Evan Cofer comments

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                                            Evan Cofer

Proof-of-concept for reasoning over the SemMedDB knowledge base, using miniKanren + heuristics + indexing.

@renesugar This is great. Thanks!

Predicting the clinical impact of human mutation with deep neural networks

# Goal Predict if a missense variant in an amino acid sequence is benign or pathogenic and greatly augment the amount of available training data by incorporating benign variants from...

3D Molecular Representations Based on the Wave Transform for Convolutional Neural Networks

Edited to match the style of other posts, and used a URL that made the DOI a bit more obvious.

DeSigN: connecting gene expression with therapeutics for drug repurposing and development

@renesugar Can you include the entire abstract and a doi-based link to the paper? I think [this issue](https://github.com/greenelab/deep-review/issues/941) is a good example of how to format it.

Adding an RNA sequence class?

This differs slightly depending on whether we want mRNA, pre-mRNA, and so on. However, as long as we use transcript or gene coordinates, things are simple. If we want mRNAs...

speed up in silico mutagenesis

I tried using `joblib` to parallelize `in_silico_mutagenesis_sequences` as follows. For `1 < n_jobs < 7` it did not perform significantly different than `n_jobs = 1`. For `n_jobs >= 7` it...

Merge clusters like "trumps" if "trump" exists. Otherwise don't.

You can probably use or modify an existing stemming or lemmatization algorithm or library for this (See https://nlp.stanford.edu/IR-book/html/htmledition/stemming-and-lemmatization-1.html for definition). I believe python's nltk already has support for both. I...

Merge clusters like "trumps" if "trump" exists. Otherwise don't.

There are almost certainly other alternatives, but NLTK is probably the most commonly used.