Uncertainty
Conformalized Gaussian processes for online uncertainty quantification over graphs
Xu, Jinwen, Lu, Qin, Giannakis, Georgios B.
Uncertainty quantification (UQ) over graphs arises in a number of safety-critical applications in network science. The Gaussian process (GP), as a classical Bayesian framework for UQ, has been developed to handle graph-structured data by devising topology-aware kernel functions. However, such GP-based approaches are limited not only by the prohibitive computational complexity, but also the strict modeling assumptions that might yield poor coverage, especially with labels arriving on the fly. To effect scalability, we devise a novel graph-aware parametric GP model by leveraging the random feature (RF)-based kernel approximation, which is amenable to efficient recursive Bayesian model updates. To further allow for adaptivity, an ensemble of graph-aware RF-based scalable GPs have been leveraged, with per-GP weight adapted to data arriving incrementally. To ensure valid coverage with robustness to model mis-specification, we wed the GP-based set predictors with the online conformal prediction framework, which post-processes the prediction sets using adaptive thresholds. Experimental results the proposed method yields improved coverage and efficient prediction sets over existing baselines by adaptively ensembling the GP models and setting the key threshold parameters in CP.
PolyGraph Discrepancy: a classifier-based metric for graph generation
Krimmel, Markus, Hartout, Philip, Borgwardt, Karsten, Chen, Dexiong
Existing methods for evaluating graph generative models primarily rely on Maximum Mean Discrepancy (MMD) metrics based on graph descriptors. While these metrics can rank generative models, they do not provide an absolute measure of performance. Their values are also highly sensitive to extrinsic parameters, namely kernel and descriptor parametrization, making them incomparable across different graph descriptors. We introduce PolyGraph Discrepancy (PGD), a new evaluation framework that addresses these limitations. It approximates the Jensen-Shannon distance of graph distributions by fitting binary classifiers to distinguish between real and generated graphs, featurized by these descriptors. The data log-likelihood of these classifiers approximates a variational lower bound on the JS distance between the two distributions. Resulting metrics are constrained to the unit interval [0,1] and are comparable across different graph descriptors. We further derive a theoretically grounded summary metric that combines these individual metrics to provide a maximally tight lower bound on the distance for the given descriptors. Thorough experiments demonstrate that PGD provides a more robust and insightful evaluation compared to MMD metrics. The PolyGraph framework for benchmarking graph generative models is made publicly available at https://github.com/BorgwardtLab/polygraph-benchmark.
Learning Mixtures of Linear Dynamical Systems (MoLDS) via Hybrid Tensor-EM Method
Mixtures of linear dynamical systems (MoLDS) provide a path to model time-series data that exhibit diverse temporal dynamics across trajectories. However, its application remains challenging in complex and noisy settings, limiting its effectiveness for neural data analysis. Tensor-based moment methods can provide global identifiability guarantees for MoLDS, but their performance degrades under noise and complexity. Commonly used expectation-maximization (EM) methods offer flexibility in fitting latent models but are highly sensitive to initialization and prone to poor local minima. Here, we propose a tensor-based method that provides identifiability guarantees for learning MoLDS, which is followed by EM updates to combine the strengths of both approaches. The novelty in our approach lies in the construction of moment tensors using the input-output data to recover globally consistent estimates of mixture weights and system parameters. These estimates can then be refined through a Kalman EM algorithm, with closed-form updates for all LDS parameters. We validate our framework on synthetic benchmarks and real-world datasets. On synthetic data, the proposed Tensor-EM method achieves more reliable recovery and improved robustness compared to either pure tensor or randomly initialized EM methods. We then analyze neural recordings from the primate somatosensory cortex while a non-human primate performs reaches in different directions. Our method successfully models and clusters different conditions as separate subsystems, consistent with supervised single-LDS fits for each condition. Finally, we apply this approach to another neural dataset where monkeys perform a sequential reaching task. These results demonstrate that MoLDS provides an effective framework for modeling complex neural data, and that Tensor-EM is a reliable approach to MoLDS learning for these applications.
Out-of-Distribution Detection from Small Training Sets using Bayesian Neural Network Classifiers
Out-of-Distribution (OOD) detection is critical to AI reliability and safety, yet in many practical settings, only a limited amount of training data is available. Bayesian Neural Networks (BNNs) are a promising class of model on which to base OOD detection, because they explicitly represent epistemic (i.e. model) uncertainty. In the small training data regime, BNNs are especially valuable because they can incorporate prior model information. We introduce a new family of Bayesian posthoc OOD scores based on expected logit vectors, and compare 5 Bayesian and 4 deterministic posthoc OOD scores. Experiments on MNIST and CIFAR-10 In-Distributions, with 5000 training samples or less, show that the Bayesian methods outperform corresponding deterministic methods.
ESS-Flow: Training-free guidance of flow-based models as inference in source space
Kalaivanan, Adhithyan, Zhao, Zheng, Sjölund, Jens, Lindsten, Fredrik
Guiding pretrained flow-based generative models for conditional generation or to produce samples with desired target properties enables solving diverse tasks without retraining on paired data. We present ESS-Flow, a gradient-free method that leverages the typically Gaussian prior of the source distribution in flow-based models to perform Bayesian inference directly in the source space using Elliptical Slice Sampling. ESS-Flow only requires forward passes through the generative model and observation process, no gradient or Jacobian computations, and is applicable even when gradients are unreliable or unavailable, such as with simulation-based observations or quantization in the generation or observation process. We demonstrate its effectiveness on designing materials with desired target properties and predicting protein structures from sparse inter-residue distance measurements. In generative modeling, we are given data samples and aim to construct a sampler that approximates the data distribution. Diffusion models (Ho et al., 2020; Song et al., 2021) and continuous normalizing flows (Lipman et al., 2023; Liu et al., 2023; Albergo et al., 2023) achieve this by transporting samples from a simple source distribution to the data distribution.
A Probabilistic Basis for Low-Rank Matrix Learning
Low rank inference on matrices is widely conducted by optimizing a cost function augmented with a penalty proportional to the nuclear norm $\Vert \cdot \Vert_*$. However, despite the assortment of computational methods for such problems, there is a surprising lack of understanding of the underlying probability distributions being referred to. In this article, we study the distribution with density $f(X)\propto e^{-λ\Vert X\Vert_*}$, finding many of its fundamental attributes to be analytically tractable via differential geometry. We use these facts to design an improved MCMC algorithm for low rank Bayesian inference as well as to learn the penalty parameter $λ$, obviating the need for hyperparameter tuning when this is difficult or impossible. Finally, we deploy these to improve the accuracy and efficiency of low rank Bayesian matrix denoising and completion algorithms in numerical experiments.