machine-learning
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cognoma
Machine learning for Project Cognoma
We're nearing the point where we'll need to implement a machine learning module to execute user queries. We're looking to create a minimum viable product. We can expand functionality later,...
In addition to gene expression, we probably should include other information on samples. This discussion will focus on identifying potential covariates and evaluating whether they make sense to include in...
@gwaygenomics presented evidence that median absolute deviation ([MAD](https://en.wikipedia.org/wiki/Median_absolute_deviation)) feature selection (selecting genes with the highest MADs) can eliminate most features without hurting performance: https://github.com/cognoma/machine-learning/pull/18#issuecomment-236265506. In fact, it appears that performance...
In #18 I propose using a grid search to fit the classifier hyperparameters ([notebook](https://github.com/dhimmel/machine-learning/blob/84a3271b8a11763616b62316cc589a40608e1852/1.TCGA-MLexample.ipynb)). We end up with average performance across cross-validation folds for many hyperparameter combinations. Here's the performance...
We need to design our results json so that we can later visualize the most important results via the results viewer from the UI team.
Going off of @gwaygenomics's post in the Cognoma repo (https://github.com/cognoma/cognoma/issues/15) , and @cgreene's suggestion this might be a good place to discuss ML-specific resources for the uninitiated, especially for others...
