9,182 research outputs found
ProtNN: Fast and Accurate Nearest Neighbor Protein Function Prediction based on Graph Embedding in Structural and Topological Space
Studying the function of proteins is important for understanding the
molecular mechanisms of life. The number of publicly available protein
structures has increasingly become extremely large. Still, the determination of
the function of a protein structure remains a difficult, costly, and time
consuming task. The difficulties are often due to the essential role of spatial
and topological structures in the determination of protein functions in living
cells. In this paper, we propose ProtNN, a novel approach for protein function
prediction. Given an unannotated protein structure and a set of annotated
proteins, ProtNN finds the nearest neighbor annotated structures based on
protein-graph pairwise similarities. Given a query protein, ProtNN finds the
nearest neighbor reference proteins based on a graph representation model and a
pairwise similarity between vector embedding of both query and reference
protein-graphs in structural and topological spaces. ProtNN assigns to the
query protein the function with the highest number of votes across the set of k
nearest neighbor reference proteins, where k is a user-defined parameter.
Experimental evaluation demonstrates that ProtNN is able to accurately classify
several datasets in an extremely fast runtime compared to state-of-the-art
approaches. We further show that ProtNN is able to scale up to a whole PDB
dataset in a single-process mode with no parallelization, with a gain of
thousands order of magnitude of runtime compared to state-of-the-art
approaches
Structured Knowledge Representation for Image Retrieval
We propose a structured approach to the problem of retrieval of images by
content and present a description logic that has been devised for the semantic
indexing and retrieval of images containing complex objects. As other
approaches do, we start from low-level features extracted with image analysis
to detect and characterize regions in an image. However, in contrast with
feature-based approaches, we provide a syntax to describe segmented regions as
basic objects and complex objects as compositions of basic ones. Then we
introduce a companion extensional semantics for defining reasoning services,
such as retrieval, classification, and subsumption. These services can be used
for both exact and approximate matching, using similarity measures. Using our
logical approach as a formal specification, we implemented a complete
client-server image retrieval system, which allows a user to pose both queries
by sketch and queries by example. A set of experiments has been carried out on
a testbed of images to assess the retrieval capabilities of the system in
comparison with expert users ranking. Results are presented adopting a
well-established measure of quality borrowed from textual information
retrieval
Query processing of spatial objects: Complexity versus Redundancy
The management of complex spatial objects in applications, such as geography and cartography,
imposes stringent new requirements on spatial database systems, in particular on efficient
query processing. As shown before, the performance of spatial query processing can be improved
by decomposing complex spatial objects into simple components. Up to now, only decomposition
techniques generating a linear number of very simple components, e.g. triangles or trapezoids, have
been considered. In this paper, we will investigate the natural trade-off between the complexity of
the components and the redundancy, i.e. the number of components, with respect to its effect on
efficient query processing. In particular, we present two new decomposition methods generating
a better balance between the complexity and the number of components than previously known
techniques. We compare these new decomposition methods to the traditional undecomposed representation
as well as to the well-known decomposition into convex polygons with respect to their
performance in spatial query processing. This comparison points out that for a wide range of query
selectivity the new decomposition techniques clearly outperform both the undecomposed representation
and the convex decomposition method. More important than the absolute gain in performance
by a factor of up to an order of magnitude is the robust performance of our new decomposition
techniques over the whole range of query selectivity
A storage and access architecture for efficient query processing in spatial database systems
Due to the high complexity of objects and queries and also due to extremely
large data volumes, geographic database systems impose stringent requirements on their
storage and access architecture with respect to efficient query processing. Performance
improving concepts such as spatial storage and access structures, approximations, object
decompositions and multi-phase query processing have been suggested and analyzed as
single building blocks. In this paper, we describe a storage and access architecture which
is composed from the above building blocks in a modular fashion. Additionally, we incorporate
into our architecture a new ingredient, the scene organization, for efficiently
supporting set-oriented access of large-area region queries. An experimental performance
comparison demonstrates that the concept of scene organization leads to considerable
performance improvements for large-area region queries by a factor of up to 150
Geospatial Narratives and their Spatio-Temporal Dynamics: Commonsense Reasoning for High-level Analyses in Geographic Information Systems
The modelling, analysis, and visualisation of dynamic geospatial phenomena
has been identified as a key developmental challenge for next-generation
Geographic Information Systems (GIS). In this context, the envisaged
paradigmatic extensions to contemporary foundational GIS technology raises
fundamental questions concerning the ontological, formal representational, and
(analytical) computational methods that would underlie their spatial
information theoretic underpinnings.
We present the conceptual overview and architecture for the development of
high-level semantic and qualitative analytical capabilities for dynamic
geospatial domains. Building on formal methods in the areas of commonsense
reasoning, qualitative reasoning, spatial and temporal representation and
reasoning, reasoning about actions and change, and computational models of
narrative, we identify concrete theoretical and practical challenges that
accrue in the context of formal reasoning about `space, events, actions, and
change'. With this as a basis, and within the backdrop of an illustrated
scenario involving the spatio-temporal dynamics of urban narratives, we address
specific problems and solutions techniques chiefly involving `qualitative
abstraction', `data integration and spatial consistency', and `practical
geospatial abduction'. From a broad topical viewpoint, we propose that
next-generation dynamic GIS technology demands a transdisciplinary scientific
perspective that brings together Geography, Artificial Intelligence, and
Cognitive Science.
Keywords: artificial intelligence; cognitive systems; human-computer
interaction; geographic information systems; spatio-temporal dynamics;
computational models of narrative; geospatial analysis; geospatial modelling;
ontology; qualitative spatial modelling and reasoning; spatial assistance
systemsComment: ISPRS International Journal of Geo-Information (ISSN 2220-9964);
Special Issue on: Geospatial Monitoring and Modelling of Environmental
Change}. IJGI. Editor: Duccio Rocchini. (pre-print of article in press
Data-Driven Shape Analysis and Processing
Data-driven methods play an increasingly important role in discovering
geometric, structural, and semantic relationships between 3D shapes in
collections, and applying this analysis to support intelligent modeling,
editing, and visualization of geometric data. In contrast to traditional
approaches, a key feature of data-driven approaches is that they aggregate
information from a collection of shapes to improve the analysis and processing
of individual shapes. In addition, they are able to learn models that reason
about properties and relationships of shapes without relying on hard-coded
rules or explicitly programmed instructions. We provide an overview of the main
concepts and components of these techniques, and discuss their application to
shape classification, segmentation, matching, reconstruction, modeling and
exploration, as well as scene analysis and synthesis, through reviewing the
literature and relating the existing works with both qualitative and numerical
comparisons. We conclude our report with ideas that can inspire future research
in data-driven shape analysis and processing.Comment: 10 pages, 19 figure
The combination of spatial access methods and computational geometry in geographic database systems
Geographic database systems, known as geographic information systems (GISs) particularly among non-computer scientists, are one of the most important applications of the very active research area named spatial database systems. Consequently following the database approach, a GIS hag to be seamless, i.e. store the complete area of interest (e.g. the whole world) in one database map. For exhibiting acceptable performance a seamless GIS hag to use spatial access methods. Due to the complexity of query and analysis operations on geographic objects, state-of-the-art computational geomeny concepts have to be used in implementing these operations. In this paper, we present GIS operations based on the compuational geomeny technique plane sweep. Specifically, we show how the two ingredients spatial access methods and computational geomeny concepts can be combined für improving the performance of GIS operations. The fruitfulness of this combination is based on the fact that spatial access methods efficiently provide the data at the time when computational geomeny algorithms need it für processing. Additionally, this combination avoids page faults and facilitates the parallelization of the algorithms.
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