William L. Hamilton

Lu Liu, William Hamilton, Guodong Long et al.

Few-shot classification aims to recognize unseen classes when presented with only a small number of samples. We consider the problem of multi-domain few-shot image classification, where unseen classes and examples come from diverse data sources. This problem has seen growing interest and has inspired the development of benchmarks such as Meta-Dataset. A key challenge in this multi-domain setting is to effectively integrate the feature representations from the diverse set of training domains. Here, we propose a Universal Representation Transformer (URT) layer, that meta-learns to leverage universal features for few-shot classification by dynamically re-weighting and composing the most appropriate domain-specific representations. In experiments, we show that URT sets a new state-of-the-art result on Meta-Dataset. Specifically, it achieves top-performance on the highest number of data sources compared to competing methods. We analyze variants of URT and present a visualization of the attention score heatmaps that sheds light on how the model performs cross-domain generalization. Our code is available at https://github.com/liulu112601/URT.

Renjie Liao, Yujia Li, Yang Song et al.

We propose a new family of efficient and expressive deep generative models of graphs, called Graph Recurrent Attention Networks (GRANs). Our model generates graphs one block of nodes and associated edges at a time. The block size and sampling stride allow us to trade off sample quality for efficiency. Compared to previous RNN-based graph generative models, our framework better captures the auto-regressive conditioning between the already-generated and to-be-generated parts of the graph using Graph Neural Networks (GNNs) with attention. This not only reduces the dependency on node ordering but also bypasses the long-term bottleneck caused by the sequential nature of RNNs. Moreover, we parameterize the output distribution per block using a mixture of Bernoulli, which captures the correlations among generated edges within the block. Finally, we propose to handle node orderings in generation by marginalizing over a family of canonical orderings. On standard benchmarks, we achieve state-of-the-art time efficiency and sample quality compared to previous models. Additionally, we show our model is capable of generating large graphs of up to 5K nodes with good quality. To the best of our knowledge, GRAN is the first deep graph generative model that can scale to this size. Our code is released at: https://github.com/lrjconan/GRAN.

Maksym Korablyov, Cheng-Hao Liu, Moksh Jain et al. · mila

Despite substantial progress in machine learning for scientific discovery in recent years, truly de novo design of small molecules which exhibit a property of interest remains a significant challenge. We introduce LambdaZero, a generative active learning approach to search for synthesizable molecules. Powered by deep reinforcement learning, LambdaZero learns to search over the vast space of molecules to discover candidates with a desired property. We apply LambdaZero with molecular docking to design novel small molecules that inhibit the enzyme soluble Epoxide Hydrolase 2 (sEH), while enforcing constraints on synthesizability and drug-likeliness. LambdaZero provides an exponential speedup in terms of the number of calls to the expensive molecular docking oracle, and LambdaZero de novo designed molecules reach docking scores that would otherwise require the virtual screening of a hundred billion molecules. Importantly, LambdaZero discovers novel scaffolds of synthesizable, drug-like inhibitors for sEH. In in vitro experimental validation, a series of ligands from a generated quinazoline-based scaffold were synthesized, and the lead inhibitor N-(4,6-di(pyrrolidin-1-yl)quinazolin-2-yl)-N-methylbenzamide (UM0152893) displayed sub-micromolar enzyme inhibition of sEH.

Vincent Mallet, Carlos G. Oliver, William L. Hamilton

Graph are a ubiquitous data representation, as they represent a flexible and compact representation. For instance, the 3D structure of RNA can be efficiently represented as $\textit{2.5D graphs}$, graphs whose nodes are nucleotides and edges represent chemical interactions. In this setting, we have biological evidence of the similarity between the edge types, as some chemical interactions are more similar than others. Machine learning on graphs have recently experienced a breakthrough with the introduction of Graph Neural Networks. This algorithm can be framed as a message passing algorithm between graph nodes over graph edges. These messages can depend on the edge type they are transmitted through, but no method currently constrains how a message is altered when the edge type changes. Motivated by the RNA use case, in this project we introduce a graph neural network layer which can leverage prior information about similarities between edges. We show that despite the theoretical appeal of including this similarity prior, the empirical performance is not enhanced on the tasks and datasets we include here.

Devin Kreuzer, Dominique Beaini, William L. Hamilton et al.

In recent years, the Transformer architecture has proven to be very successful in sequence processing, but its application to other data structures, such as graphs, has remained limited due to the difficulty of properly defining positions. Here, we present the $\textit{Spectral Attention Network}$ (SAN), which uses a learned positional encoding (LPE) that can take advantage of the full Laplacian spectrum to learn the position of each node in a given graph. This LPE is then added to the node features of the graph and passed to a fully-connected Transformer. By leveraging the full spectrum of the Laplacian, our model is theoretically powerful in distinguishing graphs, and can better detect similar sub-structures from their resonance. Further, by fully connecting the graph, the Transformer does not suffer from over-squashing, an information bottleneck of most GNNs, and enables better modeling of physical phenomenons such as heat transfer and electric interaction. When tested empirically on a set of 4 standard datasets, our model performs on par or better than state-of-the-art GNNs, and outperforms any attention-based model by a wide margin, becoming the first fully-connected architecture to perform well on graph benchmarks.

Stephen Bonner, Ian P Barrett, Cheng Ye et al.

Knowledge Graphs (KG) and associated Knowledge Graph Embedding (KGE) models have recently begun to be explored in the context of drug discovery and have the potential to assist in key challenges such as target identification. In the drug discovery domain, KGs can be employed as part of a process which can result in lab-based experiments being performed, or impact on other decisions, incurring significant time and financial costs and most importantly, ultimately influencing patient healthcare. For KGE models to have impact in this domain, a better understanding of not only of performance, but also the various factors which determine it, is required. In this study we investigate, over the course of many thousands of experiments, the predictive performance of five KGE models on two public drug discovery-oriented KGs. Our goal is not to focus on the best overall model or configuration, instead we take a deeper look at how performance can be affected by changes in the training setup, choice of hyperparameters, model parameter initialisation seed and different splits of the datasets. Our results highlight that these factors have significant impact on performance and can even affect the ranking of models. Indeed these factors should be reported along with model architectures to ensure complete reproducibility and fair comparisons of future work, and we argue this is critical for the acceptance of use, and impact of KGEs in a biomedical setting.

Andjela Mladenovic, Avishek Joey Bose, Hugo Berard et al.

Adversarial attacks expose important vulnerabilities of deep learning models, yet little attention has been paid to settings where data arrives as a stream. In this paper, we formalize the online adversarial attack problem, emphasizing two key elements found in real-world use-cases: attackers must operate under partial knowledge of the target model, and the decisions made by the attacker are irrevocable since they operate on a transient data stream. We first rigorously analyze a deterministic variant of the online threat model by drawing parallels to the well-studied $k$-secretary problem in theoretical computer science and propose Virtual+, a simple yet practical online algorithm. Our main theoretical result shows Virtual+ yields provably the best competitive ratio over all single-threshold algorithms for $k<5$ -- extending the previous analysis of the $k$-secretary problem. We also introduce the \textit{stochastic $k$-secretary} -- effectively reducing online blackbox transfer attacks to a $k$-secretary problem under noise -- and prove theoretical bounds on the performance of Virtual+ adapted to this setting. Finally, we complement our theoretical results by conducting experiments on MNIST, CIFAR-10, and Imagenet classifiers, revealing the necessity of online algorithms in achieving near-optimal performance and also the rich interplay between attack strategies and online attack selection, enabling simple strategies like FGSM to outperform stronger adversaries.

Stephen Bonner, Ian P Barrett, Cheng Ye et al.

Drug discovery and development is a complex and costly process. Machine learning approaches are being investigated to help improve the effectiveness and speed of multiple stages of the drug discovery pipeline. Of these, those that use Knowledge Graphs (KG) have promise in many tasks, including drug repurposing, drug toxicity prediction and target gene-disease prioritisation. In a drug discovery KG, crucial elements including genes, diseases and drugs are represented as entities, whilst relationships between them indicate an interaction. However, to construct high-quality KGs, suitable data is required. In this review, we detail publicly available sources suitable for use in constructing drug discovery focused KGs. We aim to help guide machine learning and KG practitioners who are interested in applying new techniques to the drug discovery field, but who may be unfamiliar with the relevant data sources. The datasets are selected via strict criteria, categorised according to the primary type of information contained within and are considered based upon what information could be extracted to build a KG. We then present a comparative analysis of existing public drug discovery KGs and a evaluation of selected motivating case studies from the literature. Additionally, we raise numerous and unique challenges and issues associated with the domain and its datasets, whilst also highlighting key future research directions. We hope this review will motivate KGs use in solving key and emerging questions in the drug discovery domain.

Dora Jambor, Komal Teru, Joelle Pineau et al.

Real-world knowledge graphs are often characterized by low-frequency relations - a challenge that has prompted an increasing interest in few-shot link prediction methods. These methods perform link prediction for a set of new relations, unseen during training, given only a few example facts of each relation at test time. In this work, we perform a systematic study on a spectrum of models derived by generalizing the current state of the art for few-shot link prediction, with the goal of probing the limits of learning in this few-shot setting. We find that a simple zero-shot baseline - which ignores any relation-specific information - achieves surprisingly strong performance. Moreover, experiments on carefully crafted synthetic datasets show that having only a few examples of a relation fundamentally limits models from using fine-grained structural information and only allows for exploiting the coarse-grained positional information of entities. Together, our findings challenge the implicit assumptions and inductive biases of prior work and highlight new directions for research in this area.

Zichao Yan, William L. Hamilton, Mathieu Blanchette

Our work is concerned with the generation and targeted design of RNA, a type of genetic macromolecule that can adopt complex structures which influence their cellular activities and functions. The design of large scale and complex biological structures spurs dedicated graph-based deep generative modeling techniques, which represents a key but underappreciated aspect of computational drug discovery. In this work, we investigate the principles behind representing and generating different RNA structural modalities, and propose a flexible framework to jointly embed and generate these molecular structures along with their sequence in a meaningful latent space. Equipped with a deep understanding of RNA molecular structures, our most sophisticated encoding and decoding methods operate on the molecular graph as well as the junction tree hierarchy, integrating strong inductive bias about RNA structural regularity and folding mechanism such that high structural validity, stability and diversity of generated RNAs are achieved. Also, we seek to adequately organize the latent space of RNA molecular embeddings with regard to the interaction with proteins, and targeted optimization is used to navigate in this latent space to search for desired novel RNA molecules.

Devendra Singh Sachan, Mostofa Patwary, Mohammad Shoeybi et al.

Recent work on training neural retrievers for open-domain question answering (OpenQA) has employed both supervised and unsupervised approaches. However, it remains unclear how unsupervised and supervised methods can be used most effectively for neural retrievers. In this work, we systematically study retriever pre-training. We first propose an approach of unsupervised pre-training with the Inverse Cloze Task and masked salient spans, followed by supervised finetuning using question-context pairs. This approach leads to absolute gains of 2+ points over the previous best result in the top-20 retrieval accuracy on Natural Questions and TriviaQA datasets. We also explore two approaches for end-to-end supervised training of the reader and retriever components in OpenQA models. In the first approach, the reader considers each retrieved document separately while in the second approach, the reader considers all the retrieved documents together. Our experiments demonstrate the effectiveness of these approaches as we obtain new state-of-the-art results. On the Natural Questions dataset, we obtain a top-20 retrieval accuracy of 84, an improvement of 5 points over the recent DPR model. In addition, we achieve good results on answer extraction, outperforming recent models like REALM and RAG by 3+ points. We further scale up end-to-end training to large models and show consistent gains in performance over smaller models.

Devendra Singh Sachan, Lingfei Wu, Mrinmaya Sachan et al.

Prior work on automated question generation has almost exclusively focused on generating simple questions whose answers can be extracted from a single document. However, there is an increasing interest in developing systems that are capable of more complex multi-hop question generation, where answering the questions requires reasoning over multiple documents. In this work, we introduce a series of strong transformer models for multi-hop question generation, including a graph-augmented transformer that leverages relations between entities in the text. While prior work has emphasized the importance of graph-based models, we show that we can substantially outperform the state-of-the-art by 5 BLEU points using a standard transformer architecture. We further demonstrate that graph-based augmentations can provide complimentary improvements on top of this foundation. Interestingly, we find that several important factors--such as the inclusion of an auxiliary contrastive objective and data filtering could have larger impacts on performance. We hope that our stronger baselines and analysis provide a constructive foundation for future work in this area.

Jiapeng Wu, Meng Cao, Jackie Chi Kit Cheung et al.

Inferring missing facts in temporal knowledge graphs (TKGs) is a fundamental and challenging task. Previous works have approached this problem by augmenting methods for static knowledge graphs to leverage time-dependent representations. However, these methods do not explicitly leverage multi-hop structural information and temporal facts from recent time steps to enhance their predictions. Additionally, prior work does not explicitly address the temporal sparsity and variability of entity distributions in TKGs. We propose the Temporal Message Passing (TeMP) framework to address these challenges by combining graph neural networks, temporal dynamics models, data imputation and frequency-based gating techniques. Experiments on standard TKG tasks show that our approach provides substantial gains compared to the previous state of the art, achieving a 10.7% average relative improvement in Hits@10 across three standard benchmarks. Our analysis also reveals important sources of variability both within and across TKG datasets, and we introduce several simple but strong baselines that outperform the prior state of the art in certain settings.

Dominique Beaini, Saro Passaro, Vincent Létourneau et al.

The lack of anisotropic kernels in graph neural networks (GNNs) strongly limits their expressiveness, contributing to well-known issues such as over-smoothing. To overcome this limitation, we propose the first globally consistent anisotropic kernels for GNNs, allowing for graph convolutions that are defined according to topologicaly-derived directional flows. First, by defining a vector field in the graph, we develop a method of applying directional derivatives and smoothing by projecting node-specific messages into the field. Then, we propose the use of the Laplacian eigenvectors as such vector field. We show that the method generalizes CNNs on an $n$-dimensional grid and is provably more discriminative than standard GNNs regarding the Weisfeiler-Lehman 1-WL test. We evaluate our method on different standard benchmarks and see a relative error reduction of 8% on the CIFAR10 graph dataset and 11% to 32% on the molecular ZINC dataset, and a relative increase in precision of 1.6% on the MolPCBA dataset. An important outcome of this work is that it enables graph networks to embed directions in an unsupervised way, thus allowing a better representation of the anisotropic features in different physical or biological problems.

Kian Ahrabian, Aarash Feizi, Yasmin Salehi et al.

Learning low-dimensional representations for entities and relations in knowledge graphs using contrastive estimation represents a scalable and effective method for inferring connectivity patterns. A crucial aspect of contrastive learning approaches is the choice of corruption distribution that generates hard negative samples, which force the embedding model to learn discriminative representations and find critical characteristics of observed data. While earlier methods either employ too simple corruption distributions, i.e. uniform, yielding easy uninformative negatives or sophisticated adversarial distributions with challenging optimization schemes, they do not explicitly incorporate known graph structure resulting in suboptimal negatives. In this paper, we propose Structure Aware Negative Sampling (SANS), an inexpensive negative sampling strategy that utilizes the rich graph structure by selecting negative samples from a node's k-hop neighborhood. Empirically, we demonstrate that SANS finds semantically meaningful negatives and is competitive with SOTA approaches while requires no additional parameters nor difficult adversarial optimization.

Carlos Oliver, Vincent Mallet, Pericles Philippopoulos et al.

RNA 3D motifs are recurrent substructures, modelled as networks of base pair interactions, which are crucial for understanding structure-function relationships. The task of automatically identifying such motifs is computationally hard, and remains a key challenge in the field of RNA structural biology and network analysis. State of the art methods solve special cases of the motif problem by constraining the structural variability in occurrences of a motif, and narrowing the substructure search space. Here, we relax these constraints by posing the motif finding problem as a graph representation learning and clustering task. This framing takes advantage of the continuous nature of graph representations to model the flexibility and variability of RNA motifs in an efficient manner. We propose a set of node similarity functions, clustering methods, and motif construction algorithms to recover flexible RNA motifs. Our tool, VeRNAl can be easily customized by users to desired levels of motif flexibility, abundance and size. We show that VeRNAl is able to retrieve and expand known classes of motifs, as well as to propose novel motifs.

Devendra Singh Sachan, Yuhao Zhang, Peng Qi et al.

Much recent work suggests that incorporating syntax information from dependency trees can improve task-specific transformer models. However, the effect of incorporating dependency tree information into pre-trained transformer models (e.g., BERT) remains unclear, especially given recent studies highlighting how these models implicitly encode syntax. In this work, we systematically study the utility of incorporating dependency trees into pre-trained transformers on three representative information extraction tasks: semantic role labeling (SRL), named entity recognition, and relation extraction. We propose and investigate two distinct strategies for incorporating dependency structure: a late fusion approach, which applies a graph neural network on the output of a transformer, and a joint fusion approach, which infuses syntax structure into the transformer attention layers. These strategies are representative of prior work, but we introduce additional model design elements that are necessary for obtaining improved performance. Our empirical analysis demonstrates that these syntax-infused transformers obtain state-of-the-art results on SRL and relation extraction tasks. However, our analysis also reveals a critical shortcoming of these models: we find that their performance gains are highly contingent on the availability of human-annotated dependency parses, which raises important questions regarding the viability of syntax-augmented transformers in real-world applications.

Avishek Joey Bose, Gauthier Gidel, Hugo Berard et al.

The existence of adversarial examples capable of fooling trained neural network classifiers calls for a much better understanding of possible attacks to guide the development of safeguards against them. This includes attack methods in the challenging non-interactive blackbox setting, where adversarial attacks are generated without any access, including queries, to the target model. Prior attacks in this setting have relied mainly on algorithmic innovations derived from empirical observations (e.g., that momentum helps), lacking principled transferability guarantees. In this work, we provide a theoretical foundation for crafting transferable adversarial examples to entire hypothesis classes. We introduce Adversarial Example Games (AEG), a framework that models the crafting of adversarial examples as a min-max game between a generator of attacks and a classifier. AEG provides a new way to design adversarial examples by adversarially training a generator and a classifier from a given hypothesis class (e.g., architecture). We prove that this game has an equilibrium, and that the optimal generator is able to craft adversarial examples that can attack any classifier from the corresponding hypothesis class. We demonstrate the efficacy of AEG on the MNIST and CIFAR-10 datasets, outperforming prior state-of-the-art approaches with an average relative improvement of $29.9\%$ and $47.2\%$ against undefended and robust models (Table 2 & 3) respectively.

Koustuv Sinha, Prasanna Parthasarathi, Jasmine Wang et al.

Evaluating the quality of a dialogue interaction between two agents is a difficult task, especially in open-domain chit-chat style dialogue. There have been recent efforts to develop automatic dialogue evaluation metrics, but most of them do not generalize to unseen datasets and/or need a human-generated reference response during inference, making it infeasible for online evaluation. Here, we propose an unreferenced automated evaluation metric that uses large pre-trained language models to extract latent representations of utterances, and leverages the temporal transitions that exist between them. We show that our model achieves higher correlation with human annotations in an online setting, while not requiring true responses for comparison during inference.

Koustuv Sinha, Shagun Sodhani, Joelle Pineau et al.

Recent research has highlighted the role of relational inductive biases in building learning agents that can generalize and reason in a compositional manner. However, while relational learning algorithms such as graph neural networks (GNNs) show promise, we do not understand how effectively these approaches can adapt to new tasks. In this work, we study the task of logical generalization using GNNs by designing a benchmark suite grounded in first-order logic. Our benchmark suite, GraphLog, requires that learning algorithms perform rule induction in different synthetic logics, represented as knowledge graphs. GraphLog consists of relation prediction tasks on 57 distinct logical domains. We use GraphLog to evaluate GNNs in three different setups: single-task supervised learning, multi-task pretraining, and continual learning. Unlike previous benchmarks, our approach allows us to precisely control the logical relationship between the different tasks. We find that the ability for models to generalize and adapt is strongly determined by the diversity of the logical rules they encounter during training, and our results highlight new challenges for the design of GNN models. We publicly release the dataset and code used to generate and interact with the dataset at https://www.cs.mcgill.ca/~ksinha4/graphlog.

Ashutosh Adhikari, Xingdi Yuan, Marc-Alexandre Côté et al.

Playing text-based games requires skills in processing natural language and sequential decision making. Achieving human-level performance on text-based games remains an open challenge, and prior research has largely relied on hand-crafted structured representations and heuristics. In this work, we investigate how an agent can plan and generalize in text-based games using graph-structured representations learned end-to-end from raw text. We propose a novel graph-aided transformer agent (GATA) that infers and updates latent belief graphs during planning to enable effective action selection by capturing the underlying game dynamics. GATA is trained using a combination of reinforcement and self-supervised learning. Our work demonstrates that the learned graph-based representations help agents converge to better policies than their text-only counterparts and facilitate effective generalization across game configurations. Experiments on 500+ unique games from the TextWorld suite show that our best agent outperforms text-based baselines by an average of 24.2%.

Avishek Joey Bose, Ariella Smofsky, Renjie Liao et al.

The choice of approximate posterior distributions plays a central role in stochastic variational inference (SVI). One effective solution is the use of normalizing flows \cut{defined on Euclidean spaces} to construct flexible posterior distributions. However, one key limitation of existing normalizing flows is that they are restricted to the Euclidean space and are ill-equipped to model data with an underlying hierarchical structure. To address this fundamental limitation, we present the first extension of normalizing flows to hyperbolic spaces. We first elevate normalizing flows to hyperbolic spaces using coupling transforms defined on the tangent bundle, termed Tangent Coupling ($\mathcal{TC}$). We further introduce Wrapped Hyperboloid Coupling ($\mathcal{W}\mathbb{H}C$), a fully invertible and learnable transformation that explicitly utilizes the geometric structure of hyperbolic spaces, allowing for expressive posteriors while being efficient to sample from. We demonstrate the efficacy of our novel normalizing flow over hyperbolic VAEs and Euclidean normalizing flows. Our approach achieves improved performance on density estimation, as well as reconstruction of real-world graph data, which exhibit a hierarchical structure. Finally, we show that our approach can be used to power a generative model over hierarchical data using hyperbolic latent variables.

Agnieszka Słowik, Abhinav Gupta, William L. Hamilton et al.

In order to communicate, humans flatten a complex representation of ideas and their attributes into a single word or a sentence. We investigate the impact of representation learning in artificial agents by developing graph referential games. We empirically show that agents parametrized by graph neural networks develop a more compositional language compared to bag-of-words and sequence models, which allows them to systematically generalize to new combinations of familiar features.

Agnieszka Słowik, Abhinav Gupta, William L. Hamilton et al.

Recent findings in neuroscience suggest that the human brain represents information in a geometric structure (for instance, through conceptual spaces). In order to communicate, we flatten the complex representation of entities and their attributes into a single word or a sentence. In this paper we use graph convolutional networks to support the evolution of language and cooperation in multi-agent systems. Motivated by an image-based referential game, we propose a graph referential game with varying degrees of complexity, and we provide strong baseline models that exhibit desirable properties in terms of language emergence and cooperation. We show that the emerged communication protocol is robust, that the agents uncover the true factors of variation in the game, and that they learn to generalize beyond the samples encountered during training.

Avishek Joey Bose, Ankit Jain, Piero Molino et al.

We consider the task of few shot link prediction on graphs. The goal is to learn from a distribution over graphs so that a model is able to quickly infer missing edges in a new graph after a small amount of training. We show that current link prediction methods are generally ill-equipped to handle this task. They cannot effectively transfer learned knowledge from one graph to another and are unable to effectively learn from sparse samples of edges. To address this challenge, we introduce a new gradient-based meta learning framework, Meta-Graph. Our framework leverages higher-order gradients along with a learned graph signature function that conditionally generates a graph neural network initialization. Using a novel set of few shot link prediction benchmarks, we show that Meta-Graph can learn to quickly adapt to a new graph using only a small sample of true edges, enabling not only fast adaptation but also improved results at convergence.

Komal K. Teru, Etienne Denis, William L. Hamilton

The dominant paradigm for relation prediction in knowledge graphs involves learning and operating on latent representations (i.e., embeddings) of entities and relations. However, these embedding-based methods do not explicitly capture the compositional logical rules underlying the knowledge graph, and they are limited to the transductive setting, where the full set of entities must be known during training. Here, we propose a graph neural network based relation prediction framework, GraIL, that reasons over local subgraph structures and has a strong inductive bias to learn entity-independent relational semantics. Unlike embedding-based models, GraIL is naturally inductive and can generalize to unseen entities and graphs after training. We provide theoretical proof and strong empirical evidence that GraIL can represent a useful subset of first-order logic and show that GraIL outperforms existing rule-induction baselines in the inductive setting. We also demonstrate significant gains obtained by ensembling GraIL with various knowledge graph embedding methods in the transductive setting, highlighting the complementary inductive bias of our method.

Jonathan Lebensold, William Hamilton, Borja Balle et al.

Reinforcement learning algorithms are known to be sample inefficient, and often performance on one task can be substantially improved by leveraging information (e.g., via pre-training) on other related tasks. In this work, we propose a technique to achieve such knowledge transfer in cases where agent trajectories contain sensitive or private information, such as in the healthcare domain. Our approach leverages a differentially private policy evaluation algorithm to initialize an actor-critic model and improve the effectiveness of learning in downstream tasks. We empirically show this technique increases sample efficiency in resource-constrained control problems while preserving the privacy of trajectories collected in an upstream task.

Koustuv Sinha, Shagun Sodhani, Jin Dong et al.

The recent success of natural language understanding (NLU) systems has been troubled by results highlighting the failure of these models to generalize in a systematic and robust way. In this work, we introduce a diagnostic benchmark suite, named CLUTRR, to clarify some key issues related to the robustness and systematicity of NLU systems. Motivated by classic work on inductive logic programming, CLUTRR requires that an NLU system infer kinship relations between characters in short stories. Successful performance on this task requires both extracting relationships between entities, as well as inferring the logical rules governing these relationships. CLUTRR allows us to precisely measure a model's ability for systematic generalization by evaluating on held-out combinations of logical rules, and it allows us to evaluate a model's robustness by adding curated noise facts. Our empirical results highlight a substantial performance gap between state-of-the-art NLU models (e.g., BERT and MAC) and a graph neural network model that works directly with symbolic inputs---with the graph-based model exhibiting both stronger generalization and greater robustness.

Charles C. Onu, Jonathan Lebensold, William L. Hamilton et al.

Despite continuing medical advances, the rate of newborn morbidity and mortality globally remains high, with over 6 million casualties every year. The prediction of pathologies affecting newborns based on their cry is thus of significant clinical interest, as it would facilitate the development of accessible, low-cost diagnostic tools\cut{ based on wearables and smartphones}. However, the inadequacy of clinically annotated datasets of infant cries limits progress on this task. This study explores a neural transfer learning approach to developing accurate and robust models for identifying infants that have suffered from perinatal asphyxia. In particular, we explore the hypothesis that representations learned from adult speech could inform and improve performance of models developed on infant speech. Our experiments show that models based on such representation transfer are resilient to different types and degrees of noise, as well as to signal loss in time and frequency domains.

Avishek Joey Bose, Andre Cianflone, William L. Hamilton

Adversarial attacks on deep neural networks traditionally rely on a constrained optimization paradigm, where an optimization procedure is used to obtain a single adversarial perturbation for a given input example. In this work we frame the problem as learning a distribution of adversarial perturbations, enabling us to generate diverse adversarial distributions given an unperturbed input. We show that this framework is domain-agnostic in that the same framework can be employed to attack different input domains with minimal modification. Across three diverse domains---images, text, and graphs---our approach generates whitebox attacks with success rates that are competitive with or superior to existing approaches, with a new state-of-the-art achieved in the graph domain. Finally, we demonstrate that our framework can efficiently generate a diverse set of attacks for a single given input, and is even capable of attacking \textit{unseen} test instances in a zero-shot manner, exhibiting attack generalization.

Avishek Joey Bose, William L. Hamilton

Learning high-quality node embeddings is a key building block for machine learning models that operate on graph data, such as social networks and recommender systems. However, existing graph embedding techniques are unable to cope with fairness constraints, e.g., ensuring that the learned representations do not correlate with certain attributes, such as age or gender. Here, we introduce an adversarial framework to enforce fairness constraints on graph embeddings. Our approach is compositional---meaning that it can flexibly accommodate different combinations of fairness constraints during inference. For instance, in the context of social recommendations, our framework would allow one user to request that their recommendations are invariant to both their age and gender, while also allowing another user to request invariance to just their age. Experiments on standard knowledge graph and recommender system benchmarks highlight the utility of our proposed framework.

Koustuv Sinha, Shagun Sodhani, William L. Hamilton et al.

Neural networks for natural language reasoning have largely focused on extractive, fact-based question-answering (QA) and common-sense inference. However, it is also crucial to understand the extent to which neural networks can perform relational reasoning and combinatorial generalization from natural language---abilities that are often obscured by annotation artifacts and the dominance of language modeling in standard QA benchmarks. In this work, we present a novel benchmark dataset for language understanding that isolates performance on relational reasoning. We also present a neural message-passing baseline and show that this model, which incorporates a relational inductive bias, is superior at combinatorial generalization compared to a traditional recurrent neural network approach.

Christopher Morris, Martin Ritzert, Matthias Fey et al.

In recent years, graph neural networks (GNNs) have emerged as a powerful neural architecture to learn vector representations of nodes and graphs in a supervised, end-to-end fashion. Up to now, GNNs have only been evaluated empirically -- showing promising results. The following work investigates GNNs from a theoretical point of view and relates them to the $1$-dimensional Weisfeiler-Leman graph isomorphism heuristic ($1$-WL). We show that GNNs have the same expressiveness as the $1$-WL in terms of distinguishing non-isomorphic (sub-)graphs. Hence, both algorithms also have the same shortcomings. Based on this, we propose a generalization of GNNs, so-called $k$-dimensional GNNs ($k$-GNNs), which can take higher-order graph structures at multiple scales into account. These higher-order structures play an essential role in the characterization of social networks and molecule graphs. Our experimental evaluation confirms our theoretical findings as well as confirms that higher-order information is useful in the task of graph classification and regression.

Petar Veličković, William Fedus, William L. Hamilton et al.

We present Deep Graph Infomax (DGI), a general approach for learning node representations within graph-structured data in an unsupervised manner. DGI relies on maximizing mutual information between patch representations and corresponding high-level summaries of graphs---both derived using established graph convolutional network architectures. The learnt patch representations summarize subgraphs centered around nodes of interest, and can thus be reused for downstream node-wise learning tasks. In contrast to most prior approaches to unsupervised learning with GCNs, DGI does not rely on random walk objectives, and is readily applicable to both transductive and inductive learning setups. We demonstrate competitive performance on a variety of node classification benchmarks, which at times even exceeds the performance of supervised learning.

Rex Ying, Jiaxuan You, Christopher Morris et al.

Recently, graph neural networks (GNNs) have revolutionized the field of graph representation learning through effectively learned node embeddings, and achieved state-of-the-art results in tasks such as node classification and link prediction. However, current GNN methods are inherently flat and do not learn hierarchical representations of graphs---a limitation that is especially problematic for the task of graph classification, where the goal is to predict the label associated with an entire graph. Here we propose DiffPool, a differentiable graph pooling module that can generate hierarchical representations of graphs and can be combined with various graph neural network architectures in an end-to-end fashion. DiffPool learns a differentiable soft cluster assignment for nodes at each layer of a deep GNN, mapping nodes to a set of clusters, which then form the coarsened input for the next GNN layer. Our experimental results show that combining existing GNN methods with DiffPool yields an average improvement of 5-10% accuracy on graph classification benchmarks, compared to all existing pooling approaches, achieving a new state-of-the-art on four out of five benchmark data sets.

Srijan Kumar, William L. Hamilton, Jure Leskovec et al.

Users organize themselves into communities on web platforms. These communities can interact with one another, often leading to conflicts and toxic interactions. However, little is known about the mechanisms of interactions between communities and how they impact users. Here we study intercommunity interactions across 36,000 communities on Reddit, examining cases where users of one community are mobilized by negative sentiment to comment in another community. We show that such conflicts tend to be initiated by a handful of communities---less than 1% of communities start 74% of conflicts. While conflicts tend to be initiated by highly active community members, they are carried out by significantly less active members. We find that conflicts are marked by formation of echo chambers, where users primarily talk to other users from their own community. In the long-term, conflicts have adverse effects and reduce the overall activity of users in the targeted communities. Our analysis of user interactions also suggests strategies for mitigating the negative impact of conflicts---such as increasing direct engagement between attackers and defenders. Further, we accurately predict whether a conflict will occur by creating a novel LSTM model that combines graph embeddings, user, community, and text features. This model can be used toreate early-warning systems for community moderators to prevent conflicts. Altogether, this work presents a data-driven view of community interactions and conflict, and paves the way towards healthier online communities.

William L. Hamilton, Rex Ying, Jure Leskovec

Machine learning on graphs is an important and ubiquitous task with applications ranging from drug design to friendship recommendation in social networks. The primary challenge in this domain is finding a way to represent, or encode, graph structure so that it can be easily exploited by machine learning models. Traditionally, machine learning approaches relied on user-defined heuristics to extract features encoding structural information about a graph (e.g., degree statistics or kernel functions). However, recent years have seen a surge in approaches that automatically learn to encode graph structure into low-dimensional embeddings, using techniques based on deep learning and nonlinear dimensionality reduction. Here we provide a conceptual review of key advancements in this area of representation learning on graphs, including matrix factorization-based methods, random-walk based algorithms, and graph neural networks. We review methods to embed individual nodes as well as approaches to embed entire (sub)graphs. In doing so, we develop a unified framework to describe these recent approaches, and we highlight a number of important applications and directions for future work.

Justine Zhang, William L. Hamilton, Cristian Danescu-Niculescu-Mizil et al.

A community's identity defines and shapes its internal dynamics. Our current understanding of this interplay is mostly limited to glimpses gathered from isolated studies of individual communities. In this work we provide a systematic exploration of the nature of this relation across a wide variety of online communities. To this end we introduce a quantitative, language-based typology reflecting two key aspects of a community's identity: how distinctive, and how temporally dynamic it is. By mapping almost 300 Reddit communities into the landscape induced by this typology, we reveal regularities in how patterns of user engagement vary with the characteristics of a community. Our results suggest that the way new and existing users engage with a community depends strongly and systematically on the nature of the collective identity it fosters, in ways that are highly consequential to community maintainers. For example, communities with distinctive and highly dynamic identities are more likely to retain their users. However, such niche communities also exhibit much larger acculturation gaps between existing users and newcomers, which potentially hinder the integration of the latter. More generally, our methodology reveals differences in how various social phenomena manifest across communities, and shows that structuring the multi-community landscape can lead to a better understanding of the systematic nature of this diversity.

William L. Hamilton, Justine Zhang, Cristian Danescu-Niculescu-Mizil et al.

Loyalty is an essential component of multi-community engagement. When users have the choice to engage with a variety of different communities, they often become loyal to just one, focusing on that community at the expense of others. However, it is unclear how loyalty is manifested in user behavior, or whether loyalty is encouraged by certain community characteristics. In this paper we operationalize loyalty as a user-community relation: users loyal to a community consistently prefer it over all others; loyal communities retain their loyal users over time. By exploring this relation using a large dataset of discussion communities from Reddit, we reveal that loyalty is manifested in remarkably consistent behaviors across a wide spectrum of communities. Loyal users employ language that signals collective identity and engage with more esoteric, less popular content, indicating they may play a curational role in surfacing new material. Loyal communities have denser user-user interaction networks and lower rates of triadic closure, suggesting that community-level loyalty is associated with more cohesive interactions and less fragmentation into subgroups. We exploit these general patterns to predict future rates of loyalty. Our results show that a user's propensity to become loyal is apparent from their first interactions with a community, suggesting that some users are intrinsically loyal from the very beginning.

William L. Hamilton, Mahdi Milani Fard, Joelle Pineau

Predictive state representations (PSRs) offer an expressive framework for modelling partially observable systems. By compactly representing systems as functions of observable quantities, the PSR learning approach avoids using local-minima prone expectation-maximization and instead employs a globally optimal moment-based algorithm. Moreover, since PSRs do not require a predetermined latent state structure as an input, they offer an attractive framework for model-based reinforcement learning when agents must plan without a priori access to a system model. Unfortunately, the expressiveness of PSRs comes with significant computational cost, and this cost is a major factor inhibiting the use of PSRs in applications. In order to alleviate this shortcoming, we introduce the notion of compressed PSRs (CPSRs). The CPSR learning approach combines recent advancements in dimensionality reduction, incremental matrix decomposition, and compressed sensing. We show how this approach provides a principled avenue for learning accurate approximations of PSRs, drastically reducing the computational costs associated with learning while also providing effective regularization. Going further, we propose a planning framework which exploits these learned models. And we show that this approach facilitates model-learning and planning in large complex partially observable domains, a task that is infeasible without the principled use of compression.