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Benchmarking natural-language parsers for biological applications using dependency graphs

Andrew B Clegg, Adrian J Shepherd
2007 BMC Bioinformatics  
Conclusion: Evaluating using dependency graphs allows parsers to be tested easily on criteria chosen according to the semantics of particular biological applications, drawing attention to important mistakes  ...  Interest is growing in the application of syntactic parsers to natural language processing problems in biology, but assessing their performance is difficult because differences in linguistic convention  ...  Acknowledgements This work was funded by the Biotechnology and Biological Sciences Research Council and AstraZeneca PLC.  ... 
doi:10.1186/1471-2105-8-24 pmid:17254351 pmcid:PMC1797812 fatcat:xdmpnmc4hndyzdmofaiyoe3fke

An overview of graph databases and their applications in the biomedical domain

Santiago Timón-Reina, Mariano Rincón, Rafael Martínez-Tomás
2021 Database: The Journal of Biological Databases and Curation  
Because of the interconnected nature of its data, the biomedical domain has been one of the early adopters of graph databases, enabling more natural representation models and better data integration workflows  ...  In this work, we survey the literature to explore the evolution, performance and how the most recent graph database solutions are applied in the biomedical domain, compiling a great variety of use cases  ...  Biological knowledge graphs While there exist multiple definitions of Knowledge Graphs (KGs) that depend on the application context (115) , we can define them as large, heterogeneous knowledgebases modeled  ... 
doi:10.1093/database/baab026 pmid:34003247 pmcid:PMC8130509 fatcat:xku5npedwzgs3ayzsuvz6iattq

GraphBreak: Tool for Network Community based Regulatory Medicine, Gene co-expression, Linkage Disequilibrium analysis, functional annotation and more [article]

Abhishek Narain Singh
2021 arXiv   pre-print
Graph-Break showed critical use case value in its downstream analysis for disease association of communities detected.  ...  For this, we present GraphBreak, a suite of tools for community detection application, such as for gene co-expression, protein interaction, regulation network, etc.Although developed for use case of eQTLs  ...  Acknowledgement The author acknowledges the makers of CONDOR as inspiration to develop and deploy graph network-based algorithms for biological purposes.  ... 
arXiv:2103.06145v1 fatcat:sd52dd2vrzhptodb6hf4zijubq

Proofs and pedagogy; science and systems: The grammar tool box

Adrian Johnstone, Elizabeth Scott
2007 Science of Computer Programming  
In this paper we focus on the overall rationale for the GTB framework; the GTB design goals; and some detailed operational flows that are supported by GTB.  ...  way that allows meaningful comparisons between them in a repeatable and easily accessible fashion whilst also allowing: (i) new theoretical ideas to be generated and explored; (ii) production quality parsers  ...  so general algorithms with quadratic or even cubic complexity may, with time, become attractive; (ii) new applications arise in non-synthetic languages (in particular in natural languages and biological  ... 
doi:10.1016/j.scico.2007.01.016 fatcat:ikkpsqqonrgz7nl7sfk3prot6u


Sofie Van Landeghem, Bernard De Baets, Yves Van de Peer, Yvan Saeys
2011 Computational intelligence  
All predictions are merged into an integrated network, useful for visualization and for deduction of new biological knowledge.  ...  Employing type-specific classifiers, this framework processes research articles to extract various biological events.  ...  Both formats have been widely used in the field of Natural Language Processing (NLP) and in BioNLP in particular.  ... 
doi:10.1111/j.1467-8640.2011.00403.x fatcat:wmvblcmuvbaznjivph2by27ebm

CPTAM: Constituency Parse Tree Aggregation Method [article]

Adithya Kulkarni, Nasim Sabetpour, Alexey Markin, Oliver Eulenstein, Qi Li
2022 arXiv   pre-print
Extensive experiments are conducted on benchmark datasets in different languages and domains.  ...  Diverse Natural Language Processing tasks employ constituency parsing to understand the syntactic structure of a sentence according to a phrase structure grammar.  ...  Government is authorized to reproduce and distribute reprints for Government purposes, notwithstanding any copyright notation hereon.  ... 
arXiv:2201.07905v1 fatcat:tnzepapil5gcfmndk2aqsggh3q

AffectiveSpace 2: Enabling Affective Intuition for Concept-Level Sentiment Analysis

Erik Cambria, Jie Fu, Federica Bisio, Soujanya Poria
AffectiveSpace 2 is a vector space model, built by means of random projection, that allows for reasoning by analogy on natural language con- cepts.  ...  Predicting the affective valence of unknown multi-word expressions is key for concept-level sentiment analysis.  ...  associated with natural language opinions.  ... 
doi:10.1609/aaai.v29i1.9230 fatcat:d2dum5tsl5bf5och4a5h2xgo7e

A logic-based relational learning approach to relation extraction: The OntoILPER system

Rinaldo Lima, Bernard Espinasse, Fred Freitas
2019 Engineering applications of artificial intelligence  
Moreover, OntoILPER uses a domain ontology that guides the background knowledge generation process and is used for storing the extracted relation instances.  ...  In this work, we present OntoILPER, a logic-based relational learning approach to Relation Extraction that uses Inductive Logic Programming for generating extraction models in the form of symbolic extraction  ...  Acknowledgment The authors would like to thank Hilario Oliveira for helping us in the implementation of the Text Preprocessing and BK Generation modules, and the National Council for Scientific and Technological  ... 
doi:10.1016/j.engappai.2018.11.001 fatcat:zbhchesxxfb5zgqsq3qexdwlkm

chemf: A purely functional chemistry toolkit

Stefan Höck, Rainer Riedl
2012 Journal of Cheminformatics  
We present our initial results with functional programming in chemistry by first describing an immutable data structure for molecular graphs together with a couple of simple algorithms to calculate basic  ...  The data structures and algorithms presented in this article perform well while at the same time they can be safely used in parallelized applications, such as computer aided drug design experiments, without  ...  Acknowledgements This project was financially supported by the ZHAW (Development of a cheminformatics toolkit as a basis for other chemistry-related software).  ... 
doi:10.1186/1758-2946-4-38 pmid:23253942 pmcid:PMC3660204 fatcat:dx3igceog5hc7pdj7wjgcautcm

A review of genomic data warehousing systems

T. Triplet, G. Butler
2013 Briefings in Bioinformatics  
Each aspect of the benchmark may be dynamically weighted by scientists using our online tool BenchDW ( to build custom warehouse profiles and tailor  ...  T.T. and G.B. designed the benchmark and the study. T.T. configured the data warehouses, performed the experiments, wrote the code for BenchDW, analyzed the data and prepared the manuscript.  ...  BioMart team, Junjun Zhang who initially developed BioXRT and now a member of the BioMart group, Richard Smith from the InterMine team, and Mario Latendresse and Peter Karp from the PathwayTools team for  ... 
doi:10.1093/bib/bbt031 pmid:23673292 fatcat:gfkpuosdz5d5fohew5xnwpfofi

Approximate Subgraph Matching-Based Literature Mining for Biomedical Events and Relations

Haibin Liu, Lawrence Hunter, Vlado Kešelj, Karin Verspoor, Neil R. Smalheiser
2013 PLoS ONE  
Extraction of such knowledge is performed by searching for an approximate subgraph isomorphism between key contextual dependencies and input sentence graphs.  ...  In this paper, we propose a novel approach for mining relations and events in the biomedical literature using approximate subgraph matching.  ...  John Wilbur for providing valuable feedback to the manuscript. This research was supported in part by the Intramural Research Program of the NIH, NLM.  ... 
doi:10.1371/journal.pone.0060954 pmid:23613763 pmcid:PMC3629260 fatcat:jpzkx4fxrneonkoivop7krlima

SAIBench: Benchmarking AI for Science

Yatao Li, Jianfeng Zhan
2022 BenchCouncil Transactions on Benchmarks, Standards and Evaluations  
We formalize the problem of scientific AI benchmarking, and propose a system called SAIBench in the hope of unifying the efforts and enabling low-friction on-boarding of new disciplines.  ...  The system approaches this goal with SAIL, a domain-specific language to decouple research problems, AI models, ranking criteria, and software/hardware configuration into reusable modules.  ...  The parser then analyzes the computation graph and synthesizes actual benchmarking code.  ... 
doi:10.1016/j.tbench.2022.100063 fatcat:akn3lnoux5gmriih7comxnkr5u

NegBio: a high-performance tool for negation and uncertainty detection in radiology reports [article]

Yifan Peng and Xiaosong Wang and Le Lu and Mohammadhadi Bagheri and Ronald Summers and Zhiyong Lu
2017 arXiv   pre-print
We evaluated NegBio on four datasets, including two public benchmarking corpora of radiology reports, a new radiology corpus that we annotated for this work, and a public corpus of general clinical texts  ...  Evaluation on these datasets demonstrates that NegBio is highly accurate for detecting negative and uncertain findings and compares favorably to a widely-used state-of-the-art system NegEx (an average  ...  Dina Demner-Fushman and Willie J Rogers for the helpful discussion, and the NIH Fellows Editorial Board for their editorial comments.  ... 
arXiv:1712.05898v2 fatcat:xialqsgjijh3feavujcarcnrde

Automatic extraction of protein-protein interactions using grammatical relationship graph

Kaixian Yu, Pei-Yau Lung, Tingting Zhao, Peixiang Zhao, Yan-Yuan Tseng, Jinfeng Zhang
2018 BMC Medical Informatics and Decision Making  
In this study, we developed a novel approach to extract bio-entity relationships information using Nature Language Processing (NLP) and a graph-theoretic algorithm.  ...  We first use a sentence parsing tool to obtain the sentence structure represented as a dependency graph where words are nodes and edges are typed dependencies.  ...  Abbreviations GRGT: Grammatical Relationship Graph for Triplets; NLP: Natural language processing; PICAD: Protein interaction corpus with annotated directions; PPI: Protein-protein interaction Acknowledgements  ... 
doi:10.1186/s12911-018-0628-4 pmid:30066644 pmcid:PMC6069288 fatcat:d3pdfurmajaxdda6457c62mmmu

Property Graph vs RDF Triple Store: A Comparison on Glycan Substructure Search

Davide Alocci, Julien Mariethoz, Oliver Horlacher, Jerven T. Bolleman, Matthew P. Campbell, Frederique Lisacek, Manuela Helmer-Citterich
2015 PLoS ONE  
In this context, Graph databases are possible software solutions for storing glycan structures and Graph query languages, such as SPARQL and Cypher, can be used to perform a substructure search.  ...  Resource description framework (RDF) and Property Graph databases are emerging technologies that are used for storing graph-structured data.  ...  Hayes for fruitful discussions and valuable advice. Author Contributions  ... 
doi:10.1371/journal.pone.0144578 pmid:26656740 pmcid:PMC4684231 fatcat:owqgwxvrgbdy5nwqtpuvsjxpmm
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