arXiv subjects

Jure Leskovec

Publications and source records attributed to Jure Leskovec.

At least 127 records · Page 7Linked to original sources

arXiv2022

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.

cs.LG↗

arXiv2022

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.

cs.LG↗

arXiv2022

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.

cs.LG↗

arXiv2022

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.

cs.CL↗

arXiv2022

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.

cs.LG↗

arXiv2022

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.

cs.CL↗

arXiv2021

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.

cs.SI↗

arXiv2021

M2P2: Multimodal Persuasion Prediction using Adaptive Fusion

Identifying persuasive speakers in an adversarial environment is a critical task. In a national election, politicians would like to have persuasive speakers campaign on their behalf. When a company faces adverse publicity, they would like to engage persuasive advocates for their position in the presence of adversaries who are critical of them. Debates represent a common platform for these forms of adversarial persuasion. This paper solves two problems: the Debate Outcome Prediction (DOP) problem predicts who wins a debate while the Intensity of Persuasion Prediction (IPP) problem predicts the change in the number of votes before and after a speaker speaks. Though DOP has been previously studied, we are the first to study IPP. Past studies on DOP fail to leverage two important aspects of multimodal data: 1) multiple modalities are often semantically aligned, and 2) different modalities may provide diverse information for prediction. Our M2P2 (Multimodal Persuasion Prediction) framework is the first to use multimodal (acoustic, visual, language) data to solve the IPP problem. To leverage the alignment of different modalities while maintaining the diversity of the cues they provide, M2P2 devises a novel adaptive fusion learning framework which fuses embeddings obtained from two modules -- an alignment module that extracts shared information between modalities and a heterogeneity module that learns the weights of different modalities with guidance from three separately trained unimodal reference models. We test M2P2 on the popular IQ2US dataset designed for DOP. We also introduce a new dataset called QPS (from Qipashuo, a popular Chinese debate TV show ) for IPP. M2P2 significantly outperforms 4 recent baselines on both datasets.

cs.CV↗

arXiv2021

SMORE: Knowledge Graph Completion and Multi-hop Reasoning in Massive Knowledge Graphs

Knowledge graphs (KGs) capture knowledge in the form of head--relation--tail triples and are a crucial component in many AI systems. There are two important reasoning tasks on KGs: (1) single-hop knowledge graph completion, which involves predicting individual links in the KG; and (2), multi-hop reasoning, where the goal is to predict which KG entities satisfy a given logical query. Embedding-based methods solve both tasks by first computing an embedding for each entity and relation, then using them to form predictions. However, existing scalable KG embedding frameworks only support single-hop knowledge graph completion and cannot be applied to the more challenging multi-hop reasoning task. Here we present Scalable Multi-hOp REasoning (SMORE), the first general framework for both single-hop and multi-hop reasoning in KGs. Using a single machine SMORE can perform multi-hop reasoning in Freebase KG (86M entities, 338M edges), which is 1,500x larger than previously considered KGs. The key to SMORE's runtime performance is a novel bidirectional rejection sampling that achieves a square root reduction of the complexity of online training data generation. Furthermore, SMORE exploits asynchronous scheduling, overlapping CPU-based data sampling, GPU-based embedding computation, and frequent CPU--GPU IO. SMORE increases throughput (i.e., training speed) over prior multi-hop KG frameworks by 2.2x with minimal GPU memory requirements (2GB for training 400-dim embeddings on 86M-node Freebase) and achieves near linear speed-up with the number of GPUs. Moreover, on the simpler single-hop knowledge graph completion task SMORE achieves comparable or even better runtime performance to state-of-the-art frameworks on both single GPU and multi-GPU settings.

cs.LG↗

arXiv2021

Modeling Heterogeneous Hierarchies with Relation-specific Hyperbolic Cones

Hierarchical relations are prevalent and indispensable for organizing human knowledge captured by a knowledge graph (KG). The key property of hierarchical relations is that they induce a partial ordering over the entities, which needs to be modeled in order to allow for hierarchical reasoning. However, current KG embeddings can model only a single global hierarchy (single global partial ordering) and fail to model multiple heterogeneous hierarchies that exist in a single KG. Here we present ConE (Cone Embedding), a KG embedding model that is able to simultaneously model multiple hierarchical as well as non-hierarchical relations in a knowledge graph. ConE embeds entities into hyperbolic cones and models relations as transformations between the cones. In particular, ConE uses cone containment constraints in different subspaces of the hyperbolic embedding space to capture multiple heterogeneous hierarchies. Experiments on standard knowledge graph benchmarks show that ConE obtains state-of-the-art performance on hierarchical reasoning tasks as well as knowledge graph completion task on hierarchical graphs. In particular, our approach yields new state-of-the-art Hits@1 of 45.3% on WN18RR and 16.1% on DDB14 (0.231 MRR). As for hierarchical reasoning task, our approach outperforms previous best results by an average of 20% across the three datasets.

cs.LG↗

arXiv2021

Postmortem memory of public figures in news and social media

Deceased public figures are often said to live on in collective memory. We quantify this phenomenon by tracking mentions of 2,362 public figures in English-language online news and social media (Twitter) one year before and after death. We measure the sharp spike and rapid decay of attention following death and model collective memory as a composition of communicative and cultural memory. Clustering reveals four patterns of post-mortem memory, and regression analysis shows that boosts in media attention are largest for pre-mortem popular anglophones who died a young, unnatural death; that long-term boosts are smallest for leaders and largest for artists; and that, while both the news and Twitter are triggered by young and unnatural deaths, the news additionally curates collective memory when old persons or leaders die. Overall, we illuminate the age-old question who is remembered by society, and the distinct roles of news and social media in collective memory formation.

cs.SI↗

arXiv2021

Combiner: Full Attention Transformer with Sparse Computation Cost

Transformers provide a class of expressive architectures that are extremely effective for sequence modeling. However, the key limitation of transformers is their quadratic memory and time complexity $\mathcal{O}(L^2)$ with respect to the sequence length in attention layers, which restricts application in extremely long sequences. Most existing approaches leverage sparsity or low-rank assumptions in the attention matrix to reduce cost, but sacrifice expressiveness. Instead, we propose Combiner, which provides full attention capability in each attention head while maintaining low computation and memory complexity. The key idea is to treat the self-attention mechanism as a conditional expectation over embeddings at each location, and approximate the conditional distribution with a structured factorization. Each location can attend to all other locations, either via direct attention, or through indirect attention to abstractions, which are again conditional expectations of embeddings from corresponding local regions. We show that most sparse attention patterns used in existing sparse transformers are able to inspire the design of such factorization for full attention, resulting in the same sub-quadratic cost ($\mathcal{O}(L\log(L))$ or $\mathcal{O}(L\sqrt{L})$). Combiner is a drop-in replacement for attention layers in existing transformers and can be easily implemented in common frameworks. An experimental evaluation on both autoregressive and bidirectional sequence tasks demonstrates the effectiveness of this approach, yielding state-of-the-art results on several image and text modeling tasks.

cs.LG↗

arXiv2021

OGB-LSC: A Large-Scale Challenge for Machine Learning on Graphs

Enabling effective and efficient machine learning (ML) over large-scale graph data (e.g., graphs with billions of edges) can have a great impact on both industrial and scientific applications. However, existing efforts to advance large-scale graph ML have been largely limited by the lack of a suitable public benchmark. Here we present OGB Large-Scale Challenge (OGB-LSC), a collection of three real-world datasets for facilitating the advancements in large-scale graph ML. The OGB-LSC datasets are orders of magnitude larger than existing ones, covering three core graph learning tasks -- link prediction, graph regression, and node classification. Furthermore, we provide dedicated baseline experiments, scaling up expressive graph ML models to the massive datasets. We show that expressive models significantly outperform simple scalable baselines, indicating an opportunity for dedicated efforts to further improve graph ML at scale. Moreover, OGB-LSC datasets were deployed at ACM KDD Cup 2021 and attracted more than 500 team registrations globally, during which significant performance improvements were made by a variety of innovative techniques. We summarize the common techniques used by the winning solutions and highlight the current best practices in large-scale graph ML. Finally, we describe how we have updated the datasets after the KDD Cup to further facilitate research advances. The OGB-LSC datasets, baseline code, and all the information about the KDD Cup are available at https://ogb.stanford.edu/docs/lsc/ .

cs.LG↗

arXiv2021

Neural Distance Embeddings for Biological Sequences

The development of data-dependent heuristics and representations for biological sequences that reflect their evolutionary distance is critical for large-scale biological research. However, popular machine learning approaches, based on continuous Euclidean spaces, have struggled with the discrete combinatorial formulation of the edit distance that models evolution and the hierarchical relationship that characterises real-world datasets. We present Neural Distance Embeddings (NeuroSEED), a general framework to embed sequences in geometric vector spaces, and illustrate the effectiveness of the hyperbolic space that captures the hierarchical structure and provides an average 22% reduction in embedding RMSE against the best competing geometry. The capacity of the framework and the significance of these improvements are then demonstrated devising supervised and unsupervised NeuroSEED approaches to multiple core tasks in bioinformatics. Benchmarked with common baselines, the proposed approaches display significant accuracy and/or runtime improvements on real-world datasets. As an example for hierarchical clustering, the proposed pretrained and from-scratch methods match the quality of competing baselines with 30x and 15x runtime reduction, respectively.

q-bio.QM↗

arXiv2021

LM-Critic: Language Models for Unsupervised Grammatical Error Correction

Training a model for grammatical error correction (GEC) requires a set of labeled ungrammatical / grammatical sentence pairs, but manually annotating such pairs can be expensive. Recently, the Break-It-Fix-It (BIFI) framework has demonstrated strong results on learning to repair a broken program without any labeled examples, but this relies on a perfect critic (e.g., a compiler) that returns whether an example is valid or not, which does not exist for the GEC task. In this work, we show how to leverage a pretrained language model (LM) in defining an LM-Critic, which judges a sentence to be grammatical if the LM assigns it a higher probability than its local perturbations. We apply this LM-Critic and BIFI along with a large set of unlabeled sentences to bootstrap realistic ungrammatical / grammatical pairs for training a corrector. We evaluate our approach on GEC datasets across multiple domains (CoNLL-2014, BEA-2019, GMEG-wiki and GMEG-yahoo) and show that it outperforms existing methods in both the unsupervised setting (+7.7 F0.5) and the supervised setting (+0.5 F0.5).

cs.CL↗

arXiv2021

Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development

Therapeutics machine learning is an emerging field with incredible opportunities for innovatiaon and impact. However, advancement in this field requires formulation of meaningful learning tasks and careful curation of datasets. Here, we introduce Therapeutics Data Commons (TDC), the first unifying platform to systematically access and evaluate machine learning across the entire range of therapeutics. To date, TDC includes 66 AI-ready datasets spread across 22 learning tasks and spanning the discovery and development of safe and effective medicines. TDC also provides an ecosystem of tools and community resources, including 33 data functions and types of meaningful data splits, 23 strategies for systematic model evaluation, 17 molecule generation oracles, and 29 public leaderboards. All resources are integrated and accessible via an open Python library. We carry out extensive experiments on selected datasets, demonstrating that even the strongest algorithms fall short of solving key therapeutics challenges, including real dataset distributional shifts, multi-scale modeling of heterogeneous data, and robust generalization to novel data points. We envision that TDC can facilitate algorithmic and scientific advances and considerably accelerate machine-learning model development, validation and transition into biomedical and clinical implementation. TDC is an open-science initiative available at https://tdcommons.ai.

cs.LG↗

arXiv2021

Multi-hop Attention Graph Neural Network

Self-attention mechanism in graph neural networks (GNNs) led to state-of-the-art performance on many graph representation learning tasks. Currently, at every layer, attention is computed between connected pairs of nodes and depends solely on the representation of the two nodes. However, such attention mechanism does not account for nodes that are not directly connected but provide important network context. Here we propose Multi-hop Attention Graph Neural Network (MAGNA), a principled way to incorporate multi-hop context information into every layer of attention computation. MAGNA diffuses the attention scores across the network, which increases the receptive field for every layer of the GNN. Unlike previous approaches, MAGNA uses a diffusion prior on attention values, to efficiently account for all paths between the pair of disconnected nodes. We demonstrate in theory and experiments that MAGNA captures large-scale structural information in every layer, and has a low-pass effect that eliminates noisy high-frequency information from graph data. Experimental results on node classification as well as the knowledge graph completion benchmarks show that MAGNA achieves state-of-the-art results: MAGNA achieves up to 5.7 percent relative error reduction over the previous state-of-the-art on Cora, Citeseer, and Pubmed. MAGNA also obtains the best performance on a large-scale Open Graph Benchmark dataset. On knowledge graph completion MAGNA advances state-of-the-art on WN18RR and FB15k-237 across four different performance metrics.

cs.LG↗

arXiv2021

Design Space for Graph Neural Networks

The rapid evolution of Graph Neural Networks (GNNs) has led to a growing number of new architectures as well as novel applications. However, current research focuses on proposing and evaluating specific architectural designs of GNNs, as opposed to studying the more general design space of GNNs that consists of a Cartesian product of different design dimensions, such as the number of layers or the type of the aggregation function. Additionally, GNN designs are often specialized to a single task, yet few efforts have been made to understand how to quickly find the best GNN design for a novel task or a novel dataset. Here we define and systematically study the architectural design space for GNNs which consists of 315,000 different designs over 32 different predictive tasks. Our approach features three key innovations: (1) A general GNN design space; (2) a GNN task space with a similarity metric, so that for a given novel task/dataset, we can quickly identify/transfer the best performing architecture; (3) an efficient and effective design space evaluation method which allows insights to be distilled from a huge number of model-task combinations. Our key results include: (1) A comprehensive set of guidelines for designing well-performing GNNs; (2) while best GNN designs for different tasks vary significantly, the GNN task space allows for transferring the best designs across different tasks; (3) models discovered using our design space achieve state-of-the-art performance. Overall, our work offers a principled and scalable approach to transition from studying individual GNN designs for specific tasks, to systematically studying the GNN design space and the task space. Finally, we release GraphGym, a powerful platform for exploring different GNN designs and tasks. GraphGym features modularized GNN implementation, standardized GNN evaluation, and reproducible and scalable experiment management.

cs.LG↗