Day #179 - Machine learning in plant breeding - Alencar Xavier's PhD defense - Already Startups are their in this Area :) - Good One Liked it

Key Summary

• ML - Part of AI for pattern recognition for problem solving, Prediction, Classification and sometimes inference
• Heritability using the animal model

ML in Plant Breeding

• Intelligent Decision making
• Maximize productivity, Minimize losses
• Plant breeding is about resource allocation 

ML Use cases (Very Interesting)

• Yields
• Select Target environments (Plants behave similarly)
• Genomic-based prediction
• Soil Classification

Dataset

• SoyNam
• Agronomic traits

Feature Variables (So many variables we can collect from a plant :), Awesome and Amazing )

• Yield Days
• Days to Flowering
• Days to maturity
• Length of Reproductive period
• Lodging Score (Scale 1 to 5)
• Average Canopy Closure (From Pictures)
• Rate of Canopy Closure
• Leaflet Shape
• Node and Pod Number in the main stem
• Pods per node
• Internal Length - Height / Number of Nodes

Analytics Steps

• Check for Multicollinearity
• Genomic relationship matrix

Unsupervised ML Use Case

• Cluster among traits
• Genetics / Interaction based
• Pearson correlation
• Phenotypic correlation
• Conditional independence (Markov random fields)
• Finding the connected traits
• Genetic and Environmental Correlations map

Patterns Identified

PCA Approach

• Reduction of Dimensionality
• Eigenvectors of matrix
• Similar story in PCA

Supervised ML (Prediction)

• Adjust Phenotypes
• Kriging
• Genotyping Density (Posterior distribution)

Related Paper #1 - 
From paper - Soil Data Analysis Using Classification Techniques and Soil Attribute Prediction

Key Soil Traits

Regression Use case - Predicting - Phosphorous attribute on least number of attributes.

Related Paper #2 - From paper A real-time phenotyping framework using machine learning for plant stress severity rating in soybean

Use cases - Image to identify Plant Rating, the Classification problem

The Image Processing Key Tasks

• From the images extract white balance and color calibration, Hue Values
• Segmentation RGB, background removal
• Noise and outlier removal

Related Paper #3 - DeepWheat: Estimating Phenotypic Traits from Crop Images with Deep Learning (DeepWheat_Estimating_Phenotypic_Traits_From_Images.pdf)

• Phenotypic - observable characteristics - made manually in the field
• Aerial images as a basis for biomass estimation
• Above-ground biomass (AGB)
• Emergence count and biomass estimation frameworks using CNN
• Randomized minimal region swapping (RMRS) algorithm for Biomass Estimation

Key Steps

• Extract all the segmented patches from the whole image 
• Input each patch image to the counting module to get the individual emergence counts for each patch
• Predicted counts for a single plot image

Good CNN Summarization - a simple stack of convolutional layers with an over-complete set of filters followed by nonlinearity and pooling serve well when the underlying concepts to be learned via abstract representation are linearly separable

Paper - A Robust Deep-Learning-Based Detector for Real-Time Tomato Plant Diseases and Pests Recognition

• Our goal is to find the more suitable deep-learning architecture for our task
• Handcrafted feature methods are the Histogram of Oriented Gradients (HOG), Scale-Invariant Feature Transform (SIFT), which are usually combined with classifiers such as Adaptive Boosting (AdaBoost)  or Support Vector Machines (SVM)

Patterns Detection

• Infection status
• Location of the symptom
• Patterns of the leaf
• Type of fungus
• Color and Shape

My Thoughts - This post has provided fundamentals on areas worked upon on Agri Startups.

• Data Collection and infrastructure is key
• Feature Variables are from Soil traits, Plant Traits, Weather Data
• The Analysis of collected data for different periods/years would provide qualitative information to predict / forecast / recommend
• Quality Assessment can also be predicted based on the trends

More Reads
Connected Components Labeling
Orange & Brown
Google Citation - Alencar Xavier



Happy Mastering DL!!!