arXiv subjects

Lizhi Wang

Publications and source records attributed to Lizhi Wang.

47 records · Page 3Linked to original sources

arXiv2021

A reinforcement learning approach to resource allocation in genomic selection

Genomic selection (GS) is a technique that plant breeders use to select individuals to mate and produce new generations of species. Allocation of resources is a key factor in GS. At each selection cycle, breeders are facing the choice of budget allocation to make crosses and produce the next generation of breeding parents. Inspired by recent advances in reinforcement learning for AI problems, we develop a reinforcement learning-based algorithm to automatically learn to allocate limited resources across different generations of breeding. We mathematically formulate the problem in the framework of Markov Decision Process (MDP) by defining state and action spaces. To avoid the explosion of the state space, an integer linear program is proposed that quantifies the trade-off between resources and time. Finally, we propose a value function approximation method to estimate the action-value function and then develop a greedy policy improvement technique to find the optimal resources. We demonstrate the effectiveness of the proposed method in enhancing genetic gain using a case study with realistic data.

q-bio.GN↗

arXiv2021

Simultaneous Corn and Soybean Yield Prediction from Remote Sensing Data Using Deep Transfer Learning

Large-scale crop yield estimation is, in part, made possible due to the availability of remote sensing data allowing for the continuous monitoring of crops throughout their growth cycle. Having this information allows stakeholders the ability to make real-time decisions to maximize yield potential. Although various models exist that predict yield from remote sensing data, there currently does not exist an approach that can estimate yield for multiple crops simultaneously, and thus leads to more accurate predictions. A model that predicts the yield of multiple crops and concurrently considers the interaction between multiple crop yields. We propose a new convolutional neural network model called YieldNet which utilizes a novel deep learning framework that uses transfer learning between corn and soybean yield predictions by sharing the weights of the backbone feature extractor. Additionally, to consider the multi-target response variable, we propose a new loss function. We conduct our experiment using data from 1,132 counties for corn and 1,076 counties for soybean across the United States. Numerical results demonstrate that our proposed method accurately predicts corn and soybean yield from one to four months before the harvest with a MAE being 8.74% and 8.70% of the average yield, respectively, and is competitive to other state-of-the-art approaches.

cs.CV↗

arXiv2021

WheatNet: A Lightweight Convolutional Neural Network for High-throughput Image-based Wheat Head Detection and Counting

For a globally recognized planting breeding organization, manually-recorded field observation data is crucial for plant breeding decision making. However, certain phenotypic traits such as plant color, height, kernel counts, etc. can only be collected during a specific time-window of a crop's growth cycle. Due to labor-intensive requirements, only a small subset of possible field observations are recorded each season. To help mitigate this data collection bottleneck in wheat breeding, we propose a novel deep learning framework to accurately and efficiently count wheat heads to aid in the gathering of real-time data for decision making. We call our model WheatNet and show that our approach is robust and accurate for a wide range of environmental conditions of the wheat field. WheatNet uses a truncated MobileNetV2 as a lightweight backbone feature extractor which merges feature maps with different scales to counter image scale variations. Then, extracted multi-scale features go to two parallel sub-networks for simultaneous density-based counting and localization tasks. Our proposed method achieves an MAE and RMSE of 3.85 and 5.19 in our wheat head counting task, respectively, while having significantly fewer parameters when compared to other state-of-the-art methods. Our experiments and comparisons with other state-of-the-art methods demonstrate the superiority and effectiveness of our proposed method.

cs.CV↗

arXiv2021

DeepCorn: A Semi-Supervised Deep Learning Method for High-Throughput Image-Based Corn Kernel Counting and Yield Estimation

The success of modern farming and plant breeding relies on accurate and efficient collection of data. For a commercial organization that manages large amounts of crops, collecting accurate and consistent data is a bottleneck. Due to limited time and labor, accurately phenotyping crops to record color, head count, height, weight, etc. is severely limited. However, this information, combined with other genetic and environmental factors, is vital for developing new superior crop species that help feed the world's growing population. Recent advances in machine learning, in particular deep learning, have shown promise in mitigating this bottleneck. In this paper, we propose a novel deep learning method for counting on-ear corn kernels in-field to aid in the gathering of real-time data and, ultimately, to improve decision making to maximize yield. We name this approach DeepCorn, and show that this framework is robust under various conditions. DeepCorn estimates the density of corn kernels in an image of corn ears and predicts the number of kernels based on the estimated density map. DeepCorn uses a truncated VGG-16 as a backbone for feature extraction and merges feature maps from multiple scales of the network to make it robust against image scale variations. We also adopt a semi-supervised learning approach to further improve the performance of our proposed method. Our proposed method achieves the MAE and RMSE of 41.36 and 60.27 in the corn kernel counting task, respectively. Our experimental results demonstrate the superiority and effectiveness of our proposed method compared to other state-of-the-art methods.

cs.CV↗

arXiv2021

Snapshot Hyperspectral Imaging Based on Weighted High-order Singular Value Regularization

Snapshot hyperspectral imaging can capture the 3D hyperspectral image (HSI) with a single 2D measurement and has attracted increasing attention recently. Recovering the underlying HSI from the compressive measurement is an ill-posed problem and exploiting the image prior is essential for solving this ill-posed problem. However, existing reconstruction methods always start from modeling image prior with the 1D vector or 2D matrix and cannot fully exploit the structurally spectral-spatial nature in 3D HSI, thus leading to a poor fidelity. In this paper, we propose an effective high-order tensor optimization based method to boost the reconstruction fidelity for snapshot hyperspectral imaging. We first build high-order tensors by exploiting the spatial-spectral correlation in HSI. Then, we propose a weight high-order singular value regularization (WHOSVR) based low-rank tensor recovery model to characterize the structure prior of HSI. By integrating the structure prior in WHOSVR with the system imaging process, we develop an optimization framework for HSI reconstruction, which is finally solved via the alternating minimization algorithm. Extensive experiments implemented on two representative systems demonstrate that our method outperforms state-of-the-art methods.

eess.IV↗

arXiv2020

High-Throughput Image-Based Plant Stand Count Estimation Using Convolutional Neural Networks

The future landscape of modern farming and plant breeding is rapidly changing due to the complex needs of our society. The explosion of collectable data has started a revolution in agriculture to the point where innovation must occur. To a commercial organization, the accurate and efficient collection of information is necessary to ensure that optimal decisions are made at key points of the breeding cycle. However, due to the shear size of a breeding program and current resource limitations, the ability to collect precise data on individual plants is not possible. In particular, efficient phenotyping of crops to record its color, shape, chemical properties, disease susceptibility, etc. is severely limited due to labor requirements and, oftentimes, expert domain knowledge. In this paper, we propose a deep learning based approach, named DeepStand, for image-based corn stand counting at early phenological stages. The proposed method adopts a truncated VGG-16 network as a backbone feature extractor and merges multiple feature maps with different scales to make the network robust against scale variation. Our extensive computational experiments suggest that our proposed method can successfully count corn stands and out-perform other state-of-the-art methods. It is the goal of our work to be used by the larger agricultural community as a way to enable high-throughput phenotyping without the use of extensive time and labor requirements.

cs.CV↗

arXiv2020

Predicting Yield Performance of Parents in Plant Breeding: A Neural Collaborative Filtering Approach

Experimental corn hybrids are created in plant breeding programs by crossing two parents, so-called inbred and tester, together. Identification of best parent combinations for crossing is challenging since the total number of possible cross combinations of parents is large and it is impractical to test all possible cross combinations due to limited resources of time and budget. In the 2020 Syngenta Crop Challenge, Syngenta released several large datasets that recorded the historical yield performances of around 4% of total cross combinations of 593 inbreds with 496 testers which were planted in 280 locations between 2016 and 2018 and asked participants to predict the yield performance of cross combinations of inbreds and testers that have not been planted based on the historical yield data collected from crossing other inbreds and testers. In this paper, we present a collaborative filtering method which is an ensemble of matrix factorization method and neural networks to solve this problem. Our computational results suggested that the proposed model significantly outperformed other models such as LASSO, random forest (RF), and neural networks. Presented method and results were produced within the 2020 Syngenta Crop Challenge.

cs.LG↗

arXiv2020

Convolutional Neural Networks for Image-based Corn Kernel Detection and Counting

Precise in-season corn grain yield estimates enable farmers to make real-time accurate harvest and grain marketing decisions minimizing possible losses of profitability. A well developed corn ear can have up to 800 kernels, but manually counting the kernels on an ear of corn is labor-intensive, time consuming and prone to human error. From an algorithmic perspective, the detection of the kernels from a single corn ear image is challenging due to the large number of kernels at different angles and very small distance among the kernels. In this paper, we propose a kernel detection and counting method based on a sliding window approach. The proposed method detect and counts all corn kernels in a single corn ear image taken in uncontrolled lighting conditions. The sliding window approach uses a convolutional neural network (CNN) for kernel detection. Then, a non-maximum suppression (NMS) is applied to remove overlapping detections. Finally, windows that are classified as kernel are passed to another CNN regression model for finding the (x,y) coordinates of the center of kernel image patches. Our experiments indicate that the proposed method can successfully detect the corn kernels with a low detection error and is also able to detect kernels on a batch of corn ears positioned at different angles.

cs.CV↗

arXiv2020

A CNN-RNN Framework for Crop Yield Prediction

Crop yield prediction is extremely challenging due to its dependence on multiple factors such as crop genotype, environmental factors, management practices, and their interactions. This paper presents a deep learning framework using convolutional neural networks (CNN) and recurrent neural networks (RNN) for crop yield prediction based on environmental data and management practices. The proposed CNN-RNN model, along with other popular methods such as random forest (RF), deep fully-connected neural networks (DFNN), and LASSO, was used to forecast corn and soybean yield across the entire Corn Belt (including 13 states) in the United States for years 2016, 2017, and 2018 using historical data. The new model achieved a root-mean-square-error (RMSE) 9% and 8% of their respective average yields, substantially outperforming all other methods that were tested. The CNN-RNN have three salient features that make it a potentially useful method for other crop yield prediction studies. (1) The CNN-RNN model was designed to capture the time dependencies of environmental factors and the genetic improvement of seeds over time without having their genotype information. (2) The model demonstrated the capability to generalize the yield prediction to untested environments without significant drop in the prediction accuracy. (3) Coupled with the backpropagation method, the model could reveal the extent to which weather conditions, accuracy of weather predictions, soil conditions, and management practices were able to explain the variation in the crop yields.

cs.LG↗

arXiv2019

Classification of Crop Tolerance to Heat and Drought: A Deep Convolutional Neural Networks Approach

Environmental stresses such as drought and heat can cause substantial yield loss in agriculture. As such, hybrid crops that are tolerant to drought and heat stress would produce more consistent yields compared to the hybrids that are not tolerant to these stresses. In the 2019 Syngenta Crop Challenge, Syngenta released several large datasets that recorded the yield performances of 2,452 corn hybrids planted in 1,560 locations between 2008 and 2017 and asked participants to classify the corn hybrids as either tolerant or susceptible to drought stress, heat stress, and combined drought and heat stress. However, no data was provided that classified any set of hybrids as tolerant or susceptible to any type of stress. In this paper, we present an unsupervised approach to solving this problem, which was recognized as one of the winners in the 2019 Syngenta Crop Challenge. Our results labeled 121 hybrids as drought tolerant, 193 as heat tolerant, and 29 as tolerant to both stresses.

cs.LG↗

arXiv2019

Crop Yield Prediction Using Deep Neural Networks

Crop yield is a highly complex trait determined by multiple factors such as genotype, environment, and their interactions. Accurate yield prediction requires fundamental understanding of the functional relationship between yield and these interactive factors, and to reveal such relationship requires both comprehensive datasets and powerful algorithms. In the 2018 Syngenta Crop Challenge, Syngenta released several large datasets that recorded the genotype and yield performances of 2,267 maize hybrids planted in 2,247 locations between 2008 and 2016 and asked participants to predict the yield performance in 2017. As one of the winning teams, we designed a deep neural network (DNN) approach that took advantage of state-of-the-art modeling and solution techniques. Our model was found to have a superior prediction accuracy, with a root-mean-square-error (RMSE) being 12% of the average yield and 50% of the standard deviation for the validation dataset using predicted weather data. With perfect weather data, the RMSE would be reduced to 11% of the average yield and 46% of the standard deviation. We also performed feature selection based on the trained DNN model, which successfully decreased the dimension of the input space without significant drop in the prediction accuracy. Our computational results suggested that this model significantly outperformed other popular methods such as Lasso, shallow neural networks (SNN), and regression tree (RT). The results also revealed that environmental factors had a greater effect on the crop yield than genotype.

cs.LG↗