Daily Papers

Geometric alignment appears in a variety of applications, ranging from domain adaptation, optimal transport, and normalizing flows in machine learning; optical flow and learned augmentation in computer vision and deformable registration within biomedical imaging. A recurring challenge is the alignment of domains whose topology is not the same; a problem that is routinely ignored, potentially introducing bias in downstream analysis. As a first step towards solving such alignment problems, we propose an unsupervised algorithm for the detection of changes in image topology. The model is based on a conditional variational auto-encoder and detects topological changes between two images during the registration step. We account for both topological changes in the image under spatial variation and unexpected transformations. Our approach is validated on two tasks and datasets: detection of topological changes in microscopy images of cells, and unsupervised anomaly detection brain imaging.

Manipulation of elastoplastic objects like dough often involves topological changes such as splitting and merging. The ability to accurately predict these topological changes that a specific action might incur is critical for planning interactions with elastoplastic objects. We present DoughNet, a Transformer-based architecture for handling these challenges, consisting of two components. First, a denoising autoencoder represents deformable objects of varying topology as sets of latent codes. Second, a visual predictive model performs autoregressive set prediction to determine long-horizon geometrical deformation and topological changes purely in latent space. Given a partial initial state and desired manipulation trajectories, it infers all resulting object geometries and topologies at each step. DoughNet thereby allows to plan robotic manipulation; selecting a suited tool, its pose and opening width to recreate robot- or human-made goals. Our experiments in simulated and real environments show that DoughNet is able to significantly outperform related approaches that consider deformation only as geometrical change.

Neural radiance fields (NeRF) achieve highly photo-realistic novel-view synthesis, but it's a challenging problem to edit the scenes modeled by NeRF-based methods, especially for dynamic scenes. We propose editable neural radiance fields that enable end-users to easily edit dynamic scenes and even support topological changes. Input with an image sequence from a single camera, our network is trained fully automatically and models topologically varying dynamics using our picked-out surface key points. Then end-users can edit the scene by easily dragging the key points to desired new positions. To achieve this, we propose a scene analysis method to detect and initialize key points by considering the dynamics in the scene, and a weighted key points strategy to model topologically varying dynamics by joint key points and weights optimization. Our method supports intuitive multi-dimensional (up to 3D) editing and can generate novel scenes that are unseen in the input sequence. Experiments demonstrate that our method achieves high-quality editing on various dynamic scenes and outperforms the state-of-the-art. Our code and captured data are available at https://chengwei-zheng.github.io/EditableNeRF/.

Clipart, a pre-made graphic art form, offers a convenient and efficient way of illustrating visual content. Traditional workflows to convert static clipart images into motion sequences are laborious and time-consuming, involving numerous intricate steps like rigging, key animation and in-betweening. Recent advancements in text-to-video generation hold great potential in resolving this problem. Nevertheless, direct application of text-to-video generation models often struggles to retain the visual identity of clipart images or generate cartoon-style motions, resulting in unsatisfactory animation outcomes. In this paper, we introduce AniClipart, a system that transforms static clipart images into high-quality motion sequences guided by text-to-video priors. To generate cartoon-style and smooth motion, we first define B\'{e}zier curves over keypoints of the clipart image as a form of motion regularization. We then align the motion trajectories of the keypoints with the provided text prompt by optimizing the Video Score Distillation Sampling (VSDS) loss, which encodes adequate knowledge of natural motion within a pretrained text-to-video diffusion model. With a differentiable As-Rigid-As-Possible shape deformation algorithm, our method can be end-to-end optimized while maintaining deformation rigidity. Experimental results show that the proposed AniClipart consistently outperforms existing image-to-video generation models, in terms of text-video alignment, visual identity preservation, and motion consistency. Furthermore, we showcase the versatility of AniClipart by adapting it to generate a broader array of animation formats, such as layered animation, which allows topological changes.

In the real world, objects reveal internal textures when sliced or cut, yet this behavior is not well-studied in 3D generation tasks today. For example, slicing a virtual 3D watermelon should reveal flesh and seeds. Given that no available dataset captures an object's full internal structure and collecting data from all slices is impractical, generative methods become the obvious approach. However, current 3D generation and inpainting methods often focus on visible appearance and overlook internal textures. To bridge this gap, we introduce FruitNinja, the first method to generate internal textures for 3D objects undergoing geometric and topological changes. Our approach produces objects via 3D Gaussian Splatting (3DGS) with both surface and interior textures synthesized, enabling real-time slicing and rendering without additional optimization. FruitNinja leverages a pre-trained diffusion model to progressively inpaint cross-sectional views and applies voxel-grid-based smoothing to achieve cohesive textures throughout the object. Our OpaqueAtom GS strategy overcomes 3DGS limitations by employing densely distributed opaque Gaussians, avoiding biases toward larger particles that destabilize training and sharp color transitions for fine-grained textures. Experimental results show that FruitNinja substantially outperforms existing approaches, showcasing unmatched visual quality in real-time rendered internal views across arbitrary geometry manipulations.

Within the graph learning community, conventional wisdom dictates that spectral convolutional networks may only be deployed on undirected graphs: Only there could the existence of a well-defined graph Fourier transform be guaranteed, so that information may be translated between spatial- and spectral domains. Here we show this traditional reliance on the graph Fourier transform to be superfluous and -- making use of certain advanced tools from complex analysis and spectral theory -- extend spectral convolutions to directed graphs. We provide a frequency-response interpretation of newly developed filters, investigate the influence of the basis used to express filters and discuss the interplay with characteristic operators on which networks are based. In order to thoroughly test the developed theory, we conduct experiments in real world settings, showcasing that directed spectral convolutional networks provide new state of the art results for heterophilic node classification on many datasets and -- as opposed to baselines -- may be rendered stable to resolution-scale varying topological perturbations.

We introduce a theoretical framework for differentiable surface evolution that allows discrete topology changes through the use of topological derivatives for variational optimization of image functionals. While prior methods for inverse rendering of geometry rely on silhouette gradients for topology changes, such signals are sparse. In contrast, our theory derives topological derivatives that relate the introduction of vanishing holes and phases to changes in image intensity. As a result, we enable differentiable shape perturbations in the form of hole or phase nucleation. We validate the proposed theory with optimization of closed curves in 2D and surfaces in 3D to lend insights into limitations of current methods and enable improved applications such as image vectorization, vector-graphics generation from text prompts, single-image reconstruction of shape ambigrams and multi-view 3D reconstruction.

Micro-Aerial Vehicles (MAVs) have the advantage of moving freely in 3D space. However, creating compact and sparse map representations that can be efficiently used for planning for such robots is still an open problem. In this paper, we take maps built from noisy sensor data and construct a sparse graph containing topological information that can be used for 3D planning. We use a Euclidean Signed Distance Field, extract a 3D Generalized Voronoi Diagram (GVD), and obtain a thin skeleton diagram representing the topological structure of the environment. We then convert this skeleton diagram into a sparse graph, which we show is resistant to noise and changes in resolution. We demonstrate global planning over this graph, and the orders of magnitude speed-up it offers over other common planning methods. We validate our planning algorithm in real maps built onboard an MAV, using RGB-D sensing.

This paper investigates how Transformer language models (LMs) fine-tuned for acceptability classification capture linguistic features. Our approach uses the best practices of topological data analysis (TDA) in NLP: we construct directed attention graphs from attention matrices, derive topological features from them, and feed them to linear classifiers. We introduce two novel features, chordality, and the matching number, and show that TDA-based classifiers outperform fine-tuning baselines. We experiment with two datasets, CoLA and RuCoLA in English and Russian, typologically different languages. On top of that, we propose several black-box introspection techniques aimed at detecting changes in the attention mode of the LMs during fine-tuning, defining the LM's prediction confidences, and associating individual heads with fine-grained grammar phenomena. Our results contribute to understanding the behavior of monolingual LMs in the acceptability classification task, provide insights into the functional roles of attention heads, and highlight the advantages of TDA-based approaches for analyzing LMs. We release the code and the experimental results for further uptake.

Language Models (LMs) are increasingly challenging the dominance of domain-specific models, including Graph Neural Networks (GNNs) and Graph Transformers (GTs), in graph learning tasks. Following this trend, we propose a novel approach that empowers off-the-shelf LMs to achieve performance comparable to state-of-the-art GNNs on node classification tasks, without requiring any architectural modification. By preserving the LM's original architecture, our approach retains a key benefit of LM instruction tuning: the ability to jointly train on diverse datasets, fostering greater flexibility and efficiency. To achieve this, we introduce two key augmentation strategies: (1) Enriching LMs' input using topological and semantic retrieval methods, which provide richer contextual information, and (2) guiding the LMs' classification process through a lightweight GNN classifier that effectively prunes class candidates. Our experiments on real-world datasets show that backbone Flan-T5 models equipped with these augmentation strategies outperform state-of-the-art text-output node classifiers and are comparable to top-performing vector-output node classifiers. By bridging the gap between specialized task-specific node classifiers and general LMs, this work paves the way for more versatile and widely applicable graph learning models. We will open-source the code upon publication.

We propose a method, named DualMesh-UDF, to extract a surface from unsigned distance functions (UDFs), encoded by neural networks, or neural UDFs. Neural UDFs are becoming increasingly popular for surface representation because of their versatility in presenting surfaces with arbitrary topologies, as opposed to the signed distance function that is limited to representing a closed surface. However, the applications of neural UDFs are hindered by the notorious difficulty in extracting the target surfaces they represent. Recent methods for surface extraction from a neural UDF suffer from significant geometric errors or topological artifacts due to two main difficulties: (1) A UDF does not exhibit sign changes; and (2) A neural UDF typically has substantial approximation errors. DualMesh-UDF addresses these two difficulties. Specifically, given a neural UDF encoding a target surface S to be recovered, we first estimate the tangent planes of S at a set of sample points close to S. Next, we organize these sample points into local clusters, and for each local cluster, solve a linear least squares problem to determine a final surface point. These surface points are then connected to create the output mesh surface, which approximates the target surface. The robust estimation of the tangent planes of the target surface and the subsequent minimization problem constitute our core strategy, which contributes to the favorable performance of DualMesh-UDF over other competing methods. To efficiently implement this strategy, we employ an adaptive Octree. Within this framework, we estimate the location of a surface point in each of the octree cells identified as containing part of the target surface. Extensive experiments show that our method outperforms existing methods in terms of surface reconstruction quality while maintaining comparable computational efficiency.

Adapting pre-trained foundation models for various downstream tasks has been prevalent in artificial intelligence. Due to the vast number of tasks and high costs, adjusting all parameters becomes unfeasible. To mitigate this, several fine-tuning techniques have been developed to update the pre-trained model weights in a more resource-efficient manner, such as through low-rank adjustments. Yet, almost all of these methods focus on linear weights, neglecting the intricacies of parameter spaces in higher dimensions like 4D. Alternatively, some methods can be adapted for high-dimensional parameter space by compressing changes in the original space into two dimensions and then employing low-rank matrix decomposition. However, these approaches destructs the structural integrity of the involved high-dimensional spaces. To tackle the diversity of dimensional spaces across different foundation models and provide a more precise representation of the changes within these spaces, this paper introduces a generalized parameter-efficient fine-tuning framework, FLoRA, designed for various dimensional parameter space. Specifically, utilizing Tucker decomposition, FLoRA asserts that changes in each dimensional parameter space are based on a low-rank core space which maintains the consistent topological structure with the original space. It then models the changes through this core space alongside corresponding weights to reconstruct alterations in the original space. FLoRA effectively preserves the structural integrity of the change of original N-dimensional parameter space, meanwhile decomposes it via low-rank tensor decomposition. Extensive experiments on computer vision, natural language processing and multi-modal tasks validate FLoRA's effectiveness. Codes are available at https://github.com/SJTU-DeepVisionLab/FLoRA.

With their non-Abelian topological charges, real multi-bandgap systems challenge the conventional topological phase classifications. As the minimal sector of multi-bandgap systems, real triple degeneracies (RTPs), which serve as real 'Weyl points', lay the foundation for the research on real topological phases. However, experimental demonstration of physical systems with global band configurations consisting of multiple RTPs in crystals has not been reported. Here we present experimental evidence of RTPs in photonic meta-crystals, characterizing them using the Euler number, and establishing their connection with both Abelian and non-Abelian charges. By considering RTPs as the basic elements, we further propose the concept of a topological compound, akin to a chemical compound, where we find that certain phases are not topologically allowed. The topological classification of RTPs in crystals demonstrated in our work plays a similar role as the 'no-go' theorem in Weyl systems.

Using a set of LambdaCDM simulations of cosmic structure formation, we study the evolving connectivity and changing topological structure of the cosmic web using state-of-the-art tools of multiscale topological data analysis (TDA). We follow the development of the cosmic web topology in terms of the evolution of Betti number curves and feature persistence diagrams of the three (topological) classes of structural features: matter concentrations, filaments and tunnels, and voids. The Betti curves specify the prominence of features as a function of density level, and their evolution with cosmic epoch reflects the changing network connections between these structural features. The persistence diagrams quantify the longevity and stability of topological features. In this study we establish, for the first time, the link between persistence diagrams, the features they show, and the gravitationally driven cosmic structure formation process. By following the diagrams' development over cosmic time, the link between the multiscale topology of the cosmic web and the hierarchical buildup of cosmic structure is established. The sharp apexes in the diagrams are intimately related to key transitions in the structure formation process. The apex in the matter concentration diagrams coincides with the density level at which, typically, they detach from the Hubble expansion and begin to collapse. At that level many individual islands merge to form the network of the cosmic web and a large number of filaments and tunnels emerge to establish its connecting bridges. The location trends of the apex possess a self-similar character that can be related to the cosmic web's hierarchical buildup. We find that persistence diagrams provide a significantly higher and more profound level of information on the structure formation process than more global summary statistics like Euler characteristic or Betti numbers.

Topological data analysis (TDA) is an area of data science that focuses on using invariants from algebraic topology to provide multiscale shape descriptors for geometric data sets such as point clouds. One of the most important such descriptors is {\em persistent homology}, which encodes the change in shape as a filtration parameter changes; a typical parameter is the feature scale. For many data sets, it is useful to simultaneously vary multiple filtration parameters, for example feature scale and density. While the theoretical properties of single parameter persistent homology are well understood, less is known about the multiparameter case. In particular, a central question is the problem of representing multiparameter persistent homology by elements of a vector space for integration with standard machine learning algorithms. Existing approaches to this problem either ignore most of the multiparameter information to reduce to the one-parameter case or are heuristic and potentially unstable in the face of noise. In this article, we introduce a new general representation framework that leverages recent results on {\em decompositions} of multiparameter persistent homology. This framework is rich in information, fast to compute, and encompasses previous approaches. Moreover, we establish theoretical stability guarantees under this framework as well as efficient algorithms for practical computation, making this framework an applicable and versatile tool for analyzing geometric and point cloud data. We validate our stability results and algorithms with numerical experiments that demonstrate statistical convergence, prediction accuracy, and fast running times on several real data sets.

Complex prediction models such as deep learning are the output from fitting machine learning, neural networks, or AI models to a set of training data. These are now standard tools in science. A key challenge with the current generation of models is that they are highly parameterized, which makes describing and interpreting the prediction strategies difficult. We use topological data analysis to transform these complex prediction models into pictures representing a topological view. The result is a map of the predictions that enables inspection. The methods scale up to large datasets across different domains and enable us to detect labeling errors in training data, understand generalization in image classification, and inspect predictions of likely pathogenic mutations in the BRCA1 gene.

We introduce a new generative model that combines latent diffusion with persistent homology to create 3D shapes with high diversity, with a special emphasis on their topological characteristics. Our method involves representing 3D shapes as implicit fields, then employing persistent homology to extract topological features, including Betti numbers and persistence diagrams. The shape generation process consists of two steps. Initially, we employ a transformer-based autoencoding module to embed the implicit representation of each 3D shape into a set of latent vectors. Subsequently, we navigate through the learned latent space via a diffusion model. By strategically incorporating topological features into the diffusion process, our generative module is able to produce a richer variety of 3D shapes with different topological structures. Furthermore, our framework is flexible, supporting generation tasks constrained by a variety of inputs, including sparse and partial point clouds, as well as sketches. By modifying the persistence diagrams, we can alter the topology of the shapes generated from these input modalities.

The natural world is full of complex systems characterized by intricate relations between their components: from social interactions between individuals in a social network to electrostatic interactions between atoms in a protein. Topological Deep Learning (TDL) provides a comprehensive framework to process and extract knowledge from data associated with these systems, such as predicting the social community to which an individual belongs or predicting whether a protein can be a reasonable target for drug development. TDL has demonstrated theoretical and practical advantages that hold the promise of breaking ground in the applied sciences and beyond. However, the rapid growth of the TDL literature has also led to a lack of unification in notation and language across Topological Neural Network (TNN) architectures. This presents a real obstacle for building upon existing works and for deploying TNNs to new real-world problems. To address this issue, we provide an accessible introduction to TDL, and compare the recently published TNNs using a unified mathematical and graphical notation. Through an intuitive and critical review of the emerging field of TDL, we extract valuable insights into current challenges and exciting opportunities for future development.

In this study, we examine the frequency and physical drivers of transformations from cool-core (CC) to non-cool-core (NCC) clusters, and vice versa, in a sample of 352 massive galaxy clusters (M_vir = 10^14-15.3 M_sun) from the TNG-Cluster magnetohydrodynamical cosmological simulation of galaxies. By identifying transformations based on the evolution of central entropy and focusing on z<2.5, we find that clusters frequently undergo such events, depending on their assembly and supermassive black hole histories. On average, clusters experience 2 to 3 transformations. Transformations can occur in both directions and can be temporary, but those to higher entropy cores, i.e. in the direction from CC to NCC states, are the vast majority. CC phases are shorter than NCC phases, and thus overall the TNG-Cluster population forms with low-entropy cores and moves towards NCC states with time. We study the role that mergers play in driving transformations, and find that mergers within ~1Gyr prior to a transformation toward higher (but not lower) entropy cores occur statistically more often than in a random control sample. Most importantly, we find examples of mergers associated with CC disruption regardless of their mass ratio or angular momentum. However, past merger activity is not a good predictor for z=0 CC status, at least based on core entropy, even though clusters undergoing more mergers eventually have the highest core entropy values at z=0. We consider the interplay between AGN feedback and evolving cluster core thermodynamics. We find that core transformations are accompanied by an increase in AGN activity, whereby frequent and repeated (kinetic) energy injections from the central SMBHs can produce a collective, long-term impact on central entropy, ultimately heating cluster cores. Whether such fast-paced periods of AGN activity are triggered by mergers is plausible, but not necessary.

Knot diagrams are among the most common visual tools in topology. Computer programs now make it possible to draw, manipulate and render them digitally, which proves to be useful in knot theory teaching and research. Still, an openly available tool to manipulate knot diagrams in a real-time, interactive way is yet to be developed. We introduce a method of operating on the geometry of the knot diagram itself without any underlying three-dimensional structure that can underpin such an application. This allows us to directly interact with vector graphics knot diagrams while at the same time computing knot invariants in ways proposed by previous work. An implementation of this method is provided.

Autoencoders have been proposed as a powerful tool for model-independent anomaly detection in high-energy physics. The operating principle is that events which do not belong to the space of training data will be reconstructed poorly, thus flagging them as anomalies. We point out that in a variety of examples of interest, the connection between large reconstruction error and anomalies is not so clear. In particular, for data sets with nontrivial topology, there will always be points that erroneously seem anomalous due to global issues. Conversely, neural networks typically have an inductive bias or prior to locally interpolate such that undersampled or rare events may be reconstructed with small error, despite actually being the desired anomalies. Taken together, these facts are in tension with the simple picture of the autoencoder as an anomaly detector. Using a series of illustrative low-dimensional examples, we show explicitly how the intrinsic and extrinsic topology of the dataset affects the behavior of an autoencoder and how this topology is manifested in the latent space representation during training. We ground this analysis in the discussion of a mock "bump hunt" in which the autoencoder fails to identify an anomalous "signal" for reasons tied to the intrinsic topology of n-particle phase space.

The enduring legacy of Euclidean geometry underpins classical machine learning, which, for decades, has been primarily developed for data lying in Euclidean space. Yet, modern machine learning increasingly encounters richly structured data that is inherently nonEuclidean. This data can exhibit intricate geometric, topological and algebraic structure: from the geometry of the curvature of space-time, to topologically complex interactions between neurons in the brain, to the algebraic transformations describing symmetries of physical systems. Extracting knowledge from such non-Euclidean data necessitates a broader mathematical perspective. Echoing the 19th-century revolutions that gave rise to non-Euclidean geometry, an emerging line of research is redefining modern machine learning with non-Euclidean structures. Its goal: generalizing classical methods to unconventional data types with geometry, topology, and algebra. In this review, we provide an accessible gateway to this fast-growing field and propose a graphical taxonomy that integrates recent advances into an intuitive unified framework. We subsequently extract insights into current challenges and highlight exciting opportunities for future development in this field.