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Questions tagged [machine-learning]

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0
votes
1answer
39 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
58 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
31 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
58 views

How I know which gene is a good predictor in this neural network or not?

I have 25 highly differentially expressed genes among responder (TRG12) and non responder (TRG45) patients to chemotherapy. I have made a neural network of these genes. Accuracy of model is 0.73 but ...
2
votes
1answer
37 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
81 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
162 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
137 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
61 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
33 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
301 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
115 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
217 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
104 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 ...