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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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 ...
simusid's user avatar
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5 votes
2 answers
302 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 ...
Rafael Coelho's user avatar
4 votes
1 answer
360 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 ...
Olli B.'s user avatar
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4 votes
2 answers
115 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 ...
Ezequiel's user avatar
4 votes
1 answer
200 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 (...
Daniel Harris's user avatar
3 votes
1 answer
264 views

Gene names from components in NMF analysis

This question was also asked on Biostars I am using Rcppml package in R for my NMF analysis, I have a matrix from single-cell analysis. I have cells scores and I wanted to know how to extract genes ...
David's user avatar
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3 votes
1 answer
114 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 ...
wrong_path's user avatar
3 votes
1 answer
125 views

Applying glmnet to identify predictors for subtypes

I am new to glmnet and other ML techniques, so apologise in advance if this sounds a trivial question. However, your guidance is very much appreciated. So, I have nearly 700 genes with their ...
Angelo's user avatar
  • 237
3 votes
1 answer
931 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 ...
Firas's user avatar
  • 33
3 votes
2 answers
973 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 ...
0x90's user avatar
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3 votes
1 answer
81 views

How to extract and visualize sequence logos from CNN kernels?

I created a basic CNN architecture using Tensorflow to classify transcription factor binding sites. My aim is to somehow extract and visualize sequence logos from the convolutional kernels. The model ...
Károly Pákozdi's user avatar
2 votes
1 answer
164 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 ...
Jim Eric Skogman's user avatar
2 votes
2 answers
37 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 ...
xie186's user avatar
  • 121
2 votes
2 answers
41 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 ...
Mendel's user avatar
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2 votes
1 answer
171 views

How to identify genomic regions / peaks associated with enhancers (TF binding sites)? Is there a tool or a formal recipe?

I am attempting to identify DNA sequences/regions associated with enhancers in my NGS sequencing data. How can I identify (from peak files/counts for chip-seq, atac etc.) genomics regions/peaks ...
Zebra Fish's user avatar
2 votes
1 answer
94 views

De novo antibody sequencing fromMS/MS Ion Trap proteomics raw signal

I've read about different proteomics tools that can do de novo assembly of MS/MS Ion Trap proteomics signatures for de novo antibody sequencing. Given the way CDR3s of antibodies are created, together ...
719016's user avatar
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2 votes
1 answer
98 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 ...
J. Doe's user avatar
  • 575
2 votes
1 answer
51 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 ...
nafizh's user avatar
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2 votes
1 answer
25 views

Is a classification tree appropriate method to use for my project?

I have about ~3000 genomes of organisms and presence (recorded as 1)/absence (recorded as 0) data of ~300 genes in them. Among 3000 genomes, we have experimental data on 20 organisms, which were ...
brownsloth's user avatar
2 votes
1 answer
100 views

Multivariate analysis of cell culture bioprocess

I am seeking statistical support for the following bacterial growth time series. In the lab, we have cell cultures growing in bioreactors. Every day we measure the concentration in mmol-1 of a set of ...
CorteZero's user avatar
  • 109
2 votes
1 answer
41 views

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 ...
Adonis Cedeño's user avatar
2 votes
1 answer
164 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 ...
Cecilia's user avatar
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2 votes
2 answers
591 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 ...
Sean's user avatar
  • 121
2 votes
1 answer
101 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. The accuracy of the model is 0.73 ...
Zizogolu's user avatar
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2 votes
1 answer
138 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 ...
Nurrakman Dwinanda W's user avatar
2 votes
0 answers
39 views

How to create a dataset of contact maps of homologous proteins?

Disclaimer: I am a machine learning researcher working on network science and want to use proteins to test an algorithm of mine using real-world data. My bioinformatics knowledge is minimal. I need to ...
Tendero's user avatar
  • 121
2 votes
1 answer
29 views

Single Node Deletion in Cheng and Church Algorithm

Cheng and Church Algorithm is a biclustering algorithm or an unsupervised learning task with which both rows and columns in a data matrix can be placed in concurrent clusters. In the original paper, ...
ShokofehVS's user avatar
2 votes
1 answer
102 views

Model optimization causes overfitting

I'm working on an ML model to predict colorectal cancer using data from the human microbiome (collected from fecal samples). My dataset is made up of metadata (containing phenotypic information on the ...
user17818805's user avatar
2 votes
0 answers
489 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 ...
Sarah's user avatar
  • 496
2 votes
2 answers
199 views

Books on application of Machine Learning in Bioinformatics

I'm looking for books on applications of machine learning and statistical data mining in bioinformatics with example codes provided in R and/or python. I came across the following two books: the first ...
The August's user avatar
1 vote
3 answers
353 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 ...
Patrick's user avatar
  • 11
1 vote
1 answer
350 views

Reproducible PyTorch Model

I'm using PyTorch (1.7.1), PyTorch Geometric (1.6.3), NVIDIA Cuda (11.2). I need to make a neural network reproducible for a competition. However, when I try: ...
이명훈's user avatar
1 vote
1 answer
59 views

Challenging benchmarks for supervised learning on sparse scRNA-seq data

One challenging aspect of modeling scRNA-seq data is data sparsity, that is, scRNA-seq measurements typically suffer from large fractions of observed zeros (i.e. dropouts), where a given gene in a ...
rvinas's user avatar
  • 123
1 vote
2 answers
219 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 ...
Dhruv Shah's user avatar
1 vote
1 answer
52 views

Intepreting and applying ordinal logistic regression coefficients to calculate probabilities?

Can someone help hint me how I can interpret ordinal logistic regression coefficients and how I can use the .L, .Q and .C terms to calculate probabilities? I am analysing a dataset, where people ...
Charles's user avatar
  • 537
1 vote
1 answer
65 views

Gene rank scores from LINCS database: Evangelista et al. 2022

The website https://maayanlab.cloud/sigcom-lincs/#/SignatureSearch/UpDown can be used to "Identify reversers and mimickers from over 1 million signatures by entering up and down gene sets .. &...
c00kieRaptor's user avatar
1 vote
1 answer
46 views

What options should I explore to improve the output of the protein reconstruction?

We developed a neural network-based protein reconstruction tool to reconstruct the main chain from only CA atoms. we generated data from some selected PDBs from the RCSB website to train an NN model. ...
user366312's user avatar
1 vote
1 answer
98 views

Is current AI able to generate RNA sequences of viruses? [closed]

After seeing a video of a combination of CRISPR and AI, and an article of someone who made two babies immune against HIV and still healthy, I wondered about something. If such complicated thing, to ...
Random user's user avatar
1 vote
2 answers
92 views

Advise on building an effect ML model for predicting important proteins for drug response

I want to create a model to predict proteins which could be associated with drug response in cancer cell lines. I have cell line proteomics data, with compound screening data they have gained for a ...
LJM's user avatar
  • 11
1 vote
1 answer
36 views

Transfer learning for a Convolutional NN for Recursion dataset

As a practice data analysis I am trying to train a convolutional neural network (CNN) on some cellular images made publicly available on Kaggle in 2019 by the company Recursion via supervised deep ...
Angus Campbell's user avatar
1 vote
1 answer
38 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. ...
webNoob13's user avatar
  • 145
1 vote
1 answer
169 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 ...
rvinas's user avatar
  • 123
1 vote
1 answer
460 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 ...
Equinox's user avatar
  • 129
1 vote
3 answers
287 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 ...
abalter's user avatar
  • 161
1 vote
0 answers
39 views

Comparing sc-seq combination and bulk-sequencing

I have expression matrices for different cell types, representing the expression of individual cells of that type. They were learned through a generative model, so I am confident they represent the ...
谢润达's user avatar
1 vote
1 answer
230 views

how to train a gene dataset with a nearest shrunken centroid classifier?

I have a data file named "geneexp.csv". the data contains information about gene expression of three different cell types (CD4 and CD8, CD19) I want to classify cells by performing the ...
homa taha's user avatar
  • 113
1 vote
0 answers
106 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 ...
Qinsheng Zhang's user avatar
1 vote
1 answer
144 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 ...
Giannis Lazaridis's user avatar
1 vote
0 answers
278 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 ...
user324810's user avatar
  • 1,115
1 vote
0 answers
32 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 ...
Arthur Frankel's user avatar