Questions tagged [machine-learning]

A subset of articial intelligence methods which 'learn' through training on real-world data sets. The model is then tested on a 'test' data set and initially assessed through an accuracy measure. The approach is specifically termed 'supervised learning'.

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1answer
41 views

Metapath2vec on Drug-ADR Heterogeneous Graph

I am new in this field and I am having some problems regarding a new project. I built a graph using Drugbank Data connected to SIDER Adverse Reactions. I used Organ- level Terms to classify the ADRs ...
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2answers
18 views

Any suggestions for cultivar identification using SSR (simple sequence repeat) markers

This is the data I have now: 30 simple sequence repeat (SSR) markers for 80 cultivars of cucumber. 10 of the 80 cultivars belong to one cultivar (let's say A). My goal is to classify an unknown ...
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1answer
29 views

Problems replicating Kover paper results

I am trying to replicate the results for the creator of this repo: https://github.com/aldro61/kover2_paper for genotype to phenotype machine learning interpretable (decision tree) prediction. ...
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9 views

How to infer the number of chaperones involved in protein folding?

Let us suppose to have the complete CDS set of an organisms. Let us suppose to want to infer the number of chaperones involved in folding a certain subclass of proteins in this data set.Is there any ...
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2answers
88 views

How does DeepVariant construct RGB images from DNA sequences?

DeepVariant is a pipeline to call genetic variants from DNA sequencing data. A major step, before feeding the CNN, is to translate these DNA sequences into images. It's unclear why and how Google ...
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1answer
24 views

Is it possible to predict protein-ligand binding kinetics using machine learning? [closed]

I would like to work on a project that involves the prediction of protein-ligand binding kinetics. What might be the feature that is relevant for the prediction?
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1answer
53 views

What are the state-of-the-art cell-type RNA-Seq deconvolution methods?

I would like to find the proportion of each cell-type in bulk RNA-Seq transcriptomics data. I am looking for some guidance on the following: What are the state-of-the-art methods? What are their ...
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1answer
55 views

How do I set a neural network to loop multiple times and average the resulting values?

I have a script in R/RStudio which creates random datasets of binomial variables, feeds them through a neural network, and calculates their likelihood ratio statistic and deviance. I'd like the script ...
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0answers
26 views

Available Protein sequence alignment dataset and HMM model

It may better to move the question here. I am new to biology and I find my algorithm may be used in the Protein sequence alignment, since it is a henced HMM model. I find that people use HMM to ...
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1answer
50 views

Generate ligands candidates based on protein shape

Recent approaches to novel drug design using machine learning (ML) and deep learning, often involve generating hundreds of potential ligands which are later tested by docking with a target protein and ...
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1answer
69 views

Problem with classification model of genomic data: every machine learing model predicts wrongly almost always the same subset of dataset

First of all, I'd like to apologize for any spelling or grammar mistakes. I'm having a problem using R for a classification problem. My dataset contains ~300.000 genomic data, and the features are ...
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2answers
479 views

BERT Language Model and Gene Sequences - How Do I Relate Clusters of Sequences?

I hope you'll indulge a question from a computer scientist with limited bioinformatics knowledge. I've been working with the Google tool for language modeling called BERT. It's generally regarded ...
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44 views

How are the scores of GeneSplicer, MaxEntScan and SpliceRegion interpreted from VEP annotations?

I am using VEP from Ensembl to annotate my VCF files with the extra plugins of GeneSplicer, MaxEntScan and SpliceRegion. However, I don't fully understand the output of these scores. I know that they ...
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17 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 to perform classification. There are some normal ...
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1answer
23 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, ...
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1answer
22 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 ....
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1answer
55 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 ...
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2answers
63 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 ...
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2answers
78 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 ...
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3answers
153 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 ...
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87 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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106 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 ...
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1answer
53 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 ?
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3answers
252 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 ...
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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 ...
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1answer
55 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. ...
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1answer
98 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 ...
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2answers
35 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
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1answer
85 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 ...
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1answer
56 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 ...
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1answer
124 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 ...
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1answer
872 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 ...
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1answer
162 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 ...
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1answer
85 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 ...
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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 ...
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0answers
449 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
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1answer
161 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 (...
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2answers
281 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 ...
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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 ...