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Probabilistic Methods · Bayesian Models and Methods

Nick Bishop, Daniel Jarne Ornia, Joel Dyer, Anisoara Calinescu, Michael Wooldridge

Simulation modeling offers a flexible approach to constructing high-fidelity synthetic representations of complex real-world systems. However, the increased complexity of such models introduces additional complications, for example when carrying out statistical inference procedures. This has motivated a large and growing literature on *likelihood-free* or *simulation-based* inference methods, which approximate (e.g., Bayesian) inference without assuming access to the simulator's intractable likelihood function. A hitherto neglected problem in the simulation-based Bayesian inference literature is the challenge of constructing minimally informative *reference priors* for complex simulation models. Such priors maximise an expected Kullback-Leibler distance from the prior to the posterior, thereby influencing posterior inferences minimally and enabling an ``objective'' approach to Bayesian inference that does not necessitate the incorporation of strong subjective prior beliefs. In this paper, we propose and test a selection of likelihood-free methods for learning reference priors for simulation models, using variational approximations to these priors and a variety of mutual information estimators. Our experiments demonstrate that good approximations to reference priors for simulation models are in this way attainable, providing a first step towards the development of likelihood-free objective Bayesian inference procedures.

Probabilistic Methods · Variational Inference

Chuanhui Liu, Xiao Wang

This paper provides a comprehensive analysis of variational inference in latent variable models for survival analysis, emphasizing the distinctive challenges associated with applying variational methods to survival data. We identify a critical weakness in the existing methodology, demonstrating how a poorly designed variational distribution may hinder the objective of survival analysis tasks—modeling time-to-event distributions. We prove that the optimal variational distribution, which perfectly bounds the log-likelihood, may depend on the censoring mechanism. To address this issue, we propose censor-dependent variational inference (CDVI), tailored for latent variable models in survival analysis. More practically, we introduce CD-CVAE, a V-structure Variational Autoencoder (VAE) designed for the scalable implementation of CDVI. Further discussion extends some existing theories and training techniques to survival analysis. Extensive experiments validate our analysis and demonstrate significant improvements in the estimation of individual survival distributions.

Applications · Chemistry, Physics, and Earth Sciences

Louis Serrano, Armand Kassaï Koupaï, Thomas Wang, Pierre ERBACHER, patrick gallinari

Solving time-dependent parametric partial differential equations (PDEs) is challenging for data-driven methods, as these models must adapt to variations in parameters such as coefficients, forcing terms, and initial conditions. State-of-the-art neural surrogates perform adaptation through gradient-based optimization and meta-learning to implicitly encode the variety of dynamics from observations. This often comes with increased inference complexity. Inspired by the in-context learning capabilities of large language models (LLMs), we introduce Zebra, a novel generative auto-regressive transformer designed to solve parametric PDEs without requiring gradient adaptation at inference. By leveraging in-context information during both pre-training and inference, Zebra dynamically adapts to new tasks by conditioning on input sequences that incorporate context example trajectories. As a generative model, Zebra can be used to generate new trajectories and allows quantifying the uncertainty of the predictions. We evaluate Zebra across a variety of challenging PDE scenarios, demonstrating its adaptability, robustness, and superior performance compared to existing approaches.

Probabilistic Methods · Variational Inference

Rogelio A. Mancisidor, Robert Jenssen, Shujian Yu, Michael Kampffmeyer

Multimodal learning with variational autoencoders (VAEs) requires estimating joint distributions to evaluate the evidence lower bound (ELBO). Current methods, the product and mixture of experts, aggregate single-modality distributions assuming independence for simplicity, which is an overoptimistic assumption. This research introduces a novel methodology for aggregating single-modality distributions by exploiting the principle of *consensus of dependent experts* (CoDE), which circumvents the aforementioned assumption. Utilizing the CoDE method, we propose a novel ELBO that approximates the joint likelihood of the multimodal data by learning the contribution of each subset of modalities. The resulting CoDE-VAE model demonstrates better performance in terms of balancing the trade-off between generative coherence and generative quality, as well as generating more precise log-likelihood estimations. CoDE-VAE further minimizes the generative quality gap as the number of modalities increases. In certain cases, it reaches a generative quality similar to that of unimodal VAEs, which is a desirable property that is lacking in most current methods. Finally, the classification accuracy achieved by CoDE-VAE is comparable to that of state-of-the-art multimodal VAE models.

Applications · Chemistry, Physics, and Earth Sciences

Guancheng Wan, Zijie Huang, Wanjia Zhao, Xiao Luo, Yizhou Sun, Wei Wang

Coupled dynamical systems govern essential phenomena across physics, biology, and engineering, where components interact through complex dependencies. While Graph Ordinary Differential Equations (GraphODE) offer a powerful framework to model these systems, their **generalization** capabilities degrade severely under limited observational training data due to two fundamental flaws: (i) the entanglement of static attributes and dynamic states in the initialization process, and (ii) the reliance on context-specific coupling patterns during training, which hinders performance in unseen scenarios. In this paper, we propose a Generalizable GraphODE with disentanglement and regularization (GREAT) to address these challenges. Through systematic analysis via the Structural Causal Model, we identify backdoor paths that undermine generalization and design two key modules to mitigate their effects. The *Dynamic-Static Equilibrium Decoupler (DyStaED)* disentangles static and dynamic states via orthogonal subspace projections, ensuring robust initialization. Furthermore, the *Causal Mediation for Coupled Dynamics (CMCD)* employs variational inference to estimate latent causal factors, reducing spurious correlations and enhancing universal coupling dynamics. Extensive experiments across diverse dynamical systems demonstrate that ours outperforms state-of-the-art methods within both in-distribution and out-of-distribution.

Deep Learning · Large Language Models

Haoyun Jiang, Haolin li, jianwei zhang, Fei Huang, Qiang Hu, Minmin Sun, Shuai Xiao, Yong Li, Junyang Lin, Jiangchao Yao

Large language models (LLMs) have demonstrated strong capabilities in handling long-context tasks, but processing such long contexts remains challenging due to the substantial memory requirements and inference latency. In this work, we discover that certain attention heads exhibit sequential consistency in their attention patterns, which can be persistently identified using a coefficient-of-variation-based algorithm. Inspired by this observation, we propose CateKV, a hybrid KV cache method that retains only critical token information for consistent heads, thereby reducing KV cache size and computational overhead, while preserving the majority of KV pairs in adaptive heads to ensure high accuracy. We show the unique characteristics of our algorithm and its extension with existing acceleration methods. Comprehensive evaluations on long-context benchmarks show that, while maintaining accuracy comparable to full attention, CateKV reduces memory usage by up to $2.72\times$ and accelerates decoding by $2.18\times$ in single-sample inputs, and boosts throughput by $3.96\times$ in batch scenarios.

Probabilistic Methods · Bayesian Models and Methods

Gábor Pituk, Vik Shirvaikar, Tom Rainforth

We empirically investigate how well popular approximate inference algorithms for Bayesian Neural Networks (BNNs) respect the theoretical properties of Bayesian belief updating. We find strong evidence on synthetic regression and real-world image classification tasks that common BNN algorithms such as variational inference, Laplace approximation, SWAG, and SGLD fail to update in a consistent manner, forget about old data under sequential updates, and violate the predictive coherence properties that would be expected of Bayesian methods. These observed behaviors imply that care should be taken when treating BNNs as true Bayesian models, particularly when using them beyond static prediction settings, such as for active, continual, or transfer learning.

Deep Learning · Generative Models and Autoencoders

Longlin Yu, Jiajun Zha, Tong Yang, Tianyu Xie, Xiangyu Zhang, Gary Chan, Cheng Zhang

Semi-implicit distributions have shown great promise in variational inference and generative modeling. Hierarchical semi-implicit models, which stack multiple semi-implicit layers, enhance the expressiveness of semi-implicit distributions and can be used to accelerate diffusion models given pretrained score networks. However, their sequential training often suffers from slow convergence. In this paper, we introduce CoSIM, a continuous semi-implicit model that extends hierarchical semi-implicit models into a continuous framework. By incorporating a continuous transition kernel, CoSIM enables efficient, simulation-free training. Furthermore, we show that CoSIM achieves consistency with a carefully designed transition kernel, offering a novel approach for multistep distillation of generative models at the distributional level. Extensive experiments on image generation demonstrate that CoSIM performs on par or better than existing diffusion model acceleration methods, achieving superior performance on FD-DINOv2.

Deep Learning · Generative Models and Autoencoders

Deqian Kong, Minglu Zhao, Dehong Xu, Bo Pang, Shu Wang, Edouardo Honig, Zhangzhang Si, Chuan Li, Jianwen Xie, Sirui Xie 等

We propose a novel class of language models, Latent Thought Models (LTMs), which incorporate explicit latent thought vectors that follow an explicit prior model in latent space. These latent thought vectors guide the autoregressive generation of ground tokens through a Transformer decoder. Training employs a dual-rate optimization process within the classical variational Bayes framework: fast learning of local variational parameters for the posterior distribution of latent vectors (inference-time computation), and slow learning of global decoder parameters. Empirical studies reveal that LTMs possess additional scaling dimensions beyond traditional Large Language Models (LLMs), such as the number of iterations in inference-time computation and number of latent thought vectors. Higher sample efficiency can be achieved by increasing training compute per token, with further gains possible by trading model size for more inference steps. Designed based on these scaling properties, LTMs demonstrate superior sample and parameter efficiency compared to autoregressive models and discrete diffusion models. They significantly outperform these counterparts in validation perplexity and zero-shot language modeling tasks. Additionally, LTMs exhibit emergent few-shot in-context reasoning capabilities that scale with model size, and achieve competitive performance in conditional and unconditional text generation. The project page is available at [https://deqiankong.github.io/blogs/ltm](https://deqiankong.github.io/blogs/ltm).

Probabilistic Methods · Bayesian Models and Methods

Dario Coscia, Max Welling, Nicola Demo, Gianluigi Rozza

Autoregressive and recurrent networks have achieved remarkable progress across various fields, from weather forecasting to molecular generation and Large Language Models. Despite their strong predictive capabilities, these models lack a rigorous framework for addressing uncertainty, which is key in scientific applications such as PDE solving, molecular generation and machine l earning Force Fields.To address this shortcoming we present BARNN: a variational Bayesian Autoregressive and Recurrent Neural Network. BARNNs aim to provide a principled way to turn any autoregressive or recurrent model into its Bayesian version. BARNN is based on the variational dropout method, allowing to apply it to large recurrent neural networks as well. We also introduce a temporal version of the“Variational Mixtures of Posteriors” prior (tVAMP-prior) to make Bayesian inference efficient and well-calibrated. Extensive experiments on PDE modelling and molecular generation demonstrate that BARNN not only achieves comparable or superior accuracy compared to existing methods, but also excels in uncertainty quantification and modelling long-range dependencies.

Deep Learning · Large Language Models

Weihua Du, Yiming Yang, Sean Welleck

Multi-sample aggregation strategies, such as majority voting and best-of-N sampling, are widely used in contemporary large language models (LLMs) to enhance predictive accuracy across various tasks. A key challenge in this process is temperature selection, which significantly impacts model performance. Existing approaches either rely on a fixed default temperature or require labeled validation data for tuning, which are often scarce and difficult to obtain. This paper addresses the challenge of automatically identifying the (near)-optimal temperature for different LLMs using multi-sample aggregation strategies, without relying on task-specific validation data. We provide a comprehensive analysis of temperature’s role in performance optimization, considering variations in model architectures, datasets, task types, model sizes, and predictive accuracy. Furthermore, we propose a novel entropy-based metric for automated temperature optimization, which consistently outperforms fixed-temperature baselines. Additionally, we incorporate a stochastic process model to enhance interpretability, offering deeper insights into the relationship between temperature and model performance.

Probabilistic Methods · Variational Inference

Ngoc Quan Pham, Tuan Truong, Quyen Tran, Tan Nguyen, Dinh Phung, Trung Le

We introduce Interactive Bayesian Distributional Robustness (IBDR), a novel Bayesian inference framework that allows modeling the interactions between particles, thereby enhancing ensemble quality through increased particle diversity. IBDR is grounded in a generalized theoretical framework that connects the distributional population loss with the approximate posterior, motivating a practical dual optimization procedure that enforces distributional robustness while fostering particle diversity. We evaluate IBDR's performance against various baseline methods using the VTAB-1K benchmark and the common reasoning language task. The results consistently show that IBDR outperforms these baselines, underscoring its effectiveness in real-world applications.

General Machine Learning · Clustering

Arhit Chakrabarti, Yang Ni, Debdeep Pati, Bani Mallick

We consider the problem of clustering grouped data for which the observations may include group-specific variables in addition to the variables that are shared across groups. This type of data is quite common; for example, in cancer genomic studies, molecular information is available for all cancers whereas cancer-specific clinical information may only be available for certain cancers. Existing grouped clustering methods only consider the shared variables but ignore valuable information from the group-specific variables. To allow for these group-specific variables to aid in the clustering, we propose a novel Bayesian nonparametric approach, termed global-local (GLocal) Dirichlet process, that models the "global-local" structure of the observations across groups. We characterize the GLocal Dirichlet process using the stick-breaking representation and the representation as a limit of a finite mixture model. We theoretically quantify the approximation errors of the truncated prior, the corresponding finite mixture model, and the associated posterior distribution. We develop a fast variational Bayes algorithm for scalable posterior inference, which we illustrate with extensive simulations and a TCGA pan-gastrointestinal cancer dataset.

Deep Learning · Large Language Models

Aniket Vashishtha, Abhinav Kumar, Atharva Pandey, Abbavaram Gowtham Reddy, Kabir Ahuja, Vineeth N Balasubramanian, Amit Sharma

For text-based AI systems to interact in the real world, causal reasoning is an essential skill. Since interventional data is costly to generate, we study to what extent an agent can learn causal reasoning from passive data. Specifically, we consider an axiomatic training setup where an agent learns from multiple demonstrations of a causal axiom (or rule), rather than incorporating the axiom as an inductive bias or inferring it from data values. A key question is whether the agent would learn to generalize from the axiom demonstrations to new scenarios. For example, if a transformer model is trained on demonstrations of the causal transitivity axiom over small graphs, would it generalize to applying the transitivity axiom over large graphs? Our results, based on a novel axiomatic training scheme, indicate that such generalization is possible. We consider the task of inferring whether a variable causes another variable, given a causal graph structure. We find that a 67 million parameter transformer model, when trained on linear causal chains (along with some noisy variations) can generalize well to new kinds of graphs, including longer causal chains, causal chains with reversed order, and graphs with branching; even when it is not explicitly trained for such settings. Our model performs at par (or even better) than many larger language models such as GPT-4, Gemini Pro, and Phi-3. Overall, our axiomatic training framework provides a new paradigm of learning causal reasoning from passive data that can be used to learn arbitrary axioms, as long as sufficient demonstrations can be generated.

Applications · Computer Vision

Hao Dai, Jagmohan Chauhan

Continual Generalized Category Discovery (C-GCD) faces a critical challenge: incrementally learning new classes from unlabeled data streams while preserving knowledge of old classes. Existing methods struggle with catastrophic forgetting, especially when unlabeled data mixes known and novel categories. We address this by analyzing C-GCD’s forgetting dynamics through a Bayesian lens, revealing that covariance misalignment between old and new classes drives performance degradation. Building on this insight, we propose Variational Bayes C-GCD (VB-CGCD), a novel framework that integrates variational inference with covariance-aware nearest-class-mean classification. VB-CGCD adaptively aligns class distributions while suppressing pseudo-label noise via stochastic variational updates. Experiments show VB-CGCD surpasses prior art by +15.21% with the overall accuracy in the final session on standard benchmarks. We also introduce a new challenging benchmark with only 10% labeled data and extended online phases—VB-CGCD achieves a 67.86% final accuracy, significantly higher than state-of-the-art (38.55%), demonstrating its robust applicability across diverse scenarios. Code is available at: https://github.com/daihao42/VB-CGCD

Deep Learning · Robustness

Jonas Möller, Lukas Pirch, Felix Weissberg, Sebastian Baunsgaard, Thorsten Eisenhofer, Konrad Rieck

Linear algebra is a cornerstone of neural network inference. The efficiency of popular frameworks, such as TensorFlow and PyTorch, critically depends on backend libraries providing highly optimized matrix multiplications and convolutions. A diverse range of these backends exists across platforms, including Intel MKL, Nvidia CUDA, and Apple Accelerate. Although these backends provide equivalent functionality, subtle variations in their implementations can lead to seemingly negligible differences during inference. In this paper, we investigate these minor discrepancies and demonstrate how they can be selectively amplified by adversaries. Specifically, we introduce *Chimera examples*, inputs to models that elicit conflicting predictions depending on the employed backend library. These inputs can even be constructed with integer values, creating a vulnerability exploitable from real-world input domains. We analyze the prevalence and extent of the underlying attack surface and propose corresponding defenses to mitigate this threat.

Probabilistic Methods · Variational Inference

Zijian Liang, Kai Niu, Changshuo Wang, Jin Xu, Ping Zhang

Recent contributions of semantic information theory reveal the set-element relationship between semantic and syntactic information, represented as synonymous relationships. In this paper, we propose a synonymous variational inference (SVI) method based on this synonymity viewpoint to re-analyze the perceptual image compression problem. It takes perceptual similarity as a typical synonymous criterion to build an ideal synonymous set (Synset), and approximate the posterior of its latent synonymous representation with a parametric density by minimizing a partial semantic KL divergence. This analysis theoretically proves that the optimization direction of perception image compression follows a triple tradeoff that can cover the existing rate-distortion-perception schemes. Additionally, we introduce synonymous image compression (SIC), a new image compression scheme that corresponds to the analytical process of SVI, and implement a progressive SIC codec to fully leverage the model's capabilities. Experimental results demonstrate comparable rate-distortion-perception performance using a single progressive SIC codec, thus verifying the effectiveness of our proposed analysis method.

General Machine Learning · Causality

Xin Wang, Shengfei Lyu, Luo Chi, Xiren Zhou, Huanhuan Chen

A key challenge in personalized healthcare is identifying optimal intervention sequences to guide temporal systems toward target outcomes, a novel problem we formalize as counterfactual target achievement. In addressing this problem, directly adopting counterfactual estimation methods face compounding errors due to the unobservability of counterfactuals. To overcome this, we propose Variational Counterfactual Intervention Planning (VCIP), which reformulates the problem by modeling the conditional likelihood of achieving target outcomes, implemented through variational inference. By leveraging the g-formula to bridge the gap between interventional and observational log-likelihoods, VCIP enables reliable training from observational data. Experiments on both synthetic and real-world datasets show that VCIP significantly outperforms existing methods in target achievement accuracy.

Deep Learning · Generative Models and Autoencoders

Jaehyeon Kim, Taehong Moon, Keon Lee, Jaewoong Cho

We introduce ResGen, an efficient Residual Vector Quantization (RVQ)-based generative model for high-fidelity generation with fast sampling. RVQ improves data fidelity by increasing the number of quantization steps, referred to as depth, but deeper quantization typically increases inference steps in generative models. To address this, ResGen directly predicts the vector embedding of collective tokens rather than individual ones, ensuring that inference steps remain independent of RVQ depth. Additionally, we formulate token masking and multi-token prediction within a probabilistic framework using discrete diffusion and variational inference. We validate the efficacy and generalizability of the proposed method on two challenging tasks across different modalities: conditional image generation on ImageNet 256×256 and zero-shot text-to-speech synthesis. Experimental results demonstrate that ResGen outperforms autoregressive counterparts in both tasks, delivering superior performance without compromising sampling speed. Furthermore, as we scale the depth of RVQ, our generative models exhibit enhanced generation fidelity or faster sampling speeds compared to similarly sized baseline models.

Deep Learning · Graph Neural Networks

Federico Errica, Henrik Christiansen, Viktor Zaverkin, Takashi Maruyama, Mathias Niepert, Francesco Alesiani

Long-range interactions are essential for the correct description of complex systems in many scientific fields. The price to pay for including them in the calculations, however, is a dramatic increase in the overall computational costs. Recently, deep graph networks have been employed as efficient, data-driven models for predicting properties of complex systems represented as graphs. These models rely on a message passing strategy that should, in principle, capture long-range information without explicitly modeling the corresponding interactions. In practice, most deep graph networks cannot really model long-range dependencies due to the intrinsic limitations of (synchronous) message passing, namely oversmoothing, oversquashing, and underreaching. This work proposes a general framework that \textit{learns to mitigate} these limitations: within a variational inference framework, we endow message passing architectures with the ability to adapt their depth and filter messages along the way. With theoretical and empirical arguments, we show that this strategy better captures long-range interactions, by competing with the state of the art on five node and graph prediction datasets.