Siqi Li

Siqi Li, Pinyan Liu, Gustavo G. Nascimento et al.

Federated learning (FL) has gained popularity in clinical research in recent years to facilitate privacy-preserving collaboration. Structured data, one of the most prevalent forms of clinical data, has experienced significant growth in volume concurrently, notably with the widespread adoption of electronic health records in clinical practice. This review examines FL applications on structured medical data, identifies contemporary limitations and discusses potential innovations. We searched five databases, SCOPUS, MEDLINE, Web of Science, Embase, and CINAHL, to identify articles that applied FL to structured medical data and reported results following the PRISMA guidelines. Each selected publication was evaluated from three primary perspectives, including data quality, modeling strategies, and FL frameworks. Out of the 1160 papers screened, 34 met the inclusion criteria, with each article consisting of one or more studies that used FL to handle structured clinical/medical data. Of these, 24 utilized data acquired from electronic health records, with clinical predictions and association studies being the most common clinical research tasks that FL was applied to. Only one article exclusively explored the vertical FL setting, while the remaining 33 explored the horizontal FL setting, with only 14 discussing comparisons between single-site (local) and FL (global) analysis. The existing FL applications on structured medical data lack sufficient evaluations of clinically meaningful benefits, particularly when compared to single-site analyses. Therefore, it is crucial for future FL applications to prioritize clinical motivations and develop designs and methodologies that can effectively support and aid clinical practice and research.

Siqi Li, Yilin Ning, Marcus Eng Hock Ong et al.

We propose FedScore, a privacy-preserving federated learning framework for scoring system generation across multiple sites to facilitate cross-institutional collaborations. The FedScore framework includes five modules: federated variable ranking, federated variable transformation, federated score derivation, federated model selection and federated model evaluation. To illustrate usage and assess FedScore's performance, we built a hypothetical global scoring system for mortality prediction within 30 days after a visit to an emergency department using 10 simulated sites divided from a tertiary hospital in Singapore. We employed a pre-existing score generator to construct 10 local scoring systems independently at each site and we also developed a scoring system using centralized data for comparison. We compared the acquired FedScore model's performance with that of other scoring models using the receiver operating characteristic (ROC) analysis. The FedScore model achieved an average area under the curve (AUC) value of 0.763 across all sites, with a standard deviation (SD) of 0.020. We also calculated the average AUC values and SDs for each local model, and the FedScore model showed promising accuracy and stability with a high average AUC value which was closest to the one of the pooled model and SD which was lower than that of most local models. This study demonstrates that FedScore is a privacy-preserving scoring system generator with potentially good generalizability.

Siqi Li, Di Miao, Qiming Wu et al.

Federated learning (FL) has shown promising potential in safeguarding data privacy in healthcare collaborations. While the term "FL" was originally coined by the engineering community, the statistical field has also explored similar privacy-preserving algorithms. Statistical FL algorithms, however, remain considerably less recognized than their engineering counterparts. Our goal was to bridge the gap by presenting the first comprehensive comparison of FL frameworks from both engineering and statistical domains. We evaluated five FL frameworks using both simulated and real-world data. The results indicate that statistical FL algorithms yield less biased point estimates for model coefficients and offer convenient confidence interval estimations. In contrast, engineering-based methods tend to generate more accurate predictions, sometimes surpassing central pooled and statistical FL models. This study underscores the relative strengths and weaknesses of both types of methods, emphasizing the need for increased awareness and their integration in future FL applications.

Mengying Yan, Ziye Tian, Siqi Li et al.

Clinical decision support tools built on electronic health records often experience performance drift due to temporal population shifts, particularly when changes in the clinical environment initially affect only a subset of patients, resulting in a transition to mixed populations. Such case-mix changes commonly arise following system-level operational updates or the emergence of new diseases, such as COVID-19. We propose TRACER (Transfer Learning-based Real-time Adaptation for Clinical Evolving Risk), a framework that identifies encounter-level transition membership and adapts predictive models using transfer learning without full retraining. In simulation studies, TRACER outperformed static models trained on historical or contemporary data. In a real-world application predicting hospital admission following emergency department visits across the COVID-19 transition, TRACER improved both discrimination and calibration. TRACER provides a scalable approach for maintaining robust predictive performance under evolving and heterogeneous clinical conditions.

Siqi Li, Yasser Shoukry

Deep neural networks are highly susceptible to adversarial attacks, which pose significant risks to security- and safety-critical applications. We present KoALA (KL-L0 Adversarial detection via Label Agreement), a novel, semantics-free adversarial detector that requires no architectural changes or adversarial retraining. KoALA operates on a simple principle: it detects an adversarial attack when class predictions from two complementary similarity metrics disagree. These metrics-KL divergence and an L0-based similarity-are specifically chosen to detect different types of perturbations. The KL divergence metric is sensitive to dense, low-amplitude shifts, while the L0-based similarity is designed for sparse, high-impact changes. We provide a formal proof of correctness for our approach. The only training required is a simple fine-tuning step on a pre-trained image encoder using clean images to ensure the embeddings align well with both metrics. This makes KOALA a lightweight, plug-and-play solution for existing models and various data modalities. Our extensive experiments on ResNet/CIFAR-10 and CLIP/Tiny-ImageNet confirm our theoretical claims. When the theorem's conditions are met, KoALA consistently and effectively detects adversarial examples. On the full test sets, KoALA achieves a precision of 0.94 and a recall of 0.81 on ResNet/CIFAR-10, and a precision of 0.66 and a recall of 0.85 on CLIP/Tiny-ImageNet.

Zhu Yufan, Hao Zeyu, Li Siqi et al.

SplaXBERT, built on ALBERT-xlarge with context-splitting and mixed precision training, achieves high efficiency in question-answering tasks on lengthy texts. Tested on SQuAD v1.1, it attains an Exact Match of 85.95% and an F1 Score of 92.97%, outperforming traditional BERT-based models in both accuracy and resource efficiency.

Yilin Ning, Siqi Li, Marcus Eng Hock Ong et al.

Risk scores are widely used for clinical decision making and commonly generated from logistic regression models. Machine-learning-based methods may work well for identifying important predictors, but such 'black box' variable selection limits interpretability, and variable importance evaluated from a single model can be biased. We propose a robust and interpretable variable selection approach using the recently developed Shapley variable importance cloud (ShapleyVIC) that accounts for variability across models. Our approach evaluates and visualizes overall variable contributions for in-depth inference and transparent variable selection, and filters out non-significant contributors to simplify model building steps. We derive an ensemble variable ranking from variable contributions, which is easily integrated with an automated and modularized risk score generator, AutoScore, for convenient implementation. In a study of early death or unplanned readmission, ShapleyVIC selected 6 of 41 candidate variables to create a well-performing model, which had similar performance to a 16-variable model from machine-learning-based ranking.