Questions tagged [features]

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What are the fastest way of feature selection in R for large dataset in Machine Learning?

I have about 100 data sets with over 100,000 rows and 27 predictor variables and multiple response variable on each dataset. I want to select the most essential Features for these datasets. I used ...
2 votes
1 answer

Help with finding an unsupervised learning algorithm for RNA sequence/structure pattern identification

I have a bunch of RNA sequences (and their optimal secondary structures) and their corresponding energy values (measured by mean free energy) and I'm trying to find a way to identify features (...
2 votes
1 answer

Differentiating molecules based on peptide sequence? How to annotate?

I want to differentiate between classical class I and non classical class I MHC molecules in a model organism using well conserved structural features within classical MHC I molecules (eg intradomain ...
2 votes
1 answer

Reduce Overfit by removing insignificant proteins through PSEA analysis

I'm training a ML model for disease prediction using protein composition as input, but overfit is present. While looking to remove proteins and reduce multi-correlation, as remove composition ...
3 votes
3 answers

Is there a JSON-based genomic feature format?

There's a variety of formats for storing genomic features (e.g. Genbank, GFF, GTF, Bedfile) but all of the ones that I'm familiar with use either a custom format (Genbank) or a CSV with defined column ...
4 votes
1 answer

Are there computational tools to extract features of DNA sequences?

I am looking for tools to extract features from short DNA sequences. For example, entropy, complexity, GC-content, etc. I have found the script from the PyFeat repo, but is there ...
0 votes
1 answer

Extract features from fasta sequences and train the classifier

I am new to the bioinformatics field. I have positive and negative protein sequences for acetylation PTM. Now, I want to train a classifier, say SVM. What will be the next step? How can I convert ...
0 votes
1 answer

Feature extraction methods that can handle inconsistent numbers of atoms for molecular dynamics

I want to compare the protein dynamics ) pH 7 versus pH 3, or ) wild type versus mutant The protein will have slightly different number of atoms at each condition, due to protonation or mutation, ...
0 votes
1 answer

How to predict protein binding to ligands?

I want to predict from protein sequence if the protein binds to metal, nuclear or small ligand. How can I do this ? Which features are relevant if I want to use them in a machine learning algorithm ?
0 votes
0 answers

Selecting genes with more contribution from PCA

I have RNA-seq data in response to treatment vs non response; By machine learning I selected three principle components likely can predict the response based on the gene expression. Now I have ...
1 vote
1 answer

What is Feature Barcoding technology?

I heard the term Feature Barcoding a lot so I find resources to understand it. I have read docs of 10xgenomics and I see that ...
3 votes
1 answer

How can the Autocovariances, autocorrelations, and autocorrelation coefficients be calculated from a Protein Amino Acid Sequence?

Given a normal protein sequence with the 20 standard amino acids, how can the 'Autocovariances', 'autocorrelations', and 'autocorrelation coefficients' of the sequence be calculated? What is meant by ...