arXiv subjects

Yi-Ju Tseng

Publications and source records attributed to Yi-Ju Tseng.

6 recordsLinked to original sources

arXiv2026

NPCNet: Navigator-Driven Pseudo Text for Deep Clustering of Early Sepsis Phenotyping

Electronic Health Records (EHRs) provide high-dimensional temporal data essential for patient modeling; however, conventional algorithmic approaches often rely on data aggregation or imputation, which distorts temporal disease trajectories. Such computational limitations are particularly critical in sepsis, a heterogeneous syndrome where clustering-based stratification plays a key role in identifying clinically distinct phenotypes for precise treatment strategies. Furthermore, existing clustering processes seldom incorporate domain-driven constraints, often resulting in phenotypes that lack clear clinical distinction. We propose a novel clustering network, NPCNet, that comprises a text embedding generator, a clustering operator, and a target navigator. We first transform EHRs into pseudo texts by discretizing continuous clinical measurements, then integrate them with static variables to construct the embeddings. The target navigator then infuses clinical knowledge into the embeddings through auxiliary tasks, constraining clustering results to better align sepsis phenotypes with clinical significance. Finally, the clustering operator employs an iterative refinement mechanism to jointly optimize phenotype centroids and patient representations under domain-driven constraints. Extensive experiments on public datasets validate that NPCNet achieves superior performance on both internal clustering benchmarks and clinical validity metrics, offering a viable pathway for precision treatment strategies in the management of sepsis.

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arXiv2026

MedM2T: A MultiModal Framework for Time-Aware Modeling with Electronic Health Record and Electrocardiogram Data

The inherent multimodality and heterogeneous temporal structures of medical data pose significant challenges for modeling. We propose MedM2T, a time-aware multimodal framework designed to address these complexities. MedM2T integrates: (i) Sparse Time Series Encoder to flexibly handle irregular and sparse time series, (ii) Hierarchical Time-Aware Fusion to capture both micro- and macro-temporal patterns from multiple dense time series, such as ECGs, and (iii) Bi-Modal Attention to extract cross-modal interactions, which can be extended to any number of modalities. To mitigate granularity gaps between modalities, MedM2T uses modality-specific pre-trained encoders and aligns resulting features within a shared encoder. We evaluated MedM2T on MIMIC-IV and MIMIC-IV-ECG datasets for three tasks that encompass chronic and acute disease dynamics: 90-day cardiovascular disease (CVD) prediction, in-hospital mortality prediction, and ICU length-of-stay (LOS) regression. MedM2T achieved superior or comparable performance relative to state-of-the-art multimodal learning frameworks and existing time series models, achieving an AUROC of 0.932 and an AUPRC of 0.670 for CVD prediction; an AUROC of 0.868 and an AUPRC of 0.470 for mortality prediction; and Mean Absolute Error (MAE) of 2.33 for LOS regression. These results highlight the robustness and broad applicability of MedM2T, positioning it as a promising tool in clinical prediction. We provide the implementation of MedM2T at https://github.com/DHLab-TSENG/MedM2T.

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arXiv2026

LF2L: Loss Fusion Horizontal Federated Learning Across Heterogeneous Feature Spaces Using External Datasets Effectively: A Case Study in Second Primary Cancer Prediction

Second primary cancer (SPC), a new cancer in patients different from previously diagnosed, is a growing concern due to improved cancer survival rates. Early prediction of SPC is essential to enable timely clinical interventions. This study focuses on lung cancer survivors treated in Taiwanese hospitals, where the limited size and geographic scope of local datasets restrict the effectiveness and generalizability of traditional machine learning approaches. To address this, we incorporate external data from the publicly available US-based Surveillance, Epidemiology, and End Results (SEER) program, significantly increasing data diversity and scale. However, the integration of multi-source datasets presents challenges such as feature inconsistency and privacy constraints. Rather than naively merging data, we proposed a loss fusion horizontal federated learning (LF2L) framework that can enable effective cross-institutional collaboration while preserving institutional privacy by avoiding data sharing. Using both common and unique features and balancing their contributions through a shared loss mechanism, our method demonstrates substantial improvements in the prediction performance of SPC. Experiment results show statistically significant improvements in AUROC and AUPRC when compared to localized, horizontal federated, and centralized learning baselines. This highlights the importance of not only acquiring external data but also leveraging it effectively to enhance model performance in real-world clinical model development.

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arXiv2025

KAT-GNN: A Knowledge-Augmented Temporal Graph Neural Network for Risk Prediction in Electronic Health Records

Clinical risk prediction using electronic health records (EHRs) is vital to facilitate timely interventions and clinical decision support. However, modeling heterogeneous and irregular temporal EHR data presents significant challenges. We propose \textbf{KAT-GNN} (Knowledge-Augmented Temporal Graph Neural Network), a graph-based framework that integrates clinical knowledge and temporal dynamics for risk prediction. KAT-GNN first constructs modality-specific patient graphs from EHRs. These graphs are then augmented using two knowledge sources: (1) ontology-driven edges derived from SNOMED CT and (2) co-occurrence priors extracted from EHRs. Subsequently, a time-aware transformer is employed to capture longitudinal dynamics from the graph-encoded patient representations. KAT-GNN is evaluated on three distinct datasets and tasks: coronary artery disease (CAD) prediction using the Chang Gung Research Database (CGRD) and in-hospital mortality prediction using the MIMIC-III and MIMIC-IV datasets. KAT-GNN achieves state-of-the-art performance in CAD prediction (AUROC: 0.9269 $\pm$ 0.0029) and demonstrated strong results in mortality prediction in MIMIC-III (AUROC: 0.9230 $\pm$ 0.0070) and MIMIC-IV (AUROC: 0.8849 $\pm$ 0.0089), consistently outperforming established baselines such as GRASP and RETAIN. Ablation studies confirm that both knowledge-based augmentation and the temporal modeling component are significant contributors to performance gains. These findings demonstrate that the integration of clinical knowledge into graph representations, coupled with a time-aware attention mechanism, provides an effective and generalizable approach for risk prediction across diverse clinical tasks and datasets.

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arXiv2025

SG-XDEAT: Sparsity-Guided Cross-Dimensional and Cross-Encoding Attention with Target-Aware Conditioning in Tabular Learning

We propose SG-XDEAT (Sparsity-Guided Cross Dimensional and Cross-Encoding Attention with Target Aware Conditioning), a novel framework designed for supervised learning on tabular data. At its core, SG-XDEAT employs a dual-stream encoder that decomposes each input feature into two parallel representations: a raw value stream and a target-conditioned (label-aware) stream. These dual representations are then propagated through a hierarchical stack of attention-based modules. SG-XDEAT integrates three key components: (i) Cross-Dimensional self-attention, which captures intra-view dependencies among features within each stream; (ii) Cross-Encoding self-attention, which enables bidirectional interaction between raw and target-aware representations; and (iii) an Adaptive Sparse Self-Attention (ASSA) mechanism, which dynamically suppresses low-utility tokens by driving their attention weights toward zero--thereby mitigating the impact of noise. Empirical results on multiple public benchmarks show consistent gains over strong baselines, confirming that jointly modeling raw and target-aware views--while adaptively filtering noise--yields a more robust deep tabular learner.

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arXiv2023

Self-supervised learning-based general laboratory progress pretrained model for cardiovascular event detection

The inherent nature of patient data poses several challenges. Prevalent cases amass substantial longitudinal data owing to their patient volume and consistent follow-ups, however, longitudinal laboratory data are renowned for their irregularity, temporality, absenteeism, and sparsity; In contrast, recruitment for rare or specific cases is often constrained due to their limited patient size and episodic observations. This study employed self-supervised learning (SSL) to pretrain a generalized laboratory progress (GLP) model that captures the overall progression of six common laboratory markers in prevalent cardiovascular cases, with the intention of transferring this knowledge to aid in the detection of specific cardiovascular event. GLP implemented a two-stage training approach, leveraging the information embedded within interpolated data and amplify the performance of SSL. After GLP pretraining, it is transferred for TVR detection. The proposed two-stage training improved the performance of pure SSL, and the transferability of GLP exhibited distinctiveness. After GLP processing, the classification exhibited a notable enhancement, with averaged accuracy rising from 0.63 to 0.90. All evaluated metrics demonstrated substantial superiority (p < 0.01) compared to prior GLP processing. Our study effectively engages in translational engineering by transferring patient progression of cardiovascular laboratory parameters from one patient group to another, transcending the limitations of data availability. The transferability of disease progression optimized the strategies of examinations and treatments, and improves patient prognosis while using commonly available laboratory parameters. The potential for expanding this approach to encompass other diseases holds great promise.

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