Browsing by Author "Gupta, Chirag"

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    GraphDHT: Scaling Graph Neural Networks' Distributed Training on Edge Devices on a Peer-to-Peer Distributed Hash Table Network
    Gupta, Chirag (Virginia Tech, 2024-01-03)
    This thesis presents an innovative strategy for distributed Graph Neural Network (GNN) training, leveraging a peer-to-peer network of heterogeneous edge devices interconnected through a Distributed Hash Table (DHT). As GNNs become increasingly vital in analyzing graph-structured data across various domains, they pose unique challenges in computational demands and privacy preservation, particularly when deployed for training on edge devices like smartphones. To address these challenges, our study introduces the Adaptive Load- Balanced Partitioning (ALBP) technique in the GraphDHT system. This approach optimizes the division of graph datasets among edge devices, tailoring partitions to the computational capabilities of each device. By doing so, ALBP ensures efficient resource utilization across the network, significantly improving upon traditional participant selection strategies that often overlook the potential of lower-performance devices. Our methodology's core is weighted graph partitioning and model aggregation in GNNs, based on partition ratios, improving training efficiency and resource use. ALBP promotes inclusive device participation in training, overcoming computational limits and privacy concerns in large-scale graph data processing. Utilizing a DHT-based system enhances privacy in the peer-to-peer setup. The GraphDHT system, tested across various datasets and GNN architectures, shows ALBP's effectiveness in distributed GNN training and its broad applicability in different domains and structures. This contributes to applied machine learning, especially in optimizing distributed learning on edge devices.
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    RECoN: Rice Environment Coexpression Network for Systems Level Analysis of Abiotic-Stress Response
    Krishnan, Arjun; Gupta, Chirag; Ambavaram, Madana M. R.; Pereira, Andy (2017-09-20)
    Transcriptional profiling is a prevalent and powerful approach for capturing the response of crop plants to environmental stresses, e.g., response of rice to drought. However, functionally interpreting the resulting genome-wide gene expression changes is severely hampered by the large gaps in our genomic knowledge about which genes work together in cellular pathways/processes in rice. Here, we present a new web resource - RECoN - that relies on a network-based approach to go beyond currently limited annotations in delineating functional and regulatory perturbations in new rice transcriptome datasets generated by a researcher. To build RECoN, we first enumerated 1,744 abiotic stress-specific gene modules covering 28,421 rice genes (> 72% of the genes in the genome). Each module contains a group of genes tightly coexpressed across a large number of environmental conditions and, thus, is likely to be functionally coherent. When a user provides a new differential expression profile, RECoN identifies modules substantially perturbed in their experiment and further suggests deregulated functional and regulatory mechanisms based on the enrichment of current annotations within the predefined modules. We demonstrate the utility of this resource by analyzing new drought transcriptomes of rice in three developmental stages, which revealed large-scale insights into the cellular processes and regulatory mechanisms involved in common and stage-specific drought responses. RECoN enables biologists to functionally explore new data from all abiotic stresses on a genome-scale and to uncover gene candidates, including those that are currently functionally uncharacterized, for engineering stress tolerance.