Elucidating Flow Matching ODE Dynamics with respect to Data Geometries

Diffusion-based generative models have become the standard for image generation. ODE-based samplers and flow matching models improve efficiency, in comparison to diffusion models, by reducing sampling steps through learned vector fields. However, the theoretical foundations of flow matching models remain limited, particularly regarding the convergence of individual sample trajectories at terminal time - a critical property that impacts sample quality and being critical assumption for models like the consistency model. In this paper, we advance the theory of flow matching models through a comprehensive analysis of sample trajectories, centered on the denoiser that drives ODE dynamics. We establish the existence, uniqueness and convergence of ODE trajectories at terminal time, ensuring stable sampling outcomes under minimal assumptions. Our analysis reveals how trajectories evolve from capturing global data features to local structures, providing the geometric characterization of per-sample behavior in flow matching models. We also explain the memorization phenomenon in diffusion-based training through our terminal time analysis. These findings bridge critical gaps in understanding flow matching models, with practical implications for sampling stability and model design.

DE-HNN: An effective neural model for Circuit Netlist representation

The run-time for optimization tools used in chip design has grown with the complexity of designs to the point where it can take several days to go through one design cycle which has become a bottleneck. Designers want fast tools that can quickly give feedback on a design. Using the input and output data of the tools from past designs, one can attempt to build a machine learning model that predicts the outcome of a design in significantly shorter time than running the tool. The accuracy of such models is affected by the representation of the design data, which is usually a netlist that describes the elements of the digital circuit and how they are connected. Graph representations for the netlist together with graph neural networks have been investigated for such models. However, the characteristics of netlists pose several challenges for existing graph learning frameworks, due to the large number of nodes and the importance of long-range interactions between nodes. To address these challenges, we represent the netlist as a directed hypergraph and propose a Directional Equivariant Hypergraph Neural Network (DE-HNN) for the effective learning of (directed) hypergraphs. Theoretically, we show that our DE-HNN can universally approximate any node or hyperedge based function that satisfies certain permutation equivariant and invariant properties natural for directed hypergraphs. We compare the proposed DE-HNN with several State-of-the-art (SOTA) machine learning models for (hyper)graphs and netlists, and show that the DE-HNN significantly outperforms them in predicting the outcome of optimized place-and-route tools directly from the input netlists. Our source code and the netlists data used are publicly available at https://github.com/YusuLab/chips.git

On the Theoretical Expressive Power and the Design Space of Higher-Order Graph Transformers

Graph transformers have recently received significant attention in graph learning, partly due to their ability to capture more global interaction via self-attention. Nevertheless, while higher-order graph neural networks have been reasonably well studied, the exploration of extending graph transformers to higher-order variants is just starting. Both theoretical understanding and empirical results are limited. In this paper, we provide a systematic study of the theoretical expressive power of order-$k$ graph transformers and sparse variants. We first show that, an order-$k$ graph transformer without additional structural information is less expressive than the $k$-Weisfeiler Lehman ($k$-WL) test despite its high computational cost. We then explore strategies to both sparsify and enhance the higher-order graph transformers, aiming to improve both their efficiency and expressiveness. Indeed, sparsification based on neighborhood information can enhance the expressive power, as it provides additional information about input graph structures. In particular, we show that a natural neighborhood-based sparse order-$k$ transformer model is not only computationally efficient, but also expressive -- as expressive as $k$-WL test. We further study several other sparse graph attention models that are computationally efficient and provide their expressiveness analysis. Finally, we provide experimental results to show the effectiveness of the different sparsification strategies.

Comparing Graph Transformers via Positional Encodings

The distinguishing power of graph transformers is closely tied to the choice of positional encoding: features used to augment the base transformer with information about the graph. There are two primary types of positional encoding: absolute positional encodings (APEs) and relative positional encodings (RPEs). APEs assign features to each node and are given as input to the transformer. RPEs instead assign a feature to each pair of nodes, e.g., graph distance, and are used to augment the attention block. A priori, it is unclear which method is better for maximizing the power of the resulting graph transformer. In this paper, we aim to understand the relationship between these different types of positional encodings. Interestingly, we show that graph transformers using APEs and RPEs are equivalent in terms of distinguishing power. In particular, we demonstrate how to interchange APEs and RPEs while maintaining their distinguishing power in terms of graph transformers. Based on our theoretical results, we provide a study on several APEs and RPEs (including the resistance distance and the recently introduced stable and expressive positional encoding (SPE)) and compare their distinguishing power in terms of transformers. We believe our work will help navigate the huge number of choices of positional encoding and will provide guidance on the future design of positional encodings for graph transformers.

Position Paper: Challenges and Opportunities in Topological Deep Learning

Topological deep learning (TDL) is a rapidly evolving field that uses topological features to understand and design deep learning models. This paper posits that TDL may complement graph representation learning and geometric deep learning by incorporating topological concepts, and can thus provide a natural choice for various machine learning settings. To this end, this paper discusses open problems in TDL, ranging from practical benefits to theoretical foundations. For each problem, it outlines potential solutions and future research opportunities. At the same time, this paper serves as an invitation to the scientific community to actively participate in TDL research to unlock the potential of this emerging field.

NN-Steiner: A Mixed Neural-algorithmic Approach for the Rectilinear Steiner Minimum Tree Problem

Recent years have witnessed rapid advances in the use of neural networks to solve combinatorial optimization problems. Nevertheless, designing the "right" neural model that can effectively handle a given optimization problem can be challenging, and often there is no theoretical understanding or justification of the resulting neural model. In this paper, we focus on the rectilinear Steiner minimum tree (RSMT) problem, which is of critical importance in IC layout design and as a result has attracted numerous heuristic approaches in the VLSI literature. Our contributions are two-fold. On the methodology front, we propose NN-Steiner, which is a novel mixed neural-algorithmic framework for computing RSMTs that leverages the celebrated PTAS algorithmic framework of Arora to solve this problem (and other geometric optimization problems). Our NN-Steiner replaces key algorithmic components within Arora's PTAS by suitable neural components. In particular, NN-Steiner only needs four neural network (NN) components that are called repeatedly within an algorithmic framework. Crucially, each of the four NN components is only of bounded size independent of input size, and thus easy to train. Furthermore, as the NN component is learning a generic algorithmic step, once learned, the resulting mixed neural-algorithmic framework generalizes to much larger instances not seen in training. Our NN-Steiner, to our best knowledge, is the first neural architecture of bounded size that has capacity to approximately solve RSMT (and variants). On the empirical front, we show how NN-Steiner can be implemented and demonstrate the effectiveness of our resulting approach, especially in terms of generalization, by comparing with state-of-the-art methods (both neural and non-neural based).

Cycle Invariant Positional Encoding for Graph Representation Learning

Cycles are fundamental elements in graph-structured data and have demonstrated their effectiveness in enhancing graph learning models. To encode such information into a graph learning framework, prior works often extract a summary quantity, ranging from the number of cycles to the more sophisticated persistence diagram summaries. However, more detailed information, such as which edges are encoded in a cycle, has not yet been used in graph neural networks. In this paper, we make one step towards addressing this gap, and propose a structure encoding module, called CycleNet, that encodes cycle information via edge structure encoding in a permutation invariant manner. To efficiently encode the space of all cycles, we start with a cycle basis (i.e., a minimal set of cycles generating the cycle space) which we compute via the kernel of the 1-dimensional Hodge Laplacian of the input graph. To guarantee the encoding is invariant w.r.t. the choice of cycle basis, we encode the cycle information via the orthogonal projector of the cycle basis, which is inspired by BasisNet proposed by Lim et al. We also develop a more efficient variant which however requires that the input graph has a unique shortest cycle basis. To demonstrate the effectiveness of the proposed module, we provide some theoretical understandings of its expressive power. Moreover, we show via a range of experiments that networks enhanced by our CycleNet module perform better in various benchmarks compared to several existing SOTA models.

Universal Representation of Permutation-Invariant Functions on Vectors and Tensors

A main object of our study is multiset functions -- that is, permutation-invariant functions over inputs of varying sizes. Deep Sets, proposed by \cite{zaheer2017deep}, provides a \emph{universal representation} for continuous multiset functions on scalars via a sum-decomposable model. Restricting the domain of the functions to finite multisets of $D$-dimensional vectors, Deep Sets also provides a \emph{universal approximation} that requires a latent space dimension of $O(N^D)$ -- where $N$ is an upper bound on the size of input multisets. In this paper, we strengthen this result by proving that universal representation is guaranteed for continuous and discontinuous multiset functions though a latent space dimension of $O(N^D)$. We then introduce \emph{identifiable} multisets for which we can uniquely label their elements using an identifier function, namely, finite-precision vectors are identifiable. Using our analysis on identifiable multisets, we prove that a sum-decomposable model for general continuous multiset functions only requires a latent dimension of $2DN$. We further show that both encoder and decoder functions of the model are continuous -- our main contribution to the existing work which lack such a guarantee. Also this provides a significant improvement over the aforementioned $O(N^D)$ bound which was derived for universal representation of continuous and discontinuous multiset functions. We then extend our results and provide special sum-decomposition structures to universally represent permutation-invariant tensor functions on identifiable tensors. These families of sum-decomposition models enables us to design deep network architectures and deploy them on a variety of learning tasks on sequences, images, and graphs.

Neural approximation of Wasserstein distance via a universal architecture for symmetric and factorwise group invariant functions

Learning distance functions between complex objects, such as the Wasserstein distance to compare point sets, is a common goal in machine learning applications. However, functions on such complex objects (e.g., point sets and graphs) are often required to be invariant to a wide variety of group actions e.g. permutation or rigid transformation. Therefore, continuous and symmetric product functions (such as distance functions) on such complex objects must also be invariant to the product of such group actions. We call these functions symmetric and factor-wise group invariant (or SFGI functions in short). In this paper, we first present a general neural network architecture for approximating SFGI functions. The main contribution of this paper combines this general neural network with a sketching idea to develop a specific and efficient neural network which can approximate the $p$-th Wasserstein distance between point sets. Very importantly, the required model complexity is independent of the sizes of input point sets. On the theoretical front, to the best of our knowledge, this is the first result showing that there exists a neural network with the capacity to approximate Wasserstein distance with bounded model complexity. Our work provides an interesting integration of sketching ideas for geometric problems with universal approximation of symmetric functions. On the empirical front, we present a range of results showing that our newly proposed neural network architecture performs comparatively or better than other models (including a SOTA Siamese Autoencoder based approach). In particular, our neural network generalizes significantly better and trains much faster than the SOTA Siamese AE. Finally, this line of investigation could be useful in exploring effective neural network design for solving a broad range of geometric optimization problems (e.g., $k$-means in a metric space).

Distances for Markov Chains, and Their Differentiation

(Directed) graphs with node attributes are a common type of data in various applications and there is a vast literature on developing metrics and efficient algorithms for comparing them. Recently, in the graph learning and optimization communities, a range of new approaches have been developed for comparing graphs with node attributes, leveraging ideas such as the Optimal Transport (OT) and the Weisfeiler-Lehman (WL) graph isomorphism test. Two state-of-the-art representatives are the OTC distance proposed by O'Connor et al., 2022 and the WL distance by Chen et al.,2022. Interestingly, while these two distances are developed based on different ideas, we observe that they both view graphs as Markov chains, and are deeply connected. Indeed, in this paper, we propose a unified framework to generate distances for Markov chains (thus including (directed) graphs with node attributes), which we call the Optimal Transport Markov (OTM) distances, that encompass both the OTC and the WL distances. We further introduce a special one-parameter family of distances within our OTM framework, called the discounted WL distance. We show that the discounted WL distance has nice theoretical properties and can address several limitations of the existing OTC and WL distances. Furthermore, contrary to the OTC and the WL distances, we show our new discounted WL distance can be differentiated (after an entropy-regularization similar to the Sinkhorn distance), making it suitable for use in learning frameworks, e.g., as the reconstruction loss in a graph generative model.