A significant gap exists between theory and practice in deep learning. Generalization and approximation error bounds are often derived for simplified models or are too loose to be informative. Many rely on the manifold hypothesis and on geometric regularity such as intrinsic dimension, curvature, and reach. Progress requires insight into data-manifold geometry and suitable benchmarks, yet existing options are polarized: analytic manifolds with known geometry but limited applicability, or real-world datasets where geometry is only coarsely estimable. We introduce a benchmarking framework for studying data geometry. We repurpose and extend dSprites and COIL-20 with additional transformation dimensions and dense, axis-aligned sampling, and pair them with finite-difference estimators that recover curvature, reach, and volume at near-ground-truth accuracy in a regime where general-purpose estimators are unreliable or difficult to deploy. The framework is intended as a controlled testbed, useful as a calibration environment for geometric estimators and a sandbox for probing theoretical assumptions. To illustrate its use, we present two application studies, namely assessing the scaling behavior of the bounds of Genovese et al. and Fefferman et al., and tracking the layer-wise geometry of a $β$-VAE, highlighting the behavior of current bounds and the value of controlled benchmarks for guiding and validating future theory. A reference implementation is available at https://github.com/koulakis/manifold-microscope.

A.1 Broader impact Our work introduces a general method for unsupervised 3D segmentation that can be used for any 3D voxel-grid data. This line of work is especially useful for analyzing biomedical data, as many different types of biomedical data are in volumetric form and lack the ground truth annotations required for fully-or semi-supervised segmentation. For example, we may wish to study diseased tissue but do not have sufficient understanding to ensure that unexplored features of interests are labelled in training data. We illustrate the potential of our proposed approach for scientific discovery applications using our example of cryo-ET data in the Appendix. The discovered features can now be analyzed for their chemical identities and functions, in diseased vs. healthy cells.

The Hausdorff distance (HD) is a robust measure of set dissimilarity, but computing it exactly on large, high-dimensional datasets is prohibitively expensive. We propose \textbf{ProHD}, a projection-guided approximation algorithm that dramatically accelerates HD computation while maintaining high accuracy. ProHD identifies a small subset of candidate "extreme" points by projecting the data onto a few informative directions (such as the centroid axis and top principal components) and computing the HD on this subset. This approach guarantees an underestimate of the true HD with a bounded additive error and typically achieves results within a few percent of the exact value. In extensive experiments on image, physics, and synthetic datasets (up to two million points in $D=256$), ProHD runs 10--100$\times$ faster than exact algorithms while attaining 5--20$\times$ lower error than random sampling-based approximations. Our method enables practical HD calculations in scenarios like large vector databases and streaming data, where quick and reliable set distance estimation is needed.

Trajectory similarity retrieval is an important part of spatiotemporal data mining, however, existing methods have the following limitations: traditional metrics are computationally expensive, while learning-based methods suffer from substantial training costs and potential instability. This paper addresses these problems by proposing Geometric Prototype Trajectory Hashing (GeoPTH), a novel, lightweight, and non-learning framework for efficient category-based trajectory retrieval. GeoPTH constructs data-dependent hash functions by using representative trajectory prototypes, i.e., small point sets preserving geometric characteristics, as anchors. The hashing process is efficient, which involves mapping a new trajectory to its closest prototype via a robust, Hausdorff metric. Extensive experiments show that GeoPTH's retrieval accuracy is highly competitive with both traditional metrics and state-of-the-art learning methods, and it significantly outperforms binary codes generated through simple binarization of the learned embeddings. Critically, GeoPTH consistently outperforms all competitors in terms of efficiency. Our work demonstrates that a lightweight, prototype-centric approach offers a practical and powerful alternative, achieving an exceptional retrieval performance and computational efficiency.

Diffusion MRI (dMRI) provides a distinctive means to probe the microstructural architecture of living tissue, facilitating applications such as brain connectivity analysis, modeling across multiple conditions, and the estimation of macrostructural features. Tractography, which emerged in the final years of the 20th century and accelerated in the early 21st century, is a technique for visualizing white matter pathways in the brain using dMRI. Most diffusion tractography methods rely on procedural streamline propagators or global energy minimization methods. Although recent advancements in deep learning have enabled tasks that were previously challenging, existing tractography approaches are often non-differentiable, limiting their integration in end-to-end learning frameworks. While progress has been made in representing streamlines in differentiable frameworks, no existing method offers fully differentiable propagation. In this work, we propose a fully differentiable solution that retains numerical fidelity with a leading streamline algorithm. The key is that our PyTorch-engineered streamline propagator has no components that block gradient flow, making it fully differentiable. We show that our method matches standard propagators while remaining differentiable. By translating streamline propagation into a differentiable PyTorch framework, we enable deeper integration of tractography into deep learning workflows, laying the foundation for a new category of macrostructural reasoning that is not only computationally robust but also scientifically rigorous.

Equation discovery from data is a core challenge in machine learning for science, requiring the recovery of concise symbolic expressions that govern complex physical and geometric phenomena. Recent approaches with large language models (LLMs) show promise in symbolic regression, but their success often hinges on memorized formulas or overly simplified functional forms. Existing benchmarks exacerbate this limitation: they focus on scalar functions, ignore domain grounding, and rely on brittle string-matching based metrics that fail to capture scientific equivalence. We introduce SurfaceBench, first comprehensive benchmark for symbolic surface discovery. SurfaceBench comprises 183 tasks across 15 categories of symbolic complexity, spanning explicit, implicit, and parametric equation representation forms. Each task includes ground-truth equations, variable semantics, and synthetically sampled three dimensional data. Unlike prior SR datasets, our tasks reflect surface-level structure, resist LLM memorization through novel symbolic compositions, and are grounded in scientific domains such as fluid dynamics, robotics, electromagnetics, and geometry. To evaluate equation discovery quality, we pair symbolic checks with geometry-aware metrics such as Chamfer and Hausdorff distances, capturing both algebraic fidelity and spatial reconstruction accuracy. Our experiments reveal that state-of-the-art frameworks, while occasionally successful on specific families, struggle to generalize across representation types and surface complexities. SurfaceBench thus establishes a challenging and diagnostic testbed that bridges symbolic reasoning with geometric reconstruction, enabling principled benchmarking of progress in compositional generalization, data-driven scientific induction, and geometry-aware reasoning with LLMs. We release the code here: https://github.com/Sanchit-404/surfacebench

Accurate segmentation of the left atrium (LA) from cardiac MRI is critical for guiding atrial fibrillation (AF) ablation and constructing biophysical cardiac models. Manual delineation is time-consuming, observer-dependent, and impractical for large-scale or time-sensitive clinical workflows. Deep learning methods, particularly convolutional architectures, have recently demonstrated superior performance in medical image segmentation tasks. In this study, we applied the nnU-Net framework, an automated, self-configuring deep learning segmentation architecture, to the Left Atrial Segmentation Challenge 2013 dataset. The dataset consists of thirty MRI scans with corresponding expert-annotated masks. The nnU-Net model automatically adapted its preprocessing, network configuration, and training pipeline to the characteristics of the MRI data. Model performance was quantitatively evaluated using the Dice similarity coefficient (DSC), and qualitative results were compared against expert segmentations. The proposed nnUNet model achieved a mean Dice score of 93.5, demonstrating high overlap with expert annotations and outperforming several traditional segmentation approaches reported in previous studies. The network exhibited robust generalization across variations in left atrial shape, contrast, and image quality, accurately delineating both the atrial body and proximal pulmonary veins.

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