920 research outputs found
Critical Transitions In a Model of a Genetic Regulatory System
We consider a model for substrate-depletion oscillations in genetic systems,
based on a stochastic differential equation with a slowly evolving external
signal. We show the existence of critical transitions in the system. We apply
two methods to numerically test the synthetic time series generated by the
system for early indicators of critical transitions: a detrended fluctuation
analysis method, and a novel method based on topological data analysis
(persistence diagrams).Comment: 19 pages, 8 figure
Algorithms to automatically quantify the geometric similarity of anatomical surfaces
We describe new approaches for distances between pairs of 2-dimensional
surfaces (embedded in 3-dimensional space) that use local structures and global
information contained in inter-structure geometric relationships. We present
algorithms to automatically determine these distances as well as geometric
correspondences. This is motivated by the aspiration of students of natural
science to understand the continuity of form that unites the diversity of life.
At present, scientists using physical traits to study evolutionary
relationships among living and extinct animals analyze data extracted from
carefully defined anatomical correspondence points (landmarks). Identifying and
recording these landmarks is time consuming and can be done accurately only by
trained morphologists. This renders these studies inaccessible to
non-morphologists, and causes phenomics to lag behind genomics in elucidating
evolutionary patterns. Unlike other algorithms presented for morphological
correspondences our approach does not require any preliminary marking of
special features or landmarks by the user. It also differs from other seminal
work in computational geometry in that our algorithms are polynomial in nature
and thus faster, making pairwise comparisons feasible for significantly larger
numbers of digitized surfaces. We illustrate our approach using three datasets
representing teeth and different bones of primates and humans, and show that it
leads to highly accurate results.Comment: Changes with respect to v1, v2: an Erratum was added, correcting the
references for one of the three datasets. Note that the datasets and code for
this paper can be obtained from the Data Conservancy (see Download column on
v1, v2
Ricci Curvature of the Internet Topology
Analysis of Internet topologies has shown that the Internet topology has
negative curvature, measured by Gromov's "thin triangle condition", which is
tightly related to core congestion and route reliability. In this work we
analyze the discrete Ricci curvature of the Internet, defined by Ollivier, Lin,
etc. Ricci curvature measures whether local distances diverge or converge. It
is a more local measure which allows us to understand the distribution of
curvatures in the network. We show by various Internet data sets that the
distribution of Ricci cuvature is spread out, suggesting the network topology
to be non-homogenous. We also show that the Ricci curvature has interesting
connections to both local measures such as node degree and clustering
coefficient, global measures such as betweenness centrality and network
connectivity, as well as auxilary attributes such as geographical distances.
These observations add to the richness of geometric structures in complex
network theory.Comment: 9 pages, 16 figures. To be appear on INFOCOM 201
- …