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Baskar Ganapathysubramanian

Publications and source records attributed to Baskar Ganapathysubramanian.

At least 73 records · Page 4Linked to original sources

Class-specific Data Augmentation for Plant Stress Classification

Data augmentation is a powerful tool for improving deep learning-based image classifiers for plant stress identification and classification. However, selecting an effective set of augmentations from a large pool of candidates remains a key challenge, particularly in imbalanced and confounding datasets. We propose an approach for automated class-specific data augmentation using a genetic algorithm. We demonstrate the utility of our approach on soybean [Glycine max (L.) Merr] stress classification where symptoms are observed on leaves; a particularly challenging problem due to confounding classes in the dataset. Our approach yields substantial performance, achieving a mean-per-class accuracy of 97.61% and an overall accuracy of 98% on the soybean leaf stress dataset. Our method significantly improves the accuracy of the most challenging classes, with notable enhancements from 83.01% to 88.89% and from 85.71% to 94.05%, respectively. A key observation we make in this study is that high-performing augmentation strategies can be identified in a computationally efficient manner. We fine-tune only the linear layer of the baseline model with different augmentations, thereby reducing the computational burden associated with training classifiers from scratch for each augmentation policy while achieving exceptional performance. This research represents an advancement in automated data augmentation strategies for plant stress classification, particularly in the context of confounding datasets. Our findings contribute to the growing body of research in tailored augmentation techniques and their potential impact on disease management strategies, crop yields, and global food security. The proposed approach holds the potential to enhance the accuracy and efficiency of deep learning-based tools for managing plant stresses in agriculture.

cs.CV↗

Multi-Sensor and Multi-temporal High-Throughput Phenotyping for Monitoring and Early Detection of Water-Limiting Stress in Soybean

Soybean production is susceptible to biotic and abiotic stresses, exacerbated by extreme weather events. Water limiting stress, i.e. drought, emerges as a significant risk for soybean production, underscoring the need for advancements in stress monitoring for crop breeding and production. This project combines multi-modal information to identify the most effective and efficient automated methods to investigate drought response. We investigated a set of diverse soybean accessions using multiple sensors in a time series high-throughput phenotyping manner to: (1) develop a pipeline for rapid classification of soybean drought stress symptoms, and (2) investigate methods for early detection of drought stress. We utilized high-throughput time-series phenotyping using UAVs and sensors in conjunction with machine learning (ML) analytics, which offered a swift and efficient means of phenotyping. The red-edge and green bands were most effective to classify canopy wilting stress. The Red-Edge Chlorophyll Vegetation Index (RECI) successfully differentiated susceptible and tolerant soybean accessions prior to visual symptom development. We report pre-visual detection of soybean wilting using a combination of different vegetation indices. These results can contribute to early stress detection methodologies and rapid classification of drought responses in screening nurseries for breeding and production applications.

cs.LG↗

Direct numerical simulation of electrokinetic transport phenomena in fluids: variational multi-scale stabilization and octree-based mesh refinement

Computational modeling of charged species transport has enabled the analysis, design, and optimization of a diverse array of electrochemical and electrokinetic devices. These systems are represented by the Poisson-Nernst-Planck (PNP) equations coupled with the Navier-Stokes (NS) equation. Direct numerical simulation (DNS) to accurately capture the spatio-temporal variation of ion concentration and current flux remains challenging due to the (a) small critical dimension of the diffuse charge layer (DCL), (b) stiff coupling due to fast charge relaxation times, large advective effects, and steep gradients close to boundaries, and (c) complex geometries exhibited by electrochemical devices. In the current study, we address these challenges by presenting a direct numerical simulation framework that incorporates (a) a variational multiscale (VMS) treatment, (b) a block-iterative strategy in conjunction with semi-implicit (for NS) and implicit (for PNP) time integrators, and (c) octree based adaptive mesh refinement. The VMS formulation provides numerical stabilization critical for capturing the electro-convective flows often observed in engineered devices. The block-iterative strategy decouples the difficulty of non-linear coupling between the NS and PNP equations and allows the use of tailored numerical schemes separately for NS and PNP equations. The carefully designed second-order, hybrid implicit methods circumvent the harsh timestep requirements of explicit time steppers, thus enabling simulations over longer time horizons. Finally, the octree-based meshing allows efficient and targeted spatial resolution of the DCL. These features are incorporated into a massively parallel computational framework, enabling the simulation of realistic engineering electrochemical devices. The numerical framework is illustrated using several challenging canonical examples.

math.NA↗

Data-driven optimal control with neural network modeling of gradient flows

Extracting physical laws from observation data is a central challenge in many diverse areas of science and engineering. We propose Optimal Control Neural Networks (OCN) to learn the laws of vector fields in dynamical systems, with no assumption on their analytical form, given data consisting of sampled trajectories. The OCN framework consists of a neural network representation and an optimal control formulation. We provide error bounds for both the solution and the vector field. The bounds are shown to depend on both the training error and the time step between the observation data. We also demonstrate the effectiveness of OCN, as well as its generalization ability, by testing on several canonical systems, including the chaotic Lorenz system.

math.DS↗

Latent Diffusion Models for Structural Component Design

Recent advances in generative modeling, namely Diffusion models, have revolutionized generative modeling, enabling high-quality image generation tailored to user needs. This paper proposes a framework for the generative design of structural components. Specifically, we employ a Latent Diffusion model to generate potential designs of a component that can satisfy a set of problem-specific loading conditions. One of the distinct advantages our approach offers over other generative approaches, such as generative adversarial networks (GANs), is that it permits the editing of existing designs. We train our model using a dataset of geometries obtained from structural topology optimization utilizing the SIMP algorithm. Consequently, our framework generates inherently near-optimal designs. Our work presents quantitative results that support the structural performance of the generated designs and the variability in potential candidate designs. Furthermore, we provide evidence of the scalability of our framework by operating over voxel domains with resolutions varying from $32^3$ to $128^3$. Our framework can be used as a starting point for generating novel near-optimal designs similar to topology-optimized designs.

cs.LG↗

Towards Foundational AI Models for Additive Manufacturing: Language Models for G-Code Debugging, Manipulation, and Comprehension

3D printing or additive manufacturing is a revolutionary technology that enables the creation of physical objects from digital models. However, the quality and accuracy of 3D printing depend on the correctness and efficiency of the G-code, a low-level numerical control programming language that instructs 3D printers how to move and extrude material. Debugging G-code is a challenging task that requires a syntactic and semantic understanding of the G-code format and the geometry of the part to be printed. In this paper, we present the first extensive evaluation of six state-of-the-art foundational large language models (LLMs) for comprehending and debugging G-code files for 3D printing. We design effective prompts to enable pre-trained LLMs to understand and manipulate G-code and test their performance on various aspects of G-code debugging and manipulation, including detection and correction of common errors and the ability to perform geometric transformations. We analyze their strengths and weaknesses for understanding complete G-code files. We also discuss the implications and limitations of using LLMs for G-code comprehension.

cs.SE↗

Optimal Surrogate Boundary Selection and Scalability Studies for the Shifted Boundary Method on Octree Meshes

The accurate and efficient simulation of Partial Differential Equations (PDEs) in and around arbitrarily defined geometries is critical for many application domains. Immersed boundary methods (IBMs) alleviate the usually laborious and time-consuming process of creating body-fitted meshes around complex geometry models (described by CAD or other representations, e.g., STL, point clouds), especially when high levels of mesh adaptivity are required. In this work, we advance the field of IBM in the context of the recently developed Shifted Boundary Method (SBM). In the SBM, the location where boundary conditions are enforced is shifted from the actual boundary of the immersed object to a nearby surrogate boundary, and boundary conditions are corrected utilizing Taylor expansions. This approach allows choosing surrogate boundaries that conform to a Cartesian mesh without losing accuracy or stability. Our contributions in this work are as follows: (a) we show that the SBM numerical error can be greatly reduced by an optimal choice of the surrogate boundary, (b) we mathematically prove the optimal convergence of the SBM for this optimal choice of the surrogate boundary, (c) we deploy the SBM on massively parallel octree meshes, including algorithmic advances to handle incomplete octrees, and (d) we showcase the applicability of these approaches with a wide variety of simulations involving complex shapes, sharp corners, and different topologies. Specific emphasis is given to Poisson's equation and the linear elasticity equations.

math.NA↗

Deep learning powered real-time identification of insects using citizen science data

Insect-pests significantly impact global agricultural productivity and quality. Effective management involves identifying the full insect community, including beneficial insects and harmful pests, to develop and implement integrated pest management strategies. Automated identification of insects under real-world conditions presents several challenges, including differentiating similar-looking species, intra-species dissimilarity and inter-species similarity, several life cycle stages, camouflage, diverse imaging conditions, and variability in insect orientation. A deep-learning model, InsectNet, is proposed to address these challenges. InsectNet is endowed with five key features: (a) utilization of a large dataset of insect images collected through citizen science; (b) label-free self-supervised learning for large models; (c) improving prediction accuracy for species with a small sample size; (d) enhancing model trustworthiness; and (e) democratizing access through streamlined MLOps. This approach allows accurate identification (>96% accuracy) of over 2500 insect species, including pollinator (e.g., butterflies, bees), parasitoid (e.g., some wasps and flies), predator species (e.g., lady beetles, mantises, dragonflies) and harmful pest species (e.g., armyworms, cutworms, grasshoppers, stink bugs). InsectNet can identify invasive species, provide fine-grained insect species identification, and work effectively in challenging backgrounds. It also can abstain from making predictions when uncertain, facilitating seamless human intervention and making it a practical and trustworthy tool. InsectNet can guide citizen science data collection, especially for invasive species where early detection is crucial. Similar approaches may transform other agricultural challenges like disease detection and underscore the importance of data collection, particularly through citizen science efforts..

cs.CV↗

Generating Finite Element Codes combining Adaptive Octrees with Complex Geometries

We present a high-level domain-specific language (DSL) interface to drive an adaptive incomplete $k$-d tree-based framework for finite element (FEM) solutions to PDEs. This DSL provides three key advances: (a) it abstracts out the complexity of implementing non-trivial FEM formulations, (b) it simplifies deploying these formulations on arbitrarily complicated and adaptively refined meshes, and (c) it exhibits good parallel performance. Taken together, the DSL interface allows end-users to rapidly and efficiently prototype new mathematical approaches, and deploy them on large clusters for solving practical problems. We illustrate this DSL by implementing a workflow for solving PDEs using the recently developed shifted boundary method (SBM). The SBM requires approximating relatively complicated integrals over boundary surfaces. Using a high-level DSL greatly simplifies this process and allows rapid exploration of variations. We demonstrate these tools on a variety of 2-D and 3-D configurations. With fewer than 20 lines of input, we can produce a parallel code that scales well to thousands of processes. This generated code is made accessible and readable to be easily modified and hand-tuned, making this tool useful even to experts with the target software.

cs.CE↗

Out-of-distribution detection algorithms for robust insect classification

Deep learning-based approaches have produced models with good insect classification accuracy; Most of these models are conducive for application in controlled environmental conditions. One of the primary emphasis of researchers is to implement identification and classification models in the real agriculture fields, which is challenging because input images that are wildly out of the distribution (e.g., images like vehicles, animals, humans, or a blurred image of an insect or insect class that is not yet trained on) can produce an incorrect insect classification. Out-of-distribution (OOD) detection algorithms provide an exciting avenue to overcome these challenge as it ensures that a model abstains from making incorrect classification prediction of non-insect and/or untrained insect class images. We generate and evaluate the performance of state-of-the-art OOD algorithms on insect detection classifiers. These algorithms represent a diversity of methods for addressing an OOD problem. Specifically, we focus on extrusive algorithms, i.e., algorithms that wrap around a well-trained classifier without the need for additional co-training. We compared three OOD detection algorithms: (i) Maximum Softmax Probability, which uses the softmax value as a confidence score, (ii) Mahalanobis distance-based algorithm, which uses a generative classification approach; and (iii) Energy-Based algorithm that maps the input data to a scalar value, called energy. We performed an extensive series of evaluations of these OOD algorithms across three performance axes: (a) \textit{Base model accuracy}: How does the accuracy of the classifier impact OOD performance? (b) How does the \textit{level of dissimilarity to the domain} impact OOD performance? and (c) \textit{Data imbalance}: How sensitive is OOD performance to the imbalance in per-class sample size?

cs.CV↗

Scalable adaptive algorithms for next-generation multiphase flow simulations

High-fidelity flow simulations are indispensable when analyzing systems exhibiting multiphase flow phenomena. The accuracy of multiphase flow simulations is strongly contingent upon the finest mesh resolution used to represent the fluid-fluid interfaces. However, the increased resolution comes at a higher computational cost. In this work, we propose algorithmic advances that aim to reduce the computational cost without compromising on the physics by selectively detecting key regions of interest (droplets/filaments) that require significantly higher resolution. The framework uses an adaptive octree-based meshing framework that is integrated with PETSc's linear algebra solvers. We demonstrate scaling of the framework up to 114,688 processes on TACC's Frontera. Finally, we deploy the framework to simulate one of the most resolved simulations of primary jet atomization. This simulation -- equivalent to 35 trillion grid points on a uniform grid -- is 64 times larger than the current state-of-the-art simulations and provides unprecedented insights into an important flow physics problem with a diverse array of engineering applications.

physics.comp-ph↗

A projection-based, semi-implicit time-stepping approach for the Cahn-Hilliard Navier-Stokes equations on adaptive octree meshes

The Cahn-Hilliard Navier-Stokes (CHNS) system provides a computationally tractable model that can be used to effectively capture interfacial dynamics in two-phase fluid flows. In this work, we present a semi-implicit, projection-based finite element framework for solving the CHNS system. We use a projection-based semi-implicit time discretization for the Navier-Stokes equation and a fully-implicit time discretization for the Cahn-Hilliard equation. We use a conforming continuous Galerkin (cG) finite element method in space equipped with a residual-based variational multiscale (RBVMS) formulation. Pressure is decoupled using a projection step, which results in two linear positive semi-definite systems for velocity and pressure, instead of the saddle point system of a pressure-stabilized method. All the linear systems are solved using an efficient and scalable algebraic multigrid (AMG) method. We deploy this approach on a massively parallel numerical implementation using parallel octree-based adaptive meshes. The overall approach allows the use of relatively large time steps with much faster time-to-solve than similar fully-implicit methods. We present comprehensive numerical experiments showing detailed comparisons with results from the literature for canonical cases, including the single bubble rise and Rayleigh-Taylor instability.

math.NA↗

Neural PDE Solvers for Irregular Domains

Neural network-based approaches for solving partial differential equations (PDEs) have recently received special attention. However, the large majority of neural PDE solvers only apply to rectilinear domains, and do not systematically address the imposition of Dirichlet/Neumann boundary conditions over irregular domain boundaries. In this paper, we present a framework to neurally solve partial differential equations over domains with irregularly shaped (non-rectilinear) geometric boundaries. Our network takes in the shape of the domain as an input (represented using an unstructured point cloud, or any other parametric representation such as Non-Uniform Rational B-Splines) and is able to generalize to novel (unseen) irregular domains; the key technical ingredient to realizing this model is a novel approach for identifying the interior and exterior of the computational grid in a differentiable manner. We also perform a careful error analysis which reveals theoretical insights into several sources of error incurred in the model-building process. Finally, we showcase a wide variety of applications, along with favorable comparisons with ground truth solutions.

cs.LG↗

CyRSoXS: A GPU-accelerated virtual instrument for Polarized Resonant Soft X-ray Scattering (P-RSoXS)

Polarized Resonant Soft X-ray scattering (P-RSoXS) has emerged as a powerful synchrotron-based tool that combines principles of X-ray scattering and X-ray spectroscopy. P-RSoXS provides unique sensitivity to molecular orientation and chemical heterogeneity in soft materials such as polymers and biomaterials. Quantitative extraction of orientation information from P-RSoXS pattern data is challenging because the scattering processes originate from sample properties that must be represented as energy-dependent three-dimensional tensors with heterogeneities at nanometer to sub-nanometer length scales. We overcome this challenge by developing an open-source virtual instrument that uses GPUs to simulate P-RSoXS patterns from real-space material representations with nanoscale resolution. Our computational framework CyRSoXS (https://github.com/usnistgov/cyrsoxs) is designed to maximize GPU performance. We demonstrate the accuracy and robustness of our approach by validating against an extensive set of test cases, which include both analytical solutions and numerical comparisons, demonstrating a speedup of over three orders relative to the current state-of-the-art simulation software. Such fast simulations open up a variety of applications that were previously computationally infeasible, including (a) pattern fitting, (b) co-simulation with the physical instrument for operando analytics, data exploration, and decision support, (c) data creation and integration into machine learning workflows, and (d) utilization in multi-modal data assimilation approaches. Finally, we abstract away the complexity of the computational framework from the end-user by exposing CyRSoXS to Python using Pybind. This eliminates I/O requirements for large-scale parameter exploration and inverse design, and democratizes usage by enabling seamless integration with a Python ecosystem (https://github.com/usnistgov/nrss).

physics.comp-ph↗

Breakup dynamics in primary jet atomization using mesh- and interface- refined Cahn-Hilliard Navier-Stokes

We present a technique to perform interface-resolved simulations of complex breakup dynamics in two-phase flows using the Cahn-Hilliard Navier-Stokes equations. The method dynamically decreases the interface thickness parameter in relevant regions and simultaneously increases local mesh resolution, preventing numerical artifacts. We perform a detailed numerical simulation of pulsed jet atomization that shows a complex cascade of break-up mechanisms involving sheet rupture and filament formation. To understand the effect of refinement on the breakup, we analyze the droplet size distribution. The proposed approach opens up resolved simulations for various multiphase flow phenomena.

physics.flu-dyn↗

A fully-coupled framework for solving Cahn-Hilliard Navier-Stokes equations: Second-order, energy-stable numerical methods on adaptive octree based meshes

We present a fully-coupled, implicit-in-time framework for solving a thermodynamically-consistent Cahn-Hilliard Navier-Stokes system that models two-phase flows. In this work, we extend the block iterative method presented in Khanwale et al. [\textit{Simulating two-phase flows with thermodynamically consistent energy stable Cahn-Hilliard Navier-Stokes equations on parallel adaptive octree based meshes}, J. Comput. Phys. (2020)], to a fully-coupled, provably second-order accurate scheme in time, while maintaining energy-stability. The new method requires fewer matrix assemblies in each Newton iteration resulting in faster solution time. The method is based on a fully-implicit Crank-Nicolson scheme in time and a pressure stabilization for an equal order Galerkin formulation. That is, we use a conforming continuous Galerkin (cG) finite element method in space equipped with a residual-based variational multiscale (RBVMS) procedure to stabilize the pressure. We deploy this approach on a massively parallel numerical implementation using parallel octree-based adaptive meshes. We present comprehensive numerical experiments showing detailed comparisons with results from the literature for canonical cases, including the single bubble rise, Rayleigh-Taylor instability, and lid-driven cavity flow problems. We analyze in detail the scaling of our numerical implementation.

math.NA↗

Stochastic Conservative Contextual Linear Bandits

Many physical systems have underlying safety considerations that require that the strategy deployed ensures the satisfaction of a set of constraints. Further, often we have only partial information on the state of the system. We study the problem of safe real-time decision making under uncertainty. In this paper, we formulate a conservative stochastic contextual bandit formulation for real-time decision making when an adversary chooses a distribution on the set of possible contexts and the learner is subject to certain safety/performance constraints. The learner observes only the context distribution and the exact context is unknown, and the goal is to develop an algorithm that selects a sequence of optimal actions to maximize the cumulative reward without violating the safety constraints at any time step. By leveraging the UCB algorithm for this setting, we propose a conservative linear UCB algorithm for stochastic bandits with context distribution. We prove an upper bound on the regret of the algorithm and show that it can be decomposed into three terms: (i) an upper bound for the regret of the standard linear UCB algorithm, (ii) a constant term (independent of time horizon) that accounts for the loss of being conservative in order to satisfy the safety constraint, and (ii) a constant term (independent of time horizon) that accounts for the loss for the contexts being unknown and only the distribution being known. To validate the performance of our approach we perform extensive simulations on synthetic data and on real-world maize data collected through the Genomes to Fields (G2F) initiative.

cs.LG↗

Case study of SARS-CoV-2 transmission risk assessment in indoor environments using cloud computing resources

Complex flow simulations are conventionally performed on HPC clusters. However, the limited availability of HPC resources and steep learning curve of executing on traditional supercomputer infrastructure has drawn attention towards deploying flow simulation software on the cloud. We showcase how a complex computational framework -- that can evaluate COVID-19 transmission risk in various indoor classroom scenarios -- can be abstracted and deployed on cloud services. The availability of such cloud-based personalized planning tools can enable educational institutions, medical institutions, public sector workers (courthouses, police stations, airports, etc.), and other entities to comprehensively evaluate various in-person interaction scenarios for transmission risk. We deploy the simulation framework on the Azure cloud framework, utilizing the Dendro-kT mesh generation tool and PETSc solvers. The cloud abstraction is provided by RocketML cloud infrastructure. We compare the performance of the cloud machines with state-of-the-art HPC machine TACC Frontera. Our results suggest that cloud-based HPC resources are a viable strategy for a diverse array of end-users to rapidly and efficiently deploy simulation software.

cs.DC↗