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Probabilistic Methods/Gaussian Processes

mu niu, Zhenwen Dai, Pokman Cheung, Yizhu Wang

This article presents a novel approach to construct Intrinsic Gaussian Processes for regression on unknown manifolds with probabilistic metrics (GPUM) in point clouds. In many real world applications, one often encounters high dimensional data (e.g.‘point cloud data’) centered around some lower dimensional unknown manifolds. The geometry of manifold is in general different from the usual Euclidean geometry. Naively applying traditional smoothing methods such as Euclidean Gaussian Processes (GPs) to manifold-valued data and so ignoring the geometry of the space can potentially lead to highly misleading predictions and inferences. A manifold embedded in a high dimensional Euclidean space can be well described by a probabilistic mapping function and the corresponding latent space. We investigate the geometrical structure of the unknown manifolds using the Bayesian Gaussian Processes latent variable models(B-GPLVM) and Riemannian geometry. The distribution of the metric tensor is learned using B-GPLVM. The boundary of the resulting manifold is defined based on the uncertainty quantification of the mapping. We use the probabilistic metric tensor to simulate Brownian Motion paths on the unknown manifold. The heat kernel is estimated as the transition density of Brownian Motion and used as the covariance functions of GPUM. The applications of GPUM are illustrated in the simulation studies on the Swiss roll, high dimensional real datasets of WiFi signals and image data examples. Its performance is compared with the Graph Laplacian GP, Graph Mat\'{e}rn GP and Euclidean GP.

Social Aspects/Privacy-preserving Statistics and Machine Learning

Hua Wang, Sheng Gao, Huanyu Zhang, Weijie Su, Milan Shen

Hyperparameter optimization, also known as hyperparameter tuning, is a widely recognized technique for improving model performance. Regrettably, when training private ML models, many practitioners often overlook the privacy risks associated with hyperparameter optimization, which could potentially expose sensitive information about the underlying dataset.Currently, the sole existing approach to allow privacy-preserving hyperparameter optimization is to uniformly and randomly select hyperparameters for a number of runs, subsequently reporting the best-performing hyperparameter.In contrast, in non-private settings, practitioners commonly utilize "adaptive" hyperparameter optimization methods such as Gaussian Process-based optimization, which select the next candidate based on information gathered from previous outputs.This substantial contrast between private and non-private hyperparameter optimization underscores a critical concern. In our paper, we introduce DP-HyPO, a pioneering framework for "adaptive" private hyperparameter optimization, aiming to bridge the gap between private and non-private hyperparameter optimization. To accomplish this, we provide a comprehensive differential privacy analysis of our framework. Furthermore, we empirically demonstrate the effectiveness of DP-HyPO on a diverse set of real-world datasets.

Miscellaneous Aspects of Machine Learning/Representation Learning

Ignavier Ng, Yujia Zheng, Xinshuai Dong, Kun Zhang

Independent component analysis (ICA) is a fundamental statistical tool used to reveal hidden generative processes from observed data. However, traditional ICA approaches struggle with the rotational invariance inherent in Gaussian distributions, often necessitating the assumption of non-Gaussianity in the underlying sources. This may limit their applicability in broader contexts. To accommodate Gaussian sources, we develop an identifiability theory that relies on second-order statistics without imposing further preconditions on the distribution of sources, by introducing novel assumptions on the connective structure from sources to observed variables. Different from recent work that focuses on potentially restrictive connective structures, our proposed assumption of structural variability is both considerably less restrictive and provably necessary. Furthermore, we propose two estimation methods based on second-order statistics and sparsity constraint. Experimental results are provided to validate our identifiability theory and estimation methods.

Jun Wu, Lisa Ainsworth, Andrew Leakey, Haixun Wang, Jingrui He

Transferable graph learning involves knowledge transferability from a source graph to a relevant target graph. The major challenge of transferable graph learning is the distribution shift between source and target graphs induced by individual node attributes and complex graph structures. To solve this problem, in this paper, we propose a generic graph-structured Gaussian process framework (GraphGP) for adaptively transferring knowledge across graphs with either homophily or heterophily assumptions. Specifically, GraphGP is derived from a novel graph structure-aware neural network in the limit on the layer width. The generalization analysis of GraphGP explicitly investigates the connection between knowledge transferability and graph domain similarity. Extensive experiments on several transferable graph learning benchmarks demonstrate the efficacy of GraphGP over state-of-the-art Gaussian process baselines.

Marga Don, Satchit Chatterji, Milena Kapralova, Ryan Amaudruz

Scope of Reproducibility — This paper aims to reproduce the study FairCal: Fairness Calibration for Face Verification by Salvador et al., focused on verifying three main claims: FairCal (introduced by the authors) achieves state‐of‐the‐art (i) global accuracy, (ii) fairness-calibrated probabilities and (iii) equality in false positive rates across sensitive attributes (i.e. predictive equality). The sensitive attribute taken into account is ethnicity.Methodology — Salvador et al. provide partial code via a GitHub repository. Additional code to generate image embeddings from three pretrained neural network models were based on existing repositories. All code was refactored to fit our needs, keeping extendability and readability in mind. Two datasets were used, namely, Balanced Faces in the Wild (BFW) and Racial Faces in the Wild (RFW). Additional experiments using Gaussian mixture models instead of K‐means clustering for FairCal validate the use of unsupervised clus‐ tering methods. The code was run on an AMD Ryzen 7 2700X CPU and NVIDIA GeForce GTX1080Ti GPU with a total runtime of around 3 hours for all experiments.Results — In most cases, we were able to reproduce results from the original paper to within 1 standard deviation, and observe similar trends. However, due to missing information about image pre‐processing, we were unable to reproduce the results exactly.What was easy — The original paper is clear and understandable. Furthermore, the authors provided a mostly working version of the code. Though the datasets are not freely available to the public, their authors supplied these to us swiftly after contacting them.What was difficult — While most of the code worked with slight changes, it was assumed there were files containing image embeddings available for both datasets, which the authors neither provided nor gave details about. We therefore pre‐processed and generated embeddings independent of the authors, which makes it more difficult to judge the overall reproducibility of their method. Additionally, we encountered difficulties while improving the efficiency and extendability of the code.Communication with original authors — We emailed the first author of the paper twice. First at the beginning of our undertaking, they were enthusiastic about our attempt, and clarified a few initial doubts about their implementation, the embeddings, and missing files. As per the writing of this paper, they have not responded to the second email.

Probabilistic Methods/Gaussian Processes

Robert Allison, Anthony Stephenson, Samuel F, Edward O Pyzer-Knapp

The accurate predictions and principled uncertainty measures provided by GP regression incur $O(n^3)$ cost which is prohibitive for modern-day large-scale applications. This has motivated extensive work on computationally efficient approximations. We introduce a new perspective by exploring robustness properties and limiting behaviour of GP nearest-neighbour (GPnn) prediction. We demonstrate through theory and simulation that as the data-size $n$ increases, accuracy of estimated parameters and GP model assumptions become increasingly irrelevant to GPnn predictive accuracy. Consequently, it is sufficient to spend small amounts of work on parameter estimation in order to achieve high MSE accuracy, even in the presence of gross misspecification. In contrast, as $n \rightarrow \infty$, uncertainty calibration and NLL are shown to remain sensitive to just one parameter, the additive noise-variance; but we show that this source of inaccuracy can be corrected for, thereby achieving both well-calibrated uncertainty measures and accurate predictions at remarkably low computational cost. We exhibit a very simple GPnn regression algorithm with stand-out performance compared to other state-of-the-art GP approximations as measured on large UCI datasets. It operates at a small fraction of those other methods' training costs, for example on a basic laptop taking about 30 seconds to train on a dataset of size $n = 1.6 \times 10^6$.

Optimization/Optimization and Learning under Uncertainty

Lin Yang, Junlong Lyu, Wenlong Lyu, Zhitang Chen

Bayesian Optimization (BO) is a sample-efficient optimization algorithm widely employed across various applications. In some challenging BO tasks, input uncertainty arises due to the inevitable randomness in the optimization process, such as machining errors, execution noise, or contextual variability. This uncertainty deviates the input from the intended value before evaluation, resulting in significant performance fluctuations in the final result. In this paper, we introduce a novel robust Bayesian Optimization algorithm, AIRBO, which can effectively identify a robust optimum that performs consistently well under arbitrary input uncertainty. Our method directly models the uncertain inputs of arbitrary distributions by empowering the Gaussian Process with the Maximum Mean Discrepancy (MMD) and further accelerates the posterior inference via Nystrom approximation. Rigorous theoretical regret bound is established under MMD estimation error and extensive experiments on synthetic functions and real problems demonstrate that our approach can handle various input uncertainties and achieve a state-of-the-art performance.

Jihao Andreas Lin, Javier Antorán, Shreyas Padhy, David Janz, José Miguel Hernández-Lobato, Alexander Terenin

Gaussian processes are a powerful framework for quantifying uncertainty and for sequential decision-making but are limited by the requirement of solving linear systems. In general, this has a cubic cost in dataset size and is sensitive to conditioning. We explore stochastic gradient algorithms as a computationally efficient method of approximately solving these linear systems: we develop low-variance optimization objectives for sampling from the posterior and extend these to inducing points. Counterintuitively, stochastic gradient descent often produces accurate predictions, even in cases where it does not converge quickly to the optimum. We explain this through a spectral characterization of the implicit bias from non-convergence. We show that stochastic gradient descent produces predictive distributions close to the true posterior both in regions with sufficient data coverage, and in regions sufficiently far away from the data. Experimentally, stochastic gradient descent achieves state-of-the-art performance on sufficiently large-scale or ill-conditioned regression tasks. Its uncertainty estimates match the performance of significantly more expensive baselines on a large-scale Bayesian~optimization~task.

Miscellaneous Aspects of Machine Learning/Online Learning, Active Learning and Bandits

Haoting Zhang, Jinghai He, Rhonda Righter, Zuo-Jun Shen, Zeyu Zheng

Contextual decision-making problems have witnessed extensive applications in various fields such as online content recommendation, personalized healthcare, and autonomous vehicles, where a core practical challenge is to select a suitable surrogate model for capturing unknown complicated reward functions. It is often the case that both high approximation accuracy and explicit uncertainty quantification are desired. In this work, we propose a neural network-accompanied Gaussian process (NN-AGP) model, which leverages neural networks to approximate the unknown and potentially complicated reward function regarding the contextual variable, and maintains a Gaussian process surrogate model with respect to the decision variable. Our model is shown to outperform existing approaches by offering better approximation accuracy thanks to the use of neural networks and possessing explicit uncertainty quantification from the Gaussian process. We also analyze the maximum information gain of the NN-AGP model and prove regret bounds for the corresponding algorithms. Moreover, we conduct experiments on both synthetic and practical problems, illustrating the effectiveness of our approach.

Applications/Chemistry and Drug Discovery

Ryan-Rhys Griffiths, Leo Klarner, Henry Moss, Aditya Ravuri, Sang Truong, Yuanqi Du, Samuel Stanton, Gary Tom, Bojana Rankovic, Arian Jamasb 等

We introduce GAUCHE, an open-source library for GAUssian processes in CHEmistry. Gaussian processes have long been a cornerstone of probabilistic machine learning, affording particular advantages for uncertainty quantification and Bayesian optimisation. Extending Gaussian processes to molecular representations, however, necessitates kernels defined over structured inputs such as graphs, strings and bit vectors. By providing such kernels in a modular, robust and easy-to-use framework, we seek to enable expert chemists and materials scientists to make use of state-of-the-art black-box optimization techniques. Motivated by scenarios frequently encountered in practice, we showcase applications for GAUCHE in molecular discovery, chemical reaction optimisation and protein design. The codebase is made available at https://github.com/leojklarner/gauche.

Applications/Computer Vision

Zheng Chen, Yulun Zhang, Ding Liu, bin xia, Jinjin Gu, Linghe Kong, Xin Yuan

Diffusion models (DMs) have recently been introduced in image deblurring and exhibited promising performance, particularly in terms of details reconstruction. However, the diffusion model requires a large number of inference iterations to recover the clean image from pure Gaussian noise, which consumes massive computational resources. Moreover, the distribution synthesized by the diffusion model is often misaligned with the target results, leading to restrictions in distortion-based metrics. To address the above issues, we propose the Hierarchical Integration Diffusion Model (HI-Diff), for realistic image deblurring. Specifically, we perform the DM in a highly compacted latent space to generate the prior feature for the deblurring process. The deblurring process is implemented by a regression-based method to obtain better distortion accuracy. Meanwhile, the highly compact latent space ensures the efficiency of the DM. Furthermore, we design the hierarchical integration module to fuse the prior into the regression-based model from multiple scales, enabling better generalization in complex blurry scenarios. Comprehensive experiments on synthetic and real-world blur datasets demonstrate that our HI-Diff outperforms state-of-the-art methods. Code and trained models are available at https://github.com/zhengchen1999/HI-Diff.

Deep Learning/Algorithms

Andres Potapczynski, Marc Finzi, Geoff Pleiss, Andrew Wilson

Many areas of machine learning and science involve large linear algebra problems, such as eigendecompositions, solving linear systems, computing matrix exponentials, and trace estimation. The matrices involved often have Kronecker, convolutional, block diagonal, sum, or product structure. In this paper, we propose a simple but general framework for large-scale linear algebra problems in machine learning, named CoLA (Compositional Linear Algebra). By combining a linear operator abstraction with compositional dispatch rules, CoLA automatically constructs memory and runtime efficient numerical algorithms. Moreover, CoLA provides memory efficient automatic differentiation, low precision computation, and GPU acceleration in both JAX and PyTorch, while also accommodating new objects, operations, and rules in downstream packages via multiple dispatch. CoLA can accelerate many algebraic operations, while making it easy to prototype matrix structures and algorithms, providing an appealing drop-in tool for virtually any computational effort that requires linear algebra. We showcase its efficacy across a broad range of applications, including partial differential equations, Gaussian processes, equivariant model construction, and unsupervised learning.

Social Aspects/Trustworthy Machine Learning

Guangyu Shen, Siyuan Cheng, Guanhong Tao, Kaiyuan Zhang, Yingqi Liu, Shengwei An, Shiqing Ma, Xiangyu Zhang

Object detection models are vulnerable to backdoor or trojan attacks, where an attacker can inject malicious triggers into the model, leading to altered behavior during inference. As a defense mechanism, trigger inversion leverages optimization to reverse-engineer triggers and identify compromised models. While existing trigger inversion methods assume that each instance from the support set is equally affected by the injected trigger, we observe that the poison effect can vary significantly across bounding boxes in object detection models due to its dense prediction nature, leading to an undesired optimization objective misalignment issue for existing trigger reverse-engineering methods. To address this challenge, we propose the first object detection backdoor detection framework Django (Detecting Trojans in Object Detection Models via Gaussian Focus Calibration). It leverages a dynamic Gaussian weighting scheme that prioritizes more vulnerable victim boxes and assigns appropriate coefficients to calibrate the optimization objective during trigger inversion. In addition, we combine Django with a novel label proposal pre-processing technique to enhance its efficiency. We evaluate Django on 3 object detection image datasets, 3 model architectures, and 2 types of attacks, with a total of 168 models. Our experimental results show that Django outperforms 6 state-of-the-art baselines, with up to 38% accuracy improvement and 10x reduced overhead. The code is available at https://github.com/PurduePAML/DJGO.

Probabilistic Methods/Bayesian Models and Methods

Alexander Immer, Emanuele Palumbo, Alexander Marx, Julia Vogt

Flexibly quantifying both irreducible aleatoric and model-dependent epistemic uncertainties plays an important role for complex regression problems. While deep neural networks in principle can provide this flexibility and learn heteroscedastic aleatoric uncertainties through non-linear functions, recent works highlight that maximizing the log likelihood objective parameterized by mean and variance can lead to compromised mean fits since the gradient are scaled by the predictive variance, and propose adjustments in line with this premise. We instead propose to use the natural parametrization of the Gaussian, which has been shown to be more stable for heteroscedastic regression based on non-linear feature maps and Gaussian processes. Further, we emphasize the significance of principled regularization of the network parameters and prediction. We therefore propose an efficient Laplace approximation for heteroscedastic neural networks that allows automatic regularization through empirical Bayes and provides epistemic uncertainties, both of which improve generalization.We showcase on a range of regression problems—including a new heteroscedastic image regression benchmark—that our methods are scalable, improve over previous approaches for heteroscedastic regression, and provide epistemic uncertainty without requiring hyperparameter tuning.

Miscellaneous Aspects of Machine Learning/Kernel methods

Alexandre Capone, Sandra Hirche, Geoff Pleiss

While Gaussian processes are a mainstay for various engineering and scientific applications, the uncertainty estimates don't satisfy frequentist guarantees and can be miscalibrated in practice. State-of-the-art approaches for designing calibrated models rely on inflating the Gaussian process posterior variance, which yields confidence intervals that are potentially too coarse. To remedy this, we present a calibration approach that generates predictive quantiles using a computation inspired by the vanilla Gaussian process posterior variance but using a different set of hyperparameters chosen to satisfy an empirical calibration constraint. This results in a calibration approach that is considerably more flexible than existing approaches, which we optimize to yield tight predictive quantiles. Our approach is shown to yield a calibrated model under reasonable assumptions. Furthermore, it outperforms existing approaches in sharpness when employed for calibrated regression.

Xinran Zhu, Kaiwen Wu, Natalie Maus, Jacob Gardner, David Bindel

Variational Gaussian processes (GPs) approximate exact GP inference by using a small set of inducing points to form a sparse approximation of the true posterior, with the fidelity of the model increasing with additional inducing points. Although the approximation error in principle can be reduced through the use of more inducing points, this leads to scaling optimization challenges and computational complexity. To achieve scalability, inducing point methods typically introduce conditional independencies and then approximations to the training and test conditional distributions. In this paper, we consider an alternative approach to modifying the training and test conditionals, in which we make them more flexible. In particular, we investigate decoupling the parametric form of the predictive mean and covariance in the conditionals, and learn independent parameters for predictive mean and covariance. We derive new evidence lower bounds (ELBO) under these more flexible conditionals, and provide two concrete examples of applying the decoupled conditionals. Empirically, we find this additional flexibility leads to improved model performance on a variety of regression tasks and Bayesian optimization (BO) applications.

Probabilistic Methods/Gaussian Processes

Amir Hossein Hosseini Akbarnejad, Gilbert Bigras, Nilanjan Ray

The analogy between Gaussian processes (GPs) and deep artificial neural networks (ANNs) has received a lot of interest, and has shown promise to unbox the blackbox of deep ANNs. Existing theoretical works put strict assumptions on the ANN (e.g. requiring all intermediate layers to be wide, or using specific activation functions). Accommodating those theoretical assumptions is hard in recent deep architectures, and those theoretical conditions need refinement as new deep architectures emerge. In this paper we derive an evidence lower-bound that encourages the GP's posterior to match the ANN's output without any requirement on the ANN. Using our method we find out that on 5 datasets, only a subset of those theoretical assumptions are sufficient. Indeed, in our experiments we used a normal ResNet-18 or feed-forward backbone with a single wide layer in the end. One limitation of training GPs is the lack of scalability with respect to the number of inducing points. We use novel computational techniques that allow us to train GPs with hundreds of thousands of inducing points and with GPU acceleration. As shown in our experiments, doing so has been essential to get a close match between the GPs and the ANNs on 5 datasets. We implement our method as a publicly available tool called GPEX: https://github.com/amirakbarnejad/gpex. On 5 datasets (4 image datasets, and 1 biological dataset) and ANNs with 2 types of functionality (classifier or attention-mechanism) we were able to find GPs whose outputs closely match those of the corresponding ANNs. After matching the GPs to the ANNs, we used the GPs' kernel functions to explain the ANNs' decisions. We provide more than 200 explanations (around 30 in the paper and the rest in the supplementary) which are highly interpretable by humans and show the ability of the obtained GPs to unbox the ANNs' decisions.

Probabilistic Methods/Bayesian Models and Methods

Shikai Fang, Xin Yu, Shibo Li, Zheng Wang, Mike Kirby, Shandian Zhe

Practical tensor data is often along with time information. Most existing temporal decomposition approaches estimate a set of fixed factors for the objects in each tensor mode, and hence cannot capture the temporal evolution of the objects' representation. More important, we lack an effective approach to capture such evolution from streaming data, which is common in real-world applications. To address these issues, we propose Streaming Factor Trajectory Learning (SFTL) for temporal tensor decomposition. We use Gaussian processes (GPs) to model the trajectory of factors so as to flexibly estimate their temporal evolution. To address the computational challenges in handling streaming data, we convert the GPs into a state-space prior by constructing an equivalent stochastic differential equation (SDE). We develop an efficient online filtering algorithm to estimate a decoupled running posterior of the involved factor states upon receiving new data. The decoupled estimation enables us to conduct standard Rauch-Tung-Striebel smoothing to compute the full posterior of all the trajectories in parallel, without the need for revisiting any previous data. We have shown the advantage of SFTL in both synthetic tasks and real-world applications.

Probabilistic Methods/Gaussian Processes

Luke Travis, Kolyan Ray

We study pointwise estimation and uncertainty quantification for a sparse variational Gaussian process method with eigenvector inducing variables. For a rescaled Brownian motion prior, we derive theoretical guarantees and limitations for the frequentist size and coverage of pointwise credible sets. For sufficiently many inducing variables, we precisely characterize the asymptotic frequentist coverage, deducing when credible sets from this variational method are conservative and when overconfident/misleading. We numerically illustrate the applicability of our results and discuss connections with other common Gaussian process priors.

Probabilistic Methods/Gaussian Processes

Siu Lun Chau, Krikamol Muandet, Dino Sejdinovic

We present a novel approach for explaining Gaussian processes (GPs) that can utilize the full analytical covariance structure present in GPs. Our method is based on the popular solution concept of Shapley values extended to stochastic cooperative games, resulting in explanations that are random variables. The GP explanations generated using our approach satisfy similar favorable axioms to standard Shapley values and possess a tractable covariance function across features and data observations. This covariance allows for quantifying explanation uncertainties and studying the statistical dependencies between explanations. We further extend our framework to the problem of predictive explanation, and propose a Shapley prior over the explanation function to predict Shapley values for new data based on previously computed ones. Our extensive illustrations demonstrate the effectiveness of the proposed approach.