A machine learning pipeline for discriminant pathways identification

Motivation: Identifying the molecular pathways more prone to disruption during a pathological process is a key task in network medicine and, more in general, in systems biology. Results: In this work we propose a pipeline that couples a machine learning solution for molecular profiling with a recent network comparison method. The pipeline can identify changes occurring between specific sub-modules of networks built in a case-control biomarker study, discriminating key groups of genes whose interactions are modified by an underlying condition. The proposal is independent from the classification algorithm used. Three applications on genomewide data are presented regarding children susceptibility to air pollution and two neurodegenerative diseases: Parkinson's and Alzheimer's. Availability: Details about the software used for the experiments discussed in this paper are provided in the Appendix

Evaluation of a Tree-based Pipeline Optimization Tool for Automating Data Science

As the field of data science continues to grow, there will be an ever-increasing demand for tools that make machine learning accessible to non-experts. 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 an open source Tree-based Pipeline Optimization Tool (TPOT) in Python and demonstrate its effectiveness on a series of simulated and real-world benchmark data sets. In particular, we show that TPOT can design machine learning pipelines that provide a significant improvement over a basic machine learning analysis while requiring little to no input nor prior knowledge from the user. We also address the tendency for TPOT to design overly complex pipelines by integrating Pareto optimization, which produces compact pipelines without sacrificing classification accuracy. As such, this work represents an important step toward fully automating machine learning pipeline design.Comment: 8 pages, 5 figures, preprint to appear in GECCO 2016, edits not yet made from reviewer comment

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

Machine Learning Pipeline for Exoplanet Classification

Planet identification has typically been a tasked performed exclusively by teams of astronomers and astrophysicists using methods and tools accessible only to those with years of academic education and training. NASA’s Exoplanet Exploration program has introduced modern satellites capable of capturing a vast array of data regarding celestial objects of interest to assist with researching these objects. The availability of satellite data has opened up the task of planet identification to individuals capable of writing and interpreting machine learning models. In this study, several classification models and datasets are utilized to assign a probability of an observation being an exoplanet. A Random Forest Classifier was selected as the optimum machine learning model to classify objects of interest in the Cumulative Kepler Object of Information table. The Random Forest Classifier obtained a cross-validated accuracy score of 98%. 968 candidate observations have a greater than 95% probability of being an exoplanet. Finally, the Random Forest Classifier was made publicly accessible by an application programming interface (API) and an Azure Container Instance web service in the Microsoft Azure cloud