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Predicting how different interventions will causally affect a specific individual is important in a variety of domains such as personalized medicine, public policy, and online marketing. There are a large number of methods to predict the effect of an existing intervention based on historical data from individuals who received it. However, in many settings it is important to predict the effects of novel interventions (e.g., a newly invented drug), which these methods do not address. Here, we consider zero-shot causal learning: predicting the personalized effects of a novel intervention. We propose CaML, a causal meta-learning framework which formulates the personalized prediction of each intervention’s effect as a task. CaML trains a single meta-model across thousands of tasks, each constructed by sampling an intervention, its recipients, and its nonrecipients. By leveraging both intervention information (e.g., a drug’s attributes) and individual features (e.g., a patient’s history), CaML is able to predict the personalized effects of novel interventions that do not exist at the time of training. Experimental results on real world datasets in large-scale medical claims and cell-line perturbations demonstrate the effectiveness of our approach. Most strikingly, CaML’s zero-shot predictions outperform even strong baselines trained directly on data from the test interventions. 

Visual question answering (VQA) requires systems to perform concept-level reasoning by unifying unstructured (e.g., the context in question and answer; “QA context”) and structured (e.g., knowledge graph for the QA context and scene; “concept graph”) multimodal knowledge. Existing works typically combine a scene graph and a concept graph of the scene by connecting corresponding visual nodes and concept nodes, then incorporate the QA context representation to perform question answering. However, these methods only perform a unidirectional fusion from unstructured knowledge to structured knowledge, limiting their potential to capture joint reasoning over the heterogeneous modalities of knowledge. To perform more expressive reasoning, we propose VQA-GNN, a new VQA model that performs bidirectional fusion between unstructured and structured multimodal knowledge to obtain unified knowledge representations. Specifically, we inter-connect the scene graph and the concept graph through a super node that represents the QA context, and introduce a new multimodal GNN technique to perform inter-modal message passing for reasoning that mitigates representational gaps between modalities. On two challenging VQA tasks (VCR and GQA), our method outperforms strong baseline VQA methods by 3.2% on VCR (Q-AR) and 4.6% on GQA, suggesting its strength in performing concept-level reasoning. Ablation studies further demonstrate the efficacy of the bidirectional fusion and multimodal GNN method in unifying unstructured and structured multimodal knowledge. 

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). 

Pretraining a language model (LM) on text has been shown to help various downstream NLP tasks. Recent works show that a knowledge graph (KG) can complement text data, offering structured background knowledge that provides a useful scaffold for reasoning. However, these works are not pretrained to learn a deep fusion of the two modalities at scale, limiting the potential to acquire fully joint representations of text and KG. Here we propose DRAGON (Deep Bidirectional Language-Knowledge Graph Pretraining), a self-supervised approach to pretraining a deeply joint language-knowledge foundation model from text and KG at scale. Specifically, our model takes pairs of text segments and relevant KG subgraphs as input and bidirectionally fuses information from both modalities. We pretrain this model by unifying two self-supervised reasoning tasks, masked language modeling and KG link prediction. DRAGON outperforms existing LM and LM+KG models on diverse downstream tasks including question answering across general and biomedical domains, with +5% absolute gain on average. In particular, DRAGON achieves notable performance on complex reasoning about language and knowledge (+10% on questions involving long contexts or multi-step reasoning) and low-resource QA (+8% on OBQA and RiddleSense), and new state-of-the-art results on various BioNLP tasks. Our code and trained models are available at https://github.com/michiyasunaga/dragon. 

The problem of answering questions using knowledge from pre-trained language models (LMs) and knowledge graphs (KGs) presents two challenges: given a QA context (question and answer choice), methods need to (i) identify relevant knowledge from large KGs, and (ii) perform joint reasoning over the QA context and KG. Here we propose a new model, QA-GNN, which addresses the above challenges through two key innovations: (i) relevance scoring, where we use LMs to estimate the importance of KG nodes relative to the given QA context, and (ii) joint reasoning, where we connect the QA context and KG to form a joint graph, and mutually update their representations through graph-based message passing. We evaluate QA-GNN on the CommonsenseQA and OpenBookQA datasets, and show its improvement over existing LM and LM+KG models, as well as its capability to perform interpretable and structured reasoning, e.g., correctly handling negation in questions. 

Answering complex natural language questions on knowledge graphs (KGQA) is a challenging task. It requires reasoning with the input natural language questions as well as a massive, incomplete heterogeneous KG. Prior methods obtain an abstract structured query graph/tree from the input question and traverse the KG for answers following the query tree. However, they inherently cannot deal with missing links in the KG. Here we present LEGO, a Latent ExecutionGuided reasOning framework to handle this challenge in KGQA. LEGO works in an iterative way, which alternates between (1) a Query Synthesizer, which synthesizes a reasoning action and grows the query tree step-by-step, and (2) a Latent Space Executor that executes the reasoning action in the latent embedding space to combat against the missing information in KG. To learn the synthesizer without step-wise supervision, we design a generic latent execution guided bottom-up search procedure to find good execution traces efficiently in the vast query space. Experimental results on several KGQA benchmarks demonstrate the effectiveness of our framework compared with previous state of the art. 

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 identical evaluation metrics. We systematically benchmark state-of-the-art methods that use unlabeled data, including domain-invariant, self-training, and self-supervised methods, and show that their success on WILDS is limited. To facilitate method development, we provide an open-source package that automates data loading and contains the model architectures and methods used in this paper. 

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 this https URL. 

Distribution shifts—where the training distribution differs from the test distribution—can substantially degrade the accuracy of machine learning (ML) systems deployed in the wild. Despite their ubiquity in the real-world deployments, these distribution shifts are under-represented in the datasets widely used in the ML community today. To address this gap, we present WILDS, a curated benchmark of 10 datasets reflecting a diverse range of distribution shifts that naturally arise in real-world applications, such as shifts across hospitals for tumor identification; across camera traps for wildlife monitoring; and across time and location in satellite imaging and poverty mapping. On each dataset, we show that standard training yields substantially lower out-of-distribution than in-distribution performance. This gap remains even with models trained by existing methods for tackling distribution shifts, underscoring the need for new methods for training models that are more robust to the types of distribution shifts that arise in practice. To facilitate method development, we provide an open source package that automates dataset loading, contains default model architectures and hyperparameters, and standardizes evaluations. The full paper, code, and leaderboards are available at https://wilds.stanford.edu.