Article
Biochemical Research Methods
Jiyu Chen, Nicholas Geard, Justin Zobel, Karin Verspoor
Summary: Two models built using our method achieved high precision for distinct annotation consistency identification tasks and were robust to updates in the GO vocabulary. Our approach demonstrates clear value for human-in-the-loop curation scenarios.
BMC BIOINFORMATICS
(2021)
Article
Computer Science, Information Systems
Lei Chai, Hailong Sun, Zizhe Wang
Summary: Crowdsourcing plays a vital role in the AI industry, but existing research primarily focuses on simple tasks like label classification, neglecting complex open-ended tasks like question answering and translation. This study introduces an error consistency-based approach for complex text annotation crowdsourcing tasks and demonstrates its effectiveness in inferring aggregated results from open-ended answers.
INFORMATION SCIENCES
(2022)
Article
Computer Science, Artificial Intelligence
Chunlin Xu, Hui Wang, Shengli Wu, Zhiwei Lin
Summary: In this paper, a novel LSTM structure, ARTree-LSTM, is proposed to handle general constituency trees. Based on this structure, a new network model called Tag Enhanced Dynamic Compositional Neural Network (TE-DCNN) is introduced for learning sentence representation. The TE-DCNN achieves state-of-the-art performance in text classification and text semantic matching tasks, demonstrating the effectiveness of incorporating syntactic tag information in sentence representation learning.
EXPERT SYSTEMS WITH APPLICATIONS
(2021)
Review
Genetics & Heredity
Kangmei Zhao, Seung Yon Rhee
Summary: Pathway enrichment analysis is crucial for interpreting omics datasets and generating hypotheses. This article discusses best practices for interpreting different types of omics data using pathway enrichment analysis and emphasizes the importance of considering intrinsic features of various types of omics data. The article also explains key components that influence the outcomes of pathway enrichment analysis and provides guidance on reporting methodological details to improve reproducibility. It aims to serve as a primer for biologists to utilize omics resources and encourage bioinformatics tool developers to enhance the power of pathway enrichment analysis.
TRENDS IN GENETICS
(2023)
Article
Physics, Multidisciplinary
Jingqiao Wu, Xiaoyue Feng, Renchu Guan, Yanchun Liang
Summary: Machine learning models can automatically discover biomedical research trends and promote the dissemination of information and knowledge. Two fusion algorithms, Tr-W2v and Ti-W2v, were proposed in this paper to improve text feature representation. Results show that the effectiveness of the fusion text representation models is better than the classical text representation model, with the Tr-W2v algorithm performing the best. Trend analyses of cancer research were conducted based on the Tr-W2v algorithm, providing valuable insights for doctors and biological researchers.
Review
Biochemical Research Methods
Jessica Andrea Carballido
Summary: This paper presents a series of steps to gain biological knowledge from microarray gene expression data. The core of the pipeline is a canonical multi-objective genetic algorithm, which selects a gene set based on differential expression and correlation between expression profiles. The methodology is exemplified using a leukemia benchmark dataset and successfully identifies a group of genes of interest.
CURRENT BIOINFORMATICS
(2022)
Article
Computer Science, Artificial Intelligence
Wenyan Guo, Qingtian Zeng, Hua Duan, Weijian Ni, Cong Liu
Summary: The study proposes a novel text similarity measure for Chinese emergency response plans by extracting process elements, generating response task vectors and response task set vectors to reflect the process semantics. Experimental results demonstrate that the proposed approach performs well in distinguishing topics and levels of emergency response plans.
EXPERT SYSTEMS WITH APPLICATIONS
(2021)
Article
Mathematics
Adrian-Gabriel Chifu, Sebastien Fournier
Summary: Subjectivity plays a crucial role in natural language understanding, particularly in user-generated text and conversational systems based on large language models. This study investigates the definition of sentence difficulty in aspect-based sentiment analysis and conducts experiments to assess and quantify the difficulty. The findings can be used to enhance the performance of aspect-based sentiment analysis.
Article
Engineering, Multidisciplinary
Seniz Demir, Berkay Topcu
Summary: This article presents a graph-based Turkish text normalizer that uses a context-tailoring approach to map non-standard words to their appropriate standard forms. The performance of the normalizer is evaluated on a tweet dataset, demonstrating its superiority over other publicly available normalizers. The evaluation analysis on multiple Turkish NLP tasks reveals that normalizing noisy texts before processing leads to remarkable performance improvements in this morphologically-rich language.
ENGINEERING SCIENCE AND TECHNOLOGY-AN INTERNATIONAL JOURNAL-JESTECH
(2022)
Article
Biochemical Research Methods
Chaoyu Zhu, Zhihao Yang, Xiaoqiong Xia, Nan Li, Fan Zhong, Lei Liu
Summary: This study focuses on developing Specific Disease Knowledge Graphs (SDKGs) and implementing multimodal reasoning to extract new reliable knowledge for specific disease fields. The construction of SDKG-11, a set including different diseases and cancers, aims to improve existing models and provide universal pre-trained knowledge. The research demonstrates the effectiveness of multimodal reasoning on all SDKGs through entity prediction tasks and validates the models' reliability in discovering new knowledge.
Article
Environmental Sciences
Yang Lan, Cheng Teng Ng, Choon Nam Ong, Liya E. Yu, Boon Huat Bay
Summary: This study investigated the effects of PM2.5 exposure on differentiated human small airway epithelial cells, highlighting the importance of using the advanced ALI model over submerged cultures. Transcriptomic analysis revealed changes in multiple signaling pathways involved in inflammation and apoptosis, suggesting that reduction of ambient PM2.5 concentrations could have a protective effect on respiratory health in humans.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2021)
Article
Biochemistry & Molecular Biology
Brad T. Sherman, Ming Hao, Ju Qiu, Xiaoli Jiao, Michael W. Baseler, H. Clifford Lane, Tomozumi Imamichi, Weizhong Chang
Summary: DAVID, a popular bioinformatics resource system, has undergone updates in 2021, including the rebuilding of the DAVID Gene system, increasing the number of gene-term records for annotation types, adding new annotations, assigning specific subgroups, and adding a species parameter for improved user experience.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Computer Science, Information Systems
Muhammad Aasim Qureshi, Muhammad Asif, Mohd Fadzil Hassan, Ghulam Mustafa, Muhammad Khurram Ehsan, Aasim Ali, Unaza Sajid
Summary: This study proposes a fully automated annotation technique for aspect level sentiment analysis and validates it using a dataset of YouTube comments. The results show that the proposed technique achieves annotation quality comparable to manual annotation, while requiring significantly less computational cost.
CMC-COMPUTERS MATERIALS & CONTINUA
(2022)
Article
Computer Science, Artificial Intelligence
Viet Bach Nguyen, Vojtech Svatek
Summary: This paper focuses on concept modeling through code lists embedded in ontologies and vocabularies. The authors propose an approach using SPARQL queries and a lightweight web application to detect and extract potential code lists, and store them in a knowledge base.
JOURNAL OF WEB SEMANTICS
(2023)
Article
Biochemistry & Molecular Biology
Xuanjin Cheng, Junran Yan, Yongxing Liu, Jiahe Wang, Stefan Taubert
Summary: Transcriptome profiling is crucial for gene regulation studies, but current tools have limitations. eVITTA addresses these limitations by providing modular analysis and visualization options, allowing customized comparisons across multiple datasets and exploration of data stored in NCBI GEO.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Oncology
Tim D. D. Somerville, Daniel H. Wiseman, Gary J. Spencer, Xu Huang, James T. Lynch, Hui Sun Leong, Emma L. Williams, Edmund Cheesman, Tim C. P. Somervaille
Article
Oncology
Dominic G. Rothwell, Nigel Smith, Daniel Morris, Hui Sun Leong, Yaoyong Li, Antoine Hollebecque, Mahmood Ayub, Louise Carter, Jenny Antonello, Lynsey Franklin, Crispin Miller, Fiona Blackhall, Caroline Dive, Ged Brady
MOLECULAR ONCOLOGY
(2016)
Correction
Biochemistry & Molecular Biology
Christopher J. Tape, Stephanie Ling, Maria Dimitriadi, Kelly M. McMahon, Jonathan D. Worboys, Hui Sun Leong, Ida C. Norrie, Crispin J. Miller, George Poulogiannis, Douglas A. Lauffenburger, Claus Jorgensen
Article
Biochemistry & Molecular Biology
Louise Carter, Dominic G. Rothwell, Barbara Mesquita, Christopher Smowton, Hui Sun Leong, Fabiola Fernandez-Gutierrez, Yaoyong Li, Deborah J. Burt, Jenny Antonello, Christopher J. Morrow, Cassandra L. Hodgkinson, Karen Morris, Lynsey Priest, Mathew Carter, Crispin Miller, Andrew Hughes, Fiona Blackhall, Caroline Dive, Ged Brady
Article
Multidisciplinary Sciences
Stuart C. Williamson, Robert L. Metcalf, Francesca Trapani, Sumitra Mohan, Jenny Antonello, Benjamin Abbott, Hui Sun Leong, Christopher P. E. Chester, Nicole Simms, Radoslaw Polanski, Daisuke Nonaka, Lynsey Priest, Alberto Fusi, Fredrika Carlsson, Anders Carlsson, Mary J. C. Hendrix, Richard E. B. Seftor, Elisabeth A. Seftor, Dominic G. Rothwell, Andrew Hughes, James Hicks, Crispin Miller, Peter Kuhn, Ged Brady, Kathryn L. Simpson, Fiona H. Blackhall, Caroline Dive
NATURE COMMUNICATIONS
(2016)
Article
Multidisciplinary Sciences
Srivatsava Naidu, Lei Shi, Peter Magee, Justin D. Middleton, Alessandro Lagana, Sudhakar Sahoo, Hui Sun Leong, Melanie Galvin, Kristopher Frese, Caroline Dive, Vincenza Guzzardo, Matteo Fassan, Michela Garofalo
SCIENTIFIC REPORTS
(2017)
Article
Cell Biology
Lei Shi, Justin Middleton, Young-Jun Jeon, Peter Magee, Dario Veneziano, Alessandro Lagana, Hui-Sun Leong, Sudhakar Sahoo, Matteo Fassan, Richard Booton, Rajesh Shah, Philip A. J. Crosbie, Michela Garofalo
CELL DEATH & DISEASE
(2018)
Article
Genetics & Heredity
Pedro Torres-Ayuso, Sudhakar Sahoo, Garry Ashton, Elvira An, Nicole Simms, Melanie Galvin, Hui Sun Leong, Kristopher K. Frese, Kathryn Simpson, Natalie Cook, Andrew Hughes, Crispin J. Miller, Richard Marais, Caroline Dive, Matthew G. Krebs, John Brognard
NPJ GENOMIC MEDICINE
(2018)
Article
Oncology
J. S. Hall, H. S. Leong, L. S. C. Armenoult, G. E. Newton, H. R. Valentine, J. J. Irlam, C. Moeller-Levet, K. A. Sikand, S. D. Pepper, C. J. Miller, C. M. L. West
BRITISH JOURNAL OF CANCER
(2011)
Article
Oncology
Martin G. McCabe, L. Magnus Baecklund, Hui Sun Leong, Koichi Ichimura, V. Peter Collins
Article
Multidisciplinary Sciences
Hui Sun Leong, Keren Dawson, Chris Wirth, Yaoyong Li, Yvonne Connolly, Duncan L. Smith, Caroline R. M. Wilkinson, Crispin J. Miller
NATURE COMMUNICATIONS
(2014)
Article
Oncology
Sumitra Mohan, Victoria Foy, Mahmood Ayub, Hui Sun Leong, Pieta Schofield, Sudhakar Sahoo, Tine Descamps, Bedirhan Kilerci, Nigel K. Smith, Mathew Carter, Lynsey Priest, Cong Zhou, T. Hedley Carr, Crispin Miller, Corinne Faivre-Finn, Fiona Blackhall, Dominic G. Rothwell, Caroline Dive, Gerard Brady
JOURNAL OF THORACIC ONCOLOGY
(2020)
Article
Oncology
Gauri Deb, Bettina Wingelhofer, Fabio M. R. Amaral, Alba Maiques-Diaz, John A. Chadwick, Gary J. Spencer, Emma L. Williams, Hui-Sun Leong, Tamara Maes, Tim C. P. Somervaille
Article
Multidisciplinary Sciences
Sumitra Mohan, Mahmood Ayub, Dominic G. Rothwell, Sakshi Gulati, Bedirhan Kilerci, Antoine Hollebecque, Hui Sun Leong, Nigel K. Smith, Sudhakar Sahoo, Tine Descamps, Cong Zhou, Richard A. Hubner, Mairead G. McNamara, Angela Lamarca, Juan W. Valle, Caroline Dive, Ged Brady
SCIENTIFIC REPORTS
(2019)
Article
Hematology
Julia E. Draper, Patrycja Sroczynska, Hui Sun Leong, Muhammad Z. H. Fadlullah, Crispin Miller, Valerie Kouskoff, Georges Lacaud