NeurIPS 2023 Papers

Supervised machine learning approaches have been increasingly used in accelerating electronic structure prediction as surrogates of first-principle computational methods, such as density functional theory (DFT). While numerous quantum chemistry datasets focus on chemical properties and atomic forces, the ability to achieve accurate and efficient prediction of the Hamiltonian matrix is highly desired, as it is the most important and fundamental physical quantity that determines the quantum states of physical systems and chemical properties. In this work, we generate a new Quantum Hamiltonian dataset, named as QH9, to provide precise Hamiltonian matrices for 999 molecular dynamics trajectories and 130,831 stable molecular geometries, based on the QM9 dataset. By designing benchmark tasks with various molecules, we show that current machine learning models have the capacity to predict Hamiltonian matrices for arbitrary molecules. Both the QH9 dataset and the baseline models are provided to the community through an open-source benchmark, which can be highly valuable for developing machine learning methods and accelerating molecular and materials design for scientific and technological applications. Our benchmark is publicly available at https://github.com/divelab/AIRS/tree/main/OpenDFT/QHBench.

Hardware-specific optimizations in machine learning (ML) frameworks can cause numerical deviations of inference results. Quite surprisingly, despite using a fixed trained model and fixed input data, inference results are not consistent across platforms, and sometimes not even deterministic on the same platform. We study the causes of these numerical deviations for convolutional neural networks (CNN) on realistic end-to-end inference pipelines and in isolated experiments. Results from 75 distinct platforms suggest that the main causes of deviations on CPUs are differences in SIMD use, and the selection of convolution algorithms at runtime on GPUs. We link the causes and propagation effects to properties of the ML model and evaluate potential mitigations. We make our research code publicly available.

Uncertainty quantification (UQ) is important for reliability assessment and enhancement of machine learning models. In deep learning, uncertainties arise not only from data, but also from the training procedure that often injects substantial noises and biases. These hinder the attainment of statistical guarantees and, moreover, impose computational challenges on UQ due to the need for repeated network retraining. Building upon the recent neural tangent kernel theory, we create statistically guaranteed schemes to principally \emph{characterize}, and \emph{remove}, the uncertainty of over-parameterized neural networks with very low computation effort. In particular, our approach, based on what we call a procedural-noise-correcting (PNC) predictor, removes the procedural uncertainty by using only \emph{one} auxiliary network that is trained on a suitably labeled dataset, instead of many retrained networks employed in deep ensembles. Moreover, by combining our PNC predictor with suitable light-computation resampling methods, we build several approaches to construct asymptotically exact-coverage confidence intervals using as low as four trained networks without additional overheads.

Deep learning-based reaction predictors have undergone significant architectural evolution. However, their reliance on reactions from the US Patent Office results in a lack of interpretable predictions and limited generalizability to other chemistry domains, such as radical and atmospheric chemistry. To address these challenges, we introduce a new reaction predictor system, RMechRP, that leverages contrastive learning in conjunction with mechanistic pathways, the most interpretable representation of chemical reactions. Specifically designed for radical reactions, RMechRP provides different levels of interpretation of chemical reactions. We develop and train multiple deep-learning models using RMechDB, a public database of radical reactions, to establish the first benchmark for predicting radical reactions. Our results demonstrate the effectiveness of RMechRP in providing accurate and interpretable predictions of radical reactions, and its potential for various applications in atmospheric chemistry.

Quantum neural networks (QNNs) have been a promising framework in pursuing near-term quantum advantage in various fields, where many applications can be viewed as learning a quantum state that encodes useful data. As a quantum analog of probability distribution learning, quantum state learning is theoretically and practically essential in quantum machine learning. In this paper, we develop a no-go theorem for learning an unknown quantum state with QNNs even starting from a high-fidelity initial state. We prove that when the loss value is lower than a critical threshold, the probability of avoiding local minima vanishes exponentially with the qubit count, while only grows polynomially with the circuit depth. The curvature of local minima is concentrated to the quantum Fisher information times a loss-dependent constant, which characterizes the sensibility of the output state with respect to parameters in QNNs. These results hold for any circuit structures, initialization strategies, and work for both fixed ansatzes and adaptive methods. Extensive numerical simulations are performed to validate our theoretical results. Our findings place generic limits on good initial guesses and adaptive methods for improving the learnability and scalability of QNNs, and deepen the understanding of prior information's role in QNNs.

Recently there has been great interest in operator learning, where networks learn operators between function spaces from an essentially infinite-dimensional perspective. In this work we present results for when the operators learned by these networks are injective and surjective. As a warmup, we combine prior work in both the finite-dimensional ReLU and operator learning setting by giving sharp conditions under which ReLU layers with linear neural operators are injective. We then consider the case when the activation function is pointwise bijective and obtain sufficient conditions for the layer to be injective. We remark that this question, while trivial in the finite-rank setting, is subtler in the infinite-rank setting and is proven using tools from Fredholm theory. Next, we prove that our supplied injective neural operators are universal approximators and that their implementation, with finite-rank neural networks, are still injective. This ensures that injectivity is not 'lost' in the transcription from analytical operators to their finite-rank implementation with networks. Finally, we conclude with an increase in abstraction and consider general conditions when subnetworks, which may have many layers, are injective and surjective and provide an exact inversion from a 'linearization.’ This section uses general arguments from Fredholm theory and Leray-Schauder degree theory for non-linear integral equations to analyze the mapping properties of neural operators in function spaces. These results apply to subnetworks formed from the layers considered in this work, under natural conditions. We believe that our work has applications in Bayesian uncertainty quantification where injectivity enables likelihood estimation and in inverse problems where surjectivity and injectivity corresponds to existence and uniqueness of the solutions, respectively.

Weight-sharing quantization has emerged as a technique to reduce energy expenditure during inference in large neural networks by constraining their weights to a limited set of values. However, existing methods often assume weights are treated solely based on value, neglecting the unique role of weight position. This paper proposes a probabilistic framework based on Bayesian neural networks (BNNs) and a variational relaxation to identify which weights can be moved to which cluster center and to what degree based on their individual position-specific learned uncertainty distributions. We introduce a new initialization setting and a regularization term, enabling the training of BNNs with complex dataset-model combinations. Leveraging the flexibility of weight values from probability distributions, we enhance noise resilience and compressibility. Our iterative clustering procedure demonstrates superior compressibility and higher accuracy compared to state-of-the-art methods on both ResNet models and the more complex transformer-based architectures. In particular, our method outperforms the state-of-the-art quantization method top-1 accuracy by 1.6\% on ImageNet using DeiT-Tiny, with its 5 million+ weights now represented by only 296 unique values. Code available at https://github.com/subiawaud/PWFN.

Temporal graphs are widely used to model dynamic systems with time-varying interactions. In real-world scenarios, the underlying mechanisms of generating future interactions in dynamic systems are typically governed by a set of recurring substructures within the graph, known as temporal motifs. Despite the success and prevalence of current temporal graph neural networks (TGNN), it remains uncertain which temporal motifs are recognized as the significant indications that trigger a certain prediction from the model, which is a critical challenge for advancing the explainability and trustworthiness of current TGNNs. To address this challenge, we propose a novel approach, called **Temp**oral **M**otifs **E**xplainer (**TempME**), which uncovers the most pivotal temporal motifs guiding the prediction of TGNNs. Derived from the information bottleneck principle, TempME extracts the most interaction-related motifs while minimizing the amount of contained information to preserve the sparsity and succinctness of the explanation. Events in the explanations generated by TempME are verified to be more spatiotemporally correlated than those of existing approaches, providing more understandable insights. Extensive experiments validate the superiority of TempME, with up to 8.21% increase in terms of explanation accuracy across six real-world datasets and up to 22.96% increase in boosting the prediction Average Precision of current TGNNs.

Learning feature interactions can be the key for multivariate predictive modeling. ReLU-activated neural networks create piecewise linear prediction models, and other nonlinear activation functions lead to models with only high-order feature interactions. Recent methods incorporate candidate polynomial terms of fixed orders into deep learning, which is subject to the issue of combinatorial explosion, or learn the orders that are difficult to adapt to different regions of the feature space. We propose a Polyhedron Attention Module (PAM) to create piecewise polynomial models where the input space is split into polyhedrons which define the different pieces and on each piece the hyperplanes that define the polyhedron boundary multiply to form the interactive terms, resulting in interactions of adaptive order to each piece. PAM is interpretable to identify important interactions in predicting a target. Theoretic analysis shows that PAM has stronger expression capability than ReLU-activated networks. Extensive experimental results demonstrate the superior classification performance of PAM on massive datasets of the click-through rate prediction and PAM can learn meaningful interaction effects in a medical problem.

Real-world data is complex and often consists of objects that can be decomposed into multiple entities (e.g. images into pixels, graphs into interconnected nodes). Randomized smoothing is a powerful framework for making models provably robust against small changes to their inputs - by guaranteeing robustness of the majority vote when randomly adding noise before classification. Yet, certifying robustness on such complex data via randomized smoothing is challenging when adversaries do not arbitrarily perturb entire objects (e.g. images) but only a subset of their entities (e.g. pixels). As a solution, we introduce hierarchical randomized smoothing: We partially smooth objects by adding random noise only on a randomly selected subset of their entities. By adding noise in a more targeted manner than existing methods we obtain stronger robustness guarantees while maintaining high accuracy. We initialize hierarchical smoothing using different noising distributions, yielding novel robustness certificates for discrete and continuous domains. We experimentally demonstrate the importance of hierarchical smoothing in image and node classification, where it yields superior robustness-accuracy trade-offs. Overall, hierarchical smoothing is an important contribution towards models that are both - certifiably robust to perturbations and accurate.

Understanding when neural networks can be learned efficiently is a fundamental question in learning theory. Existing hardness results suggest that assumptions on both the input distribution and the network's weights are necessary for obtaining efficient algorithms. Moreover, it was previously shown that depth-$2$ networks can be efficiently learned under the assumptions that the input distribution is Gaussian, and the weight matrix is non-degenerate. In this work, we study whether such assumptions may suffice for learning deeper networks and prove negative results. We show that learning depth-$3$ ReLU networks under the Gaussian input distribution is hard even in the smoothed-analysis framework, where a random noise is added to the network's parameters. It implies that learning depth-$3$ ReLU networks under the Gaussian distribution is hard even if the weight matrices are non-degenerate. Moreover, we consider depth-$2$ networks, and show hardness of learning in the smoothed-analysis framework, where both the network parameters and the input distribution are smoothed. Our hardness results are under a well-studied assumption on the existence of local pseudorandom generators.

Greedy layer-wise or module-wise training of neural networks is compelling in constrained and on-device settings where memory is limited, as it circumvents a number of problems of end-to-end back-propagation. However, it suffers from a stagnation problem, whereby early layers overfit and deeper layers stop increasing the test accuracy after a certain depth. We propose to solve this issue by introducing a simple module-wise regularization inspired by the minimizing movement scheme for gradient flows in distribution space. We call the method TRGL for Transport Regularized Greedy Learning and study it theoretically, proving that it leads to greedy modules that are regular and that progressively solve the task. Experimentally, we show improved accuracy of module-wise training of various architectures such as ResNets, Transformers and VGG, when our regularization is added, superior to that of other module-wise training methods and often to end-to-end training, with as much as 60% less memory usage.

Many common types of data can be represented as functions that map coordinates to signal values, such as pixel locations to RGB values in the case of an image. Based on this view, data can be compressed by overfitting a compact neural network to its functional representation and then encoding the network weights. However, most current solutions for this are inefficient, as quantization to low-bit precision substantially degrades the reconstruction quality. To address this issue, we propose overfitting variational Bayesian neural networks to the data and compressing an approximate posterior weight sample using relative entropy coding instead of quantizing and entropy coding it. This strategy enables direct optimization of the rate-distortion performance by minimizing the $\beta$-ELBO, and target different rate-distortion trade-offs for a given network architecture by adjusting $\beta$. Moreover, we introduce an iterative algorithm for learning prior weight distributions and employ a progressive refinement process for the variational posterior that significantly enhances performance. Experiments show that our method achieves strong performance on image and audio compression while retaining simplicity.

The growth of Graph Convolution Network (GCN) model sizes has revolutionized numerous applications, surpassing human performance in areas such as personal healthcare and financial systems. The deployment of GCNs in the cloud raises privacy concerns due to potential adversarial attacks on client data. To address security concerns, Privacy-Preserving Machine Learning (PPML) using Homomorphic Encryption (HE) secures sensitive client data. However, it introduces substantial computational overhead in practical applications. To tackle those challenges, we present LinGCN, a framework designed to reduce multiplication depth and optimize the performance of HE based GCN inference. LinGCN is structured around three key elements: (1) A differentiable structural linearization algorithm, complemented by a parameterized discrete indicator function, co-trained with model weights to meet the optimization goal. This strategy promotes fine-grained node-level non-linear location selection, resulting in a model with minimized multiplication depth. (2) A compact node-wise polynomial replacement policy with a second-order trainable activation function, steered towards superior convergence by a two-level distillation approach from an all-ReLU based teacher model. (3) an enhanced HE solution that enables finer-grained operator fusion for node-wise activation functions, further reducing multiplication level consumption in HE-based inference. Our experiments on the NTU-XVIEW skeleton joint dataset reveal that LinGCN excels in latency, accuracy, and scalability for homomorphically encrypted inference, outperforming solutions such as CryptoGCN. Remarkably, LinGCN achieves a 14.2× latency speedup relative to CryptoGCN, while preserving an inference accuracy of ~75\% and notably reducing multiplication depth. Additionally, LinGCN proves scalable for larger models, delivering a substantial 85.78\% accuracy with 6371s latency, a 10.47\% accuracy improvement over CryptoGCN.

Graph neural networks (GNNs) are commonly described as being permutation equivariant with respect to node relabeling in the graph. This symmetry of GNNs is often compared to the translation equivariance of Euclidean convolution neural networks (CNNs). However, these two symmetries are fundamentally different: The translation equivariance of CNNs corresponds to symmetries of the fixed domain acting on the image signals (sometimes known as active symmetries), whereas in GNNs any permutation acts on both the graph signals and the graph domain (sometimes described as passive symmetries). In this work, we focus on the active symmetries of GNNs, by considering a learning setting where signals are supported on a fixed graph. In this case, the natural symmetries of GNNs are the automorphisms of the graph. Since real-world graphs tend to be asymmetric, we relax the notion of symmetries by formalizing approximate symmetries via graph coarsening. We present a bias-variance formula that quantifies the tradeoff between the loss in expressivity and the gain in the regularity of the learned estimator, depending on the chosen symmetry group. To illustrate our approach, we conduct extensive experiments on image inpainting, traffic flow prediction, and human pose estimation with different choices of symmetries. We show theoretically and empirically that the best generalization performance can be achieved by choosing a suitably larger group than the graph automorphism, but smaller than the permutation group.

Interpretability methods are valuable only if their explanations faithfully describe the explained model. In this work, we consider neural networks whose predictions are invariant under a specific symmetry group. This includes popular architectures, ranging from convolutional to graph neural networks. Any explanation that faithfully explains this type of model needs to be in agreement with this invariance property. We formalize this intuition through the notion of explanation invariance and equivariance by leveraging the formalism from geometric deep learning. Through this rigorous formalism, we derive (1) two metrics to measure the robustness of any interpretability method with respect to the model symmetry group; (2) theoretical robustness guarantees for some popular interpretability methods and (3) a systematic approach to increase the invariance of any interpretability method with respect to a symmetry group. By empirically measuring our metrics for explanations of models associated with various modalities and symmetry groups, we derive a set of 5 guidelines to allow users and developers of interpretability methods to produce robust explanations.

As deep neural networks are highly expressive, it is important to find solutions with small generalization gap (the difference between the performance on the training data and unseen data). Focusing on the stochastic nature of training, we first present a theoretical analysis in which the bound of generalization gap depends on what we call inconsistency and instability of model outputs, which can be estimated on unlabeled data. Our empirical study based on this analysis shows that instability and inconsistency are strongly predictive of generalization gap in various settings. In particular, our finding indicates that inconsistency is a more reliable indicator of generalization gap than the sharpness of the loss landscape. Furthermore, we show that algorithmic reduction of inconsistency leads to superior performance. The results also provide a theoretical basis for existing methods such as co-distillation and ensemble.

As quantum chemical properties have a dependence on their geometries, graph neural networks (GNNs) using 3D geometric information have achieved high prediction accuracy in many tasks. However, they often require 3D geometries obtained from high-level quantum mechanical calculations, which are practically infeasible, limiting their applicability to real-world problems. To tackle this, we propose a new training framework, GeoTMI, that employs denoising process to predict properties accurately using easy-to-obtain geometries (corrupted versions of correct geometries, such as those obtained from low-level calculations). Our starting point was the idea that the correct geometry is the best description of the target property. Hence, to incorporate information of the correct, GeoTMI aims to maximize mutual information between three variables: the correct and the corrupted geometries and the property. GeoTMI also explicitly updates the corrupted input to approach the correct geometry as it passes through the GNN layers, contributing to more effective denoising. We investigated the performance of the proposed method using 3D GNNs for three prediction tasks: molecular properties, a chemical reaction property, and relaxed energy in a heterogeneous catalytic system. Our results showed consistent improvements in accuracy across various tasks, demonstrating the effectiveness and robustness of GeoTMI.

The choice of a graph learning (GL) model (i.e., a GL algorithm and its hyperparameter settings) has a significant impact on the performance of downstream tasks. However, selecting the right GL model becomes increasingly difficult and time consuming as more and more GL models are developed. Accordingly, it is of great significance and practical value to equip users of GL with the ability to perform a near-instantaneous selection of an effective GL model without manual intervention. Despite the recent attempts to tackle this important problem, there has been no comprehensive benchmark environment to evaluate the performance of GL model selection methods. To bridge this gap, we present GLEMOS in this work, a comprehensive benchmark for instantaneous GL model selection that makes the following contributions. (i) GLEMOS provides extensive benchmark data for fundamental GL tasks, i.e., link prediction and node classification, including the performances of 366 models on 457 graphs on these tasks. (ii) GLEMOS designs multiple evaluation settings, and assesses how effectively representative model selection techniques perform in these different settings. (iii) GLEMOS is designed to be easily extended with new models, new graphs, and new performance records. (iv) Based on the experimental results, we discuss the limitations of existing approaches and highlight future research directions. To promote research on this significant problem, we make the benchmark data and code publicly available at https://namyongpark.github.io/glemos.