All Faculty Deposits

Permanent URI for this collection

https://hdl.handle.net/10919/70873

The "All Faculty Deposits" collection contains works deposited by faculty and appointed delegates from the Elements (EFARs) system. For help with Elements, see Frequently Asked Questions on the Provost's website. In general, items can only be deposited if the item is a scholarly article that is covered by Virginia Tech's open access policy, or the item is openly licensed or in the public domain, or the item is permitted to be posted online under the journal/publisher policy, or the depositor owns the copyright. See Right to Deposit on the VTechWorks Help page. If you have questions email us at vtechworks@vt.edu.

Browse

Now showing 1 - 20 of 7526

Amonate: A Coal Camp Through Time (Part II – a comprehensive inventory)
Gilboy, Elizabeth; Gleason, Harry; Dupre, Karine; Kakkadan, Sneha; Muñoz-Vera, Gonzalo; Thomas, Jennifer; Tucker, Lisa; Rosier, Shaun; Ekberg, Caitlyn; McMahon, Carah; Dadd, Charlotte; Sincavage, Charlotte; Xiong, Jenny Xiqi; Meija, Ryan; Changani, Vaasav (Community Design Assistance Center, 2026-03-06)
This project documents the past and present of Amonate, Virginia - a former Faraday and Pocahontas Fuel Company coal camp - and identifies actionable pathways for preservation, community revitalization, and rural tourism. Led by a team from Virginia Tech in collaboration with Amonate Always, Inc., the work synthesizes historical research, field documentation, and community engagement into a comprehensive inventory and a set of near and long-term recommendations. The effort was supported through an interdisciplinary team and multiple grants. Beside key findings related to the historical significance and physical pattern of Amonate, this report presents deliverables and recommendations. As such, this study equips Amonate with the documentation, evidence, and early ideas needed to preserve its coal-camp heritage, build community capacity, and pursue incremental, feasible economic activity aligned with regional tourism patterns. The partnership among Amonate Always, CDAC/Virginia Tech, Mid-Atlantic TAB, and regional/state agencies provides a durable framework to convert momentum into sustained revitalization.
Virginia 4-H Volunteer Welcome Guide
Proudfoot, Chad (Virginia Cooperative Extension, 2026-03-20)
This guide is intended as a brief welcome and introduction to the Virginia 4-H program. It covers our history, our structure, your role, and the critical policies that ensure a safe and positive environment for all participants. Your local Virginia Cooperative Extension agent or 4-H staff members will provide more comprehensive information and training.
Informatics as a Well-Being Strategy
Uherick, Lisa; Waasdorp, C. J. (2026-03-17)
Comparison of cultural preferences and cultural practices in website design in Pakistan
Nizamani, Sehrish Basir; Nizamani, Saad; Basir, Nazish; Khoumbati, Khalil; Nizamani, Sarwat; Memon, Shahzad (Springer, 2025-11)
Purpose: Websites are typically influenced by the cultural context in which they are created and used. A website that is designed and used based on the preferences of its users and their culture is considered usable. Individuals’ cultural preferences refer to their level of cultural comfort, whereas cultural practices are shared perceptions of how people behave in a culture regularly as a whole. This article discusses the comparison of the web design preferences of users with the actual working practices of three categories of websites in Pakistan. Methods: The disparity between preferences and practices is examined utilizing Hofstede’s six cultural dimensions. Website design practices are collected through content analysis thematic coding is used to systematically categorize and analyze the data. Results: The results reflect that web design practices in Pakistan correspond to preferences in information density, information presentation, navigation, data restriction, error messages, content terminology, and gender roles. Mixed practices are observed in search results, cultural signs, colours, the purpose of images, menu choices, people’s images, user paths, the frequency of important links, input and feedback options and content density.
Nine changes needed to deliver a radical transformation in biodiversity measurement
Sutherland, William J.; Burgess, N. D.; Edwards, S. V.; Jones, J. P. G.; Soltis, P. S.; Tilman, D.; Allen, Julie M.; Andrianandrasana, H. T.; Armour, C. J.; August, T.; Bawa, K. S.; Bailey, S.; Birch, T.; Boersch-Supan, P. H.; Cavender-Bares, J.; Blaxter, M.; Chaplin-Kramer, R.; Daru, B. H.; De Palma, A.; Eisenberg, C.; Elphick, C. S.; Freckleton, R. P.; Frick, W. F.; Gonzalez, A.; Goetz, S. J.; Greenspoon, L.; Grozingeree, C. M.; Hankins, D. L.; Hazell, J.; Isaac, N. J. B.; Lambertini, M.; Lewin, H. A.; Aodha, O. M.; Madhavapeddy, A.; Milner-Gulland, E. J.; Milo, R.; O’Dwyer, J.; Purvis, A.; Salafsky, N.; Tallis, H.; Tanshi, I.; Vijay, V.; Wikelski, M.; Williams, D. R.; Woodard, S. H.; Robinson, G. E. (Proceedings of the National Academy of Sciences, 2026-03-10)
Biodiversity is declining in many parts of the world. Biological diversity measurement and monitoring are fundamental to the assessment of the causes and consequences of environmental changes, identification of key areas for the protection of biodiversity or ecosystem services, determining the effectiveness of actions, and the creation of decision-support tools critical to maintaining a sustainable planet. Biodiversity measurement is rapidly changing due to advances in citizen science, image recognition, acoustic monitoring, environmental DNA, genomics, remote sensing, and AI. In this perspective, we outline the exciting opportunities these developments offer but also consider the challenges. Our key recommendations are to 1) Capitalize on the ability of novel technology to integrate data sources 2) agree to standard methods for data collection 3) ensure new technologies are calibrated with existing data; 4) fill data gaps by using emerging technologies and increasing capacity, especially in the tropics; 5) create living safeguarded databases of trusted information to reduce the risk of poisoning by AI hallucinated, or false, information; 6) ensure data generation is valued; 7) ensure respectful incorporation of Indigenous Knowledge; 8) ensure measurements enable the quantification of effectiveness of actions, and 9) increase the resilience of global datasets to technical and societal change. Radical new collaborations are needed between computer scientists, engineers, molecular biologists, data scientists, field ecologists, citizen scientists, Indigenous peoples, policymakers, and local communities to create the rigorous, resilient, accessible biodiversity information systems required to underpin policies and practices that ensure the maintenance and restoration of ecological systems.
T-Type Labyrinth Seals Dynamic Response Evaluation Using Computational Analysis
Ashraf, Muhammad Mubashar; Untaroiu, Alexandrina (ASME International, 2026-03-06)
Effective sealing in rotating machinery is fundamental to maintaining efficiency and ensuring stable operation. Secondary leakage between high and low-pressure regions not only reduces performance but can also introduce destabilizing aerodynamic forces. Among annular gas seal technologies such as brush, hole-pattern, and honeycomb designs, labyrinth seals remain the most widely used because they are mechanically simple, reliable, and cost-effective. Recently, a modified T-type labyrinth seal has been introduced, demonstrating improved flow control and reduced flow-induced excitations compared to conventional straight-through configurations. The distinguishing feature of the T-type design is its T-shaped tooth geometry, which modifies the internal flow structure and enhances the inward radial forces associated with the Lomakin effect. This change in flow physics directly influences both leakage characteristics and rotordynamic behavior. Seal tip clearance plays a pivotal role. A smaller clearance generally reduces leakage but can alter aerodynamic stiffness and damping, thereby affecting rotor stability. Determining an appropriate clearance, therefore, requires more than a simple comparison at fixed geometry; it demands a structured parametric evaluation that captures the coupled aerodynamic and rotordynamic effects. Previous investigations have demonstrated leakage reductions of 23.6–25.3% for T-type labyrinth seals relative to straight-through designs, with axial length and tip clearance held constant. These findings point to clear performance advantages but leave open the question of optimal geometric tuning. Building on this, the present study conducts a sensitivity analysis using a design of experiments (DOE) framework coupled with steady-state computational fluid dynamics (CFD). The DOE approach enables systematic exploration of the clearance parameter space and quantifies the influence of the clearance parameter on leakage performance. In parallel, equivalent rotordynamic force coefficients are extracted from the CFD solutions to evaluate seal-induced stiffness and damping and to assess stability trends. To further establish practical relevance, the seal performance is examined across a range of pressure ratios and rotational speeds representative of aero-engine operating conditions. The results provide a coherent picture of how tip clearance governs both leakage and rotordynamic response in T-type labyrinth seals. Beyond confirming their leakage advantage, the study offers quantitative guidance for clearance selection and contributes to the broader effort to integrate aerodynamic performance and stability considerations into advanced seal design.
Assessments with Double Simultaneous Tactile Stimulation following Stroke: A Scoping Review Protocol
Paul, Arco; Holstege, Noah; Johnson, Caroline; Shalaby, Mei; Yau, Jeffrey; Chui, Kevin; Parcetich, Kevin; Comer, C. Cozette; Gurari, Netta (2026-03-24)
Intact somatosensory perception is essential to interact with our surrounding environment, including when performing basic daily tasks and learning skilled movements. Successful execution of voluntary movements depends on accurately processing and perceiving the incoming somatosensory information through integrated sensorimotor pathways. Somatosensory impairments following stroke are relatively common, affecting upwards of 85% of survivors living with stroke. Loss of tactile perception is among the most frequent occurring of the somatosensory impairments, impacting approximately 50% of these individuals in the USA. Common tactile impairments include hypoesthesia (reduced ability to feel touch), dysesthesia (abnormal tactile perception), and impaired two-point discrimination (reduced ability to discriminate between two nearby locations of touch). These impairments are often assessed using unilateral tactile stimulation on the more severely-affected (paretic) side, and, accordingly, do not capture more complex tactile impairments that can arise during bilateral interactions. One such impairment is tactile extinction (TE), a condition in which individuals can detect unilateral tactile stimuli on either side of the body but fail to perceive the same tactile stimuli on the paretic side when both sides are stimulated simultaneously. Most activities of daily living rely on coordinating touching and feeling of objects and using both upper extremities to manipulate them in a dynamic manner, such that both arms are stimulated. Tactile dysfunction that suppresses perception during such bilateral tasks can disrupt motor performance in daily activities and recovery. Therefore, understanding the nature of tactile dysfunction during bilateral tasks following stroke is valuable when considering how to effectively assess and, in turn, treat individuals. In this scoping review, we will explore approaches to assess tactile perceptual dysfunction during bilateral interactions post-stroke. Our aim is to summarize the current status of double simultaneous tactile stimulation approaches used for assessing tactile dysfunction. By considering the design of these approaches, we will identify need for further research, such as additional methods for assessment and implications of existing methods for interpreting why bilateral tactile dysfunction arises following stroke.
Investigating Toxicity of Bacteriophage Lambda N-Protein Upon Overexpression in Escherichia coli
Hite, Kristopher; Upton, Jan; Souders, Cole; Larson, Timothy J. (2026-03-09)
Over the course of two decades, cloning of a variety of native and engineered DNA fragments from bacteriophage lambda was performed as part of a capstone undergraduate course aimed at teaching fundamentals of recombinant DNA technology and regulation of gene expression in bacteria. Genomic DNA of bacteriophage lambda (λ–phage) was digested with BamHI and HindIII and the resulting DNA fragments were then ligated into similarly digested plasmid vector pUC19 to illustrate the principle of shot-gun cloning. E. coli strain TB1 was then transformed using selection for ampicillin resistance and the blue-white color screen. Upon analysis of recombinant plasmids isolated from white colonies, it became apparent that four of the five BamHI and HindIII DNA fragments were easily obtained, but one fragment was persistently missing. This 2396 bp BamHI-HindIII fragment between lambda phage genome coordinates 34500-36895 (Accession No. J02459.1) was dubbed the toxic fragment and contained the strong leftward promoter (pL) and downstream N gene encoding the transcription anti-terminator protein N, as well as the ‘rexA rexB genes. Truncation of this toxic fragment revealed that a smaller fragment (1,133 bp, spanning coordinates 34500-35632) was sufficient to confer toxicity upon cloning into pUC19. This smaller fragment contains the intact pL promoter, the open reading frame for the N-protein, and, importantly, 540 bp of 3’ untranslated DNA (UTR, which contains transcription terminator tL1). High level expression of the N-protein was hypothesized to be responsible for bacterial toxicity. This hypothesis was validated when the shorter (1,133 bp) toxic fragment was successfully transformed into strain TB1 containing pACλcI encoding lambda phage repressor protein which negatively controls expression of the N protein by binding to operators within the pL promoter. In addition, various mutations altering the pL promoter relieved toxicity. To further narrow the region of the UTR and/or N-protein responsible for bacterial toxicity, a series of truncations was created by PCR. Surprisingly, a recombinant plasmid containing the wild-type pL promoter and full length N-gene (but lacking tL1) was not toxic. Current research is focused on truncating and mutating bases within this 3’-UTR with the goal of understanding what role tL1 may be playing in toxicity
Teaching Communication in Capstone Design: The Role of the Instructor in Situated Learning
Paretti, Marie C. (ASEE, 2008-10)
Calls for engineers to communicate more effectively are ubiquitous, and engineering education literature includes numerous examples of assignments and courses that integrate writing and speaking with technical content. However, little of this literature examines in detail how engineering students develop communication skills and how those learning mechanisms influence classroom practice. To address this gap, this article synthesizes research on communication learning in college from the fields of composition and technical communication and illustrates its relevance to the engineering classroom with a case study of a capstone design course. The principles of situated learning and activity theory, in particular, provide strong evidence that the ways in which course instructors and students interact around communication tasks play a significant role in helping students develop transferable communication skills.
Sense of belonging in a scientific discipline predicts persistence intentions
Thayer, Nathan; Dayer, Ashley A.; Covino, Kristen; O'Connell, Timothy; Smith, Jennifer; Shizuka, Diazaburo (Elsevier, 2026-04-01)
Understanding the drivers of attrition of scientists in STEM fields remains a key concern. Further, diversifying the sciences and retaining marginalized scientists remains a challenge across the sciences. Here, we investigate the associations between a sense of belonging and intentions to persist in ornithology, a field of study within the sciences. Drawing on survey data gathered from members of three ornithological societies, we demonstrate that a higher sense of belonging is directly associated with stronger intentions to remain in ornithology. Further, marginalized members report, overall, a weaker sense of belonging, and stronger intentions to leave their field. Drawing on these findings, ultimately we argue for professional societies, which are uniquely positioned in the sciences to carve out disciplinary spaces outside of institutional contexts, to take actions to foster belonging in their disciplines.
Structural change in the U.S. office market after 2019: Evidence from lease-level data
Peng, Liang; Xiao, Xue (2026-03-19)
This paper examines how the leasing activities, contract features, and pricing of the Class A office leasing market have evolved since 2019 across five major U.S. markets: Los Angeles, the Bay Area, Dallas, Washington, D.C., and New York City. Using a granular dataset of 73,508 office leases from 2010 to 2024, we find a broad-based contraction in leasing volume and meaningful adjustments in contract features, including increased reliance on free rent and shifts in tenant-improvement usage. More importantly, we document structural changes in the determination of net effective rents at the lease level. In several major markets, longer leases, which were previously associated with rent discounts, began to command premiums after 2019, indicating a revaluation of contractual duration. We also find intensified spatial polarization and substantial reordering of tenant industry rent premiums, suggesting increased segmentation across geography and industry.
Measurable residual mutated NPM1 before allogeneic transplant for acute myeloid leukemia
Al-Ali, Rasha W.; Gui, Gege; Ravindra, Niveditha; Andrew, Georgia; Mukherjee, Devdeep; Wong, Zoe C.; Huang, Ying; Gerhold, Jason; Holman, Matt; Jacobsen, Austin; D'angelo, Julian; Miller, Jeffrey; Elias, Karina; Auletta, Jeffery J.; El Chaer, Firas; Devine, Steven M.; Jimenez, Antonio Martin Jimenez; De Lima, Marcos JG G.; Litzow, Mark R.; Kebriaei, Partow; Saber, Wael; Spellman, Stephen R.; Zeger, Scott L.; Page, Kristin M.; Radich, Jerald P.; Lindsley, R. Coleman; Dillon, Laura W.; Hourigan, Christopher S. (Springer Nature, 2026-02-01)
Adaptation to a Whole-Body Powered Exoskeleton: Human-Exoskeleton Coordination During Load-Handling Tasks
Park, Hanjun; Kim, Sunwook; Nussbaum, Maury A.; Srinivasan, Divya (Springer, 2026-03)
Whole-body powered exoskeletons can augment human performance and reduce physical strain in occupational settings, but little is known about how users adapt to these complex devices during practical work scenarios. We compared novice and experienced users during simulated, occupationally relevant load-handling tasks. Six novice users completed exoskeleton familiarization and stationary load-handling tasks in three sessions while five experienced users performed the tasks once. Task performance, biomechanical demands, and perceived workload were compared in each novice session vs. the experienced group. Novice performance improved substantially across sessions, with task completion time reduced by nearly 50% and movement jerk by 30%. However, performance gaps still persisted in session three, compared to the experienced users. Novices also used consistently lower angular velocities (up to 52% lower) and adopted greater hip flexion throughout the sessions. In contrast, differences in shoulder flexion, muscle activity, perceived exertion, and workload diminished more rapidly, with novices approaching experienced levels by session three. Novice users adapted to using a powered exoskeleton over multiple sessions, especially in movement patterns and muscle activation, but differences in task completion time, jerk index, and angular velocities indicated that novices did not attain the skilled coordination and efficiency of experienced users after three sessions. Our results highlight the likely need for extended familiarization and training for the current powered exoskeleton design and provide baseline data for the novice learning curve in occupational settings.
Not All Noises Are Equal: Investigating Auditory Distraction in Emergency Care Using the Tesseract Simulation Platform
Du, David; Lau, Nathan; Ojeifo, Olumide A.; Upthegrove, Tanner; Baber, Adam; Jones, Nathan A.; Parker, Sarah H. (SAGE Publications, 2025-09)
Auditory distractions in clinical environments can impair performance, yet their impact in emergency department (ED) waiting rooms remains understudied. This study investigates how distinct noise types (baby crying, conversations, and equipment alarms) and temporal patterns (continuous vs. intermittent) influence nursing triage performance. Thirty-two ED nurses completed standardized triage tasks within the Tesseract, an immersive audio-visual simulation platform replicating ED waiting room conditions. Preliminary results from 16 participants suggest that the effects of noise depend on both acoustic features and temporal structures. Subjective perceptions of distraction did not consistently align with measured outcomes. This work provides early evidence that auditory distractions influence clinical task execution in complex, task- and context-specific ways, underscoring the need for targeted mitigation strategies and soundscape-aware simulation training.
Comparative Efficacy RCT of 3 Intensive Infant/Toddler Therapies for Unilateral Cerebral Palsy
DeLuca, Stephanie C.; Ramey, Sharon L.; Darragh, Amy R.; Conaway, Mark; Heathcock, Jill C.; Lo, Warren; Gordon, Andrew M.; Trucks, Mary Rebekah; Wallace, Dory; Cabral, Thais Invencao (American Academy of Pediatrics, 2026-02-01)
Objectives: Unilateral cerebral palsy (UCP) can result in lifelong upper extremity (UE) neuromotor impairment. While both constraint-induced movement therapy (CIMT) and bimanual training have demonstrated efficacy for children with UCP, there was limited evidence to inform treatment decision-making in children aged between 6 and 24 months. Thus, we performed a comparative efficacy trial testing 3 high-dose therapist-delivered interventions, 2 CIMT interventions varied by constraint type to bimanual/no-constraint intervention for use in treating this age group of children with UCP. Patients and Methods: Fifty-eight infants/toddlers with UCP diagnosis, aged 6 to 24 months, were enrolled and randomized. Exclusion criteria were uncontrolled seizures, fragile health, prior CIMT/bimanual therapy, and recent botulinum toxin. Participants were randomly assigned (1:1:1) to 1 of 3 treatments all delivered 3 hours/d and 5 days/wk for 4 weeks: CIMT/full-time cast, CIMT/part-time splint, or bimanual/no constraint. Anonymized assessments at baseline, end of treatment (EoT), and 6 months posttreatment included the Mini–Assisting Hand Assessment (AHA) for bimanual abilities and the Bayley Scales of Infant and Toddler Development, Third Edition (Bayley-III) Fine-Motor (FM) subscale on each UE for FM abilities. Results: Fifty-three infant/toddlers completed treatment and EoT assessment (mean age, 17.2 months), and 41 completed 6-month assessment. All groups had gains from intervention: Mini-AHA scores (P < .003) and Bayley-III FM/paretic side (P < .002). Bayley-III FM/nonparetic side also improved across groups (P < .001). The CIMT/full-time cast showed larger gains on Bayley-III FM/nonparetic side when compared with bimanual/no constraint (difference, 5.9; 95% CI, 1.2-10.5; P = .015). Conclusion: The trial confirms comparable benefits from therapist-delivered CIMT and bimanual/no-constraint interventions for infants/toddlers with UCP aged between 6 and 24 months.
COVID-19 Discrimination and Social Anxiety in Burmese Refugees: The Role of Acculturation and Peer Social Support
Cole, Elli; Su, Shu; Zhang, Mengxi; Walls, Jill; Thang, Jenni (2026)
Amidst the COVID-19 pandemic, discrimination against Asian refugees surged. Discrimination is associated with higher social anxiety, which may be mediated by acculturation, yet the negative effects could be buffered by social support. This study examined whether COVID-19 anti-Asian discrimination would predict greater social anxiety in Burmese refugees through acculturation and whether social support moderated these effects. A moderated mediation analysis found that marginalization mediated the relationship between COVID-19 discrimination and social anxiety. Peer social support moderated the relationship between discrimination and social anxiety. These results add to the growing literature on the negative psychological effects of COVID-19 on Asian refugees.
Applying the Midas Touch of Reproducibility to High-Performance Computing
Minor, A. C.; Feng, Wu-chun (IEEE, 2022-09-19)
With the exponentially improving serial performance of CPUs from the 1980s and 1990s slowing to a standstill by the 2010s, the high-performance computing (HPC) community has seen parallel computing become ubiquitous, which, in turn, has led to a proliferation of parallel programming models, including CUDA, OpenACC, OpenCL, OpenMP, and SYCL. This diversity in hardware platform and programming model has forced application users to port their codes from one hardware platform to another (e.g., CUDA on NVIDIA GPU to HIP or OpenCL on AMD GPU) and demonstrate reproducibility via adhoc testing. To more rigorously ensure reproducibility between codes, we propose Midas, a system to ensure that the results of the original code match the results of the ported code by leveraging the power of snapshots to capture the state of a system before and after the execution of a kernel.
Characterization and Optimization of the Fitting of Quantum Correlation Functions
Chuang, Pi-Yueh; Shah, Niteya; Barry, Patrick; Cloet, Ian; Constantinescu, Emil M.; Sato, Nobuo; Qiu, Jian-Wei; Feng, Wu-chun (IEEE, 2024-09)
This case study presents a characterization and optimization of an application code for extracting parton distribution functions from high energy electron-proton scattering data. Profiling this application code reveals that the phase-space density computation accounts for 93% of the overall execution time for a single iteration on a single core. When executing multiple iterations in parallel on a multicore system, the application spends 78% of its overall execution time idling due to load imbalance. We address these issues by first transforming the application code from Python to C++ and then tackling the application load imbalance via a hybrid scheduling strategy that combines dynamic and static scheduling. These techniques result in a 62% reduction in CPU idle time and a 2.46x speedup in overall execution time per node. In addition, the typically enabled power-management mechanisms in supercomputers (e.g., AMD Turbo Core, Intel Turbo Boost, and RAPL) can significantly impact intra-node scalability when more than 50% of the CPU cores are used. This finding underscores the importance of understanding system interactions with power management, as they can adversely impact application performance, and highlights the necessity of intra-node scaling tests to identify performance degradation that inter-node scaling tests might otherwise overlook.
Experiences with VITIS AI for Deep Reinforcement Learning
Chaudhury, Nabayan; Gondhalekar, Atharva; Feng, Wu-chun (IEEE, 2024-09)
Deep reinforcement learning has found use cases in many applications, such as natural language processing, self-driving cars, and spacecraft control applications. Many use cases of deep reinforcement learning seek to achieve inference with low latency and high accuracy. As such, this work articulates our experiences with the AMD Vitis AI toolchain to improve the latency and accuracy of inference in deep reinforcement learning. In particular, we evaluate the soft actor-critic (SAC) model that is trained to solve the MuJoCo humanoid environment, where the objective of the humanoid agent is to learn a policy that allows it to stay in motion for as long as possible without falling over. During the training phase, we prune the model using the weight sparsity pruner from the Vitis AI optimizer at different timesteps. Our experimental results show that pruning leads to an improvement in the evaluation of the reinforcement learning policy, where the trained agent can remain balanced in the environment and accumulate higher rewards, compared to a trained agent without pruning. Specifically, we observe that pruning the network during training can deliver up to 20% better mean episode length and 23% higher reward (better accuracy), compared to a network without any pruning. Additionally, there is an improvement in decision-making latency up to 20%, which is the time between the observation of the agent's state and a control decision.
On the Scalability of Computing Genomic Diversity Using SparkLeBLAST: A Feasibility Study
Prabhu, Ritvik; Moussad, Bernard; Youssef, Karim; Vatai, Emil; Feng, Wu-chun (IEEE, 2024-09)
Studying the genomic diversity of viruses can help us understand how viruses evolve and how that evolution can impact human health. Rather than use a laborious and tedious wet-lab approach to conduct a genomic diversity study, we take a computational approach, using the ubiquitous NCBI BLAST and our parallel and distributed SparkLeBLAST, across 53 patients (40,000,000 query sequences) on Fugaku, the world's fastest homogeneous supercomputer with 158,976 nodes, where each code contains a 48-core A64FX processor and 32 GB RAM. To project how long BLAST and SparkLeBLAST would take to complete a genomic diversity study of COVID-19, we first perform a feasibility study on a subset of 50 query sequences from a single COVID-19 patient to identify bottlenecks in sequence alignment processing. We then create a model using Amdahl's law to project the run times of NCBI BLAST and SparkLeBLAST on supercomputing systems like Fugaku. Based on the data from this 50-sequence feasibility study, our model predicts that NCBI BLAST, when running on all the cores of the Fugaku supercomputer, would take approximately 26.7 years to complete the full-scale study. In contrast, SparkLeBLAST, using both our query and database segmentation, would reduce the execution time to 0.026 years (i.e., 22.9 hours) - resulting in more than a 10,000× speedup over using the ubiquitous NCBI BLAST.

Browse

Recent Submissions