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Researcher profile

Jure Leskovec

Jure Leskovec contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Machine LearningArtificial IntelligenceSocial and Information NetworksComputer VisionComputation and LanguageInformation RetrievalComputational Engineering, Finance, and Sciencecs.CYphysics.comp-phphysics.geo-ph

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Published work

37 published item(s)

preprint2026arXiv

Learning over Positive and Negative Edges with Contrastive Message Passing

Conventional approaches to learning on graphs involve message passing along existing (i.e., positive) edges to update node features. However, these approaches often disregard the potentially valuable information contained in the absence (i.e., negative) of edges. Here, we theoretically analyze the value of negative edges in graph representations and prove that in settings of low label rates, high homophily, and high edge density, access to negative edges provides significant information gain over using only positive edges. Motivated by this insight, we introduce Contrastive Message Passing (CMP), a general message passing architecture that enable graph neural network layers to reason over positive and negative edges. By imposing soft positive semidefinite constraints on the learnable weights, our approach differentially applies similarity-preserving transformations to positively connected nodes and dissimilarity-inducing transformations to negatively connected nodes. Over simulated and real datasets in varying data regimes, CMP consistently outperforms baselines in low-label settings when negative edges are informative.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

NoiseRater: Meta-Learned Noise Valuation for Diffusion Model Training

Diffusion models have achieved remarkable success across a wide range of generative tasks, yet their training paradigm largely treats injected noise as uniformly informative. In this work, we challenge this assumption and introduce NoiseRater, a meta-learning framework for instance-level noise valuation in diffusion model training. We propose a parametric noise rater that assigns importance scores to individual noise realizations conditioned on data and timestep, enabling adaptive reweighting of the training objective. The rater is trained via bilevel optimization to improve downstream validation performance after inner-loop diffusion updates. To enable efficient deployment, we further design a decoupled two-stage pipeline that transitions from soft weighting during meta-training to hard noise selection during standard training. Extensive experiments on FFHQ and ImageNet demonstrate that not all noise samples contribute equally, and that prioritizing informative noise improves both training efficiency and generation quality. Our results establish noise valuation as a complementary and previously underexplored axis for improving diffusion model training. Our code is available at: https://anonymous.4open.science/r/NoiseRater-DEB116.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

Proteo-R1: Reasoning Foundation Models for De Novo Protein Design

Deep learning in \emph{de novo} protein design has achieved atomic-level fidelity. However, existing models remain largely non-deliberative: they directly synthesize molecular geometries without explicitly reasoning about which residues or interactions are functionally essential. As a result, design decisions are entangled with continuous sampling dynamics, limiting interpretability, controllability, and systematic reuse of biochemical knowledge. We introduce \textbf{Proteo-R1}, a reasoning-guided protein design framework that explicitly decouples \emph{molecular understanding} from \emph{geometric generation}. Proteo-R1 adopts a dual-expert architecture in which a multimodal large language model (MLLM) serves as an \emph{understanding expert}, analyzing protein sequences, structures, and textual context to identify key functional residues that govern binding and specificity. These residue-level decisions are then passed as hard constraints to a separate diffusion-based \emph{generation expert}, which performs conditional co-design while respecting the fixed interaction anchors. This factorization mirrors how human experts approach molecular engineering: first, reasoning about critical interactions, then optimizing geometry subject to those constraints. By operationalizing reasoning as explicit residue-level commitments rather than latent textual guidance, Proteo-R1 achieves stable, interpretable, and modular integration of LLM reasoning with state-of-the-art geometric generative models. Code, data, and demos are available at https://smiles724.github.io/r1/.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

Surface-based Molecular Design with Multi-modal Flow Matching

Therapeutic peptides show promise in targeting previously undruggable binding sites, with recent advancements in deep generative models enabling full-atom peptide co-design for specific protein receptors. However, the critical role of molecular surfaces in protein-protein interactions (PPIs) has been underexplored. To bridge this gap, we propose an omni-design peptides generation paradigm, called SurfFlow, a novel surface-based generative algorithm that enables comprehensive co-design of sequence, structure, and surface for peptides. SurfFlow employs a multi-modality conditional flow matching (CFM) architecture to learn distributions of surface geometries and biochemical properties, enhancing peptide binding accuracy. Evaluated on the comprehensive PepMerge benchmark, SurfFlow consistently outperforms full-atom baselines across all metrics. These results highlight the advantages of considering molecular surfaces in de novo peptide discovery and demonstrate the potential of integrating multiple protein modalities for more effective therapeutic peptide discovery.

0 citations0 reviewsNo code linkedOpen access
preprint2025arXiv

End-to-End Test-Time Training for Long Context

We formulate long-context language modeling as a problem in continual learning rather than architecture design. Under this formulation, we only use a standard architecture -- a Transformer with sliding-window attention. However, our model continues learning at test time via next-token prediction on the given context, compressing the context it reads into its weights. In addition, we improve the model's initialization for learning at test time via meta-learning at training time. Overall, our method, a form of Test-Time Training (TTT), is End-to-End (E2E) both at test time (via next-token prediction) and training time (via meta-learning), in contrast to previous forms. We conduct extensive experiments with a focus on scaling properties. In particular, for 3B models trained with 164B tokens, our method (TTT-E2E) scales with context length in the same way as Transformer with full attention, while others, such as Mamba 2 and Gated DeltaNet, do not. However, similar to RNNs, TTT-E2E has constant inference latency regardless of context length, making it 2.7 times faster than full attention for 128K context. Our code is publicly available.

0 citations0 reviewsNo code linkedOpen access
preprint2024arXiv

TimeGraphs: Graph-based Temporal Reasoning

Many real-world systems exhibit temporal, dynamic behaviors, which are captured as time series of complex agent interactions. To perform temporal reasoning, current methods primarily encode temporal dynamics through simple sequence-based models. However, in general these models fail to efficiently capture the full spectrum of rich dynamics in the input, since the dynamics is not uniformly distributed. In particular, relevant information might be harder to extract and computing power is wasted for processing all individual timesteps, even if they contain no significant changes or no new information. Here we propose TimeGraphs, a novel approach that characterizes dynamic interactions as a hierarchical temporal graph, diverging from traditional sequential representations. Our approach models the interactions using a compact graph-based representation, enabling adaptive reasoning across diverse time scales. Adopting a self-supervised method, TimeGraphs constructs a multi-level event hierarchy from a temporal input, which is then used to efficiently reason about the unevenly distributed dynamics. This construction process is scalable and incremental to accommodate streaming data. We evaluate TimeGraphs on multiple datasets with complex, dynamic agent interactions, including a football simulator, the Resistance game, and the MOMA human activity dataset. The results demonstrate both robustness and efficiency of TimeGraphs on a range of temporal reasoning tasks. Our approach obtains state-of-the-art performance and leads to a performance increase of up to 12.2% on event prediction and recognition tasks over current approaches. Our experiments further demonstrate a wide array of capabilities including zero-shot generalization, robustness in case of data sparsity, and adaptability to streaming data flow.

0 citations0 reviewsNo code linkedOpen access
preprint2024arXiv

When Do Graph Neural Networks Help with Node Classification? Investigating the Impact of Homophily Principle on Node Distinguishability

Homophily principle, i.e., nodes with the same labels are more likely to be connected, has been believed to be the main reason for the performance superiority of Graph Neural Networks (GNNs) over Neural Networks on node classification tasks. Recent research suggests that, even in the absence of homophily, the advantage of GNNs still exists as long as nodes from the same class share similar neighborhood patterns. However, this argument only considers intra-class Node Distinguishability (ND) but neglects inter-class ND, which provides incomplete understanding of homophily on GNNs. In this paper, we first demonstrate such deficiency with examples and argue that an ideal situation for ND is to have smaller intra-class ND than inter-class ND. To formulate this idea and study ND deeply, we propose Contextual Stochastic Block Model for Homophily (CSBM-H) and define two metrics, Probabilistic Bayes Error (PBE) and negative generalized Jeffreys divergence, to quantify ND. With the metrics, we visualize and analyze how graph filters, node degree distributions and class variances influence ND, and investigate the combined effect of intra- and inter-class ND. Besides, we discovered the mid-homophily pitfall, which occurs widely in graph datasets. Furthermore, we verified that, in real-work tasks, the superiority of GNNs is indeed closely related to both intra- and inter-class ND regardless of homophily levels. Grounded in this observation, we propose a new hypothesis-testing based performance metric beyond homophily, which is non-linear, feature-based and can provide statistical threshold value for GNNs' the superiority. Experiments indicate that it is significantly more effective than the existing homophily metrics on revealing the advantage and disadvantage of graph-aware modes on both synthetic and benchmark real-world datasets.

0 citations0 reviewsNo code linkedOpen access
preprint2023arXiv

Learning Graph Search Heuristics

Searching for a path between two nodes in a graph is one of the most well-studied and fundamental problems in computer science. In numerous domains such as robotics, AI, or biology, practitioners develop search heuristics to accelerate their pathfinding algorithms. However, it is a laborious and complex process to hand-design heuristics based on the problem and the structure of a given use case. Here we present PHIL (Path Heuristic with Imitation Learning), a novel neural architecture and a training algorithm for discovering graph search and navigation heuristics from data by leveraging recent advances in imitation learning and graph representation learning. At training time, we aggregate datasets of search trajectories and ground-truth shortest path distances, which we use to train a specialized graph neural network-based heuristic function using backpropagation through steps of the pathfinding process. Our heuristic function learns graph embeddings useful for inferring node distances, runs in constant time independent of graph sizes, and can be easily incorporated in an algorithm such as A* at test time. Experiments show that PHIL reduces the number of explored nodes compared to state-of-the-art methods on benchmark datasets by 58.5\% on average, can be directly applied in diverse graphs ranging from biological networks to road networks, and allows for fast planning in time-critical robotics domains.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

AdaGrid: Adaptive Grid Search for Link Prediction Training Objective

One of the most important factors that contribute to the success of a machine learning model is a good training objective. Training objective crucially influences the model's performance and generalization capabilities. This paper specifically focuses on graph neural network training objective for link prediction, which has not been explored in the existing literature. Here, the training objective includes, among others, a negative sampling strategy, and various hyperparameters, such as edge message ratio which controls how training edges are used. Commonly, these hyperparameters are fine-tuned by complete grid search, which is very time-consuming and model-dependent. To mitigate these limitations, we propose Adaptive Grid Search (AdaGrid), which dynamically adjusts the edge message ratio during training. It is model agnostic and highly scalable with a fully customizable computational budget. Through extensive experiments, we show that AdaGrid can boost the performance of the models up to $1.9\%$ while being nine times more time-efficient than a complete search. Overall, AdaGrid represents an effective automated algorithm for designing machine learning training objectives.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Extending the WILDS Benchmark for Unsupervised Adaptation

Machine learning systems deployed in the wild are often trained on a source distribution but deployed on a different target distribution. Unlabeled data can be a powerful point of leverage for mitigating these distribution shifts, as it is frequently much more available than labeled data and can often be obtained from distributions beyond the source distribution as well. However, existing distribution shift benchmarks with unlabeled data do not reflect the breadth of scenarios that arise in real-world applications. In this work, we present the WILDS 2.0 update, which extends 8 of the 10 datasets in the WILDS benchmark of distribution shifts to include curated unlabeled data that would be realistically obtainable in deployment. These datasets span a wide range of applications (from histology to wildlife conservation), tasks (classification, regression, and detection), and modalities (photos, satellite images, microscope slides, text, molecular graphs). The update maintains consistency with the original WILDS benchmark by using identical labeled training, validation, and test sets, as well as the evaluation metrics. On these datasets, we systematically benchmark state-of-the-art methods that leverage unlabeled data, including domain-invariant, self-training, and self-supervised methods, and show that their success on WILDS is limited. To facilitate method development and evaluation, we provide an open-source package that automates data loading and contains all of the model architectures and methods used in this paper. Code and leaderboards are available at https://wilds.stanford.edu.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

GreaseLM: Graph REASoning Enhanced Language Models for Question Answering

Answering complex questions about textual narratives requires reasoning over both stated context and the world knowledge that underlies it. However, pretrained language models (LM), the foundation of most modern QA systems, do not robustly represent latent relationships between concepts, which is necessary for reasoning. While knowledge graphs (KG) are often used to augment LMs with structured representations of world knowledge, it remains an open question how to effectively fuse and reason over the KG representations and the language context, which provides situational constraints and nuances. In this work, we propose GreaseLM, a new model that fuses encoded representations from pretrained LMs and graph neural networks over multiple layers of modality interaction operations. Information from both modalities propagates to the other, allowing language context representations to be grounded by structured world knowledge, and allowing linguistic nuances (e.g., negation, hedging) in the context to inform the graph representations of knowledge. Our results on three benchmarks in the commonsense reasoning (i.e., CommonsenseQA, OpenbookQA) and medical question answering (i.e., MedQA-USMLE) domains demonstrate that GreaseLM can more reliably answer questions that require reasoning over both situational constraints and structured knowledge, even outperforming models 8x larger.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

ItemSage: Learning Product Embeddings for Shopping Recommendations at Pinterest

Learned embeddings for products are an important building block for web-scale e-commerce recommendation systems. At Pinterest, we build a single set of product embeddings called ItemSage to provide relevant recommendations in all shopping use cases including user, image and search based recommendations. This approach has led to significant improvements in engagement and conversion metrics, while reducing both infrastructure and maintenance cost. While most prior work focuses on building product embeddings from features coming from a single modality, we introduce a transformer-based architecture capable of aggregating information from both text and image modalities and show that it significantly outperforms single modality baselines. We also utilize multi-task learning to make ItemSage optimized for several engagement types, leading to a candidate generation system that is efficient for all of the engagement objectives of the end-to-end recommendation system. Extensive offline experiments are conducted to illustrate the effectiveness of our approach and results from online A/B experiments show substantial gains in key business metrics (up to +7% gross merchandise value/user and +11% click volume).

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Learning Backward Compatible Embeddings

Embeddings, low-dimensional vector representation of objects, are fundamental in building modern machine learning systems. In industrial settings, there is usually an embedding team that trains an embedding model to solve intended tasks (e.g., product recommendation). The produced embeddings are then widely consumed by consumer teams to solve their unintended tasks (e.g., fraud detection). However, as the embedding model gets updated and retrained to improve performance on the intended task, the newly-generated embeddings are no longer compatible with the existing consumer models. This means that historical versions of the embeddings can never be retired or all consumer teams have to retrain their models to make them compatible with the latest version of the embeddings, both of which are extremely costly in practice. Here we study the problem of embedding version updates and their backward compatibility. We formalize the problem where the goal is for the embedding team to keep updating the embedding version, while the consumer teams do not have to retrain their models. We develop a solution based on learning backward compatible embeddings, which allows the embedding model version to be updated frequently, while also allowing the latest version of the embedding to be quickly transformed into any backward compatible historical version of it, so that consumer teams do not have to retrain their models. Under our framework, we explore six methods and systematically evaluate them on a real-world recommender system application. We show that the best method, which we call BC-Aligner, maintains backward compatibility with existing unintended tasks even after multiple model version updates. Simultaneously, BC-Aligner achieves the intended task performance similar to the embedding model that is solely optimized for the intended task.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Learning Large-scale Subsurface Simulations with a Hybrid Graph Network Simulator

Subsurface simulations use computational models to predict the flow of fluids (e.g., oil, water, gas) through porous media. These simulations are pivotal in industrial applications such as petroleum production, where fast and accurate models are needed for high-stake decision making, for example, for well placement optimization and field development planning. Classical finite difference numerical simulators require massive computational resources to model large-scale real-world reservoirs. Alternatively, streamline simulators and data-driven surrogate models are computationally more efficient by relying on approximate physics models, however they are insufficient to model complex reservoir dynamics at scale. Here we introduce Hybrid Graph Network Simulator (HGNS), which is a data-driven surrogate model for learning reservoir simulations of 3D subsurface fluid flows. To model complex reservoir dynamics at both local and global scale, HGNS consists of a subsurface graph neural network (SGNN) to model the evolution of fluid flows, and a 3D-U-Net to model the evolution of pressure. HGNS is able to scale to grids with millions of cells per time step, two orders of magnitude higher than previous surrogate models, and can accurately predict the fluid flow for tens of time steps (years into the future). Using an industry-standard subsurface flow dataset (SPE-10) with 1.1 million cells, we demonstrate that HGNS is able to reduce the inference time up to 18 times compared to standard subsurface simulators, and that it outperforms other learning-based models by reducing long-term prediction errors by up to 21%.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

LinkBERT: Pretraining Language Models with Document Links

Language model (LM) pretraining can learn various knowledge from text corpora, helping downstream tasks. However, existing methods such as BERT model a single document, and do not capture dependencies or knowledge that span across documents. In this work, we propose LinkBERT, an LM pretraining method that leverages links between documents, e.g., hyperlinks. Given a text corpus, we view it as a graph of documents and create LM inputs by placing linked documents in the same context. We then pretrain the LM with two joint self-supervised objectives: masked language modeling and our new proposal, document relation prediction. We show that LinkBERT outperforms BERT on various downstream tasks across two domains: the general domain (pretrained on Wikipedia with hyperlinks) and biomedical domain (pretrained on PubMed with citation links). LinkBERT is especially effective for multi-hop reasoning and few-shot QA (+5% absolute improvement on HotpotQA and TriviaQA), and our biomedical LinkBERT sets new states of the art on various BioNLP tasks (+7% on BioASQ and USMLE). We release our pretrained models, LinkBERT and BioLinkBERT, as well as code and data at https://github.com/michiyasunaga/LinkBERT.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

MultiBiSage: A Web-Scale Recommendation System Using Multiple Bipartite Graphs at Pinterest

Graph Convolutional Networks (GCN) can efficiently integrate graph structure and node features to learn high-quality node embeddings. These embeddings can then be used for several tasks such as recommendation and search. At Pinterest, we have developed and deployed PinSage, a data-efficient GCN that learns pin embeddings from the Pin-Board graph. The Pin-Board graph contains pin and board entities and the graph captures the pin belongs to a board interaction. However, there exist several entities at Pinterest such as users, idea pins, creators, and there exist heterogeneous interactions among these entities such as add-to-cart, follow, long-click. In this work, we show that training deep learning models on graphs that captures these diverse interactions would result in learning higher-quality pin embeddings than training PinSage on only the Pin-Board graph. To that end, we model the diverse entities and their diverse interactions through multiple bipartite graphs and propose a novel data-efficient MultiBiSage model. MultiBiSage can capture the graph structure of multiple bipartite graphs to learn high-quality pin embeddings. We take this pragmatic approach as it allows us to utilize the existing infrastructure developed at Pinterest -- such as Pixie system that can perform optimized random-walks on billion node graphs, along with existing training and deployment workflows. We train MultiBiSage on six bipartite graphs including our Pin-Board graph. Our offline metrics show that MultiBiSage significantly outperforms the deployed latest version of PinSage on multiple user engagement metrics.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

On the Opportunities and Risks of Foundation Models

AI is undergoing a paradigm shift with the rise of models (e.g., BERT, DALL-E, GPT-3) that are trained on broad data at scale and are adaptable to a wide range of downstream tasks. We call these models foundation models to underscore their critically central yet incomplete character. This report provides a thorough account of the opportunities and risks of foundation models, ranging from their capabilities (e.g., language, vision, robotics, reasoning, human interaction) and technical principles(e.g., model architectures, training procedures, data, systems, security, evaluation, theory) to their applications (e.g., law, healthcare, education) and societal impact (e.g., inequity, misuse, economic and environmental impact, legal and ethical considerations). Though foundation models are based on standard deep learning and transfer learning, their scale results in new emergent capabilities,and their effectiveness across so many tasks incentivizes homogenization. Homogenization provides powerful leverage but demands caution, as the defects of the foundation model are inherited by all the adapted models downstream. Despite the impending widespread deployment of foundation models, we currently lack a clear understanding of how they work, when they fail, and what they are even capable of due to their emergent properties. To tackle these questions, we believe much of the critical research on foundation models will require deep interdisciplinary collaboration commensurate with their fundamentally sociotechnical nature.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Open-World Semi-Supervised Learning

A fundamental limitation of applying semi-supervised learning in real-world settings is the assumption that unlabeled test data contains only classes previously encountered in the labeled training data. However, this assumption rarely holds for data in-the-wild, where instances belonging to novel classes may appear at testing time. Here, we introduce a novel open-world semi-supervised learning setting that formalizes the notion that novel classes may appear in the unlabeled test data. In this novel setting, the goal is to solve the class distribution mismatch between labeled and unlabeled data, where at the test time every input instance either needs to be classified into one of the existing classes or a new unseen class needs to be initialized. To tackle this challenging problem, we propose ORCA, an end-to-end deep learning approach that introduces uncertainty adaptive margin mechanism to circumvent the bias towards seen classes caused by learning discriminative features for seen classes faster than for the novel classes. In this way, ORCA reduces the gap between intra-class variance of seen with respect to novel classes. Experiments on image classification datasets and a single-cell annotation dataset demonstrate that ORCA consistently outperforms alternative baselines, achieving 25% improvement on seen and 96% improvement on novel classes of the ImageNet dataset.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

PinnerFormer: Sequence Modeling for User Representation at Pinterest

Sequential models have become increasingly popular in powering personalized recommendation systems over the past several years. These approaches traditionally model a user's actions on a website as a sequence to predict the user's next action. While theoretically simplistic, these models are quite challenging to deploy in production, commonly requiring streaming infrastructure to reflect the latest user activity and potentially managing mutable data for encoding a user's hidden state. Here we introduce PinnerFormer, a user representation trained to predict a user's future long-term engagement using a sequential model of a user's recent actions. Unlike prior approaches, we adapt our modeling to a batch infrastructure via our new dense all-action loss, modeling long-term future actions instead of next action prediction. We show that by doing so, we significantly close the gap between batch user embeddings that are generated once a day and realtime user embeddings generated whenever a user takes an action. We describe our design decisions via extensive offline experimentation and ablations and validate the efficacy of our approach in A/B experiments showing substantial improvements in Pinterest's user retention and engagement when comparing PinnerFormer against our previous user representation. PinnerFormer is deployed in production as of Fall 2021.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

ROLAND: Graph Learning Framework for Dynamic Graphs

Graph Neural Networks (GNNs) have been successfully applied to many real-world static graphs. However, the success of static graphs has not fully translated to dynamic graphs due to the limitations in model design, evaluation settings, and training strategies. Concretely, existing dynamic GNNs do not incorporate state-of-the-art designs from static GNNs, which limits their performance. Current evaluation settings for dynamic GNNs do not fully reflect the evolving nature of dynamic graphs. Finally, commonly used training methods for dynamic GNNs are not scalable. Here we propose ROLAND, an effective graph representation learning framework for real-world dynamic graphs. At its core, the ROLAND framework can help researchers easily repurpose any static GNN to dynamic graphs. Our insight is to view the node embeddings at different GNN layers as hierarchical node states and then recurrently update them over time. We then introduce a live-update evaluation setting for dynamic graphs that mimics real-world use cases, where GNNs are making predictions and being updated on a rolling basis. Finally, we propose a scalable and efficient training approach for dynamic GNNs via incremental training and meta-learning. We conduct experiments over eight different dynamic graph datasets on future link prediction tasks. Models built using the ROLAND framework achieve on average 62.7% relative mean reciprocal rank (MRR) improvement over state-of-the-art baselines under the standard evaluation settings on three datasets. We find state-of-the-art baselines experience out-of-memory errors for larger datasets, while ROLAND can easily scale to dynamic graphs with 56 million edges. After re-implementing these baselines using the ROLAND training strategy, ROLAND models still achieve on average 15.5% relative MRR improvement over the baselines.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

ViRel: Unsupervised Visual Relations Discovery with Graph-level Analogy

Visual relations form the basis of understanding our compositional world, as relationships between visual objects capture key information in a scene. It is then advantageous to learn relations automatically from the data, as learning with predefined labels cannot capture all possible relations. However, current relation learning methods typically require supervision, and are not designed to generalize to scenes with more complicated relational structures than those seen during training. Here, we introduce ViRel, a method for unsupervised discovery and learning of Visual Relations with graph-level analogy. In a setting where scenes within a task share the same underlying relational subgraph structure, our learning method of contrasting isomorphic and non-isomorphic graphs discovers the relations across tasks in an unsupervised manner. Once the relations are learned, ViRel can then retrieve the shared relational graph structure for each task by parsing the predicted relational structure. Using a dataset based on grid-world and the Abstract Reasoning Corpus, we show that our method achieves above 95% accuracy in relation classification, discovers the relation graph structure for most tasks, and further generalizes to unseen tasks with more complicated relational structures.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Analytical Models for Motifs in Temporal Networks: Discovering Trends and Anomalies

Dynamic evolving networks capture temporal relations in domains such as social networks, communication networks, and financial transaction networks. In such networks, temporal motifs, which are repeated sequences of time-stamped edges/transactions, offer valuable information about the networks' evolution and function. However, currently no analytical models for temporal graphs exist and there are no models that would allow for scalable modeling of temporal motif frequencies over time. Here, we develop the Temporal Activity State Block Model (TASBM), to model temporal motifs in temporal graphs. We develop efficient model fitting methods and derive closed-form expressions for the expected motif frequencies and their variances in a given temporal network, thus enabling the discovery of statistically significant temporal motifs. Our TASMB framework can accurately track the changes in the expected motif frequencies over time, and also scales well to networks with tens of millions of edges/transactions as it does not require time-consuming generation of many random temporal networks and then computing motif counts for each one of them. We show that TASBM is able to model changes in temporal activity over time in a network of financial transactions, a phone call, and an email network. Additionally, we show that deviations from the expected motif counts calculated by our analytical framework correspond to anomalies in the financial transactions and phone call networks.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Driver2vec: Driver Identification from Automotive Data

With increasing focus on privacy protection, alternative methods to identify vehicle operator without the use of biometric identifiers have gained traction for automotive data analysis. The wide variety of sensors installed on modern vehicles enable autonomous driving, reduce accidents and improve vehicle handling. On the other hand, the data these sensors collect reflect drivers' habit. Drivers' use of turn indicators, following distance, rate of acceleration, etc. can be transformed to an embedding that is representative of their behavior and identity. In this paper, we develop a deep learning architecture (Driver2vec) to map a short interval of driving data into an embedding space that represents the driver's behavior to assist in driver identification. We develop a custom model that leverages performance gains of temporal convolutional networks, embedding separation power of triplet loss and classification accuracy of gradient boosting decision trees. Trained on a dataset of 51 drivers provided by Nervtech, Driver2vec is able to accurately identify the driver from a short 10-second interval of sensor data, achieving an average pairwise driver identification accuracy of 83.1% from this 10-second interval, which is remarkably higher than performance obtained in previous studies. We then analyzed performance of Driver2vec to show that its performance is consistent across scenarios and that modeling choices are sound.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

F-FADE: Frequency Factorization for Anomaly Detection in Edge Streams

Edge streams are commonly used to capture interactions in dynamic networks, such as email, social, or computer networks. The problem of detecting anomalies or rare events in edge streams has a wide range of applications. However, it presents many challenges due to lack of labels, a highly dynamic nature of interactions, and the entanglement of temporal and structural changes in the network. Current methods are limited in their ability to address the above challenges and to efficiently process a large number of interactions. Here, we propose F-FADE, a new approach for detection of anomalies in edge streams, which uses a novel frequency-factorization technique to efficiently model the time-evolving distributions of frequencies of interactions between node-pairs. The anomalies are then determined based on the likelihood of the observed frequency of each incoming interaction. F-FADE is able to handle in an online streaming setting a broad variety of anomalies with temporal and structural changes, while requiring only constant memory. Our experiments on one synthetic and six real-world dynamic networks show that F-FADE achieves state of the art performance and may detect anomalies that previous methods are unable to find.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

ForceNet: A Graph Neural Network for Large-Scale Quantum Calculations

With massive amounts of atomic simulation data available, there is a huge opportunity to develop fast and accurate machine learning models to approximate expensive physics-based calculations. The key quantity to estimate is atomic forces, where the state-of-the-art Graph Neural Networks (GNNs) explicitly enforce basic physical constraints such as rotation-covariance. However, to strictly satisfy the physical constraints, existing models have to make tradeoffs between computational efficiency and model expressiveness. Here we explore an alternative approach. By not imposing explicit physical constraints, we can flexibly design expressive models while maintaining their computational efficiency. Physical constraints are implicitly imposed by training the models using physics-based data augmentation. To evaluate the approach, we carefully design a scalable and expressive GNN model, ForceNet, and apply it to OC20 (Chanussot et al., 2020), an unprecedentedly-large dataset of quantum physics calculations. Our proposed ForceNet is able to predict atomic forces more accurately than state-of-the-art physics-based GNNs while being faster both in training and inference. Overall, our promising and counter-intuitive results open up an exciting avenue for future research.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Identity-aware Graph Neural Networks

Message passing Graph Neural Networks (GNNs) provide a powerful modeling framework for relational data. However, the expressive power of existing GNNs is upper-bounded by the 1-Weisfeiler-Lehman (1-WL) graph isomorphism test, which means GNNs that are not able to predict node clustering coefficients and shortest path distances, and cannot differentiate between different d-regular graphs. Here we develop a class of message passing GNNs, named Identity-aware Graph Neural Networks (ID-GNNs), with greater expressive power than the 1-WL test. ID-GNN offers a minimal but powerful solution to limitations of existing GNNs. ID-GNN extends existing GNN architectures by inductively considering nodes' identities during message passing. To embed a given node, ID-GNN first extracts the ego network centered at the node, then conducts rounds of heterogeneous message passing, where different sets of parameters are applied to the center node than to other surrounding nodes in the ego network. We further propose a simplified but faster version of ID-GNN that injects node identity information as augmented node features. Altogether, both versions of ID-GNN represent general extensions of message passing GNNs, where experiments show that transforming existing GNNs to ID-GNNs yields on average 40% accuracy improvement on challenging node, edge, and graph property prediction tasks; 3% accuracy improvement on node and graph classification benchmarks; and 15% ROC AUC improvement on real-world link prediction tasks. Additionally, ID-GNNs demonstrate improved or comparable performance over other task-specific graph networks.

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preprint2021arXiv

Inductive Learning on Commonsense Knowledge Graph Completion

Commonsense knowledge graph (CKG) is a special type of knowledge graph (KG), where entities are composed of free-form text. However, most existing CKG completion methods focus on the setting where all the entities are presented at training time. Although this setting is standard for conventional KG completion, it has limitations for CKG completion. At test time, entities in CKGs can be unseen because they may have unseen text/names and entities may be disconnected from the training graph, since CKGs are generally very sparse. Here, we propose to study the inductive learning setting for CKG completion where unseen entities may present at test time. We develop a novel learning framework named InductivE. Different from previous approaches, InductiveE ensures the inductive learning capability by directly computing entity embeddings from raw entity attributes/text. InductiveE consists of a free-text encoder, a graph encoder, and a KG completion decoder. Specifically, the free-text encoder first extracts the textual representation of each entity based on the pre-trained language model and word embedding. The graph encoder is a gated relational graph convolutional neural network that learns from a densified graph for more informative entity representation learning. We develop a method that densifies CKGs by adding edges among semantic-related entities and provide more supportive information for unseen entities, leading to better generalization ability of entity embedding for unseen entities. Finally, inductiveE employs Conv-TransE as the CKG completion decoder. Experimental results show that InductiveE significantly outperforms state-of-the-art baselines in both standard and inductive settings on ATOMIC and ConceptNet benchmarks. InductivE performs especially well on inductive scenarios where it achieves above 48% improvement over present methods.

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preprint2021arXiv

Model-Agnostic Graph Regularization for Few-Shot Learning

In many domains, relationships between categories are encoded in the knowledge graph. Recently, promising results have been achieved by incorporating knowledge graph as side information in hard classification tasks with severely limited data. However, prior models consist of highly complex architectures with many sub-components that all seem to impact performance. In this paper, we present a comprehensive empirical study on graph embedded few-shot learning. We introduce a graph regularization approach that allows a deeper understanding of the impact of incorporating graph information between labels. Our proposed regularization is widely applicable and model-agnostic, and boosts the performance of any few-shot learning model, including fine-tuning, metric-based, and optimization-based meta-learning. Our approach improves the performance of strong base learners by up to 2% on Mini-ImageNet and 6.7% on ImageNet-FS, outperforming state-of-the-art graph embedded methods. Additional analyses reveal that graph regularizing models result in a lower loss for more difficult tasks, such as those with fewer shots and less informative support examples.

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preprint2021arXiv

Open Graph Benchmark: Datasets for Machine Learning on Graphs

We present the Open Graph Benchmark (OGB), a diverse set of challenging and realistic benchmark datasets to facilitate scalable, robust, and reproducible graph machine learning (ML) research. OGB datasets are large-scale, encompass multiple important graph ML tasks, and cover a diverse range of domains, ranging from social and information networks to biological networks, molecular graphs, source code ASTs, and knowledge graphs. For each dataset, we provide a unified evaluation protocol using meaningful application-specific data splits and evaluation metrics. In addition to building the datasets, we also perform extensive benchmark experiments for each dataset. Our experiments suggest that OGB datasets present significant challenges of scalability to large-scale graphs and out-of-distribution generalization under realistic data splits, indicating fruitful opportunities for future research. Finally, OGB provides an automated end-to-end graph ML pipeline that simplifies and standardizes the process of graph data loading, experimental setup, and model evaluation. OGB will be regularly updated and welcomes inputs from the community. OGB datasets as well as data loaders, evaluation scripts, baseline code, and leaderboards are publicly available at https://ogb.stanford.edu .

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preprint2020arXiv

Graph Structure of Neural Networks

Neural networks are often represented as graphs of connections between neurons. However, despite their wide use, there is currently little understanding of the relationship between the graph structure of the neural network and its predictive performance. Here we systematically investigate how does the graph structure of neural networks affect their predictive performance. To this end, we develop a novel graph-based representation of neural networks called relational graph, where layers of neural network computation correspond to rounds of message exchange along the graph structure. Using this representation we show that: (1) a "sweet spot" of relational graphs leads to neural networks with significantly improved predictive performance; (2) neural network's performance is approximately a smooth function of the clustering coefficient and average path length of its relational graph; (3) our findings are consistent across many different tasks and datasets; (4) the sweet spot can be identified efficiently; (5) top-performing neural networks have graph structure surprisingly similar to those of real biological neural networks. Our work opens new directions for the design of neural architectures and the understanding on neural networks in general.

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preprint2020arXiv

Improving Query Safety at Pinterest

Query recommendations in search engines is a double edged sword, with undeniable benefits but potential of harm. Identifying unsafe queries is necessary to protect users from inappropriate query suggestions. However, identifying these is non-trivial because of the linguistic diversity resulting from large vocabularies, social-group-specific slang and typos, and because the inappropriateness of a term depends on the context. Here we formulate the problem as query-set expansion, where we are given a small and potentially biased seed set and the aim is to identify a diverse set of semantically related queries. We present PinSets, a system for query-set expansion, which applies a simple yet powerful mechanism to search user sessions, expanding a tiny seed set into thousands of related queries at nearly perfect precision, deep into the tail, along with explanations that are easy to interpret. PinSets owes its high quality expansion to using a hybrid of textual and behavioral techniques (i.e., treating queries both as compositional and as black boxes). Experiments show that, for the domain of drugs-related queries, PinSets expands 20 seed queries into 15,670 positive training examples at over 99\% precision. The generated expansions have diverse vocabulary and correctly handles words with ambiguous safety. PinSets decreased unsafe query suggestions at Pinterest by 90\%.

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preprint2020arXiv

Learning to Simulate Complex Physics with Graph Networks

Here we present a machine learning framework and model implementation that can learn to simulate a wide variety of challenging physical domains, involving fluids, rigid solids, and deformable materials interacting with one another. Our framework---which we term "Graph Network-based Simulators" (GNS)---represents the state of a physical system with particles, expressed as nodes in a graph, and computes dynamics via learned message-passing. Our results show that our model can generalize from single-timestep predictions with thousands of particles during training, to different initial conditions, thousands of timesteps, and at least an order of magnitude more particles at test time. Our model was robust to hyperparameter choices across various evaluation metrics: the main determinants of long-term performance were the number of message-passing steps, and mitigating the accumulation of error by corrupting the training data with noise. Our GNS framework advances the state-of-the-art in learned physical simulation, and holds promise for solving a wide range of complex forward and inverse problems.

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preprint2020arXiv

OCEAN: Online Task Inference for Compositional Tasks with Context Adaptation

Real-world tasks often exhibit a compositional structure that contains a sequence of simpler sub-tasks. For instance, opening a door requires reaching, grasping, rotating, and pulling the door knob. Such compositional tasks require an agent to reason about the sub-task at hand while orchestrating global behavior accordingly. This can be cast as an online task inference problem, where the current task identity, represented by a context variable, is estimated from the agent's past experiences with probabilistic inference. Previous approaches have employed simple latent distributions, e.g., Gaussian, to model a single context for the entire task. However, this formulation lacks the expressiveness to capture the composition and transition of the sub-tasks. We propose a variational inference framework OCEAN to perform online task inference for compositional tasks. OCEAN models global and local context variables in a joint latent space, where the global variables represent a mixture of sub-tasks required for the task, while the local variables capture the transitions between the sub-tasks. Our framework supports flexible latent distributions based on prior knowledge of the task structure and can be trained in an unsupervised manner. Experimental results show that OCEAN provides more effective task inference with sequential context adaptation and thus leads to a performance boost on complex, multi-stage tasks.

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preprint2020arXiv

PinnerSage: Multi-Modal User Embedding Framework for Recommendations at Pinterest

Latent user representations are widely adopted in the tech industry for powering personalized recommender systems. Most prior work infers a single high dimensional embedding to represent a user, which is a good starting point but falls short in delivering a full understanding of the user's interests. In this work, we introduce PinnerSage, an end-to-end recommender system that represents each user via multi-modal embeddings and leverages this rich representation of users to provides high quality personalized recommendations. PinnerSage achieves this by clustering users' actions into conceptually coherent clusters with the help of a hierarchical clustering method (Ward) and summarizes the clusters via representative pins (Medoids) for efficiency and interpretability. PinnerSage is deployed in production at Pinterest and we outline the several design decisions that makes it run seamlessly at a very large scale. We conduct several offline and online A/B experiments to show that our method significantly outperforms single embedding methods.

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preprint2020arXiv

Query2box: Reasoning over Knowledge Graphs in Vector Space using Box Embeddings

Answering complex logical queries on large-scale incomplete knowledge graphs (KGs) is a fundamental yet challenging task. Recently, a promising approach to this problem has been to embed KG entities as well as the query into a vector space such that entities that answer the query are embedded close to the query. However, prior work models queries as single points in the vector space, which is problematic because a complex query represents a potentially large set of its answer entities, but it is unclear how such a set can be represented as a single point. Furthermore, prior work can only handle queries that use conjunctions ($\wedge$) and existential quantifiers ($\exists$). Handling queries with logical disjunctions ($\vee$) remains an open problem. Here we propose query2box, an embedding-based framework for reasoning over arbitrary queries with $\wedge$, $\vee$, and $\exists$ operators in massive and incomplete KGs. Our main insight is that queries can be embedded as boxes (i.e., hyper-rectangles), where a set of points inside the box corresponds to a set of answer entities of the query. We show that conjunctions can be naturally represented as intersections of boxes and also prove a negative result that handling disjunctions would require embedding with dimension proportional to the number of KG entities. However, we show that by transforming queries into a Disjunctive Normal Form, query2box is capable of handling arbitrary logical queries with $\wedge$, $\vee$, $\exists$ in a scalable manner. We demonstrate the effectiveness of query2box on three large KGs and show that query2box achieves up to 25% relative improvement over the state of the art.

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preprint2020arXiv

Strategies for Pre-training Graph Neural Networks

Many applications of machine learning require a model to make accurate pre-dictions on test examples that are distributionally different from training ones, while task-specific labels are scarce during training. An effective approach to this challenge is to pre-train a model on related tasks where data is abundant, and then fine-tune it on a downstream task of interest. While pre-training has been effective in many language and vision domains, it remains an open question how to effectively use pre-training on graph datasets. In this paper, we develop a new strategy and self-supervised methods for pre-training Graph Neural Networks (GNNs). The key to the success of our strategy is to pre-train an expressive GNN at the level of individual nodes as well as entire graphs so that the GNN can learn useful local and global representations simultaneously. We systematically study pre-training on multiple graph classification datasets. We find that naive strategies, which pre-train GNNs at the level of either entire graphs or individual nodes, give limited improvement and can even lead to negative transfer on many downstream tasks. In contrast, our strategy avoids negative transfer and improves generalization significantly across downstream tasks, leading up to 9.4% absolute improvements in ROC-AUC over non-pre-trained models and achieving state-of-the-art performance for molecular property prediction and protein function prediction.

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preprint2020arXiv

Unifying Graph Convolutional Neural Networks and Label Propagation

Label Propagation (LPA) and Graph Convolutional Neural Networks (GCN) are both message passing algorithms on graphs. Both solve the task of node classification but LPA propagates node label information across the edges of the graph, while GCN propagates and transforms node feature information. However, while conceptually similar, theoretical relation between LPA and GCN has not yet been investigated. Here we study the relationship between LPA and GCN in terms of two aspects: (1) feature/label smoothing where we analyze how the feature/label of one node is spread over its neighbors; And, (2) feature/label influence of how much the initial feature/label of one node influences the final feature/label of another node. Based on our theoretical analysis, we propose an end-to-end model that unifies GCN and LPA for node classification. In our unified model, edge weights are learnable, and the LPA serves as regularization to assist the GCN in learning proper edge weights that lead to improved classification performance. Our model can also be seen as learning attention weights based on node labels, which is more task-oriented than existing feature-based attention models. In a number of experiments on real-world graphs, our model shows superiority over state-of-the-art GCN-based methods in terms of node classification accuracy.

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