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

Rapid yet accurate simulations of fluid dynamics around complex geometries is critical in a variety of engineering and scientific applications, including aerodynamics and biomedical flows. However, while scientific machine learning (SciML) has shown promise, most studies are constrained to simple geometries, leaving complex, real-world scenarios underexplored. This study 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 foundation models significantly outperform neural operators, particularly in data-limited scenarios, and that SDF representations yield superior results with sufficient training data. Despite these advancements, all models struggle with out-of-distribution generalization, highlighting a critical challenge for future SciML applications. By advancing both evaluation methodologies and modeling capabilities, this work paves the way for robust and scalable ML solutions for fluid dynamics across complex geometries.

STITCH: Surface reconstrucTion using Implicit neural representations with Topology Constraints and persistent Homology

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.

FlowBench: A Large Scale Benchmark for Flow Simulation over Complex Geometries

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.

3D Reconstruction of Protein Structures from Multi-view AFM Images using Neural Radiance Fields (NeRFs)

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.

AgEval: A Benchmark for Zero-Shot and Few-Shot Plant Stress Phenotyping with Multimodal LLMs

Plant stress phenotyping traditionally relies on expert assessments and specialized models, limiting scalability in agriculture. Recent advances in multimodal large language models (LLMs) offer potential solutions to this challenge. We present AgEval, a benchmark comprising 12 diverse plant stress phenotyping tasks, to evaluate these models' capabilities. Our study assesses zero-shot and few-shot in-context learning performance of state-of-the-art models, including Claude, GPT, Gemini, and LLaVA. Results show significant performance improvements with few-shot learning, with F1 scores increasing from 46.24% to 73.37% in 8-shot identification for the best-performing model. Few-shot examples from other classes in the dataset have negligible or negative impacts, although having the exact category example helps to increase performance by 15.38%. We also quantify the consistency of model performance across different classes within each task, finding that the coefficient of variance (CV) ranges from 26.02% to 58.03% across models, implying that subject matter expertise is needed - of 'difficult' classes - to achieve reliability in performance. AgEval establishes baseline metrics for multimodal LLMs in agricultural applications, offering insights into their promise for enhancing plant stress phenotyping at scale. Benchmark and code can be accessed at: https://anonymous.4open.science/r/AgEval/

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). SLICE-100K will be the first step in developing a multimodal foundation model for digital manufacturing.

Evaluating NeRFs for 3D Plant Geometry Reconstruction in Field Conditions

We evaluate different Neural Radiance Fields (NeRFs) techniques for reconstructing (3D) plants in varied environments, from indoor settings to outdoor fields. Traditional techniques often struggle to capture the complex details of plants, which is crucial for botanical and agricultural understanding. We evaluate three scenarios with increasing complexity and compare the results with the point cloud obtained using LiDAR as ground truth data. In the most realistic field scenario, the NeRF models achieve a 74.65% F1 score with 30 minutes of training on the GPU, highlighting the efficiency and accuracy of NeRFs in challenging environments. These findings not only demonstrate the potential of NeRF in detailed and realistic 3D plant modeling but also suggest practical approaches for enhancing the speed and efficiency of the 3D reconstruction process.

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.

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.

ZeroForge: Feedforward Text-to-Shape Without 3D Supervision

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