1,787 research outputs found
Boundary-Conforming Finite Element Methods for Twin-Screw Extruders using Spline-Based Parameterization Techniques
This paper presents a novel spline-based meshing technique that allows for
usage of boundary-conforming meshes for unsteady flow and temperature
simulations in co-rotating twin-screw extruders. Spline-based descriptions of
arbitrary screw geometries are generated using Elliptic Grid Generation. They
are evaluated in a number of discrete points to yield a coarse classical mesh.
The use of a special control mapping allows to fine-tune properties of the
coarse mesh like orthogonality at the boundaries. The coarse mesh is used as a
'scaffolding' to generate a boundary-conforming mesh out of a fine background
mesh at run-time. Storing only a coarse mesh makes the method cheap in terms of
memory storage. Additionally, the adaptation at run-time is extremely cheap
compared to computing the flow solution. Furthermore, this method circumvents
the need for expensive re-meshing and projections of solutions making it
efficient and accurate. It is incorporated into a space-time finite element
framework. We present time-dependent test cases of non-Newtonian fluids in 2D
and 3D for complex screw designs. They demonstrate the potential of the method
also for arbitrarily complex industrial applications
Fast, Autonomous Flight in GPS-Denied and Cluttered Environments
One of the most challenging tasks for a flying robot is to autonomously
navigate between target locations quickly and reliably while avoiding obstacles
in its path, and with little to no a-priori knowledge of the operating
environment. This challenge is addressed in the present paper. We describe the
system design and software architecture of our proposed solution, and showcase
how all the distinct components can be integrated to enable smooth robot
operation. We provide critical insight on hardware and software component
selection and development, and present results from extensive experimental
testing in real-world warehouse environments. Experimental testing reveals that
our proposed solution can deliver fast and robust aerial robot autonomous
navigation in cluttered, GPS-denied environments.Comment: Pre-peer reviewed version of the article accepted in Journal of Field
Robotic
An Incremental Construction of Deep Neuro Fuzzy System for Continual Learning of Non-stationary Data Streams
Existing FNNs are mostly developed under a shallow network configuration
having lower generalization power than those of deep structures. This paper
proposes a novel self-organizing deep FNN, namely DEVFNN. Fuzzy rules can be
automatically extracted from data streams or removed if they play limited role
during their lifespan. The structure of the network can be deepened on demand
by stacking additional layers using a drift detection method which not only
detects the covariate drift, variations of input space, but also accurately
identifies the real drift, dynamic changes of both feature space and target
space. DEVFNN is developed under the stacked generalization principle via the
feature augmentation concept where a recently developed algorithm, namely
gClass, drives the hidden layer. It is equipped by an automatic feature
selection method which controls activation and deactivation of input attributes
to induce varying subsets of input features. A deep network simplification
procedure is put forward using the concept of hidden layer merging to prevent
uncontrollable growth of dimensionality of input space due to the nature of
feature augmentation approach in building a deep network structure. DEVFNN
works in the sample-wise fashion and is compatible for data stream
applications. The efficacy of DEVFNN has been thoroughly evaluated using seven
datasets with non-stationary properties under the prequential test-then-train
protocol. It has been compared with four popular continual learning algorithms
and its shallow counterpart where DEVFNN demonstrates improvement of
classification accuracy. Moreover, it is also shown that the concept drift
detection method is an effective tool to control the depth of network structure
while the hidden layer merging scenario is capable of simplifying the network
complexity of a deep network with negligible compromise of generalization
performance.Comment: This paper has been published in IEEE Transactions on Fuzzy System
Safe and complete contig assembly via omnitigs
Contig assembly is the first stage that most assemblers solve when
reconstructing a genome from a set of reads. Its output consists of contigs --
a set of strings that are promised to appear in any genome that could have
generated the reads. From the introduction of contigs 20 years ago, assemblers
have tried to obtain longer and longer contigs, but the following question was
never solved: given a genome graph (e.g. a de Bruijn, or a string graph),
what are all the strings that can be safely reported from as contigs? In
this paper we finally answer this question, and also give a polynomial time
algorithm to find them. Our experiments show that these strings, which we call
omnitigs, are 66% to 82% longer on average than the popular unitigs, and 29% of
dbSNP locations have more neighbors in omnitigs than in unitigs.Comment: Full version of the paper in the proceedings of RECOMB 201
The parameterized complexity of some geometric problems in unbounded dimension
We study the parameterized complexity of the following fundamental geometric
problems with respect to the dimension : i) Given points in \Rd,
compute their minimum enclosing cylinder. ii) Given two -point sets in
\Rd, decide whether they can be separated by two hyperplanes. iii) Given a
system of linear inequalities with variables, find a maximum-size
feasible subsystem. We show that (the decision versions of) all these problems
are W[1]-hard when parameterized by the dimension . %and hence not solvable
in time, for any computable function and constant
%(unless FPT=W[1]). Our reductions also give a -time lower bound
(under the Exponential Time Hypothesis)
Efficient Algorithms for Prokaryotic Whole Genome Assembly and Finishing
De-novo genome assembly from DNA fragments is primarily based on sequence overlap information. In addition, mate-pair reads or paired-end reads provide linking information for joining gaps and bridging repeat regions. Genome assemblers in general assemble long contiguous sequences (contigs) using both overlapping reads and linked reads until the assembly runs into an ambiguous repeat region. These contigs are further bridged into scaffolds using linked read information. However, errors can be made in both phases of assembly due to high error threshold of overlap acceptance and linking based on too few mate reads. Identical as well as similar repeat regions can often cause errors in overlap and mate-pair evidence. In addition, the problem of setting the correct threshold to minimize errors and optimize assembly of reads is not trivial and often requires a time-consuming trial and error process to obtain optimal results. The typical trial-and-error with multiple assembler, which can be computationally intensive, and is very inefficient, especially when users must learn how to use a wide variety of assemblers, many of which may be serial requiring long execution time and will not return usable or accurate results. Further, we show that the comparison of assembly results may not provide the users with a clear winner under all circumstances. Therefore, we propose a novel scaffolding tool, Correlative Algorithm for Repeat Placement (CARP), capable of joining short low error contigs using mate pair reads, computationally resolved repeat structures and synteny with one or more reference organisms. The CARP tool requires a set of repeat sequences such as insertion sequences (IS) that can be found computationally found without assembling the genome. Development of methods to identify such repeating regions directly from raw sequence reads or draft genomes led to the development of the ISQuest software package. ISQuest identifies bacterial ISs and their sequence elements—inverted and direct repeats—in raw read data or contigs using flexible search parameters. ISQuest is capable of finding ISs in hundreds of partially assembled genomes within hours; making it a valuable high-throughput tool for a global search of IS and repeat elements.
The CARP tool matches very low error contigs with strong overlap using the ambiguous partial repeat sequence at the ends of the contig annotated using the repeat sequences discovered using ISQuest. These matches are verified by synteny with genomes of one or more reference organisms. We show that the CARP tool can be used to verify low mate pair evidence regions, independently find new joins and significantly reduce the number of scaffolds. Finally, we are demonstrate a novel viewer that presents to the user the computationally derived joins along with the evidence used to make the joins. The viewer allows the user to independently assess their confidence in the joins made by the finishing tools and make an informed decision of whether to invest the resources necessary to confirm a particular portion of the assembly. Further, we allow users to manually record join evidence, re-order contigs, and track the assembly finishing process
Joint segmentation of multivariate time series with hidden process regression for human activity recognition
The problem of human activity recognition is central for understanding and
predicting the human behavior, in particular in a prospective of assistive
services to humans, such as health monitoring, well being, security, etc. There
is therefore a growing need to build accurate models which can take into
account the variability of the human activities over time (dynamic models)
rather than static ones which can have some limitations in such a dynamic
context. In this paper, the problem of activity recognition is analyzed through
the segmentation of the multidimensional time series of the acceleration data
measured in the 3-d space using body-worn accelerometers. The proposed model
for automatic temporal segmentation is a specific statistical latent process
model which assumes that the observed acceleration sequence is governed by
sequence of hidden (unobserved) activities. More specifically, the proposed
approach is based on a specific multiple regression model incorporating a
hidden discrete logistic process which governs the switching from one activity
to another over time. The model is learned in an unsupervised context by
maximizing the observed-data log-likelihood via a dedicated
expectation-maximization (EM) algorithm. We applied it on a real-world
automatic human activity recognition problem and its performance was assessed
by performing comparisons with alternative approaches, including well-known
supervised static classifiers and the standard hidden Markov model (HMM). The
obtained results are very encouraging and show that the proposed approach is
quite competitive even it works in an entirely unsupervised way and does not
requires a feature extraction preprocessing step
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