ICLR 2023 论文列表

International Conference on Learning Representations

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1,575篇论文

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Learning Hierarchical Protein Representations via Complete 3D Graph Networks

Limei Wang, Haoran Liu, Yi Liu, Jerry Kurtin, Shuiwang Ji

展开摘要

We consider representation learning for proteins with 3D structures. We build 3D graphs based on protein structures and develop graph networks to learn their representations. Depending on the levels of details that we wish to capture, protein representations can be computed at different levels, \emph{e.g.}, the amino acid, backbone, or all-atom levels. Importantly, there exist hierarchical relations among different levels. In this work, we propose to develop a novel hierarchical graph network, known as ProNet, to capture the relations. Our ProNet is very flexible and can be used to compute protein representations at different levels of granularity. By treating each amino acid as a node in graph modeling as well as harnessing the inherent hierarchies, our ProNet is more effective and efficient than existing methods. We also show that, given a base 3D graph network that is complete, our ProNet representations are also complete at all levels. Experimental results show that ProNet outperforms recent methods on most datasets. In addition, results indicate that different downstream tasks may require representations at different levels. Our code is publicly available as part of the DIG library (\url{https://github.com/divelab/DIG}).

Poster
simpleKT: A Simple But Tough-to-Beat Baseline for Knowledge Tracing

Zitao Liu, Qiongqiong Liu, Jiahao Chen, Shuyan Huang, Weiqi Luo

展开摘要

Knowledge tracing (KT) is the problem of predicting students' future performance based on their historical interactions with intelligent tutoring systems. Recently, many works present lots of special methods for applying deep neural networks to KT from different perspectives like model architecture, adversarial augmentation and etc., which make the overall algorithm and system become more and more complex. Furthermore, due to the lack of standardized evaluation protocol \citep{liu2022pykt}, there is no widely agreed KT baselines and published experimental comparisons become inconsistent and self-contradictory, i.e., the reported AUC scores of DKT on ASSISTments2009 range from 0.721 to 0.821 \citep{minn2018deep,yeung2018addressing}. Therefore, in this paper, we provide a strong but simple baseline method to deal with the KT task named \textsc{simpleKT}. Inspired by the Rasch model in psychometrics, we explicitly model question-specific variations to capture the individual differences among questions covering the same set of knowledge components that are a generalization of terms of concepts or skills needed for learners to accomplish steps in a task or a problem. Furthermore, instead of using sophisticated representations to capture student forgetting behaviors, we use the ordinary dot-product attention function to extract the time-aware information embedded in the student learning interactions. Extensive experiments show that such a simple baseline is able to always rank top 3 in terms of AUC scores and achieve 57 wins, 3 ties and 16 loss against 12 DLKT baseline methods on 7 public datasets of different domains. We believe this work serves as a strong baseline for future KT research. Code is available at \url{https://github.com/pykt-team/pykt-toolkit}\footnote{We merged our model to the \textsc{pyKT} benchmark at \url{https://pykt.org/}.}.

Poster
Prompting GPT-3 To Be Reliable

Chenglei Si, Zhe Gan, Zhengyuan Yang, Shuohang Wang, Jianfeng Wang, Jordan Lee Boyd-Graber, Lijuan Wang

展开摘要

Large language models (LLMs) show impressive abilities via few-shot prompting. Commercialized APIs such as OpenAI GPT-3 further increase their use in real-world language applications. However, the crucial problem of how to improve the reliability of GPT-3 is still under-explored. While reliability is a broad and vaguely defined term, we decompose reliability into four main facets that correspond to the existing framework of ML safety and are well-recognized to be important: generalizability, social biases, calibration, and factuality. Our core contribution is to establish simple and effective prompts that improve GPT-3’s reliability as it: 1) generalizes out-of-distribution, 2) balances demographic distribution and uses natural language instructions to reduce social biases, 3) calibrates output probabilities, and 4) updates the LLM’s factual knowledge and reasoning chains. With appropriate prompts, GPT-3 is more reliable than smaller-scale supervised models on all these facets. We release all processed datasets, evaluation scripts, and model predictions. Our systematic empirical study not only sheds new insights on the reliability of prompting LLMs, but more importantly, our prompting strategies can help practitioners more reliably use LLMs like GPT-3.

Poster
Supervision Complexity and its Role in Knowledge Distillation

Hrayr Harutyunyan, Ankit Singh Rawat, Aditya Krishna Menon, Seungyeon Kim, Sanjiv Kumar

展开摘要

Despite the popularity and efficacy of knowledge distillation, there is limited understanding of why it helps. In order to study the generalization behavior of a distilled student, we propose a new theoretical framework that leverages supervision complexity: a measure of alignment between teacher-provided supervision and the student's neural tangent kernel. The framework highlights a delicate interplay among the teacher's accuracy, the student's margin with respect to the teacher predictions, and the complexity of the teacher predictions. Specifically, it provides a rigorous justification for the utility of various techniques that are prevalent in the context of distillation, such as early stopping and temperature scaling. Our analysis further suggests the use of online distillation, where a student receives increasingly more complex supervision from teachers in different stages of their training. We demonstrate efficacy of online distillation and validate the theoretical findings on a range of image classification benchmarks and model architectures.

Poster
NAGphormer: A Tokenized Graph Transformer for Node Classification in Large Graphs

Jinsong Chen, Kaiyuan Gao, Gaichao Li, Kun He

展开摘要

The graph Transformer emerges as a new architecture and has shown superior performance on various graph mining tasks. In this work, we observe that existing graph Transformers treat nodes as independent tokens and construct a single long sequence composed of all node tokens so as to train the Transformer model, causing it hard to scale to large graphs due to the quadratic complexity on the number of nodes for the self-attention computation. To this end, we propose a Neighborhood Aggregation Graph Transformer (NAGphormer) that treats each node as a sequence containing a series of tokens constructed by our proposed Hop2Token module. For each node, Hop2Token aggregates the neighborhood features from different hops into different representations and thereby produces a sequence of token vectors as one input. In this way, NAGphormer could be trained in a mini-batch manner and thus could scale to large graphs. Moreover, we mathematically show that as compared to a category of advanced Graph Neural Networks (GNNs), the decoupled Graph Convolutional Network, NAGphormer could learn more informative node representations from the multi-hop neighborhoods. Extensive experiments on benchmark datasets from small to large are conducted to demonstrate that NAGphormer consistently outperforms existing graph Transformers and mainstream GNNs. Code is available at https://github.com/JHL-HUST/NAGphormer.

Poster
Learning Structured Representations by Embedding Class Hierarchy

Siqi Zeng, Remi Tachet des Combes, Han Zhao

展开摘要

Existing models for learning representations in supervised classification problems are permutation invariant with respect to class labels. However, structured knowledge about the classes, such as hierarchical label structures, widely exists in many real-world datasets, e.g., the ImageNet and CIFAR benchmarks. How to learn representations that can preserve such structures among the classes remains an open problem. To approach this problem, given a tree of class hierarchy, we first define a tree metric between any pair of nodes in the tree to be the length of the shortest path connecting them. We then provide a method to learn the hierarchical relationship of class labels by approximately embedding the tree metric in the Euclidean space of features. More concretely, during supervised training, we propose to use the Cophenetic Correlation Coefficient (CPCC) as a regularizer for the cross-entropy loss to correlate the tree metric of classes and the Euclidean distance in the class-conditioned representations. Our proposed regularizer is computationally lightweight and easy to implement. Empirically, we demonstrate that this approach can help to learn more interpretable representations due to the preservation of the tree metric, and leads to better in-distribution generalization as well as under sub-population shifts over six real-world datasets.

Poster
A Graph Neural Network Approach to Automated Model Building in Cryo-EM Maps

Kiarash Jamali, Dari Kimanius, Sjors HW Scheres

展开摘要

Electron cryo-microscopy (cryo-EM) produces three-dimensional (3D) maps of the electrostatic potential of biological macromolecules, including proteins. At sufficient resolution, the cryo-EM maps, along with some knowledge about the imaged molecules, allow de novo atomic modelling. Typically, this is done through a laborious manual process. Recent advances in machine learning applications to protein structure prediction show potential for automating this process. Taking inspiration from these techniques, we have built ModelAngelo for automated model building of proteins in cryo-EM maps. ModelAngelo first uses a residual convolutional neural network (CNN) to initialize a graph representation with nodes assigned to individual amino acids of the proteins in the map and edges representing the protein chain. The graph is then refined with a graph neural network (GNN) that combines the cryo-EM data, the amino acid sequence data and prior knowledge about protein geometries. The GNN refines the geometry of the protein chain and classifies the amino acids for each of its nodes. The final graph is post-processed with a hidden Markov model (HMM) search to map each protein chain to entries in a user provided sequence file. Application to 28 test cases shows that ModelAngelo outperforms state-of-the-art and approximates manual building for cryo-EM maps with resolutions better than 3.5 A.

Poster
LMC: Fast Training of GNNs via Subgraph Sampling with Provable Convergence

Zhihao Shi, Xize Liang, Jie Wang

展开摘要

The message passing-based graph neural networks (GNNs) have achieved great success in many real-world applications. However, training GNNs on large-scale graphs suffers from the well-known neighbor explosion problem, i.e., the exponentially increasing dependencies of nodes with the number of message passing layers. Subgraph-wise sampling methods---a promising class of mini-batch training techniques---discard messages outside the mini-batches in backward passes to avoid the neighbor explosion problem at the expense of gradient estimation accuracy. This poses significant challenges to their convergence analysis and convergence speeds, which seriously limits their reliable real-world applications. To address this challenge, we propose a novel subgraph-wise sampling method with a convergence guarantee, namely Local Message Compensation (LMC). To the best of our knowledge, LMC is the {\it first} subgraph-wise sampling method with provable convergence. The key idea of LMC is to retrieve the discarded messages in backward passes based on a message passing formulation of backward passes. By efficient and effective compensations for the discarded messages in both forward and backward passes, LMC computes accurate mini-batch gradients and thus accelerates convergence. We further show that LMC converges to first-order stationary points of GNNs. Experiments on large-scale benchmark tasks demonstrate that LMC significantly outperforms state-of-the-art subgraph-wise sampling methods in terms of efficiency.

Top-25%
Characterizing the Influence of Graph Elements

Zizhang Chen, Peizhao Li, Hongfu Liu, Pengyu Hong

展开摘要

Influence function, a method from the robust statistics, measures the changes of model parameters or some functions about model parameters with respect to the removal or modification of training instances. It is an efficient and useful post-hoc method for studying the interpretability of machine learning models without the need of expensive model re-training. Recently, graph convolution networks (GCNs), which operate on graph data, have attracted a great deal of attention. However, there is no preceding research on the influence functions of GCNs to shed light on the effects of removing training nodes/edges from an input graph. Since the nodes/edges in a graph are interdependent in GCNs, it is challenging to derive influence functions for GCNs. To fill this gap, we started with the simple graph convolution (SGC) model that operates on an attributed graph, and formulated an influence function to approximate the changes of model parameters when a node or an edge is removed from an attributed graph. Moreover, we theoretically analyzed the error bound of the estimated influence of removing an edge. We experimentally validated the accuracy and effectiveness of our influence estimation function. In addition, we showed that the influence function of a SGC model could be used to estimate the impact of removing training nodes/edges on the test performance of the SGC without re-training the model. Finally, we demonstrated how to use influence functions to effectively guide the adversarial attacks on GCNs.

Poster
Weakly Supervised Knowledge Transfer with Probabilistic Logical Reasoning for Object Detection

Martijn Oldenhof, Adam Arany, Yves Moreau, Edward De Brouwer

展开摘要

Training object detection models usually requires instance-level annotations, such as the positions and labels of all objects present in each image. Such supervision is unfortunately not always available and, more often, only image-level information is provided, also known as weak supervision. Recent works have addressed this limitation by leveraging knowledge from a richly annotated domain. However, the scope of weak supervision supported by these approaches has been very restrictive, preventing them to use all available information. In this work, we propose ProbKT, a framework based on probabilistic logical reasoning to train object detection models with arbitrary types of weak supervision. We empirically show on different datasets that using all available information is beneficial as our ProbKT leads to significant improvement on target domain and better generalisation compared to existing baselines. We also showcase the ability of our approach to handle complex logic statements as supervision signal.

Poster
On Representing Mixed-Integer Linear Programs by Graph Neural Networks

Ziang Chen, Jialin Liu, Xinshang Wang, Wotao Yin

展开摘要

While Mixed-integer linear programming (MILP) is NP-hard in general, practical MILP has received roughly 100--fold speedup in the past twenty years. Still, many classes of MILPs quickly become unsolvable as their sizes increase, motivating researchers to seek new acceleration techniques for MILPs. With deep learning, they have obtained strong empirical results, and many results were obtained by applying graph neural networks (GNNs) to making decisions in various stages of MILP solution processes. This work discovers a fundamental limitation: there exist feasible and infeasible MILPs that all GNNs will, however, treat equally, indicating GNN's lacking power to express general MILPs. Then, we show that, by restricting the MILPs to unfoldable ones or by adding random features, there exist GNNs that can reliably predict MILP feasibility, optimal objective values, and optimal solutions up to prescribed precision. We conducted small-scale numerical experiments to validate our theoretical findings.

Poster
Gradient Boosting Performs Gaussian Process Inference

Aleksei Ustimenko, Artem Beliakov, Liudmila Prokhorenkova

展开摘要

This paper shows that gradient boosting based on symmetric decision trees can be equivalently reformulated as a kernel method that converges to the solution of a certain Kernel Ridge Regression problem. Thus, we obtain the convergence to a Gaussian Process' posterior mean, which, in turn, allows us to easily transform gradient boosting into a sampler from the posterior to provide better knowledge uncertainty estimates through Monte-Carlo estimation of the posterior variance. We show that the proposed sampler allows for better knowledge uncertainty estimates leading to improved out-of-domain detection.

Poster
ROCO: A General Framework for Evaluating Robustness of Combinatorial Optimization Solvers on Graphs

Han Lu, Zenan Li, Runzhong Wang, Qibing Ren, Xijun Li, Mingxuan Yuan, Jia Zeng, Xiaokang Yang, Junchi Yan

展开摘要

Solving combinatorial optimization (CO) on graphs has been attracting increasing interests from the machine learning community whereby data-driven approaches were recently devised to go beyond traditional manually-designated algorithms. In this paper, we study the robustness of a combinatorial solver as a blackbox regardless it is classic or learning-based though the latter can often be more interesting to the ML community. Specifically, we develop a practically feasible robustness metric for general CO solvers. A no-worse optimal cost guarantee is developed as such the optimal solutions are not required to achieve for solvers, and we tackle the non-differentiable challenge in input instance disturbance by resorting to black-box adversarial attack methods. Extensive experiments are conducted on 14 unique combinations of solvers and CO problems, and we demonstrate that the performance of state-of-the-art solvers like Gurobi can degenerate by over 20% under the given time limit bound on the hard instances discovered by our robustness metric, raising concerns about the robustness of combinatorial optimization solvers.

Poster
KnowDA: All-in-One Knowledge Mixture Model for Data Augmentation in Low-Resource NLP

Yufei Wang, Jiayi Zheng, Can Xu, Xiubo Geng, Tao Shen, Chongyang Tao, Daxin Jiang

展开摘要

This paper focuses on data augmentation for low-resource NLP tasks where the training set is limited. The existing solutions either leverage task-independent heuristic rules (e.g., Synonym Replacement) or fine-tune general-purpose pre-trained language models (e.g., GPT2) using the limited training instances to produce new synthetic data. Consequently, they have trivial task-specific knowledge and are limited to yielding low-quality synthetic data. To combat this issue, we propose Knowledge Mixture Data Augmentation Model (KnowDA), a Seq2Seq language model pretrained on a mixture of diverse NLP tasks under a novel framework of Knowledge Mixture Training (KoMT). The goal of KoMT is to condense diverse NLP task-specific knowledge into the single KnowDA model (i.e., all-in-one). The resulting KnowDA could utilize these knowledge to quickly grasp the inherent synthesis law of the target task through limited training instances. Specifically, KoMT reformulates input examples from various heterogeneous NLP tasks into a unified text-to-text format and employs denoising training objectives in different granularity to learn to reconstruct partial or complete samples. To the best of our knowledge, we are the first to attempt to apply 100+ NLP multi-task training for data augmentation. Extensive experiments show that i) the synthetic data produced by KnowDA successfully improves the performance of the strong pre-trained language models (i.e., Bert, ALBert and Deberta) by a large margin on the low-resource NLP benchmark FewGLUE, CoNLL’03 and WikiAnn; ii) KnowDA successful transfer the task knowledge to NLP tasks whose types are seen and unseen in KoMT.

Poster
LogicDP: Creating Labels for Graph Data via Inductive Logic Programming

Yuan Yang, Faramarz Fekri, James Clayton Kerce, Ali Payani

展开摘要

Graph data, such as scene graphs and knowledge graphs, see wide use in AI systems. In real-world and large applications graph data are usually incomplete, motivating graph reasoning models for missing-fact or missing-relationship inference. While these models can achieve state-of-the-art performance, they require a large amount of training data. Recent years have witnessed the rising interest in label creation with data programming (DP) methods, which aim to generate training labels from heuristic labeling functions. However, existing methods typically focus on unstructured data and are not optimized for graphs. In this work, we propose LogicDP, a data programming framework for graph data. Unlike existing DP methods, (1) LogicDP utilizes the inductive logic programming (ILP) technique and automatically discovers the labeling functions from the graph data; (2) LogicDP employs a budget-aware framework to iteratively refine the functions by querying an oracle, which significantly reduces the human efforts in function creations. Experiments show that LogicDP achieves better data efficiency in both scene graph and knowledge graph reasoning tasks.

Poster
The Best of Both Worlds: Accurate Global and Personalized Models through Federated Learning with Data-Free Hyper-Knowledge Distillation

Huancheng Chen, Chianing Wang, Haris Vikalo

展开摘要

Heterogeneity of data distributed across clients limits the performance of global models trained through federated learning, especially in the settings with highly imbalanced class distributions of local datasets. In recent years, personalized federated learning (pFL) has emerged as a potential solution to the challenges presented by heterogeneous data. However, existing pFL methods typically enhance performance of local models at the expense of the global model's accuracy. We propose FedHKD (Federated Hyper-Knowledge Distillation), a novel FL algorithm in which clients rely on knowledge distillation (KD) to train local models. In particular, each client extracts and sends to the server the means of local data representations and the corresponding soft predictions -- information that we refer to as ``hyper-knowledge". The server aggregates this information and broadcasts it to the clients in support of local training. Notably, unlike other KD-based pFL methods, FedHKD does not rely on a public dataset nor it deploys a generative model at the server. We analyze convergence of FedHKD and conduct extensive experiments on visual datasets in a variety of scenarios, demonstrating that FedHKD provides significant improvement in both personalized as well as global model performance compared to state-of-the-art FL methods designed for heterogeneous data settings.

Poster
Learning Fair Graph Representations via Automated Data Augmentations

Hongyi Ling, Zhimeng Jiang, Youzhi Luo, Shuiwang Ji, Na Zou

展开摘要

We consider fair graph representation learning via data augmentations. While this direction has been explored previously, existing methods invariably rely on certain assumptions on the properties of fair graph data in order to design fixed strategies on data augmentations. Nevertheless, the exact properties of fair graph data may vary significantly in different scenarios. Hence, heuristically designed augmentations may not always generate fair graph data in different application scenarios. In this work, we propose a method, known as Graphair, to learn fair representations based on automated graph data augmentations. Such fairness-aware augmentations are themselves learned from data. Our Graphair is designed to automatically discover fairness-aware augmentations from input graphs in order to circumvent sensitive information while preserving other useful information. Experimental results demonstrate that our Graphair consistently outperforms many baselines on multiple node classification datasets in terms of fairness-accuracy trade-off performance. In addition, results indicate that Graphair can automatically learn to generate fair graph data without prior knowledge on fairness-relevant graph properties.

Top-25%
Specformer: Spectral Graph Neural Networks Meet Transformers

Deyu Bo, Chuan Shi, Lele Wang, Renjie Liao

展开摘要

Spectral graph neural networks (GNNs) learn graph representations via spectral-domain graph convolutions. However, most existing spectral graph filters are scalar-to-scalar functions, i.e., mapping a single eigenvalue to a single filtered value, thus ignoring the global pattern of the spectrum. Furthermore, these filters are often constructed based on some fixed-order polynomials, which have limited expressiveness and flexibility. To tackle these issues, we introduce Specformer, which effectively encodes the set of all eigenvalues and performs self-attention in the spectral domain, leading to a learnable set-to-set spectral filter. We also design a decoder with learnable bases to enable non-local graph convolution. Importantly, Specformer is equivariant to permutation. By stacking multiple Specformer layers, one can build a powerful spectral GNN. On synthetic datasets, we show that our Specformer can better recover ground-truth spectral filters than other spectral GNNs. Extensive experiments of both node-level and graph-level tasks on real-world graph datasets show that our Specformer outperforms state-of-the-art GNNs and learns meaningful spectrum patterns. Code and data are available at https://github.com/bdy9527/Specformer.

Poster