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Santosh Pandey

Publications and source records attributed to Santosh Pandey.

18 recordsLinked to original sources

Concorde: Fast and Accurate CPU Performance Modeling with Compositional Analytical-ML Fusion

Cycle-level simulators such as gem5 are widely used in microarchitecture design, but they are prohibitively slow for large-scale design space explorations. We present Concorde, a new methodology for learning fast and accurate performance models of microarchitectures. Unlike existing simulators and learning approaches that emulate each instruction, Concorde predicts the behavior of a program based on compact performance distributions that capture the impact of different microarchitectural components. It derives these performance distributions using simple analytical models that estimate bounds on performance induced by each microarchitectural component, providing a simple yet rich representation of a program's performance characteristics across a large space of microarchitectural parameters. Experiments show that Concorde is more than five orders of magnitude faster than a reference cycle-level simulator, with about 2% average Cycles-Per-Instruction (CPI) prediction error across a range of SPEC, open-source, and proprietary benchmarks. This enables rapid design-space exploration and performance sensitivity analyses that are currently infeasible, e.g., in about an hour, we conducted a first-of-its-kind fine-grained performance attribution to different microarchitectural components across a diverse set of programs, requiring nearly 150 million CPI evaluations.

cs.AR

Tao: Re-Thinking DL-based Microarchitecture Simulation

Microarchitecture simulators are indispensable tools for microarchitecture designers to validate, estimate, and optimize new hardware that meets specific design requirements. While the quest for a fast, accurate and detailed microarchitecture simulation has been ongoing for decades, existing simulators excel and fall short at different aspects: (i) Although execution-driven simulation is accurate and detailed, it is extremely slow and requires expert-level experience to design. (ii) Trace-driven simulation reuses the execution traces in pursuit of fast simulation but faces accuracy concerns and fails to achieve significant speedup. (iii) Emerging deep learning (DL)-based simulations are remarkably fast and have acceptable accuracy but fail to provide adequate low-level microarchitectural performance metrics crucial for microarchitectural bottleneck analysis. Additionally, they introduce substantial overheads from trace regeneration and model re-training when simulating a new microarchitecture. Re-thinking the advantages and limitations of the aforementioned simulation paradigms, this paper introduces TAO that redesigns the DL-based simulation with three primary contributions: First, we propose a new training dataset design such that the subsequent simulation only needs functional trace as inputs, which can be rapidly generated and reused across microarchitectures. Second, we redesign the input features and the DL model using self-attention to support predicting various performance metrics. Third, we propose techniques to train a microarchitecture agnostic embedding layer that enables fast transfer learning between different microarchitectural configurations and reduces the re-training overhead of conventional DL-based simulators. Our extensive evaluation shows TAO can reduce the overall training and simulation time by 18.06x over the state-of-the-art DL-based endeavors.

cs.AR

An automated, high-resolution phenotypic assay for adult Brugia malayi and microfilaria

Brugia malayi are thread-like parasitic worms and one of the etiological agents of Lymphatic filariasis (LF). Existing anthelmintic drugs to treat LF are effective in reducing the larval microfilaria (mf) counts in human bloodstream but are less effective on adult parasites. To test potential drug candidates, we report a multi-parameter phenotypic assay based on tracking the motility of adult B. malayi and mf in vitro. For adult B. malayi, motility is characterized by the centroid velocity, path curvature, angular velocity, eccentricity, extent, and Euler Number. These parameters are evaluated in experiments with three anthelmintic drugs. For B. malayi mf, motility is extracted from the evolving body skeleton to yield positional data and bending angles at 74 key point. We achieved high-fidelity tracking of complex worm postures (self-occlusions, omega turns, body bending, and reversals) while providing a visual representation of pose estimates and behavioral attributes in both space and time scales.

q-bio.QM

Parameter extraction of Extended Floating Gate Field Effect Transistors (EGFETs): Estimating the threshold voltage, series resistance, and mobility degradation from I-V measurements

Extended Floating Gate Field Effect Transistors (EGFETs) are CMOS-compatible floating gate devices capable of detecting charges on their sensing area by the relative shifts in current-voltage (I-V) characteristics. The I-V shifts are generally computed by measuring the EGFET parameters in the strong inversion region of operation. This could lead to errors in estimating the device sensitivity because the simple I-V model ignores the mobility degradation and series resistance effects in EGFETs. Our goal is to model these parasitic effects and present methods to extract the key device parameters. We derive an analytical I-V model for EGFETs in the linear region of transistor operation, accounting for both the mobility degradation and series resistance effects. Based on the analytical model, three methods are presented to estimate the key parameters, namely the threshold voltage, series resistance, surface roughness parameter, low-field mobility, and effective mobility from the I-V characteristics, gate transconductance, and drain conductance. The peak transconductance method is used as a benchmark for comparing the extracted threshold voltages. Silicon-based EGFET devices are fabricated, and their I-V characteristics are measured with deionized water and three polyelectrolytes. From the I-V data, the parameter extraction methods are used to compute the values of the key parameters, and the suitability of each method is discussed. The gate transconductance methods show good agreement between the values for the key parameters, while the drain transconductance method gives lower values of the key parameters. There is scope to improve the presented methods by incorporating the effects of substrate bias and asymmetric series resistance for new extended-gate device architectures, including solution-based organic field-effect transistors.

eess.SP

Flexible and disposable paper- and plastic-based gel micropads for nematode handling, imaging, and chemical testing

Today, the area of point-of-care diagnostics is synonymous with paper microfluidics where cheap, disposable, and on-the-spot detection toolkits are being developed for a variety of chemical tests. In this work, we present a novel application of microfluidic paper-based analytical devices (microPADs) to study the behavior of a small model nematode, Caenorhabditis elegans. We describe schemes of microPAD fabrication on paper and plastic substrates where membranes are created in agarose and Pluronic gel. Methods are demonstrated for loading, visualizing, and transferring single and multiple nematodes. Using an anthelmintic drug, levamisole, we show that chemical testing on C. elegans is easily performed because of the open device structure. A custom program is written to automatically recognize individual worms on the microPADs and extract locomotion parameters in real-time. The combination of microPADs and the nematode tracking program provides a relatively low-cost, simple-to-fabricate imaging and screening assay (compared to standard agarose plates or polymeric microfluidic devices) for non-microfluidic, nematode laboratories.

eess.IV

Scan4CFU: Low-cost, open-source bacterial colony tracking over large areas and extended incubation times

A hallmark of bacterial populations cultured in vitro is their homogeneity of growth, where the majority of cells display identical growth rate, cell size and content. Recent insights, however, have revealed that even cells growing in exponential growth phase can be heterogeneous with respect to variables typically used to measure cell growth. Bacterial heterogeneity has important implications for how bacteria respond to environmental stresses, such as antibiotics. The phenomenon of antimicrobial persistence, for example, has been linked to a small subpopulation of cells that have entered into a state of dormancy where antibiotics are no longer effective. While methods have been developed for identifying individual non-growing cells in bacterial cultures, there has been less attention paid to how these cells may influence growth in colonies on a solid surface. In response, we have developed a low-cost, open-source platform to perform automated image capture and image analysis of bacterial colony growth on multiple nutrient agar plates simultaneously. The descriptions of the hardware and software are included, along with details about the temperature-controlled growth chamber, high-resolution scanner, and graphical interface to extract and plot the colony lag time and growth kinetics. Experiments were conducted using a wild type strain of Escherichia coli K12 to demonstrate the feasibility and operation of our setup. By automated tracking of bacterial growth kinetics in colonies, the system holds the potential to reveal new insights into understanding the impact of microbial heterogeneity on antibiotic resistance and persistence.

q-bio.QM

Effective drug combination for Caenorhabditis elegans nematodes discovered by output-driven feedback system control technique

Infections from parasitic nematodes (or roundworms) contribute to a significant disease burden and productivity losses for humans and livestock. The limited number of anthelmintics (or antinematode drugs) available today to treat these infections are rapidly losing their efficacy as multidrug resistance in parasites becomes a global health challenge. We propose an engineering approach to discover an anthelmintic drug combination that is more potent at killing wild-type Caenorhabditis elegans worms than four individual drugs. In the experiment, freely swimming single worms are enclosed in microfluidic drug environments to assess the centroid velocity and track curvature of worm movements. After analyzing the behavioral data in every iteration, the feedback system control (FSC) scheme is used to predict new drug combinations to test. Through a differential evolutionary search, the winning drug combination is reached that produces minimal centroid velocity and high track curvature, while requiring each drug in less than their EC50 concentrations. The FSC approach is model-less and does not need any information on the drug pharmacology, signaling pathways, or animal biology. Toward combating multidrug resistance, the method presented here is applicable to the discovery of new potent combinations of available anthelmintics on C. elegans, parasitic nematodes, and other small model organisms.

q-bio.QM

New methods of removing debris and high-throughput counting of cyst nematode eggs extracted from field soil

The soybean cyst nematode (SCN), Heterodera glycines, is the most damaging pathogen of soybeans in the United States. To assess the severity of nematode infestations in the field, SCN egg population densities are determined. Cysts (dead females) of the nematode must be extracted from soil samples and then ground to extract the eggs within. Sucrose centrifugation commonly is used to separate debris from suspensions of extracted nematode eggs. We present a method using OptiPrep as a density gradient medium with improved separation and recovery of extracted eggs compared to the sucrose centrifugation technique. Also, computerized methods were developed to automate the identification and counting of nematode eggs from the processed samples. In one approach, a high-resolution scanner was used to take static images of extracted eggs and debris on filter papers, and a deep learning network was trained to identify and count the eggs among the debris. In the second approach, a lensless imaging setup was developed using off-the-shelf components, and the processed egg samples were passed through a microfluidic flow chip made from double-sided adhesive tape. Holographic videos were recorded of the passing eggs and debris, and the videos were reconstructed and processed by custom software program to obtain egg counts. The performance of the software programs for egg counting was characterized with SCN-infested soil collected from two farms, and the results using these methods were compared with those obtained through manual counting.

q-bio.QM

Skin Cancer Diagnostics with an All-Inclusive Smartphone Application

Among the different types of skin cancer, melanoma is considered to be the deadliest and is difficult to treat at advanced stages. Detection of melanoma at earlier stages can lead to reduced mortality rates. Desktop-based computer-aided systems have been developed to assist dermatologists with early diagnosis. However, there is significant interest in developing portable, at-home melanoma diagnostic systems which can assess the risk of cancerous skin lesions. Here, we present a smartphone application that combines image capture capabilities with preprocessing and segmentation to extract the Asymmetry, Border irregularity, Color variegation, and Diameter (ABCD) features of a skin lesion. Using the feature sets, classification of malignancy is achieved through support vector machine classifiers. By using adaptive algorithms in the individual data-processing stages, our approach is made computationally light, user friendly, and reliable in discriminating melanoma cases from benign ones. Images of skin lesions are either captured with the smartphone camera or imported from public datasets. The entire process from image capture to classification runs on an Android smartphone equipped with a detachable 10x lens, and processes an image in less than a second. The overall performance metrics are evaluated on a public database of 200 images with Synthetic Minority Over-sampling Technique (SMOTE) (80% sensitivity, 90% specificity, 88% accuracy, and 0.85 area under curve (AUC)) and without SMOTE (55% sensitivity, 95% specificity, 90% accuracy, and 0.75 AUC). The evaluated performance metrics and computation times are comparable or better than previous methods. This all-inclusive smartphone application is designed to be easy-to-download and easy-to-navigate for the end user, which is imperative for the eventual democratization of such medical diagnostic systems.

eess.IV

Trends in Workplace Wearable Technologies and Connected-Worker Solutions for Next-Generation Occupational Safety, Health, and Productivity

The workplace influences the safety, health, and productivity of workers at multiple levels. To protect and promote total worker health, smart hardware, and software tools have emerged for the identification, elimination, substitution, and control of occupational hazards. Wearable devices enable constant monitoring of individual workers and the environment, whereas connected worker solutions provide contextual information and decision support. Here, the recent trends in commercial workplace technologies to monitor and manage occupational risks, injuries, accidents, and diseases are reviewed. Workplace safety wearables for safe lifting, ergonomics, hazard identification, sleep monitoring, fatigue management, and heat and cold stress are discussed. Examples of workplace productivity wearables for asset tracking, augmented reality, gesture and motion control, brain wave sensing, and work stress management are given. Workplace health wearables designed for work-related musculoskeletal disorders, functional movement disorders, respiratory hazards, cardiovascular health, outdoor sun exposure, and continuous glucose monitoring are shown. Connected worker platforms are discussed with information about the architecture, system modules, intelligent operations, and industry applications. Predictive analytics provide contextual information about occupational safety risks, resource allocation, equipment failure, and predictive maintenance. Altogether, these examples highlight the ground-level benefits of real-time visibility about frontline workers, work environment, distributed assets, workforce efficiency, and safety compliance

eess.SY

Robotic agricultural instrument for automated extraction of nematode cysts and eggs from soil to improve integrated pest management

Soybeans are an important crop for global food security. Every year, soybean yields are reduced by numerous soybean diseases, particularly the soybean cyst nematode (SCN). It is difficult to visually identify the presence of SCN in the field, let alone its population densities or numbers, as there are no obvious aboveground disease symptoms. The only definitive way to assess SCN population densities is to directly extract the SCN cysts from soil and then extract the eggs from cysts and count them. Extraction is typically conducted in commercial soil analysis laboratories and university plant diagnostic clinics and involves repeated steps of sieving, washing, collecting, grinding, and cleaning. Here we present a robotic instrument to reproduce and automate the functions of the conventional methods to extract nematode cysts from soil and subsequently extract eggs from the recovered nematode cysts. We incorporated mechanisms to actuate the stage system, manipulate positions of individual sieves using the gripper, recover cysts and cyst-sized objects from soil suspended in water, and grind the cysts to release their eggs. All system functions are controlled and operated by a touchscreen interface software. The performance of the robotic instrument is evaluated using soil samples infested with SCN from two farms at different locations and results were comparable to the conventional technique. Our new technology brings the benefits of automation to SCN soil diagnostics, a step towards long-term integrated pest management of this serious soybean pest.

eess.SY

Open Droplet Microfluidics for Testing Multi-Drug Resistance and Antibiotic Resilience in Bacteria

New combinations of existing antibiotics are being investigated to combat bacterial resilience. This requires detection technologies with reasonable cost, accuracy, resolution, and throughput. Here, we present a multi -drug screening platform for bacterial cultures by combining droplet microfluidics, search algorithms, and imaging with a wide field of view. We remotely alter the chemical microenvironment around cells and test 12 combinations of resistant cell types and chemicals. Fluorescence intensity readouts allow us to infer bacterial resistance to specific antibiotics within 8 hours. The platform has potential to detect and identify parameters of bacterial resilience in cell cultures, biofilms, and microbial aggregates.

eess.SP

Video Capsule Endoscopy and Ingestible Electronics: Emerging Trends in Sensors, Circuits, Materials, Telemetry, Optics, and Rapid Reading Software

Real-time monitoring of the gastrointestinal tract in a safe and comfortable manner is valuable for the diagnosis and therapy of many diseases. Within this realm, our review captures the trends in ingestible capsule systems with a focus on hardware and software technologies used for capsule endoscopy and remote patient monitoring. We introduce the structure and functions of the gastrointestinal tract, and the FDA guidelines for ingestible wireless telemetric medical devices. We survey the advanced features incorporated in ingestible capsule systems, such as microrobotics, closed-loop feedback, physiological sensing, nerve stimulation, sampling and delivery, panoramic imaging with adaptive frame rates, and rapid reading software. Examples of experimental and commercialized capsule systems are presented with descriptions of their sensors, devices, and circuits for gastrointestinal health monitoring. We also show the recent research in biocompatible materials and batteries, edible electronics, and alternative energy sources for ingestible capsule systems. The results from clinical studies are discussed for the assessment of key performance indicators related to the safety and effectiveness of ingestible capsule procedures. Lastly, the present challenges and outlook are summarized with respect to the risks to health, clinical testing and approval process, and technology adoption by patients and clinicians.

physics.med-ph

SimNet: Accurate and High-Performance Computer Architecture Simulation using Deep Learning

While discrete-event simulators are essential tools for architecture research, design, and development, their practicality is limited by an extremely long time-to-solution for realistic applications under investigation. This work describes a concerted effort, where machine learning (ML) is used to accelerate discrete-event simulation. First, an ML-based instruction latency prediction framework that accounts for both static instruction properties and dynamic processor states is constructed. Then, a GPU-accelerated parallel simulator is implemented based on the proposed instruction latency predictor, and its simulation accuracy and throughput are validated and evaluated against a state-of-the-art simulator. Leveraging modern GPUs, the ML-based simulator outperforms traditional simulators significantly.

cs.AR

TRUST: Triangle Counting Reloaded on GPUs

Triangle counting is a building block for a wide range of graph applications. Traditional wisdom suggests that i) hashing is not suitable for triangle counting, ii) edge-centric triangle counting beats vertex-centric design, and iii) communication-free and workload balanced graph partitioning is a grand challenge for triangle counting. On the contrary, we advocate that i) hashing can help the key operations for scalable triangle counting on Graphics Processing Units (GPUs), i.e., list intersection and graph partitioning, ii)vertex-centric design reduces both hash table construction cost and memory consumption, which is limited on GPUs. In addition, iii) we exploit graph and workload collaborative, and hashing-based 2D partitioning to scale vertex-centric triangle counting over 1,000 GPUswith sustained scalability. In this work, we present TRUST which performs triangle counting with the hash operation and vertex-centric mechanism at the core. To the best of our knowledge, TRUSTis the first work that achieves over one trillion Traversed Edges Per Second (TEPS) rate for triangle counting.

cs.DC

C-SAW: A Framework for Graph Sampling and Random Walk on GPUs

Many applications require to learn, mine, analyze and visualize large-scale graphs. These graphs are often too large to be addressed efficiently using conventional graph processing technologies. Many applications have requirements to analyze, transform, visualize and learn large scale graphs. These graphs are often too large to be addressed efficiently using conventional graph processing technologies. Recent literatures convey that graph sampling/random walk could be an efficient solution. In this paper, we propose, to the best of our knowledge, the first GPU-based framework for graph sampling/random walk. First, our framework provides a generic API which allows users to implement a wide range of sampling and random walk algorithms with ease. Second, offloading this framework on GPU, we introduce warp-centric parallel selection, and two optimizations for collision migration. Third, towards supporting graphs that exceed GPU memory capacity, we introduce efficient data transfer optimizations for out-of-memory sampling, such as workload-aware scheduling and batched multi-instance sampling. In its entirety, our framework constantly outperforms the state-of-the-art projects. First, our framework provides a generic API which allows users to implement a wide range of sampling and random walk algorithms with ease. Second, offloading this framework on GPU, we introduce warp-centric parallel selection, and two novel optimizations for collision migration. Third, towards supporting graphs that exceed the GPU memory capacity, we introduce efficient data transfer optimizations for out-of-memory and multi-GPU sampling, such as workload-aware scheduling and batched multi-instance sampling. Taken together, our framework constantly outperforms the state of the art projects in addition to the capability of supporting a wide range of sampling and random walk algorithms.

cs.DC

FTRANS: Energy-Efficient Acceleration of Transformers using FPGA

In natural language processing (NLP), the "Transformer" architecture was proposed as the first transduction model replying entirely on self-attention mechanisms without using sequence-aligned recurrent neural networks (RNNs) or convolution, and it achieved significant improvements for sequence to sequence tasks. The introduced intensive computation and storage of these pre-trained language representations has impeded their popularity into computation and memory-constrained devices. The field-programmable gate array (FPGA) is widely used to accelerate deep learning algorithms for its high parallelism and low latency. However, the trained models are still too large to accommodate to an FPGA fabric. In this paper, we propose an efficient acceleration framework, Ftrans, for transformer-based large scale language representations. Our framework includes enhanced block-circulant matrix (BCM)-based weight representation to enable model compression on large-scale language representations at the algorithm level with few accuracy degradation, and an acceleration design at the architecture level. Experimental results show that our proposed framework significantly reduces the model size of NLP models by up to 16 times. Our FPGA design achieves 27.07x and 81x improvement in performance and energy efficiency compared to CPU, and up to 8.80x improvement in energy efficiency compared to GPU.

cs.DC

CSI-based Fingerprinting for Indoor Localization: A Deep Learning Approach

With the fast growing demand of location-based services in indoor environments, indoor positioning based on fingerprinting has attracted a lot of interest due to its high accuracy. In this paper, we present a novel deep learning based indoor fingerprinting system using Channel State Information (CSI), which is termed DeepFi. Based on three hypotheses on CSI, the DeepFi system architecture includes an off-line training phase and an on-line localization phase. In the off-line training phase, deep learning is utilized to train all the weights of a deep network as fingerprints. Moreover, a greedy learning algorithm is used to train the weights layer-by-layer to reduce complexity. In the on-line localization phase, we use a probabilistic method based on the radial basis function to obtain the estimated location. Experimental results are presented to confirm that DeepFi can effectively reduce location error compared with three existing methods in two representative indoor environments.

cs.NI