Daily Papers

Synthesizing whole-body manipulation of articulated objects, including body motion, hand motion, and object motion, is a critical yet challenging task with broad applications in virtual humans and robotics. The core challenges are twofold. First, achieving realistic whole-body motion requires tight coordination between the hands and the rest of the body, as their movements are interdependent during manipulation. Second, articulated object manipulation typically involves high degrees of freedom and demands higher precision, often requiring the fingers to be placed at specific regions to actuate movable parts. To address these challenges, we propose a novel coordinated diffusion noise optimization framework. Specifically, we perform noise-space optimization over three specialized diffusion models for the body, left hand, and right hand, each trained on its own motion dataset to improve generalization. Coordination naturally emerges through gradient flow along the human kinematic chain, allowing the global body posture to adapt in response to hand motion objectives with high fidelity. To further enhance precision in hand-object interaction, we adopt a unified representation based on basis point sets (BPS), where end-effector positions are encoded as distances to the same BPS used for object geometry. This unified representation captures fine-grained spatial relationships between the hand and articulated object parts, and the resulting trajectories serve as targets to guide the optimization of diffusion noise, producing highly accurate interaction motion. We conduct extensive experiments demonstrating that our method outperforms existing approaches in motion quality and physical plausibility, and enables various capabilities such as object pose control, simultaneous walking and manipulation, and whole-body generation from hand-only data.

The Schr\"odinger Bridge (SB) is a powerful framework for solving generative modeling tasks such as unpaired domain translation. Most SB-related research focuses on continuous data space R^{D} and leaves open theoretical and algorithmic questions about applying SB methods to discrete data, e.g, on finite spaces S^{D}. Notable examples of such sets S are codebooks of vector-quantized (VQ) representations of modern autoencoders, tokens in texts, categories of atoms in molecules, etc. In this paper, we provide a theoretical and algorithmic foundation for solving SB in discrete spaces using the recently introduced Iterative Markovian Fitting (IMF) procedure. Specifically, we theoretically justify the convergence of discrete-time IMF (D-IMF) to SB in discrete spaces. This enables us to develop a practical computational algorithm for SB which we call Categorical Schr\"odinger Bridge Matching (CSBM). We show the performance of CSBM via a series of experiments with synthetic data and VQ representations of images.

Large-scale terrain scans are the basis for many important tasks, such as topographic mapping, forestry, agriculture, and infrastructure planning. The resulting point cloud data sets are so massive in size that even basic tasks like viewing take hours to days of pre-processing in order to create level-of-detail structures that allow inspecting the data set in their entirety in real time. In this paper, we propose a method that is capable of instantly visualizing massive country-sized scans with hundreds of billions of points. Upon opening the data set, we first load a sparse subsample of points and initialize an overview of the entire point cloud, immediately followed by a surface reconstruction process to generate higher-quality, hole-free heightmaps. As users start navigating towards a region of interest, we continue to prioritize the heightmap construction process to the user's viewpoint. Once a user zooms in closely, we load the full-resolution point cloud data for that region and update the corresponding height map textures with the full-resolution data. As users navigate elsewhere, full-resolution point data that is no longer needed is unloaded, but the updated heightmap textures are retained as a form of medium level of detail. Overall, our method constitutes a form of direct out-of-core rendering for massive point cloud data sets (terabytes, compressed) that requires no preprocessing and no additional disk space. Source code, executable, pre-trained model, and dataset are available at: https://github.com/cg-tuwien/lidarscout

We introduce a novel framework that directly learns a spectral basis for shape and manifold analysis from unstructured data, eliminating the need for traditional operator selection, discretization, and eigensolvers. Grounded in optimal-approximation theory, we train a network to decompose an implicit approximation operator by minimizing the reconstruction error in the learned basis over a chosen distribution of probe functions. For suitable distributions, they can be seen as an approximation of the Laplacian operator and its eigendecomposition, which are fundamental in geometry processing. Furthermore, our method recovers in a unified manner not only the spectral basis, but also the implicit metric's sampling density and the eigenvalues of the underlying operator. Notably, our unsupervised method makes no assumption on the data manifold, such as meshing or manifold dimensionality, allowing it to scale to arbitrary datasets of any dimension. On point clouds lying on surfaces in 3D and high-dimensional image manifolds, our approach yields meaningful spectral bases, that can resemble those of the Laplacian, without explicit construction of an operator. By replacing the traditional operator selection, construction, and eigendecomposition with a learning-based approach, our framework offers a principled, data-driven alternative to conventional pipelines. This opens new possibilities in geometry processing for unstructured data, particularly in high-dimensional spaces.

Adaptive sparse coding methods learn a possibly overcomplete set of basis functions, such that natural image patches can be reconstructed by linearly combining a small subset of these bases. The applicability of these methods to visual object recognition tasks has been limited because of the prohibitive cost of the optimization algorithms required to compute the sparse representation. In this work we propose a simple and efficient algorithm to learn basis functions. After training, this model also provides a fast and smooth approximator to the optimal representation, achieving even better accuracy than exact sparse coding algorithms on visual object recognition tasks.

Few prior works study deep learning on point sets. PointNet by Qi et al. is a pioneer in this direction. However, by design PointNet does not capture local structures induced by the metric space points live in, limiting its ability to recognize fine-grained patterns and generalizability to complex scenes. In this work, we introduce a hierarchical neural network that applies PointNet recursively on a nested partitioning of the input point set. By exploiting metric space distances, our network is able to learn local features with increasing contextual scales. With further observation that point sets are usually sampled with varying densities, which results in greatly decreased performance for networks trained on uniform densities, we propose novel set learning layers to adaptively combine features from multiple scales. Experiments show that our network called PointNet++ is able to learn deep point set features efficiently and robustly. In particular, results significantly better than state-of-the-art have been obtained on challenging benchmarks of 3D point clouds.

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.

We show how the Schur-Weyl duality that exists between the partition algebra and the symmetric group results in a stronger theoretical foundation for characterising all of the possible permutation equivariant neural networks whose layers are some tensor power of the permutation representation M_n of the symmetric group S_n. In doing so, we unify two separate bodies of literature, and we correct some of the major results that are now widely quoted by the machine learning community. In particular, we find a basis of matrices for the learnable, linear, permutation equivariant layer functions between such tensor power spaces in the standard basis of M_n by using an elegant graphical representation of a basis of set partitions for the partition algebra and its related vector spaces. Also, we show how we can calculate the number of weights that must appear in these layer functions by looking at certain paths through the McKay quiver for M_n. Finally, we describe how our approach generalises to the construction of neural networks that are equivariant to local symmetries.

Polynomial filters, a kind of Graph Neural Networks, typically use a predetermined polynomial basis and learn the coefficients from the training data. It has been observed that the effectiveness of the model is highly dependent on the property of the polynomial basis. Consequently, two natural and fundamental questions arise: Can we learn a suitable polynomial basis from the training data? Can we determine the optimal polynomial basis for a given graph and node features? In this paper, we propose two spectral GNN models that provide positive answers to the questions posed above. First, inspired by Favard's Theorem, we propose the FavardGNN model, which learns a polynomial basis from the space of all possible orthonormal bases. Second, we examine the supposedly unsolvable definition of optimal polynomial basis from Wang & Zhang (2022) and propose a simple model, OptBasisGNN, which computes the optimal basis for a given graph structure and graph signal. Extensive experiments are conducted to demonstrate the effectiveness of our proposed models.

Recent advancements in Spectral Graph Convolutional Networks (SpecGCNs) have led to state-of-the-art performance in various graph representation learning tasks. To exploit the potential of SpecGCNs, we analyze corresponding graph filters via polynomial interpolation, the cornerstone of graph signal processing. Different polynomial bases, such as Bernstein, Chebyshev, and monomial basis, have various convergence rates that will affect the error in polynomial interpolation. Although adopting Chebyshev basis for interpolation can minimize maximum error, the performance of ChebNet is still weaker than GPR-GNN and BernNet. We point out it is caused by the Gibbs phenomenon, which occurs when the graph frequency response function approximates the target function. It reduces the approximation ability of a truncated polynomial interpolation. In order to mitigate the Gibbs phenomenon, we propose to add the Gibbs damping factor with each term of Chebyshev polynomials on ChebNet. As a result, our lightweight approach leads to a significant performance boost. Afterwards, we reorganize ChebNet via decoupling feature propagation and transformation. We name this variant as ChebGibbsNet. Our experiments indicate that ChebGibbsNet is superior to other advanced SpecGCNs, such as GPR-GNN and BernNet, in both homogeneous graphs and heterogeneous graphs.

Methods of computational quantum chemistry provide accurate approximations of molecular properties crucial for computer-aided drug discovery and other areas of chemical science. However, high computational complexity limits the scalability of their applications. Neural network potentials (NNPs) are a promising alternative to quantum chemistry methods, but they require large and diverse datasets for training. This work presents a new dataset and benchmark called nabla^2DFT that is based on the nablaDFT. It contains twice as much molecular structures, three times more conformations, new data types and tasks, and state-of-the-art models. The dataset includes energies, forces, 17 molecular properties, Hamiltonian and overlap matrices, and a wavefunction object. All calculations were performed at the DFT level (omegaB97X-D/def2-SVP) for each conformation. Moreover, nabla^2DFT is the first dataset that contains relaxation trajectories for a substantial number of drug-like molecules. We also introduce a novel benchmark for evaluating NNPs in molecular property prediction, Hamiltonian prediction, and conformational optimization tasks. Finally, we propose an extendable framework for training NNPs and implement 10 models within it.

Despite their widespread success, the application of deep neural networks to functional data remains scarce today. The infinite dimensionality of functional data means standard learning algorithms can be applied only after appropriate dimension reduction, typically achieved via basis expansions. Currently, these bases are chosen a priori without the information for the task at hand and thus may not be effective for the designated task. We instead propose to adaptively learn these bases in an end-to-end fashion. We introduce neural networks that employ a new Basis Layer whose hidden units are each basis functions themselves implemented as a micro neural network. Our architecture learns to apply parsimonious dimension reduction to functional inputs that focuses only on information relevant to the target rather than irrelevant variation in the input function. Across numerous classification/regression tasks with functional data, our method empirically outperforms other types of neural networks, and we prove that our approach is statistically consistent with low generalization error. Code is available at: https://github.com/jwyyy/AdaFNN.

This paper investigates the generalization of Principal Component Analysis (PCA) to Riemannian manifolds. We first propose a new and general type of family of subspaces in manifolds that we call barycentric subspaces. They are implicitly defined as the locus of points which are weighted means of k+1 reference points. As this definition relies on points and not on tangent vectors, it can also be extended to geodesic spaces which are not Riemannian. For instance, in stratified spaces, it naturally allows principal subspaces that span several strata, which is impossible in previous generalizations of PCA. We show that barycentric subspaces locally define a submanifold of dimension k which generalizes geodesic subspaces.Second, we rephrase PCA in Euclidean spaces as an optimization on flags of linear subspaces (a hierarchy of properly embedded linear subspaces of increasing dimension). We show that the Euclidean PCA minimizes the Accumulated Unexplained Variances by all the subspaces of the flag (AUV). Barycentric subspaces are naturally nested, allowing the construction of hierarchically nested subspaces. Optimizing the AUV criterion to optimally approximate data points with flags of affine spans in Riemannian manifolds lead to a particularly appealing generalization of PCA on manifolds called Barycentric Subspaces Analysis (BSA).

The reliability with Machine Learning (ML) techniques in novel materials discovery often depend on the quality of the dataset, in addition to the relevant features used in describing the material. In this regard, the current study presents and validates a newly processed materials dataset that can be utilized for benchmark ML analysis, as it relates to the prediction and classification of deterministic target properties. Originally, the dataset was extracted from the Open Quantum Materials Database (OQMD) and contains a robust 16,323 samples of ABX3 inorganic perovskite structures. The dataset is tabular in form and is preprocessed to include sixty-one generalized input features that broadly describes the physicochemical, stability/geometrical, and Density Functional Theory (DFT) target properties associated with the elemental ionic sites in a three-dimensional ABX3 polyhedral. For validation, four different ML models are employed to predict three distinctive target properties, namely: formation energy, energy band gap, and crystal system. On experimentation, the best accuracy measurements are reported at 0.013 eV/atom MAE, 0.216 eV MAE, and 85% F1, corresponding to the formation energy prediction, band gap prediction and crystal system multi-classification, respectively. Moreover, the realized results are compared with previous literature and as such, affirms the resourcefulness of the current dataset for future benchmark materials analysis via ML techniques. The preprocessed dataset and source codes are openly available to download from github.com/chenebuah/ML_abx3_dataset.

We provide a full characterisation of all of the possible group equivariant neural networks whose layers are some tensor power of R^{n} for three symmetry groups that are missing from the machine learning literature: O(n), the orthogonal group; SO(n), the special orthogonal group; and Sp(n), the symplectic group. In particular, we find a spanning set of matrices for the learnable, linear, equivariant layer functions between such tensor power spaces in the standard basis of R^{n} when the group is O(n) or SO(n), and in the symplectic basis of R^{n} when the group is Sp(n).

We provide a full characterisation of all of the possible alternating group (A_n) equivariant neural networks whose layers are some tensor power of R^{n}. In particular, we find a basis of matrices for the learnable, linear, A_n-equivariant layer functions between such tensor power spaces in the standard basis of R^{n}. We also describe how our approach generalises to the construction of neural networks that are equivariant to local symmetries.

We consider the Similarity Sketching problem: Given a universe [u] = {0,ldots, u-1} we want a random function S mapping subsets Asubseteq [u] into vectors S(A) of size t, such that the Jaccard similarity J(A,B) = |Acap B|/|Acup B| between sets A and B is preserved. More precisely, define X_i = [S(A)[i] = S(B)[i]] and X = sum_{iin [t]} X_i. We want E[X_i]=J(A,B), and we want X to be strongly concentrated around E[X] = t cdot J(A,B) (i.e. Chernoff-style bounds). This is a fundamental problem which has found numerous applications in data mining, large-scale classification, computer vision, similarity search, etc. via the classic MinHash algorithm. The vectors S(A) are also called sketches. Strong concentration is critical, for often we want to sketch many sets B_1,ldots,B_n so that we later, for a query set A, can find (one of) the most similar B_i. It is then critical that no B_i looks much more similar to A due to errors in the sketch. The seminal ttimesMinHash algorithm uses t random hash functions h_1,ldots, h_t, and stores left ( min_{ain A} h_1(A),ldots, min_{ain A} h_t(A) right ) as the sketch of A. The main drawback of MinHash is, however, its O(tcdot |A|) running time, and finding a sketch with similar properties and faster running time has been the subject of several papers. (continued...)

Machine learning for point clouds has been attracting much attention, with many applications in various fields, such as shape recognition and material science. For enhancing the accuracy of such machine learning methods, it is often effective to incorporate global topological features, which are typically extracted by persistent homology. In the calculation of persistent homology for a point cloud, we choose a filtration for the point cloud, an increasing sequence of spaces. Since the performance of machine learning methods combined with persistent homology is highly affected by the choice of a filtration, we need to tune it depending on data and tasks. In this paper, we propose a framework that learns a filtration adaptively with the use of neural networks. In order to make the resulting persistent homology isometry-invariant, we develop a neural network architecture with such invariance. Additionally, we show a theoretical result on a finite-dimensional approximation of filtration functions, which justifies the proposed network architecture. Experimental results demonstrated the efficacy of our framework in several classification tasks.

We study the H-chromatic symmetric functions X_G^H (introduced in (arXiv:2011.06063) as a generalization of the chromatic symmetric function (CSF) X_G), which track homomorphisms from the graph G to the graph H. We focus first on the case of self-chromatic symmetric functions (self-CSFs) X_G^G, making some progress toward a conjecture from (arXiv:2011.06063) that the self-CSF, like the normal CSF, is always different for different trees. In particular, we show that the self-CSF distinguishes trees from non-trees with just one exception, we check using Sage that it distinguishes all trees on up to 12 vertices, and we show that it determines the number of legs of a spider and the degree sequence of a caterpillar given its spine length. We also show that the self-CSF detects the number of connected components of a forest, again with just one exception. Then we prove some results about the power sum expansions for H-CSFs when H is a complete bipartite graph, in particular proving that the conjecture from (arXiv:2011.06063) about p-monotonicity of ω(X_G^H) for H a star holds as long as H is sufficiently large compared to G. We also show that the self-CSFs of complete multipartite graphs form a basis for the ring Λ of symmetric functions, and we give some construction of bases for the vector space Λ^n of degree n symmetric functions using H-CSFs X_G^H where H is a fixed graph that is not a complete graph, answering a question from (arXiv:2011.06063) about whether such bases exist. However, we show that there generally do not exist such bases with G fixed, even with loops, answering another question from (arXiv:2011.06063). We also define the H-chromatic polynomial as an analogue of the chromatic polynomial, and ask when it is the same for different graphs.

We present Topological Point Cloud Clustering (TPCC), a new method to cluster points in an arbitrary point cloud based on their contribution to global topological features. TPCC synthesizes desirable features from spectral clustering and topological data analysis and is based on considering the spectral properties of a simplicial complex associated to the considered point cloud. As it is based on considering sparse eigenvector computations, TPCC is similarly easy to interpret and implement as spectral clustering. However, by focusing not just on a single matrix associated to a graph created from the point cloud data, but on a whole set of Hodge-Laplacians associated to an appropriately constructed simplicial complex, we can leverage a far richer set of topological features to characterize the data points within the point cloud and benefit from the relative robustness of topological techniques against noise. We test the performance of TPCC on both synthetic and real-world data and compare it with classical spectral clustering.

Developing robust representations of chemical structures that enable models to learn topological inductive biases is challenging. In this manuscript, we present a representation of atomistic systems. We begin by proving that our representation satisfies all structural, geometric, efficiency, and generalizability constraints. Afterward, we provide a general algorithm to encode any atomistic system. Finally, we report performance comparable to state-of-the-art methods on numerous tasks. We open-source all code and datasets. The code and data are available at https://github.com/rahulkhorana/PolyatomicComplexes.

Generative models are becoming a tool of choice for exploring the molecular space. These models learn on a large training dataset and produce novel molecular structures with similar properties. Generated structures can be utilized for virtual screening or training semi-supervised predictive models in the downstream tasks. While there are plenty of generative models, it is unclear how to compare and rank them. In this work, we introduce a benchmarking platform called Molecular Sets (MOSES) to standardize training and comparison of molecular generative models. MOSES provides a training and testing datasets, and a set of metrics to evaluate the quality and diversity of generated structures. We have implemented and compared several molecular generation models and suggest to use our results as reference points for further advancements in generative chemistry research. The platform and source code are available at https://github.com/molecularsets/moses.

We present a novel type of neural fields that uses general radial bases for signal representation. State-of-the-art neural fields typically rely on grid-based representations for storing local neural features and N-dimensional linear kernels for interpolating features at continuous query points. The spatial positions of their neural features are fixed on grid nodes and cannot well adapt to target signals. Our method instead builds upon general radial bases with flexible kernel position and shape, which have higher spatial adaptivity and can more closely fit target signals. To further improve the channel-wise capacity of radial basis functions, we propose to compose them with multi-frequency sinusoid functions. This technique extends a radial basis to multiple Fourier radial bases of different frequency bands without requiring extra parameters, facilitating the representation of details. Moreover, by marrying adaptive radial bases with grid-based ones, our hybrid combination inherits both adaptivity and interpolation smoothness. We carefully designed weighting schemes to let radial bases adapt to different types of signals effectively. Our experiments on 2D image and 3D signed distance field representation demonstrate the higher accuracy and compactness of our method than prior arts. When applied to neural radiance field reconstruction, our method achieves state-of-the-art rendering quality, with small model size and comparable training speed.

k-Clustering in R^d (e.g., k-median and k-means) is a fundamental machine learning problem. While near-linear time approximation algorithms were known in the classical setting for a dataset with cardinality n, it remains open to find sublinear-time quantum algorithms. We give quantum algorithms that find coresets for k-clustering in R^d with O(nkd^{3/2}) query complexity. Our coreset reduces the input size from n to poly(kepsilon^{-1}d), so that existing alpha-approximation algorithms for clustering can run on top of it and yield (1 + epsilon)alpha-approximation. This eventually yields a quadratic speedup for various k-clustering approximation algorithms. We complement our algorithm with a nearly matching lower bound, that any quantum algorithm must make Omega(nk) queries in order to achieve even O(1)-approximation for k-clustering.

Graph neural networks are emerging as promising methods for modeling molecular graphs, in which nodes and edges correspond to atoms and chemical bonds, respectively. Recent studies show that when 3D molecular geometries, such as bond lengths and angles, are available, molecular property prediction tasks can be made more accurate. However, computing of 3D molecular geometries requires quantum calculations that are computationally prohibitive. For example, accurate calculation of 3D geometries of a small molecule requires hours of computing time using density functional theory (DFT). Here, we propose to predict the ground-state 3D geometries from molecular graphs using machine learning methods. To make this feasible, we develop a benchmark, known as Molecule3D, that includes a dataset with precise ground-state geometries of approximately 4 million molecules derived from DFT. We also provide a set of software tools for data processing, splitting, training, and evaluation, etc. Specifically, we propose to assess the error and validity of predicted geometries using four metrics. We implement two baseline methods that either predict the pairwise distance between atoms or atom coordinates in 3D space. Experimental results show that, compared with generating 3D geometries with RDKit, our method can achieve comparable prediction accuracy but with much smaller computational costs. Our Molecule3D is available as a module of the MoleculeX software library (https://github.com/divelab/MoleculeX).

A coreset is a tiny weighted subset of an input set, that closely resembles the loss function, with respect to a certain set of queries. Coresets became prevalent in machine learning as they have shown to be advantageous for many applications. While coreset research is an active research area, unfortunately, coresets are constructed in a problem-dependent manner, where for each problem, a new coreset construction algorithm is usually suggested, a process that may take time or may be hard for new researchers in the field. Even the generic frameworks require additional (problem-dependent) computations or proofs to be done by the user. Besides, many problems do not have (provable) small coresets, limiting their applicability. To this end, we suggest an automatic practical framework for constructing coresets, which requires (only) the input data and the desired cost function from the user, without the need for any other task-related computation to be done by the user. To do so, we reduce the problem of approximating a loss function to an instance of vector summation approximation, where the vectors we aim to sum are loss vectors of a specific subset of the queries, such that we aim to approximate the image of the function on this subset. We show that while this set is limited, the coreset is quite general. An extensive experimental study on various machine learning applications is also conducted. Finally, we provide a ``plug and play" style implementation, proposing a user-friendly system that can be easily used to apply coresets for many problems. Full open source code can be found at https://github.com/alaamaalouf/AutoCoreset{https://github.com/alaamaalouf/AutoCoreset}. We believe that these contributions enable future research and easier use and applications of coresets.

Representation learning has become an invaluable approach for learning from symbolic data such as text and graphs. However, while complex symbolic datasets often exhibit a latent hierarchical structure, state-of-the-art methods typically learn embeddings in Euclidean vector spaces, which do not account for this property. For this purpose, we introduce a new approach for learning hierarchical representations of symbolic data by embedding them into hyperbolic space -- or more precisely into an n-dimensional Poincar\'e ball. Due to the underlying hyperbolic geometry, this allows us to learn parsimonious representations of symbolic data by simultaneously capturing hierarchy and similarity. We introduce an efficient algorithm to learn the embeddings based on Riemannian optimization and show experimentally that Poincar\'e embeddings outperform Euclidean embeddings significantly on data with latent hierarchies, both in terms of representation capacity and in terms of generalization ability.

Set representation has become ubiquitous in deep learning for modeling the inductive bias of neural networks that are insensitive to the input order. DeepSets is the most widely used neural network architecture for set representation. It involves embedding each set element into a latent space with dimension L, followed by a sum pooling to obtain a whole-set embedding, and finally mapping the whole-set embedding to the output. In this work, we investigate the impact of the dimension L on the expressive power of DeepSets. Previous analyses either oversimplified high-dimensional features to be one-dimensional features or were limited to analytic activations, thereby diverging from practical use or resulting in L that grows exponentially with the set size N and feature dimension D. To investigate the minimal value of L that achieves sufficient expressive power, we present two set-element embedding layers: (a) linear + power activation (LP) and (b) linear + exponential activations (LE). We demonstrate that L being poly(N, D) is sufficient for set representation using both embedding layers. We also provide a lower bound of L for the LP embedding layer. Furthermore, we extend our results to permutation-equivariant set functions and the complex field.

We study the problem of designing models for machine learning tasks defined on sets. In contrast to traditional approach of operating on fixed dimensional vectors, we consider objective functions defined on sets that are invariant to permutations. Such problems are widespread, ranging from estimation of population statistics poczos13aistats, to anomaly detection in piezometer data of embankment dams Jung15Exploration, to cosmology Ntampaka16Dynamical,Ravanbakhsh16ICML1. Our main theorem characterizes the permutation invariant functions and provides a family of functions to which any permutation invariant objective function must belong. This family of functions has a special structure which enables us to design a deep network architecture that can operate on sets and which can be deployed on a variety of scenarios including both unsupervised and supervised learning tasks. We also derive the necessary and sufficient conditions for permutation equivariance in deep models. We demonstrate the applicability of our method on population statistic estimation, point cloud classification, set expansion, and outlier detection.

With recent dramatic increases in AI system capabilities, there has been growing interest in utilizing machine learning for reasoning-heavy, quantitative tasks, particularly mathematics. While there are many resources capturing mathematics at the high-school, undergraduate, and graduate level, there are far fewer resources available that align with the level of difficulty and open endedness encountered by professional mathematicians working on open problems. To address this, we introduce a new collection of datasets, the Algebraic Combinatorics Dataset Repository (ACD Repo), representing either foundational results or open problems in algebraic combinatorics, a subfield of mathematics that studies discrete structures arising from abstract algebra. Further differentiating our dataset collection is the fact that it aims at the conjecturing process. Each dataset includes an open-ended research-level question and a large collection of examples (up to 10M in some cases) from which conjectures should be generated. We describe all nine datasets, the different ways machine learning models can be applied to them (e.g., training with narrow models followed by interpretability analysis or program synthesis with LLMs), and discuss some of the challenges involved in designing datasets like these.

Crystal structures are characterized by atomic bases within a primitive unit cell that repeats along a regular lattice throughout 3D space. The periodic and infinite nature of crystals poses unique challenges for geometric graph representation learning. Specifically, constructing graphs that effectively capture the complete geometric information of crystals and handle chiral crystals remains an unsolved and challenging problem. In this paper, we introduce a novel approach that utilizes the periodic patterns of unit cells to establish the lattice-based representation for each atom, enabling efficient and expressive graph representations of crystals. Furthermore, we propose ComFormer, a SE(3) transformer designed specifically for crystalline materials. ComFormer includes two variants; namely, iComFormer that employs invariant geometric descriptors of Euclidean distances and angles, and eComFormer that utilizes equivariant vector representations. Experimental results demonstrate the state-of-the-art predictive accuracy of ComFormer variants on various tasks across three widely-used crystal benchmarks. Our code is publicly available as part of the AIRS library (https://github.com/divelab/AIRS).

Persistent homology (PH) provides topological descriptors for geometric data, such as weighted graphs, which are interpretable, stable to perturbations, and invariant under, e.g., relabeling. Most applications of PH focus on the one-parameter case -- where the descriptors summarize the changes in topology of data as it is filtered by a single quantity of interest -- and there is now a wide array of methods enabling the use of one-parameter PH descriptors in data science, which rely on the stable vectorization of these descriptors as elements of a Hilbert space. Although the multiparameter PH (MPH) of data that is filtered by several quantities of interest encodes much richer information than its one-parameter counterpart, the scarceness of stability results for MPH descriptors has so far limited the available options for the stable vectorization of MPH. In this paper, we aim to bring together the best of both worlds by showing how the interpretation of signed barcodes -- a recent family of MPH descriptors -- as signed measures leads to natural extensions of vectorization strategies from one parameter to multiple parameters. The resulting feature vectors are easy to define and to compute, and provably stable. While, as a proof of concept, we focus on simple choices of signed barcodes and vectorizations, we already see notable performance improvements when comparing our feature vectors to state-of-the-art topology-based methods on various types of data.

Recent neural network-based wave functions have achieved state-of-the-art accuracies in modeling ab-initio ground-state potential energy surface. However, these networks can only solve different spatial arrangements of the same set of atoms. To overcome this limitation, we present Graph-learned orbital embeddings (Globe), a neural network-based reparametrization method that can adapt neural wave functions to different molecules. Globe learns representations of local electronic structures that generalize across molecules via spatial message passing by connecting molecular orbitals to covalent bonds. Further, we propose a size-consistent wave function Ansatz, the Molecular orbital network (Moon), tailored to jointly solve Schr\"odinger equations of different molecules. In our experiments, we find Moon converging in 4.5 times fewer steps to similar accuracy as previous methods or to lower energies given the same time. Further, our analysis shows that Moon's energy estimate scales additively with increased system sizes, unlike previous work where we observe divergence. In both computational chemistry and machine learning, we are the first to demonstrate that a single wave function can solve the Schr\"odinger equation of molecules with different atoms jointly.

For any graph G having n vertices and its automorphism group Aut(G), we provide a full characterisation of all of the possible Aut(G)-equivariant neural networks whose layers are some tensor power of R^{n}. In particular, we find a spanning set of matrices for the learnable, linear, Aut(G)-equivariant layer functions between such tensor power spaces in the standard basis of R^{n}.

High-fidelity human 3D models can now be learned directly from videos, typically by combining a template-based surface model with neural representations. However, obtaining a template surface requires expensive multi-view capture systems, laser scans, or strictly controlled conditions. Previous methods avoid using a template but rely on a costly or ill-posed mapping from observation to canonical space. We propose a hybrid point-based representation for reconstructing animatable characters that does not require an explicit surface model, while being generalizable to novel poses. For a given video, our method automatically produces an explicit set of 3D points representing approximate canonical geometry, and learns an articulated deformation model that produces pose-dependent point transformations. The points serve both as a scaffold for high-frequency neural features and an anchor for efficiently mapping between observation and canonical space. We demonstrate on established benchmarks that our representation overcomes limitations of prior work operating in either canonical or in observation space. Moreover, our automatic point extraction approach enables learning models of human and animal characters alike, matching the performance of the methods using rigged surface templates despite being more general. Project website: https://lemonatsu.github.io/npc/

Modern retrieval system often requires recomputing the representation of every piece of data in the gallery when updating to a better representation model. This process is known as backfilling and can be especially costly in the real world where the gallery often contains billions of samples. Recently, researchers have proposed the idea of Backward Compatible Training (BCT) where the new representation model can be trained with an auxiliary loss to make it backward compatible with the old representation. In this way, the new representation can be directly compared with the old representation, in principle avoiding the need for any backfilling. However, followup work shows that there is an inherent tradeoff where a backward compatible representation model cannot simultaneously maintain the performance of the new model itself. This paper reports our ``not-so-surprising'' finding that adding extra dimensions to the representation can help here. However, we also found that naively increasing the dimension of the representation did not work. To deal with this, we propose Backward-compatible Training with a novel Basis Transformation (BT^2). A basis transformation (BT) is basically a learnable set of parameters that applies an orthonormal transformation. Such a transformation possesses an important property whereby the original information contained in its input is retained in its output. We show in this paper how a BT can be utilized to add only the necessary amount of additional dimensions. We empirically verify the advantage of BT^2 over other state-of-the-art methods in a wide range of settings. We then further extend BT^2 to other challenging yet more practical settings, including significant change in model architecture (CNN to Transformers), modality change, and even a series of updates in the model architecture mimicking the evolution of deep learning models.

In this paper we demonstrate how sub-Riemannian geometry can be used for manifold learning and surface reconstruction by combining local linear approximations of a point cloud to obtain lower dimensional bundles. Local approximations obtained by local PCAs are collected into a rank k tangent subbundle on R^d, k<d, which we call a principal subbundle. This determines a sub-Riemannian metric on R^d. We show that sub-Riemannian geodesics with respect to this metric can successfully be applied to a number of important problems, such as: explicit construction of an approximating submanifold M, construction of a representation of the point-cloud in R^k, and computation of distances between observations, taking the learned geometry into account. The reconstruction is guaranteed to equal the true submanifold in the limit case where tangent spaces are estimated exactly. Via simulations, we show that the framework is robust when applied to noisy data. Furthermore, the framework generalizes to observations on an a priori known Riemannian manifold.

Supervised machine learning approaches have been increasingly used in accelerating electronic structure prediction as surrogates of first-principle computational methods, such as density functional theory (DFT). While numerous quantum chemistry datasets focus on chemical properties and atomic forces, the ability to achieve accurate and efficient prediction of the Hamiltonian matrix is highly desired, as it is the most important and fundamental physical quantity that determines the quantum states of physical systems and chemical properties. In this work, we generate a new Quantum Hamiltonian dataset, named as QH9, to provide precise Hamiltonian matrices for 999 or 2998 molecular dynamics trajectories and 130,831 stable molecular geometries, based on the QM9 dataset. By designing benchmark tasks with various molecules, we show that current machine learning models have the capacity to predict Hamiltonian matrices for arbitrary molecules. Both the QH9 dataset and the baseline models are provided to the community through an open-source benchmark, which can be highly valuable for developing machine learning methods and accelerating molecular and materials design for scientific and technological applications. Our benchmark is publicly available at https://github.com/divelab/AIRS/tree/main/OpenDFT/QHBench.

Quantifying the similarity between two mathematical structures or datasets constitutes a particularly interesting and useful operation in several theoretical and applied problems. Aimed at this specific objective, the Jaccard index has been extensively used in the most diverse types of problems, also motivating some respective generalizations. The present work addresses further generalizations of this index, including its modification into a coincidence index capable of accounting also for the level of relative interiority between the two compared entities, as well as respective extensions for sets in continuous vector spaces, the generalization to multiset addition, densities and generic scalar fields, as well as a means to quantify the joint interdependence between two random variables. The also interesting possibility to take into account more than two sets has also been addressed, including the description of an index capable of quantifying the level of chaining between three structures. Several of the described and suggested eneralizations have been illustrated with respect to numeric case examples. It is also posited that these indices can play an important role while analyzing and integrating datasets in modeling approaches and pattern recognition activities, including as a measurement of clusters similarity or separation and as a resource for representing and analyzing complex networks.

We investigate a general formulation for clustering and transductive few-shot learning, which integrates prototype-based objectives, Laplacian regularization and supervision constraints from a few labeled data points. We propose a concave-convex relaxation of the problem, and derive a computationally efficient block-coordinate bound optimizer, with convergence guarantee. At each iteration,our optimizer computes independent (parallel) updates for each point-to-cluster assignment. Therefore, it could be trivially distributed for large-scale clustering and few-shot tasks. Furthermore, we provides a thorough convergence analysis based on point-to-set maps. Were port comprehensive clustering and few-shot learning experiments over various data sets, showing that our method yields competitive performances, in term of accuracy and optimization quality, while scaling up to large problems. Using standard training on the base classes, without resorting to complex meta-learning and episodic-training strategies, our approach outperforms state-of-the-art few-shot methods by significant margins, across various models, settings and data sets. Surprisingly, we found that even standard clustering procedures (e.g., K-means), which correspond to particular, non-regularized cases of our general model, already achieve competitive performances in comparison to the state-of-the-art in few-shot learning. These surprising results point to the limitations of the current few-shot benchmarks, and question the viability of a large body of convoluted few-shot learning techniques in the recent literature.

The use of kernel functions is a common technique to extract important features from data sets. A quantum computer can be used to estimate kernel entries as transition amplitudes of unitary circuits. Quantum kernels exist that, subject to computational hardness assumptions, cannot be computed classically. It is an important challenge to find quantum kernels that provide an advantage in the classification of real-world data. We introduce a class of quantum kernels that can be used for data with a group structure. The kernel is defined in terms of a unitary representation of the group and a fiducial state that can be optimized using a technique called kernel alignment. We apply this method to a learning problem on a coset-space that embodies the structure of many essential learning problems on groups. We implement the learning algorithm with 27 qubits on a superconducting processor.

We propose Equiangular Basis Vectors (EBVs) for classification tasks. In deep neural networks, models usually end with a k-way fully connected layer with softmax to handle different classification tasks. The learning objective of these methods can be summarized as mapping the learned feature representations to the samples' label space. While in metric learning approaches, the main objective is to learn a transformation function that maps training data points from the original space to a new space where similar points are closer while dissimilar points become farther apart. Different from previous methods, our EBVs generate normalized vector embeddings as "predefined classifiers" which are required to not only be with the equal status between each other, but also be as orthogonal as possible. By minimizing the spherical distance of the embedding of an input between its categorical EBV in training, the predictions can be obtained by identifying the categorical EBV with the smallest distance during inference. Various experiments on the ImageNet-1K dataset and other downstream tasks demonstrate that our method outperforms the general fully connected classifier while it does not introduce huge additional computation compared with classical metric learning methods. Our EBVs won the first place in the 2022 DIGIX Global AI Challenge, and our code is open-source and available at https://github.com/NJUST-VIPGroup/Equiangular-Basis-Vectors.

Recently, pre-trained foundation models have enabled significant advancements in multiple fields. In molecular machine learning, however, where datasets are often hand-curated, and hence typically small, the lack of datasets with labeled features, and codebases to manage those datasets, has hindered the development of foundation models. In this work, we present seven novel datasets categorized by size into three distinct categories: ToyMix, LargeMix and UltraLarge. These datasets push the boundaries in both the scale and the diversity of supervised labels for molecular learning. They cover nearly 100 million molecules and over 3000 sparsely defined tasks, totaling more than 13 billion individual labels of both quantum and biological nature. In comparison, our datasets contain 300 times more data points than the widely used OGB-LSC PCQM4Mv2 dataset, and 13 times more than the quantum-only QM1B dataset. In addition, to support the development of foundational models based on our proposed datasets, we present the Graphium graph machine learning library which simplifies the process of building and training molecular machine learning models for multi-task and multi-level molecular datasets. Finally, we present a range of baseline results as a starting point of multi-task and multi-level training on these datasets. Empirically, we observe that performance on low-resource biological datasets show improvement by also training on large amounts of quantum data. This indicates that there may be potential in multi-task and multi-level training of a foundation model and fine-tuning it to resource-constrained downstream tasks.

We study the realizability of simplicial complexes with a given pair of integer sequences, representing the node degree distribution and the facet size distribution, respectively. While the s-uniform variant of the problem is NP-complete when s geq 3, we identify two populations of input sequences, most of which can be solved in polynomial time using a recursive algorithm that we contribute. Combining with a sampler for the simplicial configuration model [J.-G. Young et al., Phys. Rev. E 96, 032312 (2017)], we facilitate the efficient sampling of simplicial ensembles from arbitrary degree and size distributions. We find that, contrary to expectations based on dyadic networks, increasing the nodes' degrees reduces the number of loops in simplicial complexes. Our work unveils a fundamental constraint on the degree-size sequences and sheds light on further analysis of higher-order phenomena based on local structures.

Clustering is an unsupervised learning problem that aims to partition unlabelled data points into groups with similar features. Traditional clustering algorithms provide limited insight into the groups they find as their main focus is accuracy and not the interpretability of the group assignments. This has spurred a recent line of work on explainable machine learning for clustering. In this paper we focus on the cluster description problem where, given a dataset and its partition into clusters, the task is to explain the clusters. We introduce a new approach to explain clusters by constructing polyhedra around each cluster while minimizing either the complexity of the resulting polyhedra or the number of features used in the description. We formulate the cluster description problem as an integer program and present a column generation approach to search over an exponential number of candidate half-spaces that can be used to build the polyhedra. To deal with large datasets, we introduce a novel grouping scheme that first forms smaller groups of data points and then builds the polyhedra around the grouped data, a strategy which out-performs simply sub-sampling data. Compared to state of the art cluster description algorithms, our approach is able to achieve competitive interpretability with improved description accuracy.

Learning neural subset selection tasks, such as compound selection in AI-aided drug discovery, have become increasingly pivotal across diverse applications. The existing methodologies in the field primarily concentrate on constructing models that capture the relationship between utility function values and subsets within their respective supersets. However, these approaches tend to overlook the valuable information contained within the superset when utilizing neural networks to model set functions. In this work, we address this oversight by adopting a probabilistic perspective. Our theoretical findings demonstrate that when the target value is conditioned on both the input set and subset, it is essential to incorporate an invariant sufficient statistic of the superset into the subset of interest for effective learning. This ensures that the output value remains invariant to permutations of the subset and its corresponding superset, enabling identification of the specific superset from which the subset originated. Motivated by these insights, we propose a simple yet effective information aggregation module designed to merge the representations of subsets and supersets from a permutation invariance perspective. Comprehensive empirical evaluations across diverse tasks and datasets validate the enhanced efficacy of our approach over conventional methods, underscoring the practicality and potency of our proposed strategies in real-world contexts.

We present a new method for generating emission spectra from polycyclic aromatic hydrocarbons (PAHs) in arbitrary radiation fields. We utilize the single-photon limit for PAH heating and emission to treat individual photon absorptions as independent events. This allows the construction of a set of single-photon emission "basis spectra" that can be scaled to produce an output emission spectrum given any input heating spectrum. We find that this method produces agreement with PAH emission spectra computed accounting for multi-photon effects to within simeq10% in the 3-20~{rm mu m} wavelength range for radiation fields with intensity U<100. We use this framework to explore the dependence of PAH band ratios on the radiation field spectrum across grain sizes, finding in particular a strong dependence of the 3.3 to 11.2~mum band ratio on radiation field hardness. A Python-based tool and a set of basis spectra that can be used to generate these emission spectra are made publicly available.

We revisit the well-studied problem of approximating a matrix product, A^TB, based on small space sketches S(A) and S(B) of A in R^{n times d} and Bin R^{n times m}. We are interested in the setting where the sketches must be computed independently of each other, except for the use of a shared random seed. We prove that, when A and B are sparse, methods based on coordinated random sampling can outperform classical linear sketching approaches, like Johnson-Lindenstrauss Projection or CountSketch. For example, to obtain Frobenius norm error epsilon|A|_F|B|_F, coordinated sampling requires sketches of size O(s/epsilon^2) when A and B have at most s leq d,m non-zeros per row. In contrast, linear sketching leads to sketches of size O(d/epsilon^2) and O(m/epsilon^2) for A and B. We empirically evaluate our approach on two applications: 1) distributed linear regression in databases, a problem motivated by tasks like dataset discovery and augmentation, and 2) approximating attention matrices in transformer-based language models. In both cases, our sampling algorithms yield an order of magnitude improvement over linear sketching.

Magnitude of a finite metric space and the related notion of magnitude functions on metric spaces is an active area of research in algebraic topology. Magnitude originally arose in the context of biology, where it represents the number of effective species in an environment; when applied to a one-parameter family of metric spaces tX with scale parameter t, the magnitude captures much of the underlying geometry of the space. Prior work has mostly focussed on properties of magnitude in a global sense; in this paper we restrict the sets to finite subsets of Euclidean space and investigate its individual components. We give an explicit formula for the corrected inclusion-exclusion principle, and define a quantity associated with each point, called the moment which gives an intrinsic ordering to the points. We exploit this in order to form an algorithm which approximates the convex hull.

Neural networks are famously nonlinear. However, linearity is defined relative to a pair of vector spaces, f:XtoY. Is it possible to identify a pair of non-standard vector spaces for which a conventionally nonlinear function is, in fact, linear? This paper introduces a method that makes such vector spaces explicit by construction. We find that if we sandwich a linear operator A between two invertible neural networks, f(x)=g_y^{-1}(A g_x(x)), then the corresponding vector spaces X and Y are induced by newly defined addition and scaling actions derived from g_x and g_y. We term this kind of architecture a Linearizer. This framework makes the entire arsenal of linear algebra, including SVD, pseudo-inverse, orthogonal projection and more, applicable to nonlinear mappings. Furthermore, we show that the composition of two Linearizers that share a neural network is also a Linearizer. We leverage this property and demonstrate that training diffusion models using our architecture makes the hundreds of sampling steps collapse into a single step. We further utilize our framework to enforce idempotency (i.e. f(f(x))=f(x)) on networks leading to a globally projective generative model and to demonstrate modular style transfer.

Hyperbolic embeddings offer excellent quality with few dimensions when embedding hierarchical data structures like synonym or type hierarchies. Given a tree, we give a combinatorial construction that embeds the tree in hyperbolic space with arbitrarily low distortion without using optimization. On WordNet, our combinatorial embedding obtains a mean-average-precision of 0.989 with only two dimensions, while Nickel et al.'s recent construction obtains 0.87 using 200 dimensions. We provide upper and lower bounds that allow us to characterize the precision-dimensionality tradeoff inherent in any hyperbolic embedding. To embed general metric spaces, we propose a hyperbolic generalization of multidimensional scaling (h-MDS). We show how to perform exact recovery of hyperbolic points from distances, provide a perturbation analysis, and give a recovery result that allows us to reduce dimensionality. The h-MDS approach offers consistently low distortion even with few dimensions across several datasets. Finally, we extract lessons from the algorithms and theory above to design a PyTorch-based implementation that can handle incomplete information and is scalable.

We introduce Geometric Neural Operators (GNPs) for accounting for geometric contributions in data-driven deep learning of operators. We show how GNPs can be used (i) to estimate geometric properties, such as the metric and curvatures, (ii) to approximate Partial Differential Equations (PDEs) on manifolds, (iii) learn solution maps for Laplace-Beltrami (LB) operators, and (iv) to solve Bayesian inverse problems for identifying manifold shapes. The methods allow for handling geometries of general shape including point-cloud representations. The developed GNPs provide approaches for incorporating the roles of geometry in data-driven learning of operators.

Crystals are the foundation of numerous scientific and industrial applications. While various learning-based approaches have been proposed for crystal generation, existing methods seldom consider the space group constraint which is crucial in describing the geometry of crystals and closely relevant to many desirable properties. However, considering space group constraint is challenging owing to its diverse and nontrivial forms. In this paper, we reduce the space group constraint into an equivalent formulation that is more tractable to be handcrafted into the generation process. In particular, we translate the space group constraint into two parts: the basis constraint of the invariant logarithmic space of the lattice matrix and the Wyckoff position constraint of the fractional coordinates. Upon the derived constraints, we then propose DiffCSP++, a novel diffusion model that has enhanced a previous work DiffCSP by further taking space group constraint into account. Experiments on several popular datasets verify the benefit of the involvement of the space group constraint, and show that our DiffCSP++ achieves promising performance on crystal structure prediction, ab initio crystal generation and controllable generation with customized space groups.

Designing effective positional encodings for graphs is key to building powerful graph transformers and enhancing message-passing graph neural networks. Although widespread, using Laplacian eigenvectors as positional encodings faces two fundamental challenges: (1) Non-uniqueness: there are many different eigendecompositions of the same Laplacian, and (2) Instability: small perturbations to the Laplacian could result in completely different eigenspaces, leading to unpredictable changes in positional encoding. Despite many attempts to address non-uniqueness, most methods overlook stability, leading to poor generalization on unseen graph structures. We identify the cause of instability to be a "hard partition" of eigenspaces. Hence, we introduce Stable and Expressive Positional Encodings (SPE), an architecture for processing eigenvectors that uses eigenvalues to "softly partition" eigenspaces. SPE is the first architecture that is (1) provably stable, and (2) universally expressive for basis invariant functions whilst respecting all symmetries of eigenvectors. Besides guaranteed stability, we prove that SPE is at least as expressive as existing methods, and highly capable of counting graph structures. Finally, we evaluate the effectiveness of our method on molecular property prediction, and out-of-distribution generalization tasks, finding improved generalization compared to existing positional encoding methods.

Learning physical simulations has been an essential and central aspect of many recent research efforts in machine learning, particularly for Navier-Stokes-based fluid mechanics. Classic numerical solvers have traditionally been computationally expensive and challenging to use in inverse problems, whereas Neural solvers aim to address both concerns through machine learning. We propose a general formulation for continuous convolutions using separable basis functions as a superset of existing methods and evaluate a large set of basis functions in the context of (a) a compressible 1D SPH simulation, (b) a weakly compressible 2D SPH simulation, and (c) an incompressible 2D SPH Simulation. We demonstrate that even and odd symmetries included in the basis functions are key aspects of stability and accuracy. Our broad evaluation shows that Fourier-based continuous convolutions outperform all other architectures regarding accuracy and generalization. Finally, using these Fourier-based networks, we show that prior inductive biases, such as window functions, are no longer necessary. An implementation of our approach, as well as complete datasets and solver implementations, is available at https://github.com/tum-pbs/SFBC.

Given the exponential growth of the volume of the ball w.r.t. its radius, the hyperbolic space is capable of embedding trees with arbitrarily small distortion and hence has received wide attention for representing hierarchical datasets. However, this exponential growth property comes at a price of numerical instability such that training hyperbolic learning models will sometimes lead to catastrophic NaN problems, encountering unrepresentable values in floating point arithmetic. In this work, we carefully analyze the limitation of two popular models for the hyperbolic space, namely, the Poincar\'e ball and the Lorentz model. We first show that, under the 64 bit arithmetic system, the Poincar\'e ball has a relatively larger capacity than the Lorentz model for correctly representing points. Then, we theoretically validate the superiority of the Lorentz model over the Poincar\'e ball from the perspective of optimization. Given the numerical limitations of both models, we identify one Euclidean parametrization of the hyperbolic space which can alleviate these limitations. We further extend this Euclidean parametrization to hyperbolic hyperplanes and exhibits its ability in improving the performance of hyperbolic SVM.

The paper ``Tropical Geometry of Deep Neural Networks'' by L. Zhang et al. introduces an equivalence between integer-valued neural networks (IVNN) with ReLU_{t} and tropical rational functions, which come with a map to polytopes. Here, IVNN refers to a network with integer weights but real biases, and ReLU_{t} is defined as ReLU_{t}(x)=max(x,t) for tinRcup{-infty}. For every poset with n points, there exists a corresponding order polytope, i.e., a convex polytope in the unit cube [0,1]^n whose coordinates obey the inequalities of the poset. We study neural networks whose associated polytope is an order polytope. We then explain how posets with four points induce neural networks that can be interpreted as 2times 2 convolutional filters. These poset filters can be added to any neural network, not only IVNN. Similarly to maxout, poset pooling filters update the weights of the neural network during backpropagation with more precision than average pooling, max pooling, or mixed pooling, without the need to train extra parameters. We report experiments that support our statements. We also define the structure of algebra over the operad of posets on poset neural networks and tropical polynomials. This formalism allows us to study the composition of poset neural network arquitectures and the effect on their corresponding Newton polytopes, via the introduction of the generalization of two operations on polytopes: the Minkowski sum and the convex envelope.

In this article, we introduce a new parameterized family of topological invariants, taking the form of candidate decompositions, for multi-parameter persistence modules. We prove that our candidate decompositions are controllable approximations: when restricting to modules that can be decomposed into interval summands, we establish theoretical results about the approximation error between our candidate decompositions and the true underlying module in terms of the standard interleaving and bottleneck distances. Moreover, even when the underlying module does not admit such a decomposition, our candidate decompositions are nonetheless stable invariants; small perturbations in the underlying module lead to small perturbations in the candidate decomposition. Then, we introduce MMA (Multipersistence Module Approximation): an algorithm for computing stable instances of such invariants, which is based on fibered barcodes and exact matchings, two constructions that stem from the theory of single-parameter persistence. By design, MMA can handle an arbitrary number of filtrations, and has bounded complexity and running time. Finally, we present empirical evidence validating the generalization capabilities and running time speed-ups of MMA on several data sets.

Based on the theory of homogeneous spaces we derive geometrically optimal edge attributes to be used within the flexible message-passing framework. We formalize the notion of weight sharing in convolutional networks as the sharing of message functions over point-pairs that should be treated equally. We define equivalence classes of point-pairs that are identical up to a transformation in the group and derive attributes that uniquely identify these classes. Weight sharing is then obtained by conditioning message functions on these attributes. As an application of the theory, we develop an efficient equivariant group convolutional network for processing 3D point clouds. The theory of homogeneous spaces tells us how to do group convolutions with feature maps over the homogeneous space of positions R^3, position and orientations R^3 {times} S^2, and the group SE(3) itself. Among these, R^3 {times} S^2 is an optimal choice due to the ability to represent directional information, which R^3 methods cannot, and it significantly enhances computational efficiency compared to indexing features on the full SE(3) group. We support this claim with state-of-the-art results -- in accuracy and speed -- on five different benchmarks in 2D and 3D, including interatomic potential energy prediction, trajectory forecasting in N-body systems, and generating molecules via equivariant diffusion models.

Classification of cluster variables in cluster algebras (in particular, Grassmannian cluster algebras) is an important problem, which has direct application to computations of scattering amplitudes in physics. In this paper, we apply the tableaux method to classify cluster variables in Grassmannian cluster algebras C[Gr(k,n)] up to (k,n)=(3,12), (4,10), or (4,12) up to a certain number of columns of tableaux, using HPC clusters. These datasets are made available on GitHub. Supervised and unsupervised machine learning methods are used to analyse this data and identify structures associated to tableaux corresponding to cluster variables. Conjectures are raised associated to the enumeration of tableaux at each rank and the tableaux structure which creates a cluster variable, with the aid of machine learning.

This paper re-examines a continuous optimization framework dubbed NOTEARS for learning Bayesian networks. We first generalize existing algebraic characterizations of acyclicity to a class of matrix polynomials. Next, focusing on a one-parameter-per-edge setting, it is shown that the Karush-Kuhn-Tucker (KKT) optimality conditions for the NOTEARS formulation cannot be satisfied except in a trivial case, which explains a behavior of the associated algorithm. We then derive the KKT conditions for an equivalent reformulation, show that they are indeed necessary, and relate them to explicit constraints that certain edges be absent from the graph. If the score function is convex, these KKT conditions are also sufficient for local minimality despite the non-convexity of the constraint. Informed by the KKT conditions, a local search post-processing algorithm is proposed and shown to substantially and universally improve the structural Hamming distance of all tested algorithms, typically by a factor of 2 or more. Some combinations with local search are both more accurate and more efficient than the original NOTEARS.

A vector database is used to store high-dimensional data that cannot be characterized by traditional DBMS. Although there are not many articles describing existing or introducing new vector database architectures, the approximate nearest neighbor search problem behind vector databases has been studied for a long time, and considerable related algorithmic articles can be found in the literature. This article attempts to comprehensively review relevant algorithms to provide a general understanding of this booming research area. The basis of our framework categorises these studies by the approach of solving ANNS problem, respectively hash-based, tree-based, graph-based and quantization-based approaches. Then we present an overview of existing challenges for vector databases. Lastly, we sketch how vector databases can be combined with large language models and provide new possibilities.

Many clustering schemes are defined by optimizing an objective function defined on the partitions of the underlying set of a finite metric space. In this paper, we construct a framework for studying what happens when we instead impose various structural conditions on the clustering schemes, under the general heading of functoriality. Functoriality refers to the idea that one should be able to compare the results of clustering algorithms as one varies the data set, for example by adding points or by applying functions to it. We show that within this framework, one can prove a theorems analogous to one of J. Kleinberg, in which for example one obtains an existence and uniqueness theorem instead of a non-existence result. We obtain a full classification of all clustering schemes satisfying a condition we refer to as excisiveness. The classification can be changed by varying the notion of maps of finite metric spaces. The conditions occur naturally when one considers clustering as the statistical version of the geometric notion of connected components. By varying the degree of functoriality that one requires from the schemes it is possible to construct richer families of clustering schemes that exhibit sensitivity to density.

We consider the problem of approximating a function from L^2 by an element of a given m-dimensional space V_m, associated with some feature map varphi, using evaluations of the function at random points x_1,dots,x_n. After recalling some results on optimal weighted least-squares using independent and identically distributed points, we consider weighted least-squares using projection determinantal point processes (DPP) or volume sampling. These distributions introduce dependence between the points that promotes diversity in the selected features varphi(x_i). We first provide a generalized version of volume-rescaled sampling yielding quasi-optimality results in expectation with a number of samples n = O(mlog(m)), that means that the expected L^2 error is bounded by a constant times the best approximation error in L^2. Also, further assuming that the function is in some normed vector space H continuously embedded in L^2, we further prove that the approximation is almost surely bounded by the best approximation error measured in the H-norm. This includes the cases of functions from L^infty or reproducing kernel Hilbert spaces. Finally, we present an alternative strategy consisting in using independent repetitions of projection DPP (or volume sampling), yielding similar error bounds as with i.i.d. or volume sampling, but in practice with a much lower number of samples. Numerical experiments illustrate the performance of the different strategies.

Dynamical systems provide a comprehensive way to study complex and changing behaviors across various sciences. Many modern systems are too complicated to analyze directly or we do not have access to models, driving significant interest in learning methods. Koopman operators have emerged as a dominant approach because they allow the study of nonlinear dynamics using linear techniques by solving an infinite-dimensional spectral problem. However, current algorithms face challenges such as lack of convergence, hindering practical progress. This paper addresses a fundamental open question: When can we robustly learn the spectral properties of Koopman operators from trajectory data of dynamical systems, and when can we not? Understanding these boundaries is crucial for analysis, applications, and designing algorithms. We establish a foundational approach that combines computational analysis and ergodic theory, revealing the first fundamental barriers -- universal for any algorithm -- associated with system geometry and complexity, regardless of data quality and quantity. For instance, we demonstrate well-behaved smooth dynamical systems on tori where non-trivial eigenfunctions of the Koopman operator cannot be determined by any sequence of (even randomized) algorithms, even with unlimited training data. Additionally, we identify when learning is possible and introduce optimal algorithms with verification that overcome issues in standard methods. These results pave the way for a sharp classification theory of data-driven dynamical systems based on how many limits are needed to solve a problem. These limits characterize all previous methods, presenting a unified view. Our framework systematically determines when and how Koopman spectral properties can be learned.

For a graph G with n vertices and m edges, Lin et al. Lin define the atom--bond sum-connectivity (ABS) matrix of G such that the (i,j)^{th} entry is \[ 1 - \frac{2{d_i + d_j}} \] if vertex v_i is adjacent to the vertex v_j, and 0 otherwise. In this article, we determine the characteristic polynomial of the ABS matrix for certain specific classes of graphs. Furthermore, we compute the ABS eigenvalues and the ABS energy for these classes.

Nonlinear model order reduction has opened the door to parameter optimization and uncertainty quantification in complex physics problems governed by nonlinear equations. In particular, the computational cost of solving these equations can be reduced by means of local reduced-order bases. This article examines the benefits of a physics-informed cluster analysis for the construction of cluster-specific reduced-order bases. We illustrate that the choice of the dissimilarity measure for clustering is fundamental and highly affects the performances of the local reduced-order bases. It is shown that clustering with an angle-based dissimilarity on simulation data efficiently decreases the intra-cluster Kolmogorov N-width. Additionally, an a priori efficiency criterion is introduced to assess the relevance of a ROM-net, a methodology for the reduction of nonlinear physics problems introduced in our previous work in [T. Daniel, F. Casenave, N. Akkari, D. Ryckelynck, Model order reduction assisted by deep neural networks (ROM-net), Advanced Modeling and Simulation in Engineering Sciences 7 (16), 2020]. This criterion also provides engineers with a very practical method for ROM-nets' hyperparameters calibration under constrained computational costs for the training phase. On five different physics problems, our physics-informed clustering strategy significantly outperforms classic strategies for the construction of local reduced-order bases in terms of projection errors.

We consider the problem of constructing small coresets for k-Median in Euclidean spaces. Given a large set of data points Psubset R^d, a coreset is a much smaller set Ssubset R^d, so that the k-Median costs of any k centers w.r.t. P and S are close. Existing literature mainly focuses on the high-dimension case and there has been great success in obtaining dimension-independent bounds, whereas the case for small d is largely unexplored. Considering many applications of Euclidean clustering algorithms are in small dimensions and the lack of systematic studies in the current literature, this paper investigates coresets for k-Median in small dimensions. For small d, a natural question is whether existing near-optimal dimension-independent bounds can be significantly improved. We provide affirmative answers to this question for a range of parameters. Moreover, new lower bound results are also proved, which are the highest for small d. In particular, we completely settle the coreset size bound for 1-d k-Median (up to log factors). Interestingly, our results imply a strong separation between 1-d 1-Median and 1-d 2-Median. As far as we know, this is the first such separation between k=1 and k=2 in any dimension.

We present a vector-based method to balance chemical reactions. The algorithm builds candidates in a deterministic way, removes duplicates, and always prints coefficients in the lowest whole-number form. For redox cases, electrons and protons/hydroxide are treated explicitly, so both mass and charge are balanced. We also outline the basic principles of the vector formulation of stoichiometry, interpreting reactions as integer vectors in composition space, this geometric view supports compact visualizations of reagent-product interactions and helps surface distinct reaction families. The method enumerates valid balances for arbitrary user-specified species lists without special-case balancing rules or symbolic tricks, and it provides a clean foundation for developing new algorithmic variants (e.g., alternative objectives or constraints). On representative examples (neutralization, double displacement, decomposition, classical redox, small multicomponent sets) and a negative control, the method produced correct integer balances. When multiple balances exist, we report a canonical one - minimizing the total coefficient sum with a simple tie-breaker - without claiming global optimality beyond the solutions the search enumerates. The procedure applies per reaction and extends to reaction networks via consistent per-reaction application. We do not report runtimes, broader benchmarking and code/data release are planned.

This book introduces the mathematical foundations and techniques that lead to the development and analysis of many of the algorithms that are used in machine learning. It starts with an introductory chapter that describes notation used throughout the book and serve at a reminder of basic concepts in calculus, linear algebra and probability and also introduces some measure theoretic terminology, which can be used as a reading guide for the sections that use these tools. The introductory chapters also provide background material on matrix analysis and optimization. The latter chapter provides theoretical support to many algorithms that are used in the book, including stochastic gradient descent, proximal methods, etc. After discussing basic concepts for statistical prediction, the book includes an introduction to reproducing kernel theory and Hilbert space techniques, which are used in many places, before addressing the description of various algorithms for supervised statistical learning, including linear methods, support vector machines, decision trees, boosting, or neural networks. The subject then switches to generative methods, starting with a chapter that presents sampling methods and an introduction to the theory of Markov chains. The following chapter describe the theory of graphical models, an introduction to variational methods for models with latent variables, and to deep-learning based generative models. The next chapters focus on unsupervised learning methods, for clustering, factor analysis and manifold learning. The final chapter of the book is theory-oriented and discusses concentration inequalities and generalization bounds.

Real-valued functions on geometric data -- such as node attributes on a graph -- can be optimized using descriptors from persistent homology, allowing the user to incorporate topological terms in the loss function. When optimizing a single real-valued function (the one-parameter setting), there is a canonical choice of descriptor for persistent homology: the barcode. The operation mapping a real-valued function to its barcode is differentiable almost everywhere, and the convergence of gradient descent for losses using barcodes is relatively well understood. When optimizing a vector-valued function (the multiparameter setting), there is no unique choice of descriptor for multiparameter persistent homology, and many distinct descriptors have been proposed. This calls for the development of a general framework for differentiability and optimization that applies to a wide range of multiparameter homological descriptors. In this article, we develop such a framework and show that it encompasses well-known descriptors of different flavors, such as signed barcodes and the multiparameter persistence landscape. We complement the theory with numerical experiments supporting the idea that optimizing multiparameter homological descriptors can lead to improved performances compared to optimizing one-parameter descriptors, even when using the simplest and most efficiently computable multiparameter descriptors.

In this article, we develop an asymptotic method for constructing confidence regions for the set of all linear subspaces arising from PCA, from which we derive hypothesis tests on this set. Our method is based on the geometry of Riemannian manifolds with which some sets of linear subspaces are endowed.

Molecular pretrained representations (MPR) has emerged as a powerful approach for addressing the challenge of limited supervised data in applications such as drug discovery and material design. While early MPR methods relied on 1D sequences and 2D graphs, recent advancements have incorporated 3D conformational information to capture rich atomic interactions. However, these prior models treat molecules merely as discrete atom sets, overlooking the space surrounding them. We argue from a physical perspective that only modeling these discrete points is insufficient. We first present a simple yet insightful observation: naively adding randomly sampled virtual points beyond atoms can surprisingly enhance MPR performance. In light of this, we propose a principled framework that incorporates the entire 3D space spanned by molecules. We implement the framework via a novel Transformer-based architecture, dubbed SpaceFormer, with three key components: (1) grid-based space discretization; (2) grid sampling/merging; and (3) efficient 3D positional encoding. Extensive experiments show that SpaceFormer significantly outperforms previous 3D MPR models across various downstream tasks with limited data, validating the benefit of leveraging the additional 3D space beyond atoms in MPR models.

Matrix manifolds, such as manifolds of Symmetric Positive Definite (SPD) matrices and Grassmann manifolds, appear in many applications. Recently, by applying the theory of gyrogroups and gyrovector spaces that is a powerful framework for studying hyperbolic geometry, some works have attempted to build principled generalizations of Euclidean neural networks on matrix manifolds. However, due to the lack of many concepts in gyrovector spaces for the considered manifolds, e.g., the inner product and gyroangles, techniques and mathematical tools provided by these works are still limited compared to those developed for studying hyperbolic geometry. In this paper, we generalize some notions in gyrovector spaces for SPD and Grassmann manifolds, and propose new models and layers for building neural networks on these manifolds. We show the effectiveness of our approach in two applications, i.e., human action recognition and knowledge graph completion.

Linear time-invariant state space models (SSM) are a classical model from engineering and statistics, that have recently been shown to be very promising in machine learning through the Structured State Space sequence model (S4). A core component of S4 involves initializing the SSM state matrix to a particular matrix called a HiPPO matrix, which was empirically important for S4's ability to handle long sequences. However, the specific matrix that S4 uses was actually derived in previous work for a particular time-varying dynamical system, and the use of this matrix as a time-invariant SSM had no known mathematical interpretation. Consequently, the theoretical mechanism by which S4 models long-range dependencies actually remains unexplained. We derive a more general and intuitive formulation of the HiPPO framework, which provides a simple mathematical interpretation of S4 as a decomposition onto exponentially-warped Legendre polynomials, explaining its ability to capture long dependencies. Our generalization introduces a theoretically rich class of SSMs that also lets us derive more intuitive S4 variants for other bases such as the Fourier basis, and explains other aspects of training S4, such as how to initialize the important timescale parameter. These insights improve S4's performance to 86% on the Long Range Arena benchmark, with 96% on the most difficult Path-X task.

Graph neural networks aim to learn representations for graph-structured data and show impressive performance, particularly in node classification. Recently, many methods have studied the representations of GNNs from the perspective of optimization goals and spectral graph theory. However, the feature space that dominates representation learning has not been systematically studied in graph neural networks. In this paper, we propose to fill this gap by analyzing the feature space of both spatial and spectral models. We decompose graph neural networks into determined feature spaces and trainable weights, providing the convenience of studying the feature space explicitly using matrix space analysis. In particular, we theoretically find that the feature space tends to be linearly correlated due to repeated aggregations. Motivated by these findings, we propose 1) feature subspaces flattening and 2) structural principal components to expand the feature space. Extensive experiments verify the effectiveness of our proposed more comprehensive feature space, with comparable inference time to the baseline, and demonstrate its efficient convergence capability.

Recent success in training deep neural networks have prompted active investigation into the features learned on their intermediate layers. Such research is difficult because it requires making sense of non-linear computations performed by millions of parameters, but valuable because it increases our ability to understand current models and create improved versions of them. In this paper we investigate the extent to which neural networks exhibit what we call convergent learning, which is when the representations learned by multiple nets converge to a set of features which are either individually similar between networks or where subsets of features span similar low-dimensional spaces. We propose a specific method of probing representations: training multiple networks and then comparing and contrasting their individual, learned representations at the level of neurons or groups of neurons. We begin research into this question using three techniques to approximately align different neural networks on a feature level: a bipartite matching approach that makes one-to-one assignments between neurons, a sparse prediction approach that finds one-to-many mappings, and a spectral clustering approach that finds many-to-many mappings. This initial investigation reveals a few previously unknown properties of neural networks, and we argue that future research into the question of convergent learning will yield many more. The insights described here include (1) that some features are learned reliably in multiple networks, yet other features are not consistently learned; (2) that units learn to span low-dimensional subspaces and, while these subspaces are common to multiple networks, the specific basis vectors learned are not; (3) that the representation codes show evidence of being a mix between a local code and slightly, but not fully, distributed codes across multiple units.

This paper studies the problem of recovering cameras from a set of fundamental matrices. A set of fundamental matrices is said to be compatible if a set of cameras exists for which they are the fundamental matrices. We focus on the complete graph, where fundamental matrices for each pair of cameras are given. Previous work has established necessary and sufficient conditions for compatibility as rank and eigenvalue conditions on the n-view fundamental matrix obtained by concatenating the individual fundamental matrices. In this work, we show that the eigenvalue condition is redundant. We provide explicit homogeneous polynomials that describe necessary and sufficient conditions for compatibility in terms of the fundamental matrices and their epipoles. In this direction, we find that quadruple-wise compatibility is enough to ensure global compatibility for any number of cameras. We demonstrate that for four cameras, compatibility is generically described by triple-wise conditions and one additional equation involving all fundamental matrices.

We study the problem of recovering an underlying 3D shape from a set of images. Existing learning based approaches usually resort to recurrent neural nets, e.g., GRU, or intuitive pooling operations, e.g., max/mean poolings, to fuse multiple deep features encoded from input images. However, GRU based approaches are unable to consistently estimate 3D shapes given different permutations of the same set of input images as the recurrent unit is permutation variant. It is also unlikely to refine the 3D shape given more images due to the long-term memory loss of GRU. Commonly used pooling approaches are limited to capturing partial information, e.g., max/mean values, ignoring other valuable features. In this paper, we present a new feed-forward neural module, named AttSets, together with a dedicated training algorithm, named FASet, to attentively aggregate an arbitrarily sized deep feature set for multi-view 3D reconstruction. The AttSets module is permutation invariant, computationally efficient and flexible to implement, while the FASet algorithm enables the AttSets based network to be remarkably robust and generalize to an arbitrary number of input images. We thoroughly evaluate FASet and the properties of AttSets on multiple large public datasets. Extensive experiments show that AttSets together with FASet algorithm significantly outperforms existing aggregation approaches.

Hyperdimensional computing (HDC) is a biologically-inspired framework which represents symbols with high-dimensional vectors, and uses vector operations to manipulate them. The ensemble of a particular vector space and a prescribed set of vector operations (including one addition-like for "bundling" and one outer-product-like for "binding") form a *vector symbolic architecture* (VSA). While VSAs have been employed in numerous applications and have been studied empirically, many theoretical questions about VSAs remain open. We analyze the *representation capacities* of four common VSAs: MAP-I, MAP-B, and two VSAs based on sparse binary vectors. "Representation capacity' here refers to bounds on the dimensions of the VSA vectors required to perform certain symbolic tasks, such as testing for set membership i in S and estimating set intersection sizes |X cap Y| for two sets of symbols X and Y, to a given degree of accuracy. We also analyze the ability of a novel variant of a Hopfield network (a simple model of associative memory) to perform some of the same tasks that are typically asked of VSAs. In addition to providing new bounds on VSA capacities, our analyses establish and leverage connections between VSAs, "sketching" (dimensionality reduction) algorithms, and Bloom filters.

Catalyst discovery and optimization is key to solving many societal and energy challenges including solar fuels synthesis, long-term energy storage, and renewable fertilizer production. Despite considerable effort by the catalysis community to apply machine learning models to the computational catalyst discovery process, it remains an open challenge to build models that can generalize across both elemental compositions of surfaces and adsorbate identity/configurations, perhaps because datasets have been smaller in catalysis than related fields. To address this we developed the OC20 dataset, consisting of 1,281,040 Density Functional Theory (DFT) relaxations (~264,890,000 single point evaluations) across a wide swath of materials, surfaces, and adsorbates (nitrogen, carbon, and oxygen chemistries). We supplemented this dataset with randomly perturbed structures, short timescale molecular dynamics, and electronic structure analyses. The dataset comprises three central tasks indicative of day-to-day catalyst modeling and comes with pre-defined train/validation/test splits to facilitate direct comparisons with future model development efforts. We applied three state-of-the-art graph neural network models (CGCNN, SchNet, Dimenet++) to each of these tasks as baseline demonstrations for the community to build on. In almost every task, no upper limit on model size was identified, suggesting that even larger models are likely to improve on initial results. The dataset and baseline models are both provided as open resources, as well as a public leader board to encourage community contributions to solve these important tasks.

Recent work on mini-batch consistency (MBC) for set functions has brought attention to the need for sequentially processing and aggregating chunks of a partitioned set while guaranteeing the same output for all partitions. However, existing constraints on MBC architectures lead to models with limited expressive power. Additionally, prior work has not addressed how to deal with large sets during training when the full set gradient is required. To address these issues, we propose a Universally MBC (UMBC) class of set functions which can be used in conjunction with arbitrary non-MBC components while still satisfying MBC, enabling a wider range of function classes to be used in MBC settings. Furthermore, we propose an efficient MBC training algorithm which gives an unbiased approximation of the full set gradient and has a constant memory overhead for any set size for both train- and test-time. We conduct extensive experiments including image completion, text classification, unsupervised clustering, and cancer detection on high-resolution images to verify the efficiency and efficacy of our scalable set encoding framework. Our code is available at github.com/jeffwillette/umbc

We derive a Fast Multipole Method (FMM) where a low-rank approximation of the kernel is obtained using the Empirical Interpolation Method (EIM). Contrary to classical interpolation-based FMM, where the interpolation points and basis are fixed beforehand, the EIM is a nonlinear approximation method which constructs interpolation points and basis which are adapted to the kernel under consideration. The basis functions are obtained using evaluations of the kernel itself. We restrict ourselves to translation-invariant kernels, for which a modified version of the EIM approximation can be used in a multilevel FMM context; we call the obtained algorithm Empirical Interpolation Fast Multipole Method (EIFMM). An important feature of the EIFMM is a built-in error estimation of the interpolation error made by the low-rank approximation of the far-field behavior of the kernel: the algorithm selects the optimal number of interpolation points required to ensure a given accuracy for the result, leading to important gains for inhomogeneous kernels.

We consider the problem of simultaneously clustering and learning a linear representation of data lying close to a union of low-dimensional manifolds, a fundamental task in machine learning and computer vision. When the manifolds are assumed to be linear subspaces, this reduces to the classical problem of subspace clustering, which has been studied extensively over the past two decades. Unfortunately, many real-world datasets such as natural images can not be well approximated by linear subspaces. On the other hand, numerous works have attempted to learn an appropriate transformation of the data, such that data is mapped from a union of general non-linear manifolds to a union of linear subspaces (with points from the same manifold being mapped to the same subspace). However, many existing works have limitations such as assuming knowledge of the membership of samples to clusters, requiring high sampling density, or being shown theoretically to learn trivial representations. In this paper, we propose to optimize the Maximal Coding Rate Reduction metric with respect to both the data representation and a novel doubly stochastic cluster membership, inspired by state-of-the-art subspace clustering results. We give a parameterization of such a representation and membership, allowing efficient mini-batching and one-shot initialization. Experiments on CIFAR-10, -20, -100, and TinyImageNet-200 datasets show that the proposed method is much more accurate and scalable than state-of-the-art deep clustering methods, and further learns a latent linear representation of the data.

We present Manifold Diffusion Fields (MDF), an approach to learn generative models of continuous functions defined over Riemannian manifolds. Leveraging insights from spectral geometry analysis, we define an intrinsic coordinate system on the manifold via the eigen-functions of the Laplace-Beltrami Operator. MDF represents functions using an explicit parametrization formed by a set of multiple input-output pairs. Our approach allows to sample continuous functions on manifolds and is invariant with respect to rigid and isometric transformations of the manifold. Empirical results on several datasets and manifolds show that MDF can capture distributions of such functions with better diversity and fidelity than previous approaches.

In order to properly train a machine learning model, data must be properly collected. To guarantee a proper data collection, verifying that the collected data set holds certain properties is a possible solution. For example, guaranteeing that the data set contains samples across the whole input space, or that the data set is balanced w.r.t. different classes. We present a formal approach for verifying a set of arbitrarily stated properties over a data set. The proposed approach relies on the transformation of the data set into a first order logic formula, which can be later verified w.r.t. the different properties also stated in the same logic. A prototype tool, which uses the z3 solver, has been developed; the prototype can take as an input a set of properties stated in a formal language and formally verify a given data set w.r.t. to the given set of properties. Preliminary experimental results show the feasibility and performance of the proposed approach, and furthermore the flexibility for expressing properties of interest.

Recent advances in large language models (LLMs) have demonstrated notable progress on many mathematical benchmarks. However, most of these benchmarks only feature problems grounded in junior and senior high school subjects, contain only multiple-choice questions, and are confined to a limited scope of elementary arithmetic operations. To address these issues, this paper introduces an expansive benchmark suite SciBench that aims to systematically examine the reasoning capabilities required for complex scientific problem solving. SciBench contains two carefully curated datasets: an open set featuring a range of collegiate-level scientific problems drawn from mathematics, chemistry, and physics textbooks, and a closed set comprising problems from undergraduate-level exams in computer science and mathematics. Based on the two datasets, we conduct an in-depth benchmark study of two representative LLMs with various prompting strategies. The results reveal that current LLMs fall short of delivering satisfactory performance, with an overall score of merely 35.80%. Furthermore, through a detailed user study, we categorize the errors made by LLMs into ten problem-solving abilities. Our analysis indicates that no single prompting strategy significantly outperforms others and some strategies that demonstrate improvements in certain problem-solving skills result in declines in other skills. We envision that SciBench will catalyze further developments in the reasoning abilities of LLMs, thereby ultimately contributing to scientific research and discovery.

Foundation models, or large atomistic models (LAMs), aim to universally represent the ground-state potential energy surface (PES) of atomistic systems as defined by density functional theory (DFT). The scaling law is pivotal in the development of large models, suggesting that their generalizability in downstream tasks consistently improves with increased model size, expanded training datasets, and larger computational budgets. In this study, we present DPA3, a multi-layer graph neural network founded on line graph series (LiGS), designed explicitly for the era of LAMs. We demonstrate that the generalization error of the DPA3 model adheres to the scaling law. The scalability in the number of model parameters is attained by stacking additional layers within DPA3. Additionally, the model employs a dataset encoding mechanism that decouples the scaling of training data size from the model size within its multi-task training framework. When trained as problem-oriented potential energy models, the DPA3 model exhibits superior accuracy in the majority of benchmark cases, encompassing systems with diverse features, including molecules, bulk materials, surface and cluster catalysts, two-dimensional materials, and battery materials. When trained as a LAM on the OpenLAM-v1 dataset, the DPA-3.1-3M model exhibits state-of-the-art performance in the LAMBench benchmark suite for LAMs, demonstrating lowest overall zero-shot generalization error across 17 downstream tasks from a broad spectrum of research domains. This performance suggests superior accuracy as an out-of-the-box potential model, requiring minimal fine-tuning data for downstream scientific applications.

The exploration of linear subspaces, particularly scattered subspaces, has garnered considerable attention across diverse mathematical disciplines in recent years, notably within finite geometries and coding theory. Scattered subspaces play a pivotal role in analyzing various geometric structures such as blocking sets, two-intersection sets, complete arcs, caps in affine and projective spaces over finite fields and rank metric codes. This paper introduces a new infinite family of h-subspaces, along with their associated MRD codes. Additionally, it addresses the task of determining the generalized weights of these codes. Notably, we demonstrate that these MRD codes exhibit some larger generalized weights compared to those previously identified.

Current approaches to chemical map generation from hyperspectral images are based on models such as partial least squares (PLS) regression, generating pixel-wise predictions that do not consider spatial context and suffer from a high degree of noise. This study proposes an end-to-end deep learning approach using a modified version of U-Net and a custom loss function to directly obtain chemical maps from hyperspectral images, skipping all intermediate steps required for traditional pixel-wise analysis. We compare the U-Net with the traditional PLS regression on a real dataset of pork belly samples with associated mean fat reference values. The U-Net obtains a test set root mean squared error of between 9% and 13% lower than that of PLS regression on the task of mean fat prediction. At the same time, U-Net generates fine detail chemical maps where 99.91% of the variance is spatially correlated. Conversely, only 2.53% of the variance in the PLS-generated chemical maps is spatially correlated, indicating that each pixel-wise prediction is largely independent of neighboring pixels. Additionally, while the PLS-generated chemical maps contain predictions far beyond the physically possible range of 0-100%, U-Net learns to stay inside this range. Thus, the findings of this study indicate that U-Net is superior to PLS for chemical map generation.

Autoregressive point cloud generation has long lagged behind diffusion-based approaches in quality. The performance gap stems from the fact that autoregressive models impose an artificial ordering on inherently unordered point sets, forcing shape generation to proceed as a sequence of local predictions. This sequential bias emphasizes short-range continuity but undermines the model's capacity to capture long-range dependencies, hindering its ability to enforce global structural properties such as symmetry, consistent topology, and large-scale geometric regularities. Inspired by the level-of-detail (LOD) principle in shape modeling, we propose PointNSP, a coarse-to-fine generative framework that preserves global shape structure at low resolutions and progressively refines fine-grained geometry at higher scales through a next-scale prediction paradigm. This multi-scale factorization aligns the autoregressive objective with the permutation-invariant nature of point sets, enabling rich intra-scale interactions while avoiding brittle fixed orderings. Experiments on ShapeNet show that PointNSP establishes state-of-the-art (SOTA) generation quality for the first time within the autoregressive paradigm. In addition, it surpasses strong diffusion-based baselines in parameter, training, and inference efficiency. Finally, in dense generation with 8,192 points, PointNSP's advantages become even more pronounced, underscoring its scalability potential.

Machine learning interatomic potentials (MLIPs) balance high accuracy and lower costs compared to density functional theory calculations, but their performance often depends on the size and diversity of training datasets. Large datasets improve model accuracy and generalization but are computationally expensive to produce and train on, while smaller datasets risk discarding rare but important atomic environments and compromising MLIP accuracy/reliability. Here, we develop an information-theoretical framework to quantify the efficiency of dataset compression methods and propose an algorithm that maximizes this efficiency. By framing atomistic dataset compression as an instance of the minimum set cover (MSC) problem over atom-centered environments, our method identifies the smallest subset of structures that contains as much information as possible from the original dataset while pruning redundant information. The approach is extensively demonstrated on the GAP-20 and TM23 datasets, and validated on 64 varied datasets from the ColabFit repository. Across all cases, MSC consistently retains outliers, preserves dataset diversity, and reproduces the long-tail distributions of forces even at high compression rates, outperforming other subsampling methods. Furthermore, MLIPs trained on MSC-compressed datasets exhibit reduced error for out-of-distribution data even in low-data regimes. We explain these results using an outlier analysis and show that such quantitative conclusions could not be achieved with conventional dimensionality reduction methods. The algorithm is implemented in the open-source QUESTS package and can be used for several tasks in atomistic modeling, from data subsampling, outlier detection, and training improved MLIPs at a lower cost.

We study the complexity of sampling from a distribution over all index subsets of the set {1,...,n} with the probability of a subset S proportional to the determinant of the submatrix L_S of some ntimes n p.s.d. matrix L, where L_S corresponds to the entries of L indexed by S. Known as a determinantal point process, this distribution is used in machine learning to induce diversity in subset selection. In practice, we often wish to sample multiple subsets S with small expected size k = E[|S|] ll n from a very large matrix L, so it is important to minimize the preprocessing cost of the procedure (performed once) as well as the sampling cost (performed repeatedly). For this purpose, we propose a new algorithm which, given access to L, samples exactly from a determinantal point process while satisfying the following two properties: (1) its preprocessing cost is n cdot poly(k), i.e., sublinear in the size of L, and (2) its sampling cost is poly(k), i.e., independent of the size of L. Prior to our results, state-of-the-art exact samplers required O(n^3) preprocessing time and sampling time linear in n or dependent on the spectral properties of L. We also give a reduction which allows using our algorithm for exact sampling from cardinality constrained determinantal point processes with ncdotpoly(k) time preprocessing.

Hyperbolic space has proven to be well-suited for capturing hierarchical relations in data, such as trees and directed acyclic graphs. Prior work introduced the concept of entailment cones, which uses partial orders defined by nested cones in the Poincar\'e ball to model hierarchies. Here, we introduce the ``shadow cones" framework, a physics-inspired entailment cone construction. Specifically, we model partial orders as subset relations between shadows formed by a light source and opaque objects in hyperbolic space. The shadow cones framework generalizes entailment cones to a broad class of formulations and hyperbolic space models beyond the Poincar\'e ball. This results in clear advantages over existing constructions: for example, shadow cones possess better optimization properties over constructions limited to the Poincar\'e ball. Our experiments on datasets of various sizes and hierarchical structures show that shadow cones consistently and significantly outperform existing entailment cone constructions. These results indicate that shadow cones are an effective way to model partial orders in hyperbolic space, offering physically intuitive and novel insights about the nature of such structures.

We present a novel framework for learning on CW-complex structured data points. Recent advances have discussed CW-complexes as ideal learning representations for problems in cheminformatics. However, there is a lack of available machine learning methods suitable for learning on CW-complexes. In this paper we develop notions of convolution and attention that are well defined for CW-complexes. These notions enable us to create the first Hodge informed neural network that can receive a CW-complex as input. We illustrate and interpret this framework in the context of supervised prediction.

Prediction sets capture uncertainty by predicting sets of labels rather than individual labels, enabling downstream decisions to conservatively account for all plausible outcomes. Conformal inference algorithms construct prediction sets guaranteed to contain the true label with high probability. These guarantees fail to hold in the face of distribution shift, which is precisely when reliable uncertainty quantification can be most useful. We propose a novel algorithm for constructing prediction sets with PAC guarantees in the label shift setting. This method estimates the predicted probabilities of the classes in a target domain, as well as the confusion matrix, then propagates uncertainty in these estimates through a Gaussian elimination algorithm to compute confidence intervals for importance weights. Finally, it uses these intervals to construct prediction sets. We evaluate our approach on five datasets: the CIFAR-10, ChestX-Ray and Entity-13 image datasets, the tabular CDC Heart dataset, and the AGNews text dataset. Our algorithm satisfies the PAC guarantee while producing smaller, more informative, prediction sets compared to several baselines.

A fuzzy theoretic analytical approach was recently introduced that leads to efficient and robust models while addressing automatically the typical issues associated to parametric deep models. However, a formal conceptualization of the fuzzy theoretic analytical deep models is still not available. This paper introduces using measure theoretic basis the notion of membership-mapping for representing data points through attribute values (motivated by fuzzy theory). A property of the membership-mapping, that can be exploited for data representation learning, is of providing an interpolation on the given data points in the data space. An analytical approach to the variational learning of a membership-mappings based data representation model is considered.

Given a K-vertex simplex in a d-dimensional space, suppose we measure n points on the simplex with noise (hence, some of the observed points fall outside the simplex). Vertex hunting is the problem of estimating the K vertices of the simplex. A popular vertex hunting algorithm is successive projection algorithm (SPA). However, SPA is observed to perform unsatisfactorily under strong noise or outliers. We propose pseudo-point SPA (pp-SPA). It uses a projection step and a denoise step to generate pseudo-points and feed them into SPA for vertex hunting. We derive error bounds for pp-SPA, leveraging on extreme value theory of (possibly) high-dimensional random vectors. The results suggest that pp-SPA has faster rates and better numerical performances than SPA. Our analysis includes an improved non-asymptotic bound for the original SPA, which is of independent interest.

This work presents a graph neural network (GNN) framework for solving the maximum independent set (MIS) problem, inspired by dynamic programming (DP). Specifically, given a graph, we propose a DP-like recursive algorithm based on GNNs that firstly constructs two smaller sub-graphs, predicts the one with the larger MIS, and then uses it in the next recursive call. To train our algorithm, we require annotated comparisons of different graphs concerning their MIS size. Annotating the comparisons with the output of our algorithm leads to a self-training process that results in more accurate self-annotation of the comparisons and vice versa. We provide numerical evidence showing the superiority of our method vs prior methods in multiple synthetic and real-world datasets.

We study the matrix models pi:C(S_N^+)to M_N(C(X)) which are flat, in the sense that the standard generators of C(S_N^+) are mapped to rank 1 projections. Our first result is a generalization of the Pauli matrix construction at N=4, using finite groups and 2-cocycles. Our second result is the construction of a universal representation of C(S_N^+), inspired from the Sinkhorn algorithm, that we conjecture to be inner faithful.

We study the implications of the modeling choice to use a graph, instead of a hypergraph, to represent real-world interconnected systems whose constituent relationships are of higher order by nature. Such a modeling choice typically involves an underlying projection process that maps the original hypergraph onto a graph, and is common in graph-based analysis. While hypergraph projection can potentially lead to loss of higher-order relations, there exists very limited studies on the consequences of doing so, as well as its remediation. This work fills this gap by doing two things: (1) we develop analysis based on graph and set theory, showing two ubiquitous patterns of hyperedges that are root to structural information loss in all hypergraph projections; we also quantify the combinatorial impossibility of recovering the lost higher-order structures if no extra help is provided; (2) we still seek to recover the lost higher-order structures in hypergraph projection, and in light of (1)'s findings we propose to relax the problem into a learning-based setting. Under this setting, we develop a learning-based hypergraph reconstruction method based on an important statistic of hyperedge distributions that we find. Our reconstruction method is evaluated on 8 real-world datasets under different settings, and exhibits consistently good performance. We also demonstrate benefits of the reconstructed hypergraphs via use cases of protein rankings and link predictions.

Point cloud analysis (such as 3D segmentation and detection) is a challenging task, because of not only the irregular geometries of many millions of unordered points, but also the great variations caused by depth, viewpoint, occlusion, etc. Current studies put much focus on the adaption of neural networks to the complex geometries of point clouds, but are blind to a fundamental question: how to learn an appropriate point embedding space that is aware of both discriminative semantics and challenging variations? As a response, we propose a clustering based supervised learning scheme for point cloud analysis. Unlike current de-facto, scene-wise training paradigm, our algorithm conducts within-class clustering on the point embedding space for automatically discovering subclass patterns which are latent yet representative across scenes. The mined patterns are, in turn, used to repaint the embedding space, so as to respect the underlying distribution of the entire training dataset and improve the robustness to the variations. Our algorithm is principled and readily pluggable to modern point cloud segmentation networks during training, without extra overhead during testing. With various 3D network architectures (i.e., voxel-based, point-based, Transformer-based, automatically searched), our algorithm shows notable improvements on famous point cloud segmentation datasets (i.e.,2.0-2.6% on single-scan and 2.0-2.2% multi-scan of SemanticKITTI, 1.8-1.9% on S3DIS, in terms of mIoU). Our algorithm also demonstrates utility in 3D detection, showing 2.0-3.4% mAP gains on KITTI.

It is well noted that coordinate based MLPs benefit -- in terms of preserving high-frequency information -- through the encoding of coordinate positions as an array of Fourier features. Hitherto, the rationale for the effectiveness of these positional encodings has been solely studied through a Fourier lens. In this paper, we strive to broaden this understanding by showing that alternative non-Fourier embedding functions can indeed be used for positional encoding. Moreover, we show that their performance is entirely determined by a trade-off between the stable rank of the embedded matrix and the distance preservation between embedded coordinates. We further establish that the now ubiquitous Fourier feature mapping of position is a special case that fulfills these conditions. Consequently, we present a more general theory to analyze positional encoding in terms of shifted basis functions. To this end, we develop the necessary theoretical formulae and empirically verify that our theoretical claims hold in practice. Codes available at https://github.com/osiriszjq/Rethinking-positional-encoding.

Clustering is a NP-hard problem. Thus, no optimal algorithm exists, heuristics are applied to cluster the data. Heuristics can be very resource-intensive, if not applied properly. For substantially large data sets computational efficiencies can be achieved by reducing the input space if a minimal loss of information can be achieved. Clustering algorithms, in general, face two common problems: 1) these converge to different settings with different initial conditions and; 2) the number of clusters has to be arbitrarily decided beforehand. This problem has become critical in the realm of big data. Recently, clustering algorithms have emerged which can speedup computations using parallel processing over the grid but face the aforementioned problems. Goals: Our goals are to find methods to cluster data which: 1) guarantee convergence to the same settings irrespective of the initial conditions; 2) eliminate the need to establish the number of clusters beforehand, and 3) can be applied to cluster large datasets. Methods: We introduce a method that combines probabilistic and combinatorial clustering methods to produce repeatable and compact clusters that are not sensitive to initial conditions. This method harnesses the power of k-means (a combinatorial clustering method) to cluster/partition very large dimensional datasets and uses the Gaussian Mixture Model (a probabilistic clustering method) to validate the k-means partitions. Results: We show that this method produces very compact clusters that are not sensitive to initial conditions. This method can be used to identify the most 'separable' set in a dataset which increases the 'clusterability' of a dataset. This method also eliminates the need to specify the number of clusters in advance.

Persistent homology, a technique from computational topology, has recently shown strong empirical performance in the context of graph classification. Being able to capture long range graph properties via higher-order topological features, such as cycles of arbitrary length, in combination with multi-scale topological descriptors, has improved predictive performance for data sets with prominent topological structures, such as molecules. At the same time, the theoretical properties of persistent homology have not been formally assessed in this context. This paper intends to bridge the gap between computational topology and graph machine learning by providing a brief introduction to persistent homology in the context of graphs, as well as a theoretical discussion and empirical analysis of its expressivity for graph learning tasks.

Accurate thermochemical data with sub-chemical accuracy (i.e., within pm1 kcal mol^{-1} from sufficiently accurate experimental or theoretical reference data) is essential for the development and improvement of computational chemistry methods. Challenging thermochemical properties such as heats of formation and total atomization energies (TAEs) are of particular interest because they rigorously test the ability of computational chemistry methods to accurately describe complex chemical transformations involving multiple bond rearrangements. Yet, existing thermochemical datasets that confidently reach this level of accuracy are limited in either size or scope. Datasets with highly accurate reference values include a small number of data points, and larger datasets provide less accurate data or only cover a narrow portion of the chemical space. The existing datasets are therefore insufficient for developing data-driven methods with predictive accuracy over a large chemical space. The Microsoft Research Accurate Chemistry Collection (MSR-ACC) will address this challenge. Here, it offers the MSR-ACC/TAE25 dataset of 76,879 total atomization energies obtained at the CCSD(T)/CBS level via the W1-F12 thermochemical protocol. The dataset is constructed to exhaustively cover chemical space for all elements up to argon by enumerating and sampling chemical graphs, thus avoiding bias towards any particular subspace of the chemical space (such as drug-like, organic, or experimentally observed molecules). With this first dataset in MSR-ACC, we enable data-driven approaches for developing predictive computational chemistry methods with unprecedented accuracy and scope.

Characteristic classes, which are abstract topological invariants associated with vector bundles, have become an important notion in modern physics with surprising real-world consequences. As a representative example, the incredible properties of topological insulators, which are insulators in their bulk but conductors on their surface, can be completely characterized by a specific characteristic class associated with their electronic band structure, the first Chern class. Given their importance to next generation computing and the computational challenge of calculating them using first-principles approaches, there is a need to develop machine learning approaches to predict the characteristic classes associated with a material system. To aid in this program we introduce the {Haldane bundle dataset}, which consists of synthetically generated complex line bundles on the 2-torus. We envision this dataset, which is not as challenging as noisy and sparsely measured real-world datasets but (as we show) still difficult for off-the-shelf architectures, to be a testing ground for architectures that incorporate the rich topological and geometric priors underlying characteristic classes.

Many machine learning tasks such as multiple instance learning, 3D shape recognition, and few-shot image classification are defined on sets of instances. Since solutions to such problems do not depend on the order of elements of the set, models used to address them should be permutation invariant. We present an attention-based neural network module, the Set Transformer, specifically designed to model interactions among elements in the input set. The model consists of an encoder and a decoder, both of which rely on attention mechanisms. In an effort to reduce computational complexity, we introduce an attention scheme inspired by inducing point methods from sparse Gaussian process literature. It reduces the computation time of self-attention from quadratic to linear in the number of elements in the set. We show that our model is theoretically attractive and we evaluate it on a range of tasks, demonstrating the state-of-the-art performance compared to recent methods for set-structured data.

Molecule pretraining has quickly become the go-to schema to boost the performance of AI-based drug discovery. Naturally, molecules can be represented as 2D topological graphs or 3D geometric point clouds. Although most existing pertaining methods focus on merely the single modality, recent research has shown that maximizing the mutual information (MI) between such two modalities enhances the molecule representation ability. Meanwhile, existing molecule multi-modal pretraining approaches approximate MI based on the representation space encoded from the topology and geometry, thus resulting in the loss of critical structural information of molecules. To address this issue, we propose MoleculeSDE. MoleculeSDE leverages group symmetric (e.g., SE(3)-equivariant and reflection-antisymmetric) stochastic differential equation models to generate the 3D geometries from 2D topologies, and vice versa, directly in the input space. It not only obtains tighter MI bound but also enables prosperous downstream tasks than the previous work. By comparing with 17 pretraining baselines, we empirically verify that MoleculeSDE can learn an expressive representation with state-of-the-art performance on 26 out of 32 downstream tasks.

To characterize the location (mean, median) of a set of graphs, one needs a notion of centrality that is adapted to metric spaces, since graph sets are not Euclidean spaces. A standard approach is to consider the Frechet mean. In this work, we equip a set of graphs with the pseudometric defined by the norm between the eigenvalues of their respective adjacency matrix. Unlike the edit distance, this pseudometric reveals structural changes at multiple scales, and is well adapted to studying various statistical problems for graph-valued data. We describe an algorithm to compute an approximation to the sample Frechet mean of a set of undirected unweighted graphs with a fixed size using this pseudometric.

Much of the success of deep learning is drawn from building architectures that properly respect underlying symmetry and structure in the data on which they operate - a set of considerations that have been united under the banner of geometric deep learning. Often problems in the physical sciences deal with relatively small sets of points in two- or three-dimensional space wherein translation, rotation, and permutation equivariance are important or even vital for models to be useful in practice. In this work, we present rotation- and permutation-equivariant architectures for deep learning on these small point clouds, composed of a set of products of terms from the geometric algebra and reductions over those products using an attention mechanism. The geometric algebra provides valuable mathematical structure by which to combine vector, scalar, and other types of geometric inputs in a systematic way to account for rotation invariance or covariance, while attention yields a powerful way to impose permutation equivariance. We demonstrate the usefulness of these architectures by training models to solve sample problems relevant to physics, chemistry, and biology.

In this note we establish a 1-to-1 correspondence between the class of generalized quadrangles with ovoids and the class of balanced incomplete block designs that posses a non-triangular local resolution system and have the appropriate parameters. We present a non-triangular local resolution system for a difference family BIBD construction of Sprott.

We introduce methods for obtaining pretrained Geometric Neural Operators (GNPs) that can serve as basal foundation models for use in obtaining geometric features. These can be used within data processing pipelines for machine learning tasks and numerical methods. We show how our GNPs can be trained to learn robust latent representations for the differential geometry of point-clouds to provide estimates of metric, curvature, and other shape-related features. We demonstrate how our pre-trained GNPs can be used (i) to estimate the geometric properties of surfaces of arbitrary shape and topologies with robustness in the presence of noise, (ii) to approximate solutions of geometric partial differential equations (PDEs) on manifolds, and (iii) to solve equations for shape deformations such as curvature driven flows. We release codes and weights for using GNPs in the package geo_neural_op. This allows for incorporating our pre-trained GNPs as components for reuse within existing and new data processing pipelines. The GNPs also can be used as part of numerical solvers involving geometry or as part of methods for performing inference and other geometric tasks.

We introduce 3DShape2VecSet, a novel shape representation for neural fields designed for generative diffusion models. Our shape representation can encode 3D shapes given as surface models or point clouds, and represents them as neural fields. The concept of neural fields has previously been combined with a global latent vector, a regular grid of latent vectors, or an irregular grid of latent vectors. Our new representation encodes neural fields on top of a set of vectors. We draw from multiple concepts, such as the radial basis function representation and the cross attention and self-attention function, to design a learnable representation that is especially suitable for processing with transformers. Our results show improved performance in 3D shape encoding and 3D shape generative modeling tasks. We demonstrate a wide variety of generative applications: unconditioned generation, category-conditioned generation, text-conditioned generation, point-cloud completion, and image-conditioned generation.

Accurate potential energy surface (PES) descriptions are essential for atomistic simulations of materials. Universal machine learning interatomic potentials (UMLIPs)^{1-3} offer a computationally efficient alternative to density functional theory (DFT)^4 for PES modeling across the periodic table. However, their accuracy today is fundamentally constrained due to a reliance on DFT relaxation data.^{5,6} Here, we introduce MatPES, a foundational PES dataset comprising sim 400,000 structures carefully sampled from 281 million molecular dynamics snapshots that span 16 billion atomic environments. We demonstrate that UMLIPs trained on the modestly sized MatPES dataset can rival, or even outperform, prior models trained on much larger datasets across a broad range of equilibrium, near-equilibrium, and molecular dynamics property benchmarks. We also introduce the first high-fidelity PES dataset based on the revised regularized strongly constrained and appropriately normed (r^2SCAN) functional^7 with greatly improved descriptions of interatomic bonding. The open source MatPES initiative emphasizes the importance of data quality over quantity in materials science and enables broad community-driven advancements toward more reliable, generalizable, and efficient UMLIPs for large-scale materials discovery and design.

We study the approximability of an existing framework for clustering edge-colored hypergraphs, which is closely related to chromatic correlation clustering and is motivated by machine learning and data mining applications where the goal is to cluster a set of objects based on multiway interactions of different categories or types. We present improved approximation guarantees based on linear programming, and show they are tight by proving a matching integrality gap. Our results also include new approximation hardness results, a combinatorial 2-approximation whose runtime is linear in the hypergraph size, and several new connections to well-studied objectives such as vertex cover and hypergraph multiway cut.

In statistics, independent, identically distributed random samples do not carry a natural ordering, and their statistics are typically invariant with respect to permutations of their order. Thus, an n-sample in a space M can be considered as an element of the quotient space of M^n modulo the permutation group. The present paper takes this definition of sample space and the related concept of orbit types as a starting point for developing a geometric perspective on statistics. We aim at deriving a general mathematical setting for studying the behavior of empirical and population means in spaces ranging from smooth Riemannian manifolds to general stratified spaces. We fully describe the orbifold and path-metric structure of the sample space when M is a manifold or path-metric space, respectively. These results are non-trivial even when M is Euclidean. We show that the infinite sample space exists in a Gromov-Hausdorff type sense and coincides with the Wasserstein space of probability distributions on M. We exhibit Fr\'echet means and k-means as metric projections onto 1-skeleta or k-skeleta in Wasserstein space, and we define a new and more general notion of polymeans. This geometric characterization via metric projections applies equally to sample and population means, and we use it to establish asymptotic properties of polymeans such as consistency and asymptotic normality.

Foundation models applied to bio-molecular space hold promise to accelerate drug discovery. Molecular representation is key to building such models. Previous works have typically focused on a single representation or view of the molecules. Here, we develop a multi-view foundation model approach, that integrates molecular views of graph, image and text. Single-view foundation models are each pre-trained on a dataset of up to 200M molecules and then aggregated into combined representations. Our multi-view model is validated on a diverse set of 18 tasks, encompassing ligand-protein binding, molecular solubility, metabolism and toxicity. We show that the multi-view models perform robustly and are able to balance the strengths and weaknesses of specific views. We then apply this model to screen compounds against a large (>100 targets) set of G Protein-Coupled receptors (GPCRs). From this library of targets, we identify 33 that are related to Alzheimer's disease. On this subset, we employ our model to identify strong binders, which are validated through structure-based modeling and identification of key binding motifs.

Deep models have achieved impressive progress in solving partial differential equations (PDEs). A burgeoning paradigm is learning neural operators to approximate the input-output mappings of PDEs. While previous deep models have explored the multiscale architectures and various operator designs, they are limited to learning the operators as a whole in the coordinate space. In real physical science problems, PDEs are complex coupled equations with numerical solvers relying on discretization into high-dimensional coordinate space, which cannot be precisely approximated by a single operator nor efficiently learned due to the curse of dimensionality. We present Latent Spectral Models (LSM) toward an efficient and precise solver for high-dimensional PDEs. Going beyond the coordinate space, LSM enables an attention-based hierarchical projection network to reduce the high-dimensional data into a compact latent space in linear time. Inspired by classical spectral methods in numerical analysis, we design a neural spectral block to solve PDEs in the latent space that approximates complex input-output mappings via learning multiple basis operators, enjoying nice theoretical guarantees for convergence and approximation. Experimentally, LSM achieves consistent state-of-the-art and yields a relative gain of 11.5% averaged on seven benchmarks covering both solid and fluid physics. Code is available at https://github.com/thuml/Latent-Spectral-Models.

Generative models have advanced significantly in sampling material systems with continuous variables, such as atomistic structures. However, their application to discrete variables, like atom types or spin states, remains underexplored. In this work, we introduce a Boltzmann generator built on discrete flow matching, specifically tailored for systems with discrete phase-space coordinates (e.g., the Ising model or crystalline compounds). This approach enables a single model to sample free energy surfaces over a wide temperature range with minimal training overhead. In addition, the model generation is scalable to larger lattice sizes than those in the training set. We demonstrate the effectiveness of our approach on the 2D Ising model, showing efficient and reliable free energy sampling. This framework provides a scalable and computationally efficient solution for discrete coordinate systems and can be extended to sample the alchemical degrees of freedom in crystalline compounds.