Bayesian Inference
Structuring GUI Elements through Vision Language Models: Towards Action Space Generation
Xu, Yi, Zhang, Yesheng, Liu, Jiajia, Chen, Jingdong
Multimodal large language models (MLLMs) have emerged as pivotal tools in enhancing human-computer interaction. In this paper we focus on the application of MLLMs in the field of graphical user interface (GUI) elements structuring, where they assist in processing user instructions based on screen contents. Despite the promise of MLLMs, their performance in precisely generating UI element coordinates, a critical aspect of GUI understanding, is hindered by the nature of next-token prediction training. This challenge arises from the semantic void surrounding numerical UI coordinates in language representation spaces, necessitating a substantial and diverse dataset to bolster visual module capabilities. T o address these limitations, we introduce an IoU-Augmented Maximum Likelihood (IAML) training paradigm. Specifically, our approach involves a novel pipeline for IoU-based coordinate sampling to augment the training data, which considers the proximity to ground truth coordinates. This data augmentation strategy is then employed to fine-tune MLLMs under the IAML paradigm, which is designed to mitigate the exposure bias problem inherent in traditional maximum likelihood estimation. Through extensive experiments, we demonstrate the superior performance of our IAML training approach over traditional training paradigms.
Privacy Auditing Synthetic Data Release through Local Likelihood Attacks
Ward, Joshua, Wang, Chi-Hua, Cheng, Guang
Auditing the privacy leakage of synthetic data is an important but unresolved problem. Most existing privacy auditing frameworks for synthetic data rely on heuristics and unreasonable assumptions to attack the failure modes of generative models, exhibiting limited capability to describe and detect the privacy exposure of training data through synthetic data release. In this paper, we study designing Membership Inference Attacks (MIAs) that specifically exploit the observation that tabular generative models tend to significantly overfit to certain regions of the training distribution. Here, we propose Generative Likelihood Ratio Attack (Gen-LRA), a novel, computationally efficient No-Box MIA that, with no assumption of model knowledge or access, formulates its attack by evaluating the influence a test observation has in a surrogate model's estimation of a local likelihood ratio over the synthetic data. Assessed over a comprehensive benchmark spanning diverse datasets, model architectures, and attack parameters, we find that Gen-LRA consistently dominates other MIAs for generative models across multiple performance metrics. These results underscore Gen-LRA's effectiveness as a privacy auditing tool for the release of synthetic data, highlighting the significant privacy risks posed by generative model overfitting in real-world applications.
Priors Matter: Addressing Misspecification in Bayesian Deep Q-Learning
van der Vaart, Pascal R., Yorke-Smith, Neil, Spaan, Matthijs T. J.
Uncertainty quantification in reinforcement learning can greatly improve exploration and robustness. Approximate Bayesian approaches have recently been popularized to quantify uncertainty in model-free algorithms. However, so far the focus has been on improving the accuracy of the posterior approximation, instead of studying the accuracy of the prior and likelihood assumptions underlying the posterior. In this work, we demonstrate that there is a cold posterior effect in Bayesian deep Q-learning, where contrary to theory, performance increases when reducing the temperature of the posterior. To identify and overcome likely causes, we challenge common assumptions made on the likelihood and priors in Bayesian model-free algorithms. We empirically study prior distributions and show through statistical tests that the common Gaussian likelihood assumption is frequently violated. We argue that developing more suitable likelihoods and priors should be a key focus in future Bayesian reinforcement learning research and we offer simple, implementable solutions for better priors in deep Q-learning that lead to more performant Bayesian algorithms.
Controllable 3D Molecular Generation for Structure-Based Drug Design Through Bayesian Flow Networks and Gradient Integration
Choi, Seungyeon, Kim, Hwanhee, Park, Chihyun, Lee, Dahyeon, Lee, Seungyong, Kim, Yoonju, Park, Hyoungjoon, Kwon, Sein, Jo, Youngwan, Park, Sanghyun
Recent advances in Structure-based Drug Design (SBDD) have leveraged generative models for 3D molecular generation, predominantly evaluating model performance by binding affinity to target proteins. However, practical drug discovery necessitates high binding affinity along with synthetic feasibility and selectivity, critical properties that were largely neglected in previous evaluations. To address this gap, we identify fundamental limitations of conventional diffusion-based generative models in effectively guiding molecule generation toward these diverse pharmacological properties. We propose CByG, a novel framework extending Bayesian Flow Network into a gradient-based conditional generative model that robustly integrates property-specific guidance. Additionally, we introduce a comprehensive evaluation scheme incorporating practical benchmarks for binding affinity, synthetic feasibility, and selectivity, overcoming the limitations of conventional evaluation methods. Extensive experiments demonstrate that our proposed CByG framework significantly outperforms baseline models across multiple essential evaluation criteria, highlighting its effectiveness and practicality for real-world drug discovery applications.
Normalized Maximum Likelihood Code-Length on Riemannian Manifold Data Spaces
Fukuzawa, Kota, Suzuki, Atsushi, Yamanishi, Kenji
--In recent years, with the large-scale expansion of graph data, there has been an increased focus on Riemannian manifold data spaces other than Euclidean space. In particular, the development of hyperbolic spaces has been remarkable, and they have high expressive power for graph data with hierarchical structures. Normalized Maximum Likelihood (NML) is employed in regret minimization and model selection. However, existing formulations of NML have been developed primarily in Euclidean spaces and are inherently dependent on the choice of coordinate systems, making it non-trivial to extend NML to Riemannian manifolds. In this study, we define a new NML that reflects the geometric structure of Riemannian manifolds, called the Riemannian manifold NML (Rm-NML). This Rm-NML is invariant under coordinate transformations and coincides with the conventional NML under the natural parameterization in Euclidean space. We extend existing computational techniques for NML to the setting of Riemannian manifolds. Furthermore, we derive a method to simplify the computation of Rm-NML on Riemannian symmetric spaces, which encompass data spaces of growing interest such as hyperbolic spaces. T o illustrate the practical application of our proposed method, we explicitly computed the Rm-NML for normal distributions on hyperbolic spaces. With the recent increase in the scale of graph data, Riemannian manifold data spaces other than Euclidian spaces are attracting attention as latent spaces suitable for graph embedding [1, 2]. For example, hyperbolic spaces have been demonstrated to possess high expressive power for graph data with hierarchical structures [3]. Spherical spaces are particularly effective in representing graph data with cyclic structures [4]. Notably, research on hyperbolic spaces has been particularly remarkable[3]. Specifically, in the field of representation learning, methods that embed hierarchical structures into hyperbolic space have successfully represented such relationships using significantly lower-dimensional space compared to conventional methods based on Euclidean space, while preserving the essential relational information[2].
Towards Trustworthy Amortized Bayesian Model Comparison
Kucharskรฝ, ล imon, Mishra, Aayush, Habermann, Daniel, Radev, Stefan T., Bรผrkner, Paul-Christian
Amortized Bayesian model comparison (BMC) enables fast probabilistic ranking of models via simulation-based training of neural surrogates. However, the reliability of neural surrogates deteriorates when simulation models are misspecified - the very case where model comparison is most needed. Thus, we supplement simulation-based training with a self-consistency (SC) loss on unlabeled real data to improve BMC estimates under empirical distribution shifts. Using a numerical experiment and two case studies with real data, we compare amortized evidence estimates with and without SC against analytic or bridge sampling benchmarks. SC improves calibration under model misspecification when having access to analytic likelihoods. However, it offers limited gains with neural surrogate likelihoods, making it most practical for trustworthy BMC when likelihoods are exact.
Transfer Learning for Classification under Decision Rule Drift with Application to Optimal Individualized Treatment Rule Estimation
In this paper, we extend the transfer learning classification framework from regression function-based methods to decision rules. We propose a novel methodology for modeling posterior drift through Bayes decision rules. By exploiting the geometric transformation of the Bayes decision boundary, our method reformulates the problem as a low-dimensional empirical risk minimization problem. Under mild regularity conditions, we establish the consistency of our estimators and derive the risk bounds. Moreover, we illustrate the broad applicability of our method by adapting it to the estimation of optimal individualized treatment rules. Extensive simulation studies and analyses of real-world data further demonstrate both superior performance and robustness of our approach.
Latent Variable Modeling for Robust Causal Effect Estimation
Morimura, Tetsuro, Oka, Tatsushi, Suzuki, Yugo, Moriwaki, Daisuke
Latent variable models provide a powerful framework for incorporating and inferring unobserved factors in observational data. In causal inference, they help account for hidden factors influencing treatment or outcome, thereby addressing challenges posed by missing or unmeasured covariates. This paper proposes a new framework that integrates latent variable modeling into the double machine learning (DML) paradigm to enable robust causal effect estimation in the presence of such hidden factors. We consider two scenarios: one where a latent variable affects only the outcome, and another where it may influence both treatment and outcome. To ensure tractability, we incorporate latent variables only in the second stage of DML, separating representation learning from latent inference. We demonstrate the robustness and effectiveness of our method through extensive experiments on both synthetic and real-world datasets.
A Unified Theory of Language
A unified theory of language combines a Bayesian cognitive linguistic model of language processing, with the proposal that language evolved by sexual selection for the display of intelligence. The theory accounts for the major facts of language, including its speed and expressivity, and data on language diversity, pragmatics, syntax and semantics. The computational element of the theory is based on Construction Grammars. These give an account of the syntax and semantics of the worlds languages, using constructions and unification. Two novel elements are added to construction grammars: an account of language pragmatics, and an account of fast, precise language learning. Constructions are represented in the mind as graph like feature structures. People use slow general inference to understand the first few examples they hear of any construction. After that it is learned as a feature structure, and is rapidly applied by unification. All aspects of language (phonology, syntax, semantics, and pragmatics) are seamlessly computed by fast unification; there is no boundary between semantics and pragmatics. This accounts for the major puzzles of pragmatics, and for detailed pragmatic phenomena. Unification is Bayesian maximum likelihood pattern matching. This gives evolutionary continuity between language processing in the human brain, and Bayesian cognition in animal brains. Language is the basis of our mind reading abilities, our cooperation, self esteem and emotions; the foundations of human culture and society.
Unfolding AlphaFold's Bayesian Roots in Probability Kinematics
Hamelryck, Thomas, Mardia, Kanti V.
We present a novel theoretical interpretation of AlphaFold1 that reveals the potential of generalized Bayesian updating for probabilistic deep learning. The seminal breakthrough of AlphaFold1 in protein structure prediction by deep learning relied on a learned potential energy function, in contrast to the later end-to-end architectures of AlphaFold2 and AlphaFold3. While this potential was originally justified by referring to physical potentials of mean force (PMFs), we reinterpret AlphaFold1's potential as an instance of {\em probability kinematics} -- also known as {\em Jeffrey conditioning} -- a principled but under-recognised generalization of conventional Bayesian updating. Probability kinematics accommodates uncertain or {\em soft} evidence in the form of updated probabilities over a partition. This perspective reveals AlphaFold1's potential as a form of generalized Bayesian updating, rather than a thermodynamic potential. To confirm our probabilistic framework's scope and precision, we analyze a synthetic 2D model in which an angular random walk prior is updated with evidence on distances via probability kinematics, mirroring AlphaFold1's approach. This theoretical contribution connects AlphaFold1 to a broader class of well-justified Bayesian methods, allowing precise quantification, surpassing merely qualitative heuristics based on PMFs. Our contribution is theoretical: we replace AlphaFold1's heuristic analogy with a principled probabilistic framework, tested in a controlled synthetic setting where correctness can be assessed. More broadly, our results point to the considerable promise of probability kinematics for probabilistic deep learning, by allowing the formulation of complex models from a few simpler components.