41,783 research outputs found
A computational framework to emulate the human perspective in flow cytometric data analysis
Background: In recent years, intense research efforts have focused on developing methods for automated flow cytometric data analysis. However, while designing such applications, little or no attention has been paid to the human perspective that is absolutely central to the manual gating process of identifying and characterizing cell populations. In particular, the assumption of many common techniques that cell populations could be modeled reliably with pre-specified distributions may not hold true in real-life samples, which can have populations of arbitrary shapes and considerable inter-sample variation.
<p/>Results: To address this, we developed a new framework flowScape for emulating certain key aspects of the human perspective in analyzing flow data, which we implemented in multiple steps. First, flowScape begins with creating a mathematically rigorous map of the high-dimensional flow data landscape based on dense and sparse regions defined by relative concentrations of events around modes. In the second step, these modal clusters are connected with a global hierarchical structure. This representation allows flowScape to perform ridgeline analysis for both traversing the landscape and isolating cell populations at different levels of resolution. Finally, we extended manual gating with a new capacity for constructing templates that can identify target populations in terms of their relative parameters, as opposed to the more commonly used absolute or physical parameters. This allows flowScape to apply such templates in batch mode for detecting the corresponding populations in a flexible, sample-specific manner. We also demonstrated different applications of our framework to flow data analysis and show its superiority over other analytical methods.
<p/>Conclusions: The human perspective, built on top of intuition and experience, is a very important component of flow cytometric data analysis. By emulating some of its approaches and extending these with automation and rigor, flowScape provides a flexible and robust framework for computational cytomics
Multi-view constrained clustering with an incomplete mapping between views
Multi-view learning algorithms typically assume a complete bipartite mapping
between the different views in order to exchange information during the
learning process. However, many applications provide only a partial mapping
between the views, creating a challenge for current methods. To address this
problem, we propose a multi-view algorithm based on constrained clustering that
can operate with an incomplete mapping. Given a set of pairwise constraints in
each view, our approach propagates these constraints using a local similarity
measure to those instances that can be mapped to the other views, allowing the
propagated constraints to be transferred across views via the partial mapping.
It uses co-EM to iteratively estimate the propagation within each view based on
the current clustering model, transfer the constraints across views, and then
update the clustering model. By alternating the learning process between views,
this approach produces a unified clustering model that is consistent with all
views. We show that this approach significantly improves clustering performance
over several other methods for transferring constraints and allows multi-view
clustering to be reliably applied when given a limited mapping between the
views. Our evaluation reveals that the propagated constraints have high
precision with respect to the true clusters in the data, explaining their
benefit to clustering performance in both single- and multi-view learning
scenarios
Fast, scalable, Bayesian spike identification for multi-electrode arrays
We present an algorithm to identify individual neural spikes observed on
high-density multi-electrode arrays (MEAs). Our method can distinguish large
numbers of distinct neural units, even when spikes overlap, and accounts for
intrinsic variability of spikes from each unit. As MEAs grow larger, it is
important to find spike-identification methods that are scalable, that is, the
computational cost of spike fitting should scale well with the number of units
observed. Our algorithm accomplishes this goal, and is fast, because it
exploits the spatial locality of each unit and the basic biophysics of
extracellular signal propagation. Human intervention is minimized and
streamlined via a graphical interface. We illustrate our method on data from a
mammalian retina preparation and document its performance on simulated data
consisting of spikes added to experimentally measured background noise. The
algorithm is highly accurate
A Map of the Inorganic Ternary Metal Nitrides
Exploratory synthesis in novel chemical spaces is the essence of solid-state
chemistry. However, uncharted chemical spaces can be difficult to navigate,
especially when materials synthesis is challenging. Nitrides represent one such
space, where stringent synthesis constraints have limited the exploration of
this important class of functional materials. Here, we employ a suite of
computational materials discovery and informatics tools to construct a large
stability map of the inorganic ternary metal nitrides. Our map clusters the
ternary nitrides into chemical families with distinct stability and
metastability, and highlights hundreds of promising new ternary nitride spaces
for experimental investigation--from which we experimentally realized 7 new Zn-
and Mg-based ternary nitrides. By extracting the mixed metallicity, ionicity,
and covalency of solid-state bonding from the DFT-computed electron density, we
reveal the complex interplay between chemistry, composition, and electronic
structure in governing large-scale stability trends in ternary nitride
materials
The Whole is Greater than the Sum of the Parts: Optimizing the Joint Science Return from LSST, Euclid and WFIRST
The focus of this report is on the opportunities enabled by the combination
of LSST, Euclid and WFIRST, the optical surveys that will be an essential part
of the next decade's astronomy. The sum of these surveys has the potential to
be significantly greater than the contributions of the individual parts. As is
detailed in this report, the combination of these surveys should give us
multi-wavelength high-resolution images of galaxies and broadband data covering
much of the stellar energy spectrum. These stellar and galactic data have the
potential of yielding new insights into topics ranging from the formation
history of the Milky Way to the mass of the neutrino. However, enabling the
astronomy community to fully exploit this multi-instrument data set is a
challenging technical task: for much of the science, we will need to combine
the photometry across multiple wavelengths with varying spectral and spatial
resolution. We identify some of the key science enabled by the combined surveys
and the key technical challenges in achieving the synergies.Comment: Whitepaper developed at June 2014 U. Penn Workshop; 28 pages, 3
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MIDAS prototype Multispectral Interactive Digital Analysis System for large area earth resources surveys. Volume 2: Charge coupled device investigation
MIDAS is a third-generation, fast, low cost, multispectral recognition system able to keep pace with the large quantity and high rates of data acquisition from large regions with present and projected sensors. MIDAS, for example, can process a complete ERTS frame in forty seconds and provide a color map of sixteen constituent categories in a few minutes. A principal objective of the MIDAS Program is to provide a system well interfaced with the human operator and thus to obtain large overall reductions in turn-around time and significant gains in throughput. The need for advanced onboard spacecraft processing of remotely sensed data is stated and approaches to this problem are described which are feasible through the use of charge coupled devices. Tentative mechanizations for the required processing operations are given in large block form. These initial designs can serve as a guide to circuit/system designers
Multi-View Face Recognition From Single RGBD Models of the Faces
This work takes important steps towards solving the following problem of current interest: Assuming that each individual in a population can be modeled by a single frontal RGBD face image, is it possible to carry out face recognition for such a population using multiple 2D images captured from arbitrary viewpoints? Although the general problem as stated above is extremely challenging, it encompasses subproblems that can be addressed today. The subproblems addressed in this work relate to: (1) Generating a large set of viewpoint dependent face images from a single RGBD frontal image for each individual; (2) using hierarchical approaches based on view-partitioned subspaces to represent the training data; and (3) based on these hierarchical approaches, using a weighted voting algorithm to integrate the evidence collected from multiple images of the same face as recorded from different viewpoints. We evaluate our methods on three datasets: a dataset of 10 people that we created and two publicly available datasets which include a total of 48 people. In addition to providing important insights into the nature of this problem, our results show that we are able to successfully recognize faces with accuracies of 95% or higher, outperforming existing state-of-the-art face recognition approaches based on deep convolutional neural networks
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