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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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
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
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2 votes
1 answer
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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
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
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
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1 vote
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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
1 vote
0 answers
150 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 ...
Charles's user avatar
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Prediction of DNA binding motif from sequence/structure of TF/regulator protein?

Do you know if it is actually possible to predict with good accuracy a DNA binding motif from only the sequence/structure of the DNA-binding protein?
Icarus's user avatar
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1 answer
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How evaluate biclustering algorithm over real datasets containing labels?

I have a set of real data containing labels. However, in some biclustering algorithms (e.g., Cheng and Church Algorithm), originally authors applied gene expression data like Yeast without having ...
ShokofehVS's user avatar
0 votes
0 answers
81 views

How can I convert protein distance maps and sequences to a pdb files?

How can I convert protein distance maps and sequences to pdb files? For the same problem, in the case of a model predicting the structure of a protein, such as AlphaFold, how do we convert the ...
이명훈's user avatar
0 votes
0 answers
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Build protein-protein interaction prediction deep learning model

I'm an undergraduate biology student and my thesis is on designing a deep learning architecture to predict whether two proteins interact or not given their primary sequences. I have read some papers ...
Anh Vu Tien's user avatar
-1 votes
1 answer
40 views

Feature-selection microbiome data to build a model to predict cancer

I want to build a machine learning model to predict colorectal cancer based on 16S rRNA microbiome data (stool samples). I have filtered the data using filtering approach by Duvallet(removing samples ...
user17818805's user avatar