206 research outputs found
Convex Optimization for Binary Classifier Aggregation in Multiclass Problems
Multiclass problems are often decomposed into multiple binary problems that
are solved by individual binary classifiers whose results are integrated into a
final answer. Various methods, including all-pairs (APs), one-versus-all (OVA),
and error correcting output code (ECOC), have been studied, to decompose
multiclass problems into binary problems. However, little study has been made
to optimally aggregate binary problems to determine a final answer to the
multiclass problem. In this paper we present a convex optimization method for
an optimal aggregation of binary classifiers to estimate class membership
probabilities in multiclass problems. We model the class membership probability
as a softmax function which takes a conic combination of discrepancies induced
by individual binary classifiers, as an input. With this model, we formulate
the regularized maximum likelihood estimation as a convex optimization problem,
which is solved by the primal-dual interior point method. Connections of our
method to large margin classifiers are presented, showing that the large margin
formulation can be considered as a limiting case of our convex formulation.
Numerical experiments on synthetic and real-world data sets demonstrate that
our method outperforms existing aggregation methods as well as direct methods,
in terms of the classification accuracy and the quality of class membership
probability estimates.Comment: Appeared in Proceedings of the 2014 SIAM International Conference on
Data Mining (SDM 2014
Small Footprint High Flow Rate Microdevice for Rare Target Cell Capture
A novel high flow rate cell capture design was introduced to overcome the limitations of the current technologies or methods for rare target cell capture. Even though the rare target cell capture using BioMEMS technology has great potential for cancer diagnosis, previous rare cell capture research could not overcome the limitations of low flow rate or low recovery rate. Rare cell research requires precise sample preparation for accurate results. A new method of preparation for a single or a precise number of target cell was introduced. Current sample preparation methods which are not suitable for rare cell research, such as CTC capture or single cell analysis do not provide precise cell counts below 100. A cell collection chip was designed and used with a polyimide removed capillary tube to collect an exact number of target cells under a microscope. To optimize the dimensions of the high flow rate design, CFD (Fluent v6.3, ANSYS, Inc., Canonsburg, PA, USA) simulation was used. The design focused on a high flow rate at inlet and low axial and lateral velocities in the cell capture regions with a small footprint. Based on the simulation results, the dimensions for several prototypes were determined and fabricated in PMMA. The CTCs, MCF-7 cells, were captured flow rates up to 750 ĀµL/min from 40% red blood cells with 80% recovery rate using the high flow rate device
Biochemical and genetic characterization of bacteriophage 21 holin: S21 as a membrane protein and beyond
The fate of phage-infected bacteria is determined by the holin, a small membrane
protein that triggers disruption of the membrane at a programmed time, allowing a
lysozyme to attack the cell wall. S2168, the holin of phage 21, has two transmembrane
domains (TMDs) with a predicted N-in, C-in topology. Surprisingly, TMD1 of S2168
was found to be dispensable for function, to behave as a SAR ("signal-anchor-release")
domain in exiting the membrane to the periplasm, and to engage in homotypic
interactions in the soluble phase. The departure of TMD1 from the bilayer coincides
with the lethal triggering of the holin and is accelerated by membrane depolarization.
Basic residues added at the N-terminus of S2168 prevent the escape of TMD1 to the
periplasm and block hole formation by TMD2. Lysis thus depends on dynamic topology,
in that removal of the inhibitory TMD1 from the bilayer frees TMD2 for programmed
formation of lethal membrane lesions. Like the holin S of Ī», the holin of lambdoid phage
21 (S21) controls lysis by forming holes in the membrane. However, unlike SĪ», these
holes are small, serving only to depolarize the membrane facilitating the release and
activation of the SAR endolysin, R21. We were able to demonstrate that, unlike SĪ», S2168 forms a āpinholeā, thus macromolecules easily pass through SĪ» but not S21 holes. This
result again supports our interpretation: when S21 triggers, it only needs to collapse the
membrane potential, thus causing release and activation of the membrane-tethered
inactive SAR endolysin, but does not form holes in the membrane large enough to allow
passage of a pre-folded, active cytoplasmic endolysin. The lysis defective S2168 mutant
alleles were isolated throughout the S21 gene. Although the majority of lysis defective
mutations occurred in the codons for the TMD2 domain, two mutations were found in
the codons for the TMD1. This result suggests that only the TMD2 domain of S2168 is
likely to participate in actual hole formation. One can assume that two mutant alleles of
TMD1 are involved in two different interactions: (a) TMD1-TMD1 intermolecular
interaction, (b) TMD1-TMD2 intramolecular interaction. We showed that there is a
specific TMD1-TMD2 interaction. In terms of TMD1-TMD2 interaction, the mutated
residues of the two TMD1 mutants might prevent a departure of TMD1 from TMD2,
resulting in the lysis defective phenotype. Hopefully, these findings deliver some hints
about the mechanism of S2168 hole formation and further provoke more extensive work
which is required to provide a definite answer to many questions regarding this matter
Frequency Domain Spectral Element Model for the Vibration Analysis of a Thin Plate with Arbitrary Boundary Conditions
We propose a new spectral element model for finite rectangular plate elements with arbitrary boundary conditions. The new spectral element model is developed by modifying the boundary splitting method used in our previous study so that the four corner nodes of a finite rectangular plate element become active. Thus, the new spectral element model can be applied to any finite rectangular plate element with arbitrary boundary conditions, while the spectral element model introduced in the our previous study is valid only for finite rectangular plate elements with four fixed corner nodes. The new spectral element model can be used as a generic finite element model because it can be assembled in any plate direction. The accuracy and computational efficiency of the new spectral element model are validated by a comparison with exact solutions, solutions obtained by the standard finite element method, and solutions from the commercial finite element analysis package ANSYS
The Connection between Star-Forming Galaxies, AGN Host Galaxies and Early-Type Galaxies in the SDSS
We present a study of the connection between star-forming galaxies, AGN host
galaxies, and normal early-type galaxies in the Sloan Digital Sky Survey
(SDSS). Using the SDSS DR5 and DR4plus data, we select our early-type galaxy
sample in the color versus color-gradient space, and we classify the spectral
types of the selected early-type galaxies into normal, star-forming, Seyfert,
and LINER classes, using several spectral line flux ratios. We investigate the
slope in the fundamental space for each class of early-type galaxies and find
that there are obvious differences in the slopes of the fundamental planes
(FPs) among the different classes of early-type galaxies, in the sense that the
slopes for Seyferts and star-forming galaxies are flatter than those for normal
galaxies and LINERs. This may be the first identification of the systematic
variation of the FP slope among the subclasses of early-type galaxies. The
difference in the FP slope might be caused by the difference in the degree of
nonhomology among different classes or by the difference of gas contents in
their merging progenitors. One possible scenario is that the AGN host galaxies
and star-forming galaxies are formed by gas-rich merging and that they may
evolve into normal early-type galaxies after finishing their star formation or
AGN activities.Comment: 5 pages with emulateapj, 2 figures, accepted for publication in the
Astrophysical Journal Letter
Embracing Limited and Imperfect Data: A Review on Plant Stress Recognition Using Deep Learning
Plant stress recognition has witnessed significant improvements in recent
years with the advent of deep learning. A large-scale and annotated training
dataset is required to achieve decent performance; however, collecting it is
frequently difficult and expensive. Therefore, deploying current deep
learning-based methods in real-world applications may suffer primarily from
limited and imperfect data. Embracing them is a promising strategy that has not
received sufficient attention. From this perspective, a systematic survey was
conducted in this study, with the ultimate objective of monitoring plant growth
by implementing deep learning, which frees humans and potentially reduces the
resultant losses from plant stress. We believe that our paper has highlighted
the importance of embracing this limited and imperfect data and enhanced its
relevant understanding
Capella: A Space-only High-frequency Radio VLBI Network Formed by a Constellation of Small Satellites
Very long baseline radio interferometry (VLBI) with ground-based
observatories is limited by the size of Earth, the geographic distribution of
antennas, and the transparency of the atmosphere. In this whitepaper, we
present Capella, a tentative design of a space-only VLBI system. Using four
small (<500 kg) satellites on two orthogonal polar low-Earth orbits, and
single-band heterodyne receivers operating at frequencies around 690 GHz, the
interferometer is able to achieve angular resolutions of approximately 7
microarcsec. Within a total observing time of three days, a near-complete uv
plane coverage can be reached, with a 1-sigma point source sensitivity as good
as about 6~mJy for an instantaneous bandwidth of 1 GHz. The required downlink
data rates of >10 Gbps can be reached through near-infrared laser
communication; depending on the actual downlink speed, one or multiple ground
communication stations are necessary. We note that all key technologies
required for the Capella system are already available, some of them
off-the-shelf. Data can be correlated using dedicated versions of existing
Fourier transform (FX) software correlators; dedicated routines will be needed
to handle the effects of orbital motion, including relativistic corrections.
With the specifications assumed in this whitepaper, Capella will be able to
address a range of science cases, including: photon rings around supermassive
black holes; the acceleration and collimation zones of plasma jets emitted from
the vicinity of supermassive black holes; the chemical composition of accretion
flows into active galactic nuclei through observations of molecular absorption
lines; mapping supermassive binary black holes; the magnetic activity of stars;
and nova eruptions of symbiotic binary stars - and, like any substantially new
observing technique, has the potential for unexpected discoveries.Comment: 18 pages, 2 figures, 1 table. Whitepaper version 1.0. Living
document, will be updated when necessar
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