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Publications
Towards Graph Foundation Models: A Study on the Generalization of Positional and Structural Encodings
Recent advances in integrating positional and structural encodings (PSEs) into graph neural networks (GNNs) have significantly enhanced thei… (voir plus)r performance across various graph learning tasks. However, the general applicability of these encodings and their potential to serve as foundational representations for graphs remain uncertain. This paper investigates the fine-tuning efficiency, scalability with sample size, and generalization capability of learnable PSEs across diverse graph datasets. Specifically, we evaluate their potential as universal pre-trained models that can be easily adapted to new tasks with minimal fine-tuning and limited data. Furthermore, we assess the expressivity of the learned representations, particularly, when used to augment downstream GNNs. We demonstrate through extensive benchmarking and empirical analysis that PSEs generally enhance downstream models. However, some datasets may require specific PSE-augmentations to achieve optimal performance. Nevertheless, our findings highlight their significant potential to become integral components of future graph foundation models. We provide new insights into the strengths and limitations of PSEs, contributing to the broader discourse on foundation models in graph learning.
This work addresses the limitations of deep neural networks (DNNs) in generalizing beyond training data due to spurious correlations. Recent… (voir plus) research has demonstrated that models trained with empirical risk minimization learn both core and spurious features, often upweighting spurious ones in the final classification, which can frequently lead to poor performance on minority groups. Deep Feature Reweighting alleviates this issue by retraining the model's last classification layer using a group-balanced held-out validation set. However, relying on spurious feature labels during training or validation limits practical application, as spurious features are not always known or costly to annotate. Our preliminary experiments reveal that ERM-trained models exhibit higher gradient norms on minority group samples in the hold-out dataset. Leveraging these insights, we propose an alternative approach called GradTune, which fine-tunes the last classification layer using high-gradient norm samples. Our results on four well-established benchmarks demonstrate that the proposed method can achieve competitive performance compared to existing methods without requiring group labels during training or validation.
Many real-world processes are characterized by complex spatio-temporal dependencies, from climate dynamics to disease spread. Here, we intro… (voir plus)duce a new neural network architecture to model such dynamics at scale: the \emph{Space-Time Encoder}. Building on recent advances in \emph{location encoders}, models that take as inputs geographic coordinates, we develop a method that takes in geographic and temporal information simultaneously and learns smooth, continuous functions in both space and time. The inputs are first transformed using positional encoding functions and then fed into neural networks that allow the learning of complex functions. We implement a prototype of the \emph{Space-Time Encoder}, discuss the design choices of the novel temporal encoding, and demonstrate its utility in climate model emulation. We discuss the potential of the method across use cases, as well as promising avenues for further methodological innovation.
Spurious correlations in the data, where multiple cues are predictive of the target labels, often lead to a phenomenon known as shortcut lea… (voir plus)rning, where a model relies on erroneous, easy-to-learn cues while ignoring reliable ones. In this work, we propose
Diffusion Probabilistic Models (DPMs) are powerful generative models that have achieved unparalleled success in a number of generative tasks… (voir plus). In this work, we aim to build inductive biases into the training and sampling of diffusion models to better accommodate the target distribution of the data to model. For topologically structured data, we devise a frequency-based noising operator to purposefully manipulate, and set, these inductive biases. We first show that appropriate manipulations of the noising forward process can lead DPMs to focus on particular aspects of the distribution to learn. We show that different datasets necessitate different inductive biases, and that appropriate frequency-based noise control induces increased generative performance compared to standard diffusion. Finally, we demonstrate the possibility of ignoring information at particular frequencies while learning. We show this in an image corruption and recovery task, where we train a DPM to recover the original target distribution after severe noise corruption.
This paper presents a practical application of Relative Trajectory Balance (RTB), a recently introduced off-policy reinforcement learning (R… (voir plus)L) objective that can asymptotically solve Bayesian inverse problems optimally. We extend the original work by using RTB to train conditional diffusion model posteriors from pretrained unconditional priors for challenging linear and non-linear inverse problems in vision, and science. We use the objective alongside techniques such as off-policy backtracking exploration to improve training. Importantly, our results show that existing training-free diffusion posterior methods struggle to perform effective posterior inference in latent space due to inherent biases.
Personalized machine learning models have gained significant importance in various domains, including healthcare. However, designing efficie… (voir plus)nt personalized models remains a challenge. Traditional approaches often involve training multiple sub-models for different population sub-groups, which can be costly and does not always guarantee improved performance across all sub-groups. This paper presents a novel approach to improving model performance at the sub-group level by leveraging bias and training a joint model. Our method involves a two-step process: first, we train a model to predict group attributes, and then we use this model to learn data-dependent biases to modulate a second model for diagnosis prediction. Our results demonstrate that this joint architecture achieves consistent performance gains across all sub-groups in the Heart dataset. Furthermore, in the mortality dataset, it improves performance in two of the four sub-groups. A comparison of our method with the traditional decoupled personalization method demonstrated a greater performance gain in the sub-groups with less harm. This approach offers a more effective and scalable solution for personalization of models, which could have positive impact in healthcare and other areas that require predictive models which take sub-group information into account.
