arXiv subjects

Laura L. Tupper

Publications and source records attributed to Laura L. Tupper.

4 recordsLinked to original sources

arXiv2022

Classifying Contaminated Cell Cultures using Time Series Features

We examine the use of time series data, derived from Electric Cell-substrate Impedance Sensing (ECIS), to differentiate between standard mammalian cell cultures and those infected with a mycoplasma organism. With the goal of interpretable results, we perform low-dimensional feature-based classification, extracting application-relevant features from the ECIS time courses. We can achieve very high classification accuracy using only two features, which depend on the cell line under examination. Initial results also show the existence of experimental variation between plates and suggest types of features that may prove more robust to such variation. Our paper is the first to perform a broad examination of ECIS time course features in the context of detecting contamination; to combine different types of features to achieve classification accuracy while preserving interpretability; and to describe and suggest possibilities for ameliorating plate-to-plate variation.

q-bio.QM↗

arXiv2019

Cell Line Classification Using Electric Cell-substrate Impedance Sensing (ECIS)

We consider cell line classification using multivariate time series data obtained from electric cell-substrate impedance sensing (ECIS) technology. The ECIS device, which monitors the attachment and spreading of mammalian cells in real time through the collection of electrical impedance data, has historically been used to study one cell line at a time. However, we show that if applied to data from multiple cell lines, ECIS can be used to classify unknown or potentially mislabeled cells, which may help to mitigate the current crisis of reproducibility in the biological literature. We assess a range of approaches to this new problem, testing different classification methods and deriving a dictionary of 29 features to characterize ECIS data. Our analysis also makes use of simultaneous multi-frequency ECIS data, where previous studies have focused on only one frequency. In classification tests on fifteen mammalian cell lines, we obtain very high out-of-sample accuracy. These preliminary findings provide a baseline for future large-scale studies in this field.

q-bio.QM↗

arXiv2016

Mixed Data and Classification of Transit Stops

An analysis of the characteristics and behavior of individual bus stops can reveal clusters of similar stops, which can be of use in making routing and scheduling decisions, as well as determining what facilities to provide at each stop. This paper provides an exploratory analysis, including several possible clustering results, of a dataset provided by the Regional Transit Service of Rochester, NY. The dataset describes ridership on public buses, recording the time, location, and number of entering and exiting passengers each time a bus stops. A description of the overall behavior of bus ridership is followed by a stop-level analysis. We compare multiple measures of stop similarity, based on location, route information, and ridership volume over time.

stat.AP↗

arXiv2015

Band Depth Clustering for Nonstationary Time Series and Wind Speed Behavior

We explore the behavior of wind speed over time, using the Eastern Wind Dataset published by the National Renewable Energy Laboratory. This dataset gives wind speeds over three years at hundreds of potential wind farm sites. Wind speed analysis is necessary to the integration of wind energy into the power grid; short-term variability in wind speed affects decisions about usage of other power sources, so that the shape of the wind speed curve becomes as important as the overall level. To assess differences in intra-day time series, we propose a functional distance measure, the band distance, which extends the band depth of Lopez-Pintado and Romo (2009). This measure emphasizes the shape of time series or functional observations relative to other members of a dataset, and allows clustering of observations without reliance on pointwise Euclidean distance. To emphasize short-term variability, we examine the short-time Fourier transform of the nonstationary speed time series; we can also adjust for seasonal effects, and use these standardizations as input for the band distance. We show that these approaches to characterizing the data go beyond mean-dependent standard clustering methods, such as k-means, to provide more shape-influenced cluster representatives useful for power grid decisions.

stat.AP↗