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Researcher profile

Lifang He

Lifang He contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Machine LearningArtificial IntelligenceSocial and Information NetworksComputer VisionNeurons and CognitionBiomoleculesComputation and LanguageCryptography and SecurityDigital LibrariesDistributed, Parallel, and Cluster Computingeess.IVphysics.med-phQuantitative MethodsSymbolic Computation

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Published work

18 published item(s)

preprint2026arXiv

Digital Twin AI: Opportunities and Challenges from Large Language Models to World Models

Digital twins, as precise digital representations of physical systems, have evolved from passive simulation tools into intelligent and autonomous entities through the integration of artificial intelligence technologies. This paper presents a unified four-stage framework that systematically characterizes AI integration across the digital twin lifecycle, spanning modeling, mirroring, intervention, and autonomous management. By synthesizing existing technologies and practices, we distill a unified four-stage framework that systematically characterizes how AI methodologies are embedded across the digital twin lifecycle: (1) modeling the physical twin through physics-based and physics-informed AI approaches, (2) mirroring the physical system into a digital twin with real-time synchronization, (3) intervening in the physical twin through predictive modeling, anomaly detection, and optimization strategies, and (4) achieving autonomous management through large language models, foundation models, and intelligent agents. We analyze the synergy between physics-based modeling and data-driven learning, highlighting the shift from traditional numerical solvers to physics-informed and foundation models for physical systems. Furthermore, we examine how generative AI technologies, including large language models and generative world models, transform digital twins into proactive and self-improving cognitive systems capable of reasoning, communication, and creative scenario generation. Through a cross-domain review spanning eleven application domains, including healthcare, aerospace, smart manufacturing, robotics, and smart cities, we identify common challenges related to scalability, explainability, and trustworthiness, and outline directions for responsible AI-driven digital twin systems.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

Spatio-Temporal Graph Deep Learning with Stochastic Differential Equations for Uncovering Alzheimer's Disease Progression

Identifying objective neuroimaging biomarkers to forecast Alzheimer's disease (AD) progression is crucial for timely intervention. However, this task remains challenging due to the complex dysfunctions in the spatio-temporal characteristics of underlying brain networks, which are often overlooked by existing methods. To address these limitations, we develop an interpretable spatio-temporal graph neural network framework to predict future AD progression, leveraging dual Stochastic Differential Equations (SDEs) to model the irregularly-sampled longitudinal functional magnetic resonance imaging (fMRI) data. We validate our approach on two independent cohorts, including the Open Access Series of Imaging Studies (OASIS-3) and the Alzheimer's Disease Neuroimaging Initiative (ADNI). Our framework effectively learns sparse regional and connective importance probabilities, enabling the identification of key brain circuit abnormalities associated with disease progression. Notably, we detect the parahippocampal cortex, prefrontal cortex, and parietal lobule as salient regions, with significant disruptions in the ventral attention, dorsal attention, and default mode networks. These abnormalities correlate strongly with longitudinal AD-related clinical symptoms. Moreover, our interpretability strategy reveals both established and novel neural systems-level and sex-specific biomarkers, offering new insights into the neurobiological mechanisms underlying AD progression. Our findings highlight the potential of spatio-temporal graph-based learning for early, individualized prediction of AD progression, even in the context of irregularly-sampled longitudinal imaging data.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

Supervised Deep Multimodal Matrix Factorization for Interpretable Brain Network Analysis

We present Supervised Deep Multimodal Matrix Factorization (SD3MF), an interpretable framework for integrative brain network analysis that generalizes Symmetric Nonnegative Matrix Tri-Factorization (SNMTF) from unsupervised single-graph clustering to supervised prediction over populations of multimodal graphs. SD3MF learns deep hierarchical factorizations for each modality together with a shared latent representation that aligns subjects across views. An encoder-decoder formulation jointly optimizes graph reconstruction and supervised prediction, while adaptive weights enable data-driven multimodal fusion. By representing each subject through community-level interaction matrices, the model yields interpretable and discriminative features. Experiments on multimodal connectome datasets show that SD3MF consistently outperforms strong deep learning baselines such as CNNs and GNNs, while enabling biologically interpretable insights. Code for reproducibility is available at: https://github.com/amjadseyedi/SD3MF.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

Towards a Virtual Neuroscientist: Autonomous Neuroimaging Analysis via Multi-Agent Collaboration

Transforming neuroimaging data into clinically actionable biomarkers is a knowledge-intensive and labor-intensive process. Standardized workflows such as fMRIPrep have improved robustness and efficiency, but they are statically configured and cannot reason about downstream objectives, deliberate over alternative strategies, or close the loop between intermediate evidence and subsequent decisions in the way a human researcher would. This lack of closed-loop adaptation often leaves domain experts trapped in a cycle of manual trial-and-error to tune parameters and remediate pipeline failures, severely constraining the scalability of clinical biomarker development. To bridge this gap, we introduce NIAgent, a multi-agent system for autonomous end-to-end neuroimaging analysis. Unlike conventional flat tool-calling agents, NIAgent adopts a code-centric execution paradigm where specialist agents collaboratively synthesize and optimize executable programs over composable domain-specific primitives. This design enables robust, long-horizon workflow construction that adapts dynamically to runtime observations. Furthermore, we propose a hierarchical verification framework for autonomous quality control, integrating cohort-level metric screening with agentic visual inspection to drive evidence-grounded workflow remediation. Experiments on ADHD-200 and ADNI demonstrate that NIAgent outperforms standard workflow-based baselines in predictive performance while exhibiting sophisticated agentic behaviors, including strategy exploration and adaptive refinement.

0 citations0 reviewsNo code linkedOpen access
preprint2024arXiv

Homophily-Related: Adaptive Hybrid Graph Filter for Multi-View Graph Clustering

Recently there is a growing focus on graph data, and multi-view graph clustering has become a popular area of research interest. Most of the existing methods are only applicable to homophilous graphs, yet the extensive real-world graph data can hardly fulfill the homophily assumption, where the connected nodes tend to belong to the same class. Several studies have pointed out that the poor performance on heterophilous graphs is actually due to the fact that conventional graph neural networks (GNNs), which are essentially low-pass filters, discard information other than the low-frequency information on the graph. Nevertheless, on certain graphs, particularly heterophilous ones, neglecting high-frequency information and focusing solely on low-frequency information impedes the learning of node representations. To break this limitation, our motivation is to perform graph filtering that is closely related to the homophily degree of the given graph, with the aim of fully leveraging both low-frequency and high-frequency signals to learn distinguishable node embedding. In this work, we propose Adaptive Hybrid Graph Filter for Multi-View Graph Clustering (AHGFC). Specifically, a graph joint process and graph joint aggregation matrix are first designed by using the intrinsic node features and adjacency relationship, which makes the low and high-frequency signals on the graph more distinguishable. Then we design an adaptive hybrid graph filter that is related to the homophily degree, which learns the node embedding based on the graph joint aggregation matrix. After that, the node embedding of each view is weighted and fused into a consensus embedding for the downstream task. Experimental results show that our proposed model performs well on six datasets containing homophilous and heterophilous graphs.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Data-Efficient Brain Connectome Analysis via Multi-Task Meta-Learning

Brain networks characterize complex connectivities among brain regions as graph structures, which provide a powerful means to study brain connectomes. In recent years, graph neural networks have emerged as a prevalent paradigm of learning with structured data. However, most brain network datasets are limited in sample sizes due to the relatively high cost of data acquisition, which hinders the deep learning models from sufficient training. Inspired by meta-learning that learns new concepts fast with limited training examples, this paper studies data-efficient training strategies for analyzing brain connectomes in a cross-dataset setting. Specifically, we propose to meta-train the model on datasets of large sample sizes and transfer the knowledge to small datasets. In addition, we also explore two brain-network-oriented designs, including atlas transformation and adaptive task reweighing. Compared to other pre-training strategies, our meta-learning-based approach achieves higher and stabler performance, which demonstrates the effectiveness of our proposed solutions. The framework is also able to derive new insights regarding the similarities among datasets and diseases in a data-driven fashion.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Deep Embedded Multi-View Clustering via Jointly Learning Latent Representations and Graphs

With the representation learning capability of the deep learning models, deep embedded multi-view clustering (MVC) achieves impressive performance in many scenarios and has become increasingly popular in recent years. Although great progress has been made in this field, most existing methods merely focus on learning the latent representations and ignore that learning the latent graph of nodes also provides available information for the clustering task. To address this issue, in this paper we propose Deep Embedded Multi-view Clustering via Jointly Learning Latent Representations and Graphs (DMVCJ), which utilizes the latent graphs to promote the performance of deep embedded MVC models from two aspects. Firstly, by learning the latent graphs and feature representations jointly, the graph convolution network (GCN) technique becomes available for our model. With the capability of GCN in exploiting the information from both graphs and features, the clustering performance of our model is significantly promoted. Secondly, based on the adjacency relations of nodes shown in the latent graphs, we design a sample-weighting strategy to alleviate the noisy issue, and further improve the effectiveness and robustness of the model. Experimental results on different types of real-world multi-view datasets demonstrate the effectiveness of DMVCJ.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Deep learning for drug repurposing: methods, databases, and applications

Drug development is time-consuming and expensive. Repurposing existing drugs for new therapies is an attractive solution that accelerates drug development at reduced experimental costs, specifically for Coronavirus Disease 2019 (COVID-19), an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, comprehensively obtaining and productively integrating available knowledge and big biomedical data to effectively advance deep learning models is still challenging for drug repurposing in other complex diseases. In this review, we introduce guidelines on how to utilize deep learning methodologies and tools for drug repurposing. We first summarized the commonly used bioinformatics and pharmacogenomics databases for drug repurposing. Next, we discuss recently developed sequence-based and graph-based representation approaches as well as state-of-the-art deep learning-based methods. Finally, we present applications of drug repurposing to fight the COVID-19 pandemic, and outline its future challenges.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

From Known to Unknown: Quality-aware Self-improving Graph Neural Network for Open Set Social Event Detection

State-of-the-art Graph Neural Networks (GNNs) have achieved tremendous success in social event detection tasks when restricted to a closed set of events. However, considering the large amount of data needed for training a neural network and the limited ability of a neural network in handling previously unknown data, it remains a challenge for existing GNN-based methods to operate in an open set setting. To address this problem, we design a Quality-aware Self-improving Graph Neural Network (QSGNN) which extends the knowledge from known to unknown by leveraging the best of known samples and reliable knowledge transfer. Specifically, to fully exploit the labeled data, we propose a novel supervised pairwise loss with an additional orthogonal inter-class relation constraint to train the backbone GNN encoder. The learnt, already-known events further serve as strong reference bases for the unknown ones, which greatly prompts knowledge acquisition and transfer. When the model is generalized to unknown data, to ensure the effectiveness and reliability, we further leverage the reference similarity distribution vectors for pseudo pairwise label generation, selection and quality assessment. Following the diversity principle of active learning, our method selects diverse pair samples with the generated pseudo labels to fine-tune the GNN encoder. Besides, we propose a novel quality-guided optimization in which the contributions of pseudo labels are weighted based on consistency. We thoroughly evaluate our model on two large real-world social event datasets. Experiments demonstrate that our model achieves state-of-the-art results and extends well to unknown events.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Interpretable Graph Convolutional Network of Multi-Modality Brain Imaging for Alzheimer's Disease Diagnosis

Identification of brain regions related to the specific neurological disorders are of great importance for biomarker and diagnostic studies. In this paper, we propose an interpretable Graph Convolutional Network (GCN) framework for the identification and classification of Alzheimer's disease (AD) using multi-modality brain imaging data. Specifically, we extended the Gradient Class Activation Mapping (Grad-CAM) technique to quantify the most discriminative features identified by GCN from brain connectivity patterns. We then utilized them to find signature regions of interest (ROIs) by detecting the difference of features between regions in healthy control (HC), mild cognitive impairment (MCI), and AD groups. We conducted the experiments on the ADNI database with imaging data from three modalities, including VBM-MRI, FDG-PET, and AV45-PET, and showed that the ROI features learned by our method were effective for enhancing the performances of both clinical score prediction and disease status identification. It also successfully identified biomarkers associated with AD and MCI.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Joint Embedding of Structural and Functional Brain Networks with Graph Neural Networks for Mental Illness Diagnosis

Multimodal brain networks characterize complex connectivities among different brain regions from both structural and functional aspects and provide a new means for mental disease analysis. Recently, Graph Neural Networks (GNNs) have become a de facto model for analyzing graph-structured data. However, how to employ GNNs to extract effective representations from brain networks in multiple modalities remains rarely explored. Moreover, as brain networks provide no initial node features, how to design informative node attributes and leverage edge weights for GNNs to learn is left unsolved. To this end, we develop a novel multiview GNN for multimodal brain networks. In particular, we regard each modality as a view for brain networks and employ contrastive learning for multimodal fusion. Then, we propose a GNN model which takes advantage of the message passing scheme by propagating messages based on degree statistics and brain region connectivities. Extensive experiments on two real-world disease datasets (HIV and Bipolar) demonstrate the effectiveness of our proposed method over state-of-the-art baselines.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Multi-level Feature Learning for Contrastive Multi-view Clustering

Multi-view clustering can explore common semantics from multiple views and has attracted increasing attention. However, existing works punish multiple objectives in the same feature space, where they ignore the conflict between learning consistent common semantics and reconstructing inconsistent view-private information. In this paper, we propose a new framework of multi-level feature learning for contrastive multi-view clustering to address the aforementioned issue. Our method learns different levels of features from the raw features, including low-level features, high-level features, and semantic labels/features in a fusion-free manner, so that it can effectively achieve the reconstruction objective and the consistency objectives in different feature spaces. Specifically, the reconstruction objective is conducted on the low-level features. Two consistency objectives based on contrastive learning are conducted on the high-level features and the semantic labels, respectively. They make the high-level features effectively explore the common semantics and the semantic labels achieve the multi-view clustering. As a result, the proposed framework can reduce the adverse influence of view-private information. Extensive experiments on public datasets demonstrate that our method achieves state-of-the-art clustering effectiveness.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Task Modifiers for HTN Planning and Acting

The ability of an agent to change its objectives in response to unexpected events is desirable in dynamic environments. In order to provide this capability to hierarchical task network (HTN) planning, we propose an extension of the paradigm called task modifiers, which are functions that receive a task list and a state and produce a new task list. We focus on a particular type of problems in which planning and execution are interleaved and the ability to handle exogenous events is crucial. To determine the efficacy of this approach, we evaluate the performance of our task modifier implementation in two environments, one of which is a simulation that differs substantially from traditional HTN domains.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Heterogeneous Similarity Graph Neural Network on Electronic Health Records

Mining Electronic Health Records (EHRs) becomes a promising topic because of the rich information they contain. By learning from EHRs, machine learning models can be built to help human experts to make medical decisions and thus improve healthcare quality. Recently, many models based on sequential or graph models are proposed to achieve this goal. EHRs contain multiple entities and relations and can be viewed as a heterogeneous graph. However, previous studies ignore the heterogeneity in EHRs. On the other hand, current heterogeneous graph neural networks cannot be simply used on an EHR graph because of the existence of hub nodes in it. To address this issue, we propose Heterogeneous Similarity Graph Neural Network (HSGNN) analyze EHRs with a novel heterogeneous GNN. Our framework consists of two parts: one is a preprocessing method and the other is an end-to-end GNN. The preprocessing method normalizes edges and splits the EHR graph into multiple homogeneous graphs while each homogeneous graph contains partial information of the original EHR graph. The GNN takes all homogeneous graphs as input and fuses all of them into one graph to make a prediction. Experimental results show that HSGNN outperforms other baselines in the diagnosis prediction task.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

KG-BART: Knowledge Graph-Augmented BART for Generative Commonsense Reasoning

Generative commonsense reasoning which aims to empower machines to generate sentences with the capacity of reasoning over a set of concepts is a critical bottleneck for text generation. Even the state-of-the-art pre-trained language generation models struggle at this task and often produce implausible and anomalous sentences. One reason is that they rarely consider incorporating the knowledge graph which can provide rich relational information among the commonsense concepts. To promote the ability of commonsense reasoning for text generation, we propose a novel knowledge graph augmented pre-trained language generation model KG-BART, which encompasses the complex relations of concepts through the knowledge graph and produces more logical and natural sentences as output. Moreover, KG-BART can leverage the graph attention to aggregate the rich concept semantics that enhances the model generalization on unseen concept sets. Experiments on benchmark CommonGen dataset verify the effectiveness of our proposed approach by comparing with several strong pre-trained language generation models, particularly KG-BART outperforms BART by 5.80, 4.60, in terms of BLEU-3, 4. Moreover, we also show that the generated context by our model can work as background scenarios to benefit downstream commonsense QA tasks.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Pairwise Learning for Name Disambiguation in Large-Scale Heterogeneous Academic Networks

Name disambiguation aims to identify unique authors with the same name. Existing name disambiguation methods always exploit author attributes to enhance disambiguation results. However, some discriminative author attributes (e.g., email and affiliation) may change because of graduation or job-hopping, which will result in the separation of the same author's papers in digital libraries. Although these attributes may change, an author's co-authors and research topics do not change frequently with time, which means that papers within a period have similar text and relation information in the academic network. Inspired by this idea, we introduce Multi-view Attention-based Pairwise Recurrent Neural Network (MA-PairRNN) to solve the name disambiguation problem. We divided papers into small blocks based on discriminative author attributes and blocks of the same author will be merged according to pairwise classification results of MA-PairRNN. MA-PairRNN combines heterogeneous graph embedding learning and pairwise similarity learning into a framework. In addition to attribute and structure information, MA-PairRNN also exploits semantic information by meta-path and generates node representation in an inductive way, which is scalable to large graphs. Furthermore, a semantic-level attention mechanism is adopted to fuse multiple meta-path based representations. A Pseudo-Siamese network consisting of two RNNs takes two paper sequences in publication time order as input and outputs their similarity. Results on two real-world datasets demonstrate that our framework has a significant and consistent improvement of performance on the name disambiguation task. It was also demonstrated that MA-PairRNN can perform well with a small amount of training data and have better generalization ability across different research areas.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Lifelong Property Price Prediction: A Case Study for the Toronto Real Estate Market

We present Luce, the first life-long predictive model for automated property valuation. Luce addresses two critical issues of property valuation: the lack of recent sold prices and the sparsity of house data. It is designed to operate on a limited volume of recent house transaction data. As a departure from prior work, Luce organizes the house data in a heterogeneous information network (HIN) where graph nodes are house entities and attributes that are important for house price valuation. We employ a Graph Convolutional Network (GCN) to extract the spatial information from the HIN for house-related data like geographical locations, and then use a Long Short Term Memory (LSTM) network to model the temporal dependencies for house transaction data over time. Unlike prior work, Luce can make effective use of the limited house transactions data in the past few months to update valuation information for all house entities within the HIN. By providing a complete and up-to-date house valuation dataset, Luce thus massively simplifies the downstream valuation task for the targeting properties. We demonstrate the benefit of Luce by applying it to large, real-life datasets obtained from the Toronto real estate market. Extensive experimental results show that Luce not only significantly outperforms prior property valuation methods but also often reaches and sometimes exceeds the valuation accuracy given by independent experts when using the actual realization price as the ground truth.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Not Just Cloud Privacy: Protecting Client Privacy in Teacher-Student Learning

Ensuring the privacy of sensitive data used to train modern machine learning models is of paramount importance in many areas of practice. One recent popular approach to study these concerns is using the differential privacy via a "teacher-student" model, wherein the teacher provides the student with useful, but noisy, information, hopefully allowing the student model to perform well on a given task. However, these studies only solve the privacy concerns of the teacher by assuming the student owns a public but unlabelled dataset. In real life, the student also has privacy concerns on its unlabelled data, so as to inquire about privacy protection on any data sent to the teacher. In this work, we re-design the privacy-preserving "teacher-student" model consisting of adopting both private arbitrary masking and local differential privacy, which protects the sensitive information of each student sample. However, the traditional training of teacher model is not robust on any perturbed data. We use the adversarial learning techniques to improve the robustness of the perturbed sample that supports returning good feedback without having all private information of each student sample. The experimental results demonstrate the effectiveness of our new privacy-preserving "teacher-student" model.

0 citations0 reviewsNo code linkedOpen access