Adarsh Krishnamurthy

Muhammad Arbab Arshad, Talukder Zaki Jubery, Tirtho Roy et al.

As Vision Language Models (VLMs) become increasingly accessible to farmers and agricultural experts, there is a growing need to evaluate their potential in specialized tasks. We present AgEval, a comprehensive benchmark for assessing VLMs' capabilities in plant stress phenotyping, offering a solution to the challenge of limited annotated data in agriculture. Our study explores how general-purpose VLMs can be leveraged for domain-specific tasks with only a few annotated examples, providing insights into their behavior and adaptability. AgEval encompasses 12 diverse plant stress phenotyping tasks, evaluating zero-shot and few-shot in-context learning performance of state-of-the-art models including Claude, GPT, Gemini, and LLaVA. Our results demonstrate VLMs' rapid adaptability to specialized tasks, with the best-performing model showing an increase in F1 scores from 46.24% to 73.37% in 8-shot identification. To quantify performance disparities across classes, we introduce metrics such as the coefficient of variation (CV), revealing that VLMs' training impacts classes differently, with CV ranging from 26.02% to 58.03%. We also find that strategic example selection enhances model reliability, with exact category examples improving F1 scores by 15.38% on average. AgEval establishes a framework for assessing VLMs in agricultural applications, offering valuable benchmarks for future evaluations. Our findings suggest that VLMs, with minimal few-shot examples, show promise as a viable alternative to traditional specialized models in plant stress phenotyping, while also highlighting areas for further refinement. Results and benchmark details are available at: https://github.com/arbab-ml/AgEval

Anushrut Jignasu, Kelly O. Marshall, Ankush Kumar Mishra et al.

G-code (Geometric code) or RS-274 is the most widely used computer numerical control (CNC) and 3D printing programming language. G-code provides machine instructions for the movement of the 3D printer, especially for the nozzle, stage, and extrusion of material for extrusion-based additive manufacturing. Currently, there does not exist a large repository of curated CAD models along with their corresponding G-code files for additive manufacturing. To address this issue, we present Slice-100K, a first-of-its-kind dataset of over 100,000 G-code files, along with their tessellated CAD model, LVIS (Large Vocabulary Instance Segmentation) categories, geometric properties, and renderings. We build our dataset from triangulated meshes derived from Objaverse-XL and Thingi10K datasets. We demonstrate the utility of this dataset by finetuning GPT-2 on a subset of the dataset for G-code translation from a legacy G-code format (Sailfish) to a more modern, widely used format (Marlin). Our dataset can be found at https://github.com/idealab-isu/Slice-100K. Slice-100K will be the first step in developing a multimodal foundation model for digital manufacturing.

Ali Rabeh, Suresh Murugaiyan, Adarsh Krishnamurthy et al.

Fast, geometry-generalizing surrogates for unsteady flow remain challenging. We present a time-dependent, geometry-aware Deep Operator Network that predicts velocity fields for moderate-Re flows around parametric and non-parametric shapes. The model encodes geometry via a signed distance field (SDF) trunk and flow history via a CNN branch, trained on 841 high-fidelity simulations. On held-out shapes, it attains $\sim 5\%$ relative L2 single-step error and up to 1000X speedups over CFD. We provide physics-centric rollout diagnostics, including phase error at probes and divergence norms, to quantify long-horizon fidelity. These reveal accurate near-term transients but error accumulation in fine-scale wakes, most pronounced for sharp-cornered geometries. We analyze failure modes and outline practical mitigations. Code, splits, and scripts are openly released at: https://github.com/baskargroup/TimeDependent-DeepONet to support reproducibility and benchmarking.

Ethan Herron, Jaydeep Rade, Anushrut Jignasu et al.

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.

Ronak Tali, Ali Rabeh, Cheng-Hau Yang et al.

Simulating fluid flow around arbitrary shapes is key to solving various engineering problems. However, simulating flow physics across complex geometries remains numerically challenging and computationally resource-intensive, particularly when using conventional PDE solvers. Machine learning methods offer attractive opportunities to create fast and adaptable PDE solvers. However, benchmark datasets to measure the performance of such methods are scarce, especially for flow physics across complex geometries. We introduce FlowBench, a dataset for neural simulators with over 10K samples, which is currently larger than any publicly available flow physics dataset. FlowBench contains flow simulation data across complex geometries (\textit{parametric vs. non-parametric}), spanning a range of flow conditions (\textit{Reynolds number and Grashoff number}), capturing a diverse array of flow phenomena (\textit{steady vs. transient; forced vs. free convection}), and for both 2D and 3D. FlowBench contains over 10K data samples, with each sample the outcome of a fully resolved, direct numerical simulation using a well-validated simulator framework designed for modeling transport phenomena in complex geometries. For each sample, we include velocity, pressure, and temperature field data at 3 different resolutions and several summary statistics features of engineering relevance (such as coefficients of lift and drag, and Nusselt numbers). %Additionally, we include masks and signed distance fields for each shape. We envision that FlowBench will enable evaluating the interplay between complex geometry, coupled flow phenomena, and data sufficiency on the performance of current, and future, neural PDE solvers. We enumerate several evaluation metrics to help rank order the performance of neural PDE solvers. We benchmark the performance of several baseline methods including FNO, CNO, WNO, and DeepONet.

Anushrut Jignasu, Kelly Marshall, Baskar Ganapathysubramanian et al.

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.

Biswajit Khara, Ethan Herron, Zhanhong Jiang et al.

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.

Jaydeep Rade, Soumik Sarkar, Anwesha Sarkar et al.

Recent developments in deep learning-based methods demonstrated its potential to predict the 3D protein structures using inputs such as protein sequences, Cryo-Electron microscopy (Cryo-EM) images of proteins, etc. However, these methods struggle to predict the protein complexes (PC), structures with more than one protein. In this work, we explore the atomic force microscope (AFM) assisted deep learning-based methods to predict the 3D structure of PCs. The images produced by AFM capture the protein structure in different and random orientations. These multi-view images can help train the neural network to predict the 3D structure of protein complexes. However, obtaining the dataset of actual AFM images is time-consuming and not a pragmatic task. We propose a virtual AFM imaging pipeline that takes a 'PDB' protein file and generates multi-view 2D virtual AFM images using volume rendering techniques. With this, we created a dataset of around 8K proteins. We train a neural network for 3D reconstruction called Pix2Vox++ using the synthesized multi-view 2D AFM images dataset. We compare the predicted structure obtained using a different number of views and get the intersection over union (IoU) value of 0.92 on the training dataset and 0.52 on the validation dataset. We believe this approach will lead to better prediction of the structure of protein complexes.

Stefan Druc, Aditya Balu, Peter Wooldridge et al.

We explore the interpretability of 3D geometric deep learning models in the context of Computer-Aided Design (CAD). The field of parametric CAD can be limited by the difficulty of expressing high-level design concepts in terms of a few numeric parameters. In this paper, we use a deep learning architectures to encode high dimensional 3D shapes into a vectorized latent representation that can be used to describe arbitrary concepts. Specifically, we train a simple auto-encoder to parameterize a dataset of complex shapes. To understand the latent encoded space, we use the idea of Concept Activation Vectors (CAV) to reinterpret the latent space in terms of user-defined concepts. This allows modification of a reference design to exhibit more or fewer characteristics of a chosen concept or group of concepts. We also test the statistical significance of the identified concepts and determine the sensitivity of a physical quantity of interest across the dataset.

Stefan Druc, Peter Wooldridge, Adarsh Krishnamurthy et al.

Deep learning is becoming increasingly adopted in business and industry due to its ability to transform large quantities of data into high-performing models. These models, however, are generally regarded as black boxes, which, in spite of their performance, could prevent their use. In this context, the field of eXplainable AI attempts to develop techniques that temper the impenetrable nature of the models and promote a level of understanding of their behavior. Here we present our contribution to XAI methods in the form of a framework that we term SpecXAI, which is based on the spectral characterization of the entire network. We show how this framework can be used to not only understand the network but also manipulate it into a linear interpretable symbolic representation.

Kibon Ku, Talukder Z. Jubery, Adarsh Krishnamurthy et al.

Advances in hyperspectral imaging (HSI) and 3D reconstruction have enabled accurate, high-throughput characterization of agricultural produce quality and plant phenotypes, both essential for advancing agricultural sustainability and breeding programs. HSI captures detailed biochemical features of produce, while 3D geometric data substantially improves morphological analysis. However, integrating these two modalities at scale remains challenging, as conventional approaches involve complex hardware setups incompatible with automated phenotyping systems. Recent advances in neural radiance fields (NeRF) offer computationally efficient 3D reconstruction but typically require moving-camera setups, limiting throughput and reproducibility in standard indoor agricultural environments. To address these challenges, we introduce HSI-SC-NeRF, a stationary-camera multi-channel NeRF framework for high-throughput hyperspectral 3D reconstruction targeting postharvest inspection of agricultural produce. Multi-view hyperspectral data is captured using a stationary camera while the object rotates within a custom-built Teflon imaging chamber providing diffuse, uniform illumination. Object poses are estimated via ArUco calibration markers and transformed to the camera frame of reference through simulated pose transformations, enabling standard NeRF training on stationary-camera data. A multi-channel NeRF formulation optimizes reconstruction across all hyperspectral bands jointly using a composite spectral loss, supported by a two-stage training protocol that decouples geometric initialization from radiometric refinement. Experiments on three agricultural produce samples demonstrate high spatial reconstruction accuracy and strong spectral fidelity across the visible and near-infrared spectrum, confirming the suitability of HSI-SC-NeRF for integration into automated agricultural workflows.

Jaydeep Rade, Ethan Herron, Soumik Sarkar et al.

Recent advancements in deep learning for predicting 3D protein structures have shown promise, particularly when leveraging inputs like protein sequences and Cryo-Electron microscopy (Cryo-EM) images. However, these techniques often fall short when predicting the structures of protein complexes (PCs), which involve multiple proteins. In our study, we investigate using atomic force microscopy (AFM) combined with deep learning to predict the 3D structures of PCs. AFM generates height maps that depict the PCs in various random orientations, providing a rich information for training a neural network to predict the 3D structures. We then employ the pre-trained UpFusion model (which utilizes a conditional diffusion model for synthesizing novel views) to train an instance-specific NeRF model for 3D reconstruction. The performance of UpFusion is evaluated through zero-shot predictions of 3D protein structures using AFM images. The challenge, however, lies in the time-intensive and impractical nature of collecting actual AFM images. To address this, we use a virtual AFM imaging process that transforms a `PDB' protein file into multi-view 2D virtual AFM images via volume rendering techniques. We extensively validate the UpFusion architecture using both virtual and actual multi-view AFM images. Our results include a comparison of structures predicted with varying numbers of views and different sets of views. This novel approach holds significant potential for enhancing the accuracy of protein complex structure predictions with further fine-tuning of the UpFusion network.

Kelly O. Marshall, Minh Pham, Ameya Joshi et al.

Current state-of-the-art methods for text-to-shape generation either require supervised training using a labeled dataset of pre-defined 3D shapes, or perform expensive inference-time optimization of implicit neural representations. In this work, we present ZeroForge, an approach for zero-shot text-to-shape generation that avoids both pitfalls. To achieve open-vocabulary shape generation, we require careful architectural adaptation of existing feed-forward approaches, as well as a combination of data-free CLIP-loss and contrastive losses to avoid mode collapse. Using these techniques, we are able to considerably expand the generative ability of existing feed-forward text-to-shape models such as CLIP-Forge. We support our method via extensive qualitative and quantitative evaluations

Mohammed Musthafa Rafi, Adarsh Krishnamurthy, Aditya Balu

The proliferation of AI-generated content has created an absurd communication theater where senders use LLMs to inflate simple ideas into verbose content, recipients use LLMs to compress them back into summaries, and as a consequence neither party engage with authentic content. LAAC (LLM as a Communicator) proposes a paradigm shift - positioning LLMs as intelligent communication intermediaries that capture the sender's intent through structured dialogue and facilitate genuine knowledge exchange with recipients. Rather than perpetuating cycles of AI-generated inflation and compression, LAAC enables authentic communication across diverse contexts including academic papers, proposals, professional emails, and cross-platform content generation. However, deploying LLMs as trusted communication intermediaries raises critical questions about information fidelity, consistency, and reliability. This position paper systematically evaluates the trustworthiness requirements for LAAC's deployment across multiple communication domains. We investigate three fundamental dimensions: (1) Information Capture Fidelity - accuracy of intent extraction during sender interviews across different communication types, (2) Reproducibility - consistency of structured knowledge across multiple interaction instances, and (3) Query Response Integrity - reliability of recipient-facing responses without hallucination, source conflation, or fabrication. Through controlled experiments spanning multiple LAAC use cases, we assess these trust dimensions using LAAC's multi-agent architecture. Preliminary findings reveal measurable trust gaps that must be addressed before LAAC can be reliably deployed in high-stakes communication scenarios.

Shreyan Ganguly, Angona Biswas, Jaydeep Rade et al.

Foundation vision-language models (VLMs) excel on natural images, but their utility for biomedical microscopy remains underexplored. In this paper, we investigate how in-context learning enables state-of-the-art VLMs to perform few-shot object detection when large annotated datasets are unavailable, as is often the case with microscopic images. We introduce the Micro-OD benchmark, a curated collection of 252 images specifically curated for in-context learning, with bounding-box annotations spanning 11 cell types across four sources, including two in-lab expert-annotated sets. We systematically evaluate eight VLMs under few-shot conditions and compare variants with and without implicit test-time reasoning tokens. We further implement a hybrid Few-Shot Object Detection (FSOD) pipeline that combines a detection head with a VLM-based few-shot classifier, which enhances the few-shot performance of recent VLMs on our benchmark. Across datasets, we observe that zero-shot performance is weak due to the domain gap; however, few-shot support consistently improves detection, with marginal gains achieved after six shots. We observe that models with reasoning tokens are more effective for end-to-end localization, whereas simpler variants are more suitable for classifying pre-localized crops. Our results highlight in-context adaptation as a practical path for microscopy, and our benchmark provides a reproducible testbed for advancing open-vocabulary detection in biomedical imaging.

Qisai Liu, Alloy Das, Zhanhong Jiang et al.

Foundation models like the Segment Anything Model (SAM) demonstrate impressive zero-shot generalization but frequently degrade under diverse real-world illumination, particularly for instance segmentation. In this work, we address this limitation by developing \textit{Lighting Convolutional-Attention (\lca{})}, an adapter module that enhances segmentation robustness without fine-tuning the heavy backbone. \lca{} employs a dual-branch architecture to process RGB features alongside contrast maps, enabling physically motivated sensitivity to structural changes rather than illumination artifacts. We optimize \lca{} through a pairwise training strategy, introducing a targeted loss term that explicitly penalizes discrepancies between clean images and their corresponding illumination variants. To evaluate and support this architecture, we conduct a comprehensive empirical study across multiple existing benchmarks and present a novel Unity-based synthetic dataset specifically designed to accurately replicate complex real-world lighting conditions. Extensive experimental results demonstrate that our approach successfully bridges the domain gap, delivering superior lighting-robust segmentation.

Hossein Zaremehrjerdi, Shreyan Ganguly, Ashlyn Rairdin et al.

Agricultural decision-making involves complex, context-specific reasoning, where choices about crops, practices, and interventions depend heavily on geographic, climatic, and economic conditions. Traditional large language models (LLMs) often fall short in navigating this nuanced problem due to limited reasoning capacity. We hypothesize that recent advances in large reasoning models (LRMs) can better handle such structured, domain-specific inference. To investigate this, we introduce AgReason, the first expert-curated open-ended science benchmark with 100 questions for agricultural reasoning. Evaluations across thirteen open-source and proprietary models reveal that LRMs outperform conventional ones, though notable challenges persist, with the strongest Gemini-based baseline achieving 36% accuracy. We also present AgThoughts, a large-scale dataset of 44.6K question-answer pairs generated with human oversight and equipped with synthetically generated reasoning traces. Using AgThoughts, we develop AgThinker, a suite of small reasoning models that can be run on consumer-grade GPUs, and show that our dataset can be effective in unlocking agricultural reasoning abilities in LLMs. Our project page is here: https://baskargroup.github.io/Ag_reasoning/

Mozhgan Hadadi, Mehdi Saraeian, Jackson Godbersen et al.

This study introduces a robust framework for generating procedural 3D models of maize (Zea mays) plants from LiDAR point cloud data, offering a scalable alternative to traditional field-based phenotyping. Our framework leverages Non-Uniform Rational B-Spline (NURBS) surfaces to model the leaves of maize plants, combining Particle Swarm Optimization (PSO) for an initial approximation of the surface and a differentiable programming framework for precise refinement of the surface to fit the point cloud data. In the first optimization phase, PSO generates an approximate NURBS surface by optimizing its control points, aligning the surface with the LiDAR data, and providing a reliable starting point for refinement. The second phase uses NURBS-Diff, a differentiable programming framework, to enhance the accuracy of the initial fit by refining the surface geometry and capturing intricate leaf details. Our results demonstrate that, while PSO establishes a robust initial fit, the integration of differentiable NURBS significantly improves the overall quality and fidelity of the reconstructed surface. This hierarchical optimization strategy enables accurate 3D reconstruction of maize leaves across diverse genotypes, facilitating the subsequent extraction of complex traits like phyllotaxy. We demonstrate our approach on diverse genotypes of field-grown maize plants. All our codes are open-source to democratize these phenotyping approaches.

Muhammad Arbab Arshad, Talukder Jubery, James Afful et al.

We evaluate different Neural Radiance Fields (NeRFs) techniques for the 3D reconstruction of plants in varied environments, from indoor settings to outdoor fields. Traditional methods usually fail to capture the complex geometric details of plants, which is crucial for phenotyping and breeding studies. We evaluate the reconstruction fidelity of NeRFs in three scenarios with increasing complexity and compare the results with the point cloud obtained using LiDAR as ground truth. In the most realistic field scenario, the NeRF models achieve a 74.6% F1 score after 30 minutes of training on the GPU, highlighting the efficacy of NeRFs for 3D reconstruction in challenging environments. Additionally, we propose an early stopping technique for NeRF training that almost halves the training time while achieving only a reduction of 7.4% in the average F1 score. This optimization process significantly enhances the speed and efficiency of 3D reconstruction using NeRFs. Our findings demonstrate the potential of NeRFs in detailed and realistic 3D plant reconstruction and suggest practical approaches for enhancing the speed and efficiency of NeRFs in the 3D reconstruction process.

Nasla Saleem, Talukder Zaki Jubery, Aditya Balu et al.

High-density planting is a widely adopted strategy to enhance maize productivity, yet it introduces challenges such as increased interplant competition and shading, which can limit light capture and overall yield potential. In response, some maize plants naturally reorient their canopies to optimize light capture, a process known as canopy reorientation. Understanding this adaptive response and its impact on light capture is crucial for maximizing agricultural yield potential. This study introduces an end-to-end framework that integrates realistic 3D reconstructions of field-grown maize with photosynthetically active radiation (PAR) modeling to assess the effects of phyllotaxy and planting density on light interception. In particular, using 3D point clouds derived from field data, virtual fields for a diverse set of maize genotypes were constructed and validated against field PAR measurements. Using this framework, we present detailed analyses of the impact of canopy orientations, plant and row spacings, and planting row directions on PAR interception throughout a typical growing season. Our findings highlight significant variations in light interception efficiency across different planting densities and canopy orientations. By elucidating the relationship between canopy architecture and light capture, this study offers valuable guidance for optimizing maize breeding and cultivation strategies across diverse agricultural settings.

Ali Rabeh, Ethan Herron, Aditya Balu et al.

Rapid and accurate simulations of fluid dynamics around complicated geometric bodies are critical in a variety of engineering and scientific applications, including aerodynamics and biomedical flows. However, while scientific machine learning (SciML) has shown considerable promise, most studies in this field are limited to simple geometries, and complex, real-world scenarios are underexplored. This paper addresses this gap by benchmarking diverse SciML models, including neural operators and vision transformer-based foundation models, for fluid flow prediction over intricate geometries. Using a high-fidelity dataset of steady-state flows across various geometries, we evaluate the impact of geometric representations -- Signed Distance Fields (SDF) and binary masks -- on model accuracy, scalability, and generalization. Central to this effort is the introduction of a novel, unified scoring framework that integrates metrics for global accuracy, boundary layer fidelity, and physical consistency to enable a robust, comparative evaluation of model performance. Our findings demonstrate that newer foundation models significantly outperform neural operators, particularly in data-limited scenarios, and that SDF representations yield superior results with sufficient training data. Despite these promises, all models struggle with out-of-distribution generalization, highlighting a critical challenge for future SciML applications. By advancing both evaluation models and modeling capabilities, our work paves the way for robust and scalable ML solutions for fluid dynamics across complex geometries.

Anushrut Jignasu, Ethan Herron, Zhanhong Jiang et al.

We present STITCH, a novel approach for neural implicit surface reconstruction of a sparse and irregularly spaced point cloud while enforcing topological constraints (such as having a single connected component). We develop a new differentiable framework based on persistent homology to formulate topological loss terms that enforce the prior of a single 2-manifold object. Our method demonstrates excellent performance in preserving the topology of complex 3D geometries, evident through both visual and empirical comparisons. We supplement this with a theoretical analysis, and provably show that optimizing the loss with stochastic (sub)gradient descent leads to convergence and enables reconstructing shapes with a single connected component. Our approach showcases the integration of differentiable topological data analysis tools for implicit surface reconstruction.

Samundra Karki, Adarsh Krishnamurthy, Baskar Ganapathysubramanian

Implicit Neural Representations (INRs) provide compact models of geometry, but it is unclear when their learned shapes can be edited without retraining. We show that the Gram operator induced by the INR's penultimate features admits deformation eigenmodes that parameterize a family of realizable edits of the SDF zero level set. A key finding is that these modes are not intrinsic to the geometry alone: they are reliably recoverable only when the Gram operator is estimated from sufficiently rich sampling distributions. We derive a single closed-form update that performs geometric edits to the INR without optimization by leveraging the deformation modes. We characterize theoretically the precise set of deformations that are feasible under this one-shot update, and show that editing is well-posed exactly within the span of these deformation modes.

Mozhgan Hadadi, Talukder Z. Jubery, Patrick S. Schnable et al.

Accurate 3D plant models are crucial for computational phenotyping and physics-based simulation; however, current approaches face significant limitations. Learning-based reconstruction methods require extensive species-specific training data and lack editability. Procedural modeling offers parametric control but demands specialized expertise in geometric modeling and an in-depth understanding of complex procedural rules, making it inaccessible to domain scientists. We present FloraForge, an LLM-assisted framework that enables domain experts to generate biologically accurate, fully parametric 3D plant models through iterative natural language Plant Refinements (PR), minimizing programming expertise. Our framework leverages LLM-enabled co-design to refine Python scripts that generate parameterized plant geometries as hierarchical B-spline surface representations with botanical constraints with explicit control points and parametric deformation functions. This representation can be easily tessellated into polygonal meshes with arbitrary precision, ensuring compatibility with functional structural plant analysis workflows such as light simulation, computational fluid dynamics, and finite element analysis. We demonstrate the framework on maize, soybean, and mung bean, fitting procedural models to empirical point cloud data through manual refinement of the Plant Descriptor (PD), human-readable files. The pipeline generates dual outputs: triangular meshes for visualization and triangular meshes with additional parametric metadata for quantitative analysis. This approach uniquely combines LLM-assisted template creation, mathematically continuous representations enabling both phenotyping and rendering, and direct parametric control through PD. The framework democratizes sophisticated geometric modeling for plant science while maintaining mathematical rigor.

Juntao Zhang, Angona Biswas, Jaydeep Rade et al.

Atomic Force Microscopy (AFM) enables high-resolution surface imaging at the nanoscale, yet the output is often degraded by artifacts introduced by environmental noise, scanning imperfections, and tip-sample interactions. To address this challenge, a lightweight and fully automated framework for artifact detection and restoration in AFM image analysis is presented. The pipeline begins with a classification model that determines whether an AFM image contains artifacts. If necessary, a lightweight semantic segmentation network, custom-designed and trained on AFM data, is applied to generate precise artifact masks. These masks are adaptively expanded based on their structural orientation and then inpainted using a directional neighbor-based interpolation strategy to preserve 3D surface continuity. A localized Gaussian smoothing operation is then applied for seamless restoration. The system is integrated into a user-friendly GUI that supports real-time parameter adjustments and batch processing. Experimental results demonstrate the effective artifact removal while preserving nanoscale structural details, providing a robust, geometry-aware solution for high-fidelity AFM data interpretation.

Jaydeep Rade, Md Hasibul Hasan Hasib, Meric Ozturk et al.

AI-based in silico methods have improved protein structure prediction but often struggle with large protein complexes (PCs) involving multiple interacting proteins due to missing 3D spatial cues. Experimental techniques like Cryo-EM are accurate but costly and time-consuming. We present ProFusion, a hybrid framework that integrates a deep learning model with Atomic Force Microscopy (AFM), which provides high-resolution height maps from random orientations, naturally yielding multi-view data for 3D reconstruction. However, generating a large-scale AFM imaging data set sufficient to train deep learning models is impractical. Therefore, we developed a virtual AFM framework that simulates the imaging process and generated a dataset of ~542,000 proteins with multi-view synthetic AFM images. We train a conditional diffusion model to synthesize novel views from unposed inputs and an instance-specific Neural Radiance Field (NeRF) model to reconstruct 3D structures. Our reconstructed 3D protein structures achieve an average Chamfer Distance within the AFM imaging resolution, reflecting high structural fidelity. Our method is extensively validated on experimental AFM images of various PCs, demonstrating strong potential for accurate, cost-effective protein complex structure prediction and rapid iterative validation using AFM experiments.

Kibon Ku, Talukder Z Jubery, Elijah Rodriguez et al.

This paper presents a NeRF-based framework for point cloud (PCD) reconstruction, specifically designed for indoor high-throughput plant phenotyping facilities. Traditional NeRF-based reconstruction methods require cameras to move around stationary objects, but this approach is impractical for high-throughput environments where objects are rapidly imaged while moving on conveyors or rotating pedestals. To address this limitation, we develop a variant of NeRF-based PCD reconstruction that uses a single stationary camera to capture images as the object rotates on a pedestal. Our workflow comprises COLMAP-based pose estimation, a straightforward pose transformation to simulate camera movement, and subsequent standard NeRF training. A defined Region of Interest (ROI) excludes irrelevant scene data, enabling the generation of high-resolution point clouds (10M points). Experimental results demonstrate excellent reconstruction fidelity, with precision-recall analyses yielding an F-score close to 100.00 across all evaluated plant objects. Although pose estimation remains computationally intensive with a stationary camera setup, overall training and reconstruction times are competitive, validating the method's feasibility for practical high-throughput indoor phenotyping applications. Our findings indicate that high-quality NeRF-based 3D reconstructions are achievable using a stationary camera, eliminating the need for complex camera motion or costly imaging equipment. This approach is especially beneficial when employing expensive and delicate instruments, such as hyperspectral cameras, for 3D plant phenotyping. Future work will focus on optimizing pose estimation techniques and further streamlining the methodology to facilitate seamless integration into automated, high-throughput 3D phenotyping pipelines.

Ali Rabeh, Adarsh Krishnamurthy, Baskar Ganapathysubramanian

Accurate modeling of fluid dynamics around complex geometries is critical for applications such as aerodynamic optimization and biomedical device design. While advancements in numerical methods and high-performance computing have improved simulation capabilities, the computational cost of high-fidelity 3D flow simulations remains a significant challenge. Scientific machine learning (SciML) offers an efficient alternative, enabling rapid and reliable flow predictions. In this study, we evaluate Deep Operator Networks (DeepONet) and Geometric-DeepONet, a variant that incorporates geometry information via signed distance functions (SDFs), on steady-state 3D flow over complex objects. Our dataset consists of 1,000 high-fidelity simulations spanning Reynolds numbers from 10 to 1,000, enabling comprehensive training and evaluation across a range of flow regimes. To assess model generalization, we test our models on a random and extrapolatory train-test splitting. Additionally, we explore a derivative-informed training strategy that augments standard loss functions with velocity gradient penalties and incompressibility constraints, improving physics consistency in 3D flow prediction. Our results show that Geometric-DeepONet improves boundary-layer accuracy by up to 32% compared to standard DeepONet. Moreover, incorporating derivative constraints enhances gradient accuracy by 25% in interpolation tasks and up to 45% in extrapolatory test scenarios, suggesting significant improvement in generalization capabilities to unseen 3D Reynolds numbers.

Elvis Kimara, Mozhgan Hadadi, Jackson Godbersen et al.

The development of artificial intelligence (AI) and machine learning (ML) based tools for 3D phenotyping, especially for maize, has been limited due to the lack of large and diverse 3D datasets. 2D image datasets fail to capture essential structural details such as leaf architecture, plant volume, and spatial arrangements that 3D data provide. To address this limitation, we present MaizeField3D (https://baskargroup.github.io/MaizeField3D/), a curated dataset of 3D point clouds of field-grown maize plants from a diverse genetic panel, designed to be AI-ready for advancing agricultural research. Our dataset includes 1,045 high-quality point clouds of field-grown maize collected using a terrestrial laser scanner (TLS). Point clouds of 520 plants from this dataset were segmented and annotated using a graph-based segmentation method to isolate individual leaves and stalks, ensuring consistent labeling across all samples. This labeled data was then used for fitting procedural models that provide a structured parametric representation of the maize plants. The leaves of the maize plants in the procedural models are represented using Non-Uniform Rational B-Spline (NURBS) surfaces that were generated using a two-step optimization process combining gradient-free and gradient-based methods. We conducted rigorous manual quality control on all datasets, correcting errors in segmentation, ensuring accurate leaf ordering, and validating metadata annotations. The dataset also includes metadata detailing plant morphology and quality, alongside multi-resolution subsampled point cloud data (100k, 50k, 10k points), which can be readily used for different downstream computational tasks. MaizeField3D will serve as a comprehensive foundational dataset for AI-driven phenotyping, plant structural analysis, and 3D applications in agricultural research.

Biswajit Khara, Aditya Balu, Ameya Joshi et al.

We consider a mesh-based approach for training a neural network to produce field predictions of solutions to parametric partial differential equations (PDEs). This approach contrasts current approaches for "neural PDE solvers" that employ collocation-based methods to make point-wise predictions of solutions to PDEs. This approach has the advantage of naturally enforcing different boundary conditions as well as ease of invoking well-developed PDE theory -- including analysis of numerical stability and convergence -- to obtain capacity bounds for our proposed neural networks in discretized domains. We explore our mesh-based strategy, called NeuFENet, using a weighted Galerkin loss function based on the Finite Element Method (FEM) on a parametric elliptic PDE. The weighted Galerkin loss (FEM loss) is similar to an energy functional that produces improved solutions, satisfies a priori mesh convergence, and can model Dirichlet and Neumann boundary conditions. We prove theoretically, and illustrate with experiments, convergence results analogous to mesh convergence analysis deployed in finite element solutions to PDEs. These results suggest that a mesh-based neural network approach serves as a promising approach for solving parametric PDEs with theoretical bounds.

Minsu Cho, Aditya Balu, Ameya Joshi et al.

The paradigm of differentiable programming has significantly enhanced the scope of machine learning via the judicious use of gradient-based optimization. However, standard differentiable programming methods (such as autodiff) typically require that the machine learning models be differentiable, limiting their applicability. Our goal in this paper is to use a new, principled approach to extend gradient-based optimization to functions well modeled by splines, which encompass a large family of piecewise polynomial models. We derive the form of the (weak) Jacobian of such functions and show that it exhibits a block-sparse structure that can be computed implicitly and efficiently. Overall, we show that leveraging this redesigned Jacobian in the form of a differentiable "layer" in predictive models leads to improved performance in diverse applications such as image segmentation, 3D point cloud reconstruction, and finite element analysis.

Anjana Deva Prasad, Aditya Balu, Harshil Shah et al.

Boundary representations (B-reps) using Non-Uniform Rational B-splines (NURBS) are the de facto standard used in CAD, but their utility in deep learning-based approaches is not well researched. We propose a differentiable NURBS module to integrate NURBS representations of CAD models with deep learning methods. We mathematically define the derivatives of the NURBS curves or surfaces with respect to the input parameters (control points, weights, and the knot vector). These derivatives are used to define an approximate Jacobian used for performing the "backward" evaluation to train the deep learning models. We have implemented our NURBS module using GPU-accelerated algorithms and integrated it with PyTorch, a popular deep learning framework. We demonstrate the efficacy of our NURBS module in performing CAD operations such as curve or surface fitting and surface offsetting. Further, we show its utility in deep learning for unsupervised point cloud reconstruction and enforce analysis constraints. These examples show that our module performs better for certain deep learning frameworks and can be directly integrated with any deep-learning framework requiring NURBS.

Aditya Balu, Sergio Botelho, Biswajit Khara et al.

We consider the distributed training of large-scale neural networks that serve as PDE solvers producing full field outputs. We specifically consider neural solvers for the generalized 3D Poisson equation over megavoxel domains. A scalable framework is presented that integrates two distinct advances. First, we accelerate training a large model via a method analogous to the multigrid technique used in numerical linear algebra. Here, the network is trained using a hierarchy of increasing resolution inputs in sequence, analogous to the 'V', 'W', 'F', and 'Half-V' cycles used in multigrid approaches. In conjunction with the multi-grid approach, we implement a distributed deep learning framework which significantly reduces the time to solve. We show the scalability of this approach on both GPU (Azure VMs on Cloud) and CPU clusters (PSC Bridges2). This approach is deployed to train a generalized 3D Poisson solver that scales well to predict output full-field solutions up to the resolution of 512x512x512 for a high dimensional family of inputs.

Jaydeep Rade, Aditya Balu, Ethan Herron et al.

Topology optimization has emerged as a popular approach to refine a component's design and increase its performance. However, current state-of-the-art topology optimization frameworks are compute-intensive, mainly due to multiple finite element analysis iterations required to evaluate the component's performance during the optimization process. Recently, machine learning (ML)-based topology optimization methods have been explored by researchers to alleviate this issue. However, previous ML approaches have mainly been demonstrated on simple two-dimensional applications with low-resolution geometry. Further, current methods are based on a single ML model for end-to-end prediction, which requires a large dataset for training. These challenges make it non-trivial to extend current approaches to higher resolutions. In this paper, we develop deep learning-based frameworks consistent with traditional topology optimization algorithms for 3D topology optimization with a reasonably fine (high) resolution. We achieve this by training multiple networks, each learning a different step of the overall topology optimization methodology, making the framework more consistent with the topology optimization algorithm. We demonstrate the application of our framework on both 2D and 3D geometries. The results show that our approach predicts the final optimized design better (5.76x reduction in total compliance MSE in 2D; 2.03x reduction in total compliance MSE in 3D) than current ML-based topology optimization methods.

Sambit Ghadai, Xian Lee, Aditya Balu et al.

3D object recognition accuracy can be improved by learning the multi-scale spatial features from 3D spatial geometric representations of objects such as point clouds, 3D models, surfaces, and RGB-D data. Current deep learning approaches learn such features either using structured data representations (voxel grids and octrees) or from unstructured representations (graphs and point clouds). Learning features from such structured representations is limited by the restriction on resolution and tree depth while unstructured representations creates a challenge due to non-uniformity among data samples. In this paper, we propose an end-to-end multi-level learning approach on a multi-level voxel grid to overcome these drawbacks. To demonstrate the utility of the proposed multi-level learning, we use a multi-level voxel representation of 3D objects to perform object recognition. The multi-level voxel representation consists of a coarse voxel grid that contains volumetric information of the 3D object. In addition, each voxel in the coarse grid that contains a portion of the object boundary is subdivided into multiple fine-level voxel grids. The performance of our multi-level learning algorithm for object recognition is comparable to dense voxel representations while using significantly lower memory.

Sambit Ghadai, Aditya Balu, Adarsh Krishnamurthy et al.

3D Convolutional Neural Networks (3D-CNN) have been used for object recognition based on the voxelized shape of an object. However, interpreting the decision making process of these 3D-CNNs is still an infeasible task. In this paper, we present a unique 3D-CNN based Gradient-weighted Class Activation Mapping method (3D-GradCAM) for visual explanations of the distinct local geometric features of interest within an object. To enable efficient learning of 3D geometries, we augment the voxel data with surface normals of the object boundary. We then train a 3D-CNN with this augmented data and identify the local features critical for decision-making using 3D GradCAM. An application of this feature identification framework is to recognize difficult-to-manufacture drilled hole features in a complex CAD geometry. The framework can be extended to identify difficult-to-manufacture features at multiple spatial scales leading to a real-time design for manufacturability decision support system.

Aditya Balu, Sambit Ghadai, Gavin Young et al.

this is a duplicate submission(original is arXiv:1612.02141). Hence want to withdraw it

Aditya Balu, Sambit Ghadai, Kin Gwn Lore et al.

3D convolutional neural networks (3D-CNN) have been used for object recognition based on the voxelized shape of an object. In this paper, we present a 3D-CNN based method to learn distinct local geometric features of interest within an object. In this context, the voxelized representation may not be sufficient to capture the distinguishing information about such local features. To enable efficient learning, we augment the voxel data with surface normals of the object boundary. We then train a 3D-CNN with this augmented data and identify the local features critical for decision-making using 3D gradient-weighted class activation maps. An application of this feature identification framework is to recognize difficult-to-manufacture drilled hole features in a complex CAD geometry. The framework can be extended to identify difficult-to-manufacture features at multiple spatial scales leading to a real-time decision support system for design for manufacturability.