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Causal discovery uncovers complex relationships between variables, enhancing predictions, decision-making, and insights into real-world systems, especially in nonlinear multivariate time series. However, most existing methods primarily…

Causal inference is capable of estimating the treatment effect (i.e., the causal effect of treatment on the outcome) to benefit the decision making in various domains. One fundamental challenge in this research is that the treatment…

Across research disciplines, cluster randomized trials (CRTs) are commonly implemented to evaluate interventions delivered to groups of participants, such as communities and clinics. Despite advances in the design and analysis of CRTs,…

Illuminating the interconnections between drugs and genes is an important topic in drug development and precision medicine. Currently, computational predictions of drug-gene interactions mainly focus on the binding interactions without…

Drug-target interaction is fundamental in understanding how drugs affect biological systems, and accurately predicting drug-target affinity (DTA) is vital for drug discovery. Recently, deep learning methods have emerged as a significant…

New biological assays like Perturb-seq link highly parallel CRISPR interventions to a high-dimensional transcriptomic readout, providing insight into gene regulatory networks. Causal gene regulatory networks can be represented by directed…

The identification of drug-target interactions (DTI) is critical for drug discovery and repositioning, as it reveals potential therapeutic uses of existing drugs, accelerating development and reducing costs. However, most existing models…

Patients with Acute Kidney Injury (AKI) increase mortality, morbidity, and long-term adverse events. Therefore, early identification of AKI may improve renal function recovery, decrease comorbidities, and further improve patients' survival.…

The first step in drug discovery is finding drug molecule moieties with medicinal activity against specific targets. Therefore, it is crucial to investigate the interaction between drug-target proteins and small chemical molecules. However,…

Empirical researchers routinely invoke the no-interference or \textit{individualistic treatment response} (ITR) assumption to identify causal effects in observational studies, despite concerns that interference across units may arise in…

Identifying novel drug-target interactions (DTI) is a critical and rate limiting step in drug discovery. While deep learning models have been proposed to accelerate the identification process, we show that state-of-the-art models fail to…

A longstanding goal in computational educational research is to develop explainable knowledge tracing (KT) models. Deep Knowledge Tracing (DKT), which leverages a Recurrent Neural Network (RNN) to predict student knowledge and performance…

Background: In silico drug-target interaction (DTI) prediction plays an integral role in drug repositioning: the discovery of new uses for existing drugs. One popular method of drug repositioning is network-based DTI prediction, which uses…

Subgraph-based methods have proven to be effective and interpretable in predicting drug-drug interactions (DDIs), which are essential for medical practice and drug development. Subgraph selection and encoding are critical stages in these…

Drug-drug interaction (DDI) is a vital information when physicians and pharmacists intend to co-administer two or more drugs. Thus, several DDI databases are constructed to avoid mistakenly combined use. In recent years, automatically…

Causal inference methods are widely applied in various decision-making domains such as precision medicine, optimal policy and economics. Central to these applications is the treatment effect estimation of intervention strategies. Current…

Discovering causal structures from data is a challenging inference problem of fundamental importance in all areas of science. The appealing properties of neural networks have recently led to a surge of interest in differentiable neural…

Estimating treatment effects (TE) from observational data is a critical yet complex task in many fields, from healthcare and economics to public policy. While recent advances in machine learning and causal inference have produced powerful…

Data-driven societal event forecasting methods exploit relevant historical information to predict future events. These methods rely on historical labeled data and cannot accurately predict events when data are limited or of poor quality.…

We propose a novel neural method to extract drug-drug interactions (DDIs) from texts using external drug molecular structure information. We encode textual drug pairs with convolutional neural networks and their molecular pairs with graph…