NeurIPS 2023 Papers

Precise hardware performance models play a crucial role in code optimizations. They can assist compilers in making heuristic decisions or aid autotuners in identifying the optimal configuration for a given program. For example, the autotuner for XLA, a machine learning compiler, discovered 10–20\% speedup on state-of-the-art models serving substantial production traffic at Google. Although there exist a few datasets for program performance prediction, they target small sub-programs such as basic blocks or kernels. This paper introduces TpuGraphs, a performance prediction dataset on full tensor programs, represented as computational graphs, running on Tensor Processing Units (TPUs). Each graph in the dataset represents the main computation of a machine learning workload, e.g., a training epoch or an inference step. Each data sample contains a computational graph, a compilation configuration, and the execution time of the graph when compiled with the configuration. The graphs in the dataset are collected from open-source machine learning programs, featuring popular model architectures (e.g., ResNet, EfficientNet, Mask R-CNN, and Transformer). TpuGraphs provides 25x more graphs than the largest graph property prediction dataset (with comparable graph sizes), and 770x larger graphs on average compared to existing performance prediction datasets on machine learning programs. This graph-level prediction task on large graphs introduces new challenges in learning, ranging from scalability, training efficiency, to model quality.

Given varying prompts regarding a factoid question, can a large language model (LLM) reliably generate factually correct answers? Existing LLMs may generate distinct responses for different prompts. In this paper, we study the problem of quantifying knowledge contained in an LLM regarding a given set of facts. We propose KaRR, a statistical approach to assess factual knowledge for LLMs. The main idea is to estimate the ratio of LLM generating text corresponding to the answer entity given diverse prompts of the subject and the querying relation, versus it generating by random chances. Our assessment suite contains a comprehensive set of 994,123 entities and 600 relations, with 1,395,905 text aliases. We use our method to evaluate 20 LLMs of various sizes, including LLaMA, Alpaca, OPT, etc. Experiments show that our results have a strong correlation (0.43 Kendall's $\tau$) with the results of human assessment on LLMs. Our results reveal that the knowledge in LLMs with the same backbone architecture adheres to the scaling law, while tuning on instruction-following data sometimes compromises the model's capability to generate factually correct text reliably.

In-context learning is the ability of a pretrained model to adapt to novel and diverse downstream tasks by conditioning on prompt examples, without optimizing any parameters. While large language models have demonstrated this ability, how in-context learning could be performed over graphs is unexplored. In this paper, we develop \textbf{Pr}etraining \textbf{O}ver \textbf{D}iverse \textbf{I}n-Context \textbf{G}raph S\textbf{y}stems (PRODIGY), the first pretraining framework that enables in-context learning over graphs. The key idea of our framework is to formulate in-context learning over graphs with a novel \emph{prompt graph} representation, which connects prompt examples and queries. We then propose a graph neural network architecture over the prompt graph and a corresponding family of in-context pretraining objectives. With PRODIGY, the pretrained model can directly perform novel downstream classification tasks on unseen graphs via in-context learning. We provide empirical evidence of the effectiveness of our framework by showcasing its strong in-context learning performance on tasks involving citation networks and knowledge graphs. Our approach outperforms the in-context learning accuracy of contrastive pretraining baselines with hard-coded adaptation by 18\% on average across all setups. Moreover, it also outperforms standard finetuning with limited data by 33\% on average with in-context learning.

In $\mathbb{R}^d$, it is well-known that cumulants provide an alternative to moments that can achieve the same goals with numerous benefits such as lower variance estimators. In this paper we extend cumulants to reproducing kernel Hilbert spaces (RKHS) using tools from tensor algebras and show that they are computationally tractable by a kernel trick. These kernelized cumulants provide a new set of all-purpose statistics; the classical maximum mean discrepancy and Hilbert-Schmidt independence criterion arise as the degree one objects in our general construction. We argue both theoretically and empirically (on synthetic, environmental, and traffic data analysis) that going beyond degree one has several advantages and can be achieved with the same computational complexity and minimal overhead in our experiments.

Finding the proper depth $d$ of a graph convolutional network (GCN) that provides strong representation ability has drawn significant attention, yet nonetheless largely remains an open problem for the graph learning community. Although noteworthy progress has been made, the depth or the number of layers of a corresponding GCN is realized by a series of graph convolution operations, which naturally makes $d$ a positive integer ($d \in \mathbb{N}+$). An interesting question is whether breaking the constraint of $\mathbb{N}+$ by making $d$ a real number ($d \in \mathbb{R}$) can bring new insights into graph learning mechanisms. In this work, by redefining GCN's depth $d$ as a trainable parameter continuously adjustable within $(-\infty,+\infty)$, we open a new door of controlling its signal processing capability to model graph homophily/heterophily (nodes with similar/dissimilar labels/attributes tend to be inter-connected). A simple and powerful GCN model TEDGCN, is proposed to retain the simplicity of GCN and meanwhile automatically search for the optimal $d$ without the prior knowledge regarding whether the input graph is homophilic or heterophilic. Negative-valued $d$ intrinsically enables high-pass frequency filtering functionality via augmented topology for graph heterophily. Extensive experiments demonstrate the superiority of TEDGCN on node classification tasks for a variety of homophilic and heterophilic graphs.

Recent studies on Graph Neural Networks(GNNs) provide both empirical and theoretical evidence supporting their effectiveness in capturing structural patterns on both homophilic and certain heterophilic graphs. Notably, most real-world homophilic and heterophilic graphs are comprised of a mixture of nodes in both homophilic and heterophilic structural patterns, exhibiting a structural disparity. However, the analysis of GNN performance with respect to nodes exhibiting different structural patterns, e.g., homophilic nodes in heterophilic graphs, remains rather limited. In the present study, we provide evidence that Graph Neural Networks(GNNs) on node classification typically perform admirably on homophilic nodes within homophilic graphs and heterophilic nodes within heterophilic graphs while struggling on the opposite node set, exhibiting a performance disparity. We theoretically and empirically identify effects of GNNs on testing nodes exhibiting distinct structural patterns. We then propose a rigorous, non-i.i.d PAC-Bayesian generalization bound for GNNs, revealing reasons for the performance disparity, namely the aggregated feature distance and homophily ratio difference between training and testing nodes. Furthermore, we demonstrate the practical implications of our new findings via (1) elucidating the effectiveness of deeper GNNs; and (2) revealing an over-looked distribution shift factor on graph out-of-distribution problem and proposing a new scenario accordingly.

Multi-hop logical reasoning over knowledge graph plays a fundamental role in many artificial intelligence tasks. Recent complex query embedding methods for reasoning focus on static KGs, while temporal knowledge graphs have not been fully explored. Reasoning over TKGs has two challenges: 1. The query should answer entities or timestamps; 2. The operators should consider both set logic on entity set and temporal logic on timestamp set. To bridge this gap, we introduce the multi-hop logical reasoning problem on TKGs and then propose the first temporal complex query embedding named Temporal Feature-Logic Embedding framework (TFLEX) to answer the temporal complex queries. Specifically, we utilize fuzzy logic to compute the logic part of the Temporal Feature-Logic embedding, thus naturally modeling all first-order logic operations on the entity set. In addition, we further extend fuzzy logic on timestamp set to cope with three extra temporal operators (**After**, **Before** and **Between**). Experiments on numerous query patterns demonstrate the effectiveness of our method.

Facial expression data is characterized by a significant imbalance, with most collected data showing happy or neutral expressions and fewer instances of fear or disgust. This imbalance poses challenges to facial expression recognition (FER) models, hindering their ability to fully understand various human emotional states. Existing FER methods typically report overall accuracy on highly imbalanced test sets but exhibit low performance in terms of the mean accuracy across all expression classes. In this paper, our aim is to address the imbalanced FER problem. Existing methods primarily focus on learning knowledge of minor classes solely from minor-class samples. However, we propose a novel approach to extract extra knowledge related to the minor classes from both major and minor class samples. Our motivation stems from the belief that FER resembles a distribution learning task, wherein a sample may contain information about multiple classes. For instance, a sample from the major class surprise might also contain useful features of the minor class fear. Inspired by that, we propose a novel method that leverages re-balanced attention maps to regularize the model, enabling it to extract transformation invariant information about the minor classes from all training samples. Additionally, we introduce re-balanced smooth labels to regulate the cross-entropy loss, guiding the model to pay more attention to the minor classes by utilizing the extra information regarding the label distribution of the imbalanced training data. Extensive experiments on different datasets and backbones show that the two proposed modules work together to regularize the model and achieve state-of-the-art performance under the imbalanced FER task. Code is available at https://github.com/zyh-uaiaaaa.

Feature selection (FS) plays an important role in machine learning, which extracts important features and accelerates the learning process. In this paper, we propose a deep FS method that simultaneously conducts feature selection and differentiable $ k $-NN graph learning based on the Dirichlet Energy. The Dirichlet Energy identifies important features by measuring their smoothness on the graph structure, and facilitates the learning of a new graph that reflects the inherent structure in new feature subspace. We employ Optimal Transport theory to address the non-differentiability issue of learning $ k $-NN graphs in neural networks, which theoretically makes our method applicable to other graph neural networks for dynamic graph learning. Furthermore, the proposed framework is interpretable, since all modules are designed algorithmically. We validate the effectiveness of our model with extensive experiments on both synthetic and real-world datasets.

Dynamic graph neural networks (DGNNs) are increasingly pervasive in exploiting spatio-temporal patterns on dynamic graphs. However, existing works fail to generalize under distribution shifts, which are common in real-world scenarios. As the generation of dynamic graphs is heavily influenced by latent environments, investigating their impacts on the out-of-distribution (OOD) generalization is critical. However, it remains unexplored with the following two major challenges: **(1)** How to properly model and infer the complex environments on dynamic graphs with distribution shifts? **(2)** How to discover invariant patterns given inferred spatio-temporal environments? To solve these challenges, we propose a novel **E**nvironment-**A**ware dynamic **G**raph **LE**arning (**EAGLE**) framework for OOD generalization by modeling complex coupled environments and exploiting spatio-temporal invariant patterns. Specifically, we first design the environment-aware EA-DGNN to model environments by multi-channel environments disentangling. Then, we propose an environment instantiation mechanism for environment diversification with inferred distributions. Finally, we discriminate spatio-temporal invariant patterns for out-of-distribution prediction by the invariant pattern recognition mechanism and perform fine-grained causal interventions node-wisely with a mixture of instantiated environment samples. Experiments on real-world and synthetic dynamic graph datasets demonstrate the superiority of our method against state-of-the-art baselines under distribution shifts. To the best of our knowledge, we are the first to study OOD generalization on dynamic graphs from the environment learning perspective.

A machine learning model is traditionally considered robust if its prediction remains (almost) constant under input perturbations with small norm. However, real-world tasks like molecular property prediction or point cloud segmentation have inherent equivariances, such as rotation or permutation equivariance. In such tasks, even perturbations with large norm do not necessarily change an input's semantic content. Furthermore, there are perturbations for which a model's prediction explicitly needs to change. For the first time, we propose a sound notion of adversarial robustness that accounts for task equivariance. We then demonstrate that provable robustness can be achieved by (1) choosing a model that matches the task's equivariances (2) certifying traditional adversarial robustness. Certification methods are, however, unavailable for many models, such as those with continuous equivariances. We close this gap by developing the framework of equivariance-preserving randomized smoothing, which enables architecture-agnostic certification. We additionally derive the first architecture-specific graph edit distance certificates, i.e. sound robustness guarantees for isomorphism equivariant tasks like node classification. Overall, a sound notion of robustness is an important prerequisite for future work at the intersection of robust and geometric machine learning.

Homophily is a graph property describing the tendency of edges to connect similar nodes; the opposite is called heterophily. It is often believed that heterophilous graphs are challenging for standard message-passing graph neural networks (GNNs), and much effort has been put into developing efficient methods for this setting. However, there is no universally agreed-upon measure of homophily in the literature. In this work, we show that commonly used homophily measures have critical drawbacks preventing the comparison of homophily levels across different datasets. For this, we formalize desirable properties for a proper homophily measure and verify which measures satisfy which properties. In particular, we show that a measure that we call adjusted homophily satisfies more desirable properties than other popular homophily measures while being rarely used in graph machine learning literature. Then, we go beyond the homophily-heterophily dichotomy and propose a new characteristic that allows one to further distinguish different sorts of heterophily. The proposed label informativeness (LI) characterizes how much information a neighbor's label provides about a node's label. We prove that this measure satisfies important desirable properties. We also observe empirically that LI better agrees with GNN performance compared to homophily measures, which confirms that it is a useful characteristic of the graph structure.

Text-attributed graphs (TAGs) are prevalent in various real-world scenarios, where each node is associated with a text description. The cornerstone of representation learning on TAGs lies in the seamless integration of textual semantics within individual nodes and the topological connections across nodes. Recent advancements in pre-trained language models (PLMs) and graph neural networks (GNNs) have facilitated effective learning on TAGs, garnering increased research interest. However, the absence of meaningful benchmark datasets and standardized evaluation procedures for TAGs has impeded progress in this field. In this paper, we propose CS-TAG, a comprehensive and diverse collection of challenging benchmark datasets for TAGs. The CS-TAG datasets are notably large in scale and encompass a wide range of domains, spanning from citation networks to purchase graphs. In addition to building the datasets, we conduct extensive benchmark experiments over CS-TAG with various learning paradigms, including PLMs, GNNs, PLM-GNN co-training methods, and the proposed novel topological pre-training of language models. In a nutshell, we provide an overview of the CS-TAG datasets, standardized evaluation procedures, and present baseline experiments. The entire CS-TAG project is publicly accessible at \url{https://github.com/sktsherlock/TAG-Benchmark}.

Pre-training on graph neural networks (GNNs) aims to learn transferable knowledge for downstream tasks with unlabeled data, and it has recently become an active research area. The success of graph pre-training models is often attributed to the massive amount of input data. In this paper, however, we identify the curse of big data phenomenon in graph pre-training: more training data do not necessarily lead to better downstream performance. Motivated by this observation, we propose a better-with-less framework for graph pre-training: fewer, but carefully chosen data are fed into a GNN model to enhance pre-training. The proposed pre-training pipeline is called the data-active graph pre-training (APT) framework, and is composed of a graph selector and a pre-training model. The graph selector chooses the most representative and instructive data points based on the inherent properties of graphs as well as predictive uncertainty. The proposed predictive uncertainty, as feedback from the pre-training model, measures the confidence level of the model in the data. When fed with the chosen data, on the other hand, the pre-training model grasps an initial understanding of the new, unseen data, and at the same time attempts to remember the knowledge learned from previous data. Therefore, the integration and interaction between these two components form a unified framework (APT), in which graph pre-training is performed in a progressive and iterative way. Experiment results show that the proposed APT is able to obtain an efficient pre-training model with fewer training data and better downstream performance.

While contextual bandit has a mature theory, effectively leveraging different feedback patterns to enhance the pace of learning remains unclear. Bandits with feedback graphs, which interpolates between the full information and bandit regimes, provides a promising framework to mitigate the statistical complexity of learning. In this paper, we propose and analyze an approach to contextual bandits with feedback graphs based upon reduction to regression. The resulting algorithms are computationally practical and achieve established minimax rates, thereby reducing the statistical complexity in real-world applications.

Knowledge Distillation (KD) has emerged as a promising approach for compressing large Pre-trained Language Models (PLMs). The performance of KD relies on how to effectively formulate and transfer the knowledge from the teacher model to the student model. Prior arts mainly focus on directly aligning output features from the transformer block, which may impose overly strict constraints on the student model's learning process and complicate the training process by introducing extra parameters and computational cost. Moreover, our analysis indicates that the different relations within self-attention, as adopted in other works, involves more computation complexities and can easily be constrained by the number of heads, potentially leading to suboptimal solutions. To address these issues, we propose a novel approach that builds relationships directly from output features. Specifically, we introduce token-level and sequence-level relations concurrently to fully exploit the knowledge from the teacher model. Furthermore, we propose a correlation-based distillation loss to alleviate the exact match properties inherent in traditional KL divergence or MSE loss functions. Our method, dubbed FCD, presents a simple yet effective method to compress various architectures (BERT, RoBERTa, and GPT) and model sizes (base-size and large-size). Extensive experimental results demonstrate that our distilled, smaller language models significantly surpass existing KD methods across various NLP tasks.

Graph neural networks (GNNs) have shown state-of-the-art performances in various applications. However, GNNs often struggle to capture long-range dependencies in graphs due to oversmoothing. In this paper, we generalize the concept of oversmoothing from undirected to directed graphs. To this aim, we extend the notion of Dirichlet energy by considering a directed symmetrically normalized Laplacian. As vanilla graph convolutional networks are prone to oversmooth, we adopt a neural graph ODE framework. Specifically, we propose fractional graph Laplacian neural ODEs, which describe non-local dynamics. We prove that our approach allows propagating information between distant nodes while maintaining a low probability of long-distance jumps. Moreover, we show that our method is more flexible with respect to the convergence of the graph’s Dirichlet energy, thereby mitigating oversmoothing. We conduct extensive experiments on synthetic and real-world graphs, both directed and undirected, demonstrating our method’s versatility across diverse graph homophily levels. Our code is available at https://github.com/RPaolino/fLode

Multi-hop Knowledge Graph Question Answering (KGQA) is a task that involves retrieving nodes from a knowledge graph (KG) to answer natural language questions. Recent GNN-based approaches formulate this task as a KG path searching problem, where messages are sequentially propagated from the seed node towards the answer nodes. However, these messages are past-oriented, and they do not consider the full KG context. To make matters worse, KG nodes often represent pronoun entities and are sometimes encrypted, being uninformative in selecting between paths. To address these problems, we propose Neural Tree Search (NuTrea), a tree search-based GNN model that incorporates the broader KG context. Our model adopts a message-passing scheme that probes the unreached subtree regions to boost the past-oriented embeddings. In addition, we introduce the Relation Frequency-Inverse Entity Frequency (RF-IEF) node embedding that considers the global KG context to better characterize ambiguous KG nodes. The general effectiveness of our approach is demonstrated through experiments on three major multi-hop KGQA benchmark datasets, and our extensive analyses further validate its expressiveness and robustness. Overall, NuTrea provides a powerful means to query the KG with complex natural language questions. Code is available at https://github.com/mlvlab/NuTrea.

The causal revolution has stimulated interest in understanding complex relationships in various fields. Most of the existing methods aim to discover causal relationships among all variables within a complex large-scale graph. However, in practice, only a small subset of variables in the graph are relevant to the outcomes of interest. Consequently, causal estimation with the full causal graph---particularly given limited data---could lead to numerous *falsely discovered, spurious* variables that exhibit high correlation with, but exert no causal impact on, the target outcome. In this paper, we propose learning a class of *necessary and sufficient causal graphs (NSCG)* that exclusively comprises causally relevant variables for an outcome of interest, which we term *causal features*. The key idea is to employ *probabilities of causation* to systematically evaluate the importance of features in the causal graph, allowing us to identify a subgraph relevant to the outcome of interest. To learn NSCG from data, we develop a *necessary and sufficient causal structural learning (NSCSL)* algorithm, by establishing theoretical properties and relationships between probabilities of causation and natural causal effects of features. Across empirical studies of simulated and real data, we demonstrate that NSCSL outperforms existing algorithms and can reveal crucial yeast genes for target heritable traits of interest.