92,161 research outputs found
Toward a multilevel representation of protein molecules: comparative approaches to the aggregation/folding propensity problem
This paper builds upon the fundamental work of Niwa et al. [34], which
provides the unique possibility to analyze the relative aggregation/folding
propensity of the elements of the entire Escherichia coli (E. coli) proteome in
a cell-free standardized microenvironment. The hardness of the problem comes
from the superposition between the driving forces of intra- and inter-molecule
interactions and it is mirrored by the evidences of shift from folding to
aggregation phenotypes by single-point mutations [10]. Here we apply several
state-of-the-art classification methods coming from the field of structural
pattern recognition, with the aim to compare different representations of the
same proteins gathered from the Niwa et al. data base; such representations
include sequences and labeled (contact) graphs enriched with chemico-physical
attributes. By this comparison, we are able to identify also some interesting
general properties of proteins. Notably, (i) we suggest a threshold around 250
residues discriminating "easily foldable" from "hardly foldable" molecules
consistent with other independent experiments, and (ii) we highlight the
relevance of contact graph spectra for folding behavior discrimination and
characterization of the E. coli solubility data. The soundness of the
experimental results presented in this paper is proved by the statistically
relevant relationships discovered among the chemico-physical description of
proteins and the developed cost matrix of substitution used in the various
discrimination systems.Comment: 17 pages, 3 figures, 46 reference
Using Description Logics for RDF Constraint Checking and Closed-World Recognition
RDF and Description Logics work in an open-world setting where absence of
information is not information about absence. Nevertheless, Description Logic
axioms can be interpreted in a closed-world setting and in this setting they
can be used for both constraint checking and closed-world recognition against
information sources. When the information sources are expressed in well-behaved
RDF or RDFS (i.e., RDF graphs interpreted in the RDF or RDFS semantics) this
constraint checking and closed-world recognition is simple to describe. Further
this constraint checking can be implemented as SPARQL querying and thus
effectively performed.Comment: Extended version of a paper of the same name that will appear in
AAAI-201
Activity recognition from videos with parallel hypergraph matching on GPUs
In this paper, we propose a method for activity recognition from videos based
on sparse local features and hypergraph matching. We benefit from special
properties of the temporal domain in the data to derive a sequential and fast
graph matching algorithm for GPUs.
Traditionally, graphs and hypergraphs are frequently used to recognize
complex and often non-rigid patterns in computer vision, either through graph
matching or point-set matching with graphs. Most formulations resort to the
minimization of a difficult discrete energy function mixing geometric or
structural terms with data attached terms involving appearance features.
Traditional methods solve this minimization problem approximately, for instance
with spectral techniques.
In this work, instead of solving the problem approximatively, the exact
solution for the optimal assignment is calculated in parallel on GPUs. The
graphical structure is simplified and regularized, which allows to derive an
efficient recursive minimization algorithm. The algorithm distributes
subproblems over the calculation units of a GPU, which solves them in parallel,
allowing the system to run faster than real-time on medium-end GPUs
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