Clinical trials are pivotal for developing new medical treatments, yet they typically pose some risks such as patient mortality, adverse events, and enrollment failure that waste immense efforts spanning over a decade. Applying artificial intelligence (AI) to forecast or simulate key events in clinical trials holds great potential for providing insights to guide trial designs. However, complex data collection and question definition requiring medical expertise and a deep understanding of trial designs have hindered the involvement of AI thus far. This paper tackles these challenges by presenting a comprehensive suite of meticulously curated AIready datasets covering multi-modal data (e.g., drug molecule, disease code, text, categorical/numerical features) and 8 crucial prediction challenges in clinical trial design, encompassing prediction of trial duration, patient dropout rate, serious adverse event, mortality rate, trial approval outcome, trial failure reason, drug dose finding, design of eligibility criteria. Furthermore, we provide basic validation methods for each task to ensure the datasets' usability and reliability. We anticipate that the availability of such open-access datasets will catalyze the development of advanced AI approaches for clinical trial design, ultimately advancing clinical trial research and accelerating medical solution development.

Forecasting project expenses is a crucial step for businesses to avoid budget overruns and project failures. Traditionally, this has been done by financial analysts or data science techniques such as time-series analysis. However, these approaches can be uncertain and produce results that differ from the planned budget, especially at the start of a project with limited data points. This paper proposes a constrained non-negative matrix completion model that predicts expenses by learning the likelihood of the project correlating with certain expense patterns in the latent space. The model is constrained on three probability simplexes, two of which are on the factor matrices and the third on the missing entries. Additionally, the predicted expense values are guaranteed to meet the budget constraint without the need of post-processing. An inexact alternating optimization algorithm is developed to solve the associated optimization problem and is proven to converge to a stationary point. Results from two real datasets demonstrate the effectiveness of the proposed method in comparison to state-of-the-art algorithms.

Despite many efforts to address the disparities, the underrepresentation of gender, racial, and ethnic minorities in clinical trials remains a problem and undermines the efficacy of treatments on minorities. This paper focuses on the trial site selection task and proposes FRAMM, a deep reinforcement learning framework for fair trial site selection. We focus on addressing two real-world challenges that affect fair trial sites selection: the data modalities are often not complete for many potential trial sites, and the site selection needs to simultaneously optimize for both enrollment and diversity since the problem is necessarily a trade-off between the two with the only possible way to increase diversity post-selection being through limiting enrollment via caps. To address the missing data challenge, FRAMM has a modality encoder with a masked cross-attention mechanism for handling missing data, bypassing data imputation and the need for complete data in training. To handle the need for making efficient trade-offs, FRAMM uses deep reinforcement learning with a specifically designed reward function that simultaneously optimizes for both enrollment and fairness. We evaluate FRAMM using 4,392 real-world clinical trials ranging from 2016 to 2021 and show that FRAMM outperforms the leading baseline in enrollment-only settings while also achieving large gains in diversity. Specifically, it is able to produce a 9% improvement in diversity with similar enrollment levels over the leading baselines. That improved diversity is further manifested in achieving up to a 14% increase in Hispanic enrollment, 27% increase in Black enrollment, and 60% increase in Asian enrollment compared to selecting sites with an enrollment-only model.

Respiratory syncytial virus (RSV) is one of the most dangerous respiratory diseases for infants and young children. Due to the nonpharmaceutical intervention (NPI) imposed in the COVID-19 outbreak, the seasonal transmission pattern of RSV has been discontinued in 2020 and then shifted months ahead in 2021 in the northern hemisphere. It is critical to understand how COVID-19 impacts RSV and build predictive algorithms to forecast the timing and intensity of RSV reemergence in post-COVID-19 seasons. In this paper, we propose a deep coupled tensor factorization machine, dubbed as DeCom, for post COVID-19 RSV prediction. DeCom leverages tensor factorization and residual modeling. It enables us to learn the disrupted RSV transmission reliably under COVID-19 by taking both the regular seasonal RSV transmission pattern and the NPI into consideration. Experimental results on a real RSV dataset show that DeCom is more accurate than the state-of-the-art RSV prediction algorithms and achieves up to 46% lower root mean square error and 49% lower mean absolute error for country-level prediction compared to the baselines.

Tensor completion aims at imputing missing entries from a partially observed tensor. Existing tensor completion methods often assume either multi-linear or nonlinear relationships between latent components. However, real-world tensors have much more complex patterns where both multi-linear and nonlinear relationships may coexist. In such cases, the existing methods are insufficient to describe the data structure. This paper proposes a Joint mUlti-linear and nonLinear IdentificAtion (JULIA) framework for large-scale tensor completion. JULIA unifies the multi-linear and nonlinear tensor completion models with several advantages over the existing methods: 1) Flexible model selection, i.e., it fits a tensor by assigning its values as a combination of multi-linear and nonlinear components; 2) Compatible with existing nonlinear tensor completion methods; 3) Efficient training based on a well-designed alternating optimization approach. Experiments on six real large-scale tensors demonstrate that JULIA outperforms many existing tensor completion algorithms. Furthermore, JULIA can improve the performance of a class of nonlinear tensor completion methods. The results show that in some large-scale tensor completion scenarios, baseline methods with JULIA are able to obtain up to 55% lower root mean-squared-error and save 67% computational complexity.

Deep learning is revolutionizing predictive healthcare, including recommending medications to patients with complex health conditions. Existing approaches focus on predicting all medications for the current visit, which often overlaps with medications from previous visits. A more clinically relevant task is to identify medication changes. In this paper, we propose a new recurrent residual network, named MICRON, for medication change prediction. MICRON takes the changes in patient health records as input and learns to update a hidden medication vector and the medication set recurrently with a reconstruction design. The medication vector is like the memory cell that encodes longitudinal information of medications. Unlike traditional methods that require the entire patient history for prediction, MICRON has a residual-based inference that allows for sequential updating based only on new patient features (e.g., new diagnoses in the recent visit) more efficiently. We evaluated MICRON on real inpatient and outpatient datasets. MICRON achieves 3.5% and 7.8% relative improvements over the best baseline in F1 score, respectively. MICRON also requires fewer parameters, which significantly reduces the training time to 38.3s per epoch with 1.5x speed-up.

Despite deep learning (DL) success in classification problems, DL classifiers do not provide a sound mechanism to decide when to refrain from predicting. Recent works tried to control the overall prediction risk with classification with rejection options. However, existing works overlook the different significance of different classes. We introduce Set-classifier with Class-specific RIsk Bounds (SCRIB) to tackle this problem, assigning multiple labels to each example. Given the output of a black-box model on the validation set, SCRIB constructs a set-classifier that controls the class-specific prediction risks with a theoretical guarantee. The key idea is to reject when the set classifier returns more than one label. We validated SCRIB on several medical applications, including sleep staging on electroencephalogram (EEG) data, X-ray COVID image classification, and atrial fibrillation detection based on electrocardiogram (ECG) data. SCRIB obtained desirable class-specific risks, which are 35\%-88\% closer to the target risks than baseline methods.

The attention mechanism has demonstrated superior performance for inference over nodes in graph neural networks (GNNs), however, they result in a high computational burden during both training and inference. We propose FastGAT, a method to make attention based GNNs lightweight by using spectral sparsification to generate an optimal pruning of the input graph. This results in a per-epoch time that is almost linear in the number of graph nodes as opposed to quadratic. We theoretically prove that spectral sparsification preserves the features computed by the GAT model, thereby justifying our FastGAT algorithm. We experimentally evaluate FastGAT on several large real world graph datasets for node classification tasks under both inductive and transductive settings. FastGAT can dramatically reduce (up to 10x) the computational time and memory requirements, allowing the usage of attention based GNNs on large graphs. Graphs are efficient representations of pairwise relations, with many real-world applications including product co-purchasing network ((McAuley et al., 2015)), coauthor network ((Hamilton et al., 2017b)), etc. Graph neural networks (GNN) have become popular as a tool for inference from graph based data. By leveraging the geometric structure of the graph, GNNs learn improved representations of the graph nodes and edges that can lead to better performance in various inference tasks ((Kipf & Welling, 2016; Hamilton et al., 2017a; Veličković et al., 2018)). More recently, the attention mechanism has demonstrated superior performance for inference over nodes in GNNs ((Veličković et al., 2018; Xinyi & Chen, 2019; Thekumparampil et al., 2018; Lee et al., 2020; Bianchi et al., 2019; Knyazev et al., 2019)). However, attention based GNNs suffer from huge computational cost. This may hinder the applicability of the attention mechanism to large graphs.

Rare diseases affecting 350 million individuals are commonly associated with delay in diagnosis or misdiagnosis. To improve those patients' outcome, rare disease detection is an important task for identifying patients with rare conditions based on longitudinal medical claims. In this paper, we present a deep learning method for detecting patients with exocrine pancreatic insufficiency (EPI) (a rare disease). The contribution includes 1) a large longitudinal study using 7 years medical claims from 1.8 million patients including 29,149 EPI patients, 2) a new deep learning model using generative adversarial networks (GANs) to boost rare disease class, and also leveraging recurrent neural networks to model patient sequence data, 3) an accurate prediction with 0.56 PR-AUC which outperformed benchmark models in terms of precision and recall.

Many computational models were proposed to extract temporal patterns from clinical time series for each patient and among patient group for predictive healthcare. However, the common relations among patients (e.g., share the same doctor) were rarely considered. In this paper, we represent patients and clinicians relations by bipartite graphs addressing for example from whom a patient get a diagnosis. We then solve for the top eigenvectors of the graph Laplacian, and include the eigenvectors as latent representations of the similarity between patient-clinician pairs into a time-sensitive prediction model. We conducted experiments using real-world data to predict the initiation of first-line treatment for Chronic Lymphocytic Leukemia (CLL) patients. Results show that relational similarity can improve prediction over multiple baselines, for example a 5% incremental over long-short term memory baseline in terms of area under precision-recall curve.