Questions tagged [machine-learning]

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1answer
24 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
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3answers
138 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
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0answers
43 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
46 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
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1answer
62 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
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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
65 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
40 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
97 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
328 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
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1answer
141 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
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1answer
67 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
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1answer
43 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
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0answers
351 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
119 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
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2answers
245 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
105 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 ...