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Jul 28

Aperiodic Structures Never Collapse: Fibonacci Hierarchies for Lossless Compression

We study whether an aperiodic hierarchy can provide a structural advantage for lossless compression over periodic alternatives. We show that Fibonacci quasicrystal tilings avoid the finite-depth collapse that affects periodic hierarchies: usable n-gram lookup positions remain non-zero at every level, while periodic tilings collapse after O(log p) levels for period p. This yields an aperiodic hierarchy advantage: dictionary reuse remains available across all scales instead of vanishing beyond a finite depth. Our analysis gives four main consequences. First, the Golden Compensation property shows that the exponential decay in the number of positions is exactly balanced by the exponential growth in phrase length, so potential coverage remains scale-invariant with asymptotic value Wvarphi/5. Second, using the Sturmian complexity law p(n)=n+1, we show that Fibonacci/Sturmian hierarchies maximize codebook coverage efficiency among binary aperiodic tilings. Third, under long-range dependence, the resulting hierarchy achieves lower coding entropy than comparable periodic hierarchies. Fourth, redundancy decays super-exponentially with depth, whereas periodic systems remain locked at the depth where collapse occurs. We validate these results with Quasicryth, a lossless text compressor built on a ten-level Fibonacci hierarchy with phrase lengths {2,3,5,8,13,21,34,55,89,144}. In controlled A/B experiments with identical codebooks, the aperiodic advantage over a Period-5 baseline grows from 36{,}243 B at 3 MB to 11{,}089{,}469 B at 1 GB, explained by the activation of deeper hierarchy levels. On enwik9, Quasicryth achieves 225{,}918{,}349 B (22.59%), with 20{,}735{,}733 B saved by the Fibonacci tiling relative to no tiling.

  • 1 authors
·
Mar 16 2

NeuralRemaster: Phase-Preserving Diffusion for Structure-Aligned Generation

Standard diffusion corrupts data using Gaussian noise whose Fourier coefficients have random magnitudes and random phases. While effective for unconditional or text-to-image generation, corrupting phase components destroys spatial structure, making it ill-suited for tasks requiring geometric consistency, such as re-rendering, simulation enhancement, and image-to-image translation. We introduce Phase-Preserving Diffusion φ-PD, a model-agnostic reformulation of the diffusion process that preserves input phase while randomizing magnitude, enabling structure-aligned generation without architectural changes or additional parameters. We further propose Frequency-Selective Structured (FSS) noise, which provides continuous control over structural rigidity via a single frequency-cutoff parameter. φ-PD adds no inference-time cost and is compatible with any diffusion model for images or videos. Across photorealistic and stylized re-rendering, as well as sim-to-real enhancement for driving planners, φ-PD produces controllable, spatially aligned results. When applied to the CARLA simulator, φ-PD improves CARLA-to-Waymo planner performance by 50\%. The method is complementary to existing conditioning approaches and broadly applicable to image-to-image and video-to-video generation. Videos, additional examples, and code are available on our https://yuzeng-at-tri.github.io/ppd-page/{project page}.

  • 6 authors
·
Dec 4, 2025 2

Cylindric plane partitions, Lambda determinants, Commutants in semicircular systems

This thesis is divided into three parts. The first part deals with cylindric plane partitions. The second with lambda-determinants and the third with commutators in semi-circular systems. For more detailed abstract please see inside. Cylindric plane partitions may be thought of as a natural generalization of reverse plane partitions. A generating series for the enumeration of cylindric plane partitions was recently given by Borodin. The first result of section one is a new bijective proof of Borodin's identity which makes use of Fomin's growth diagram framework for generalized RSK correspondences. The second result is a (q,t)-analog of Borodin's identity which extends previous work by Okada in the reverse plane partition case. The third result is an explicit combinatorial interpretation of the Macdonald weight occurring in the (q,t)-analog using the non-intersecting lattice path model for cylindric plane partitions. Alternating sign matrices were discovered by Robbins and Rumsey whilst studying λ-determinants. In the second part of this thesis we prove a multi-parameter generalization of the λ-determinant, generalizing a recent result by di Francesco. Like the original λ-determinant, our formula exhibits the Laurent phenomenon. Semicircular systems were first introduced by Voiculescu as a part of his study of von Neumann algebras. In the third part of this thesis we study certain commutator subalgebras of the semicircular system. We find a projection matrix with an interesting self-similar structure. Making use of our projection formula we given an alternative, elementary proof that the semicircular system is a factor.

  • 1 authors
·
Oct 25, 2021

Efficient Encoding of Graphics Primitives with Simplex-based Structures

Grid-based structures are commonly used to encode explicit features for graphics primitives such as images, signed distance functions (SDF), and neural radiance fields (NeRF) due to their simple implementation. However, in n-dimensional space, calculating the value of a sampled point requires interpolating the values of its 2^n neighboring vertices. The exponential scaling with dimension leads to significant computational overheads. To address this issue, we propose a simplex-based approach for encoding graphics primitives. The number of vertices in a simplex-based structure increases linearly with dimension, making it a more efficient and generalizable alternative to grid-based representations. Using the non-axis-aligned simplicial structure property, we derive and prove a coordinate transformation, simplicial subdivision, and barycentric interpolation scheme for efficient sampling, which resembles transformation procedures in the simplex noise algorithm. Finally, we use hash tables to store multiresolution features of all interest points in the simplicial grid, which are passed into a tiny fully connected neural network to parameterize graphics primitives. We implemented a detailed simplex-based structure encoding algorithm in C++ and CUDA using the methods outlined in our approach. In the 2D image fitting task, the proposed method is capable of fitting a giga-pixel image with 9.4% less time compared to the baseline method proposed by instant-ngp, while maintaining the same quality and compression rate. In the volumetric rendering setup, we observe a maximum 41.2% speedup when the samples are dense enough.

  • 2 authors
·
Nov 26, 2023

Model-agnostic search for the quasinormal modes of gravitational wave echoes

Post-merger gravitational wave echoes provide a unique opportunity to probe the near-horizon structure of astrophysical black holes, that may be modified due to non-perturbative quantum gravity phenomena. However, since the waveform is subject to large theoretical uncertainties, it is necessary to develop model-agnostic search methods for detecting echoes from observational data. A promising strategy is to identify the characteristic quasinormal modes (QNMs) associated with echoes, {\it in frequency space}, which complements existing searches of quasiperiodic pulses in time. In this study, we build upon our previous work targeting these modes by incorporating relative phase information to optimize the Bayesian search algorithm. Using a new phase-marginalized likelihood, the performance can be significantly improved for well-resolved QNMs. This enables an efficient model-agnostic search for QNMs of different shapes by using a simple search template. To demonstrate the robustness of the search algorithm, we construct four complementary benchmarks for the echo waveform that span a diverse range of different theoretical possibilities for the near-horizon structure. We then validate our Bayesian search algorithms by injecting the benchmark models into different realizations of Gaussian noise. Using two types of phase-marginalized likelihoods, we find that the search algorithm can efficiently detect the corresponding QNMs. Therefore, our search strategy provides a concrete Bayesian and model-agnostic approach to "quantum black hole seismology".

  • 4 authors
·
Aug 2, 2023

Accelerating the Search for Superconductors Using Machine Learning

Prediction of critical temperature (T_c) of a superconductor remains a significant challenge in condensed matter physics. While the BCS theory explains superconductivity in conventional superconductors, there is no framework to predict T_c of unconventional, higher T_{c} superconductors. Quantum Structure Diagrams (QSD) were successful in establishing structure-property relationship for superconductors, quasicrystals, and ferroelectric materials starting from chemical composition. Building on the QSD ideas, we demonstrate that the principal component analysis of superconductivity data uncovers the clustering of various classes of superconductors. We use machine learning analysis and cleaned databases of superconductors to develop predictive models of T_c of a superconductor using its chemical composition. Earlier studies relied on datasets with inconsistencies, leading to suboptimal predictions. To address this, we introduce a data-cleaning workflow to enhance the statistical quality of superconducting databases by eliminating redundancies and resolving inconsistencies. With this improvised database, we apply a supervised machine learning framework and develop a Random Forest model to predict superconductivity and T_c as a function of descriptors motivated from Quantum Structure Diagrams. We demonstrate that this model generalizes effectively in reasonably accurate prediction of T_{c} of compounds outside the database. We further employ our model to systematically screen materials across materials databases as well as various chemically plausible combinations of elements and predict Tl_{5}Ba_{6}Ca_{6}Cu_{9}O_{29} to exhibit superconductivity with a T_{c} sim 105 K. Being based on the descriptors used in QSD's, our model bypasses structural information and predicts T_{c} merely from the chemical composition.

  • 2 authors
·
May 17, 2025

d-SEAMS: Deferred Structural Elucidation Analysis for Molecular Simulations

Structural analyses are an integral part of computational research on nucleation and supercooled water, whose accuracy and efficiency can impact the validity and feasibility of such studies. The underlying molecular mechanisms of these often elusive and computationally expensive processes can be inferred from the evolution of ice-like structures, determined using appropriate structural analysis techniques. We present d-SEAMS, a free and open-source post-processing engine for the analysis of molecular dynamics trajectories, which is specifically able to qualitatively classify ice structures, in both strong confinement and bulk systems. For the first time, recent algorithms for confined ice structure determination have been implemented, along with topological network criteria for bulk ice structure determination. Recognizing the need for customization in structural analysis, d-SEAMS has a unique code architecture, built with `nix`, employing a `YAML`-`Lua` scripting pipeline. The software has been designed to be user-friendly and easy to extend. The engine outputs are compatible with popular graphics software suites, allowing for immediate visual insights into the systems studied. We demonstrate the features of d-SEAMS by using it to analyze nucleation in the bulk regime and for quasi-one and quasi-two-dimensional systems. Structural time evolution and quantitative metrics are determined for heterogenous ice nucleation on a silver-exposed beta-AgI surface, homogenous ice nucleation, flat monolayer square ice formation and freezing of an ice nanotube.

  • 3 authors
·
Sep 21, 2019 1

Sycophancy as Material Failure under Pushback Loading: A Multi-Axis Characterization Across Three Loading Cases and up to Seventeen Material Charges

Sycophancy in LLMs is documented across 70+ papers, but expert agreement on construct boundaries remains low (ICC=.184; Ye et al., 2026). The construct fragments because behavioral classification depends on which surface form is privileged. We adopt a materials-science framing: conversation as test specimen under load, LLM-model as material charge, pushback as progressive load, stance-flip as material failure. We characterize this failure across three loading cases (debate n=1000; false-presuppositions n=3400; ethical-setting n=3400; 10-17 material charges per case; 7800 specimens total) using 14 turn-level axis-measurements spanning velocity, damage accumulation, frame-drift, brittleness, and direction stability, plus three speaker-resolved axes from an independent pipeline. The measurements are Hooke-coupled (σ= E cdot varepsilon analog) and reproduce across loading cases with effects up to |r_{rb}| = 0.35 on debate; the sign structure adds a second pattern: the ethical-setting case inverts the velocity and accumulation blocks. Variance composition partitions into two profiles: debate is charge-dominated (brittle-fracture-like: the material grade decides), false-presuppositions and ethical-setting are topic-dominated (creep-like: the load decides); the ratios (2.03 vs 0.13/0.17) are estimator-dependent, for debate even in direction. Cross-judge reliability (GPT-4o vs Haiku 4.5) shows debate scoring is judge-robust (Cohen's κ= 0.88) while false-presupposition scoring is judge-sensitive (κ= 0.36) -- a caveat single-judge benchmarks must report. This is the methodological move Ye et al.'s diagnosis calls for: a multi-axis characterization that does not depend on which surface form of the construct one privileges.

  • 1 authors
·
Jun 14

Procedural Generation of Grain Orientations using the Wave Function Collapse Algorithm

Statistics of grain sizes and orientations in metals correlate to the material's mechanical properties. Reproducing representative volume elements for further analysis of deformation and failure in metals, like 316L stainless steel, is particularly important due to their wide use in manufacturing goods today. Two approaches, initially created for video games, were considered for the procedural generation of representative grain microstructures. The first is the Wave Function Collapse (WFC) algorithm, and the second is constraint propagation and probabilistic inference through Markov Junior, a free and open-source software. This study aimed to investigate these two algorithms' effectiveness in using reference electron backscatter diffraction (EBSD) maps and recreating a statistically similar one that could be used in further research. It utilized two stainless steel EBSD maps as references to test both algorithms. First, the WFC algorithm was too constricting and, thus, incapable of producing images that resembled EBSDs. The second, MarkovJunior, was much more effective in creating a Voronoi tessellation that could be used to create an EBSD map in Python. When comparing the results between the reference and the generated EBSD, we discovered that the orientation and volume fractions were extremely similar. With the study, it was concluded that MarkovJunior is an effective machine learning tool that can reproduce representative grain microstructures.

  • 3 authors
·
Nov 20, 2023

A Topological and Operator Algebraic Framework for Asynchronous Lattice Dynamical Systems

I introduce a novel mathematical framework integrating topological dynamics, operator algebras, and ergodic geometry to study lattices of asynchronous metric dynamical systems. Each node in the lattice carries an internal flow represented by a one-parameter family of operators, evolving on its own time scale. I formalize stratified state spaces capturing multiple levels of synchronized behavior, define an asynchronous evolution metric that quantifies phase-offset distances between subsystems, and characterize emergent coherent topologies arising when subsystems synchronize. Within this framework, I develop formal operators for the evolution of each subsystem and give precise conditions under which phase-aligned synchronization occurs across the lattice. The main results include: (1) the existence and uniqueness of coherent (synchronized) states under a contractive coupling condition, (2) stability of these coherent states and criteria for their emergence as a collective phase transition in a continuous operator topology, and (3) the influence of symmetries, with group-invariant coupling leading to flow-invariant synchrony subspaces and structured cluster dynamics. Proofs are given for each theorem, demonstrating full mathematical rigor. In a final section, I discuss hypothetical applications of this framework to symbolic lattice systems (e.g. subshifts), to invariant group actions on dynamical lattices, and to operator fields over stratified manifolds in the spirit of noncommutative geometry. Throughout, I write in the first person to emphasize the exploratory nature of this work. The paper avoids any reference to cosmology or observers, focusing instead on clean, formal mathematics suitable for a broad array of dynamical systems.

  • 1 authors
·
May 14, 2025

anyakrakusuma: A Python Library for Entropic Schrödinger Bridges on Idealized Geometries

We present anyakrakusuma, an open-source Python library that solves the discrete static Schrödinger bridge problem, the entropically regularized counterpart of optimal transport, through a log-domain Sinkhorn--Knopp iteration and reconstructs the entropic interpolation between two empirical point clouds. The solver is paired with a diagnostic pipeline that characterizes the optimal coupling and the intermediate distributions through information-theoretic and geometric measures. We exercise the library on four idealized planar cases spanning a circle-to-circle dilation, a spiral-to-mixture fragmentation, a rigid reorientation of two moons, and a Lissajous-to-trefoil deformation. The log-domain formulation is necessary rather than merely convenient at the parameters studied, where the cost-to-regularization ratio reaches four hundred and the Gibbs kernel underflows double precision across most of its range; the iteration nonetheless attains a marginal residual of 10^{-9} and unit marginal fidelity in every case. Residual histories decay geometrically over approximately eight decades at per-iteration contraction factors between 0.966 and 0.976, which are local rates near the fixed point that lie many orders of magnitude below the worst-case Hilbert-metric bound. The covariance analysis recovers an imposed ninety-degree reorientation to within 0.07^circ, roughly forty times smaller than its uncertainty, across a masked interval of near-isotropy on which the principal axis is unobservable. The diagnostics are reported with explicit attention to the regimes in which each is well defined, including the differential entropy, which is meaningful only on the open interpolation interval. The presented cases are constructed rather than measured; quantitative application to empirical point clouds requires further study.

  • 10 authors
·
Jul 19

Scalable Diffusion for Materials Generation

Generative models trained on internet-scale data are capable of generating novel and realistic texts, images, and videos. A natural next question is whether these models can advance science, for example by generating novel stable materials. Traditionally, models with explicit structures (e.g., graphs) have been used in modeling structural relationships in scientific data (e.g., atoms and bonds in crystals), but generating structures can be difficult to scale to large and complex systems. Another challenge in generating materials is the mismatch between standard generative modeling metrics and downstream applications. For instance, common metrics such as the reconstruction error do not correlate well with the downstream goal of discovering stable materials. In this work, we tackle the scalability challenge by developing a unified crystal representation that can represent any crystal structure (UniMat), followed by training a diffusion probabilistic model on these UniMat representations. Our empirical results suggest that despite the lack of explicit structure modeling, UniMat can generate high fidelity crystal structures from larger and more complex chemical systems, outperforming previous graph-based approaches under various generative modeling metrics. To better connect the generation quality of materials to downstream applications, such as discovering novel stable materials, we propose additional metrics for evaluating generative models of materials, including per-composition formation energy and stability with respect to convex hulls through decomposition energy from Density Function Theory (DFT). Lastly, we show that conditional generation with UniMat can scale to previously established crystal datasets with up to millions of crystals structures, outperforming random structure search (the current leading method for structure discovery) in discovering new stable materials.

  • 7 authors
·
Oct 18, 2023

Modular versus Hierarchical: A Structural Signature of Topic Popularity in Mathematical Research

Mathematical researchers, especially those in early-career positions, face critical decisions about topic specialization with limited information about the collaborative environments of different research areas. The aim of this paper is to study how the popularity of a research topic is associated with the structure of that topic's collaboration network, as observed by a suite of measures capturing organizational structure at several scales. We apply these measures to 1,938 algorithmically discovered topics across 121,391 papers sourced from arXiv metadata during the period 2020--2025. Our analysis, which controls for the confounding effects of network size, reveals a structural dichotomy--we find that popular topics organize into modular "schools of thought," while niche topics maintain hierarchical core-periphery structures centered around established experts. This divide is not an artifact of scale, but represents a size-independent structural pattern correlated with popularity. We also document a "constraint reversal": after controlling for size, researchers in popular fields face greater structural constraints on collaboration opportunities, contrary to conventional expectations. Our findings suggest that topic selection is an implicit choice between two fundamentally different collaborative environments, each with distinct implications for a researcher's career. To make these structural patterns transparent to the research community, we developed the Math Research Compass (https://mathresearchcompass.com), an interactive platform providing data on topic popularity and collaboration patterns across mathematical topics.

  • 1 authors
·
Jun 28, 2025

Coherent Structures Governing Transport at Turbulent Interfaces

In an experiment on a turbulent jet, we detect interfacial turbulent layers in a frame that moves, on average, along with the \tnti. This significantly prolongs the observation time of scalar and velocity structures and enables the measurement of two types of Lagrangian coherent structures. One structure, the finite-time Lyapunov field (FTLE), quantifies advective transport barriers of fluid parcels while the other structure highlights barriers of diffusive momentum transport. These two complementary structures depend on large-scale and small-scale motion and are therefore associated with the growth of the turbulent region through engulfment or nibbling, respectively. We detect the \tnti\ from cluster analysis, where we divide the measured scalar field into four clusters. Not only the \tnti\ can be found this way, but also the next, internal, turbulent-turbulent interface. Conditional averages show that these interfaces are correlated with barriers of advective and diffusive transport when the Lagrangian integration time is smaller than the integral time scale. Diffusive structures decorrelate faster since they have a smaller timescale. Conditional averages of these structures at internal turbulent-turbulent interfaces show the same pattern with a more pronounced jump at the interface indicative of a shear layer. This is quite an unexpected outcome, as the internal interface is now defined not by the presence or absence of vorticity, but by conditional vorticity corresponding to two uniform concentration zones. The long-time diffusive momentum flux along Lagrangian paths represents the growth of the turbulent flow into the irrotational domain, a direct demonstration of nibbling. The diffusive flux parallel to the \tnti\ appears to be concentrated in a diffusive superlayer whose width is comparable with the Taylor microscale, which is relatively invariant in time.

  • 5 authors
·
Dec 17, 2024

DiffCrysGen: A Score-Based Diffusion Model for Design of Diverse Inorganic Crystalline Materials

Crystal structure generation is a foundational challenge in materials discovery, particularly in designing functional inorganic crystalline materials with desired properties. Most existing diffusion-based generative models for crystals rely on complex, hand-crafted priors and modular architectures to separately model atom types, atomic positions, and lattice parameters. These methods often require customized diffusion processes and conditional denoising, which can introduce additional model complexities and inconsistencies. Here we introduce DiffCrysGen, a fully data-driven, score-based diffusion model that jointly learns the distribution of all structural components in crystalline materials. With crystal structure representation as unified 2D matrices, DiffCrysGen bypasses the need for task-specific priors or decoupled modules, enabling end-to-end generation of atom types, fractional coordinates, and lattice parameters within a single framework. Our model learns crystallographic symmetry and chemical validity directly from large-scale datasets, allowing it to scale to complex materials discovery tasks. As a demonstration, we applied DiffCrysGen to the design of rare-earth-free magnetic materials with high saturation magnetization, showing its effectiveness in generating stable, diverse, and property-aligned candidates for sustainable magnet applications.

  • 3 authors
·
May 12, 2025

UltraShape 1.0: High-Fidelity 3D Shape Generation via Scalable Geometric Refinement

In this report, we introduce UltraShape 1.0, a scalable 3D diffusion framework for high-fidelity 3D geometry generation. The proposed approach adopts a two-stage generation pipeline: a coarse global structure is first synthesized and then refined to produce detailed, high-quality geometry. To support reliable 3D generation, we develop a comprehensive data processing pipeline that includes a novel watertight processing method and high-quality data filtering. This pipeline improves the geometric quality of publicly available 3D datasets by removing low-quality samples, filling holes, and thickening thin structures, while preserving fine-grained geometric details. To enable fine-grained geometry refinement, we decouple spatial localization from geometric detail synthesis in the diffusion process. We achieve this by performing voxel-based refinement at fixed spatial locations, where voxel queries derived from coarse geometry provide explicit positional anchors encoded via RoPE, allowing the diffusion model to focus on synthesizing local geometric details within a reduced, structured solution space. Our model is trained exclusively on publicly available 3D datasets, achieving strong geometric quality despite limited training resources. Extensive evaluations demonstrate that UltraShape 1.0 performs competitively with existing open-source methods in both data processing quality and geometry generation. All code and trained models will be released to support future research.

  • 13 authors
·
Dec 24, 2025 4

Scalar field dark energy models: Current and forecast constraints

Recent results from Type Ia supernovae (SNe Ia) and baryon acoustic oscillations (BAO), in combination with cosmic microwave background (CMB) measurements, have focused renewed attention on dark energy models with a time-varying equation-of-state parameter, w(z). In this paper, we describe the simplest, physically motivated models of evolving dark energy that are consistent with the recent data, a broad subclass of the so-called thawing scalar field models that we dub w_ϕCDM. We provide a quasi-universal, quasi-one-parameter functional fit to the scalar-field w_ϕ(z) that captures the behavior of these models more informatively than the standard w_0w_a phenomenological parametrization; their behavior is completely described by the current value of the equation-of-state parameter, w_0=w(z=0). Combining current data from BAO (DESI Data Release 2), the CMB (Planck and ACT), large-scale structure (DES Year-3 3times2pt), SNe Ia (DES-SN5YR), and strong lensing (TDCOSMO + SLACS), for w_ϕCDM we obtain w_0=-0.904_{-0.033}^{+0.034}, 2.9σ discrepant from the Λ cold dark matter (ΛCDM) model. The Bayesian evidence ratio substantially favors this w_ϕCDM model over ΛCDM. The data combination that yields the strongest discrepancy with ΛCDM is BAO+SNe Ia, for which w_0=-0.837^{+0.044}_{-0.045}, 3.6σ discrepant from ΛCDM and with a Bayesian evidence ratio strongly in favor. We find that the so-called S_8 tension between the CMB and large-scale structure is slightly reduced in these models, while the Hubble tension is slightly increased. We forecast constraints on these models from near-future surveys (DESI-extension and the Vera C. Rubin Observatory LSST), showing that the current best-fit w_ϕCDM model will be distinguishable from ΛCDM at over 9σ.

  • 2 authors
·
Jul 28, 2025

GraphShaper: Geometry-aware Alignment for Improving Transfer Learning in Text-Attributed Graphs

Graph foundation models represent a transformative paradigm for learning transferable representations across diverse graph domains. Recent methods leverage large language models to unify graph and text modalities into a shared representation space using contrastive learning. However, systematic evaluations reveal significant performance degradation at structural boundaries where distinct topological patterns converge, with accuracy losses exceeding 20 percentage points. This issue arises from a key limitation: current methods assume all graph structures can be encoded within a single Euclidean space. In reality, tree structures require hyperbolic geometry to preserve hierarchical branching, while cyclic patterns depend on spherical geometry for closure properties. At structural boundaries, nodes experience conflicting geometric constraints that uniform encoding spaces cannot resolve. This raises a crucial challenge: Can alignment frameworks be designed to respect the intrinsic geometric diversity of graph structures? We introduce GraphShaper, a geometry-aware framework that enhances graph encoding through multi-geometric specialization. Our approach employs expert networks tailored to different geometric spaces, dynamically computing fusion weights to adaptively integrate geometric properties based on local structural characteristics. This adaptive fusion preserves structural integrity before alignment with text embeddings. Extensive experiments demonstrate that GraphShaper achieves 9.47\% accuracy improvements on citation networks and 7.63\% on social networks in zero-shot settings.

  • 9 authors
·
Oct 13, 2025

General teleparallel geometric theory of defects

We revisit the geometric theory of defects. In the differential-geometric models of defects that have been adopted since the 1950s, dislocations have been associated with torsion, disclinations with the full curvature, and point defects with the first kind trace of non-metricity. The mainstream formulation exhibits several conceptual and technical shortcomings, most notably a hierarchy inconsistency, the non-exictence of a genuine metric formulation, and the potential emergence of Ostrogradsky-type instabilities. These issues have motivated us to develop a new framework, namely a generalized teleparallel geometric theory of defects. In our model, dislocations are identified with the trace of torsion, disclinations with the second kind trace of the non-metricity, and point defects with the first kind trace of the non-metricity. In addition, we retain the scalar part torsion as a free parameter for describing some possible unknown degrees of freedom in the theory of defects. The proposed geometric theory of defects is free from all of the aforementioned drawbacks and is therefore worthy of further investigation. To ensure the coherence and completeness of the discussion, we begin our analysis with elastic deformations, then summarize the existing metric-affine geometric theory of defects, and finally proceed to our original contribution, namely the new theory introduced here. We formulate the entire theory in Eulerian coordinates. Naturally, all results can be reformulated in Lagrangian coordinates as well. All analyses and formulae are expressed in the language of exterior algebra and are carried out in coordinate-independent orthonormal frames.

  • 3 authors
·
Feb 1

Modeling and design of heterogeneous hierarchical bioinspired spider web structures using generative deep learning and additive manufacturing

Spider webs are incredible biological structures, comprising thin but strong silk filament and arranged into complex hierarchical architectures with striking mechanical properties (e.g., lightweight but high strength, achieving diverse mechanical responses). While simple 2D orb webs can easily be mimicked, the modeling and synthesis of 3D-based web structures remain challenging, partly due to the rich set of design features. Here we provide a detailed analysis of the heterogenous graph structures of spider webs, and use deep learning as a way to model and then synthesize artificial, bio-inspired 3D web structures. The generative AI models are conditioned based on key geometric parameters (including average edge length, number of nodes, average node degree, and others). To identify graph construction principles, we use inductive representation sampling of large experimentally determined spider web graphs, to yield a dataset that is used to train three conditional generative models: 1) An analog diffusion model inspired by nonequilibrium thermodynamics, with sparse neighbor representation, 2) a discrete diffusion model with full neighbor representation, and 3) an autoregressive transformer architecture with full neighbor representation. All three models are scalable, produce complex, de novo bio-inspired spider web mimics, and successfully construct graphs that meet the design objectives. We further propose algorithm that assembles web samples produced by the generative models into larger-scale structures based on a series of geometric design targets, including helical and parametric shapes, mimicking, and extending natural design principles towards integration with diverging engineering objectives. Several webs are manufactured using 3D printing and tested to assess mechanical properties.

  • 3 authors
·
Apr 11, 2023

SciForma: Structure-Faithful Generation of Scientific Diagrams

Structural fidelity is essential to scientific methodology diagrams. To communicate research logic, these diagrams must faithfully render components, directional relations, and textual annotations. Since a single error, such as a reversed arrow or an unreadable equation, can invalidate the entire figure, structural fidelity is inherently conjunctive: correctness on one axis cannot compensate for failure on another. Current open-source models fail to satisfy this criterion. Supervised fine-tuning (SFT) learns plausible layouts but cannot reliably ensure structural correctness, while scalar reward-based post-training obscures which structural dimension has failed. To address this, we introduce SciForma, a framework for the structure faithful generation of scientific methodology diagrams. Specifically, SciForma decomposes diagram quality into three structural axes: Component, Arrow, and Text, guided by a structural inventory. Built on this foundation, we curate SciFormaData-700K for structured training and SciFormaBench-2K for logic-verified evaluation. To close the gap left by SFT, we develop Multi-Dimensional Conjunctive Preference Optimization (M-DPO), which enforces simultaneous correctness across all axes and adaptively routes gradients to the most deficient dimension in post-training. The same structural inventory also enables iterative editing at inference time to correct residual errors. This combination allows SciForma-9B to exceed all open-source baselines and GPT-Image-1.5 on both SciFormaBench-2K and AIBench, bringing open scientific diagram generation close to proprietary-level structural fidelity. Our code and data will be available at: https://github.com/microsoft/SciForma.

Denotational validation of higher-order Bayesian inference

We present a modular semantic account of Bayesian inference algorithms for probabilistic programming languages, as used in data science and machine learning. Sophisticated inference algorithms are often explained in terms of composition of smaller parts. However, neither their theoretical justification nor their implementation reflects this modularity. We show how to conceptualise and analyse such inference algorithms as manipulating intermediate representations of probabilistic programs using higher-order functions and inductive types, and their denotational semantics. Semantic accounts of continuous distributions use measurable spaces. However, our use of higher-order functions presents a substantial technical difficulty: it is impossible to define a measurable space structure over the collection of measurable functions between arbitrary measurable spaces that is compatible with standard operations on those functions, such as function application. We overcome this difficulty using quasi-Borel spaces, a recently proposed mathematical structure that supports both function spaces and continuous distributions. We define a class of semantic structures for representing probabilistic programs, and semantic validity criteria for transformations of these representations in terms of distribution preservation. We develop a collection of building blocks for composing representations. We use these building blocks to validate common inference algorithms such as Sequential Monte Carlo and Markov Chain Monte Carlo. To emphasize the connection between the semantic manipulation and its traditional measure theoretic origins, we use Kock's synthetic measure theory. We demonstrate its usefulness by proving a quasi-Borel counterpart to the Metropolis-Hastings-Green theorem.

  • 10 authors
·
Nov 8, 2017

A Geometric Theory of Cosmological Structure via Entropic Curvature in Wasserstein Space

We construct a geometric framework for cosmological large-scale structure based on optimal transport theory and Wasserstein geometry. In this framework, Ricci curvature on the probability measure space P_2(M) is characterized by the geodesic convexity of entropy and is formulated as the response of probability distributions to optimal transport. We introduce effective Ricci curvatures K_{eff}^{(infty)} and K_{eff}^{(N)} associated with Kullback--Leibler-type and Rényi-type entropies, corresponding respectively to the curvature-dimension conditions CD(K,infty) and CD(K,N). By localizing these curvatures to finite scales using local and reference measures, we construct curvature indicators applicable to observational data. Under a local quadratic approximation, the effective curvature reduces to the Hessian of the log-density, showing that conventional Hessian-based structure classifications arise as a limiting case of the present framework. We further show that effective curvature depends on observational scale and formulate this dependence as a scale flow, distinct from Ricci flow because it describes a change of resolution rather than a time evolution of geometry. Treating curvature as a random field then extends the statistical description of density fields: curvature statistics are given by higher-order weighted integrals of the power spectrum and by spatial derivatives of the correlation function, emphasizing geometric rather than amplitude information. This framework provides a unified connection between optimal transport geometry and cosmological structure analysis, and offers a new perspective on multiscale structure and nonlinear statistics.

  • 1 authors
·
Mar 31

Cosmic reflections I: the structural diversity of simulated and observed low-mass galaxy analogues

Dwarf galaxies serve as powerful laboratories for investigating the underlying physics of galaxy evolution including the impact of baryonic feedback processes and environmental influences. We compare the visual and structural properties of dwarf galaxies in ultra-deep HSC-SSP imaging of the COSMOS field with those measured from realistic HSC-like synthetic observations of dwarfs generated by the Illustris TNG50 and NewHorizon simulations. Using S\'ersic profile fitting and non-parametric morphological metrics (Gini, M_{20}, asymmetry, and concentration), we evaluate the diversity of structural properties in observed and simulated galaxies. Our analysis shows that NewHorizon and TNG50 galaxies lie at opposite extremes of observed structural trends: NewHorizon produces diffuse, extended galaxies with shallow S\'ersic indices, while TNG50 yields compact, concentrated systems with steep indices. Both simulations reproduce observed structural trends more closely at higher stellar masses (M_{star}sim10^{9.5} {rm M_{odot}}) but fail to capture the full diversity of COSMOS dwarfs at lower masses. Non-parametric metrics further show that NewHorizon galaxies exhibit more uneven, clumpy light distributions while TNG50 galaxies have smoother but excessively concentrated profiles. These structural differences reflect underlying differences in their physical prescriptions and are likely driven by differing approaches to ISM physics, supernova feedback and star formation in addition to differences in numerical resolution. Our findings highlight the unique power of low-mass galaxies to constrain differences in simulation physics, especially star formation and feedback. Upcoming surveys from facilities like the Vera C. Rubin Observatory and Euclid will enable more rigorous comparisons with simulations, offering deeper insights into the physical processes shaping galaxy evolution.

  • 13 authors
·
May 7, 2025

Microstructural Geometry Revealed by NMR Lineshape Analysis

We introduce a technique for extracting microstructural geometry from NMR lineshape analysis in porous materials at angstrom-scale resolution with the use of weak magnetic field gradients. Diverging from the generally held view of FID signals undergoing simple exponential decay, we show that a detailed analysis of the line shape can unravel structural geometry on much smaller scales than previously thought. While the original q-space PFG NMR relies on strong magnetic field gradients in order to achieve high spatial resolution, our current approach reaches comparable or higher resolution using much weaker gradients. As a model system, we simulated gas diffusion for xenon confined within carbon nanotubes over a range of temperatures and nanotube diameters in order to unveil manifestations of confinement in the diffusion behavior. We report a multiscale scheme that couples the above MD simulations with the generalized Langevin equation to estimate the transport properties of interest for this problem, such as diffusivity coefficients and NMR lineshapes, using the Green-Kubo correlation function to correctly evaluate time-dependent diffusion. Our results highlight how NMR methodologies can be adapted as effective means towards structural investigation at very small scales when dealing with complicated geometries. This method is expected to find applications in materials science, catalysis, biomedicine and other areas.

  • 2 authors
·
Oct 12, 2024

Ghost on the Shell: An Expressive Representation of General 3D Shapes

The creation of photorealistic virtual worlds requires the accurate modeling of 3D surface geometry for a wide range of objects. For this, meshes are appealing since they 1) enable fast physics-based rendering with realistic material and lighting, 2) support physical simulation, and 3) are memory-efficient for modern graphics pipelines. Recent work on reconstructing and statistically modeling 3D shape, however, has critiqued meshes as being topologically inflexible. To capture a wide range of object shapes, any 3D representation must be able to model solid, watertight, shapes as well as thin, open, surfaces. Recent work has focused on the former, and methods for reconstructing open surfaces do not support fast reconstruction with material and lighting or unconditional generative modelling. Inspired by the observation that open surfaces can be seen as islands floating on watertight surfaces, we parameterize open surfaces by defining a manifold signed distance field on watertight templates. With this parameterization, we further develop a grid-based and differentiable representation that parameterizes both watertight and non-watertight meshes of arbitrary topology. Our new representation, called Ghost-on-the-Shell (G-Shell), enables two important applications: differentiable rasterization-based reconstruction from multiview images and generative modelling of non-watertight meshes. We empirically demonstrate that G-Shell achieves state-of-the-art performance on non-watertight mesh reconstruction and generation tasks, while also performing effectively for watertight meshes.

  • 7 authors
·
Oct 23, 2023

Non-Gaussianity in D3-brane inflation

We update predictions for observables in the "delicate" D3/anti-D3 inflationary model on the conifold. We use a full CMB likelihood calculation to assess goodness-of-fit, which is necessary because in this model the zeta power spectrum often cannot be modelled as a power-law over observable scales. For the first time we are able to provide accurate forecasts for the amplitude of three-point correlations. In a significant portion of its parameter space the model follows Maldacena's single-field prediction fNL ~ -(5/12)(ns-1) if nt << 1. Therefore |fNL| is usually small when the power spectrum satisfies observational constraints. In a small number of cases the bispectrum is instead dominated by effects from rapid switching between angular minima. The resulting amplitudes are larger, but mostly with unacceptable spectral behaviour. In the most extreme case we obtain |fNLeq| ~ 75 at kt/3 = 0.002/Mpc. It has been suggested that the quasi-single field inflation ("QSFI") mechanism could produce significant 3-point correlations in this model. We do observe rare shifts in amplitude between equilateral and squeezed configurations that could possibly be associated with QSFI effects, but more investigation is needed to establish the full bispectrum shape. There is evidence of "shape" running between equilateral and squeezed configurations that may be inherited from the scale dependence of the spectrum. We explore the dependence of observables on discrete choices such as the truncation point of the potential. Our analysis illustrates the advantages of a standard format for information exchange within the inflationary model-building and testing community.

  • 3 authors
·
Feb 9, 2022

Unified Micromechanics Theory of Composites

We consider the matrix composite materials (CM) of either random (statistically homogeneous or inhomogeneous), periodic, or deterministic (neither random nor periodic) structures. CMs exhibit linear or nonlinear behavior, coupled or uncoupled multi-physical phenomena, locally elastic, weakly nonlocal (strain gradient and stress gradient), or strongly nonlocal (strain-type and displacement-type, peridynamics) phase properties. A modified Computational Analytical Micromechanics (CAM) approach introduces an exact Additive General Integral Equation (AGIE) for CMs of any structure and phase properties mentioned above. The unified iteration solution of static AGIEs is adapted to the body force with compact support serving as a fundamentally new universal training parameter. The approach also establishes a critical threshold for filtering out unsuitable sub-datasets of effective parameters through a novel Representative Volume Element (RVE) concept, which extends Hill's classical framework. This RVE concept eliminates sample size, boundary layer, and edge effects, making it applicable to CMs of any structure and phase properties, regardless of local or nonlocal, linear or nonlinear. Incorporating this new RVE concept into machine learning and neural network techniques enables the construction of any unpredefined surrogate nonlocal operators. The methodology is structured as a modular, block-based framework, allowing independent development and refinement of software components. This flexible, robust AGIE-CAM framework integrates data-driven, multi-scale, and multi-physics modeling, accelerating research in CM of any microtopology and phase properties considered. The AGIE-CAM framework represents a groundbreaking paradigm shift in the micromechanics of composites, redefining the very philosophy that underpins our understanding of their behavior at the microscopic level.

  • 1 authors
·
Mar 15, 2025

SymTRELLIS: Symmetry-Enforced Voxel Latents for 3D Generation

Single-view 3D generative models have achieved impressive visual quality, yet they are not designed to satisfy structural or functional requirements, and in practice, often fall short. Symmetry is one such requirement: violations, even subtle ones, on symmetry can render a model physically unusable. We present SymTRELLIS, a method that enforces arbitrary finite point group symmetries (rotational, reflectional, and polyhedral) during the flow-based 3D generation of TRELLIS.2, without retraining the underlying VAE or flow model. Our key idea is to approximate the latent-space action of spatial transformations as a learned linear operator on voxel latents, implemented as a lightweight spatial-transform latent mapper trained on generic, non-symmetric 3D data. At generation time, we enforce symmetry by averaging predicted flow velocities across all symmetry-equivalent transformations at each ODE step, a process we call velocity symmetrization. The symmetry specification can be estimated automatically from an initial TRELLIS.2 generation or supplied by the user, enabling deliberate fold manipulation beyond what the input image suggests. On a curated benchmark of 266 strictly symmetric objects spanning 2- to 20-fold rotations and polyhedral symmetry groups, SymTRELLIS substantially reduces all symmetry error metrics compared to TRELLIS.2, Hunyuan3D-2.1, and TripoSG, while maintaining reconstruction accuracy comparable to the base model.

symtrellis SymTRELLIS
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Jun 1

Analytical simulations of the resonant transmission of electrons in a closed nanocircuit for terahertz applications where a tunneling junction is shunted by a metallic nanowire

Earlier, in the CINT program at Los Alamos National Laboratory, we focused ultrafast mode-locked lasers on the tip-sample junction of a scanning tunneling microscope to generate currents at hundreds of harmonics of the laser pulse repetition frequency. Each harmonic has a signal-to-noise ratio of 20 dB with a 10-dB linewidth of only 3 Hz. Now we model closed quantum nanocircuits with rectangular, triangular, or delta-function barrier, shunted by a beryllium filament for quasi-coherent electron transport over mean-free paths as great as 68 nm. The time-independent Schrödinger equation is solved with the boundary conditions that the wavefunction and its derivative are continuous at both connections. These four boundary conditions are used to form a four-by-four complex matrix equation with only zeros in the right-hand column vector which is required to have a non-trivial solution with each of the closed nanocircuits. Each model has four parameters: (1) the barrier length, (2) the height and shape of the barrier, (3) the length of the pre-barrier, and (4) the electron energy. Any three of these may be specified and then the fourth is varied to bring the determinant to zero to find the solutions on lines or surfaces in the space defined by the four parameters. First, we use a simplistic model having a rectangular barrier. The second model has a triangular barrier as a first approximation to field emission, and we are considering applying this approach for a self-contained nanoscale extension of our earlier effort to generate the harmonics at Los Alamos. The third model has a delta-function barrier, and the fourth model is an extension of the first one where the width of the rectangular barrier is varied inversely with its height.

  • 1 authors
·
Oct 24, 2023

Machine-Learning Surrogate Model for Accelerating the Search of Stable Ternary Alloys

The prediction of phase diagrams in the search for new phases is a complex and computationally intensive task. Density functional theory provides, in many situations, the desired accuracy, but its throughput becomes prohibitively limited as the number of species involved grows, even when used with local and semi-local functionals. Here, we explore the possibility of integrating machine-learning models in the workflow for the construction of ternary convex hull diagrams. In particular, we train a set of spectral neighbour-analysis potentials (SNAPs) over readily available binary phases and we establish whether this is good enough to predict the energies of novel ternaries. Such a strategy does not require any new calculations specific for the construction of the model, but just avails of data stored in binary-phase-diagram repositories. We find that a so-constructed SNAP is capable of accurate total-energy estimates for ternary phases close to the equilibrium geometry but, in general, is not able to perform atomic relaxation. This is because during a typical relaxation path a given phase traverses regions in the parameter space poorly represented by the training set. Different metrics are then investigated to assess how an unknown structure is well described by a given SNAP model, and we find that the standard deviation of an ensemble of SNAPs provides a fast and non-specie-specific metric.

  • 4 authors
·
Mar 28, 2023

On the statistical theory of self-gravitating collisionless dark matter flow: Scale and redshift variation of velocity and density distributions

This paper studies the scale and redshift variation of density and velocity distributions in self-gravitating collisionless dark matter flow by a halo-based non-projection approach. All particles are divided into halo and out-of-halo particles for redshift variation of distributions. Without projecting particle fields onto a structured grid, the scale variation is analyzed by identifying all particle pairs on different scales r. We demonstrate that: i) Delaunay tessellation can be used to reconstruct the density field. The density correlation, spectrum, and dispersion functions were obtained, modeled, and compared with the N-body simulation; ii) the velocity distributions are symmetric on both small and large scales and are non-symmetric with a negative skewness on intermediate scales due to the inverse energy cascade at a constant rate varepsilon_u; iii) On small scales, the even order moments of pairwise velocity Delta u_L follow a two-thirds law (-varepsilon_ur)^{2/3}, while the odd order moments follow a linear scaling langle(Delta u_L)^{2n+1}rangle=(2n+1)langle(Delta u_L)^{2n}ranglelangleDelta u_Lrangler; iv) The scale variation of the velocity distributions was studied for longitudinal velocities u_L or u_L^{'}, pairwise velocity (velocity difference) Delta u_L=u_L^{'}-u_L and velocity sum Sigma u_L=u^{'}_L+u_L. Fully developed velocity fields are never Gaussian on any scale, despite that they can initially be Gaussian; v) On small scales, u_L and Sigma u_L can be modeled by a X distribution to maximize the system entropy; vi) On large scales, Delta u_L and Sigma u_L can be modeled by a logistic or a X distribution; vii) the redshift variation of the velocity distributions follows the evolution of the X distribution involving a shape parameter alpha(z) decreasing with time.

  • 1 authors
·
Feb 14, 2022

Magic sizes enable minimal-complexity, high-fidelity assembly of programmable shells

Recent advances in synthetic methods enable designing subunits that self-assemble into structures with well-defined sizes and architectures, but yields are frequently suppressed by the formation of off-target metastable structures. Increasing the complexity (number of distinct inter-subunit interaction types) can inhibit off-target structures, but leads to slower kinetics and higher synthesis costs. Here, we use icosahedral shells formed of programmable triangular subunits as a model system, and identify design principles that produce the highest target yield at the lowest complexity. We use a symmetry-based construction to create a range of design complexities, starting from the maximal symmetry Caspar-Klug assembly up to the fully addressable, zero-symmetry assembly. Kinetic Monte Carlo simulations reveal that the most prominent defects leading to off-target assemblies are a class of disclinations. We derive symmetry-based rules for identifying the optimal (lowest-complexity, highest-symmetry) design that inhibits these disclinations, leading to robust, high-fidelity assembly of targets with arbitrarily large sizes. Optimal complexity varies non-monotonically with target size, with `magic' sizes appearing for high-symmetry designs in which symmetry axes do not intersect vertices of the triangular net. The optimal designs at magic sizes require 12 times fewer inequivalent interaction-types than the (minimal symmetry) fully addressable construction.

  • 6 authors
·
Nov 6, 2024