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Protein-Protein Interaction subsection #575

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zietzm opened this issue Jul 12, 2017 · 3 comments

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@zietzm
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commented Jul 12, 2017

In reading through the Study section, I came across an area that I thought may be of interest but which was not yet covered by the review-- protein-protein interaction. Since classical machine learning approaches like SVM, random forest, etc. and things like Bayesian networks have been predominant, I think this section would be a potentially meaningful presentation of a good opportunity for deep learning. I found a few papers in which deep learning was applied to this topic and put them below.

  1. Sequence-based prediction of protein protein interaction using a deep-learning algorithm
  2. Deep Recurrent Neural Network for Protein Function Prediction from Sequence
  3. Structure-based prediction of protein–protein interactions on a genome-wide scale
  4. A novel method based on new adaptive LVQ neural network for predicting protein–protein interactions from protein sequences

One aspect of PPI prediction that stands out is the diversity in features used between different studies. In fact, there was a preprint just released whose purpose is to outline some of the various features for machine learning PPI prediction. This seems like a good indication in my mind that this field would be a prime target for further research that incorporates deep learning.

If this seems like a meaningful subsection to include, perhaps a suitable location would be just below the protein secondary and tertiary structure section. Right here, greenelab/deep-review/sections/04_study.md seems like it would be a logical location.

@agitter agitter added the study label Jul 13, 2017

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commented Jul 13, 2017

@zietzm protein-protein interactions are definitely an area of interest. We had no reason to exclude this topic in the version, simply a lack of a contributor to research and write about it. Would you be interested in leading this for the revised draft?

If so, I suggest that you create separate issues for the papers above so we can discuss them individually. In addition to PPI prediction, this sub-section could also cover PPI network analysis. As @mrwns pointed out in #543, PPI networks are also popular for graph representation learning and graph convolutions, topics I'm excited about. #241 could also be reviewed to see if it fits in a new PPI sub-section.

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commented Jul 14, 2017

Thanks for the quick reply, and yes, I would be very interested in contributing! I will get on those things today.

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commented Jan 15, 2018

Closed by #638

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