arXiv subjects

Ya-Wei Eileen Lin

Publications and source records attributed to Ya-Wei Eileen Lin.

9 recordsLinked to original sources

arXiv2026

Beyond Structural Symmetries: Linear Mode Connectivity via Neuron Identifiability

Many striking phenomena in deep learning, such as linear mode connectivity and the structured behavior of training dynamics, are closely tied to parameter symmetries: transformations that leave the realized function unchanged. Despite growing attention to parameter symmetries, the exact interplay between parameters, data, and representations remains underexplored. To investigate this, we develop a theoretical framework of effective function classes, i.e., the set of functions a neuron can realize on its input support, and the norm cost of realizing them. We then formalize effective symmetry breaking via neuron identifiability across independent training runs. Our analysis shows that neural networks can admit large families of approximately equivalent solutions even in structurally asymmetric models. We further show that neuron identifiability enables representation merging without prior alignment, and characterize when such merging admits a linear low-loss path. These findings highlight the role of effective function classes in affecting the loss landscape.

cs.LG↗

arXiv2026

Beyond Oversquashing: Understanding Signal Propagation in GNNs Via Observables

Graph Neural Networks (GNNs) perform computations on graphs by routing the signal between graph regions using a graph shift operator or a message passing scheme. Often, the propagation of the signal leads to a loss of information, where the signal tends to diffuse across the graph instead of being deliberately routed between regions of interest. Two notions that depict this phenomenon are oversmoothing and oversquashing. In this paper, we propose an alternative approach for modeling signal propagation, inspired by quantum mechanics, using the notion of observables. Specifically, we model the place in the graph where the signal lies, how much the signal is concentrated there, and how much of the signal is propagated towards a location of interest when applying a GNN. Using these new concepts, we prove that standard spectral GNNs have poor signal propagation capabilities. We then propose a new type of spectral GNN, termed Schrödinger GNN, which we show has a superior capacity to route the signal across the graph.

cs.LG↗

arXiv2026

Adaptive Canonicalization with Application to Invariant Anisotropic Geometric Networks

Canonicalization is a widely used strategy in equivariant machine learning, enforcing symmetry in neural networks by mapping each input to a standard form. Yet, it often introduces discontinuities that can affect stability during training, limit generalization, and complicate universal approximation theorems. In this paper, we address this by introducing adaptive canonicalization, a general framework in which the canonicalization depends both on the input and the network. Specifically, we present the adaptive canonicalization based on prior maximization, where the standard form of the input is chosen to maximize the predictive confidence of the network. We prove that this construction yields continuous and symmetry-respecting models that admit universal approximation properties. We propose two applications of our setting: (i) resolving eigenbasis ambiguities in spectral graph neural networks, and (ii) handling rotational symmetries in point clouds. We empirically validate our methods on molecular and protein classification, as well as point cloud classification tasks. Our adaptive canonicalization outperforms the three other common solutions to equivariant machine learning: data augmentation, standard canonicalization, and equivariant architectures.

cs.LG↗

arXiv2026

LieAugmenter: Equivariant Learning by Discovering Symmetries with Learnable Augmentations

Data augmentation is a powerful mechanism in equivariant machine learning, encouraging symmetry by training networks to produce consistent outputs under transformed inputs. Yet, effective augmentation typically requires the underlying symmetry to be specified a priori, which can limit generalization when symmetries are unknown or only approximately valid. To address this, we introduce LieAugmenter, an end-to-end framework that discovers task-relevant continuous symmetries through learnable augmentations. Specifically, the augmentation generator is parameterized using the theory of Lie groups and trained jointly with the prediction network using the augmented views. The learned augmentations are task-adaptive, enabling effective and interpretable symmetry discovery. We provide a theoretical analysis of identifiability and show that our method yields symmetry-respecting models for the identified groups. Empirically, LieAugmenter outperforms baselines on image classification, as well as on the prediction of N-body dynamics and molecular properties. In addition, it can also provide an interpretable signature for detecting the absence of symmetries.

cs.LG↗

arXiv2025

Joint Hierarchical Representation Learning of Samples and Features via Informed Tree-Wasserstein Distance

High-dimensional data often exhibit hierarchical structures in both modes: samples and features. Yet, most existing approaches for hierarchical representation learning consider only one mode at a time. In this work, we propose an unsupervised method for jointly learning hierarchical representations of samples and features via Tree-Wasserstein Distance (TWD). Our method alternates between the two data modes. It first constructs a tree for one mode, then computes a TWD for the other mode based on that tree, and finally uses the resulting TWD to build the second mode's tree. By repeatedly alternating through these steps, the method gradually refines both trees and the corresponding TWDs, capturing meaningful hierarchical representations of the data. We provide a theoretical analysis showing that our method converges. We show that our method can be integrated into hyperbolic graph convolutional networks as a pre-processing technique, improving performance in link prediction and node classification tasks. In addition, our method outperforms baselines in sparse approximation and unsupervised Wasserstein distance learning tasks on word-document and single-cell RNA-sequencing datasets.

cs.LG↗

arXiv2025

Finsler Multi-Dimensional Scaling: Manifold Learning for Asymmetric Dimensionality Reduction and Embedding

Dimensionality reduction is a fundamental task that aims to simplify complex data by reducing its feature dimensionality while preserving essential patterns, with core applications in data analysis and visualisation. To preserve the underlying data structure, multi-dimensional scaling (MDS) methods focus on preserving pairwise dissimilarities, such as distances. They optimise the embedding to have pairwise distances as close as possible to the data dissimilarities. However, the current standard is limited to embedding data in Riemannian manifolds. Motivated by the lack of asymmetry in the Riemannian metric of the embedding space, this paper extends the MDS problem to a natural asymmetric generalisation of Riemannian manifolds called Finsler manifolds. Inspired by Euclidean space, we define a canonical Finsler space for embedding asymmetric data. Due to its simplicity with respect to geodesics, data representation in this space is both intuitive and simple to analyse. We demonstrate that our generalisation benefits from the same theoretical convergence guarantees. We reveal the effectiveness of our Finsler embedding across various types of non-symmetric data, highlighting its value in applications such as data visualisation, dimensionality reduction, directed graph embedding, and link prediction.

cs.CV↗

arXiv2025

Tree-Wasserstein Distance for High Dimensional Data with a Latent Feature Hierarchy

Finding meaningful distances between high-dimensional data samples is an important scientific task. To this end, we propose a new tree-Wasserstein distance (TWD) for high-dimensional data with two key aspects. First, our TWD is specifically designed for data with a latent feature hierarchy, i.e., the features lie in a hierarchical space, in contrast to the usual focus on embedding samples in hyperbolic space. Second, while the conventional use of TWD is to speed up the computation of the Wasserstein distance, we use its inherent tree as a means to learn the latent feature hierarchy. The key idea of our method is to embed the features into a multi-scale hyperbolic space using diffusion geometry and then present a new tree decoding method by establishing analogies between the hyperbolic embedding and trees. We show that our TWD computed based on data observations provably recovers the TWD defined with the latent feature hierarchy and that its computation is efficient and scalable. We showcase the usefulness of the proposed TWD in applications to word-document and single-cell RNA-sequencing datasets, demonstrating its advantages over existing TWDs and methods based on pre-trained models.

cs.LG↗

arXiv2024

Equivariant Machine Learning on Graphs with Nonlinear Spectral Filters

Equivariant machine learning is an approach for designing deep learning models that respect the symmetries of the problem, with the aim of reducing model complexity and improving generalization. In this paper, we focus on an extension of shift equivariance, which is the basis of convolution networks on images, to general graphs. Unlike images, graphs do not have a natural notion of domain translation. Therefore, we consider the graph functional shifts as the symmetry group: the unitary operators that commute with the graph shift operator. Notably, such symmetries operate in the signal space rather than directly in the spatial space. We remark that each linear filter layer of a standard spectral graph neural network (GNN) commutes with graph functional shifts, but the activation function breaks this symmetry. Instead, we propose nonlinear spectral filters (NLSFs) that are fully equivariant to graph functional shifts and show that they have universal approximation properties. The proposed NLSFs are based on a new form of spectral domain that is transferable between graphs. We demonstrate the superior performance of NLSFs over existing spectral GNNs in node and graph classification benchmarks.

cs.LG↗

arXiv2023

Hyperbolic Diffusion Embedding and Distance for Hierarchical Representation Learning

Finding meaningful representations and distances of hierarchical data is important in many fields. This paper presents a new method for hierarchical data embedding and distance. Our method relies on combining diffusion geometry, a central approach to manifold learning, and hyperbolic geometry. Specifically, using diffusion geometry, we build multi-scale densities on the data, aimed to reveal their hierarchical structure, and then embed them into a product of hyperbolic spaces. We show theoretically that our embedding and distance recover the underlying hierarchical structure. In addition, we demonstrate the efficacy of the proposed method and its advantages compared to existing methods on graph embedding benchmarks and hierarchical datasets.

cs.LG↗