposed to be a one class classifier, where on training phase, it only fed 'normal' data however the normal ...
63 views

### What is the probability of the first positive event in an sequence of binary events where sequences have finite but random lengths?

I have a time series of observations from a longitudinal study of individual objects. These observations are seen as discrete sequences of features, one sequence per object. The sequences have ...
14 views

### Combining probabilities with different amount of evidence in sequence learning

Let us think of a simple case of sequence prediction. Based on 20 observed items, b was observed 16 times, c 3 times, and d only 1 time. The sequence is as follows: ...
37 views

### What are the best packages for HMM sequence analysis?

I have a sequence of events and I want to learn discrete probabilities of transitions between them and to predict next item in a sequence. Can you point me on good papers and Python or R package for ...
30 views

### simple temporal classification with LSTM

I'm working on a sequence labeling for specific type of data using LSTM network. However at the moment i'm trying the algorithm with some toy data. I've written the matlab code to implement the ...
13 views

### How the total pseudo R2 is calculated with the “dissmfac” function in TraMineR?

I am using the discrepancy analysis in TraMineR. I performed univariate analysis with "dissassoc" to measure the effect of each variable. Then, I did a multi-factors analysis using "dissmfac" to ...
25 views

### Clustering and differentially expressed genes in RNAseq

I have performed differential analysis with DESeq2, edgeR and voom-limma. My goal was to evaluate each methods on my data. Now I would like to perform clustering with the genes found differentially ...
28 views

### Optimal matching distances

If I have two sequences: 1: A-B-C-D 1: X-A-B-C-D and I do: library(TraMineR) seqdist(sequence1, sequence2, method = "OM") ...
24 views

### How to build a model that maps strings to lists of strings?

I have a mapping from strings to rows in a data table. Each strings maps to exactly one row in a table but the opposite is not generally true (one row can be "bound" to different strings. For example ...
79 views

### How to prove cooperation from behavioural sequences

Situation: Two birds (male and female) protect their eggs in nest against an intruder. Each bird can use either attack or threat for protection, and be either present or absent. There is a pattern ...
6 views

### Representing pairs of proteins as feature vectors

I am attempting to predict whether two proteins will interact or not (binary classification task - pair of proteins as input and 1 or 0 for output indicating interaction). I have thousands of positive ...
41 views

### What is the optimal observation sequence length to train HMM?

I want to train HMM based on 11000 files each has a long sequence, this huge number to train, training time is too much, how I will choose the t = observation length to train HMM?
22 views

### Analysis of classification result

Assume you observed a system for 24 hours and collected data points each minute (each data points contain some host information like cpu_usage,... All elements are numeric). Also, there is a trained ...
15 views

### Sequence analysis with multiple sequences

I would like to recognize different states in a sequence of multiple vectors. To make it little more clear, here is an example: I have 2 (or more) vectors in a sequence: head position(HP) and eye ...
27 views

### Length-dependent indel costs in OMA algorithm?

I re-read this article after a long time (this time paying attention to the fine print) and noticed that they use indel costs that depend on sequence length in their OMA. They argue that it is done to ...
714 views

### Using Keras LSTM RNN for variable length sequence prediction

I have a set of sequences. Each sequence is the form $\{(s_1,l_1),(s_2,l_2) \ldots\}$ where $s_i$'s are real valued numbers and $l_i$s are labels from a fixed alphabet. It is important to note that ...
25 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 ...
72 views

### Distinguish long and short term fluctuations in time series

I have a sequence of events $(e_1,e_2,\dotsc,e_n)$, and each event $(e_i)$ is described by two features $(t_i,F1,F2)$, where $t_i$ is the time of capturing the event. The events $(e_i)$ are captured ...
15 views

### Method for inferring tree structure from messy sequence data

I have data about case events in criminal cases. These data are in the form of sequence like ...
63 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 ...
27 views

### Mining sequential associations using entropy measures

Assume I have a sequence that looks like this: A-A-A-B-A-A-C-A-A-B-C Let's say I want to predict to use the sequences of letter that occur between one letter and ...
114 views

### RNNLIB: How to get CTC output label sequence locations?

I'm using Alex's RNNLIB (http://sourceforge.net/projects/rnnl/) with CTC output on one of my projects. I am up to the step that I have successfully trained a network with 3 hidden layers (with an ...
42 views

### Calculating the significance of lift

The lift (in data mining, especially for sequential association rules), is calculated as: "by dividing the confidence by the unconditional probability of the consequent" (https://en.wikipedia.org/...
46 views

### Position-dependent substitution cost matrix for sequence alignment

Many sequence alignment algorithms and those which measure similarity between sequences require specification of a cost matrix defined on the sequence alphabet. However, the cost incurred does not ...
22 views

### How do I calculate the inter-rater agreement for sequence alignments?

I am having this task of aligning one sequence of sentences to another sequence of sentences. Let's say we have sequence 1 and sequence 2 as an example of the task: Sequence 1:  A B C D E  F ...
27 views

### Sequential pattern mining on mutiple sequences

Can someone give me a hint about a good approach to find a frequent patterns in a multiple sequences. Each sequences is a combination of 7 characters M,E,N,S,U,R,G. The length of each sequences is ...
16 views

### Domain of sequence information

The larger project is to build an SVM model using protein sequence information as input. From the sequence [C,E,D,T....] I generate sequence based variables. For example, mass is represented by [121....
575 views

### similarity measure between two different ordered sequences

I know we can quantify the similarity between two sequences with the same length and same elements by rank order correlation. But how to measure similarity between two sequences of different length, ...
149 views

### Comparing mutation frequency between a case and a pool of controls

I"m working in genomics and trying to come up with the appropriate statistical test for my question. To call mutations in a tumor's DNA, we use sequencing that samples from the total population of ...
366 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 ...
750 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 ...
87 views

### Central limit theorem for sum of differences

I have a quick question. If we have a sequence of i.i.d random variables, $X_1,X_2,X_3,\ldots,X_n$. Then, we make sequence below: $$S=X_1-X_2+X_3-X_4+\ldots+X_n$$ Does central limit theorem work in ...
80 views

### How to interpret p-values in output of seqecmpgroup()?

The seqecmpgroup() function returns a table that, among other things, include p-values for each identified subsequence. How should these be interpreted? I can see ...
142 views

### How to do centroid clustering of sequences?

I want to cluster sequences using centroids. In the hclust package it is noted that "Method "centroid" is typically meant to be used with squared Euclidean ...
121 views

78 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 ...
326 views

### Visualize process data

I have a dataset of order processing with 8 million rows with following columns: HistoryId - Identity column of the records ...
137 views

### Predicting on data consisting of many independent short time series?

I have a dataset which contains many (hundreds) of short (3-30 obs) timeseries of different lengths. Each series is currently represented as a number indicating how long it took to the next event. To ...
118 views

### modeling changing items in market basket analysis

I'm performing a "dynamic" market basket analysis where a customer transaction is traced from the beginning (here it has an initial basket of product) to the finalized purchase (where there is the ...
96 views

### Finding all largest sequences

What would be a good / efficient algorithm or approach to find all the largest sequences within a list of chains with varying lengths? For instance these chains: ...
289 views

### Statistical test to assess differences between two sequencing methods

To asses differences between two DNA sequencing methods (454 and MiSeq) I have made artificial mixtures of different bacteria in the lab (mock communities). An Example might be (numbers are ...
89 views

### Hypergeometric test

I have compared 1370 genes which are obtained from ChIP-sequencing analysis and 652 genes which are differentially regulated genes obtained by analyzing affymetrix 430.2.0 mouse array. When I ...