Skip to main content

Questions tagged [bioinformatics]

The discipline at the crossroads of computing and the biological sciences, which involves organizing, maintaining, and analyzing data from such fields as molecular biology, genetics, and genomics

Filter by
Sorted by
Tagged with
0 votes
0 answers
13 views

Which parameters of the Sholl analysis summary do I need to compare to get descriptive graphs about the complexity of single neurons?

For my master thesis I am working with Purkinje cells from Zebrafish with a condition that makes these neurons less complex. I am treating them with a construct that is hypothesized to improve this ...
Elvira's user avatar
  • 1
0 votes
0 answers
16 views

Reinstalling Orange Add-on over again

After I upgraded to the latest orange version (3.36.2), I observed that whenever I install an add-on, for instance, Bioinformatics, when I close and reopen the orange software, all the new add-ons are ...
Ayodeji Samuel's user avatar
2 votes
0 answers
146 views

Seeking an RNA Sequence Tokenizer akin to OpenAI's tiktoken for Text

I want to train a language model tailored specifically for RNA sequences. Given the success of language models in the NLP domain, I believe there's significant potential to extract intricate patterns, ...
0x90's user avatar
  • 173
0 votes
1 answer
295 views

Splitting CSV data with missing target variable using train_test_split in Python

I have a dataset in CSV format that consists of a training dataset with around 300 instances and a test dataset with around 100 instances. The issue is that the target variable (the column we want to ...
Yasmine Bzgn's user avatar
0 votes
2 answers
47 views

Difficulty loading data/running model on custom dataset derrived from DNA sequence data - TypeError when attempting to run model

I am a student who has some limited experience with keras, and for a new project recently decided to learn how to use pytorch to implement my models. I'm a beginner with both, so apologies in advance ...
Moss_and_Bones's user avatar
0 votes
1 answer
898 views

Sequence Embedding using embedding layer: how does the network architecture influence it? [closed]

I want to obtain a dense vector representation of protein sequences so that I can meaningfully represent them in an embedding space. We can consider them as sequences of letters, in particular there ...
HelpNeederStudent's user avatar
1 vote
1 answer
112 views

Understanding how Long Short-Term Memory works in classification of sequences of symbols

I want to use a LSTM neural network to classify sequences of protein according to the host species. For example, I have these sequences of letters (toy example, just to understand): ...
HelpNeederStudent's user avatar
1 vote
0 answers
14 views

What are some strategies to deal with label sparsity when training a protein function prediction model?

The protein function prediction task requires you to take a sequence of amino acids (think words in a sentence, but if there are only 20 words), and output the functions that protein can take. There ...
luongminh97's user avatar
1 vote
0 answers
32 views

What is important for Pharmaceutical companies to answer with Big Data Analysis?

I am a data scientist, and I have some biological background (genetics). I have been asked to give a talk for our customers from pharmaceutical industry. I should show them how they benefit from Big ...
Rebecca's user avatar
  • 143
2 votes
2 answers
2k views

How to decide on using xgboost with imputation or without it and keeping missing values?

I have a large genetic dataset that I am using xgboost on to score most likely disease causing genes - giving the genes a score between 0-1 of likelihood. I try to avoid features with a lot of ...
DN1's user avatar
  • 175
0 votes
2 answers
2k views

Remove all characters following a certain character in a column of a dataset

I have a data set like the following, and the first column contains the groupings. However, some are labelled slightly differently. I need to remove all characters following the punctuation used (...
NewtoR's user avatar
  • 1
2 votes
1 answer
368 views

How to interpret a specific feature importance?

Apologies for a very case specific question. I have a dataset of genes, with which I am using machine learning to predict if a gene causes a disease. One of the features I have is a beta value (which ...
DN1's user avatar
  • 175
2 votes
2 answers
4k views

How to make a classification problem into a regression problem?

I have data describing genes which each get 1 of 4 labels, I use this to train models to predict/label other unlabelled genes. I have a huge class imbalance with 10k genes in 1 label and 50-100 genes ...
DN1's user avatar
  • 175
2 votes
0 answers
139 views

FFR and FAR calculating for multiclasss biometric face recognition system

I am implementing a face recognition system using facenet and svc Ml algorithm i have like 20 classes or more and I'm getting 98% accuracy im trying to calculate the FAR and FRR and the EER I'm ...
Mustafa Alahmid's user avatar
0 votes
1 answer
118 views

Clustering analysis for observations with lists as data

So I have several samples analyzed for their chemical composition. After data analysis, for each sample, I have a list of compounds found and their corresponding relative abundance. Some compounds are ...
quarksome's user avatar
0 votes
0 answers
151 views

How to compare genetic profiles or vcf files in Python?

I have hundreds of vcf file where each vcf file contains genome profile for a tissue. A portion of the vcf file is as follows: I can read each vcf file into a dataframe. So it would be hundreds of ...
studentcoder's user avatar
1 vote
0 answers
60 views

Best model for Antimicrobial Resistance (AMR) prediction?

Some classes of problem are best solved by a specific class of machine learning model, due to the structure of the data (e.g. CNN's for computer vision tasks). Prediction of bacterial resistance/...
iacob's user avatar
  • 309
1 vote
0 answers
37 views

Bioinformatics add-on [closed]

I would like to ask you why there are no Volcano-plot or MA-plot widgets in bioinformatics add-on already? As I can see it in the youtube video tutorial (two years ago, version 3.3). In the latest ...
PePr's user avatar
  • 11
0 votes
1 answer
69 views

How to split temporal sequences to sub-sequences in a meaningful yet unsupervised manner?

I have a biological process that undergoes some cellular event which I am observing. I have a series of events, with different temporal gaps between them. For example ...
Lafayette's user avatar
  • 604
0 votes
1 answer
68 views

Bioinformatics widget

Why is there are no Volcano-plot or MA-plot in bioinformatics widget?
Fatty's user avatar
  • 9
1 vote
0 answers
50 views

How to Implement Biological Neuron Activations in Artificial Neural Networks

In artificial neural networks, activation functions are used for neurons, i.e. the sigmoid activation: Which can be implemented in code as (in Python): ...
Larry's user avatar
  • 180
3 votes
2 answers
6k views

Autoencoder for anomaly detection from feature vectors

I am trying to use an autoencoder (as described here https://blog.keras.io/building-autoencoders-in-keras.html#) for anomaly detection. I am using a ~1700 feature vector (rather than images, which ...
Lafayette's user avatar
  • 604
4 votes
7 answers
147k views

Remove part of string in R

I have a table in R. It just has two columns and many rows. Each element is a string that contains some characters and some numbers. I need number part of the element. How can I have number part? For ...
mahtab's user avatar
  • 41
1 vote
1 answer
2k views

Feature selection for gene expression dataset

I am searching for a feature selection algorithm which selects features that are: relevant to discriminate groups of samples (for each sample a group label is provided) endowed with high variance ...
gc5's user avatar
  • 879
1 vote
1 answer
45 views

Why is there such a wide range of prices for whole genome sequencing services?

Below is a list of labs around the country that offer genetic sequencing. What would be the reasons why they each cost a different amount if the end result is that you get a 90GB hard drive with 3+ ...
JustBeingHelpful's user avatar
6 votes
0 answers
102 views

Meta-analysis of public 16S data

I am trying to start a meta-analysis for which I want to extract some 16S-based information from public databases. Moreover, I want to relate this information with any metadata found in the associated ...
André Soares's user avatar
1 vote
1 answer
343 views

R: Comparing dissimilarity between metabolic models with discrete wavelet transformation

I’m working on comparing bacteria metabolic models. Each model has a set of metabolites (around 2000) and their concentration for 200 time points. I’m in the process of comparing the models to cluster ...
SriniShine's user avatar
4 votes
2 answers
195 views

What kind of research can be done with genomic data?

It is well known that science has given us large amounts of free accessible data, such as https://www.1000genomes.org and https://www.ncbi.nlm.nih.gov/genbank. How can we play around with the data and ...
SmallChess's user avatar
  • 3,570