Questions tagged [deep-learning]

The tag has no usage guidance.

Filter by
Sorted by
Tagged with
-1
votes
1answer
49 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: ...
0
votes
0answers
17 views

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 ...
2
votes
1answer
50 views

Important genes beyond PAM50 for breast cancer classification

Note: this question has also been asked on Biostars I am currently trying to complete a Breast Cancer Classification task using Neural Networks. I have experimented with using my full dataset of gene ...
0
votes
1answer
27 views

how to get access to genotypes and phenotypes used for a GWAS

I'm a master's student working on genomic prediction of complex traits using deep learning. i'm looking for a dataset of human genotypes and phenotypes that has been used for a GWAS. The only thing i ...
1
vote
0answers
29 views

Calling variants with DeepVariant on targeted NGS sequencing (custom library)

I am seeking advice regarding DeepVariant analysis. To avoid false positives I'm using several variant callers and then the resulting common set will be considered as TP variants. One of the callers ...
1
vote
1answer
55 views

What datasets are available out there for prediction based on DNA sequences? [closed]

I am looking for publicly available data for a genomics deep learning project. My goal is to compare different architectures to predict biological insights from DNA sequences. I have heard about ...
1
vote
1answer
213 views

How to predict with the pre-trained DNABERT model?

I was curious to give DNA BERT a try. This is a BERT (Bidirectional Encoder Representations from Transformers) model that was trained on short (k=3,4,5, or 6) k-...
2
votes
1answer
53 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 ...
3
votes
2answers
251 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 ...