Stay updated with our latest findings, methods explored, challenges overcome, and concepts learned during the project lifecycle. We'll share insights into applying machine learning to rice genomics.
ML Model Study & Basic Yield Prediction Pipeline
Update: Q4 2025
We studied several advanced machine learning models suited for genomic data and implemented an initial analysis pipeline for yield prediction as a baseline.... Our review included promising architectures like Nucleonet, AgroNet, and the Nucleotide Transformer, evaluating their potential applicability. Concurrently, we built a basic pipeline incorporating SNP/phenotype data preparation, preprocessing, cleaning, Principal Component Analysis (PCA) for dimensionality reduction, and applied Ordinary Least Squares (OLS) regression as a foundational step for predicting yield.
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Field Insights & Expert Consultation
Update: Q4 2025
Gained valuable practical insights through a field visit to Padma Shri awardee Sh Sathyanarayana Beleri and discussed genomic selection methods with IRRI India expert... Mr. Krishna T Sundaram. The visit to Sh Beleri in Kasaragod provided a grounding perspective on rice cultivation and conservation practices. The interactive session with Mr. Sundaram from the International Rice Research Institute India delved into crucial details regarding advanced genomic selection techniques and specific data analysis approaches relevant to our project goals, helping refine our strategy.
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Developing Our Analysis Pipeline & Exploring Genomic Tools
Update: Q4 2025
Work commenced with reading several related research papers and structuring a Python-based analysis pipeline and exploring key genomic ... research techniques required for the project's complex data. This involved designing the preliminary workflow stages for handling SNP and phenotype data, and investigating essential tools and methods including various data imputation techniques, linkage disequilibrium (LD) analysis strategies, and the implementation specifics of techniques like imputation to ensure robust analysis.
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Attended 2 Workshops
Posted on: 2025-02-01
The project recently facilitated two significant national workshops. The first..., a 7-day intensive on JAMOVI (January 19-25, 2025), covered fundamental data handling, hypothesis testing, correlation, regression, and various statistical tests. Following this, a second workshop (January 28 - February 1, 2025) focused on Experimental Designs using R/JAMOVI/SPSS, encompassing R basics, common experimental designs (CRD, RBD, Split-Plot), ANOVA, and graphical representation of results, including a case study. Our Project Associate, Saumya Dwivedi, attended both workshops, instructed by Dr. D S Dhakre of Statistical Point, gaining valuable skills for analyzing project data.
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