Questions tagged [machine-learning]
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26
questions
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0answers
14 views
Portals besides the National Cancer Institute GDC Data Portal for downloading histology slides
I am downloading sample slides (in svs format) from the GDC Portal for a convolutional neural network model, but I also need normal tissue slides. There are some normal tissue slides that are adjacent ...
0
votes
1answer
19 views
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
1answer
18 views
Why my bim file doesn't match to my ped file as the Plink documentation suggests?
Plink documentation about .bim says the columns 5 and 6 are the Allele 1 and Allele 2 respectively.
The documentation about the .ped in turn, says "...The first six fields are the same as those in a ....
0
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1answer
26 views
Use of Electronic Phenotype in EHR
May I know what's the use of Electronic Phenotyping using EHR data?
I did refer this link but have few questions
I understand that ...
2
votes
2answers
32 views
What is the significance of enrichment factor regarding machine learning methods?
I'm fairly new to the field of bioinformatics and ran into a question while reading a paper I found on bioRxiv. The overall setting of the paper is using multi-task deep neural networks for kinase ...
0
votes
2answers
49 views
What kind of analysis is practically done on GSE data files?
I have a GSE data file in csv file format containing fields such as: ID, adj.P.Val, P.Value, t, B, logFC, Gene.symbol, Gene.title. In which adj.P.Val, P.Value, t, B, logFC fields being numeric. What ...
-1
votes
1answer
67 views
16S species-level taxonomic assignment--what is the current state of the art?
We currently use DADA2 for picking ASVs and the assignTaxonomy funciton for assingment to genera. Google does bring up various recent articles on species-level ...
0
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0answers
54 views
length of 'dimnames' [1686] must match that of 'dims' [3]
Please if anyone has experience with the use of the BSEQ-SC package for the deconvolution of bulk RNA sequencing data with single cell RNA sequencing data I will be very grateful for your suggestion.
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0answers
80 views
Error using bseqsc
I will be very grateful for any hint on how to overcome the error. I wish to deconvolve my bulk RNA seq data obtained from the lungs of mice using single cell RNA seq data. For practice, I am ...
0
votes
1answer
46 views
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 ?
1
vote
3answers
209 views
Deep learning RNA sequences
Currently I'm working on a project, which combines deep learning with RNA sequences. I'll try to predict pseudotorsion angles [1] from raw rna sequence. The ideas is to train a neural network with raw ...
1
vote
0answers
45 views
Is the visual cortex of a newborn baby immediately capable of object detection or is this skill learned over time, and if so, how? [closed]
Is the visual cortex of newborn babies right off the bat capable of making sense of raw visual data, for instance, converting the constant stream of raw RGB images perceived by the eyes into a ...
0
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1answer
52 views
Finding the members in a confusion matrix
I have inferred a confusion matrix of training and test set by neural network. I want to know which members are in the confusion matrix.
...
-3
votes
1answer
82 views
Recommendation for a binary dataset for Computational Biology open access (as in a dataset with 1 and 0 that can be used to apply ML techniques? [closed]
I have a couple of modified ML methods that I want to test with biological binary data - specifically binary gene expression data - e.g. https://eprints.soton.ac.uk/69359/1/Thesis.pdf that might ...
2
votes
2answers
33 views
General framework for fusing biological networks
I know that there are different types of biological networks. Protein-protein interaction, gene interaction, metabolic networks, gene expression networks, etc. Each of these networks can be ...
2
votes
1answer
84 views
How I know which gene is a good predictor in this neural network or not?
I have 25 highly differentially expressed genes among and patients to chemotherapy.
I have made a neural network of these genes. Accuracy of model is 0.73 but I don't know from 25 genes how I could ...
2
votes
1answer
45 views
De novo motif discovery in protein sequences
I am trying to build a features matrix to be used for Random Forest based classification. I'd like to add, as features, short motifs which are common to all the protein sequences belonging to a ...
2
votes
1answer
120 views
Question about research in bioinformatics for Computer Science student [closed]
I am a computer science student, who was interested in taking research in the field of bioinformatics.
The first research idea I had was to make a model that could predict the possibility of type 2 ...
3
votes
1answer
855 views
Integrative analysis of omics studies using machine learning
I would like to use public omics datasets (ChIP-seq, RNA-seq, and ATAC-seq) from different studies to do an integrative analysis as follow:
Normalise samples, within each type of omics, from ...
3
votes
1answer
145 views
Machine learning using protein-sequences
I'm participating in a bioinformatics machine-learning seminar at my university. The main task is predicting binary classification of protein-protein interactions using sequence data as input.
One ...
2
votes
1answer
79 views
Link Prediction in Bipartite Networks between biological pathways and drugs
Currently I'm building a big matrix (using microarray, mass spectrometry, RNAseq data) that consist by pathways (rows) and treatment/drugs (columns).
The values of that matrix are scores that ...
2
votes
1answer
47 views
Proteins that cannot form biofilm?
I am trying to build a machine learning training set for bacterial protein sequences that form biofilm, and that cannot. I collected the positive sequences from the GO ontology website but for ...
2
votes
0answers
410 views
How to prevent sklearn Imputer(missing_values=“NaN”, strategy=“mean”, axis=0).fit_transform(data) from removing columns with only NA in them [closed]
I am trying to test a preexisting python machine learning script with a subset of my genetic data. One of the feature columns I am using happens to only have NA values in it. I lose this column when ...
4
votes
1answer
140 views
Preparing binary matrix data for Scikit classification algorithms
I made this post in regular stack overflow but I was told about this awesome feature by @nbryans.
I am a researcher (my programming knowledge is small) conducting analysis on a set of antibiotic (...
5
votes
2answers
271 views
Rule Extraction from nnet results
I used a script in R language that uses nnet library to predict promoter bacteria and i would like to know how to extract rules from this neural network results.
As my input of the neural network i ...
4
votes
2answers
107 views
How can I use annotations to remove variants not relevant to cancer risk?
I currently have ~180 whole germlines and around 10M SNPs/indels. I would like to build a predictive model using Machine Learning (ML) techniques to predict cancer risk according to these germline ...
