added naive clustering (topk), added per-pdb roc curves, using new data set configuration
fixed per-pdb roc curves, minor fix in peptalk
added per-cutoff testing of configs and datasets
added cluster atoms function for visualization
adapting cluster stats to dual pred_data
added confusion table to compare dbscan with naive clustering
minor changes to performance_topk, plus finding extreme cases subsequently
added some properties to dataset struct, started replacing PepTalkResult
implemented clustering in Classifier class
order dbscan clusters by the sum of their confidence scores
moved scoring methods to Classifier
added cluster accuracy score
updated clustering with two kinds of naive clustering, added accuracy score, removed cruft
eliminated pred_data stuff in clustering-new
refactored precision/recall method to use masks
updated precision/recall/fscore calculation
adding box plot section comparing clustering methods more compactly
minor fixes to clustering notebook
commented out caching by joblib, to avoid attribute error with numpy and joblib
changed LinearSVC to solve dual problem, because it produces better
coefficients.