NeurIPS 2023 Papers

Transformers have achieved great success in machine learning applications. Normalization techniques, such as Layer Normalization (LayerNorm, LN) and Root Mean Square Normalization (RMSNorm), play a critical role in accelerating and stabilizing the training of Transformers. While LayerNorm recenters and rescales input vectors, RMSNorm only rescales the vectors by their RMS value. Despite being more computationally efficient, RMSNorm may compromise the representation ability of Transformers. There is currently no consensus regarding the preferred normalization technique, as some models employ LayerNorm while others utilize RMSNorm, especially in recent large language models. It is challenging to convert Transformers with one normalization to the other type. While there is an ongoing disagreement between the two normalization types, we propose a solution to unify two mainstream Transformer architectures, Pre-LN and Pre-RMSNorm Transformers. By removing the inherent redundant mean information in the main branch of Pre-LN Transformers, we can reduce LayerNorm to RMSNorm, achieving higher efficiency. We further propose the Compressed RMSNorm (CRMSNorm) and Pre-CRMSNorm Transformer based on a lossless compression of the zero-mean vectors. We formally establish the equivalence of Pre-LN, Pre-RMSNorm, and Pre-CRMSNorm Transformer variants in both training and inference. It implies that Pre-LN Transformers can be substituted with Pre-(C)RMSNorm counterparts at almost no cost, offering the same arithmetic functionality along with free efficiency improvement. Experiments demonstrate that we can reduce the training and inference time of Pre-LN Transformers by 1% - 10%.

Artificial intelligence for scientific discovery has recently generated significant interest within the machine learning and scientific communities, particularly in the domains of chemistry, biology, and material discovery. For these scientific problems, molecules serve as the fundamental building blocks, and machine learning has emerged as a highly effective and powerful tool for modeling their geometric structures. Nevertheless, due to the rapidly evolving process of the field and the knowledge gap between science ({\eg}, physics, chemistry, \& biology) and machine learning communities, a benchmarking study on geometrical representation for such data has not been conducted. To address such an issue, in this paper, we first provide a unified view of the current symmetry-informed geometric methods, classifying them into three main categories: invariance, equivariance with spherical frame basis, and equivariance with vector frame basis. Then we propose a platform, coined Geom3D, which enables benchmarking the effectiveness of geometric strategies. Geom3D contains 16 advanced symmetry-informed geometric representation models and 14 geometric pretraining methods over 52 diverse tasks, including small molecules, proteins, and crystalline materials. We hope that Geom3D can, on the one hand, eliminate barriers for machine learning researchers interested in exploring scientific problems; and, on the other hand, provide valuable guidance for researchers in computational chemistry, structural biology, and materials science, aiding in the informed selection of representation techniques for specific applications. The source code is available on \href{https://github.com/chao1224/Geom3D}{the GitHub repository}.

In this paper, we propose a novel and powerful method to harness Bayesian optimization for variational quantum eigensolvers (VQEs) - a hybrid quantum-classical protocol used to approximate the ground state of a quantum Hamiltonian. Specifically, we derive a *VQE-kernel* which incorporates important prior information about quantum circuits: the kernel feature map of the VQE-kernel exactly matches the known functional form of the VQE's objective function and thereby significantly reduces the posterior uncertainty. Moreover, we propose a novel acquisition function for Bayesian optimization called \emph{Expected Maximum Improvement over Confident Regions} (EMICoRe) which can actively exploit the inductive bias of the VQE-kernel by treating regions with low predictive uncertainty as indirectly "observed". As a result, observations at as few as three points in the search domain are sufficient to determine the complete objective function along an entire one-dimensional subspace of the optimization landscape. Our numerical experiments demonstrate that our approach improves over state-of-the-art baselines.

We study a spiked Wigner problem with an inhomogeneous noise profile. Our aim in this problem is to recover the signal passed through an inhomogeneous low-rank matrix channel. While the information-theoretic performances are well-known, we focus on the algorithmic problem. First, we derive an approximate message-passing algorithm (AMP) for the inhomogeneous problem and show that its rigorous state evolution coincides with the information-theoretic optimal Bayes fixed-point equations. Second, we deduce a simple and efficient spectral method that outperforms PCA and is shown to match the information-theoretic transition.

Spectral clustering has gained popularity for clustering non-convex data due to its simplicity and effectiveness. It is essential to construct a similarity graph using a high-quality affinity measure that models the local neighborhood relations among the data samples. However, incomplete data can lead to inaccurate affinity measures, resulting in degraded clustering performance. To address these issues, we propose an imputation-free framework with two novel approaches to improve spectral clustering on incomplete data. Firstly, we introduce a new kernel correction method that enhances the quality of the kernel matrix estimated on incomplete data with a theoretical guarantee, benefiting classical spectral clustering on pre-defined kernels. Secondly, we develop a series of affinity learning methods that equip the self-expressive framework with $\ell_p$-norm to construct an intrinsic affinity matrix with an adaptive extension. Our methods outperform existing data imputation and distance calibration techniques on benchmark datasets, offering a promising solution to spectral clustering on incomplete data in various real-world applications.

We introduce a data-driven learning framework that assimilates two powerful ideas: ideal large eddy simulation (LES) from turbulence closure modeling and neural stochastic differential equations (SDE) for stochastic modeling. The ideal LES models the LES flow by treating each full-order trajectory as a random realization of the underlying dynamics, as such, the effect of small-scales is marginalized to obtain the deterministic evolution of the LES state. However, ideal LES is analytically intractable. In our work, we use a latent neural SDE to model the evolution of the stochastic process and an encoder-decoder pair for transforming between the latent space and the desired ideal flow field. This stands in sharp contrast to other types of neural parameterization of closure models where each trajectory is treated as a deterministic realization of the dynamics. We show the effectiveness of our approach (niLES – neural ideal LES) on two challenging chaotic dynamical systems: Kolmogorov flow at a Reynolds number of 20,000 and flow past a cylinder at Reynolds number 500. Compared to competing methods, our method can handle non-uniform geometries using unstructured meshes seamlessly. In particular, niLES leads to trajectories with more accurate statistics and enhances stability, particularly for long-horizon rollouts. (Source codes and datasets will be made publicly available.)

Deep neural networks are notorious for defying theoretical treatment. However, when the number of parameters in each layer tends to infinity, the network function is a Gaussian process (GP) and quantitatively predictive description is possible. Gaussian approximation allows one to formulate criteria for selecting hyperparameters, such as variances of weights and biases, as well as the learning rate. These criteria rely on the notion of criticality defined for deep neural networks. In this work we describe a new practical way to diagnose criticality. We introduce *partial Jacobians* of a network, defined as derivatives of preactivations in layer $l$ with respect to preactivations in layer $l_0\leq l$. We derive recurrence relations for the norms of partial Jacobians and utilize these relations to analyze criticality of deep fully connected neural networks with LayerNorm and/or residual connections. We derive and implement a simple and cheap numerical test that allows one to select optimal initialization for a broad class of deep neural networks; containing fully connected, convolutional and normalization layers. Using these tools we show quantitatively that proper stacking of the LayerNorm (applied to preactivations) and residual connections leads to an architecture that is critical for any initialization. Finally, we apply our methods to analyze ResNet and MLP-Mixer architectures; demonstrating the everywhere-critical regime.

While Gaussian processes are a mainstay for various engineering and scientific applications, the uncertainty estimates don't satisfy frequentist guarantees and can be miscalibrated in practice. State-of-the-art approaches for designing calibrated models rely on inflating the Gaussian process posterior variance, which yields confidence intervals that are potentially too coarse. To remedy this, we present a calibration approach that generates predictive quantiles using a computation inspired by the vanilla Gaussian process posterior variance but using a different set of hyperparameters chosen to satisfy an empirical calibration constraint. This results in a calibration approach that is considerably more flexible than existing approaches, which we optimize to yield tight predictive quantiles. Our approach is shown to yield a calibrated model under reasonable assumptions. Furthermore, it outperforms existing approaches in sharpness when employed for calibrated regression.

We introduce GAUCHE, an open-source library for GAUssian processes in CHEmistry. Gaussian processes have long been a cornerstone of probabilistic machine learning, affording particular advantages for uncertainty quantification and Bayesian optimisation. Extending Gaussian processes to molecular representations, however, necessitates kernels defined over structured inputs such as graphs, strings and bit vectors. By providing such kernels in a modular, robust and easy-to-use framework, we seek to enable expert chemists and materials scientists to make use of state-of-the-art black-box optimization techniques. Motivated by scenarios frequently encountered in practice, we showcase applications for GAUCHE in molecular discovery, chemical reaction optimisation and protein design. The codebase is made available at https://github.com/leojklarner/gauche.

Bayesian bandit algorithms with approximate Bayesian inference have been widely used in real-world applications. However, there is a large discrepancy between the superior practical performance of these approaches and their theoretical justification. Previous research only indicates a negative theoretical result: Thompson sampling could have a worst-case linear regret $\Omega(T)$ with a constant threshold on the inference error measured by one $\alpha$-divergence. To bridge this gap, we propose an Enhanced Bayesian Upper Confidence Bound (EBUCB) framework that can efficiently accommodate bandit problems in the presence of approximate inference. Our theoretical analysis demonstrates that for Bernoulli multi-armed bandits, EBUCB can achieve the optimal regret order $O(\log T)$ if the inference error measured by two different $\alpha$-divergences is less than a constant, regardless of how large this constant is. To our best knowledge, our study provides the first theoretical regret bound that is better than $o(T)$ in the setting of constant approximate inference error. Furthermore, in concordance with the negative results in previous studies, we show that only one bounded $\alpha$-divergence is insufficient to guarantee a sub-linear regret.

We study a novel variant of the parameterized bandits problem in which the learner can observe additional auxiliary feedback that is correlated with the observed reward. The auxiliary feedback is readily available in many real-life applications, e.g., an online platform that wants to recommend the best-rated services to its users can observe the user's rating of service (rewards) and collect additional information like service delivery time (auxiliary feedback). In this paper, we first develop a method that exploits auxiliary feedback to build a reward estimator with tight confidence bounds, leading to a smaller regret. We then characterize the regret reduction in terms of the correlation coefficient between reward and its auxiliary feedback. Experimental results in different settings also verify the performance gain achieved by our proposed method.

High-energy collisions at the Large Hadron Collider (LHC) provide valuable insights into open questions in particle physics. However, detector effects must be corrected before measurements can be compared to certain theoretical predictions or measurements from other detectors. Methods to solve this inverse problem of mapping detector observations to theoretical quantities of the underlying collision are essential parts of many physics analyses at the LHC. We investigate and compare various generative deep learning methods to approximate this inverse mapping. We introduce a novel unified architecture, termed latent variational diffusion models, which combines the latent learning of cutting-edge generative art approaches with an end-to-end variational framework. We demonstrate the effectiveness of this approach for reconstructing global distributions of theoretical kinematic quantities, as well as for ensuring the adherence of the learned posterior distributions to known physics constraints. Our unified approach achieves a distribution-free distance to the truth of over 20 times smaller than non-latent state-of-the-art baseline and 3 times smaller than traditional latent diffusion models.

Data-driven machine learning approaches are being increasingly used to solve partial differential equations (PDEs). They have shown particularly striking successes when training an operator, which takes as input a PDE in some family, and outputs its solution. However, the architectural design space, especially given structural knowledge of the PDE family of interest, is still poorly understood. We seek to remedy this gap by studying the benefits of weight-tied neural network architectures for steady-state PDEs. To achieve this, we first demonstrate that the solution of most steady-state PDEs can be expressed as a fixed point of a non-linear operator. Motivated by this observation, we propose FNO-DEQ, a deep equilibrium variant of the FNO architecture that directly solves for the solution of a steady-state PDE as the infinite-depth fixed point of an implicit operator layer using a black-box root solver and differentiates analytically through this fixed point resulting in $\mathcal{O}(1)$ training memory. Our experiments indicate that FNO-DEQ-based architectures outperform FNO-based baselines with $4\times$ the number of parameters in predicting the solution to steady-state PDEs such as Darcy Flow and steady-state incompressible Navier-Stokes. Finally, we show FNO-DEQ is more robust when trained with datasets with more noisy observations than the FNO-based baselines, demonstrating the benefits of using appropriate inductive biases in architectural design for different neural network based PDE solvers. Further, we show a universal approximation result that demonstrates that FNO-DEQ can approximate the solution to any steady-state PDE that can be written as a fixed point equation.

Analysis of compressible turbulent flows is essential for applications related to propulsion, energy generation, and the environment. Here, we present BLASTNet 2.0, a 2.2 TB network-of-datasets containing 744 full-domain samples from 34 high-fidelity direct numerical simulations, which addresses the current limited availability of 3D high-fidelity reacting and non-reacting compressible turbulent flow simulation data. With this data, we benchmark a total of 49 variations of five deep learning approaches for 3D super-resolution - which can be applied for improving scientific imaging, simulations, turbulence models, as well as in computer vision applications. We perform neural scaling analysis on these models to examine the performance of different machine learning (ML) approaches, including two scientific ML techniques. We demonstrate that (i) predictive performance can scale with model size and cost, (ii) architecture matters significantly, especially for smaller models, and (iii) the benefits of physics-based losses can persist with increasing model size. The outcomes of this benchmark study are anticipated to offer insights that can aid the design of 3D super-resolution models, especially for turbulence models, while this data is expected to foster ML methods for a broad range of flow physics applications. This data is publicly available with download links and browsing tools consolidated at https://blastnet.github.io.

Fourier neural operators (FNOs) can learn highly nonlinear mappings between function spaces, and have recently become a popular tool for learning responses of complex physical systems. However, to achieve good accuracy and efficiency, FNOs rely on the Fast Fourier transform (FFT), which is restricted to modeling problems on rectangular domains. To lift such a restriction and permit FFT on irregular geometries as well as topology changes, we introduce domain agnostic Fourier neural operator (DAFNO), a novel neural operator architecture for learning surrogates with irregular geometries and evolving domains. The key idea is to incorporate a smoothed characteristic function in the integral layer architecture of FNOs, and leverage FFT to achieve rapid computations, in such a way that the geometric information is explicitly encoded in the architecture. In our empirical evaluation, DAFNO has achieved state-of-the-art accuracy as compared to baseline neural operator models on two benchmark datasets of material modeling and airfoil simulation. To further demonstrate the capability and generalizability of DAFNO in handling complex domains with topology changes, we consider a brittle material fracture evolution problem. With only one training crack simulation sample, DAFNO has achieved generalizability to unseen loading scenarios and substantially different crack patterns from the trained scenario. Our code and data accompanying this paper are available at https://github.com/ningliu-iga/DAFNO.

Innovation is a major driver of economic and social development, and information about many kinds of innovation is embedded in semi-structured data from patents and patent applications. Though the impact and novelty of innovations expressed in patent data are difficult to measure through traditional means, machine learning offers a promising set of techniques for evaluating novelty, summarizing contributions, and embedding semantics. In this paper, we introduce the Harvard USPTO Patent Dataset (HUPD), a large-scale, well-structured, and multi-purpose corpus of English-language patent applications filed to the United States Patent and Trademark Office (USPTO) between 2004 and 2018. With more than 4.5 million patent documents, HUPD is two to three times larger than comparable corpora. Unlike other NLP patent datasets, HUPD contains the inventor-submitted versions of patent applications, not the final versions of granted patents, allowing us to study patentability at the time of filing using NLP methods for the first time. It is also novel in its inclusion of rich structured data alongside the text of patent filings: By providing each application’s metadata along with all of its text fields, HUPD enables researchers to perform new sets of NLP tasks that leverage variation in structured covariates. As a case study on the types of research HUPD makes possible, we introduce a new task to the NLP community -- patent acceptance prediction. We additionally show the structured metadata provided in HUPD allows us to conduct explicit studies of concept shifts for this task. We find that performance on patent acceptance prediction decays when models trained in one context are evaluated on different innovation categories and over time. Finally, we demonstrate how HUPD can be used for three additional tasks: Multi-class classification of patent subject areas, language modeling, and abstractive summarization. Put together, our publicly-available dataset aims to advance research extending language and classification models to diverse and dynamic real-world data distributions.

Offline Reinforcement Learning (RL) has demonstrated promising results in various applications by learning policies from previously collected datasets, reducing the need for online exploration and interactions. However, real-world scenarios usually involve partial observability, which brings crucial challenges of the deployment of offline RL methods: i) the policy trained on data with full observability is not robust against the masked observations during execution, and ii) the information of which parts of observations are masked is usually unknown during training. In order to address these challenges, we present Offline RL with DiscrEte pRoxy representations (ORDER), a probabilistic framework which leverages novel state representations to improve the robustness against diverse masked observabilities. Specifically, we propose a discrete representation of the states and use a proxy representation to recover the states from masked partial observable trajectories. The training of ORDER can be compactly described as the following three steps. i) Learning the discrete state representations on data with full observations, ii) Training the decision module based on the discrete representations, and iii) Training the proxy discrete representations on the data with various partial observations, aligning with the discrete representations. We conduct extensive experiments to evaluate ORDER, showcasing its effectiveness in offline RL for diverse partially observable scenarios and highlighting the significance of discrete proxy representations in generalization performance. ORDER is a flexible framework to employ any offline RL algorithms and we hope that ORDER can pave the way for the deployment of RL policy against various partial observabilities in the real world.

A popular heuristic method for improving clustering results is to apply dimensionality reduction before running clustering algorithms. It has been observed that spectral-based dimensionality reduction tools, such as PCA or SVD, improve the performance of clustering algorithms in many applications. This phenomenon indicates that spectral method not only serves as a dimensionality reduction tool, but also contributes to the clustering procedure in some sense. It is an interesting question to understand the behavior of spectral steps in clustering problems. As an initial step in this direction, this paper studies the power of vanilla-SVD algorithm in the stochastic block model (SBM). We show that, in the symmetric setting, vanilla-SVD algorithm recovers all clusters correctly. This result answers an open question posed by Van Vu (Combinatorics Probability and Computing, 2018) in the symmetric setting.

Recently, the Deep Learning community has become interested in evolutionary optimization (EO) as a means to address hard optimization problems, e.g. meta-learning through long inner loop unrolls or optimizing non-differentiable operators. One core reason for this trend has been the recent innovation in hardware acceleration and compatible software -- making distributed population evaluations much easier than before. Unlike for gradient descent-based methods though, there is a lack of hyperparameter understanding and best practices for EO – arguably due to severely less `graduate student descent' and benchmarking being performed for EO methods. Additionally, classical benchmarks from the evolutionary community provide few practical insights for Deep Learning applications. This poses challenges for newcomers to hardware-accelerated EO and hinders significant adoption. Hence, we establish a new benchmark of EO methods (NEB) tailored toward Deep Learning applications and exhaustively evaluate traditional and meta-learned EO. We investigate core scientific questions including resource allocation, fitness shaping, normalization, regularization & scalability of EO. The benchmark is open-sourced at https://github.com/neuroevobench/neuroevobench under Apache-2.0 license.