Yubai Yuan

Yuanchen Wu, Yubai Yuan

We consider the problem of active learning on graphs, which has crucial applications in many real-world networks where labeling node responses is expensive. In this paper, we propose an offline active learning method that selects nodes to query by explicitly incorporating information from both the network structure and node covariates. Building on graph signal recovery theories and the random spectral sparsification technique, the proposed method adopts a two-stage biased sampling strategy that takes both informativeness and representativeness into consideration for node querying. Informativeness refers to the complexity of graph signals that are learnable from the responses of queried nodes, while representativeness refers to the capacity of queried nodes to control generalization errors given noisy node-level information. We establish a theoretical relationship between generalization error and the number of nodes selected by the proposed method. Our theoretical results demonstrate the trade-off between informativeness and representativeness in active learning. Extensive numerical experiments show that the proposed method is competitive with existing graph-based active learning methods, especially when node covariates and responses contain noises. Additionally, the proposed method is applicable to both regression and classification tasks on graphs.

Yuanchen Wu, Yubai Yuan

Estimating causal effects on networks is important for both scientific research and practical applications. Unlike traditional settings that assume the Stable Unit Treatment Value Assumption (SUTVA), interference allows an intervention/treatment on one unit to affect the outcomes of others. Understanding both direct and spillover effects is critical in fields such as epidemiology, political science, and economics. Causal inference on networks faces two main challenges. First, causal effects are typically heterogeneous, varying with unit features and local network structure. Second, connected units often exhibit dependence due to network homophily, creating confounding between structural correlations and causal effects. In this paper, we propose a two-stage method to estimate heterogeneous direct and spillover effects on networks. The first stage uses graph neural networks to estimate nuisance components that depend on the complex network topology. In the second stage, we adjust for network confounding using these estimates and infer causal effects through a novel attention-based interference model. Our approach balances expressiveness and interpretability, enabling downstream tasks such as identifying influential neighborhoods and recovering the sign of spillover effects. We integrate the two stages using Neyman orthogonalization and cross-fitting, which ensures that errors from nuisance estimation contribute only at higher order. As a result, our causal effect estimates are robust to bias and misspecification in modeling causal effects under network dependencies.

Yubai Yuan, Babak Shahbaba, Norbert Fortin et al.

Detecting dynamic patterns of task-specific responses shared across heterogeneous datasets is an essential and challenging problem in many scientific applications in medical science and neuroscience. In our motivating example of rodent electrophysiological data, identifying the dynamical patterns in neuronal activity associated with ongoing cognitive demands and behavior is key to uncovering the neural mechanisms of memory. One of the greatest challenges in investigating a cross-subject biological process is that the systematic heterogeneity across individuals could significantly undermine the power of existing machine learning methods to identify the underlying biological dynamics. In addition, many technically challenging neurobiological experiments are conducted on only a handful of subjects where rich longitudinal data are available for each subject. The low sample sizes of such experiments could further reduce the power to detect common dynamic patterns among subjects. In this paper, we propose a novel heterogeneous data integration framework based on optimal transport to extract shared patterns in complex biological processes. The key advantages of the proposed method are that it can increase discriminating power in identifying common patterns by reducing heterogeneity unrelated to the signal by aligning the extracted latent spatiotemporal information across subjects. Our approach is effective even with a small number of subjects, and does not require auxiliary matching information for the alignment. In particular, our method can align longitudinal data across heterogeneous subjects in a common latent space to capture the dynamics of shared patterns while utilizing temporal dependency within subjects.

Yujia Deng, Yubai Yuan, Haoda Fu et al.

In this paper we propose an active metric learning method for clustering with pairwise constraints. The proposed method actively queries the label of informative instance pairs, while estimating underlying metrics by incorporating unlabeled instance pairs, which leads to a more accurate and efficient clustering process. In particular, we augment the queried constraints by generating more pairwise labels to provide additional information in learning a metric to enhance clustering performance. Furthermore, we increase the robustness of metric learning by updating the learned metric sequentially and penalizing the irrelevant features adaptively. In addition, we propose a novel active query strategy that evaluates the information gain of instance pairs more accurately by incorporating the neighborhood structure, which improves clustering efficiency without extra labeling cost. In theory, we provide a tighter error bound of the proposed metric learning method utilizing augmented queries compared with methods using existing constraints only. Furthermore, we also investigate the improvement using the active query strategy instead of random selection. Numerical studies on simulation settings and real datasets indicate that the proposed method is especially advantageous when the signal-to-noise ratio between significant features and irrelevant features is low.

Yubai Yuan, Annie Qu

Link prediction infers potential links from observed networks, and is one of the essential problems in network analyses. In contrast to traditional graph representation modeling which only predicts two-way pairwise relations, we propose a novel tensor-based joint network embedding approach on simultaneously encoding pairwise links and hyperlinks onto a latent space, which captures the dependency between pairwise and multi-way links in inferring potential unobserved hyperlinks. The major advantage of the proposed embedding procedure is that it incorporates both the pairwise relationships and subgroup-wise structure among nodes to capture richer network information. In addition, the proposed method introduces a hierarchical dependency among links to infer potential hyperlinks, and leads to better link prediction. In theory we establish the estimation consistency for the proposed embedding approach, and provide a faster convergence rate compared to link prediction utilizing pairwise links or hyperlinks only. Numerical studies on both simulation settings and Facebook ego-networks indicate that the proposed method improves both hyperlink and pairwise link prediction accuracy compared to existing link prediction algorithms.