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Fuzzy set intersection based paired-end short-read alignment [article]

William J Bolosky, Arun Subramaniyan, Matei Zaharia, Ravi Pandya, Taylor Sittler, David Patterson
2021 bioRxiv   pre-print
Much genomic data comes in the form of paired-end reads: two reads that represent genetic material with a small gap between. We present a new algorithm for aligning both reads in a pair simultaneously by fuzzily intersecting the sets of candidate alignment locations for each read. This algorithm is often much faster and produces alignments that result in variant calls having roughly the same concordance as the best competing aligners.
doi:10.1101/2021.11.23.469039 fatcat:sz473yuo45c5xhpmfs6fxmgaua

Accelerating Maximal-Exact-Match Seeding with Enumerated Radix Trees [article]

Arun Subramaniyan, Jack Wadden, Kush Goliya, Nathan Ozog, Xiao Wu, Satish Narayanasamy, David Blaauw, Reetuparna Das
2020 bioRxiv   pre-print
prototype an FPGA implementation of ERT on Amazon EC2 F1 cloud and observe 1.6× higher seeding throughput over a 48-thread optimized CPU-ERT implementation.Availability and implementationhttps://github.com/arun-sub  ... 
doi:10.1101/2020.03.23.003897 fatcat:ih3uy7tabjc7zjr774uqez2nva

Selective Cache Line Replication Scheme in Shared Last Level Cache

Nitin Chaturvedi, Arun Subramaniyan, S. Gurunarayanan
2015 Procedia Computer Science  
In current multi-core systems with the shared last level cache (LLC) physically distributed across all the cores, both initial data placement and subsequent placement of data close to the requesting core can contribute to reducing memory access latency and power consumption. This paper extends a replication scheme that balances between access latency and cache capacity in shared NUCA designs by selectively replicating frequently used cache lines close to the requesting cores. Our scheme reduces
more » ... completion time by 15% and improves energy consumption by 27% when compared to the Static-NUCA (S-NUCA) management scheme, when simulated on an eight core system.
doi:10.1016/j.procs.2015.01.022 fatcat:5sm4uxomgfdzhl5vteg3b35lby

Reliability-Based Design Optimization of Load Sharing Systems Using SSI-Markov Models

Arun Bala Bala Subramaniyan, Rong Pan, Xiaoping Du
2019 Designs  
This paper presents a novel single loop approach to design the components of the load sharing systems by optimally allocating the failure probabilities to each component, thereby satisfying the overall system reliability requirement. The Reliability–Based Design Optimization (RBDO) of load sharing systems is computationally intensive due to the dynamic nature of component failure probabilities, since the failure of one component will vary the failure probabilities of other working components.
more » ... ny RBDO methods have been successfully utilized to design individual components, however using these methods for handling system level reliability constraints is still a challenging task. This is because of a drop in accuracy and computational efficiency, especially when considering a load sharing system, where there is dependency in failure probabilities of components. The key idea is to integrate Stress–Strength Interference (SSI) theory with discrete (or) continuous time-discrete state Markov model for the reliability assessment of system, with the states being the condition of components (working/failed). This method takes advantage of the state transition probability matrix to represent the dynamic nature of the system performance. A numerical example of a simple load sharing system with two I-Beams is presented to illustrate and evaluate the performance of the proposed methodology.
doi:10.3390/designs3030034 fatcat:yoijj2inkndnjmrb2hmld6zizy

Neural Cache: Bit-Serial In-Cache Acceleration of Deep Neural Networks [article]

Charles Eckert, Xiaowei Wang, Jingcheng Wang, Arun Subramaniyan, Ravi Iyer, Dennis Sylvester, David Blaauw, Reetuparna Das
2018 arXiv   pre-print
This paper presents the Neural Cache architecture, which re-purposes cache structures to transform them into massively parallel compute units capable of running inferences for Deep Neural Networks. Techniques to do in-situ arithmetic in SRAM arrays, create efficient data mapping and reducing data movement are proposed. The Neural Cache architecture is capable of fully executing convolutional, fully connected, and pooling layers in-cache. The proposed architecture also supports quantization
more » ... che. Our experimental results show that the proposed architecture can improve inference latency by 18.3x over state-of-art multi-core CPU (Xeon E5), 7.7x over server class GPU (Titan Xp), for Inception v3 model. Neural Cache improves inference throughput by 12.4x over CPU (2.2x over GPU), while reducing power consumption by 50% over CPU (53% over GPU).
arXiv:1805.03718v1 fatcat:d72fse5przg43h5ojhqydsl64i

Continuum interpretation of virial stress in molecular simulations

Arun K. Subramaniyan, C.T. Sun
2008 International Journal of Solids and Structures  
The equivalence of the virial stress and Cauchy stress is reviewed using both theoretical arguments and numerical simulations. Using thermoelasticity problems as examples, we numerically demonstrate that virial stress is equivalent to the continuum Cauchy stress. Neglecting the velocity terms in the definition of virial stress as many authors have recently suggested, can cause significant errors in interpreting MD simulation results at elevated temperatures (T > 0 K).
doi:10.1016/j.ijsolstr.2008.03.016 fatcat:mkktldfeenghjnhogvs6x4tcqy

Fatigue Crack Growth Life Assessment for Industrial Applications using Re-meshing and Bayesian Hybrid Techniques

Adrian Loghin, Balajee Ananthasayanam, Jeff LeMonds, Arun Subramaniyan, Felipe Viana
2016 Procedia Structural Integrity  
During their operation, modern aircraft engine components are subjected to increasingly demanding operating conditions, especially the high pressure turbine (HPT) blades. Such conditions cause these parts to undergo different types of time-dependent degradation, one of which is creep. A model using the finite element method (FEM) was developed, in order to be able to predict the creep behaviour of HPT blades. Flight data records (FDR) for a specific aircraft, provided by a commercial aviation
more » ... mpany, were used to obtain thermal and mechanical data for three different flight cycles. In order to create the 3D model needed for the FEM analysis, a HPT blade scrap was scanned, and its chemical composition and material properties were obtained. The data that was gathered was fed into the FEM model and different simulations were run, first with a simplified 3D rectangular block shape, in order to better establish the model, and then with the real 3D mesh obtained from the blade scrap. The overall expected behaviour in terms of displacement was observed, in particular at the trailing edge of the blade. Therefore such a model can be useful in the goal of predicting turbine blade life, given a set of FDR data. Abstract In this study, two different techniques are outlined for assessment of fatigue crack growth life of industrial components: i) a finite element based approach (3DFAS, GE proprietary) using re-meshing techniques that allows automatic propagation of cracks under realistic loading conditions and ii) novel approach using Bayesian hybrid methods (BHM) that significantly improves the efficiency of life assessment computation of the former approach. Parallel processing of a set of three dimensional crack geometries using 3DFAS and Ansys™ is used to create a crack propagation space that is further used to build metamodels required to assess propagation life for an asymmetrically grown planar crack. Verification of the 3DFAS-BHM procedure against automatic (serial mode) finite element crack propagation simulation (using 3DFAS) is provided. Abstract In this study, two different techniques are outlined for assessment of fatigue crack growth life of industrial components: i) a finite element based approach (3DFAS, GE proprietary) using re-meshing techniques that allows automatic propagation of cracks under realistic loading conditions and ii) novel approach using Bayesian hybrid methods (BHM) that significantly improves the efficiency of life assessment computation of the former approach. Parallel processing of a set of three dimensional crack geometries using 3DFAS and Ansys™ is used to create a crack propagation space that is further used to build metamodels required to assess propagation life for an asymmetrically grown planar crack. Verification of the 3DFAS-BHM procedure against automatic (serial mode) finite element crack propagation simulation (using 3DFAS) is provided.
doi:10.1016/j.prostr.2016.06.311 fatcat:khpi2mmhgndydhm5r2horctj34

Experimental Investigation of Power Signatures for Cavitation and Water Hammer in an Industrial Parallel Pumping System

V.K. Arun Shankar, Umashankar Subramaniyan, Padmanaban Sanjeevikumar, Jens Bo Holm-Nielsen, Frede Blaabjerg, S. Paramasivam
2019 Energies  
Among the total energy consumption by utilities, pumping systems contribute 30%. It is evident that a tremendous energy saving potential is achievable by improving the energy efficiency and reducing faults in the pumping system. Thus, optimal operation of centrifugal pumps throughout the operating region is desired for improved energy efficiency and extended lifetime of the pumping system. The major harmful operations in centrifugal pumps include cavitation and water hammering. The pump faults
more » ... re simulated in a real-time experimental setup and the operating point of the pump is estimated correspondingly. In this article, the experimental power quality and vibration measurements of cascade pumps during cavitation and water hammering is recorded for different operating conditions. The results are compared with the normal operating conditions of the pumping system for fault prediction and parameter estimation in a cascade water pumping system. Moreover, the Fast Fourier Transform (FFT) analysis comparison of normal and water hammering (faulty condition) highlights the frequency response of the pumping system. Also, the various power quality issues, i.e., voltage, current, total harmonic distortion, power factor, and active, reactive, and apparent power for a cascade multipump control is discussed in this article. The vibration, FFT, and various power quality measurements serve as input data for the classification of faulty pump operating condition in contrast with the normal operation of pumping system.
doi:10.3390/en12071351 fatcat:zjiizec6i5be7evr23sm45pfrm

Promotion of sanitation and hygiene in a rural area of South India: A community-based study

Nagapraveen Veerapu, P Subramaniyan, BA Praveenkumar, G Arun
2016 Journal of Family Medicine and Primary Care  
Globally, billions of people do not have access to improved sanitation and many defecate in the open air. Poor hand washing practices and limited access to sanitation facilities perpetuate the transmission of disease-causing germs. The objectives of the study were to find out the level of knowledge, attitudes, and practices (KAPs) on sanitary latrine, footwear, and hand washing among rural people and to assess the improvement in KAP after health education intervention. Materials and Methods: A
more » ... ealth education intervention study was conducted from November 2012 to January 2014 in a rural area of Kuppam, Andhra Pradesh, South India among the people aged 15 years and above. The individuals were selected by multistage random sampling and interviewed using a structured questionnaire. After a baseline KAP assessment, intervention activities were conducted twice. The intervention activities were group level talks and discussions, free soap distribution, and display of posters at anganwadi centers. Post-KAP was assessed twice, and the significance of difference was found by using McNemar's test. Results: After the intervention, there was a significant improvement in the overall KAPs among the subjects in post test-1 and post test-2 (P 1 < 0.0001, P 2 < 0.0001), respectively. Conclusions: Health education as an intervention has significantly increased KAP more than 30%. Hence, it is imperative that education interventions are needed to bring or sustain positive change.
doi:10.4103/2249-4863.197305 pmid:28217588 pmcid:PMC5290765 fatcat:4bdy3smeufeflhqeogttn3u2be

Crush Characteristics and Energy Absorption of Thin-Walled Tubes with Through-Hole Crush Initiators

S. Kanna Subramaniyan, Arun Kumar Kananasan, Mohd Radzi Mohamed Yunus, Shahruddin Mahzan, Mohd Imran Ghazali
2014 Applied Mechanics and Materials  
An experimental investigation was conducted to compare the crush characteristics and energy absorption capacity of circular and square tubes with located through-hole crush initiator. Circular through-holes were fabricated at three different configurations based on location into steel tubes which had a length of 200 mm. Furthermore, two different side configurations along the tube were considered for introducing the crush initiators. The results found that adding crush initiator onto the tubes
more » ... ere effectively reduced the initial peak force of a thin-walled circular and square tubes under axial quasi-static loading. The peak crush force was reduced within a range 3-10% and 5-16% for circular and square tubes respectively when compared with corresponding tubes without crush initiator. Moreover, the energy absorption capacity of the tubes was independent with the incorporation of through-hole crush initiators. However, the energy absorption of circular and square tubes were slightly decreases when compared with the tubes fabricated four sided crush initiation and tubes without crush initiator. Overall, the effect of location and number of crush initiation proved significantly influences the initial peak forces while maintain the energy absorbed.
doi:10.4028/www.scientific.net/amm.606.181 fatcat:zokxemzch5fdrefdvljtyeedve

Functional dependence among elderly people in a rural community of Andhra Pradesh, South India

Nagapraveen Veerapu, Praveenkumar A., Subramaniyan P., Arun G.
2016 International Journal of Community Medicine and Public Health  
The ageing process leads to decrease in body stamina and immunity and makes the elderly more prone to diseases and dependence. 5 Particularly the loss of functional capacity is associated with increased functional dependence, and increased need for care. 2 ABSTRACT Background: The elderly people constitute about 8% of the world's population. Loss of functional capacity of an elderly person leads to dependence on others and increased need for formal and informal care. The objectives of this
more » ... were to find out the prevalence of functional dependence among the elderly people and its association with certain socio-demographic factors. Methods: A cross-sectional study was conducted from November 2013 to October 2014 in a rural area of Andhra Pradesh, South India. A Sample of 252 elderly individuals, aged 60 years and above were selected from the villages by probability sampling method and interviewed by using structured questionnaire. Activities of daily living (ADL) were assessed by Katz Index scale and Instrumental activities of daily living (IADL) were assessed by using Lawton Scale. Regression analysis was used to find the association between functional dependence and determinants. Results: The prevalence of functional dependence was found to be 21.8% for ADL and 57.1% for IADL. The highest percentage of dependence for ADL was related to urinary continence/evacuation (12.7%), followed by getting bath (7.5%). Regarding the IADL, the highest percentage of dependence was related to managing money (44.8%) followed by preparation of meals (32.5%). After adjusting independent variables, functional dependence was found to increase with increasing age, lower education and lower Socio-Economic status. Conclusions: More than half of the elderly were functionally dependent. National health programs for the elderly and voluntary organizations should take effort to identify and limit the progression of functional dependence and provide adequate care.
doi:10.18203/2394-6040.ijcmph20162051 fatcat:2ujdswbpszfdfgrdneglhhb6xm

Research directions for an open unit manufacturing process repository: A collaborative vision

William Z. Bernstein, Arun Bala Subramaniyan, Alexander Brodsky, Ian C. Garretson, Karl R. Haapala, Don Libes, K.C. Morris, Rong Pan, Vittal Prabhu, Arkopaul Sarkar, Arvind Shankar Raman, Zhenhua Wu
2018 Manufacturing Letters  
The design of manufacturing systems can see dramatic improvements through the use of digital technologies for modeling and simulation prior to deployment. At the 2017 ASME International Manufacturing Science and Engineering Conference held jointly with the 45th SME North American Manufacturing Research Conference, researchers met within a workshop to discuss structuring and presenting research for modeling manufacturing processes to support life cycle assessment. Workshop participants explored
more » ... vision for using standard formats to represent manufacturing processes in a community-based repository and identified research opportunities and challenges. This paper places these resulting research directions into a plan for implementing the vision.
doi:10.1016/j.mfglet.2017.12.007 fatcat:gm2yksk72fgwzlt3ufv5rgqmyu

Comparison of telemedicine with in-person care for follow-up after elective neurosurgery: results of a cost-effectiveness analysis of 1200 patients using patient-perceived utility scores

Sumit Thakar, Niranjana Rajagopal, Subramaniyan Mani, Maya Shyam, Saritha Aryan, Arun S. Rao, Rakshith Srinivasa, Dilip Mohan, Alangar S. Hegde
2018 Neurosurgical Focus  
FOCUS Neurosurg Focus 44 (5): E17, 2018 T he application of telemedicine (TM) in neurosurgical care has been underexplored, with most of the existing studies being related to telemedicine for trauma (teletrauma) 3,4,17 and stroke (telestroke). 24, 29 In a lower-middle-income economy like India, where a majority of the population resides in rural areas and has limited access to specialty services such as neurosurgery, 25 the need for evaluating the cost-effectiveness of TM becomes all the more
more » ... portant. While there have been many feasibility studies in TM across specialties, 2 there are only a few studies that have addressed the economic utility of TM. In one of the largest TM-related studies in neurosurgery, we ABBREVIATIONS CEA = cost-effectiveness analysis; CGHS = Central Government Health Scheme; ICER = incremental cost-effectiveness ratio; INR = Indian rupee; TM = telemedicine. ACCOMPANYING EDITORIAL OBJECTIVE The utility of telemedicine (TM) in neurosurgery is underexplored, with most of the studies relating to teletrauma or telestroke programs. In this study, the authors evaluate the cost-effectiveness of TM consultations for followup care of a large population of patients who underwent neurosurgical procedures. METHODS A decision-analytical model was used to assess the cost-effectiveness of TM for elective post-neurosurgical care patients from a predominantly nonurban cohort in West Bengal, India. The model compared TM care via a nodal center in West Bengal to routine, in-person, per-episode care at the provider site in Bangalore, India. Cost and effectiveness data relating to 1200 patients were collected for a 52-month period. The effectiveness of TM care was calculated using efficiency in terms of the percentage of successful TM consultations, as well as patient-perceived utility values for overall experience of the type of health care access that they received. Incremental cost-effectiveness ratio (ICER) analysis was done using the 4-quadrant charting of the cost-effectiveness plane. One-way sensitivity and tornado analyses were performed to identify thresholds where the care strategy would change. RESULTS The overall utility for the 3 TM scenarios was found to be higher (89%) than for the utility of routine care (80%). TM was found to be more cost-effective (Indian rupee [INR] 2630 per patient) compared to routine care (INR 6848 per patient). The TM strategy "dominates" that of routine care by being more effective and less expensive (ICER value of -39,400 INR/unit of effectiveness). Sensitivity analysis revealed that cost-effectiveness of TM was most sensitive to changes in the number of TM patients, utility and success rate of TM, and travel distance to the TM center. CONCLUSIONS TM care dominates the in-person care strategy by providing more effective and less expensive followup care for a remote post-neurosurgical care population in India. In the authors' setting, this benefit of TM is sustainable even if half the TM consultations turn out to be unsuccessful. The viability of TM as a cost-effective care protocol is attributed to a combination of factors, like an adequate patient volume utilizing TM, patient utility, success rate of TM, and the patient travel distance. https://thejns.org/doi/abs/10.3171/2018.2.FOCUS17543
doi:10.3171/2018.2.focus17543 pmid:29712532 fatcat:5c54pue43rga3dmkrqyipxvjz4

A Methodology for Updating Prognostic Models via Kalman Filters

Venkatesh Rajagopalan, Arun Subramaniyan
unpublished
Prognostic models are built to predict the future evolution of the state or health of a system. Typical applications of these models include predictions of damage (like crack, wear) and estimation of remaining useful life of a component. Prog-nostic models may be data based, based on known physics of the system or can be hybrid, i.e., built through a combination of data and physics. To build such models, one needs either data from the field (i.e., real-world operations) or sim-ulations/tests
more » ... t qualitatively represent field observations. Often, field data is not easy to obtain and is limited in its availability. Thus, models are built with simulation or test data and then validated with field observations when they become available. This necessitates a procedure that allows for refinement of models to better represent real-world behavior without having to run expensive simulations or tests repeatedly. Further, a single prognostic model developed for an entire fleet may need to be updated with measurements obtained from individual units. In this paper, we describe a novel methodology, based on the Unscented Kalman Filter, that not only allows for updating such "fleet" models, but also guarantees improvement over the existing model.
fatcat:piqwohzsljhutnbh2gjcgp3xxa

An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates

Ann M. Mc Cartney, Medhat Mahmoud, Michael Jochum, Daniel Paiva Agustinho, Barry Zorman, Ahmad Al Khleifat, Fawaz Dabbaghie, Rupesh K Kesharwani, Moritz Smolka, Moez Dawood, Dreycey Albin, Elbay Aliyev (+50 others)
2021 F1000Research  
In October 2020, 62 scientists from nine nations worked together remotely in the Second Baylor College of Medicine & DNAnexus hackathon, focusing on different related topics on Structural Variation, Pan-genomes, and SARS-CoV-2 related research. The overarching focus was to assess the current status of the field and identify the remaining challenges. Furthermore, how to combine the strengths of the different interests to drive research and method development forward. Over the four days, eight
more » ... ups each designed and developed new open-source methods to improve the identification and analysis of variations among species, including humans and SARS-CoV-2. These included improvements in SV calling, genotyping, annotations and filtering. Together with advancements in benchmarking existing methods. Furthermore, groups focused on the diversity of SARS-CoV-2. Daily discussion summary and methods are available publicly at https://github.com/collaborativebioinformatics provides valuable insights for both participants and the research community.
doi:10.12688/f1000research.51477.2 fatcat:4wph6zknrrefxoizjzigqxz5be
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