Understanding the geometry of neural network loss landscapes is a central question in deep learning, with implications for generalization and optimization. A striking phenomenon is linear mode connectivity (LMC), where independently trained models can be connected by low-or zero-barrier paths, despite appearing to lie in separate loss basins. However, this is often obscured by symmetries in parameter space--such as neuron permutations--which make functionally equivalent models appear dissimilar. Prior work has predominantly focused on neuron reordering through permutations, but such approaches are limited in scope and fail to capture the richer symmetries exhibited by modern architectures such as Transformers. In this work, we introduce a unified framework that captures four symmetry classes--permutations, semi-permutations, orthogonal transformations, and general invertible maps--broadening the set of valid reparameterizations and subsuming many previous approaches as special cases. Crucially, this generalization enables, for the first time, the discovery of low-and zero-barrier linear interpolation paths between independently trained Vision Transformers and GPT-2 models. Furthermore, our framework extends beyond pairwise alignment, to multi-model and width-heterogeneous settings, enabling alignment across architectures of different sizes. These results reveal deeper structure in the loss landscape and underscore the importance of symmetry-aware analysis for understanding model space geometry. Our code is available here.

Large Language Models (LLMs) enable a new form of digital experimentation where treatments combine human and model-generated content in increasingly sophisticated ways. The main methodological challenge in this setting is representing these high-dimensional treatments without losing their semantic meaning or rendering analysis intractable. Here we address this problem by focusing on learning low-dimensional representations that capture the underlying structure of such treatments. These representations enable downstream applications such as guiding generative models to produce meaningful treatment variants and facilitating adaptive assignment in online experiments. We propose double kernel representation learning, which models the causal effect through the inner product of kernel-based representations of treatments and user covariates. We develop an alternating-minimization algorithm that learns these representations efficiently from data and provide convergence guarantees under a low-rank factor model. As an application of this framework, we introduce an adaptive design strategy for online experimentation and demonstrate the method's effectiveness through numerical experiments.

Deep neural networks using state space models as layers are well suited for longrange sequence tasks but can be challenging to compress after training. We use that regularizing the sum of Hankel singular values of state space models leads to a fast decay of these singular values and thus to compressible models. To make the proposed Hankel singular value regularization scalable, we develop an algorithm to efficiently compute the Hankel singular values during training iterations by exploiting the specific block-diagonal structure of the system matrices that we use in our state space model parametrization. Experiments on Long Range Arena benchmarks demonstrate that the regularized state space layers are up to 10 more compressible than standard state space layers while maintaining high accuracy.

Natural gradient methods significantly accelerate the training of Physics-Informed Neural Networks (PINNs), but are often prohibitively costly. We introduce a suite of techniques to improve the accuracy and efficiency of energy natural gradient descent (ENGD) for PINNs. First, we leverage the Woodbury formula to dramatically reduce the computational complexity of ENGD. Second, we adapt the Subsampled Projected-Increment Natural Gradient Descent algorithm from the variational Monte Carlo literature to accelerate the convergence. Third, we explore the use of randomized algorithms to further reduce the computational cost in the case of large batch sizes. We find that randomization accelerates progress in the early stages of training for low-dimensional problems, and we identify key barriers to attaining acceleration in other scenarios. Our numerical experiments demonstrate that our methods outperform previous approaches, achieving the same L2 error as the original ENGD up to 75 faster.

We develop an analytical framework for understanding how the generated distribution evolves during diffusion model training. Leveraging a Gaussian-equivalence principle, we solve the full-batch gradient-flow dynamics of linear and convolutional denoisers and integrate the resulting probability-flow ODE, yielding analytic expressions for the generated distribution. The theory exposes a universal inverse-variance spectral law: the time for an eigen-or Fourier mode to match its target variance scales as τ λ 1, so high-variance (coarse) structure is mastered orders of magnitude sooner than low-variance (fine) detail. Extending the analysis to deep linear networks and circulant full-width convolutions shows that weight sharing merely multiplies learning rates--accelerating but not eliminating the bias--whereas local convolution introduces a qualitatively different bias. Experiments on Gaussian and natural-image datasets confirm the spectral law persists in deep MLP-based UNet.

Crossmodal matching in single-cell omics is essential for explaining biological regulatory mechanisms and enhancing downstream analyses. However, current single-cell crossmodal models often suffer from three limitations: sparse modality signals, underutilization of biological attributes, and insufficient modeling of regulatory interactions. These challenges hinder generalization in data-scarce settings and restrict the ability to uncover fine-grained biologically meaningful crossmodal relationships. Here, we present a novel framework which reformulates crossmodal matching as a graph classification task on Attributed Bipartite Graphs (ABGs). It models single-cell ATAC-RNA data as an ABG, where each expressed ATAC and RNA is treated as a distinct node with unique IDs and biological features. To model crossmodal interaction patterns on the constructed ABG, we propose Bi2Former, a biologically-driven bipartite graph transformer that learns interpretable attention over ATAC-RNA pairs. This design enables the model to effectively learn and explain biological regulatory relationships between ATAC and RNA modalities. Extensive experiments demonstrate that Bi2Former achieves state-of-the-art performance in crossmodal matching across diverse datasets, remains robust under sparse training data, generalizes to unseen cell types and datasets, and reveals biologically meaningful regulatory patterns.

In this paper, we address the challenges associated with merging low-rank adaptations of large neural networks. With the rise of parameter-efficient adaptation techniques, such as Low-Rank Adaptation (LoRA), model fine-tuning has become more accessible. While fine-tuning models with LoRA is highly efficient, existing merging methods often sacrifice this efficiency by merging fully-sized weight matrices. We propose the Core Space merging framework, which enables the merging of LoRA-adapted models within a common alignment basis, thereby preserving the efficiency of low-rank adaptation while substantially improving accuracy across tasks. We further provide a formal proof that projection into Core Space ensures no loss of information and provide a complexity analysis showing the efficiency gains. Extensive empirical results demonstrate that Core Space significantly improves existing merging techniques and achieves state-of-the-art results on both vision and language tasks while utilizing a fraction of the computational resources.

This work tackles the fundamental challenges in Federated Learning (FL) posed by arbitrary client participation and data heterogeneity, prevalent characteristics in practical FL settings. It is well-established that popular FedAvg-style algorithms struggle with exact convergence and can suffer from slow convergence rates since a decaying learning rate is required to mitigate these scenarios. To address these issues, we introduce the concept of stochastic matrix and the corresponding timevarying graphs as a novel modeling tool to accurately capture the dynamics of arbitrary client participation and the local update procedure. Leveraging this approach, we offer a fresh decentralized perspective on designing FL algorithms and present FOCUS, Federated Optimization with Exact Convergence via Push-pull Strategy, a provably convergent algorithm designed to effectively overcome the previously mentioned two challenges. More specifically, we provide a rigorous proof demonstrating that FOCUS achieves exact convergence with a linear rate regardless of the arbitrary client participation, establishing it as the first work to demonstrate this significant result.

Graphon models provide a flexible nonparametric framework for estimating latent connectivity probabilities in networks, enabling a range of downstream applications such as link prediction and data augmentation. However, accurate graphon estimation typically requires a large graph, whereas in practice, one often only observes a small-sized network. One approach to addressing this issue is to adopt a transfer learning framework, which aims to improve estimation in a small target graph by leveraging structural information from a larger, related source graph. In this paper, we propose a novel method, namely GTRANS, a transfer learning framework that integrates neighborhood smoothing and Gromov-Wasserstein optimal transport to align and transfer structural patterns between graphs. To prevent negative transfer, GTRANS includes an adaptive debiasing mechanism that identifies and corrects for target-specific deviations via residual smoothing. We provide theoretical guarantees on the stability of the estimated alignment matrix and demonstrate the effectiveness of GTRANS in improving the accuracy of target graph estimation through extensive synthetic and real data experiments. These improvements translate directly to enhanced performance in downstream applications, such as the graph classification task and the link prediction task.

A common challenge in the natural sciences is to disentangle distinct, unknown sources from observations. Examples of this source separation task include deblending galaxies in a crowded field, distinguishing the activity of individual neurons from overlapping signals, and separating seismic events from an ambient background. Traditional analyses often rely on simplified source models that fail to accurately reproduce the data. Recent advances have shown that diffusion models can directly learn complex prior distributions from noisy, incomplete data. In this work, we show that diffusion models can solve the source separation problem without explicit assumptions about the source. Our method relies only on multiple views, or the property that different sets of observations contain different linear transformations of the unknown sources. We show that our method succeeds even when no source is individually observed and the observations are noisy, incomplete, and vary in resolution. The learned diffusion models enable us to sample from the source priors, evaluate the probability of candidate sources, and draw from the joint posterior of the source distribution given an observation. We demonstrate the effectiveness of our method on a range of synthetic problems as well as real-world galaxy observations.