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In time-series analysis, many recent works seek to provide a unified view and representation for time-series across multiple domains, leading to the development of foundation models for time-series data. Despite diverse modeling techniques, existing models are black boxes and fail to provide insights and explanations about their representations. In this paper, we present VQShape, a pre-trained, generalizable, and interpretable model for time-series representation learning and classification. By introducing a novel representation for time-series data, we forge a connection between the latent space of VQShape and shape-level features. Using vector quantization, we show that time-series from different domains can be described using a unified set of low-dimensional codes, where each code can be represented as an abstracted shape in the time domain. On classification tasks, we show that the representations of VQShape can be utilized to build interpretable classifiers, achieving comparable performance to specialist models. Additionally, in zero-shot learning, VQShape and its codebook can generalize to previously unseen datasets and domains that are not included in the pre-training process. The code and pre-trained weights are available at https://github.com/YunshiWen/VQShape., Comment: Accepted by Neural Information Processing Systems (NeurIPS) 2024

Sampling is an established technique to scale graph neural networks to large graphs. Current approaches however assume the graphs to be homogeneous in terms of relations and ignore relation types, critically important in biomedical graphs. Multi-relational graphs contain various types of relations that usually come with variable frequency and have different importance for the problem at hand. We propose an approach to modeling the importance of relation types for neighborhood sampling in graph neural networks and show that we can learn the right balance: relation-type probabilities that reflect both frequency and importance. Our experiments on drug-drug interaction prediction show that state-of-the-art graph neural networks profit from relation-dependent sampling in terms of both accuracy and efficiency.

Missing node attributes is a common problem in real-world graphs. Graph neural networks have been demonstrated power in graph representation learning while their performance is affected by the completeness of graph information. Most of them are not specified for missing-attribute graphs and fail to leverage incomplete attribute information effectively. In this paper, we propose an innovative node representation learning framework, Wasserstein Graph Neural Network (WGNN), to mitigate the problem. To make the most of limited observed attribute information and capture the uncertainty caused by missing values, we express nodes as low-dimensional distributions derived from the decomposition of the attribute matrix. Furthermore, we strengthen the expressiveness of representations by developing a novel message passing schema that aggregates distributional information from neighbors in the Wasserstein space. We test WGNN in node classification tasks under two missing-attribute cases on both synthetic and real-world datasets. In addition, we find WGNN suitable to recover missing values and adapt them to tackle matrix completion problems with graphs of users and items. Experimental results on both tasks demonstrate the superiority of our method.

While the celebrated graph neural networks yield effective representations for individual nodes of a graph, there has been relatively less success in extending to the task of graph similarity learning. Recent work on graph similarity learning has considered either global-level graph-graph interactions or low-level node-node interactions, however ignoring the rich cross-level interactions (e.g., between each node of one graph and the other whole graph). In this paper, we propose a multi-level graph matching network (MGMN) framework for computing the graph similarity between any pair of graph-structured objects in an end-to-end fashion. In particular, the proposed MGMN consists of a node-graph matching network for effectively learning cross-level interactions between each node of one graph and the other whole graph, and a siamese graph neural network to learn global-level interactions between two input graphs. Furthermore, to compensate for the lack of standard benchmark datasets, we have created and collected a set of datasets for both the graph-graph classification and graph-graph regression tasks with different sizes in order to evaluate the effectiveness and robustness of our models. Comprehensive experiments demonstrate that MGMN consistently outperforms state-of-the-art baseline models on both the graph-graph classification and graph-graph regression tasks. Compared with previous work, MGMN also exhibits stronger robustness as the sizes of the two input graphs increase., Comment: Accepted by IEEE Transactions on Neural Networks and Learning Systems (IEEE TNNLS)

There is a growing interest in applying deep learning (DL) to healthcare, driven by the availability of data with multiple feature channels in rich-data environments (e.g., intensive care units). However, in many other practical situations, we can only access data with much fewer feature channels in a poor-data environments (e.g., at home), which often results in predictive models with poor performance. How can we boost the performance of models learned from such poor-data environment by leveraging knowledge extracted from existing models trained using rich data in a related environment? To address this question, we develop a knowledge infusion framework named CHEER that can succinctly summarize such rich model into transferable representations, which can be incorporated into the poor model to improve its performance. The infused model is analyzed theoretically and evaluated empirically on several datasets. Our empirical results showed that CHEER outperformed baselines by 5.60% to 46.80% in terms of the macro-F1 score on multiple physiological datasets., Comment: Published in TKDE

There have been more than 850,000 confirmed cases and over 48,000 deaths from the human coronavirus disease 2019 (COVID-19) pandemic, caused by novel severe acute respiratory syndrome coronavirus (SARS-CoV-2), in the United States alone. However, there are currently no proven effective medications against COVID-19. Drug repurposing offers a promising way for the development of prevention and treatment strategies for COVID-19. This study reports an integrative, network-based deep learning methodology to identify repurposable drugs for COVID-19 (termed CoV-KGE). Specifically, we built a comprehensive knowledge graph that includes 15 million edges across 39 types of relationships connecting drugs, diseases, genes, pathways, and expressions, from a large scientific corpus of 24 million PubMed publications. Using Amazon AWS computing resources, we identified 41 repurposable drugs (including indomethacin, toremifene and niclosamide) whose therapeutic association with COVID-19 were validated by transcriptomic and proteomic data in SARS-CoV-2 infected human cells and data from ongoing clinical trials. While this study, by no means recommends specific drugs, it demonstrates a powerful deep learning methodology to prioritize existing drugs for further investigation, which holds the potential of accelerating therapeutic development for COVID-19.

Hierarchical abstractions are a methodology for solving large-scale graph problems in various disciplines. Coarsening is one such approach: it generates a pyramid of graphs whereby the one in the next level is a structural summary of the prior one. With a long history in scientific computing, many coarsening strategies were developed based on mathematically driven heuristics. Recently, resurgent interests exist in deep learning to design hierarchical methods learnable through differentiable parameterization. These approaches are paired with downstream tasks for supervised learning. In practice, however, supervised signals (e.g., labels) are scarce and are often laborious to obtain. In this work, we propose an unsupervised approach, coined OTCoarsening, with the use of optimal transport. Both the coarsening matrix and the transport cost matrix are parameterized, so that an optimal coarsening strategy can be learned and tailored for a given set of graphs. We demonstrate that the proposed approach produces meaningful coarse graphs and yields competitive performance compared with supervised methods for graph classification and regression., Comment: AAAI 2021. Code is available at https://github.com/matenure/OTCoarsening

Gaining more comprehensive knowledge about drug-drug interactions (DDIs) is one of the most important tasks in drug development and medical practice. Recently graph neural networks have achieved great success in this task by modeling drugs as nodes and drug-drug interactions as links and casting DDI predictions as link prediction problems. However, correlations between link labels (e.g., DDI types) were rarely considered in existing works. We propose the graph energy neural network (GENN) to explicitly model link type correlations. We formulate the DDI prediction task as a structure prediction problem and introduce a new energy-based model where the energy function is defined by graph neural networks. Experiments on two real-world DDI datasets demonstrated that GENN is superior to many baselines without consideration of link type correlations and achieved $13.77\%$ and $5.01\%$ PR-AUC improvement on the two datasets, respectively. We also present a case study in which \mname can better capture meaningful DDI correlations compared with baseline models.

Benchmark data sets are an indispensable ingredient of the evaluation of graph-based machine learning methods. We release a new data set, compiled from International Planning Competitions (IPC), for benchmarking graph classification, regression, and related tasks. Apart from the graph construction (based on AI planning problems) that is interesting in its own right, the data set possesses distinctly different characteristics from popularly used benchmarks. The data set, named IPC, consists of two self-contained versions, grounded and lifted, both including graphs of large and skewedly distributed sizes, posing substantial challenges for the computation of graph models such as graph kernels and graph neural networks. The graphs in this data set are directed and the lifted version is acyclic, offering the opportunity of benchmarking specialized models for directed (acyclic) structures. Moreover, the graph generator and the labeling are computer programmed; thus, the data set may be extended easily if a larger scale is desired. The data set is accessible from \url{https://github.com/IBM/IPC-graph-data}., Comment: ICML 2019 Workshop on Learning and Reasoning with Graph-Structured Data. The data set is accessible from https://github.com/IBM/IPC-graph-data

Graph representation learning resurges as a trending research subject owing to the widespread use of deep learning for Euclidean data, which inspire various creative designs of neural networks in the non-Euclidean domain, particularly graphs. With the success of these graph neural networks (GNN) in the static setting, we approach further practical scenarios where the graph dynamically evolves. Existing approaches typically resort to node embeddings and use a recurrent neural network (RNN, broadly speaking) to regulate the embeddings and learn the temporal dynamics. These methods require the knowledge of a node in the full time span (including both training and testing) and are less applicable to the frequent change of the node set. In some extreme scenarios, the node sets at different time steps may completely differ. To resolve this challenge, we propose EvolveGCN, which adapts the graph convolutional network (GCN) model along the temporal dimension without resorting to node embeddings. The proposed approach captures the dynamism of the graph sequence through using an RNN to evolve the GCN parameters. Two architectures are considered for the parameter evolution. We evaluate the proposed approach on tasks including link prediction, edge classification, and node classification. The experimental results indicate a generally higher performance of EvolveGCN compared with related approaches. The code is available at \url{https://github.com/IBM/EvolveGCN}., Comment: AAAI 2020. The code is available at https://github.com/IBM/EvolveGCN

Automated planning is one of the foundational areas of AI. Since no single planner can work well for all tasks and domains, portfolio-based techniques have become increasingly popular in recent years. In particular, deep learning emerges as a promising methodology for online planner selection. Owing to the recent development of structural graph representations of planning tasks, we propose a graph neural network (GNN) approach to selecting candidate planners. GNNs are advantageous over a straightforward alternative, the convolutional neural networks, in that they are invariant to node permutations and that they incorporate node labels for better inference. Additionally, for cost-optimal planning, we propose a two-stage adaptive scheduling method to further improve the likelihood that a given task is solved in time. The scheduler may switch at halftime to a different planner, conditioned on the observed performance of the first one. Experimental results validate the effectiveness of the proposed method against strong baselines, both deep learning and non-deep learning based. The code is available at \url{https://github.com/matenure/GNN_planner}., Comment: AAAI 2020. Code is released at https://github.com/matenure/GNN_planner. Data set is released at https://github.com/IBM/IPC-graph-data

Deep generative models have achieved remarkable success in various data domains, including images, time series, and natural languages. There remain, however, substantial challenges for combinatorial structures, including graphs. One of the key challenges lies in the difficulty of ensuring semantic validity in context. For examples, in molecular graphs, the number of bonding-electron pairs must not exceed the valence of an atom; whereas in protein interaction networks, two proteins may be connected only when they belong to the same or correlated gene ontology terms. These constraints are not easy to be incorporated into a generative model. In this work, we propose a regularization framework for variational autoencoders as a step toward semantic validity. We focus on the matrix representation of graphs and formulate penalty terms that regularize the output distribution of the decoder to encourage the satisfaction of validity constraints. Experimental results confirm a much higher likelihood of sampling valid graphs in our approach, compared with others reported in the literature., Comment: NIPS 2018

Recent progress in deep learning is revolutionizing the healthcare domain including providing solutions to medication recommendations, especially recommending medication combination for patients with complex health conditions. Existing approaches either do not customize based on patient health history, or ignore existing knowledge on drug-drug interactions (DDI) that might lead to adverse outcomes. To fill this gap, we propose the Graph Augmented Memory Networks (GAMENet), which integrates the drug-drug interactions knowledge graph by a memory module implemented as a graph convolutional networks, and models longitudinal patient records as the query. It is trained end-to-end to provide safe and personalized recommendation of medication combination. We demonstrate the effectiveness and safety of GAMENet by comparing with several state-of-the-art methods on real EHR data. GAMENet outperformed all baselines in all effectiveness measures, and also achieved 3.60% DDI rate reduction from existing EHR data., Comment: AAAI 2019; change the template and fix some typos

In many situations, we need to build and deploy separate models in related environments with different data qualities. For example, an environment with strong observation equipments (e.g., intensive care units) often provides high-quality multi-modal data, which are acquired from multiple sensory devices and have rich-feature representations. On the other hand, an environment with poor observation equipment (e.g., at home) only provides low-quality, uni-modal data with poor-feature representations. To deploy a competitive model in a poor-data environment without requiring direct access to multi-modal data acquired from a rich-data environment, this paper develops and presents a knowledge distillation (KD) method (RDPD) to enhance a predictive model trained on poor data using knowledge distilled from a high-complexity model trained on rich, private data. We evaluated RDPD on three real-world datasets and shown that its distilled model consistently outperformed all baselines across all datasets, especially achieving the greatest performance improvement over a model trained only on low-quality data by 24.56% on PR-AUC and 12.21% on ROC-AUC, and over that of a state-of-the-art KD model by 5.91% on PR-AUC and 4.44% on ROC-AUC., Comment: Published in IJCAI 2019

Drug similarity has been studied to support downstream clinical tasks such as inferring novel properties of drugs (e.g. side effects, indications, interactions) from known properties. The growing availability of new types of drug features brings the opportunity of learning a more comprehensive and accurate drug similarity that represents the full spectrum of underlying drug relations. However, it is challenging to integrate these heterogeneous, noisy, nonlinear-related information to learn accurate similarity measures especially when labels are scarce. Moreover, there is a trade-off between accuracy and interpretability. In this paper, we propose to learn accurate and interpretable similarity measures from multiple types of drug features. In particular, we model the integration using multi-view graph auto-encoders, and add attentive mechanism to determine the weights for each view with respect to corresponding tasks and features for better interpretability. Our model has flexible design for both semi-supervised and unsupervised settings. Experimental results demonstrated significant predictive accuracy improvement. Case studies also showed better model capacity (e.g. embed node features) and interpretability., Comment: IJCAI 2018