College of Agriculture and Life Sciences (CALS)

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Browsing College of Agriculture and Life Sciences (CALS) by Department "Center for Advanced Innovation in Agriculture"

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    ASAS-NANP SYMPOSIUM: prospects for interactive and dynamic graphics in the era of data-rich animal science
    Morota, Gota; Cheng, Hao; Cook, Dianne; Tanaka, Emi (2021-02)
    Statistical graphics, and data visualization, play an essential but under-utilized, role for data analysis in animal science, and also to visually illustrate the concepts, ideas, or outputs of research and in curricula. The recent rise in web technologies and ubiquitous availability of web browsers enables easier sharing of interactive and dynamic graphics. Interactivity and dynamic feedback enhance humancomputer interaction and data exploration. Web applications such as decision support systems coupled with multimedia tools synergize with interactive and dynamic graphics. However, the importance of graphics for effectively communicating data, understanding data uncertainty, and the state of the field of interactive and dynamic graphics is underappreciated in animal science. To address this gap, we describe the current state of graphical methodology and technology that might be more broadly adopted. This includes an explanation of a conceptual framework for effective graphics construction. The ideas and technology are illustrated using publicly available animal datasets. We foresee that many new types of big and complex data being generated in precision livestock farming create exciting opportunities for applying interactive and dynamic graphics to improve data analysis and make data-supported decisions.
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    Assessing the Role of Cyberbiosecurity in Agriculture: A Case Study
    Drape, Tiffany A.; Magerkorth, Noah; Sen, Anuradha; Simpson, Joseph; Seibel, Megan M.; Murch, Randall Steven; Duncan, Susan E. (Frontiers, 2021-08-19)
    Agriculture has adopted the use of smart technology to help meet growing food demands. This increased automation and associated connectivity increases the risk of farms being targeted by cyber-attacks. Increasing frequency of cybersecurity breaches in many industries illustrates the need for securing our food supply chain. The uniqueness of biological data, the complexity of integration across the food and agricultural system, and the importance of this system to the U.S. bioeconomy and public welfare suggests an urgency as well as unique challenges that are not common across all industries. To identify and address the gaps in awareness and knowledge as well as encourage collaborations, Virginia Tech hosted a virtual workshop consisting of professionals from agriculture, cybersecurity, government, and academia. During the workshop, thought leaders and influencers discussed 1) common food and agricultural system challenges, scenarios, outcomes and risks to various sectors of the system; 2) cyberbiosecurity strategies for the system, gaps in workforce and training, and research and policy needs. The meeting sessions were transcribed and analyzed using qualitative methodology. The most common themes that emerged were challenges, solutions, viewpoints, common vocabulary. From the results of the analysis, it is evident that none of the participating groups had available cybersecurity training and resources. Participants were uncertain about future pathways for training, implementation, and outreach related to cyberbiosecurity. Recommendations include creating training and education, continued interdisciplinary collaboration, and recruiting government involvement to speed up better security practices related to cyberbiosecurity.
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    Comparison of Single-Breed and Multi-Breed Training Populations for Infrared Predictions of Novel Phenotypes in Holstein Cows
    Mota, Lucio Flavio Macedo; Pegolo, Sara; Baba, Toshimi; Morota, Gota; Peñagaricano, Francisco; Bittante, Giovanni; Cecchinato, Alessio (MDPI, 2021-07-02)
    In general, Fourier-transform infrared (FTIR) predictions are developed using a single-breed population split into a training and a validation set. However, using populations formed of different breeds is an attractive way to design cross-validation scenarios aimed at increasing prediction for difficult-to-measure traits in the dairy industry. This study aimed to evaluate the potential of FTIR prediction using training set combining specialized and dual-purpose dairy breeds to predict different phenotypes divergent in terms of biological meaning, variability, and heritability, such as body condition score (BCS), serum β-hydroxybutyrate (BHB), and kappa casein (k-CN) in the major cattle breed, i.e., Holstein-Friesian. Data were obtained from specialized dairy breeds: Holstein (468 cows) and Brown Swiss (657 cows), and dual-purpose breeds: Simmental (157 cows), Alpine Grey (75 cows), and Rendena (104 cows), giving a total of 1461 cows from 41 multi-breed dairy herds. The FTIR prediction model was developed using a gradient boosting machine (GBM), and predictive ability for the target phenotype in Holstein cows was assessed using different cross-validation (CV) strategies: a within-breed scenario using 10-fold cross-validation, for which the Holstein population was randomly split into 10 folds, one for validation and the remaining nine for training (10-fold_HO); an across-breed scenario (BS_HO) where the Brown Swiss cows were used as the training set and the Holstein cows as the validation set; a specialized multi-breed scenario (BS+HO_10-fold), where the entire Brown Swiss and Holstein populations were combined then split into 10 folds, and a multi-breed scenario (Multi-breed), where the training set comprised specialized (Holstein and Brown Swiss) and dual-purpose (Simmental, Alpine Grey, and Rendena) dairy cows, combined with nine folds of the Holstein cows. Lastly a Multi-breed CV2 scenario was implemented, assuming the same number of records as the reference scenario and using the same proportions as the multi-breed. Within-Holstein, FTIR predictions had a predictive ability of 0.63 for BCS, 0.81 for BHB, and 0.80 for k-CN. Using a specific breed (Brown Swiss) as the training set for prediction in the Holstein population reduced the prediction accuracy by 10% for BCS, 7% for BHB, and 11% for k-CN. Notably, the combination of Holstein and Brown Swiss cows in the training set increased the predictive ability of the model by 6%, which was 0.66 for BCS, 0.85 for BHB, and 0.87 for k-CN. Using multiple specialized and dual-purpose animals in the training set outperforms the 10-fold_HO (standard) approach, with an increase in predictive ability of 8% for BCS, 7% for BHB, and 10% for k-CN. When the Multi-breed CV2 was implemented, no improvement was observed. Our findings suggest that FTIR prediction of different phenotypes in the Holstein breed can be improved by including different specialized and dual-purpose breeds in the training population. Our study also shows that predictive ability is enhanced when the size of the training population and the phenotypic variability are increased.
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    Forecasting dynamic body weight of nonrestrained pigs from images using an RGB-D sensor camera
    Yu, Haipeng; Lee, Kiho; Morota, Gota (Oxford University Press, 2021-01-01)
    Average daily gain is an indicator of the growth rate, feed efficiency, and current health status of livestock species including pigs. Continuous monitoring of daily gain in pigs aids producers to optimize their growth performance while ensuring animal welfare and sustainability, such as reducing stress reactions and feed waste. Computer vision has been used to predict live body weight from video images without direct handling of the pig. In most studies, videos were taken while pigs were immobilized at a weighing station or feeding area to facilitate data collection. An alternative approach is to capture videos while pigs are allowed to move freely within their own housing environment, which can be easily applied to the production system as no special imaging station needs to be established. The objective of this study was to establish a computer vision system by collecting RGB-D videos to capture top-view red, green, and blue (RGB) and depth images of nonrestrained, growing pigs to predict their body weight over time. Over a period of 38 d, eight growers were video recorded for approximately 3 min/d, at the rate of six frames per second, and manually weighed using an electronic scale. An image-processing pipeline in Python using OpenCV was developed to process the images. Specifically, each pig within the RGB frame was segmented by a thresholding algorithm, and the contour of the pig was identified to extract its length and width. The height of a pig was estimated from the depth images captured by the infrared depth sensor. Quality control included removing pigs that were touching the fence and sitting, as well as those showing extremely distorted shape or motion blur owing to their frequent movement. Fitting all of the morphological image descriptors simultaneously in linear mixed models yielded prediction coefficients of determination of 0.72-0.98, 0.65-0.95, 0.51-0.94, and 0.49-0.93 for 1-, 2-, 3-, and 4-d ahead forecasting, respectively, of body weight in time series cross-validation. Based on the results, we conclude that our RGB-D sensor-based imaging system coupled with the Python image-processing pipeline could potentially provide an effective approach to predict the live body weight of nonrestrained pigs from images.