arXiv subjects

Baskar Ganapathysubramanian

Publications and source records attributed to Baskar Ganapathysubramanian.

At least 37 records · Page 2Linked to original sources

arXiv2026

InSpecLearn4SDL: Interpretable Spectral Features Predict Conductivity in Self-Driving Doped Conjugated Polymer Labs

To accelerate materials discovery using self-driving labs (SDLs), we present a machine learning pipeline that predicts the electrical conductivity of doped conjugated polymers using rapid, non-destructive optical spectroscopy. Our approach automates spectral featurization by combining a genetic algorithm with adaptive area-under-the-curve (AUC) computations, creating a quantitative structure-property relationship (QSPR) that links optical response and processing parameters to conductivity. By incorporating SHAP-guided selection and domain-knowledge-based feature expansion, the model matches expert-curated performance while theoretically reducing experimental effort by $\sim 33\%$ by minimizing the need for costly direct conductivity measurements. Notably, the model recovers known physical descriptors in pBTTT and identifies informative tail-state regions correlated with polymer bleaching upon successful doping. This generic, interpretable, small-data-friendly methodology can be extended to other spectroscopic modalities, such as Raman or FTIR, providing a framework for autonomous decision-making in SDLs.

cond-mat.mtrl-sci↗

arXiv2025

Towards smart canopies: Algorithmic design of maize canopy architectures that maximize light use efficiency

We present a computational framework that integrates functional-structural plant modeling (FSPM) with an evolutionary algorithm to optimize three-dimensional maize canopy architecture for enhanced light interception under high-density planting. The optimization revealed an emergent ideotype characterized by two distinct strategies: a vertically stratified leaf profile (steep, narrow upper leaves for penetration; broad, horizontal lower leaves for capture) and a radially tiled azimuthal arrangement that breaks the conventional distichous symmetry of maize to minimize self and mutual shading. Reverse ray-tracing simulations show that this architecture intercepts significantly more photosynthetically active radiation (PAR) than virtual canopies parameterized from high-performing field hybrids, with gains that generalize across multiple U.S. latitudes and planting densities. The optimized trait combinations align with characteristics of modern density-tolerant cultivars, supporting biological plausibility. Because recent gene editing advances enable more independent control of architectural traits, the designs identified here are increasingly feasible. By uncovering effective, non-intuitive trait configurations, our approach provides a scalable, predictive tool to guide breeding targets, improve light-use efficiency, and ultimately support sustainable yield gains.

q-bio.QM↗

arXiv2025

FloraForge: LLM-Assisted Procedural Generation of Editable and Analysis-Ready 3D Plant Geometric Models For Agricultural Applications

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.

cs.CV↗

arXiv2025

Predicting Time-Dependent Flow Over Complex Geometries Using Operator Networks

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.

physics.flu-dyn↗

arXiv2025

Crossmodal learning for Crop Canopy Trait Estimation

Recent advances in plant phenotyping have driven widespread adoption of multi sensor platforms for collecting crop canopy reflectance data. This includes the collection of heterogeneous data across multiple platforms, with Unmanned Aerial Vehicles (UAV) seeing significant usage due to their high performance in crop monitoring, forecasting, and prediction tasks. Similarly, satellite missions have been shown to be effective for agriculturally relevant tasks. In contrast to UAVs, such missions are bound to the limitation of spatial resolution, which hinders their effectiveness for modern farming systems focused on micro-plot management. In this work, we propose a cross modal learning strategy that enriches high-resolution satellite imagery with UAV level visual detail for crop canopy trait estimation. Using a dataset of approximately co registered satellite UAV image pairs collected from replicated plots of 84 hybrid maize varieties across five distinct locations in the U.S. Corn Belt, we train a model that learns fine grained spectral spatial correspondences between sensing modalities. Results show that the generated UAV-like representations from satellite inputs consistently outperform real satellite imagery on multiple downstream tasks, including yield and nitrogen prediction, demonstrating the potential of cross-modal correspondence learning to bridge the gap between satellite and UAV sensing in agricultural monitoring.

cs.CV↗

arXiv2025

Slice-100K: A Multimodal Dataset for Extrusion-based 3D Printing

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.

cs.CV↗

arXiv2025

High-Resolution Thermal Simulation Framework for Extrusion-based Additive Manufacturing of Complex Geometries

Accurate simulation of the printing process is essential for improving print quality, reducing waste, and optimizing the printing parameters of extrusion-based additive manufacturing. Traditional additive manufacturing simulations are very compute-intensive and are not scalable to simulate even moderately sized geometries. In this paper, we propose a general framework for creating a digital twin of the dynamic printing process by performing physics simulations with the intermediate print geometries. Our framework takes a general extrusion-based additive manufacturing G-code, generates an analysis-suitable voxelized geometry representation from the print schedule, and performs physics-based (transient thermal) simulations of the printing process. Our approach leverages adaptive octree meshes for both geometry representation as well as for fast simulations to address real-time predictions. We demonstrate the effectiveness of our method by simulating the printing of complex geometries at high voxel resolutions with both sparse and dense infills. Our results show that this approach scales to high voxel resolutions and can predict the transient heat distribution as the print progresses. Because the simulation runs faster than real print time, the same engine could, in principle, feed thermal predictions back to the machine controller (e.g., to adjust fan speed or extrusion rate). The present study establishes the computational foundations for a real-time digital twin, which can be used for closed control loop control in the future.

cs.GR↗

arXiv2025

Direct Flow Simulations with Implicit Neural Representation of Complex Geometry

Implicit neural representations have emerged as a powerful approach for encoding complex geometries as continuous functions. These implicit models are widely used in computer vision and 3D content creation, but their integration into scientific computing workflows, such as finite element or finite volume simulations, remains limited. One reason is that conventional simulation pipelines require explicit geometric inputs (meshes), forcing INR-based shapes to be converted to meshes--a step that introduces approximation errors, computational overhead, and significant manual effort. Immersed boundary methods partially alleviate this issue by allowing simulations on background grids without body-fitted meshes. However, they still require an explicit boundary description and can suffer from numerical artifacts, such as sliver cut cells. The shifted boundary method (SBM) eliminates the need for explicit geometry by using grid-aligned surrogate boundaries, making it inherently compatible with implicit shape representations. Here, we present a framework that directly couples neural implicit geometries with SBM to perform high-fidelity fluid flow simulations without any intermediate mesh generation. By leveraging neural network inference, our approach computes the surrogate boundary and distance vectors required by SBM on-the-fly directly from the INR, thus completely bypassing traditional geometry processing. We demonstrate this approach on canonical 2D and 3D flow benchmarks (lid-driven cavity flows) and complex geometries (gyroids, the Stanford bunny, and AI-generated shapes), achieving simulation accuracy comparable to conventional mesh-based methods. This work highlights a novel pathway for integrating AI-driven geometric representations into computational physics, establishing INRs as a versatile and scalable tool for simulations and removing a long-standing bottleneck in geometry handling.

cs.GR↗

arXiv2025

MaizeField3D: A Curated 3D Point Cloud and Procedural Model Dataset of Field-Grown Maize from a Diversity Panel

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.

cs.CV↗

arXiv2025

Mechanics Simulation with Implicit Neural Representations of Complex Geometries

Implicit Neural Representations (INRs), characterized by neural network-encoded signed distance fields, provide a powerful means to represent complex geometries continuously and efficiently. While successful in computer vision and generative modeling, integrating INRs into computational analysis workflows, such as finite element simulations, remains underdeveloped. In this work, we propose a computational framework that seamlessly combines INRs with the Shifted Boundary Method (SBM) for high-fidelity linear elasticity simulations without explicit geometry transformations. By directly querying the neural implicit geometry, we obtain the surrogate boundaries and distance vectors essential for SBM, effectively eliminating the meshing step. We demonstrate the efficacy and robustness of our approach through elasticity simulations on complex geometries (Stanford Bunny, Eiffel Tower, gyroids) sourced from triangle soups and point clouds. Our method showcases significant computational advantages and accuracy, underscoring its potential in biomedical, geophysical, and advanced manufacturing applications.

cs.CE↗

arXiv2025

TerraIncognita: A Dynamic Benchmark for Species Discovery Using Frontier Models

The rapid global loss of biodiversity, particularly among insects, represents an urgent ecological crisis. Current methods for insect species discovery are manual, slow, and severely constrained by taxonomic expertise, hindering timely conservation actions. We introduce TerraIncognita, a dynamic benchmark designed to evaluate state-of-the-art multimodal models for the challenging problem of identifying unknown, potentially undescribed insect species from image data. Our benchmark dataset combines a mix of expertly annotated images of insect species likely known to frontier AI models, and images of rare and poorly known species, for which few/no publicly available images exist. These images were collected from underexplored biodiversity hotspots, realistically mimicking open-world discovery scenarios faced by ecologists. The benchmark assesses models' proficiency in hierarchical taxonomic classification, their capability to detect and abstain from out-of-distribution (OOD) samples representing novel species, and their ability to generate explanations aligned with expert taxonomic knowledge. Notably, top-performing models achieve over 90\% F1 at the Order level on known species, but drop below 2\% at the Species level, highlighting the sharp difficulty gradient from coarse to fine taxonomic prediction (Order $\rightarrow$ Family $\rightarrow$ Genus $\rightarrow$ Species). TerraIncognita will be updated regularly, and by committing to quarterly dataset expansions (of both known and novel species), will provide an evolving platform for longitudinal benchmarking of frontier AI methods. All TerraIncognita data, results, and future updates are available \href{https://baskargroup.github.io/TerraIncognita/}{here}.

cs.CV↗

arXiv2025

Towards Large Reasoning Models for Agriculture

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/

cs.LG↗

arXiv2025

MPFBench: A Large Scale Dataset for SciML of Multi-Phase-Flows: Droplet and Bubble Dynamics

Multiphase fluid dynamics, such as falling droplets and rising bubbles, are critical to many industrial applications. However, simulating these phenomena efficiently is challenging due to the complexity of instabilities, wave patterns, and bubble breakup. This paper investigates the potential of scientific machine learning (SciML) to model these dynamics using neural operators and foundation models. We apply sequence-to-sequence techniques on a comprehensive dataset generated from 11,000 simulations, comprising 1 million time snapshots, produced with a well-validated Lattice Boltzmann method (LBM) framework. The results demonstrate the ability of machine learning models to capture transient dynamics and intricate fluid interactions, paving the way for more accurate and computationally efficient SciML-based solvers for multiphase applications.

physics.flu-dyn↗

arXiv2025

SC-NeRF: NeRF-based Point Cloud Reconstruction using a Stationary Camera for Agricultural Applications

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.

cs.CV↗

arXiv2025

Geometry Matters: Benchmarking Scientific ML Approaches for Flow Prediction around Complex Geometries

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.

cs.LG↗

arXiv2025

Optimizing Navigation And Chemical Application in Precision Agriculture With Deep Reinforcement Learning And Conditional Action Tree

This paper presents a novel reinforcement learning (RL)-based planning scheme for optimized robotic management of biotic stresses in precision agriculture. The framework employs a hierarchical decision-making structure with conditional action masking, where high-level actions direct the robot's exploration, while low-level actions optimize its navigation and efficient chemical spraying in affected areas. The key objectives of optimization include improving the coverage of infected areas with limited battery power and reducing chemical usage, thus preventing unnecessary spraying of healthy areas of the field. Our numerical experimental results demonstrate that the proposed method, Hierarchical Action Masking Proximal Policy Optimization (HAM-PPO), significantly outperforms baseline practices, such as LawnMower navigation + indiscriminate spraying (Carpet Spray), in terms of yield recovery and resource efficiency. HAM-PPO consistently achieves higher yield recovery percentages and lower chemical costs across a range of infection scenarios. The framework also exhibits robustness to observation noise and generalizability under diverse environmental conditions, adapting to varying infection ranges and spatial distribution patterns.

cs.RO↗

arXiv2025

3D Neural Operator-Based Flow Surrogates around 3D geometries: Signed Distance Functions and Derivative Constraints

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.

cs.LG↗

arXiv2025

3D Multiphase Heterogeneous Microstructure Generation Using Conditional Latent Diffusion Models

The ability to generate 3D multiphase microstructures on-demand with targeted attributes can greatly accelerate the design of advanced materials. Here, we present a conditional latent diffusion model (LDM) framework that rapidly synthesizes high-fidelity 3D multiphase microstructures tailored to user specifications. Using this approach, we generate diverse two-phase and three-phase microstructures at high resolution (volumes of $128 \times 128 \times 64$ voxels, representing $>10^6$ voxels each) within seconds, overcoming the scalability and time limitations of traditional simulation-based methods. Key design features, such as desired volume fractions and tortuosities, are incorporated as controllable inputs to guide the generative process, ensuring that the output structures meet prescribed statistical and topological targets. Moreover, the framework predicts corresponding manufacturing (processing) parameters for each generated microstructure, helping to bridge the gap between digital microstructure design and experimental fabrication. While demonstrated on organic photovoltaic (OPV) active-layer morphologies, the flexible architecture of our approach makes it readily adaptable to other material systems and microstructure datasets. By combining computational efficiency, adaptability, and experimental relevance, this framework addresses major limitations of existing methods and offers a powerful tool for accelerated materials discovery.

cond-mat.mtrl-sci↗