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Deep Learning · Generative Models and Autoencoders

Siddharth Ramchandran, Manuel Haussmann, Harri Lähdesmäki

Bayesian optimisation (BO) using a Gaussian process (GP)-based surrogate model is a powerful tool for solving black-box optimisation problems but does not scale well to high-dimensional data. Previous works have proposed to use variational autoencoders (VAEs) to project high-dimensional data onto a low-dimensional latent space and to implement BO in the inferred latent space. In this work, we propose a conditional generative model for efficient high-dimensional BO that uses a GP surrogate model together with GP prior VAEs. A GP prior VAE extends the standard VAE by conditioning the generative and inference model on auxiliary covariates, capturing complex correlations across samples with a GP. Our model incorporates the observed target quantity values as auxiliary covariates learning a structured latent space that is better suited for the GP-based BO surrogate model. It handles partially observed auxiliary covariates using a unifying probabilistic framework and can also incorporate additional auxiliary covariates that may be available in real-world applications. We demonstrate that our method improves upon existing latent space BO methods on simulated datasets as well as on commonly used benchmarks.

Applications · Physics

Yehui Tang, Mabiao Long, Junchi Yan

Quantum state property estimation (QPE) is a fundamental challenge in quantum many-body problems in physics and chemistry, involving the prediction of characteristics such as correlation and entanglement entropy through statistical analysis of quantum measurement data. Recent advances in deep learning have provided powerful solutions, predominantly using auto-regressive models. These models generally assume an intrinsic ordering among qubits, aiming to approximate the classical probability distribution through sequential training. However, unlike natural language, the entanglement structure of qubits lacks an inherent ordering, hurting the motivation of such models. In this paper, we introduce a novel, non-autoregressive generative model called \textbf{\model}, designed for \underline{\textbf{Qua}}ntum state property estimation using \underline{\textbf{Di}}ffusion \underline{\textbf{M}}odels. \model progressively denoises Gaussian noise into the distribution corresponding to the quantum state, encouraging equal, unbiased treatment of all qubits. \model learns to map physical variables to properties of the ground state of the parameterized Hamiltonian during offline training. Afterwards one can sample from the learned distribution conditioned on previously unseen physical variables to collect measurement records and employ post-processing to predict properties of unknown quantum states. We evaluate \model on large-scale QPE tasks using classically simulated data on the 1D anti-ferromagnetic Heisenberg model with the system size up to 100 qubits. Numerical results demonstrate that \model outperforms baseline models, particularly auto-regressive approaches, under conditions of limited measurement data during training and reduced sample complexity during inference.

Theory · Learning Theory

Yuchen Liang, Peizhong Ju, Yingbin Liang, Ness Shroff

Accelerated diffusion models hold the potential to significantly enhance the efficiency of standard diffusion processes. Theoretically, these models have been shown to achieve faster convergence rates than the standard $\mathcal O(1/\epsilon^2)$ rate of vanilla diffusion models, where $\epsilon$ denotes the target accuracy. However, current theoretical studies have established the acceleration advantage only for restrictive target distribution classes, such as those with smoothness conditions imposed along the entire sampling path or with bounded support. In this work, we significantly broaden the target distribution classes with a new accelerated stochastic DDPM sampler. In particular, we show that it achieves accelerated performance for three broad distribution classes not considered before. Our first class relies on the smoothness condition posed only to the target density $q_0$, which is far more relaxed than the existing smoothness conditions posed to all $q_t$ along the entire sampling path. Our second class requires only a finite second moment condition, allowing for a much wider class of target distributions than the existing finite-support condition. Our third class is Gaussian mixture, for which our result establishes the first acceleration guarantee. Moreover, among accelerated DDPM type samplers, our results specialized for bounded-support distributions show an improved dependency on the data dimension $d$. Our analysis introduces a novel technique for establishing performance guarantees via constructing a tilting factor representation of the convergence error and utilizing Tweedie's formula to handle Taylor expansion terms. This new analytical framework may be of independent interest.

Applications · Computer Vision

Lin-Zhuo Chen, Kangjie Liu, Youtian Lin, Zhihao Li, Siyu Zhu, Xun Cao, Yao Yao

3D Gaussian Splatting (3DGS) has achieved excellent rendering quality with fast training and rendering speed. However, its optimization process lacks explicit geometric constraints, leading to suboptimal geometric reconstruction in regions with sparse or no observational input views. In this work, we try to mitigate the issue by incorporating a pre-trained matching prior to the 3DGS optimization process. We introduce Flow Distillation Sampling (FDS), a technique that leverages pre-trained geometric knowledge to bolster the accuracy of the Gaussian radiance field. Our method employs a strategic sampling technique to target unobserved views adjacent to the input views, utilizing the optical flow calculated from the matching model (Prior Flow) to guide the flow analytically calculated from the 3DGS geometry (Radiance Flow). Comprehensive experiments in depth rendering, mesh reconstruction, and novel view synthesis showcase the significant advantages of FDS over state-of-the-art methods. Additionally, our interpretive experiments and analysis aim to shed light on the effects of FDS on geometric accuracy and rendering quality, potentially providing readers with insights into its performance.

Applications · Genetics, Cell Biology, Health, etc

Zhenyi Zhang, Tiejun Li, Peijie Zhou

Reconstructing dynamics using samples from sparsely time-resolved snapshots is an important problem in both natural sciences and machine learning. Here, we introduce a new deep learning approach for solving regularized unbalanced optimal transport (RUOT) and inferring continuous unbalanced stochastic dynamics from observed snapshots. Based on the RUOT form, our method models these dynamics without requiring prior knowledge of growth and death processes or additional information, allowing them to be learned directly from data. Theoretically, we explore the connections between the RUOT and Schrödinger bridge problem and discuss the key challenges and potential solutions. The effectiveness of our method is demonstrated with a synthetic gene regulatory network, high-dimensional Gaussian Mixture Model, and single-cell RNA-seq data from blood development. Compared with other methods, our approach accurately identifies growth and transition patterns, eliminates false transitions, and constructs the Waddington developmental landscape. Our code is available at: [https://github.com/zhenyiizhang/DeepRUOT](https://github.com/zhenyiizhang/DeepRUOT).

Probabilistic Methods · Gaussian Processes

Weibin Chen, Azhir Mahmood, Michel Tsamados, So Takao

The rapid growth of earth observation systems calls for a scalable approach to interpolate remote-sensing observations. These methods in principle, should acquire more information about the observed field as data grows. Gaussian processes (GPs) are candidate model choices for interpolation. However, due to their poor scalability, they usually rely on inducing points for inference, which restricts their expressivity. Moreover, commonly imposed assumptions such as stationarity prevents them from capturing complex patterns in the data. While deep GPs can overcome this issue, training and making inference with them are difficult, again requiring crude approximations via inducing points. In this work, we instead approach the problem through Bayesian deep learning, where spatiotemporal fields are represented by deep neural networks, whose layers share the inductive bias of stationary GPs on the plane/sphere via random feature expansions. This allows one to (1) capture high frequency patterns in the data, and (2) use mini-batched gradient descent for large scale training. We experiment on various remote sensing data at local/global scales, showing that our approach produce competitive or superior results to existing methods, with well-calibrated uncertainties.

Social Aspects · Fairness, Equity, Justice and Safety

Yepeng Liu, Yiren Song, Hai Ci, Yu Zhang, Haofan Wang, Mike Zheng Shou, Yuheng Bu

Image watermark techniques provide an effective way to assert ownership, deter misuse, and trace content sources, which has become increasingly essential in the era of large generative models. A critical attribute of watermark techniques is their robustness against various manipulations. In this paper, we introduce a watermark removal approach capable of effectively nullifying state-of-the-art watermarking techniques. Our primary insight involves regenerating the watermarked image starting from a \textbf{clean Gaussian noise} via a controllable diffusion model, utilizing the extracted semantic and spatial features from the watermarked image. The semantic control adapter and the spatial control network are specifically trained to control the denoising process towards ensuring image quality and enhancing consistency between the cleaned image and the original watermarked image. To achieve a smooth trade-off between watermark removal performance and image consistency, we further propose an adjustable and controllable regeneration scheme. This scheme adds varying numbers of noise steps to the latent representation of the watermarked image, followed by a controlled denoising process starting from this noisy latent representation. As the number of noise steps increases, the latent representation progressively approaches clean Gaussian noise, facilitating the desired trade-off. We apply our watermark removal methods across various watermarking techniques, and the results demonstrate that our methods offer superior visual consistency/quality and enhanced watermark removal performance compared to existing regeneration approaches. Our code is available at \url{https://github.com/yepengliu/CtrlRegen}.

Toni Liu, Nicolas Boulle, Raphaël Sarfati, Christopher Earls

Large language models (LLMs) demonstrate remarkable emergent abilities to perform in-context learning across various tasks, including time series forecasting. This work investigates LLMs' ability to estimate probability density functions (PDFs) from data observed in-context; such density estimation (DE) is a fundamental task underlying many probabilistic modeling problems. We leverage the Intensive Principal Component Analysis (InPCA) to visualize and analyze the in-context learning dynamics of LLaMA-2 models. Our main finding is that these LLMs all follow similar learning trajectories in a low-dimensional InPCA space, which are distinct from those of traditional density estimation methods like histograms and Gaussian kernel density estimation (KDE). We interpret the LLaMA in-context DE process as a KDE with an adaptive kernel width and shape. This custom kernel model captures a significant portion of LLaMA's behavior despite having only two parameters. We further speculate on why LLaMA's kernel width and shape differs from classical algorithms, providing insights into the mechanism of in-context probabilistic reasoning in LLMs.Our codebase, along with a 3D visualization of an LLM's in-context learning trajectory, is publicly available at https://github.com/AntonioLiu97/LLMICL_inPCA.

Miscellaneous Aspects of Machine Learning · Causality

Bao Duong, Sunil Gupta, Thin Nguyen

Existing score-based methods for directed acyclic graph (DAG) learning from observational data struggle to recover the causal graph accurately and sample-efficiently. To overcome this, in this study, we propose DrBO (DAG recovery via Bayesian Optimization)—a novel DAG learning framework leveraging Bayesian optimization (BO) to find high-scoring DAGs. We show that, by sophisticatedly choosing the promising DAGs to explore, we can find higher-scoring ones much more efficiently. To address the scalability issues of conventional BO in DAG learning, we replace Gaussian Processes commonly employed in BO with dropout neural networks, trained in a continual manner, which allows for (i) flexibly modeling the DAG scores without overfitting, (ii) incorporation of uncertainty into the estimated scores, and (iii) scaling with the number of evaluations. As a result, DrBO is computationally efficient and can find the accurate DAG in fewer trials and less time than existing state-of-the-art methods. This is demonstrated through an extensive set of empirical evaluations on many challenging settings with both synthetic and real data. Our implementation is available at https://github.com/baosws/DrBO.

Reinforcement Learning · Everything Else

Tetsuro Morimura, Satoshi Hayakawa

Reward evaluation of episodes becomes a bottleneck in a broad range of reinforcement learning tasks. Our aim in this paper is to select a small but representative subset of a large batch of episodes, only on which we actually compute rewards for more efficient policy gradient iterations. We build a Gaussian process modeling of discounted returns or rewards to derive a positive definite kernel on the space of episodes, run an ``episodic" kernel quadrature method to compress the information of sample episodes, and pass the reduced episodes to the policy network for gradient updates. We present the theoretical background of this procedure as well as its numerical illustrations in MuJoCo tasks.

Deep Learning · Generative Models and Autoencoders

Haitao Yang, Yuan Dong, Hanwen Jiang, Dejia Xu, Georgios Pavlakos, Qixing Huang

Using the latent diffusion model has proven effective in developing novel 3D generation techniques. To harness the latent diffusion model, a key challenge is designing a high-fidelity and efficient representation that links the latent space and the 3D space. In this paper, we introduce Atlas Gaussians, a novel representation for feed-forward native 3D generation. Atlas Gaussians represent a shape as the union of local patches, and each patch can decode 3D Gaussians. We parameterize a patch as a sequence of feature vectors and design a learnable function to decode 3D Gaussians from the feature vectors. In this process, we incorporate UV-based sampling, enabling the generation of a sufficiently large, and theoretically infinite, number of 3D Gaussian points. The large amount of 3D Gaussians enables the generation of high-quality details. Moreover, due to local awareness of the representation, the transformer-based decoding procedure operates on a patch level, ensuring efficiency. We train a variational autoencoder to learn the Atlas Gaussians representation, and then apply a latent diffusion model on its latent space for learning 3D Generation. Experiments show that our approach outperforms the prior arts of feed-forward native 3D generation. Project page: https://yanghtr.github.io/projects/atlas_gaussians.

Applications · Computer Vision

Xiaoyu Xiong, Changyu Hu, Chunru Lin, Pingchuan Ma, Chuang Gan, Tao Du

We present TopoGaussian, a holistic, particle-based pipeline for inferring the interior structure of an opaque object from easily accessible photos and videos as input. Traditional mesh-based approaches require tedious and error-prone mesh filling and fixing process, while typically output rough boundary surface. Our pipeline combines Gaussian Splatting with a novel, versatile particle-based differentiable simulator that simultaneously accommodates constitutive model, actuator, and collision, without interference with mesh. Based on the gradients from this simulator, we provide flexible choice of topology representation for optimization, including particle, neural implicit surface, and quadratic surface. The resultant pipeline takes easily accessible photos and videos as input and outputs the topology that matches the physical characteristics of the input. We demonstrate the efficacy of our pipeline on a synthetic dataset and four real-world tasks with 3D-printed prototypes. Compared with existing mesh-based method, our pipeline is 5.26x faster on average with improved shape quality. These results highlight the potential of our pipeline in 3D vision, soft robotics, and manufacturing applications.

Applications · Computer Vision

Hongze CHEN, Zehong Lin, Jun Zhang

We present GI-GS, a novel inverse rendering framework that leverages 3D Gaussian Splatting (3DGS) and deferred shading to achieve photo-realistic novel view synthesis and relighting. In inverse rendering, accurately modeling the shading processes of objects is essential for achieving high-fidelity results. Therefore, it is critical to incorporate global illumination to account for indirect lighting that reaches an object after multiple bounces across the scene. Previous 3DGS-based methods have attempted to model indirect lighting by characterizing indirect illumination as learnable lighting volumes or additional attributes of each Gaussian, while using baked occlusion to represent shadow effects. These methods, however, fail to accurately model the complex physical interactions between light and objects, making it impossible to construct realistic indirect illumination during relighting. To address this limitation, we propose to calculate indirect lighting using efficient path tracing with deferred shading. In our framework, we first render a G-buffer to capture the detailed geometry and material properties of the scene. Then, we perform physically-based rendering (PBR) only for direct lighting. With the G-buffer and previous rendering results, the indirect lighting can be calculated through a lightweight path tracing. Our method effectively models indirect lighting under any given lighting conditions, thereby achieving better novel view synthesis and competitive relighting. Quantitative and qualitative results show that our GI-GS outperforms existing baselines in both rendering quality and efficiency. Project page: https://stopaimme.github.io/GI-GS-site/.

Hengyu Fu, Zehao Dou, Jiawei Guo, Mengdi Wang, Minshuo Chen

Diffusion Transformer, the backbone of Sora for video generation, successfully scales the capacity of diffusion models, pioneering new avenues for high-fidelity sequential data generation. Unlike static data such as images, sequential data consists of consecutive data frames indexed by time, exhibiting rich spatial and temporal dependencies. These dependencies represent the underlying dynamic model and are critical to validate the generated data. In this paper, we make the first theoretical step towards bridging diffusion transformers for capturing spatial-temporal dependencies. Specifically, we establish score approximation and distribution estimation guarantees of diffusion transformers for learning Gaussian process data with covariance functions of various decay patterns. We highlight how the spatial-temporal dependencies are captured and affect learning efficiency. Our study proposes a novel transformer approximation theory, where the transformer acts to unroll an algorithm. We support our theoretical results by numerical experiments, providing strong evidence that spatial-temporal dependencies are captured within attention layers, aligning with our approximation theory.

Deep Learning · Attention Mechanisms

Piotr Indyk, Michael Kapralov, Kshiteej Jitesh Sheth, Tal Wagner

Motivated by the problem of fast processing of attention matrices, we study fast algorithms for computing matrix-vector products for asymmetric Gaussian Kernel matrices $K\in \mathbb{R}^{n\times n}$. $K$'s columns are indexed by a set of $n$ keys $k_1,k_2\ldots, k_n\in \mathbb{R}^d$, rows by a set of $n$ queries $q_1,q_2,\ldots,q_n\in \mathbb{R}^d $, and its $i,j$ entry is $K_{ij} = e^{-\|q_i-k_j\|_2^2/2\sigma^2}$ for some bandwidth parameter $\sigma>0$. Given a vector $x\in \mathbb{R}^n$ and error parameter $\epsilon>0$, our task is to output a $y\in \mathbb{R}^n$ such that $\|Kx-y\|_2\leq \epsilon \|x\|_2$ in time subquadratic in $n$ and linear in $d$. Our algorithms rely on the following modelling assumption about the matrices $K$: the sum of the entries of $K$ scales linearly in $n$, as opposed to worst case quadratic growth. We validate this assumption experimentally, for Gaussian kernel matrices encountered in various settings such as fast attention computation in LLMs. Under this assumption, we obtain the first subquadratic time algorithm for kernel matrix-vector multiplication for unrestricted vectors.

Deep Learning · Theory

Zechen Zhang, Haim Sompolinsky

The infinite width limit of random neural networks is known to result in Neural Networks as Gaussian Process (NNGP) (Lee et al. (2018)), characterized by task-independent kernels. It is widely accepted that larger network widths contribute to improved generalization (Park et al. (2019)). However, this work challenges this notion by investigating the narrow width limit of the Bayesian Parallel BranchingNeural Network (BPB-NN), an architecture that resembles neural networks with residual blocks. We demonstrate that when the width of a BPB-NN is significantly smaller compared to the number of training examples, each branch exhibits more robust learning due to a symmetry breaking of branches in kernel renormalization. Surprisingly, the performance of a BPB-NN in the narrow width limit is generally superior to or comparable to that achieved in the wide width limit in bias-limited scenarios. Furthermore, the readout norms of each branch in the narrow width limit are mostly independent of the architectural hyperparameters but generally reflective of the nature of the data. We demonstrate such phenomenon primarily in the branching graph neural networks, where each branch represents a different order of convolutions of the graph; we also extend the results to other more general architectures such as the residual-MLP and demonstrate that the narrow width effect is a general feature of the branching networks. Our results characterize a newly defined narrow-width regime for parallel branching networks in general.

Optimization · Zero-order and Black-box Optimization

Taiwo Adebiyi, Bach Do, Ruda Zhang

Bayesian optimization devolves the global optimization of a costly objective function to the global optimization of a sequence of acquisition functions. This inner-loop optimization can be catastrophically difficult if it involves posterior sample paths, especially in higher dimensions. We introduce an efficient global optimization strategy for posterior samples based on global rootfinding. It provides gradient-based optimizers with two sets of judiciously selected starting points, designed to combine exploration and exploitation. The number of starting points can be kept small without sacrificing optimization quality. Remarkably, even with just one point from each set, the global optimum is discovered most of the time. The algorithm scales practically linearly to high dimensions, breaking the curse of dimensionality. For Gaussian process Thompson sampling (GP-TS), we demonstrate remarkable improvement in both inner- and outer-loop optimization, surprisingly outperforming alternatives like EI and GP-UCB in most cases. Our approach also improves the performance of other posterior sample-based acquisition functions, such as variants of entropy search. Furthermore, we propose a sample-average formulation of GP-TS, which has a parameter to explicitly control exploitation and can be computed at the cost of one posterior sample.

Probabilistic Methods · Bayesian Models and Methods

Chukwudi Paul Obite, Zhi Chang, Keyan Wu, Shiwei Lan

The effectiveness of statistical and machine learning methods depends on how well data features are characterized. Developing informative and interpretable latent representations with controlled complexity is essential for visualizing data structure and for facilitating efficient model building through dimensionality reduction. Latent variable models, such as Gaussian Process Latent Variable Models (GP-LVM), have become popular for learning complex, nonlinear representations as alternatives to Principal Component Analysis (PCA). In this paper, we propose a novel class of latent variable models based on the recently introduced Q-exponential process (QEP), which generalizes GP-LVM with a tunable complexity parameter, $q>0$. Our approach, the \emph{Q-exponential Process Latent Variable Model (QEP-LVM)}, subsumes GP-LVM as a special case when $q=2$, offering greater flexibility in managing representation complexity while enhancing interpretability. To ensure scalability, we incorporate sparse variational inference within a Bayesian training framework. We establish connections between QEP-LVM and probabilistic PCA, demonstrating its superior performance through experiments on datasets such as the Swiss roll, oil flow, and handwritten digits.

Theory · Probabilistic Methods

David Dalton, Alan Lazarus, Hao Gao, Dirk Husmeier

We introduce a framework for designing boundary constrained Gaussian process (BCGP) priors for exact enforcement of linear boundary conditions, and apply it to the machine learning of (initial) boundary value problems involving linear partial differential equations (PDEs).In contrast to existing work, we illustrate how to design boundary constrained mean and kernel functions for all classes of boundary conditions typically used in PDE modelling, namely Dirichlet, Neumann, Robin and mixed conditions. Importantly, this is done in a manner which allows for both forward and inverse problems to be naturally accommodated. We prove that the BCGP kernel has a universal representational capacity under Dirichlet conditions, and establish a formal equivalence between BCGPs and boundary-constrained neural networks (BCNNs) of infinite width.Finally, extensive numerical experiments are performed involving several linear PDEs, the results of which demonstrate the effectiveness and robustness of BCGP inference in the presence of sparse, noisy data.

Reinforcement Learning · Deep RL

Yu Heng Hung, Kai-Jie Lin, Yu-Heng Lin, Chien-Yi Wang, Cheng Sun, Ping-Chun Hsieh

Bayesian optimization (BO) offers an efficient pipeline for optimizing black-box functions with the help of a Gaussian process prior and an acquisition function (AF). Recently, in the context of single-objective BO, learning-based AFs witnessed promising empirical results given its favorable non-myopic nature. Despite this, the direct extension of these approaches to multi-objective Bayesian optimization (MOBO) suffer from the hypervolume identifiability issue, which results from the non-Markovian nature of MOBO problems. To tackle this, inspired by the non-Markovian RL literature and the success of Transformers in language modeling, we present a generalized deep Q-learning framework and propose BOFormer, which substantiates this framework for MOBO via sequence modeling. Through extensive evaluation, we demonstrate that BOFormer constantly achieves better performance than the benchmark rule-based and learning-based algorithms in various synthetic MOBO and real-world multi-objective hyperparameter optimization problems.