37,259 research outputs found
Recurrence networks - A novel paradigm for nonlinear time series analysis
This paper presents a new approach for analysing structural properties of
time series from complex systems. Starting from the concept of recurrences in
phase space, the recurrence matrix of a time series is interpreted as the
adjacency matrix of an associated complex network which links different points
in time if the evolution of the considered states is very similar. A critical
comparison of these recurrence networks with similar existing techniques is
presented, revealing strong conceptual benefits of the new approach which can
be considered as a unifying framework for transforming time series into complex
networks that also includes other methods as special cases.
It is demonstrated that there are fundamental relationships between the
topological properties of recurrence networks and the statistical properties of
the phase space density of the underlying dynamical system. Hence, the network
description yields new quantitative characteristics of the dynamical complexity
of a time series, which substantially complement existing measures of
recurrence quantification analysis
Geometry of the ergodic quotient reveals coherent structures in flows
Dynamical systems that exhibit diverse behaviors can rarely be completely
understood using a single approach. However, by identifying coherent structures
in their state spaces, i.e., regions of uniform and simpler behavior, we could
hope to study each of the structures separately and then form the understanding
of the system as a whole. The method we present in this paper uses trajectory
averages of scalar functions on the state space to: (a) identify invariant sets
in the state space, (b) form coherent structures by aggregating invariant sets
that are similar across multiple spatial scales. First, we construct the
ergodic quotient, the object obtained by mapping trajectories to the space of
trajectory averages of a function basis on the state space. Second, we endow
the ergodic quotient with a metric structure that successfully captures how
similar the invariant sets are in the state space. Finally, we parametrize the
ergodic quotient using intrinsic diffusion modes on it. By segmenting the
ergodic quotient based on the diffusion modes, we extract coherent features in
the state space of the dynamical system. The algorithm is validated by
analyzing the Arnold-Beltrami-Childress flow, which was the test-bed for
alternative approaches: the Ulam's approximation of the transfer operator and
the computation of Lagrangian Coherent Structures. Furthermore, we explain how
the method extends the Poincar\'e map analysis for periodic flows. As a
demonstration, we apply the method to a periodically-driven three-dimensional
Hill's vortex flow, discovering unknown coherent structures in its state space.
In the end, we discuss differences between the ergodic quotient and
alternatives, propose a generalization to analysis of (quasi-)periodic
structures, and lay out future research directions.Comment: Submitted to Elsevier Physica D: Nonlinear Phenomen
A Force-Directed Approach for Offline GPS Trajectory Map Matching
We present a novel algorithm to match GPS trajectories onto maps offline (in
batch mode) using techniques borrowed from the field of force-directed graph
drawing. We consider a simulated physical system where each GPS trajectory is
attracted or repelled by the underlying road network via electrical-like
forces. We let the system evolve under the action of these physical forces such
that individual trajectories are attracted towards candidate roads to obtain a
map matching path. Our approach has several advantages compared to traditional,
routing-based, algorithms for map matching, including the ability to account
for noise and to avoid large detours due to outliers in the data whilst taking
into account the underlying topological restrictions (such as one-way roads).
Our empirical evaluation using real GPS traces shows that our method produces
better map matching results compared to alternative offline map matching
algorithms on average, especially for routes in dense, urban areas.Comment: 10 pages, 12 figures, accepted version of article submitted to ACM
SIGSPATIAL 2018, Seattle, US
Path Similarity Analysis: a Method for Quantifying Macromolecular Pathways
Diverse classes of proteins function through large-scale conformational
changes; sophisticated enhanced sampling methods have been proposed to generate
these macromolecular transition paths. As such paths are curves in a
high-dimensional space, they have been difficult to compare quantitatively, a
prerequisite to, for instance, assess the quality of different sampling
algorithms. The Path Similarity Analysis (PSA) approach alleviates these
difficulties by utilizing the full information in 3N-dimensional trajectories
in configuration space. PSA employs the Hausdorff or Fr\'echet path
metrics---adopted from computational geometry---enabling us to quantify path
(dis)similarity, while the new concept of a Hausdorff-pair map permits the
extraction of atomic-scale determinants responsible for path differences.
Combined with clustering techniques, PSA facilitates the comparison of many
paths, including collections of transition ensembles. We use the closed-to-open
transition of the enzyme adenylate kinase (AdK)---a commonly used testbed for
the assessment enhanced sampling algorithms---to examine multiple microsecond
equilibrium molecular dynamics (MD) transitions of AdK in its substrate-free
form alongside transition ensembles from the MD-based dynamic importance
sampling (DIMS-MD) and targeted MD (TMD) methods, and a geometrical targeting
algorithm (FRODA). A Hausdorff pairs analysis of these ensembles revealed, for
instance, that differences in DIMS-MD and FRODA paths were mediated by a set of
conserved salt bridges whose charge-charge interactions are fully modeled in
DIMS-MD but not in FRODA. We also demonstrate how existing trajectory analysis
methods relying on pre-defined collective variables, such as native contacts or
geometric quantities, can be used synergistically with PSA, as well as the
application of PSA to more complex systems such as membrane transporter
proteins.Comment: 9 figures, 3 tables in the main manuscript; supplementary information
includes 7 texts (S1 Text - S7 Text) and 11 figures (S1 Fig - S11 Fig) (also
available from journal site
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