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Leiva-Araos, Andres

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Leiva-Araos

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  • Publication
    Leveraging LLMs for Efficient Topic Reviews
    (2024) Gana, Bady; Leiva-Araos, Andres; Allende-Cid, Héctor; García, José
    This paper presents the topic review (TR), a novel semi-automatic framework designed to enhance the efficiency and accuracy of literature reviews. By leveraging the capabilities of large language models (LLMs), TR addresses the inefficiencies and error-proneness of traditional review methods, especially in rapidly evolving fields. The framework significantly improves literature review processes by integrating advanced text mining and machine learning techniques. Through a case study approach, TR offers a step-by-step methodology that begins with query generation and refinement, followed by semi-automated text mining to identify relevant articles. LLMs are then employed to extract and categorize key themes and concepts, facilitating an in-depth literature analysis. This approach demonstrates the transformative potential of natural language processing in literature reviews. With an average similarity of 69.56% between generated and indexed keywords, TR effectively manages the growing volume of scientific publications, providing researchers with robust strategies for complex text synthesis and advancing knowledge in various domains. An expert analysis highlights a positive Fleiss’ Kappa score, underscoring the significance and interpretability of the results.
  • Publication
    Transcriptome Data Analysis Applied to Grapevine Growth Stage Identification
    (2024) Altimiras, Francisco; Pavéz, Leonardo; Pourreza, Alireza; Yañez, Osvaldo; González-Rodríguez, Lisdelys; García, José; Galaz, Claudio; Leiva-Araos, Andres; Allende-Cid, Héctor
    In agricultural production, it is fundamental to characterize the phenological stage of plants to ensure a good evaluation of the development, growth and health of crops. Phenological characterization allows for the early detection of nutritional deficiencies in plants that diminish the growth and productive yield and drastically affect the quality of their fruits. Currently, the phenological estimation of development in grapevine (Vitis vinifera) is carried out using four different schemes: Baillod and Baggiolini, Extended BBCH, Eichhorn and Lorenz, and Modified E-L. Phenological estimation requires the exhaustive evaluation of crops, which makes it intensive in terms of labor, personnel, and the time required for its application. In this work, we propose a new phenological classification based on transcriptional measures of certain genes to accurately estimate the stage of development of grapevine. There are several genomic information databases for Vitis vinifera, and the function of thousands of their genes has been widely characterized. The application of advanced molecular biology, including the massive parallel sequencing of RNA (RNA-seq), and the handling of large volumes of data provide state-of-the-art tools for the determination of phenological stages, on a global scale, of the molecular functions and processes of plants. With this aim, we applied a bioinformatic pipeline for the high-throughput quantification of RNA-seq datasets and further analysis of gene ontology terms. We identified differentially expressed genes in several datasets, and then, we associated them with the corresponding phenological stage of development. Differentially expressed genes were classified using count-based expression analysis and clustering and annotated using gene ontology data. This work contributes to the use of transcriptome data and gene expression analysis for the classification of development in plants, with a wide range of industrial applications in agriculture.