Browsing by Author "Ha, Sook Shin"

Now showing 1 - 7 of 7
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    AI-ML Powered Pig Behavior Classification and Body Weight Prediction
    Bharadwaj, Sanjana Manjunath (Virginia Tech, 2024-05-31)
    Precision livestock farming technologies have been widely researched over the last decade. These technologies help in monitoring animal health and welfare parameters in a continuous, automated fashion. Under this umbrella of precision livestock farming, this study focuses on activity classification and body weight prediction in pigs. Activity monitoring is essential for understanding the health and growth of pigs. To automate this task effectively, we propose efficient and accurate sensor-based deep learning (DL) solutions. Among these, the 2D Residual Networks emerged as the best performing model, achieving an accuracy of 95.6%. This accuracy was 15.6% higher than that of other machine learning approaches. Additionally, accurate pig weight estimation is crucial for pork production, as it provides valuable insights into growth rates, disease prevalence, and overall health. Traditional manual methods of estimating pig weights are time-consuming and labor-intensive. To address this issue, we propose a novel approach that utilizes deep learning techniques on depth images for weight prediction. Through a custom image preprocessing pipeline, we train DL models to extract meaningful information from depth images for weight prediction. Our findings show that XceptionNet gives promising results, with a mean absolute error of 2.82 kg and a mean absolute percentage error of 7.42%. In comparison, the best performing statistical model, support vector machine, achieved a mean absolute error of 4.51 kg mean absolute percentage error of 15.56%.
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    Apply Machine Learning on Cattle Behavior Classification Using Accelerometer Data
    Zhao, Zhuqing (Virginia Tech, 2022-04-15)
    We used a 50Hz sampling frequency to collect tri-axle acceleration from the cows. For the traditional Machine learning approach, we segmented the data to calculate features, selected the important features, and applied machine learning algorithms for classification. We compared the performance of various models and found a robust model with relatively low computation and high accuracy. For the deep learning approach, we designed an end-to-end trainable Convolutional Neural Networks (CNN) to predict activities for given segments, applied distillation, and quantization to reduce model size. In addition to the fixed window size approach, we used CNN to predict dense labels that each data point has an individual label, inspired by semantic segmentation. In this way, we could have a more precise measurement for the composition of activities. Summarily, physically monitoring the well-being of crowded animals is labor-intensive, so we proposed a solution for timely and efficient measuring of cattle’s daily activities using wearable sensors and machine learning models.
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    Dimensionality Reduction, Feature Selection and Visualization of Biological Data
    Ha, Sook Shin (Virginia Tech, 2012-08-08)
    Due to the high dimensionality of most biological data, it is a difficult task to directly analyze, model and visualize the data to gain biological insight. Thus, dimensionality reduction becomes an imperative pre-processing step in analyzing and visualizing high-dimensional biological data. Two major approaches to dimensionality reduction in genomic analysis and biomarker identification studies are: Feature extraction, creating new features by combining existing ones based on a mapping technique; and feature selection, choosing an optimal subset of all features based on an objective function. In this dissertation, we show how our innovative reduction schemes effectively reduce the dimensionality of DNA gene expression data to extract biologically interpretable and relevant features which result in enhancing the biomarker identification process. To construct biologically interpretable features and facilitate Muscular Dystrophy (MD) subtypes classification, we extract molecular features from MD microarray data by constructing sub-networks using a novel integrative scheme which utilizes protein-protein interaction (PPI) network, functional gene sets information and mRNA profiling data. The workflow includes three major steps: First, by combining PPI network structure and gene-gene co-expression relationship into a new distance metric, we apply affinity propagation clustering (APC) to build gene sub-networks; secondly, we further incorporate functional gene sets knowledge to complement the physical interaction information; finally, based on the constructed sub-network and gene set features, we apply multi-class support vector machine (MSVM) for MD sub-type classification and highlight the biomarkers contributing to the sub-type prediction. The experimental results show that our scheme could construct sub-networks that are more relevant to MD than those constructed by the conventional approach. Furthermore, our integrative strategy substantially improved the prediction accuracy, especially for those ‘hard-to-classify' sub-types. Conventionally, pathway-based analysis assumes that genes in a pathway equally contribute to a biological function, thus assigning uniform weight to genes. However, this assumption has been proven incorrect and applying uniform weight in the pathway analysis may not be an adequate approach for tasks like molecular classification of diseases, as genes in a functional group may have different differential power. Hence, we propose to use different weights for the pathway analysis which resulted in the development of four weighting schemes. We applied them in two existing pathway analysis methods using both real and simulated gene expression data for pathways. Weighting changes pathway scoring and brings up some new significant pathways, leading to the detection of disease-related genes that are missed under uniform weight. To help us understand our MD expression data better and derive scientific insight from it, we have explored a suite of visualization tools. Particularly, for selected top performing MD sub-networks, we displayed the network view using Cytoscape; functional annotations using IPA and DAVID functional analysis tools; expression pattern using heat-map and parallel coordinates plot; and MD associated pathways using KEGG pathway diagrams. We also performed weighted MD pathway analysis, and identified overlapping sub-networks across different weight schemes and different MD subtypes using Venn Diagrams, which resulted in the identification of a new sub-network significantly associated with MD. All those graphically displayed data and information helped us understand our MD data and the MD subtypes better, resulting in the identification of several potentially MD associated biomarker pathways and genes.
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    High performance Deep Learning based Digital Pre-distorters for RF Power Amplifiers
    Kudupudi, Rajesh (Virginia Tech, 2022-01-25)
    In this work, we present different deep learning-based digital pre-distorters and compare them based on their performance towards improving the linearity of highly non-linear power amplifiers. The simulation results show that BiLSTM based DPDs work the best in terms of improving the linearity performance. We also compare two methodologies of direct learning and indirect learning to develop deep learning-based digital pre-distorters (DL-DPDs) models and evaluate their improvement on the linearity of Power Amplifiers (PA). We carry out a theoretical analysis on the differences between these training methodologies and verify their performance with simulation results on class-AB and class-F⁻¹ PAs. The simulation results show that both the learning methods lead to an improvement of more than 12 dB and 11dB in the linearity of class-AB and class-F⁻¹ PAs respectively, with indirect learning DL-DPD offering marginally better performance. Moreover, we compare the DL-DPD with memory polynomial models and show that using the former gives a significant improvement over the memory polynomials. Furthermore, we discuss the advantages of exploiting a BiLSTM based neural network architecture for designing direct/indirect DPDs. We demonstrate that BiLSTM DPD can be used to pre distort signals of any size without the drop in linearity. Moreover, based on the insights we develop a frequency domain loss using which further increased the linearity of the PA.
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    Low-Power Wireless Sensor Node with Edge Computing for Pig Behavior Classifications
    Xu, Yuezhong (Virginia Tech, 2024-04-25)
    A wireless sensor node (WSN) system, capable of sensing animal motion and transmitting motion data wirelessly, is an effective and efficient way to monitor pigs' activity. However, the raw sensor data sampling and transmission consumes lots of power such that WSNs' battery have to be frequently charged or replaced. The proposed work solves this issue through WSN edge computing solution, in which a Random Forest Classifier (RFC) is trained and implemented into WSNs. The implementation of RFC on WSNs does not save power, but the RFC predicts animal behavior such that WSNs can adaptively adjust the data sampling frequency to reduce power consumption. In addition, WSNs can transmit less data by sending RFC predictions instead of raw sensor data to save power. The proposed RFC classifies common animal activities: eating, drinking, laying, standing, and walking with a F-1 score of 93%. The WSN power consumption is reduced by 25% with edge computing intelligence, compare to WSN power that samples and transmits raw sensor data periodically at 10 Hz.
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    SAMPLS: A prompt engineering approach using Segment-Anything-Model for PLant Science research
    Sivaramakrishnan, Upasana (Virginia Tech, 2024-05-30)
    Comparative anatomical studies of diverse plant species are vital for the understanding of changes in gene functions such as those involved in solute transport and hormone signaling in plant roots. The state-of-the-art method for confocal image analysis called PlantSeg utilized U-Net for cell wall segmentation. U-Net is a neural network model that requires training with a large amount of manually labeled confocal images and lacks generalizability. In this research, we test a foundation model called the Segment Anything Model (SAM) to evaluate its zero-shot learning capability and whether prompt engineering can reduce the effort and time consumed in dataset annotation, facilitating a semi-automated training process. Our proposed method improved the detection rate of cells and reduced the error rate as compared to state-of-the-art segmentation tools. We also estimated the IoU scores between the proposed method and PlantSeg to reveal the trade-off between accuracy and detection rate for different quality of data. By addressing the challenges specific to confocal images, our approach offers a robust solution for studying plant structure. Our findings demonstrated the efficiency of SAM in confocal image segmentation, showcasing its adaptability and performance as compared to existing tools. Overall, our research highlights the potential of foundation models like SAM in specialized domains and underscores the importance of tailored approaches for achieving accurate semantic segmentation in confocal imaging.
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    Trustworthy Soft Sensing in Water Supply Systems using Deep Learning
    Sreng, Chhayly (Virginia Tech, 2024-05-22)
    In many industrial and scientific applications, accurate sensor measurements are crucial. Instruments such as nitrate sensors are vulnerable to environmental conditions, calibration drift, high maintenance costs, and degrading. Researchers have turned to advanced computational methods, including mathematical modeling, statistical analysis, and machine learning, to overcome these limitations. Deep learning techniques have shown promise in outperforming traditional methods in many applications by achieving higher accuracy, but they are often criticized as 'black-box' models due to their lack of transparency. This thesis presents a framework for deep learning-based soft sensors that can quantify the robustness of soft sensors by estimating predictive uncertainty and evaluating performance across various scenarios. The framework facilitates comparisons between hard and soft sensors. To validate the framework, I conduct experiments using data generated by AI and Cyber for Water and Ag (ACWA), a cyber-physical system water-controlled environment testbed. Afterwards, the framework is tested on real-world environment data from Alexandria Renew Enterprise (AlexRenew), establishing its applicability and effectiveness in practical settings.