Automating biomedical data science through tree-based pipeline optimization

Over the past decade, data science and machine learning has grown from a mysterious art form to a staple tool across a variety of fields in academia, business, and government. In this paper, we introduce the concept of tree-based pipeline optimization for automating one of the most tedious parts of machine learning---pipeline design. We implement a Tree-based Pipeline Optimization Tool (TPOT) and demonstrate its effectiveness on a series of simulated and real-world genetic data sets. In particular, we show that TPOT can build machine learning pipelines that achieve competitive classification accuracy and discover novel pipeline operators---such as synthetic feature constructors---that significantly improve classification accuracy on these data sets. We also highlight the current challenges to pipeline optimization, such as the tendency to produce pipelines that overfit the data, and suggest future research paths to overcome these challenges. As such, this work represents an early step toward fully automating machine learning pipeline design.Comment: 16 pages, 5 figures, to appear in EvoBIO 2016 proceeding

MBT: A Memory-Based Part of Speech Tagger-Generator

We introduce a memory-based approach to part of speech tagging. Memory-based learning is a form of supervised learning based on similarity-based reasoning. The part of speech tag of a word in a particular context is extrapolated from the most similar cases held in memory. Supervised learning approaches are useful when a tagged corpus is available as an example of the desired output of the tagger. Based on such a corpus, the tagger-generator automatically builds a tagger which is able to tag new text the same way, diminishing development time for the construction of a tagger considerably. Memory-based tagging shares this advantage with other statistical or machine learning approaches. Additional advantages specific to a memory-based approach include (i) the relatively small tagged corpus size sufficient for training, (ii) incremental learning, (iii) explanation capabilities, (iv) flexible integration of information in case representations, (v) its non-parametric nature, (vi) reasonably good results on unknown words without morphological analysis, and (vii) fast learning and tagging. In this paper we show that a large-scale application of the memory-based approach is feasible: we obtain a tagging accuracy that is on a par with that of known statistical approaches, and with attractive space and time complexity properties when using {\em IGTree}, a tree-based formalism for indexing and searching huge case bases.} The use of IGTree has as additional advantage that optimal context size for disambiguation is dynamically computed.Comment: 14 pages, 2 Postscript figure

Non-uniform Feature Sampling for Decision Tree Ensembles

We study the effectiveness of non-uniform randomized feature selection in decision tree classification. We experimentally evaluate two feature selection methodologies, based on information extracted from the provided dataset: $(i)$ \emph{leverage scores-based} and $(ii)$ \emph{norm-based} feature selection. Experimental evaluation of the proposed feature selection techniques indicate that such approaches might be more effective compared to naive uniform feature selection and moreover having comparable performance to the random forest algorithm [3]Comment: 7 pages, 7 figures, 1 tabl