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

Diagnosis of Influenza from Lower Respiratory Tract Sampling after Negative Upper Respiratory Tract Sampling

In this retrospective cohort study, we demonstrate that PCR-confirmed diagnoses of influenza were made solely by lower respiratory sampling in 6.9% of cases, as traditional upper respiratory tract tests were negative, indeterminate or not performed. Clinical features of these cases are presented. Clinicians should consider lower respiratory tract sampling in select cases of influenza-like illness for diagnosis

Geomorphic process fingerprints in submarine canyons

This paper is not subject to U.S. copyright. The definitive version was published in Marine Geology 337 (2013): 53-66, doi:10.1016/j.margeo.2013.01.005.Submarine canyons are common features of continental margins worldwide. They are conduits that funnel vast quantities of sediment from the continents to the deep sea. Though it is known that submarine canyons form primarily from erosion induced by submarine sediment flows, we currently lack quantitative, empirically based expressions that describe the morphology of submarine canyon networks. Multibeam bathymetry data along the entire passive US Atlantic margin (USAM) and along the active central California margin near Monterey Bay provide an opportunity to examine the fine-scale morphology of 171 slope-sourced canyons. Log–log regression analyses of canyon thalweg gradient (S) versus up-canyon catchment area (A) are used to examine linkages between morphological domains and the generation and evolution of submarine sediment flows. For example, canyon reaches of the upper continental slope are characterized by steep, linear and/or convex longitudinal profiles, whereas reaches farther down canyon have distinctly concave longitudinal profiles. The transition between these geomorphic domains is inferred to represent the downslope transformation of debris flows into erosive, canyon-flushing turbidity flows. Over geologic timescales this process appears to leave behind a predictable geomorphic fingerprint that is dependent on the catchment area of the canyon head. Catchment area, in turn, may be a proxy for the volume of sediment released during geomorphically significant failures along the upper continental slope. Focused studies of slope-sourced submarine canyons may provide new insights into the relationships between fine-scale canyon morphology and down-canyon changes in sediment flow dynamics

Evaluation of a urine pooling strategy for the rapid and cost-efficient prevalence classification of schistosomiasis

A key epidemiologic feature of schistosomiasis is its focal distribution, which has important implications for the spatial targeting of preventive chemotherapy programs. We evaluated the diagnostic accuracy of a urine pooling strategy using a point-of-care circulating cathodic antigen (POC-CCA) cassette test for detection of Schistosoma mansoni, and employed simulation modeling to test the classification accuracy and efficiency of this strategy in determining where preventive chemotherapy is needed in low-endemicity settings.; We performed a cross-sectional study involving 114 children aged 6-15 years in six neighborhoods in Azaguié Ahoua, south Côte d'Ivoire to characterize the sensitivity and specificity of the POC-CCA cassette test with urine samples that were tested individually and in pools of 4, 8, and 12. We used a Bayesian latent class model to estimate test characteristics for individual POC-CCA and quadruplicate Kato-Katz thick smears on stool samples. We then developed a microsimulation model and used lot quality assurance sampling to test the performance, number of tests, and total cost per school for each pooled testing strategy to predict the binary need for school-based preventive chemotherapy using a 10% prevalence threshold for treatment.; The sensitivity of the urine pooling strategy for S. mansoni diagnosis using pool sizes of 4, 8, and 12 was 85.9%, 79.5%, and 65.4%, respectively, when POC-CCA trace results were considered positive, and 61.5%, 47.4%, and 30.8% when POC-CCA trace results were considered negative. The modeled specificity ranged from 94.0-97.7% for the urine pooling strategies (when POC-CCA trace results were considered negative). The urine pooling strategy, regardless of the pool size, gave comparable and often superior classification performance to stool microscopy for the same number of tests. The urine pooling strategy with a pool size of 4 reduced the number of tests and total cost compared to classical stool microscopy.; This study introduces a method for rapid and efficient S. mansoni prevalence estimation through examining pooled urine samples with POC-CCA as an alternative to widely used stool microscopy

Seabed fluid expulsion along the upper slope and outer shelf of the U.S. Atlantic continental margin

Author Posting. © American Geophysical Union, 2014. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geophysical Research Letters 41 (2014): 96-101, doi:10.1002/2013GL058048.Identifying the spatial distribution of seabed fluid expulsion features is crucial for understanding the substrate plumbing system of any continental margin. A 1100 km stretch of the U.S. Atlantic margin contains more than 5000 pockmarks at water depths of 120 m (shelf edge) to 700 m (upper slope), mostly updip of the contemporary gas hydrate stability zone (GHSZ). Advanced attribute analyses of high-resolution multichannel seismic reflection data reveal gas-charged sediment and probable fluid chimneys beneath pockmark fields. A series of enhanced reflectors, inferred to represent hydrate-bearing sediments, occur within the GHSZ. Differential sediment loading at the shelf edge and warming-induced gas hydrate dissociation along the upper slope are the proposed mechanisms that led to transient changes in substrate pore fluid overpressure, vertical fluid/gas migration, and pockmark formation.The U.S. Geological Survey and the U.S. Nuclear Regulatory Commission funded this research.2014-07-0

Identification of buried lunar impact craters from GRAIL data and implications for the nearside maria

Gravity observations from the dual Gravity Recovery and Interior Laboratory (GRAIL) spacecraft have revealed more than 100 quasi‐circular mass anomalies, 26–300 km in diameter, on the lunar nearside. These anomalies are interpreted to be impact craters filled primarily by mare deposits, and their characteristics are consistent with those of impact structures that formed prior to, and during, intervals of flooding of feldspathic terrane by mare basalt lavas. We determine that mare deposits have an average density contrast of 850⁺³⁰⁰₋₂₀₀ kg m⁻³ relative to the surrounding crust. The presence of a large population of volcanically buried craters with minimal topographic expression and diameters up to 300 km requires an average nearside mare thickness of at least 1.5 km and local lenses of mare basalt as thick as ~7 km

Gene Ontology Analysis of Pairwise Genetic Associations in Two Genome-Wide Studies of Sporadic ALS

It is increasingly clear that common human diseases have a complex genetic architecture characterized by both additive and nonadditive genetic effects. The goal of the present study was to determine whether patterns of both additive and nonadditive genetic associations aggregate in specific functional groups as defined by the Gene Ontology (GO)