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Deep Learning · Generative Models and Autoencoders

Kushagra Pandey, Farrin Marouf Sofian, Felix Draxler, Theofanis Karaletsos, Stephan Mandt

Diffusion models exhibit excellent sample quality, but existing guidance methods often require additional model training or are limited to specific tasks. We revisit guidance in diffusion models from the perspective of variational inference and control, introducing \emph{Diffusion Trajectory Matching (DTM)} that enables guiding pretrained diffusion trajectories to satisfy a terminal cost. DTM unifies a broad class of guidance methods and enables novel instantiations. We introduce a new method within this framework that achieves state-of-the-art results on several linear, non-linear, and blind inverse problems without requiring additional model training or specificity to pixel or latent space diffusion models. Our code will be available at https://github.com/czi-ai/oc-guidance.

Probabilistic Methods · Gaussian Processes

Xinxing Shi, Xiaoyu Jiang, Mauricio Álvarez

Gaussian Process (GP) Variational Autoencoders (VAEs) extend standard VAEs by replacing the fully factorised Gaussian prior with a GP prior, thereby capturing richer correlations among latent variables. However, performing exact GP inference in large-scale GPVAEs is computationally prohibitive, often forcing existing approaches to rely on restrictive kernel assumptions or large sets of inducing points. In this work, we propose a neighbour-driven approximation strategy that exploits local adjacencies in the latent space to achieve scalable GPVAE inference. By confining computations to the nearest neighbours of each data point, our method preserves essential latent dependencies, allowing more flexible kernel choices and mitigating the need for numerous inducing points. Through extensive experiments on tasks including representation learning, data imputation, and conditional generation, we demonstrate that our approach outperforms other GPVAE variants in both predictive performance and computational efficiency.

General Machine Learning

Chao Yang, Shuting Cui, Yang Yang, Shuang Li

Understanding human mental states—such as intentions and desires—is crucial for natural AI-human collaboration. However, this is challenging because human actions occur irregularly over time, and the underlying mental states that drive these actions are unobserved. To tackle this, we propose a novel framework that combines a logic-informed temporal point process (TPP) with amortized variational Expectation-Maximization (EM). Our key innovation is integrating logic rules as priors to guide the TPP’s intensity function, allowing the model to capture the interplay between actions and mental events while reducing dependence on large datasets. To handle the intractability of mental state inference, we introduce a discrete-time renewal process to approximate the posterior. By jointly optimizing model parameters, logic rules, and inference networks, our approach infers entire mental event sequences and adaptively predicts future actions. Experiments on both synthetic and real-world datasets show that our method outperforms existing approaches in accurately inferring mental states and predicting actions, demonstrating its effectiveness in modeling human cognitive processes.

Deep Learning · Generative Models and Autoencoders

Ching-Hua Lee, Chouchang Yang, Jaejin Cho, Yashas Malur Saidutta, Rakshith Sharma Srinivasa, Yilin Shen, Hongxia Jin

Denoising diffusion probabilistic models (DDPMs) can be utilized to recover a clean signal from its degraded observation(s) by conditioning the model on the degraded signal. The degraded signals are themselves contaminated versions of the clean signals; due to this correlation, they may encompass certain useful information about the target clean data distribution. However, existing adoption of the standard Gaussian as the prior distribution in turn discards such information when shaping the prior, resulting in sub-optimal performance. In this paper, we propose to improve conditional DDPMs for signal restoration by leveraging a more informative prior that is jointly learned with the diffusion model. The proposed framework, called RestoreGrad, seamlessly integrates DDPMs into the variational autoencoder (VAE) framework, taking advantage of the correlation between the degraded and clean signals to encode a better diffusion prior. On speech and image restoration tasks, we show that RestoreGrad demonstrates faster convergence (5-10 times fewer training steps) to achieve better quality of restored signals over existing DDPM baselines and improved robustness to using fewer sampling steps in inference time (2-2.5 times fewer), advocating the advantages of leveraging jointly learned prior for efficiency improvements in the diffusion process.

Probabilistic Methods · Variational Inference

Terje Mildner, Oliver Hamelijnck, Paris Giampouras, Theodoros Damoulas

We introduce FedGVI, a probabilistic Federated Learning (FL) framework that is robust to both prior and likelihood misspecification. FedGVI addresses limitations in both frequentist and Bayesian FL by providing unbiased predictions under model misspecification, with calibrated uncertainty quantification. Our approach generalises previous FL approaches, specifically Partitioned Variational Inference (Ashman et al., 2022), by allowing robust and conjugate updates, decreasing computational complexity at the clients. We offer theoretical analysis in terms of fixed-point convergence, optimality of the cavity distribution, and provable robustness to likelihood misspecification. Further, we empirically demonstrate the effectiveness of FedGVI in terms of improved robustness and predictive performance on multiple synthetic and real world classification data sets.

Probabilistic Methods · Bayesian Models and Methods

Nuojin Cheng, Leonard Papenmeier, Stephen Becker, Luigi Nardi

Bayesian optimization is a widely used method for optimizing expensive black-box functions, with Expected Improvement being one of the most commonly used acquisition functions. In contrast, information-theoretic acquisition functions aim to reduce uncertainty about the function’s optimum and are often considered fundamentally distinct from EI. In this work, we challenge this prevailing perspective by introducing a unified theoretical framework, Variational Entropy Search, which reveals that EI and information-theoretic acquisition functions are more closely related than previously recognized. We demonstrate that EI can be interpreted as a variational inference approximation of the popular information-theoretic acquisition function, named Max-value Entropy Search. Building on this insight, we propose VES-Gamma, a novel acquisition function that balances the strengths of EI and MES. Extensive empirical evaluations across both low- and high-dimensional synthetic and real-world benchmarks demonstrate that VES-Gamma is competitive with state-of-the-art acquisition functions and in many cases outperforms EI and MES.

Nuojin Cheng, Leonard Papenmeier, Stephen Becker, Luigi Nardi

Bayesian optimization is a widely used method for optimizing expensive black-box functions, with Expected Improvement being one of the most commonly used acquisition functions. In contrast, information-theoretic acquisition functions aim to reduce uncertainty about the function’s optimum and are often considered fundamentally distinct from EI. In this work, we challenge this prevailing perspective by introducing a unified theoretical framework, Variational Entropy Search, which reveals that EI and information-theoretic acquisition functions are more closely related than previously recognized. We demonstrate that EI can be interpreted as a variational inference approximation of the popular information-theoretic acquisition function, named Max-value Entropy Search. Building on this insight, we propose VES-Gamma, a novel acquisition function that balances the strengths of EI and MES. Extensive empirical evaluations across both low- and high-dimensional synthetic and real-world benchmarks demonstrate that VES-Gamma is competitive with state-of-the-art acquisition functions and in many cases outperforms EI and MES.

Deep Learning · Large Language Models

Jixian Zhou, Fang DONG(董方), Ruijun Huang, Hengjie Cao, Mengyi Chen, Yifeng Yang, Anrui Chen, Mingzhi Dong, Yujiang Wang, Dongsheng Li 等

Mixture-of-Experts (MoE) is widely adopted to deploy Large Language Models (LLMs) on edge devices with limited memory budgets.Although MoE is, in theory, an inborn memory-friendly architecture requiring only a few activated experts to reside in the memory for inference, current MoE architectures cannot effectively fulfill this advantage and will yield intolerable inference latencies of LLMs on memory-constrained devices. Our investigation pinpoints the essential cause as the remarkable temporal inconsistencies of inter-token expert activations, which generate overly frequent expert swapping demands dominating the latencies. To this end, we propose a novel MoE architecture, Oracle-MoE, to fulfill the real on-device potential of MoE-based LLMs. Oracle-MoE route tokens in a highly compact space suggested by attention scores, termed the *oracle space*, to effectively maintain the semantic locality across consecutive tokens to reduce expert activation variations, eliminating massive swapping demands. Theoretical analysis proves that Oracle-MoE is bound to provide routing decisions with better semantic locality and, therefore, better expert activation consistencies. Experiments on the pretrained GPT-2 architectures of different sizes (200M, 350M, 790M, and 2B) and downstream tasks demonstrate that without compromising task performance, our Oracle-MoE has achieved state-of-the-art inference speeds across varying memory budgets, revealing its substantial potential for LLM deployments in industry.

Probabilistic Methods · Variational Inference

Xuesong Wang, He Zhao, Edwin V. Bonilla

Neural Processes (NPs) are deep probabilistic models that represent stochastic processes by conditioning their prior distributions on a set of context points. Despite their advantages in uncertainty estimation for complex distributions, NPs enforce parameterization coupling between the conditional prior model and the posterior model. We show that this coupling amounts to prior misspecification and revisit the NP objective to address this issue. More specifically, we propose Rényi Neural Processes (RNP), a method that replaces the standard KL divergence with the Rényi divergence, dampening the effects of the misspecified prior during posterior updates. We validate our approach across multiple benchmarks including regression and image inpainting tasks, and show significant performance improvements of RNPs in real-world problems. Our extensive experiments show consistently better log-likelihoods over state-of-the-art NP models.

Probabilistic Methods · Variational Inference

Junbin Liu, Farzan Farnia, Wing-Kin Ma

Multilayer matrix factorization (MMF) has recently emerged as a generalized model of, and potentially a more expressive approach than, the classic matrix factorization.This paper considers MMF under a probabilistic formulation, and our focus is on inference methods under variational inference.The challenge in this context lies in determining a variational process that leads to a computationally efficient and accurate approximation of the maximum likelihood inference. One well-known example is the variational autoencoder (VAE), which uses neural networks for the variational process.In this work, we take insight from variational diffusion models in the context of generative models to develop variational inference for MMF.We propose a dimension-reducing diffusion process that results in a new way to interact with the layered structures of the MMF model.Experimental results demonstrate that the proposed diffusion variational inference method leads to improved performance scores compared to several existing methods, including the VAE.

General Machine Learning · Causality

Kun Wang, Sumanth Varambally, Duncan Watson-Parris, Yian Ma, Rose Yu

Many important phenomena in scientific fields like climate, neuroscience, and epidemiology are naturally represented as spatiotemporal gridded data with complex interactions. Inferring causal relationships from these data is a challenging problem compounded by the high dimensionality of such data and the correlations between spatially proximate points. We present SPACY (SPAtiotemporal Causal discoverY), a novel framework based on variational inference, designed to model latent time series and their causal relationships from spatiotemporal data. SPACY alleviates the high-dimensional challenge by discovering causal structures in the latent space. To aggregate spatially proximate, correlated grid points, we use spatial factors, parametrized by spatial kernel functions, to map observational time series to latent representations. Theoretically, we generalize the problem to a continuous spatial domain and establish identifiability when the observations arise from a nonlinear, invertible function of the product of latent series and spatial factors. Using this approach, we avoid assumptions that are often unverifiable, including those about instantaneous effects or sufficient variability. Empirically, SPACY outperforms state-of-the-art baselines on synthetic data, even in challenging settings where existing methods struggle, while remaining scalable for large grids. SPACY also identifies key known phenomena from real-world climate data. An implementation of SPACY is available at \url{https://github.com/Rose-STL-Lab/SPACY/}

Probabilistic Methods · Variational Inference

Tobias Pielok, Bernd Bischl, David Rügamer

Recent years have witnessed growing interest in semi-implicit variational inference (SIVI) methods due to their ability to rapidly generate samples from complex distributions. However, since the likelihood of these samples is non-trivial to estimate in high dimensions, current research focuses on finding effective SIVI training routines. Although unbiased implicit variational inference (UIVI) has largely been dismissed as imprecise and computationally prohibitive because of its inner MCMC loop, we revisit this method and show that UIVI's MCMC loop can be effectively replaced via importance sampling and the optimal proposal distribution can be learned stably by minimizing an expected forward Kullback–Leibler divergence without bias. Our refined approach demonstrates superior performance or parity with state-of-the-art methods on established SIVI benchmarks.

Probabilistic Methods · Variational Inference

Yuta Tarumi, Keisuke Fukuda, Shin-ichi Maeda

Data assimilation for nonlinear state space models (SSMs) is inherently challenging due to non-Gaussian posteriors. We propose Deep Bayesian Filtering (DBF), a novel approach to data assimilation in nonlinear SSMs. DBF introduces latent variables $h_t$ in addition to physical variables $z_t$, ensuring Gaussian posteriors by (i) constraining state transitions in the latent space to be linear and (ii) learning a Gaussian inverse observation operator $r(h_t|o_t)$. This structured posterior design enables analytical recursive computation, avoiding the accumulation of Monte Carlo sampling errors over time steps. DBF optimizes these operators and other latent SSM parameters by maximizing the evidence lower bound. Experiments demonstrate that DBF outperforms existing methods in scenarios with highly non-Gaussian posteriors.

Probabilistic Methods · Variational Inference

Zhe Wang, Jiaxin Shi, Nicolas Heess, Arthur Gretton, Michalis Titsias

Autoregressive models (ARMs) have become the workhorse for sequence generation tasks, since many problems can be modeled as next-token prediction. While there appears to be a natural ordering for text (i.e., left-to-right), for many data types, such as graphs, the canonical ordering is less obvious. To address this problem, we introduce a variant of ARM that generates high-dimensional data using a probabilistic ordering that is sequentially inferred from data. This model incorporates a trainable probability distribution, referred to as an order-policy, that dynamically decides the autoregressive order in a state-dependent manner. To train the model, we introduce a variational lower bound on the exact log-likelihood, which we optimize with stochastic gradient estimation. We demonstrate experimentally that our method can learn meaningful autoregressive orderings in image and graph generation. On the challenging domain of molecular graph generation, we achieve state-of-the-art results on the QM9 and ZINC250k benchmarks, evaluated using the Fréchet ChemNet Distance (FCD), Synthetic Accessibility Score (SAS), Quantitative Estimate of Drug-likeness (QED).

Probabilistic Methods · Gaussian Processes

Jihao Andreas Lin, Sebastian Ament, Maximilian Balandat, David Eriksson, Jose Miguel Hernandez-Lobato, Eytan Bakshy

Applying Gaussian processes (GPs) to very large datasets remains a challenge due to limited computational scalability. Matrix structures, such as the Kronecker product, can accelerate operations significantly, but their application commonly entails approximations or unrealistic assumptions. In particular, the most common path to creating a Kronecker-structured kernel matrix is by evaluating a product kernel on gridded inputs that can be expressed as a Cartesian product. However, this structure is lost if any observation is missing, breaking the Cartesian product structure, which frequently occurs in real-world data such as time series. To address this limitation, we propose leveraging latent Kronecker structure, by expressing the kernel matrix of observed values as the projection of a latent Kronecker product. In combination with iterative linear system solvers and pathwise conditioning, our method facilitates inference of exact GPs while requiring substantially fewer computational resources than standard iterative methods. We demonstrate that our method outperforms state-of-the-art sparse and variational GPs on real-world datasets with up to five million examples, including robotics, automated machine learning, and climate applications.

Applications · Neuroscience, Cognitive Science

Belle Liu, Jacob I Sacks, Matthew Golub

Neural recording technologies now enable simultaneous recording of population activity across multiple brain regions, motivating the development of data-driven models of communication between recorded brain regions. Existing models can struggle to disentangle communication from the effects of unrecorded regions and local neural population dynamics. Here, we introduce Multi-Region Latent Factor Analysis via Dynamical Systems (MR-LFADS), a sequential variational autoencoder composed of region-specific recurrent networks. MR-LFADS features structured information bottlenecks, data-constrained communication, and unsupervised inference of unobserved inputs--features that specifically support disentangling of inter-regional communication, inputs from unobserved regions, and local population dynamics. MR-LFADS outperforms existing approaches at identifying communication across dozens of simulations of task-trained multi-region networks. Applied to large-scale electrophysiology, MR-LFADS predicts brain-wide effects of circuit perturbations that were not seen during model fitting. These validations on synthetic and real neural data suggest that MR-LFADS could serve as a powerful tool for uncovering the principles of brain-wide information processing.

General Machine Learning · Transfer, Multitask and Meta-learning

Junyu Luo, Yuhao Tang, Yiwei Fu, Xiao Luo, Zhizhuo KOU, Zhiping Xiao, Wei Ju, Wentao Zhang, Ming Zhang

Unsupervised Graph Domain Adaptation (UGDA) leverages labeled source domain graphs to achieve effective performance in unlabeled target domains despite distribution shifts. However, existing methods often yield suboptimal results due to the entanglement of causal-spurious features and the failure of global alignment strategies. We propose SLOGAN (Sparse Causal Discovery with Generative Intervention), a novel approach that achieves stable graph representation transfer through sparse causal modeling and dynamic intervention mechanisms. Specifically, SLOGAN first constructs a sparse causal graph structure, leveraging mutual information bottleneck constraints to disentangle sparse, stable causal features while compressing domain-dependent spurious correlations through variational inference. To address residual spurious correlations, we innovatively design a generative intervention mechanism that breaks local spurious couplings through cross-domain feature recombination while maintaining causal feature semantic consistency via covariance constraints. Furthermore, to mitigate error accumulation in target domain pseudo-labels, we introduce a category-adaptive dynamic calibration strategy, ensuring stable discriminative learning. Extensive experiments on multiple real-world datasets demonstrate that SLOGAN significantly outperforms existing baselines.

Probabilistic Methods · Variational Inference

Abhinav Agrawal, Justin Domke

Predictive posterior densities (PPDs) are essential in approximate inference for quantifying predictive uncertainty and comparing inference methods. Typically, PPDs are estimated by simple Monte Carlo (MC) averages. In this paper, we expose a critical under-recognized issue: the signal-to-noise ratio (SNR) of the simple MC estimator can sometimes be extremely low, leading to unreliable estimates. Our main contribution is a theoretical analysis demonstrating that even with exact inference, SNR can decay rapidly with an increase in (a) the mismatch between training and test data, (b) the dimensionality of the latent space, or (c) the size of test data relative to training data. Through several examples, we empirically verify these claims and show that these factors indeed lead to poor SNR and unreliable PPD estimates (sometimes, estimates are off by hundreds of nats even with a million samples). While not the primary focus, we also explore an adaptive importance sampling approach as an illustrative way to mitigate the problem, where we learn the proposal distribution by maximizing a variational proxy to the SNR. Taken together, our findings highlight an important challenge and provide essential insights for reliable estimation.

Social Aspects · Safety

Jingwei Li, Jing Dong, Tianxing He, Jingzhao Zhang

Given the rising popularity of AI-generated art and the associated copyright concerns, identifying whether an artwork was used to train a diffusion model is an important research topic. The work approaches this problem from the membership inference attack (MIA) perspective. We first identify the limitation of applying existing MIA methods for proprietary diffusion models: the required access of internal U-nets.To address the above problem, we introduce a novel membership inference attack method that uses only the image-to-image variation API and operates without access to the model's internal U-net. Our method is based on the intuition that the model can more easily obtain an unbiased noise prediction estimate for images from the training set. By applying the API multiple times to the target image, averaging the outputs, and comparing the result to the original image, our approach can classify whether a sample was part of the training set. We validate our method using DDIM and Stable Diffusion setups and further extend both our approach and existing algorithms to the Diffusion Transformer architecture. Our experimental results consistently outperform previous methods.

Deep Learning · Generative Models and Autoencoders

Floor Eijkelboom, Heiko Zimmermann, Sharvaree Vadgama, Erik Bekkers, Max Welling, Christian Andersson Naesseth, Jan-Willem van de Meent

We derive a controlled generation objective within the framework of Variational Flow Matching (VFM),which casts flow matching as a variational inference problem.We demonstrate that controlled generation can be implemented two ways: (1) by way of end-to-end training of conditional generative models, or (2) as a Bayesian inference problem, enabling post hoc control of unconditional models without retraining. Furthermore, we establish the conditions required for equivariant generation and provide an equivariant formulation of VFM tailored for molecular generation, ensuring invariance to rotations, translations, and permutations. We evaluate our approach on both uncontrolled and controlled molecular generation, achieving state-of-the-art performance on uncontrolled generation and outperforming state-of-the-art models in controlled generation, both with end-to-end training and in the Bayesian inference setting. This work strengthens the connection between flow-based generative modeling and Bayesian inference, offering a scalable and principled framework for constraint-driven and symmetry-aware generation.