scholarly journals Dealing with the Ambiguity of Glycan Substructure Search

2021 ◽  
Author(s):  
Vincenzo Daponte ◽  
Catherine Hayes ◽  
Julien Mariethoz ◽  
Frederique Lisacek
Keyword(s):  
Knowledge Base ◽  
Large Scale ◽  
Logical Structure ◽  
Glycan Structure ◽  
Substructure Search ◽  
Advanced Search

The level of ambiguity in describing glycan structure has significantly increased with the upsurge of large scale glycomics and glycoproteomics experiments. Consequently, an ontology-based model appears as an appropriate solution for navigating this data. However, navigation is not sufficient and the model should also enable advanced search and comparison. A new ontology with a tree logical structure is introduced to represent glycan structures irrespective of the precision of molecular details. The model heavily relies on the GlycoCT encoding of glycan structures. Its implementation in the GlySTreeM knowledge base was validated with GlyConnect data and benchmarked with the Glycowork library. GlySTreeM is shown to be fast, consistent, reliable and more flexible than existing solutions for matching parts of or whole glycan structures. The model is also well suited to painless future expansion. Availability:https://glyconnect.expasy.org/glystreem/wiki

scholarly journals Dealing with the Ambiguity of Glycan Substructure Search

Molecules ◽  
2021 ◽  
Vol 27 (1) ◽  
pp. 65
Author(s):  
Vincenzo Daponte ◽  
Catherine Hayes ◽  
Julien Mariethoz ◽  
Frederique Lisacek
Keyword(s):  
Knowledge Base ◽  
Large Scale ◽  
Logical Structure ◽  
Glycan Structure ◽  
Substructure Search ◽  
Advanced Search

The level of ambiguity in describing glycan structure has significantly increased with the upsurge of large-scale glycomics and glycoproteomics experiments. Consequently, an ontology-based model appears as an appropriate solution for navigating these data. However, navigation is not sufficient and the model should also enable advanced search and comparison. A new ontology with a tree logical structure is introduced to represent glycan structures irrespective of the precision of molecular details. The model heavily relies on the GlycoCT encoding of glycan structures. Its implementation in the GlySTreeM knowledge base was validated with GlyConnect data and benchmarked with the Glycowork library. GlySTreeM is shown to be fast, consistent, reliable and more flexible than existing solutions for matching parts of or whole glycan structures. The model is also well suited for painless future expansion.

Virtual Gas Turbines Part I: A Top-Down Geometry Modelling Environment for Turbomachinery Application

2021 ◽  
Author(s):  
Davendu Y. Kulkarni ◽  
Gan Lu ◽  
Feng Wang ◽  
Luca di Mare
Keyword(s):  
Gas Turbine ◽  
Gas Turbines ◽  
Large Scale ◽  
Logical Structure ◽  
System Level ◽  
Top Down ◽  
Design Intent ◽  
Geometry Model ◽  
Feature Based ◽  
Modelling Environment

Abstract The gas turbine engine design involves multi-disciplinary, multi-fidelity iterative design-analysis processes. These highly intertwined processes are nowadays incorporated in automated design frameworks to facilitate high-fidelity, fully coupled, large-scale simulations. The most tedious and time-consuming step in such simulations is the construction of a common geometry database that ensures geometry consistency at every step of the design iteration, is accessible to multi-disciplinary solvers and allows system-level analysis. This paper presents a novel design-intent-driven geometry modelling environment that is based on a top-down feature-based geometry model generation method. In the proposed object-oriented environment, each feature entity possesses a separate identity, denotes an abstract geometry, and carries a set of characteristics. These geometry features are organised in a turbomachinery feature taxonomy. The engine geometry is represented by a tree-like logical structure of geometry features, wherein abstract features outline the engine architecture, while the detailed geometry is defined by lower-level features. This top-down flexible arrangement of feature-tree enables the design intent to be preserved throughout the design process, allows the design to be modified freely and supports the design intent variations to be propagated throughout the geometry automatically. The application of the proposed feature-based geometry modelling environment is demonstrated by generating a whole-engine computational geometry. This geometry modelling environment provides an efficient means of rapidly populating complex turbomachinery assemblies. The generated engine geometry is fully scalable, easily modifiable and is re-usable for generating the geometry models of new engines or their derivatives. This capability also enables fast multi-fidelity simulation and optimisation of various gas turbine systems.

Constructing and Utilizing Video Ontology for Accurate and Fast Retrieval

2011 ◽  
Vol 2 (4) ◽  
pp. 59-75 ◽  
Author(s):  
Kimiaki Shirahama ◽  
Kuniaki Uehara
Keyword(s):  
Knowledge Base ◽  
Large Scale ◽  
Video Retrieval ◽  
Computational Cost ◽  
Semantic Content ◽  
Video Data ◽  
Experimental Results ◽  
Huge Number ◽  
Dempster Shafer Theory ◽  
Shafer Theory

This paper examines video retrieval based on Query-By-Example (QBE) approach, where shots relevant to a query are retrieved from large-scale video data based on their similarity to example shots. This involves two crucial problems: The first is that similarity in features does not necessarily imply similarity in semantic content. The second problem is an expensive computational cost to compute the similarity of a huge number of shots to example shots. The authors have developed a method that can filter a large number of shots irrelevant to a query, based on a video ontology that is knowledge base about concepts displayed in a shot. The method utilizes various concept relationships (e.g., generalization/specialization, sibling, part-of, and co-occurrence) defined in the video ontology. In addition, although the video ontology assumes that shots are accurately annotated with concepts, accurate annotation is difficult due to the diversity of forms and appearances of the concepts. Dempster-Shafer theory is used to account the uncertainty in determining the relevance of a shot based on inaccurate annotation of this shot. Experimental results on TRECVID 2009 video data validate the effectiveness of the method.

Predicting Lexical Answer Types in Open Domain QA

2012 ◽  
Vol 8 (3) ◽  
pp. 74-88 ◽  
Author(s):  
Alfio Massimiliano Gliozzo ◽  
Aditya Kalyanpur
Keyword(s):  
Knowledge Acquisition ◽  
Knowledge Base ◽  
Large Scale ◽  
Question Answering ◽  
General Purpose ◽  
Open Domain ◽  
Lexical Knowledge ◽  
Research Challenge ◽  
Lexical Knowledge Base

Automatic open-domain Question Answering has been a long standing research challenge in the AI community. IBM Research undertook this challenge with the design of the DeepQA architecture and the implementation of Watson. This paper addresses a specific subtask of Deep QA, consisting of predicting the Lexical Answer Type (LAT) of a question. Our approach is completely unsupervised and is based on PRISMATIC, a large-scale lexical knowledge base automatically extracted from a Web corpus. Experiments on the Jeopardy! data shows that it is possible to correctly predict the LAT in a substantial number of questions. This approach can be used for general purpose knowledge acquisition tasks such as frame induction from text.

COMBINING DEFAULT LOGIC DATABASES

1994 ◽  
Vol 03 (03) ◽  
pp. 319-348 ◽  
Author(s):  
CHITTA BARAL ◽  
SARIT KRAUS ◽  
JACK MINKER ◽  
V. S. SUBRAHMANIAN
Keyword(s):  
Knowledge Representation ◽  
Knowledge Base ◽  
Large Scale ◽  
Future Generation ◽  
Knowledge Bases ◽  
Default Logic ◽  
Integrity Constraints ◽  
Specialized Knowledge ◽  
The Past ◽  
The Future

During the past decade, it has become increasingly clear that the future generation of large-scale knowledge bases will consist, not of one single isolated knowledge base, but a multiplicity of specialized knowledge bases that contain knowledge about different domains of expertise. These knowledge bases will work cooperatively, pooling together their varied bodies of knowledge, so as to be able to solve complex problems that no single knowledge base, by itself, would have been able to address successfully. In any such situation, inconsistencies are bound to arise. In this paper, we address the question: "Suppose we have a set of knowledge bases, KB1, …, KBn, each of which uses default logic as the formalism for knowledge representation, and a set of integrity constraints IC. What knowledge base constitutes an acceptable combination of KB1, …, KBn?"

Workflows Científicos com Apoio de Bases de Conhecimento em Tempo Real

2020 ◽  
Author(s):  
Victor S. Bursztyn ◽  
Jonas Dias ◽  
Marta Mattoso
Keyword(s):  
Knowledge Base ◽  
Domain Knowledge ◽  
Large Scale ◽  
Workflow Engine ◽  
Workflow Execution ◽  
Human In The Loop ◽  
Domain Specific ◽  
Political Sciences ◽  
Provenance Data ◽  
Domain Specific Knowledge

One major challenge in large-scale experiments is the analytical capacity to contrast ongoing results with domain knowledge. We approach this challenge by constructing a domain-specific knowledge base, which is queried during workflow execution. We introduce K-Chiron, an integrated solution that combines a state-of-the-art automatic knowledge base construction (KBC) system to Chiron, a well-established workflow engine. In this work we experiment in the context of Political Sciences to show how KBC may be used to improve human-in-the-loop (HIL) support in scientific experiments. While HIL in traditional domain expert supervision is done offline, in K-Chiron it is done online, i.e. at runtime. We achieve results in less laborious ways, to the point of enabling a breed of experiments that could be unfeasible with traditional HIL. Finally, we show how provenance data could be leveraged with KBC to enable further experimentation in more dynamic settings.

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