NeurIPS 2024 Papers

Reliable prediction of protein variant effects is crucial for both protein optimization and for advancing biological understanding. For practical use in protein engineering, it is important that we can also provide reliable uncertainty estimates for our predictions, and while prediction accuracy has seen much progress in recent years, uncertainty metrics are rarely reported. We here provide a Gaussian process regression model, Kermut, with a novel composite kernel for modeling mutation similarity, which obtains state-of-the-art performance for supervised protein variant effect prediction while also offering estimates of uncertainty through its posterior. An analysis of the quality of the uncertainty estimates demonstrates that our model provides meaningful levels of overall calibration, but that instance-specific uncertainty calibration remains more challenging.

Generalizable 3D Gaussian splitting (3DGS) can reconstruct new scenes from sparse-view observations in a feed-forward inference manner, eliminating the need for scene-specific retraining required in conventional 3DGS. However, existing methods rely heavily on epipolar priors, which can be unreliable in complex real-world scenes, particularly in non-overlapping and occluded regions. In this paper, we propose eFreeSplat, an efficient feed-forward 3DGS-based model for generalizable novel view synthesis that operates independently of epipolar line constraints. To enhance multiview feature extraction with 3D perception, we employ a self-supervised Vision Transformer (ViT) with cross-view completion pre-training on large-scale datasets. Additionally, we introduce an Iterative Cross-view Gaussians Alignment method to ensure consistent depth scales across different views. Our eFreeSplat represents a new paradigm for generalizable novel view synthesis. We evaluate eFreeSplat on wide-baseline novel view synthesis tasks using the RealEstate10K and ACID datasets. Extensive experiments demonstrate that eFreeSplat surpasses state-of-the-art baselines that rely on epipolar priors, achieving superior geometry reconstruction and novel view synthesis quality.

We study clustering under anisotropic Gaussian Mixture Models (GMMs), where covariance matrices from different clusters are unknown and are not necessarily the identity matrix. We analyze two anisotropic scenarios: homogeneous, with identical covariance matrices, and heterogeneous, with distinct matrices per cluster. For these models, we derive minimax lower bounds that illustrate the critical influence of covariance structures on clustering accuracy. To solve the clustering problem, we consider a variant of Lloyd's algorithm, adapted to estimate and utilize covariance information iteratively. We prove that the adjusted algorithm not only achieves the minimax optimality but also converges within a logarithmic number of iterations, thus bridging the gap between theoretical guarantees and practical efficiency.

In this paper, we propose Generalizable and Animatable Gaussian head Avatar (GAGA) for one-shot animatable head avatar reconstruction. Existing methods rely on neural radiance fields, leading to heavy rendering consumption and low reenactment speeds. To address these limitations, we generate the parameters of 3D Gaussians from a single image in a single forward pass. The key innovation of our work is the proposed dual-lifting method, which produces high-fidelity 3D Gaussians that capture identity and facial details. Additionally, we leverage global image features and the 3D morphable model to construct 3D Gaussians for controlling expressions. After training, our model can reconstruct unseen identities without specific optimizations and perform reenactment rendering at real-time speeds. Experiments show that our method exhibits superior performance compared to previous methods in terms of reconstruction quality and expression accuracy. We believe our method can establish new benchmarks for future research and advance applications of digital avatars.

3D Gaussian splatting (3DGS) has shown promising results in image rendering and surface reconstruction. However, its potential in volumetric reconstruction tasks, such as X-ray computed tomography, remains under-explored. This paper introduces R$^2$-Gaussian, the first 3DGS-based framework for sparse-view tomographic reconstruction. By carefully deriving X-ray rasterization functions, we discover a previously unknown \emph{integration bias} in the standard 3DGS formulation, which hampers accurate volume retrieval. To address this issue, we propose a novel rectification technique via refactoring the projection from 3D to 2D Gaussians. Our new method presents three key innovations: (1) introducing tailored Gaussian kernels, (2) extending rasterization to X-ray imaging, and (3) developing a CUDA-based differentiable voxelizer. Experiments on synthetic and real-world datasets demonstrate that our method outperforms state-of-the-art approaches in accuracy and efficiency. Crucially, it delivers high-quality results in 4 minutes, which is 12$\times$ faster than NeRF-based methods and on par with traditional algorithms.

Recently, Gaussian splatting has received more and more attention in the field of static scene rendering. Due to the low computational overhead and inherent flexibility of explicit representations, plane-based explicit methods are popular ways to predict deformations for Gaussian-based dynamic scene rendering models. However, plane-based methods rely on the inappropriate low-rank assumption and excessively decompose the space-time 4D encoding, resulting in overmuch feature overlap and unsatisfactory rendering quality. To tackle these problems, we propose Grid4D, a dynamic scene rendering model based on Gaussian splatting and employing a novel explicit encoding method for the 4D input through the hash encoding. Different from plane-based explicit representations, we decompose the 4D encoding into one spatial and three temporal 3D hash encodings without the low-rank assumption. Additionally, we design a novel attention module that generates the attention scores in a directional range to aggregate the spatial and temporal features. The directional attention enables Grid4D to more accurately fit the diverse deformations across distinct scene components based on the spatial encoded features. Moreover, to mitigate the inherent lack of smoothness in explicit representation methods, we introduce a smooth regularization term that keeps our model from the chaos of deformation prediction. Our experiments demonstrate that Grid4D significantly outperforms the state-of-the-art models in visual quality and rendering speed.

Equivariant deep learning architectures exploit symmetries in learning problems to improve the sample efficiency of neural-network-based models and their ability to generalise. However, when modelling real-world data, learning problems are often not *exactly* equivariant, but only approximately. For example, when estimating the global temperature field from weather station observations, local topographical features like mountains break translation equivariance. In these scenarios, it is desirable to construct architectures that can flexibly depart from exact equivariance in a data-driven way. Current approaches to achieving this cannot usually be applied out-of-the-box to any architecture and symmetry group. In this paper, we develop a general approach to achieving this using existing equivariant architectures. Our approach is agnostic to both the choice of symmetry group and model architecture, making it widely applicable. We consider the use of approximately equivariant architectures in neural processes (NPs), a popular family of meta-learning models. We demonstrate the effectiveness of our approach on a number of synthetic and real-world regression experiments, showing that approximately equivariant NP models can outperform both their non-equivariant and strictly equivariant counterparts.

The premise of semi-supervised learning (SSL) is that combining labeled and unlabeled data yields significantly more accurate models. Despite empirical successes, the theoretical understanding of SSL is still far from complete. In this work, we study SSL for high dimensional sparse Gaussian classification. To construct an accurate classifier a key task is feature selection, detecting the few variables that separate the two classes. For this SSL setting, we analyze information theoretic lower bounds for accurate feature selection as well as computational lower bounds, assuming the low-degree likelihood hardness conjecture. Our key contribution is the identification of a regime in the problem parameters (dimension, sparsity, number of labeled and unlabeled samples) where SSL is guaranteed to be advantageous for classification. Specifically, there is a regime where it is possible to construct in polynomial time an accurate SSL classifier. However, any computationally efficient supervised or unsupervised learning schemes, that separately use only the labeled or unlabeled data would fail. Our work highlights the provable benefits of combining labeled and unlabeled data for classification and feature selection in high dimensions. We present simulations that complement our theoretical analysis.

We consider the problem of active learning for global sensitivity analysis of expensive black-box functions. Our aim is to efficiently learn the importance of different input variables, e.g., in vehicle safety experimentation, we study the impact of the thickness of various components on safety objectives. Since function evaluations are expensive, we use active learning to prioritize experimental resources where they yield the most value. We propose novel active learning acquisition functions that directly target key quantities of derivative-based global sensitivity measures (DGSMs) under Gaussian process surrogate models. We showcase the first application of active learning directly to DGSMs, and develop tractable uncertainty reduction and information gain acquisition functions for these measures. Through comprehensive evaluation on synthetic and real-world problems, our study demonstrates how these active learning acquisition strategies substantially enhance the sample efficiency of DGSM estimation, particularly with limited evaluation budgets. Our work paves the way for more efficient and accurate sensitivity analysis in various scientific and engineering applications.

Bayesian optimization is a popular framework for efficiently tackling black-box search problems. As a rule, these algorithms operate by iteratively choosing what to evaluate next until some predefined budget has been exhausted. We investigate replacing this de facto stopping rule with criteria based on the probability that a point satisfies a given set of conditions. We focus on the prototypical example of an $(\epsilon, \delta)$-criterion: stop when a solution has been found whose value is within $\epsilon > 0$ of the optimum with probability at least $1 - \delta$ under the model. For Gaussian process priors, we show that Bayesian optimization satisfies this criterion under mild technical assumptions. Further, we give a practical algorithm for evaluating Monte Carlo stopping rules in a manner that is both sample efficient and robust to estimation error. These findings are accompanied by empirical results which demonstrate the strengths and weaknesses of the proposed approach.

Although 3D Gaussian Splatting has been widely studied because of its realistic and efficient novel-view synthesis, it is still challenging to extract a high-quality surface from the point-based representation. Previous works improve the surface by incorporating geometric priors from the off-the-shelf normal estimator. However, there are two main limitations: 1) Supervising normal rendered from 3D Gaussians updates only the rotation parameter while neglecting other geometric parameters; 2) The inconsistency of predicted normal maps across multiple views may lead to severe reconstruction artifacts. In this paper, we propose a Depth-Normal regularizer that directly couples normal with other geometric parameters, leading to full updates of the geometric parameters from normal regularization. We further propose a confidence term to mitigate inconsistencies of normal predictions across multiple views. Moreover, we also introduce a densification and splitting strategy to regularize the size and distribution of 3D Gaussians for more accurate surface modeling. Compared with Gaussian-based baselines, experiments show that our approach obtains better reconstruction quality and maintains competitive appearance quality at faster training speed and 100+ FPS rendering. Our code will be made open-source upon paper acceptance.

We develop a technique to design efficiently computable estimators for sparse linear regression in the simultaneous presence of two adversaries: oblivious and adaptive. Consider the model $y^*=X^*\beta^*+ \eta$ where $X^*$ is an $n\times d$ random design matrix, $\beta^*\in \mathbb{R}^d$ is a $k$-sparse vector, and the noise $\eta$ is independent of $X^*$ and chosen by the \emph{oblivious adversary}. Apart from the independence of $X^*$, we only require a small fraction entries of $\eta$ to have magnitude at most $1$. The \emph{adaptive adversary} is allowed to arbitrarily corrupt an $\varepsilon$-fraction of the samples $(X_1^*, y_1^*),\ldots, (X_n^*, y_n^*)$. Given the $\varepsilon$-corrupted samples $(X_1, y_1),\ldots, (X_n, y_n)$, the goal is to estimate $\beta^*$. We assume that the rows of $X^*$ are iid samples from some $d$-dimensional distribution $\mathcal{D}$ with zero mean and (unknown) covariance matrix $\Sigma$ with bounded condition number. We design several robust algorithms that outperform the state of the art even in the special case of Gaussian noise $\eta \sim N(0,1)^n$. In particular, we provide a polynomial-time algorithm that with high probability recovers $\beta^*$ up to error $O(\sqrt{\varepsilon})$ as long as $n \ge \tilde{O}(k^2/\varepsilon)$, only assuming some bounds on the third and the fourth moments of $\mathcal{D}$. In addition, prior to this work, even in the special case of Gaussian design $\mathcal{D} = N(0,\Sigma)$ and noise $\eta \sim N(0,1)$, no polynomial time algorithm was known to achieve error $o(\sqrt{\varepsilon})$ in the sparse setting $n < d^2$. We show that under some assumptions on the fourth and the eighth moments of $\mathcal{D}$, there is a polynomial-time algorithm that achieves error $o(\sqrt{\varepsilon})$ as long as $n \ge \tilde{O}(k^4 / \varepsilon^3)$. For Gaussian distribution $\mathcal{D} = N(0,\Sigma)$, this algorithm achieves error $O(\varepsilon^{3/4})$. Moreover, our algorithm achieves error $o(\sqrt{\varepsilon})$ for all log-concave distributions if $\varepsilon \le 1/\text{polylog(d)}$. Our algorithms are based on the filtering of the covariates that uses sum-of-squares relaxations, and weighted Huber loss minimization with $\ell_1$ regularizer. We provide a novel analysis of weighted penalized Huber loss that is suitable for heavy-tailed designs in the presence of two adversaries. Furthermore, we complement our algorithmic results with Statistical Query lower bounds, providing evidence that our estimators are likely to have nearly optimal sample complexity.

Reinforcement learning algorithms typically rely on the assumption that the environment dynamics and value function can be expressed in terms of a Markovian state representation. However, when state information is only partially observable, how can an agent learn such a state representation, and how can it detect when it has found one? We introduce a metric that can accomplish both objectives, without requiring access to---or knowledge of---an underlying, unobservable state space. Our metric, the λ-discrepancy, is the difference between two distinct temporal difference (TD) value estimates, each computed using TD(λ) with a different value of λ. Since TD(λ=0) makes an implicit Markov assumption and TD(λ=1) does not, a discrepancy between these estimates is a potential indicator of a non-Markovian state representation. Indeed, we prove that the λ-discrepancy is exactly zero for all Markov decision processes and almost always non-zero for a broad class of partially observable environments. We also demonstrate empirically that, once detected, minimizing the λ-discrepancy can help with learning a memory function to mitigate the corresponding partial observability. We then train a reinforcement learning agent that simultaneously constructs two recurrent value networks with different λ parameters and minimizes the difference between them as an auxiliary loss. The approach scales to challenging partially observable domains, where the resulting agent frequently performs significantly better (and never performs worse) than a baseline recurrent agent with only a single value network.

Diffusion models (DMs) have shown remarkable capabilities in generating realistic high-quality images, audios, and videos. They benefit significantly from extensive pre-training on large-scale datasets, including web-crawled data with paired data and conditions, such as image-text and image-class pairs. Despite rigorous filtering, these pre-training datasets often inevitably contain corrupted pairs where conditions do not accurately describe the data. This paper presents the first comprehensive study on the impact of such corruption in pre-training data of DMs. We synthetically corrupt ImageNet-1K and CC3M to pre-train and evaluate over $50$ conditional DMs. Our empirical findings reveal that various types of slight corruption in pre-training can significantly enhance the quality, diversity, and fidelity of the generated images across different DMs, both during pre-training and downstream adaptation stages. Theoretically, we consider a Gaussian mixture model and prove that slight corruption in the condition leads to higher entropy and a reduced 2-Wasserstein distance to the ground truth of the data distribution generated by the corruptly trained DMs. Inspired by our analysis, we propose a simple method to improve the training of DMs on practical datasets by adding condition embedding perturbations (CEP). CEP significantly improves the performance of various DMs in both pre-training and downstream tasks. We hope that our study provides new insights into understanding the data and pre-training processes of DMs.

Despite the remarkable empirical performance of Transformers, their theoretical understanding remains elusive. Here, we consider a deep multi-head self-attention network, that is closely related to Transformers yet analytically tractable. We develop a statistical mechanics theory of Bayesian learning in this model, deriving exact equations for the network's predictor statistics under the finite-width thermodynamic limit, i.e., $N,P\rightarrow\infty$, $P/N=\mathcal{O}(1)$, where $N$ is the network width and $P$ is the number of training examples. Our theory shows that the predictor statistics are expressed as a sum of independent kernels, each one pairing different "attention paths", defined as information pathways through different attention heads across layers. The kernels are weighted according to a "task-relevant kernel combination" mechanism that aligns the total kernel with the task labels. As a consequence, this interplay between attention paths enhances generalization performance. Experiments confirm our findings on both synthetic and real-world sequence classification tasks. Finally, our theory explicitly relates the kernel combination mechanism to properties of the learned weights, allowing for a qualitative transfer of its insights to models trained via gradient descent. As an illustration, we demonstrate an efficient size reduction of the network, by pruning those attention heads that are deemed less relevant by our theory.

It is well known that eigenfunctions of a kernel play a crucial role in kernel regression. Through several examples, we demonstrate that even with the same set of eigenfunctions, the order of these functions significantly impacts regression outcomes. Simplifying the model by diagonalizing the kernel, we introduce an over-parameterized gradient descent in the realm of sequence model to capture the effects of various orders of a fixed set of eigen-functions. This method is designed to explore the impact of varying eigenfunction orders. Our theoretical results show that the over-parameterization gradient flow can adapt to the underlying structure of the signal and significantly outperform the vanilla gradient flow method. Moreover, we also demonstrate that deeper over-parameterization can further enhance the generalization capability of the model. These results not only provide a new perspective on the benefits of over-parameterization and but also offer insights into the adaptivity and generalization potential of neural networks beyond the kernel regime.

Machine learning models provide alternatives for efficiently recognizing complex patterns from data, but the main concern in applying them to modeling physical systems stems from their physics-agnostic design, leading to learning methods that lack interpretability, robustness, and data efficiency. This paper mitigates this concern by incorporating the Helmholtz-Hodge decomposition into a Gaussian process model, leading to a versatile framework that simultaneously learns the curl-free and divergence-free components of a dynamical system. Learning a predictive model in this form facilitates the exploitation of symmetry priors. In addition to improving predictive power, these priors make the model indentifiable, thus the identified features can be linked to comprehensible scientific properties of the system. We show that compared to baseline models, our model achieves better predictive performance on several benchmark dynamical systems while allowing physically meaningful decomposition of the systems from noisy and sparse data.

In this work, we study the generalizability of diffusion models by looking into the hidden properties of the learned score functions, which are essentially a series of deep denoisers trained on various noise levels. We observe that as diffusion models transition from memorization to generalization, their corresponding nonlinear diffusion denoisers exhibit increasing linearity. This discovery leads us to investigate the linear counterparts of the nonlinear diffusion models, which are a series of linear models trained to match the function mappings of the nonlinear diffusion denoisers. Surprisingly, these linear denoisers are approximately the optimal denoisers for a multivariate Gaussian distribution characterized by the empirical mean and covariance of the training dataset. This finding implies that diffusion models have the inductive bias towards capturing and utilizing the Gaussian structure (covariance information) of the training dataset for data generation. We empirically demonstrate that this inductive bias is a unique property of diffusion models in the generalization regime, which becomes increasingly evident when the model's capacity is relatively small compared to the training dataset size. In the case that the model is highly overparameterized, this inductive bias emerges during the initial training phases before the model fully memorizes its training data. Our study provides crucial insights into understanding the notable strong generalization phenomenon recently observed in real-world diffusion models.

This paper studies the problem of estimating physical properties (system identification) through visual observations. To facilitate geometry-aware guidance in physical property estimation, we introduce a novel hybrid framework that leverages 3D Gaussian representation to not only capture explicit shapes but also enable the simulated continuum to render object masks as 2D shape surrogates during training. We propose a new dynamic 3D Gaussian framework based on motion factorization to recover the object as 3D Gaussian point sets across different time states. Furthermore, we develop a coarse-to-fine filling strategy to generate the density fields of the object from the Gaussian reconstruction, allowing for the extraction of object continuums along with their surfaces and the integration of Gaussian attributes into these continuum. In addition to the extracted object surfaces, the Gaussian-informed continuum also enables the rendering of object masks during simulations, serving as 2D-shape guidance for physical property estimation. Extensive experimental evaluations demonstrate that our pipeline achieves state-of-the-art performance across multiple benchmarks and metrics. Additionally, we illustrate the effectiveness of the proposed method through real-world demonstrations, showcasing its practical utility. Our project page is at https://jukgei.github.io/project/gic.