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  1. Abstract Most diseases disrupt multiple proteins, and drugs treat such diseases by restoring the functions of the disrupted proteins. How drugs restore these functions, however, is often unknown as a drug’s therapeutic effects are not limited to the proteins that the drug directly targets. Here, we develop the multiscale interactome, a powerful approach to explain disease treatment. We integrate disease-perturbed proteins, drug targets, and biological functions into a multiscale interactome network. We then develop a random walk-based method that captures how drug effects propagate through a hierarchy of biological functions and physical protein-protein interactions. On three key pharmacological tasks, themore »multiscale interactome predicts drug-disease treatment, identifies proteins and biological functions related to treatment, and predicts genes that alter a treatment’s efficacy and adverse reactions. Our results indicate that physical interactions between proteins alone cannot explain treatment since many drugs treat diseases by affecting the biological functions disrupted by the disease rather than directly targeting disease proteins or their regulators. We provide a general framework for explaining treatment, even when drugs seem unrelated to the diseases they are recommended for.« less
    Free, publicly-accessible full text available December 1, 2022
  2. 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 amore »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.« less
  3. Dynamic social interaction networks are an important abstraction to model time-stamped social interactions such as eye contact, speaking and listening between people. These networks typically contain informative while subtle patterns that reflect people’s social characters and relationship, and therefore attract the attentions of a lot of social scientists and computer scientists. Previous approaches on extracting those patterns primarily rely on sophisticated expert knowledge of psychology and social science, and the obtained features are often overly task-specific. More generic models based on representation learning of dynamic networks may be applied, but the unique properties of social interactions cause severe model mismatchmore »and degenerate the quality of the obtained representations. Here we fill this gap by proposing a novel framework, termed TEmporal network-DIffusion Convolutional networks (TEDIC), for generic representation learning on dynamic social interaction networks. We make TEDIC a good fit by designing two components: 1) Adopt diffusion of node attributes over a combination of the original network and its complement to capture long-hop interactive patterns embedded in the behaviors of people making or avoiding contact; 2) Leverage temporal convolution networks with hierarchical set-pooling operation to flexibly extract patterns from different-length interactions scattered over a long time span. The design also endows TEDIC with certain self-explaining power. We evaluate TEDIC over five real datasets for four different social character prediction tasks including deception detection, dominance identification, nervousness detection and community detection. TEDIC not only consistently outperforms previous SOTA’s, but also provides two important pieces of social insight. In addition, it exhibits favorable societal characteristics by remaining unbiased to people from different regions. Our project website is:« less
  4. 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, wemore »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« less
  5. 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 jointmore »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.« less
  6. Source code (Context) and its parsed abstract syntax tree (AST; Structure) are two complementary representations of the same computer program. Traditionally, designers of machine learning models have relied predominantly either on Structure or Context. We propose a new model, which jointly learns on Context and Structure of source code. In contrast to previous approaches, our model uses only language-agnostic features, i.e., source code and features that can be computed directly from the AST. Besides obtaining state-of-the-art on monolingual code summarization on all five programming languages considered in this work, we propose the first multilingual code summarization model. We show thatmore »jointly training on non-parallel data from multiple programming languages improves results on all individual languages, where the strongest gains are on low-resource languages. Remarkably, multilingual training only from Context does not lead to the same improvements, highlighting the benefits of combining Structure and Context for representation learning on code.« less
  7. Temporal networks serve as abstractions of many real-world dynamic systems. These networks typically evolve according to certain laws, such as the law of triadic closure, which is universal in social networks. Inductive representation learning of temporal networks should be able to capture such laws and further be applied to systems that follow the same laws but have not been unseen during the training stage. Previous works in this area depend on either network node identities or rich edge attributes and typically fail to extract these laws. Here, we propose Causal Anonymous Walks (CAWs) to inductively represent a temporal network. CAWsmore »are extracted by temporal random walks and work as automatic retrieval of temporal network motifs to represent network dynamics while avoiding the time-consuming selection and counting of those motifs. CAWs adopt a novel anonymization strategy that replaces node identities with the hitting counts of the nodes based on a set of sampled walks to keep the method inductive, and simultaneously establish the correlation between motifs. We further propose a neural-network model CAW-N to encode CAWs, and pair it with a CAW sampling strategy with constant memory and time cost to support online training and inference. CAW-N is evaluated to predict links over 6 real temporal networks and uniformly outperforms previous SOTA methods by averaged 15% AUC gain in the inductive setting. CAW-N also outperforms previous methods in 5 out of the 6 networks in the transductive setting.« less
  8. Developing algorithms that are able to generalize to a novel task given only a few labeled examples represents a fundamental challenge in closing the gap between machine- and human-level performance. The core of human cognition lies in the structured, reusable concepts that help us to rapidly adapt to new tasks and provide reasoning behind our decisions. However, existing meta-learning methods learn complex representations across prior labeled tasks without imposing any structure on the learned representations. Here we propose COMET, a meta-learning method that improves generalization ability by learning to learn along human-interpretable concept dimensions. Instead of learning a joint unstructuredmore »metric space, COMET learns mappings of high-level concepts into semi-structured metric spaces, and effectively combines the outputs of independent concept learners. We evaluate our model on few-shot tasks from diverse domains, including fine-grained image classification, document categorization and cell type annotation on a novel dataset from a biological domain developed in our work. COMET significantly outperforms strong meta-learning baselines, achieving 6–15% relative improvement on the most challenging 1-shot learning tasks, while unlike existing methods providing interpretations behind the model’s predictions.« less
  9. 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 messagemore »passing. To embed a given node, IDGNN 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.« less