Bridging the Data Scarcity in Venous Thromboembolism Detection: A Deep Learning Framework for Large-scale Irregular Clinical Time Series

Abstract

Venous thromboembolism (VTE) is a common and life-threatening complication in cancer patients after treatment. Early risk assessment and detection of VTE primarily rely on clinical indicators, such as blood test results. However, existing studies are limited to static or snapshot-based models, failing to capture the evolving dynamics of disease progression, as deep time-series modeling is hindered by the lack of longitudinal clinical data. To address this gap, we introduce CliTsVTE, a large-scale clinical time-series dataset curated for VTE modeling, comprising 501,063 samples from 26,022 patients over seven years across nine cancer types. The dataset contains continuous time gaps between consecutive time points. Unlike many benchmarks, CliTsVTE reflects real-world clinical settings and presents unique challenges in continuous irregular time-series modeling with long-term irregularity and varying data granularity, which makes missingness significantly consequential. To tackle this, we propose a deep learning framework integrating multiple sequential backbones with an adversarially regularized autoencoder (ARAE) that learns latent representations to eliminate missingness. Experiments on CliTsVTE show that our best model achieves 88.7% accuracy and an AUC of 0.952, significantly outperforming traditional time-point models and regular time-series benchmarks. These results establish a strong benchmark for deep modeling of continuous irregularity in clinical time-series data and highlight the potential of AI-driven large-scale clinical datasets in solving real-world medical research challenges.