Bing Yao

Jiahao Shao, Xudong Wang, Anam Nawaz Khan et al.

Breast cancer recurrence, a leading cause of long-term mortality among survivors, requires timely and accurate risk assessment to guide follow-up care and treatment planning. Traditional predictive models, often limited to either structured or unstructured data alone, struggle to capture the full clinical context. This study examines the impact of integrating multi-modal clinical data, including treatment records, pathology reports, and clinician notes, on recurrence prediction. By integrating a rule-based regular expression extraction mechanism with a rigorous precedence-based conflict reconciliation strategy, our approach effectively recovers definitive tumor characteristics from free-text pathology narratives to augment structured records. We also benchmark performance against commonly used feature sets from prior breast cancer studies to assess the added value of multi-modal integration. Single-source and multi-modal inputs are evaluated across a range of machine learning models. Results show that multi-modal integration consistently improves predictive accuracy compared to single-modal methods.

Zekai Wang, Stavros Stavrakis, Bing Yao

Cardiac disease is the leading cause of death in the US. Accurate heart disease detection is of critical importance for timely medical treatment to save patients' lives. Routine use of electrocardiogram (ECG) is the most common method for physicians to assess the electrical activities of the heart and detect possible abnormal cardiac conditions. Fully utilizing the ECG data for reliable heart disease detection depends on developing effective analytical models. In this paper, we propose a two-level hierarchical deep learning framework with Generative Adversarial Network (GAN) for automatic diagnosis of ECG signals. The first-level model is composed of a Memory-Augmented Deep auto-Encoder with GAN (MadeGAN), which aims to differentiate abnormal signals from normal ECGs for anomaly detection. The second-level learning aims at robust multi-class classification for different arrhythmias identification, which is achieved by integrating the transfer learning technique to transfer knowledge from the first-level learning with the multi-branching architecture to handle the data-lacking and imbalanced data issue. We evaluate the performance of the proposed framework using real-world medical data from the MIT-BIH arrhythmia database. Experimental results show that our proposed model outperforms existing methods that are commonly used in current practice.

Jiahao Shao, Anam Nawaz Khan, Christopher Brett et al.

Pathology reports serve as the definitive record for breast cancer staging, yet their unstructured format impedes large-scale data curation. While Large Language Models (LLMs) offer semantic reasoning, their deployment is often limited by high computational costs and hallucination risks. This study introduces a parameter-efficient, multi-task framework for automating the extraction of Tumor-Node-Metastasis (TNM) staging, histologic grade, and biomarkers. We fine-tune a Llama-3-8B-Instruct encoder using Low-Rank Adaptation (LoRA) on a curated, expert-verified dataset of 10,677 reports. Unlike generative approaches, our architecture utilizes parallel classification heads to enforce consistent schema adherence. Experimental results demonstrate that the model achieves a Macro F1 score of 0.976, successfully resolving complex contextual ambiguities and heterogeneous reporting formats that challenge traditional extraction methods including rule-based natural language processing (NLP) pipelines, zero-shot LLMs, and single-task LLM baselines. The proposed adapter-efficient, multi-task architecture enables reliable, scalable pathology-derived cancer staging and biomarker profiling, with the potential to enhance clinical decision support and accelerate data-driven oncology research.

Jianxin Xie, Bing Yao, Zheyu Jiang

Soil moisture is a key hydrological parameter that has significant importance to human society and the environment. Accurate modeling and monitoring of soil moisture in crop fields, especially in the root zone (top 100 cm of soil), is essential for improving agricultural production and crop yield with the help of precision irrigation and farming tools. Realizing the full sensor data potential depends greatly on advanced analytical and predictive domain-aware models. In this work, we propose a physics-constrained deep learning (P-DL) framework to integrate physics-based principles on water transport and water sensing signals for effective reconstruction of the soil moisture dynamics. We adopt three different optimizers, namely Adam, RMSprop, and GD, to minimize the loss function of P-DL during the training process. In the illustrative case study, we demonstrate the empirical convergence of Adam optimizers outperforms the other optimization methods in both mini-batch and full-batch training.

Xizhuo Zhang, Bing Yao

Rapid developments in advanced sensing and imaging have significantly enhanced information visibility, opening opportunities for predictive modeling of complex dynamic systems. However, sensing signals acquired from such complex systems are often distributed across 3D geometries and rapidly evolving over time, posing significant challenges in spatiotemporal predictive modeling. This paper proposes a geometry-aware active learning framework for modeling spatiotemporal dynamic systems. Specifically, we propose a geometry-aware spatiotemporal Gaussian Process (G-ST-GP) to effectively integrate the temporal correlations and geometric manifold features for reliable prediction of high-dimensional dynamic behaviors. In addition, we develop an adaptive active learning strategy to strategically identify informative spatial locations for data collection and further maximize the prediction accuracy. This strategy achieves the adaptive trade-off between the prediction uncertainty in the G-ST-GP model and the space-filling design guided by the geodesic distance across the 3D geometry. We implement the proposed framework to model the spatiotemporal electrodynamics in a 3D heart geometry. Numerical experiments show that our framework outperforms traditional methods lacking the mechanism of geometric information incorporation or effective data collection.

Xizhuo Zhang, Bing Yao

Recent advances in sensing and imaging technologies have enabled the collection of high-dimensional spatiotemporal data across complex geometric domains. However, effective modeling of such data remains challenging due to irregular spatial structures, rapid temporal dynamics, and the need to jointly predict multiple interrelated physical variables. This paper presents a physics-augmented multi-task Gaussian Process (P-M-GP) framework tailored for spatiotemporal dynamic systems. Specifically, we develop a geometry-aware, multi-task Gaussian Process (M-GP) model to effectively capture intrinsic spatiotemporal structure and inter-task dependencies. To further enhance the model fidelity and robustness, we incorporate governing physical laws through a physics-based regularization scheme, thereby constraining predictions to be consistent with governing dynamical principles. We validate the proposed P-M-GP framework on a 3D cardiac electrodynamics modeling task. Numerical experiments demonstrate that our method significantly improves prediction accuracy over existing methods by effectively incorporating domain-specific physical constraints and geometric prior.

Zekai Wang, Bing Yao

Spatiotemporal dynamics forecasting is inherently challenging, particularly in systems defined over irregular geometric domains, due to the need to jointly capture complex spatial correlations and nonlinear temporal dynamics. To tackle these challenges, we propose TK-GCN, a two-stage framework that integrates geometry-aware spatial encoding with long-range temporal modeling. In the first stage, a Koopman-enhanced Graph Convolutional Network (K-GCN) is developed to embed the high-dimensional dynamics distributed on spatially irregular domains into a latent space where the evolution of system states is approximately linear. By leveraging Koopman operator theory, this stage enhances the temporal consistency during the latent learning. In the second stage, a Transformer module is employed to model the temporal progression within the Koopman-encoded latent space. Through the self-attention mechanism, the Transformer captures long-range temporal dependencies, enabling accurate forecasting over extended horizons. We evaluate TK-GCN in spatiotemporal cardiac dynamics forecasting and benchmark its performance against several state-of-the-art baselines. Experimental results and ablation studies show that TK-GCN consistently delivers superior predictive accuracy across a range of forecast horizons, demonstrating its capability to effectively model complex spatial structures and nonlinear temporal dynamics.

Zekai Wang, Tieming Liu, Bing Yao

The era of big data has made vast amounts of clinical data readily available, particularly in the form of electronic health records (EHRs), which provides unprecedented opportunities for developing data-driven diagnostic tools to enhance clinical decision making. However, the application of EHRs in data-driven modeling faces challenges such as irregularly spaced multi-variate time series, issues of incompleteness, and data imbalance. Realizing the full data potential of EHRs hinges on the development of advanced analytical models. In this paper, we propose a novel Missingness-aware mUlti-branching Self-Attention Encoder (MUSE-Net) to cope with the challenges in modeling longitudinal EHRs for data-driven disease prediction. The proposed MUSE-Net is composed by four novel modules including: (1) a multi-task Gaussian process (MGP) with missing value masks for data imputation; (2) a multi-branching architecture to address the data imbalance problem; (3) a time-aware self-attention encoder to account for the irregularly spaced time interval in longitudinal EHRs; (4) interpretable multi-head attention mechanism that provides insights into the importance of different time points in disease prediction, allowing clinicians to trace model decisions. We evaluate the proposed MUSE-Net using both synthetic and real-world datasets. Experimental results show that our MUSE-Net outperforms existing methods that are widely used to investigate longitudinal signals.

Bing Yao, Jing Su, Fei Ma et al.

Making topological authentication from theory to practical application is an important and challenging task. More and more researchers pay attention on coming quantum computation, privacy data protection, lattices and cryptography. Research show the advantages of topological authentications through graph operations, various matrices, graph colorings and graph labelings are: related with two or more different mathematical areas, be not pictures, there are huge number of colorings and labelings, rooted on modern mathematics, diversity of asymmetric ciphers, simplicity and convenience, easily created, irreversibility, computational security, provable security, and so on. Topological authentications based on various graph homomorphisms, degree-sequence homomorphisms, graph-set homomorphisms. Randomly topological coding and topological authentications are based on Hanzi authentication, randomly adding-edge-removing operation, randomly leaf-adding algorithms, graph random increasing techniques, operation graphic lattice and dynamic networked models and their spanning trees and maximum leaf spanning trees. Realization of topological authentication is an important topic, we study: number-based strings generated from colored graphs, particular graphs (complete graphs, trees, planar graphs), some methods of generating public-keys. some techniques of topologically asymmetric cryptosystem are: W-type matching labelings, dual-type labelings, reciprocal-type labelings, topological homomorphisms, indexed colorings, graphic lattices, degree-sequence lattices, every-zero Cds-matrix groups of degree-sequences, every-zero graphic groups, graphic lattices having coloring closure property, self-similar networked lattices.

Bing Yao, Fei Ma

In order to make more complex number-based strings from topological coding for defending against the intelligent attacks equipped with quantum computing and providing effective protection technology for the age of quantum computing, we will introduce set-colored graphs admitting set-colorings that has been considerable cryptanalytic significance, and especially related with hypergraphs. We use the set-coloring of graphs to reflect the intersection of elements, and add other constraint requirements to express more connections between sets (as hyperedges). Since we try to find some easy and effective techniques based on graph theory for practical application, we use intersected-graphs admitting set-colorings defined on hyperedge sets to observe topological structures of hypergraphs, string-type Topcode-matrix, set-type Topcode-matrix, graph-type Topcode-matrix, hypergraph-type Topcode-matrix, matrix-type Topcode-matrix \emph{etc}. We will show that each connected graph is the intersected-graph of some hypergraph and investigate hypergraph's connectivity, colorings of hypergraphs, hypergraph homomorphism, hypernetworks, scale-free network generator, compound hypergraphs having their intersected-graphs with vertices to be hypergraphs (for high-dimensional extension diagram). Naturally, we get various graphic lattices, such as edge-coincided intersected-graph lattice, vertex-coincided intersected-graph lattice, edge-hamiltonian graphic lattice, hypergraph lattice and intersected-network lattice. Many techniques in this article can be translated into polynomial algorithms, since we are aiming to apply hypergraphs and graph set-colorings to homomorphic encryption and asymmetric cryptograph.

Jianxin Xie, Bing Yao

The rapid developments in advanced sensing and imaging bring about a data-rich environment, facilitating the effective modeling, monitoring, and control of complex systems. For example, the body-sensor network captures multi-channel information pertinent to the electrical activity of the heart (i.e., electrocardiograms (ECG)), which enables medical scientists to monitor and detect abnormal cardiac conditions. However, the high-dimensional sensing data are generally complexly structured and realizing the full data potential depends to a great extent on advanced analytical and predictive methods. This paper presents a physics-constrained deep learning (P-DL) framework for high-dimensional inverse ECG modeling. This method integrates the physical laws of the complex system with the advanced deep learning infrastructure for effective prediction of the system dynamics. The proposed P-DL approach is implemented to solve the inverse ECG model and predict the time-varying distribution of electric potentials in the heart from the ECG data measured by the body-surface sensor network. Experimental results show that the proposed P-DL method significantly outperforms existing methods that are commonly used in current practice.

Bing Yao, Hui Sun, Xiaohui Zhang et al.

Graphical passwords (GPWs) are convenient for mobile equipments with touch screen. Topological graphic passwords (Topsnut-gpws) can be saved in computer by classical matrices and run quickly than the existing GPWs. We research Topsnut-gpws by the matching of view, since they have many advantages. We discuss: configuration matching partition, coloring/labelling matching partition, set matching partition, matching chain, etc. And, we introduce new graph labellings for enriching Topsnut-matchings and show that these labellings can be realized for trees or spanning trees of networks. In theoretical works we explore Graph Labelling Analysis, and show that every graph admits our extremal labellings and set-type labellings in graph theory. Many of the graph labellings mentioned are related with problems of set matching partitions to number theory, and yield new objects and new problems to graph theory.

Bing Yao, Hui Sun, Hongyu Wang et al.

Graphical passwords (GPWs) have been studied over 20 years. We are motivated from QR codes that can be considered GPWs, are successfully applied in today's world. However, one need such GPWs that can be use conveniently and have higher level security in information networks. We aim to GPWs for mobile devices with touch screen. No more researching papers of GPWs by means of techniques of graph theory that are already used in a wide range of scientific areas, especially, dynamic networks. Our investigation is devoted to designing new type of graphical passwords by methods of graph theory, such as various topological structures and colorings (labellings). We develop the idea of "topological structure plus number theory" in maximal planar graphs, and provide new techniques for designing new type of GPWs, and furthermore we do theoretical analysis on these new type of GPWs.