3 votes

Why can't AlphaFold predict the consequences of point-mutations?

Other have addressed why AlphaFold2 cannot really get the necessary signal from MSA (Multiple Sequence Alignment) and memory to properly model a variant, but I thought I'd add my observations/rants. I ...
Matteo Ferla's user avatar
  • 4,234
3 votes

Important genes beyond PAM50 for breast cancer classification

There is a CSV table in this paper with 33 sets of genes.
user66081's user avatar
  • 151
2 votes

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

Good question and the Janggu link is cool. Thanks! Kaggle is/was heavily image recognition. There isn't an MNIST type data set in genomics, in case anyone is wondering this is a classic natural ...
M__'s user avatar
  • 12.3k
2 votes

Reproducible PyTorch Model

There is this nice function from Kaggle: ...
Soerendip's user avatar
  • 1,295
2 votes

How many protein sequences do we usually have for each species?

I'm going to start by assuming that you don't actually want 10 protein sequences from the same species, even though you write this in your comment on M__'s (deleted) answer. This will not be a very ...
Maximilian Press's user avatar
1 vote

Why does DNABert use overlapping k-mers as input?

NLP and vectorisation is used to trap non-linearity which is highly applicable to sentences written in English. Vectorisation of k-mers for an overlapping sliding window is weird because it's trying ...
M__'s user avatar
  • 12.3k
1 vote
Accepted

How many protein sequences do we usually have for each species?

Just to add to Maximilian Press's answer. I happen to know about human immunology and I think Maximilian Press has a good idea. Genetic studies and immunological studies per se in cellular immunology ...
M__'s user avatar
  • 12.3k
1 vote

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

Summary answer Although I'm unhappy about how the paper is written and possibly the methodology, the following sentence is likely (almost certainly) to be the answer. The coefficient (aka weight) is ...
M__'s user avatar
  • 12.3k
1 vote
Accepted

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

The first step is to assess the accuracy, recall and precision of the model then look at confusion matrix. Thereafter consider ROC AUC and if all those are fine ... it's biological. If the model is ...
M__'s user avatar
  • 12.3k
1 vote

Why can't AlphaFold predict the consequences of point-mutations?

As marcin points out in the comments: by "AphaFold (AF) has not been trained to predict structural consequences of point mutations" it is meant "AF is not able to tell you whether your ...
O.Laprevote's user avatar
1 vote

Why can't AlphaFold predict the consequences of point-mutations?

This answer is from common knowledge rather than specific infield expertise. The question could be more expertly answered by other members. If you really want to pursue this type of calculation, it's ...
M__'s user avatar
  • 12.3k
1 vote
Accepted

Transfer learning for a Convolutional NN for Recursion dataset

learn = cnn_learner(data, models.resnet50, metrics=error_rate) resnet50 is one of many pre-trained 2D CNN computer vision ...
M__'s user avatar
  • 12.3k
1 vote

How to predict with the pre-trained DNABERT model?

I don't why this RNN k-mer Pytorch model is not producing an output. I do know that, "rnn_dropout": 0.0, ... is bad news for any ANN (artificial neural ...
M__'s user avatar
  • 12.3k
1 vote

Metapath2vec on Drug-ADR Heterogeneous Graph

Clearly the additional references do put Metapath2vec into good use. Its a many to many ML relationship. Most catagorization/classification particularly in deep learning is many to one. So thats the ...
M__'s user avatar
  • 12.3k
1 vote
Accepted

How does DeepVariant construct RGB images from DNA sequences?

Actually the paper has made it clear how they did it. You just have to read the supplementary materials closer. In their figure from the paper: A is Red, C is Green, G is blue, and T is Yellow (G+R), ...
SmallChess's user avatar
  • 2,699

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