NeurIPS 2023 Papers

Deep neural networks are known to be vulnerable to adversarial attacks (AA). For an image recognition task, this means that a small perturbation of the original can result in the image being misclassified. Design of such attacks as well as methods of adversarial training against them are subject of intense research. We re-cast the problem using techniques of Wasserstein distributionally robust optimization (DRO) and obtain novel contributions leveraging recent insights from DRO sensitivity analysis. We consider a set of distributional threat models. Unlike the traditional pointwise attacks, which assume a uniform bound on perturbation of each input data point, distributional threat models allow attackers to perturb inputs in a non-uniform way. We link these more general attacks with questions of out-of-sample performance and Knightian uncertainty. To evaluate the distributional robustness of neural networks, we propose a first-order AA algorithm and its multistep version. Our attack algorithms include Fast Gradient Sign Method (FGSM) and Projected Gradient Descent (PGD) as special cases. Furthermore, we provide a new asymptotic estimate of the adversarial accuracy against distributional threat models. The bound is fast to compute and first-order accurate, offering new insights even for the pointwise AA. It also naturally yields out-of-sample performance guarantees. We conduct numerical experiments on CIFAR-10, CIFAR-100, ImageNet datasets using DNNs on RobustBench to illustrate our theoretical results. Our code is available at https://github.com/JanObloj/W-DRO-Adversarial-Methods.

Graph Neural Networks (GNNs) have received significant attention recently, but training them at a large scale remains a challenge. Mini-batch training coupled with sampling is used to alleviate this challenge. However, existing approaches either suffer from the neighborhood explosion phenomenon or have suboptimal performance. To address these issues, we propose a new sampling algorithm called LAyer-neighBOR sampling (LABOR). It is designed to be a direct replacement for Neighbor Sampling (NS) with the same fanout hyperparameter while sampling up to 7 times fewer vertices, without sacrificing quality. By design, the variance of the estimator of each vertex matches NS from the point of view of a single vertex. Moreover, under the same vertex sampling budget constraints, LABOR converges faster than existing layer sampling approaches and can use up to 112 times larger batch sizes compared to NS.

We introduce MLFMF, a collection of data sets for benchmarking recommendation systems used to support formalization of mathematics with proof assistants. These systems help humans identify which previous entries (theorems, constructions, datatypes, and postulates) are relevant in proving a new theorem or carrying out a new construction. Each data set is derived from a library of formalized mathematics written in proof assistants Agda or Lean. The collection includes the largest Lean 4 library Mathlib, and some of the largest Agda libraries: the standard library, the library of univalent mathematics Agda-unimath, and the TypeTopology library. Each data set represents the corresponding library in two ways: as a heterogeneous network, and as a list of s-expressions representing the syntax trees of all the entries in the library. The network contains the (modular) structure of the library and the references between entries, while the s-expressions give complete and easily parsed information about every entry. We report baseline results using standard graph and word embeddings, tree ensembles, and instance-based learning algorithms. The MLFMF data sets provide solid benchmarking support for further investigation of the numerous machine learning approaches to formalized mathematics. The methodology used to extract the networks and the s-expressions readily applies to other libraries, and is applicable to other proof assistants. With more than $250\,000$ entries in total, this is currently the largest collection of formalized mathematical knowledge in machine learnable format.

To quantify uncertainty, conformal prediction methods are gaining continuously more interest and have already been successfully applied to various domains. However, they are difficult to apply to time series as the autocorrelative structure of time series violates basic assumptions required by conformal prediction. We propose HopCPT, a novel conformal prediction approach for time series that not only copes with temporal structures but leverages them. We show that our approach is theoretically well justified for time series where temporal dependencies are present. In experiments, we demonstrate that our new approach outperforms state-of-the-art conformal prediction methods on multiple real-world time series datasets from four different domains.

Graph neural networks (GNNs) have found extensive applications in learning from graph data. However, real-world graphs often possess diverse structures and comprise nodes and edges of varying types. To bolster the generalization capacity of GNNs, it has become customary to augment training graph structures through techniques like graph augmentations and large-scale pre-training on a wider array of graphs. Balancing this diversity while avoiding increased computational costs and the notorious trainability issues of GNNs is crucial. This study introduces the concept of Mixture-of-Experts (MoE) to GNNs, with the aim of augmenting their capacity to adapt to a diverse range of training graph structures, without incurring explosive computational overhead. The proposed Graph Mixture of Experts (GMoE) model empowers individual nodes in the graph to dynamically and adaptively select more general information aggregation experts. These experts are trained to capture distinct subgroups of graph structures and to incorporate information with varying hop sizes, where those with larger hop sizes specialize in gathering information over longer distances. The effectiveness of GMoE is validated through a series of experiments on a diverse set of tasks, including graph, node, and link prediction, using the OGB benchmark. Notably, it enhances ROC-AUC by $1.81\%$ in ogbg-molhiv and by $1.40\%$ in ogbg-molbbbp, when compared to the non-MoE baselines. Our code is publicly available at https://github.com/VITA-Group/Graph-Mixture-of-Experts.

Time perception is critical in our daily life. An important feature of time perception is temporal scaling (TS): the ability to generate temporal sequences (e.g., motor actions) at different speeds. However, it is largely unknown about the math principle underlying temporal scaling in recurrent circuits in the brain. To shed insight, the present study investigates the temporal scaling from the Lie group point of view. We propose a canonical nonlinear recurrent circuit dynamics, modeled as a continuous attractor network, whose neuronal population responses embed a temporal sequence that is TS equivariant. Furthermore, we found the TS group operators can be explicitly represented by a control input fed into the recurrent circuit, where the input gain determines the temporal scaling factor (group parameter), and the spatial offset between the control input and network state emerges the generator. The neuronal responses in the recurrent circuit are also consistent with experimental findings. We illustrated that the recurrent circuit can drive a feedforward circuit to generate complex temporal sequences with different time scales, even in the case of negative time scaling (''time reversal''). Our work for the first time analytically links the abstract temporal scaling group and concrete neural circuit dynamics.

Recent years have witnessed a significant increase in the storage density of NAND flash memory, making it a critical component in modern electronic devices. However, with the rise in storage capacity comes an increased likelihood of errors in data storage and retrieval. The growing number of errors poses ongoing challenges for system designers and engineers, in terms of the characterization, modeling, and optimization of NAND-based systems. We present a novel approach for modeling and preventing errors by utilizing the capabilities of generative and unsupervised machine learning methods. As part of our research, we constructed and trained a neural modulator that translates information bits into programming operations on each memory cell in NAND devices. Our modulator, tailored explicitly for flash memory channels, provides a smart writing scheme that reduces programming errors as well as compensates for data degradation over time. Specifically, the modulator is based on an auto-encoder architecture with an additional channel model embedded between the encoder and the decoder. A conditional generative adversarial network (cGAN) was used to construct the channel model. Optimized for the end-of-life work-point, the learned memory system outperforms the prior art by up to 56\% in raw bit error rate (RBER) and extends the lifetime of the flash memory block by up to 25\%.

While Graph Neural Networks (GNNs) recently became powerful tools in graph learning tasks, considerable efforts have been spent on improving GNNs' structural encoding ability. A particular line of work proposed subgraph GNNs that use subgraph information to improve GNNs' expressivity and achieved great success. However, such effectivity sacrifices the efficiency of GNNs by enumerating all possible subgraphs. In this paper, we analyze the necessity of complete subgraph enumeration and show that a model can achieve a comparable level of expressivity by considering a small subset of the subgraphs. We then formulate the identification of the optimal subset as a combinatorial optimization problem and propose Magnetic Graph Neural Network (MAG-GNN), a reinforcement learning (RL) boosted GNN, to solve the problem. Starting with a candidate subgraph set, MAG-GNN employs an RL agent to iteratively update the subgraphs to locate the most expressive set for prediction. This reduces the exponential complexity of subgraph enumeration to the constant complexity of a subgraph search algorithm while keeping good expressivity. We conduct extensive experiments on many datasets, showing that MAG-GNN achieves competitive performance to state-of-the-art methods and even outperforms many subgraph GNNs. We also demonstrate that MAG-GNN effectively reduces the running time of subgraph GNNs.

Adaptive methods with non-diagonal preconditioning have shown state-of-the-art results on various tasks. However, their computational complexity and memory requirement makes it challenging to scale these methods to modern neural network architectures. To address this challenge, some previous works have adopted block-diagonal preconditioners. However, the memory cost of storing the block-diagonal matrix remains substantial, leading to the use of smaller block sizes and ultimately resulting in suboptimal performance. To reduce the time and memory complexity without sacrificing performance, we propose approximating each diagonal block of the second moment matrix by low-rank matrices and enforcing the same basis for the blocks within each layer. We provide theoretical justification for such sharing and design an algorithm to efficiently maintain this shared-basis block low-rank approximation during training. Our results on a deep autoencoder and a transformer benchmark demonstrate that the proposed method outperforms first-order methods with slightly more time and memory usage, while also achieving competitive or superior performance compared to other second-order methods with less time and memory usage.

Controlling the parameters' norm often yields good generalisation when training neural networks. Beyond simple intuitions, the relation between regularising parameters' norm and obtained estimators remains theoretically misunderstood. For one hidden ReLU layer networks with unidimensional data, this work shows the parameters' norm required to represent a function is given by the total variation of its second derivative, weighted by a $\sqrt{1+x^2}$ factor. Notably, this weighting factor disappears when the norm of bias terms is not regularised. The presence of this additional weighting factor is of utmost significance as it is shown to enforce the uniqueness and sparsity (in the number of kinks) of the minimal norm interpolator. Conversely, omitting the bias' norm allows for non-sparse solutions. Penalising the bias terms in the regularisation, either explicitly or implicitly, thus leads to sparse estimators.

Computational lithography provides algorithmic and mathematical support for resolution enhancement in optical lithography, which is the critical step in semiconductor manufacturing. The time-consuming lithography simulation and mask optimization processes limit the practical application of inverse lithography technology (ILT), a promising solution to the challenges of advanced-node lithography. Although various machine learning methods for ILT have shown promise for reducing the computational burden, this field is in lack of a dataset that can train the models thoroughly and evaluate the performance comprehensively. To boost the development of AI-driven computational lithography, we present the LithoBench dataset, a collection of circuit layout tiles for deep-learning-based lithography simulation and mask optimization. LithoBench consists of more than 120k tiles that are cropped from real circuit designs or synthesized according to the layout topologies of famous ILT testcases. The ground truths are generated by a famous lithography model in academia and an advanced ILT method. Based on the data, we provide a framework to design and evaluate deep neural networks (DNNs) with the data. The framework is used to benchmark state-of-the-art models on lithography simulation and mask optimization. We hope LithoBench can promote the research and development of computational lithography. LithoBench is available at https://anonymous.4open.science/r/lithobench-APPL.

Sparse high-dimensional functions have arisen as a rich framework to study the behavior of gradient-descent methods using shallow neural networks, and showcasing its ability to perform feature learning beyond linear models. Amongst those functions, the simplest are single-index models $f(x) = \phi( x \cdot \theta^*)$, where the labels are generated by an arbitrary non-linear link function $\phi$ of an unknown one-dimensional projection $\theta^*$ of the input data. By focusing on Gaussian data, several recent works have built a remarkable picture, where the so-called information exponent (related to the regularity of the link function) controls the required sample complexity. In essence, these tools exploit the stability and spherical symmetry of Gaussian distributions. In this work, we explore extensions of this picture beyond the Gaussian setting, where both stability or symmetry might be violated. Focusing on the planted setting where $\phi$ is known, our main results establish that Stochastic Gradient Descent recovers the unknown direction $\theta^*$ with constant probability in the high-dimensional regime, under mild assumptions that significantly extend ~[Yehudai and Shamir,20].

The recent success of neural networks as implicit representation of data has driven growing interest in neural functionals: models that can process other neural networks as input by operating directly over their weight spaces. Nevertheless, constructing expressive and efficient neural functional architectures that can handle high-dimensional weight-space objects remains challenging. This paper uses the attention mechanism to define a novel set of permutation equivariant weight-space layers and composes them into deep equivariant models called neural functional Transformers (NFTs). NFTs respect weight-space permutation symmetries while incorporating the advantages of attention, which have exhibited remarkable success across multiple domains. In experiments processing the weights of feedforward MLPs and CNNs, we find that NFTs match or exceed the performance of prior weight-space methods. We also leverage NFTs to develop Inr2Array, a novel method for computing permutation invariant latent representations from the weights of implicit neural representations (INRs). Our proposed method improves INR classification accuracy by up to $+17\\%$ over existing methods. We provide an implementation of our layers at https://github.com/AllanYangZhou/nfn.

Training neural networks sequentially in time to approximate solution fields of time-dependent partial differential equations can be beneficial for preserving causality and other physics properties; however, the sequential-in-time training is numerically challenging because training errors quickly accumulate and amplify over time. This work introduces Neural Galerkin schemes that update randomized sparse subsets of network parameters at each time step. The randomization avoids overfitting locally in time and so helps prevent the error from accumulating quickly over the sequential-in-time training, which is motivated by dropout that addresses a similar issue of overfitting due to neuron co-adaptation. The sparsity of the update reduces the computational costs of training without losing expressiveness because many of the network parameters are redundant locally at each time step. In numerical experiments with a wide range of evolution equations, the proposed scheme with randomized sparse updates is up to two orders of magnitude more accurate at a fixed computational budget and up to two orders of magnitude faster at a fixed accuracy than schemes with dense updates.

The Kohn-Sham equations underlie many important applications such as the discovery of new catalysts. Recent machine learning work on catalyst modeling has focused on prediction of the energy, but has so far not yet demonstrated significant out-of-distribution generalization. Here we investigate another approach based on the pointwise learning of the Kohn-Sham charge-density. On a new dataset of bulk catalysts with charge densities, we show density models can generalize to new structures with combinations of elements not seen at train time, a form of combinatorial generalization. We show that over 80% of binary and ternary test cases achieve faster convergence than standard baselines in Density Functional Theory, amounting to an average reduction of 13% in the number of iterations required to reach convergence, which may be of independent interest. Our results suggest that density learning is a viable alternative, trading greater inference costs for a step towards combinatorial generalization, a key property for applications.

Graph Neural Network (GNN) architectures are defined by their implementations of update and aggregation modules. While many works focus on new ways to parametrise the update modules, the aggregation modules receive comparatively little attention. Because it is difficult to parametrise aggregation functions, currently most methods select a ``standard aggregator'' such as mean, sum, or max. While this selection is often made without any reasoning, it has been shown that the choice in aggregator has a significant impact on performance, and the best choice in aggregator is problem-dependent. Since aggregation is a lossy operation, it is crucial to select the most appropriate aggregator in order to minimise information loss. In this paper, we present GenAgg, a generalised aggregation operator, which parametrises a function space that includes all standard aggregators. In our experiments, we show that GenAgg is able to represent the standard aggregators with much higher accuracy than baseline methods. We also show that using GenAgg as a drop-in replacement for an existing aggregator in a GNN often leads to a significant boost in performance across various tasks.

Feature visualization has gained significant popularity as an explainability method, particularly after the influential work by Olah et al. in 2017. Despite its success, its widespread adoption has been limited due to issues in scaling to deeper neural networks and the reliance on tricks to generate interpretable images. Here, we describe MACO, a simple approach to address these shortcomings. It consists in optimizing solely an image's phase spectrum while keeping its magnitude constant to ensure that the generated explanations lie in the space of natural images. Our approach yields significantly better results -- both qualitatively and quantitatively -- unlocking efficient and interpretable feature visualizations for state-of-the-art neural networks. We also show that our approach exhibits an attribution mechanism allowing to augment feature visualizations with spatial importance. Furthermore, we enable quantitative evaluation of feature visualizations by introducing 3 metrics: transferability, plausibility, and alignment with natural images. We validate our method on various applications and we introduce a website featuring MACO visualizations for all classes of the ImageNet dataset, which will be made available upon acceptance. Overall, our study unlocks feature visualizations for the largest, state-of-the-art classification networks without resorting to any parametric prior image model, effectively advancing a field that has been stagnating since 2017 (Olah et al, 2017).

We present an approach for analyzing message passing graph neural networks (MPNNs) based on an extension of graphon analysis to a so called graphon-signal analysis. A MPNN is a function that takes a graph and a signal on the graph (a graph-signal) and returns some value. Since the input space of MPNNs is non-Euclidean, i.e., graphs can be of any size and topology, properties such as generalization are less well understood for MPNNs than for Euclidean neural networks. We claim that one important missing ingredient in past work is a meaningful notion of graph-signal similarity measure, that endows the space of inputs to MPNNs with a regular structure. We present such a similarity measure, called the graphon-signal cut distance, which makes the space of all graph-signals a dense subset of a compact metric space -- the graphon-signal space. Informally, two deterministic graph-signals are close in cut-distance if they ``look like'' they were sampled from the same random graph-signal model. Hence, our cut distance is a natural notion of graph-signal similarity, which allows comparing any pair of graph-signals of any size and topology. We prove that MPNNs are Lipschitz continuous functions over the graphon-signal metric space. We then give two applications of this result: 1) a generalization bound for MPNNs, and, 2) the stability of MPNNs to subsampling of graph-signals. Our results apply to any regular enough MPNN on any distribution of graph-signals, making the analysis rather universal.

We propose a novel neural network-based approach to modeling protein dynamics using an implicit representation of a protein’s surface in 3D and time. Our method utilizes the zero-level set of signed distance functions (SDFs) to represent protein surfaces, enabling temporally and spatially continuous representations of protein dynamics. Our experimental results demonstrate that our model accurately captures protein dynamic trajectories and can interpolate and extrapolate in 3D and time. Importantly, this is the first study to introduce this method and successfully model large-scale protein dynamics. This approach offers a promising alternative to current methods, overcoming the limitations of first-principles-based and deep learning methods, and provides a more scalable and efficient approach to modeling protein dynamics. Additionally, our surface representation approach simplifies calculations and allows identifying movement trends and amplitudes of protein domains, making it a useful tool for protein dynamics research. Codes are available at https://github.com/Sundw-818/DSR, and we have a project webpage that shows some video results, https://sundw-818.github.io/DSR/.