Rebekka Burkholz

Jonas Fischer, Rebekka Burkholz, Jilles Vreeken

Low-dimensional embeddings and visualizations are an indispensable tool for analysis of high-dimensional data. State-of-the-art methods, such as tSNE and UMAP, excel in unveiling local structures hidden in high-dimensional data and are therefore routinely applied in standard analysis pipelines in biology. We show, however, that these methods fail to reconstruct local properties, such as relative differences in densities (Fig. 1) and that apparent differences in cluster size can arise from computational artifact caused by differing sample sizes (Fig. 2). Providing a theoretical analysis of this issue, we then suggest dtSNE, which approximately conserves local densities. In an extensive study on synthetic benchmark and real world data comparing against five state-of-the-art methods, we empirically show that dtSNE provides similar global reconstruction, but yields much more accurate depictions of local distances and relative densities.

Advait Gadhikar, Sohom Mukherjee, Rebekka Burkholz

Random masks define surprisingly effective sparse neural network models, as has been shown empirically. The resulting sparse networks can often compete with dense architectures and state-of-the-art lottery ticket pruning algorithms, even though they do not rely on computationally expensive prune-train iterations and can be drawn initially without significant computational overhead. We offer a theoretical explanation of how random masks can approximate arbitrary target networks if they are wider by a logarithmic factor in the inverse sparsity $1 / \log(1/\text{sparsity})$. This overparameterization factor is necessary at least for 3-layer random networks, which elucidates the observed degrading performance of random networks at higher sparsity. At moderate to high sparsity levels, however, our results imply that sparser networks are contained within random source networks so that any dense-to-sparse training scheme can be turned into a computationally more efficient sparse-to-sparse one by constraining the search to a fixed random mask. We demonstrate the feasibility of this approach in experiments for different pruning methods and propose particularly effective choices of initial layer-wise sparsity ratios of the random source network. As a special case, we show theoretically and experimentally that random source networks also contain strong lottery tickets.

Nimrah Mustafa, Aleksandar Bojchevski, Rebekka Burkholz

While the expressive power and computational capabilities of graph neural networks (GNNs) have been theoretically studied, their optimization and learning dynamics, in general, remain largely unexplored. Our study undertakes the Graph Attention Network (GAT), a popular GNN architecture in which a node's neighborhood aggregation is weighted by parameterized attention coefficients. We derive a conservation law of GAT gradient flow dynamics, which explains why a high portion of parameters in GATs with standard initialization struggle to change during training. This effect is amplified in deeper GATs, which perform significantly worse than their shallow counterparts. To alleviate this problem, we devise an initialization scheme that balances the GAT network. Our approach i) allows more effective propagation of gradients and in turn enables trainability of deeper networks, and ii) attains a considerable speedup in training and convergence time in comparison to the standard initialization. Our main theorem serves as a stepping stone to studying the learning dynamics of positive homogeneous models with attention mechanisms.

Rebekka Burkholz

The strong lottery ticket hypothesis has highlighted the potential for training deep neural networks by pruning, which has inspired interesting practical and theoretical insights into how neural networks can represent functions. For networks with ReLU activation functions, it has been proven that a target network with depth $L$ can be approximated by the subnetwork of a randomly initialized neural network that has double the target's depth $2L$ and is wider by a logarithmic factor. We show that a depth $L+1$ network is sufficient. This result indicates that we can expect to find lottery tickets at realistic, commonly used depths while only requiring logarithmic overparametrization. Our novel construction approach applies to a large class of activation functions and is not limited to ReLUs.

Rebekka Burkholz

The Lottery Ticket Hypothesis continues to have a profound practical impact on the quest for small scale deep neural networks that solve modern deep learning tasks at competitive performance. These lottery tickets are identified by pruning large randomly initialized neural networks with architectures that are as diverse as their applications. Yet, theoretical insights that attest their existence have been mostly focused on deep fully-connected feed forward networks with ReLU activation functions. We prove that also modern architectures consisting of convolutional and residual layers that can be equipped with almost arbitrary activation functions can contain lottery tickets with high probability.

Advait Gadhikar, Rebekka Burkholz

The training success, training speed and generalization ability of neural networks rely crucially on the choice of random parameter initialization. It has been shown for multiple architectures that initial dynamical isometry is particularly advantageous. Known initialization schemes for residual blocks, however, miss this property and suffer from degrading separability of different inputs for increasing depth and instability without Batch Normalization or lack feature diversity. We propose a random initialization scheme, RISOTTO, that achieves perfect dynamical isometry for residual networks with ReLU activation functions even for finite depth and width. It balances the contributions of the residual and skip branches unlike other schemes, which initially bias towards the skip connections. In experiments, we demonstrate that in most cases our approach outperforms initialization schemes proposed to make Batch Normalization obsolete, including Fixup and SkipInit, and facilitates stable training. Also in combination with Batch Normalization, we find that RISOTTO often achieves the overall best result.

Dong Sun, Rahul Nittala, Rebekka Burkholz

Despite their practical success, it remains unclear why Mixture of Experts (MoE) models can outperform dense networks beyond sheer parameter scaling. We study an iso-parameter regime where inputs exhibit latent modular structure but are corrupted by feature noise, a proxy for noisy internal activations. We show that sparse expert activation acts as a noise filter: compared to a dense estimator, MoEs achieve lower generalization error under feature noise, improved robustness to perturbations, and faster convergence speed. Empirical results on synthetic data and real-world language tasks corroborate the theoretical insights, demonstrating consistent robustness and efficiency gains from sparse modular computation.

Levy Chaves, Chao Zhou, Rebekka Burkholz et al.

Model merging integrates multiple task-specific models into a single consolidated one. Recent research has made progress in improving merging performance for in-distribution or multi-task scenarios, but domain generalization in model merging remains underexplored. We investigate how merging models fine-tuned on distinct domains affects generalization to unseen domains. Through an analysis of parameter competition in the task matrix using singular value decomposition, we show that merging models trained under different distribution shifts induces stronger conflicts between their subspaces compared to traditional multi-task settings. To mitigate this issue, we propose SCORE (Subspace COnflict-Resolving mErging), a method designed to alleviate such singular subspace conflicts. SCORE finds a shared orthogonal basis by computing the principal components of the concatenated leading singular vectors of all models. It then projects each task matrix into the shared basis, pruning off-diagonal components to remove conflicting singular directions. SCORE consistently outperforms, on average, existing model merging approaches in domain generalization settings across a variety of architectures and model scales, demonstrating its effectiveness and scalability.

Celia Rubio-Madrigal, Rebekka Burkholz

Graph neural networks (GNNs) are widely believed to excel at node representation learning through trainable neighborhood aggregations. We challenge this view by introducing Fixed Aggregation Features (FAFs), a training-free approach that transforms graph learning tasks into tabular problems. This simple shift enables the use of well-established tabular methods, offering strong interpretability and the flexibility to deploy diverse classifiers. Across 14 benchmarks, well-tuned multilayer perceptrons trained on FAFs rival or outperform state-of-the-art GNNs and graph transformers on 12 tasks -- often using only mean aggregation. The only exceptions are the Roman Empire and Minesweeper datasets, which typically require unusually deep GNNs. To explain the theoretical possibility of non-trainable aggregations, we connect our findings to Kolmogorov-Arnold representations and discuss when mean aggregation can be sufficient. In conclusion, our results call for (i) richer benchmarks benefiting from learning diverse neighborhood aggregations, (ii) strong tabular baselines as standard, and (iii) employing and advancing tabular models for graph data to gain new insights into related tasks.

Adarsh Jamadandi, Celia Rubio-Madrigal, Rebekka Burkholz

Message Passing Graph Neural Networks are known to suffer from two problems that are sometimes believed to be diametrically opposed: over-squashing and over-smoothing. The former results from topological bottlenecks that hamper the information flow from distant nodes and are mitigated by spectral gap maximization, primarily, by means of edge additions. However, such additions often promote over-smoothing that renders nodes of different classes less distinguishable. Inspired by the Braess phenomenon, we argue that deleting edges can address over-squashing and over-smoothing simultaneously. This insight explains how edge deletions can improve generalization, thus connecting spectral gap optimization to a seemingly disconnected objective of reducing computational resources by pruning graphs for lottery tickets. To this end, we propose a more effective spectral gap optimization framework to add or delete edges and demonstrate its effectiveness on large heterophilic datasets.

Celia Rubio-Madrigal, Adarsh Jamadandi, Rebekka Burkholz

Maximizing the spectral gap through graph rewiring has been proposed to enhance the performance of message-passing graph neural networks (GNNs) by addressing over-squashing. However, as we show, minimizing the spectral gap can also improve generalization. To explain this, we analyze how rewiring can benefit GNNs within the context of stochastic block models. Since spectral gap optimization primarily influences community strength, it improves performance when the community structure aligns with node labels. Building on this insight, we propose three distinct rewiring strategies that explicitly target community structure, node labels, and their alignment: (a) community structure-based rewiring (ComMa), a more computationally efficient alternative to spectral gap optimization that achieves similar goals; (b) feature similarity-based rewiring (FeaSt), which focuses on maximizing global homophily; and (c) a hybrid approach (ComFy), which enhances local feature similarity while preserving community structure to optimize label-community alignment. Extensive experiments confirm the effectiveness of these strategies and support our theoretical insights.

Abbavaram Gowtham Reddy, Celia Rubio-Madrigal, Rebekka Burkholz et al.

Distribution shifts introduce uncertainty that undermines the robustness and generalization capabilities of machine learning models. While conventional wisdom suggests that learning causal-invariant representations enhances robustness to such shifts, recent empirical studies present a counterintuitive finding: (i) empirical risk minimization (ERM) can rival or even outperform state-of-the-art out-of-distribution (OOD) generalization methods, and (ii) its OOD generalization performance improves when all available covariates, not just causal ones, are utilized. Drawing on both empirical and theoretical evidence, we attribute this phenomenon to hidden confounding. Shifts in hidden confounding induce changes in data distributions that violate assumptions commonly made by existing OOD generalization approaches. Under such conditions, we prove that effective generalization requires learning environment-specific relationships, rather than relying solely on invariant ones. Furthermore, we show that models augmented with proxies for hidden confounders can mitigate the challenges posed by hidden confounding shifts. These findings offer new theoretical insights and practical guidance for designing robust OOD generalization algorithms and principled covariate selection strategies.

Advait Gadhikar, Tom Jacobs, Chao Zhou et al.

The performance gap between training sparse neural networks from scratch (PaI) and dense-to-sparse training presents a major roadblock for efficient deep learning. According to the Lottery Ticket Hypothesis, PaI hinges on finding a problem specific parameter initialization. As we show, to this end, determining correct parameter signs is sufficient. Yet, they remain elusive to PaI. To address this issue, we propose Sign-In, which employs a dynamic reparameterization that provably induces sign flips. Such sign flips are complementary to the ones that dense-to-sparse training can accomplish, rendering Sign-In as an orthogonal method. While our experiments and theory suggest performance improvements of PaI, they also carve out the main open challenge to close the gap between PaI and dense-to-sparse training.

Chao Zhou, Tom Jacobs, Advait Gadhikar et al.

Finetuning large pretrained neural networks is known to be resource-intensive, both in terms of memory and computational cost. To mitigate this, a common approach is to restrict training to a subset of the model parameters. By analyzing the relationship between gradients and weights during finetuning, we observe a notable pattern: large gradients are often associated with small-magnitude weights. This correlation is more pronounced in finetuning settings than in training from scratch. Motivated by this observation, we propose NANOADAM, which dynamically updates only the small-magnitude weights during finetuning and offers several practical advantages: first, this criterion is gradient-free -- the parameter subset can be determined without gradient computation; second, it preserves large-magnitude weights, which are likely to encode critical features learned during pretraining, thereby reducing the risk of catastrophic forgetting; thirdly, it permits the use of larger learning rates and consistently leads to better generalization performance in experiments. We demonstrate this for both NLP and vision tasks.

Tom Jacobs, Advait Gadhikar, Celia Rubio-Madrigal et al.

Understanding the implicit bias of optimization algorithms has become central to explaining the generalization behavior of deep learning models. For instance, the hyperbolic implicit bias induced by the overparameterization $m \odot w$--though effective in promoting sparsity--can result in a small effective learning rate, which slows down convergence. To overcome this obstacle, we propose HAM (Hyperbolic Aware Minimization), which alternates between an optimizer step and a new hyperbolic mirror step. We derive the Riemannian gradient flow for its combination with gradient descent, leading to improved convergence and a similar beneficial hyperbolic geometry as $m \odot w$ for feature learning. We provide an interpretation of the the algorithm by relating it to natural gradient descent, and an exact characterization of its implicit bias for underdetermined linear regression. HAM's implicit bias consistently boosts performance--even of dense training, as we demonstrate in experiments across diverse tasks, including vision, graph and node classification, and large language model fine-tuning. HAM is especially effective in combination with different sparsification methods, improving upon the state of the art. The hyperbolic step requires minimal computational and memory overhead, it succeeds even with small batch sizes, and its implementation integrates smoothly with existing optimizers.

Advait Gadhikar, Sree Harsha Nelaturu, Rebekka Burkholz

The success of iterative pruning methods in achieving state-of-the-art sparse networks has largely been attributed to improved mask identification and an implicit regularization induced by pruning. We challenge this hypothesis and instead posit that their repeated cyclic training schedules enable improved optimization. To verify this, we show that pruning at initialization is significantly boosted by repeated cyclic training, even outperforming standard iterative pruning methods. The dominant mechanism how this is achieved, as we conjecture, can be attributed to a better exploration of the loss landscape leading to a lower training loss. However, at high sparsity, repeated cyclic training alone is not enough for competitive performance. A strong coupling between learnt parameter initialization and mask seems to be required. Standard methods obtain this coupling via expensive pruning-training iterations, starting from a dense network. To achieve this with sparse training instead, we propose SCULPT-ing, i.e., repeated cyclic training of any sparse mask followed by a single pruning step to couple the parameters and the mask, which is able to match the performance of state-of-the-art iterative pruning methods in the high sparsity regime at reduced computational cost.

Nimrah Mustafa, Rebekka Burkholz

Graph Attention Networks (GATs) are designed to provide flexible neighborhood aggregation that assigns weights to neighbors according to their importance. In practice, however, GATs are often unable to switch off task-irrelevant neighborhood aggregation, as we show experimentally and analytically. To address this challenge, we propose GATE, a GAT extension that holds three major advantages: i) It alleviates over-smoothing by addressing its root cause of unnecessary neighborhood aggregation. ii) Similarly to perceptrons, it benefits from higher depth as it can still utilize additional layers for (non-)linear feature transformations in case of (nearly) switched-off neighborhood aggregation. iii) By down-weighting connections to unrelated neighbors, it often outperforms GATs on real-world heterophilic datasets. To further validate our claims, we construct a synthetic test bed to analyze a model's ability to utilize the appropriate amount of neighborhood aggregation, which could be of independent interest.

Intekhab Hossain, Jonas Fischer, Rebekka Burkholz et al.

The practical utility of machine learning models in the sciences often hinges on their interpretability. It is common to assess a model's merit for scientific discovery, and thus novel insights, by how well it aligns with already available domain knowledge--a dimension that is currently largely disregarded in the comparison of neural network models. While pruning can simplify deep neural network architectures and excels in identifying sparse models, as we show in the context of gene regulatory network inference, state-of-the-art techniques struggle with biologically meaningful structure learning. To address this issue, we propose DASH, a generalizable framework that guides network pruning by using domain-specific structural information in model fitting and leads to sparser, better interpretable models that are more robust to noise. Using both synthetic data with ground truth information, as well as real-world gene expression data, we show that DASH, using knowledge about gene interaction partners within the putative regulatory network, outperforms general pruning methods by a large margin and yields deeper insights into the biological systems being studied.

Jonas Fischer, Rebekka Burkholz

The lottery ticket hypothesis has sparked the rapid development of pruning algorithms that aim to reduce the computational costs associated with deep learning during training and model deployment. Currently, such algorithms are primarily evaluated on imaging data, for which we lack ground truth information and thus the understanding of how sparse lottery tickets could be. To fill this gap, we develop a framework that allows us to plant and hide winning tickets with desirable properties in randomly initialized neural networks. To analyze the ability of state-of-the-art pruning to identify tickets of extreme sparsity, we design and hide such tickets solving four challenging tasks. In extensive experiments, we observe similar trends as in imaging studies, indicating that our framework can provide transferable insights into realistic problems. Additionally, we can now see beyond such relative trends and highlight limitations of current pruning methods. Based on our results, we conclude that the current limitations in ticket sparsity are likely of algorithmic rather than fundamental nature. We anticipate that comparisons to planted tickets will facilitate future developments of efficient pruning algorithms.

Rebekka Burkholz, Nilanjana Laha, Rajarshi Mukherjee et al.

The lottery ticket hypothesis conjectures the existence of sparse subnetworks of large randomly initialized deep neural networks that can be successfully trained in isolation. Recent work has experimentally observed that some of these tickets can be practically reused across a variety of tasks, hinting at some form of universality. We formalize this concept and theoretically prove that not only do such universal tickets exist but they also do not require further training. Our proofs introduce a couple of technical innovations related to pruning for strong lottery tickets, including extensions of subset sum results and a strategy to leverage higher amounts of depth. Our explicit sparse constructions of universal function families might be of independent interest, as they highlight representational benefits induced by univariate convolutional architectures.

Jonas Fischer, Advait Gadhikar, Rebekka Burkholz

The strong lottery ticket hypothesis holds the promise that pruning randomly initialized deep neural networks could offer a computationally efficient alternative to deep learning with stochastic gradient descent. Common parameter initialization schemes and existence proofs, however, are focused on networks with zero biases, thus foregoing the potential universal approximation property of pruning. To fill this gap, we extend multiple initialization schemes and existence proofs to nonzero biases, including explicit 'looks-linear' approaches for ReLU activation functions. These do not only enable truly orthogonal parameter initialization but also reduce potential pruning errors. In experiments on standard benchmark data, we further highlight the practical benefits of nonzero bias initialization schemes, and present theoretically inspired extensions for state-of-the-art strong lottery ticket pruning.

Alkis Gotovos, Rebekka Burkholz, John Quackenbush et al.

Modeling the time evolution of discrete sets of items (e.g., genetic mutations) is a fundamental problem in many biomedical applications. We approach this problem through the lens of continuous-time Markov chains, and show that the resulting learning task is generally underspecified in the usual setting of cross-sectional data. We explore a perhaps surprising remedy: including a number of additional independent items can help determine time order, and hence resolve underspecification. This is in sharp contrast to the common practice of limiting the analysis to a small subset of relevant items, which is followed largely due to poor scaling of existing methods. To put our theoretical insight into practice, we develop an approximate likelihood maximization method for learning continuous-time Markov chains, which can scale to hundreds of items and is orders of magnitude faster than previous methods. We demonstrate the effectiveness of our approach on synthetic and real cancer data.

Rebekka Burkholz, John Quackenbush

Cascade models are central to understanding, predicting, and controlling epidemic spreading and information propagation. Related optimization, including influence maximization, model parameter inference, or the development of vaccination strategies, relies heavily on sampling from a model. This is either inefficient or inaccurate. As alternative, we present an efficient message passing algorithm that computes the probability distribution of the cascade size for the Independent Cascade Model on weighted directed networks and generalizations. Our approach is exact on trees but can be applied to any network topology. It approximates locally tree-like networks well, scales to large networks, and can lead to surprisingly good performance on more dense networks, as we also exemplify on real world data.

Rebekka Burkholz, Alina Dubatovka

Deep learning relies on good initialization schemes and hyperparameter choices prior to training a neural network. Random weight initializations induce random network ensembles, which give rise to the trainability, training speed, and sometimes also generalization ability of an instance. In addition, such ensembles provide theoretical insights into the space of candidate models of which one is selected during training. The results obtained so far rely on mean field approximations that assume infinite layer width and that study average squared signals. We derive the joint signal output distribution exactly, without mean field assumptions, for fully-connected networks with Gaussian weights and biases, and analyze deviations from the mean field results. For rectified linear units, we further discuss limitations of the standard initialization scheme, such as its lack of dynamical isometry, and propose a simple alternative that overcomes these by initial parameter sharing.