Xuan Kan

Yue Yu, Xuan Kan, Hejie Cui et al. · cmu

Functional magnetic resonance imaging (fMRI) has become one of the most common imaging modalities for brain function analysis. Recently, graph neural networks (GNN) have been adopted for fMRI analysis with superior performance. Unfortunately, traditional functional brain networks are mainly constructed based on similarities among region of interests (ROI), which are noisy and agnostic to the downstream prediction tasks and can lead to inferior results for GNN-based models. To better adapt GNNs for fMRI analysis, we propose TBDS, an end-to-end framework based on \underline{T}ask-aware \underline{B}rain connectivity \underline{D}AG (short for Directed Acyclic Graph) \underline{S}tructure generation for fMRI analysis. The key component of TBDS is the brain network generator which adopts a DAG learning approach to transform the raw time-series into task-aware brain connectivities. Besides, we design an additional contrastive regularization to inject task-specific knowledge during the brain network generation process. Comprehensive experiments on two fMRI datasets, namely Adolescent Brain Cognitive Development (ABCD) and Philadelphia Neuroimaging Cohort (PNC) datasets demonstrate the efficacy of TBDS. In addition, the generated brain networks also highlight the prediction-related brain regions and thus provide unique interpretations of the prediction results. Our implementation will be published to https://github.com/yueyu1030/TBDS upon acceptance.

Xuan Kan, Wei Dai, Hejie Cui et al.

Human brains are commonly modeled as networks of Regions of Interest (ROIs) and their connections for the understanding of brain functions and mental disorders. Recently, Transformer-based models have been studied over different types of data, including graphs, shown to bring performance gains widely. In this work, we study Transformer-based models for brain network analysis. Driven by the unique properties of data, we model brain networks as graphs with nodes of fixed size and order, which allows us to (1) use connection profiles as node features to provide natural and low-cost positional information and (2) learn pair-wise connection strengths among ROIs with efficient attention weights across individuals that are predictive towards downstream analysis tasks. Moreover, we propose an Orthonormal Clustering Readout operation based on self-supervised soft clustering and orthonormal projection. This design accounts for the underlying functional modules that determine similar behaviors among groups of ROIs, leading to distinguishable cluster-aware node embeddings and informative graph embeddings. Finally, we re-standardize the evaluation pipeline on the only one publicly available large-scale brain network dataset of ABIDE, to enable meaningful comparison of different models. Experiment results show clear improvements of our proposed Brain Network Transformer on both the public ABIDE and our restricted ABCD datasets. The implementation is available at https://github.com/Wayfear/BrainNetworkTransformer.

Xuan Kan, Hejie Cui, Joshua Lukemire et al.

Functional magnetic resonance imaging (fMRI) is one of the most common imaging modalities to investigate brain functions. Recent studies in neuroscience stress the great potential of functional brain networks constructed from fMRI data for clinical predictions. Traditional functional brain networks, however, are noisy and unaware of downstream prediction tasks, while also incompatible with the deep graph neural network (GNN) models. In order to fully unleash the power of GNNs in network-based fMRI analysis, we develop FBNETGEN, a task-aware and interpretable fMRI analysis framework via deep brain network generation. In particular, we formulate (1) prominent region of interest (ROI) features extraction, (2) brain networks generation, and (3) clinical predictions with GNNs, in an end-to-end trainable model under the guidance of particular prediction tasks. Along with the process, the key novel component is the graph generator which learns to transform raw time-series features into task-oriented brain networks. Our learnable graphs also provide unique interpretations by highlighting prediction-related brain regions. Comprehensive experiments on two datasets, i.e., the recently released and currently largest publicly available fMRI dataset Adolescent Brain Cognitive Development (ABCD), and the widely-used fMRI dataset PNC, prove the superior effectiveness and interpretability of FBNETGEN. The implementation is available at https://github.com/Wayfear/FBNETGEN.

Ran Xu, Hejie Cui, Yue Yu et al. · gatech

Clinical natural language processing requires methods that can address domain-specific challenges, such as complex medical terminology and clinical contexts. Recently, large language models (LLMs) have shown promise in this domain. Yet, their direct deployment can lead to privacy issues and are constrained by resources. To address this challenge, we delve into synthetic clinical text generation using LLMs for clinical NLP tasks. We propose an innovative, resource-efficient approach, ClinGen, which infuses knowledge into the process. Our model involves clinical knowledge extraction and context-informed LLM prompting. Both clinical topics and writing styles are drawn from external domain-specific knowledge graphs and LLMs to guide data generation. Our extensive empirical study across 7 clinical NLP tasks and 16 datasets reveals that ClinGen consistently enhances performance across various tasks, effectively aligning the distribution of real datasets and significantly enriching the diversity of generated training instances. Our code is available at \url{https://github.com/ritaranx/ClinGen}.

Ran Xu, Yue Yu, Hejie Cui et al.

Training deep neural networks (DNNs) with limited supervision has been a popular research topic as it can significantly alleviate the annotation burden. Self-training has been successfully applied in semi-supervised learning tasks, but one drawback of self-training is that it is vulnerable to the label noise from incorrect pseudo labels. Inspired by the fact that samples with similar labels tend to share similar representations, we develop a neighborhood-based sample selection approach to tackle the issue of noisy pseudo labels. We further stabilize self-training via aggregating the predictions from different rounds during sample selection. Experiments on eight tasks show that our proposed method outperforms the strongest self-training baseline with 1.83% and 2.51% performance gain for text and graph datasets on average. Our further analysis demonstrates that our proposed data selection strategy reduces the noise of pseudo labels by 36.8% and saves 57.3% of the time when compared with the best baseline. Our code and appendices will be uploaded to https://github.com/ritaranx/NeST.

Hejie Cui, Wei Dai, Yanqiao Zhu et al.

Mapping the connectome of the human brain using structural or functional connectivity has become one of the most pervasive paradigms for neuroimaging analysis. Recently, Graph Neural Networks (GNNs) motivated from geometric deep learning have attracted broad interest due to their established power for modeling complex networked data. Despite their superior performance in many fields, there has not yet been a systematic study of how to design effective GNNs for brain network analysis. To bridge this gap, we present BrainGB, a benchmark for brain network analysis with GNNs. BrainGB standardizes the process by (1) summarizing brain network construction pipelines for both functional and structural neuroimaging modalities and (2) modularizing the implementation of GNN designs. We conduct extensive experiments on datasets across cohorts and modalities and recommend a set of general recipes for effective GNN designs on brain networks. To support open and reproducible research on GNN-based brain network analysis, we host the BrainGB website at https://braingb.us with models, tutorials, examples, as well as an out-of-box Python package. We hope that this work will provide useful empirical evidence and offer insights for future research in this novel and promising direction.

Yi Yang, Yanqiao Zhu, Hejie Cui et al.

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.

Hejie Cui, Jiaying Lu, Ran Xu et al.

This comprehensive review aims to provide an overview of the current state of Healthcare Knowledge Graphs (HKGs), including their construction, utilization models, and applications across various healthcare and biomedical research domains. We thoroughly analyzed existing literature on HKGs, covering their construction methodologies, utilization techniques, and applications in basic science research, pharmaceutical research and development, clinical decision support, and public health. The review encompasses both model-free and model-based utilization approaches and the integration of HKGs with large language models (LLMs). We searched Google Scholar for relevant papers on HKGs and classified them into the following topics: HKG construction, HKG utilization, and their downstream applications in various domains. We also discussed their special challenges and the promise for future work. The review highlights the potential of HKGs to significantly impact biomedical research and clinical practice by integrating vast amounts of biomedical knowledge from multiple domains. The synergy between HKGs and LLMs offers promising opportunities for constructing more comprehensive knowledge graphs and improving the accuracy of healthcare applications. HKGs have emerged as a powerful tool for structuring medical knowledge, with broad applications across biomedical research, clinical decision-making, and public health. This survey serves as a roadmap for future research and development in the field of HKGs, highlighting the potential of combining knowledge graphs with advanced machine learning models for healthcare transformation.

Xuan Kan, Zimu Li, Hejie Cui et al.

Biological networks are commonly used in biomedical and healthcare domains to effectively model the structure of complex biological systems with interactions linking biological entities. However, due to their characteristics of high dimensionality and low sample size, directly applying deep learning models on biological networks usually faces severe overfitting. In this work, we propose R-MIXUP, a Mixup-based data augmentation technique that suits the symmetric positive definite (SPD) property of adjacency matrices from biological networks with optimized training efficiency. The interpolation process in R-MIXUP leverages the log-Euclidean distance metrics from the Riemannian manifold, effectively addressing the swelling effect and arbitrarily incorrect label issues of vanilla Mixup. We demonstrate the effectiveness of R-MIXUP with five real-world biological network datasets on both regression and classification tasks. Besides, we derive a commonly ignored necessary condition for identifying the SPD matrices of biological networks and empirically study its influence on the model performance. The code implementation can be found in Appendix E.

Xuan Kan, Antonio Aodong Chen Gu, Hejie Cui et al.

Recent neuroimaging studies have highlighted the importance of network-centric brain analysis, particularly with functional magnetic resonance imaging. The emergence of Deep Neural Networks has fostered a substantial interest in predicting clinical outcomes and categorizing individuals based on brain networks. However, the conventional approach involving static brain network analysis offers limited potential in capturing the dynamism of brain function. Although recent studies have attempted to harness dynamic brain networks, their high dimensionality and complexity present substantial challenges. This paper proposes a novel methodology, Dynamic bRAin Transformer (DART), which combines static and dynamic brain networks for more effective and nuanced brain function analysis. Our model uses the static brain network as a baseline, integrating dynamic brain networks to enhance performance against traditional methods. We innovatively employ attention mechanisms, enhancing model explainability and exploiting the dynamic brain network's temporal variations. The proposed approach offers a robust solution to the low signal-to-noise ratio of blood-oxygen-level-dependent signals, a recurring issue in direct DNN modeling. It also provides valuable insights into which brain circuits or dynamic networks contribute more to final predictions. As such, DRAT shows a promising direction in neuroimaging studies, contributing to the comprehensive understanding of brain organization and the role of neural circuits.

Xuan Kan, Yonghui Xiao, Tien-Ju Yang et al.

This work explores the challenge of enhancing Automatic Speech Recognition (ASR) model performance across various user-specific domains while preserving user data privacy. We employ federated learning and parameter-efficient domain adaptation methods to solve the (1) massive data requirement of ASR models from user-specific scenarios and (2) the substantial communication cost between servers and clients during federated learning. We demonstrate that when equipped with proper adapters, ASR models under federated tuning can achieve similar performance compared with centralized tuning ones, thus providing a potential direction for future privacy-preserved ASR services. Besides, we investigate the efficiency of different adapters and adapter incorporation strategies under the federated learning setting.

Hejie Cui, Xinyu Fang, Zihan Zhang et al.

Images contain rich relational knowledge that can help machines understand the world. Existing methods on visual knowledge extraction often rely on the pre-defined format (e.g., sub-verb-obj tuples) or vocabulary (e.g., relation types), restricting the expressiveness of the extracted knowledge. In this work, we take a first exploration to a new paradigm of open visual knowledge extraction. To achieve this, we present OpenVik which consists of an open relational region detector to detect regions potentially containing relational knowledge and a visual knowledge generator that generates format-free knowledge by prompting the large multimodality model with the detected region of interest. We also explore two data enhancement techniques for diversifying the generated format-free visual knowledge. Extensive knowledge quality evaluations highlight the correctness and uniqueness of the extracted open visual knowledge by OpenVik. Moreover, integrating our extracted knowledge across various visual reasoning applications shows consistent improvements, indicating the real-world applicability of OpenVik.

Junjie Wu, Xuan Kan, Zihao He et al.

Multimodal Large Language Models (MLLMs) have been widely adopted as MLLM-as-a-Judges due to their strong alignment with human judgment across various visual tasks. However, most existing judge models are optimized for single-task scenarios and struggle to generalize to diverse contexts, which is a critical requirement for reliable evaluation. To address this limitation, we propose Multi-Task Reinforcement Learning for MLLM-as-a-Judge (MT-RL-Judge), a framework that jointly optimizes the judge model across multiple tasks, leveraging the generalization capabilities of RL. Experimental results against several strong baselines demonstrate that MT-RL-Judge outperforms strong baselines in both judgment consistency and correlation with human preferences. Furthermore, our approach exhibits robust generalization on out-of-distribution tasks, further validating its effectiveness.

Wei Dai, Hejie Cui, Xuan Kan et al.

Brain networks, graphical models such as those constructed from MRI, have been widely used in pathological prediction and analysis of brain functions. Within the complex brain system, differences in neuronal connection strengths parcellate the brain into various functional modules (network communities), which are critical for brain analysis. However, identifying such communities within the brain has been a nontrivial issue due to the complexity of neuronal interactions. In this work, we propose a novel interpretable transformer-based model for joint hierarchical cluster identification and brain network classification. Extensive experimental results on real-world brain network datasets show that with the help of hierarchical clustering, the model achieves increased accuracy and reduced runtime complexity while providing plausible insight into the functional organization of brain regions. The implementation is available at https://github.com/DDVD233/THC.

Hejie Cui, Xinyu Fang, Ran Xu et al.

Electronic Health Records (EHRs) have become increasingly popular to support clinical decision-making and healthcare in recent decades. EHRs usually contain heterogeneous information, such as structural data in tabular form and unstructured data in textual notes. Different types of information in EHRs can complement each other and provide a more complete picture of the health status of a patient. While there has been a lot of research on representation learning of structured EHR data, the fusion of different types of EHR data (multimodal fusion) is not well studied. This is mostly because of the complex medical coding systems used and the noise and redundancy present in the written notes. In this work, we propose a new framework called MINGLE, which integrates both structures and semantics in EHR effectively. Our framework uses a two-level infusion strategy to combine medical concept semantics and clinical note semantics into hypergraph neural networks, which learn the complex interactions between different types of data to generate visit representations for downstream prediction. Experiment results on two EHR datasets, the public MIMIC-III and private CRADLE, show that MINGLE can effectively improve predictive performance by 11.83% relatively, enhancing semantic integration as well as multimodal fusion for structural and textual EHR data.

Kaiqiao Han, Yi Yang, Zijie Huang et al.

Brain network analysis is vital for understanding the neural interactions regarding brain structures and functions, and identifying potential biomarkers for clinical phenotypes. However, widely used brain signals such as Blood Oxygen Level Dependent (BOLD) time series generated from functional Magnetic Resonance Imaging (fMRI) often manifest three challenges: (1) missing values, (2) irregular samples, and (3) sampling misalignment, due to instrumental limitations, impacting downstream brain network analysis and clinical outcome predictions. In this work, we propose a novel model called BrainODE to achieve continuous modeling of dynamic brain signals using Ordinary Differential Equations (ODE). By learning latent initial values and neural ODE functions from irregular time series, BrainODE effectively reconstructs brain signals at any time point, mitigating the aforementioned three data challenges of brain signals altogether. Comprehensive experimental results on real-world neuroimaging datasets demonstrate the superior performance of BrainODE and its capability of addressing the three data challenges.

Bo Pan, Xuan Kan, Kaitai Zhang et al.

Large language models (LLMs) have become widely adopted as automated judges for evaluating AI-generated content. Despite their success, aligning LLM-based evaluations with human judgments remains challenging. While supervised fine-tuning on human-labeled data can improve alignment, it is costly and inflexible, requiring new training for each task or dataset. Recent progress in auto prompt optimization (APO) offers a more efficient alternative by automatically improving the instructions that guide LLM judges. However, existing APO methods primarily target text-only evaluations and remain underexplored in multimodal settings. In this work, we study auto prompt optimization for multimodal LLM-as-a-judge, particularly for evaluating AI-generated images. We identify a key bottleneck: multimodal models can only process a limited number of visual examples due to context window constraints, which hinders effective trial-and-error prompt refinement. To overcome this, we propose BLPO, a bi-level prompt optimization framework that converts images into textual representations while preserving evaluation-relevant visual cues. Our bi-level optimization approach jointly refines the judge prompt and the I2T prompt to maintain fidelity under limited context budgets. Experiments on four datasets and three LLM judges demonstrate the effectiveness of our method.

Shuai Huang, Xuan Kan, James J. Lah et al.

Current atlas-based approaches to brain network analysis rely heavily on standardized anatomical or connectivity-driven brain atlases. However, these fixed atlases often introduce significant limitations, such as spatial misalignment across individuals, functional heterogeneity within predefined regions, and atlas-selection biases, collectively undermining the reliability and interpretability of the derived brain networks. To address these challenges, we propose a novel atlas-free brain network transformer (atlas-free BNT) that leverages individualized brain parcellations derived directly from subject-specific resting-state fMRI data. Our approach computes ROI-to-voxel connectivity features in a standardized voxel-based feature space, which are subsequently processed using the BNT architecture to produce comparable subject-level embeddings. Experimental evaluations on sex classification and brain-connectome age prediction tasks demonstrate that our atlas-free BNT consistently outperforms state-of-the-art atlas-based methods, including elastic net, BrainGNN, Graphormer and the original BNT. Our atlas-free approach significantly improves the precision, robustness, and generalizability of brain network analyses. This advancement holds great potential to enhance neuroimaging biomarkers and clinical diagnostic tools for personalized precision medicine.

Xuan Kan, Hejie Cui, Ying Guo et al.

Recent studies in neuroscience show great potential of functional brain networks constructed from fMRI data for popularity modeling and clinical predictions. However, existing functional brain networks are noisy and unaware of downstream prediction tasks, while also incompatible with recent powerful machine learning models of GNNs. In this work, we develop an end-to-end trainable pipeline to extract prominent fMRI features, generate brain networks, and make predictions with GNNs, all under the guidance of downstream prediction tasks. Preliminary experiments on the PNC fMRI data show the superior effectiveness and unique interpretability of our framework.

Xuan Kan, Hejie Cui, Carl Yang

Relation prediction among entities in images is an important step in scene graph generation (SGG), which further impacts various visual understanding and reasoning tasks. Existing SGG frameworks, however, require heavy training yet are incapable of modeling unseen (i.e.,zero-shot) triplets. In this work, we stress that such incapability is due to the lack of commonsense reasoning,i.e., the ability to associate similar entities and infer similar relations based on general understanding of the world. To fill this gap, we propose CommOnsense-integrAted sCenegrapHrElation pRediction (COACHER), a framework to integrate commonsense knowledge for SGG, especially for zero-shot relation prediction. Specifically, we develop novel graph mining pipelines to model the neighborhoods and paths around entities in an external commonsense knowledge graph, and integrate them on top of state-of-the-art SGG frameworks. Extensive quantitative evaluations and qualitative case studies on both original and manipulated datasets from Visual Genome demonstrate the effectiveness of our proposed approach.

Chris Xiaoxuan Lu, Xuan Kan, Bowen Du et al.

Facial recognition is a key enabling component for emerging Internet of Things (IoT) services such as smart homes or responsive offices. Through the use of deep neural networks, facial recognition has achieved excellent performance. However, this is only possibly when trained with hundreds of images of each user in different viewing and lighting conditions. Clearly, this level of effort in enrolment and labelling is impossible for wide-spread deployment and adoption. Inspired by the fact that most people carry smart wireless devices with them, e.g. smartphones, we propose to use this wireless identifier as a supervisory label. This allows us to curate a dataset of facial images that are unique to a certain domain e.g. a set of people in a particular office. This custom corpus can then be used to finetune existing pre-trained models e.g. FaceNet. However, due to the vagaries of wireless propagation in buildings, the supervisory labels are noisy and weak.We propose a novel technique, AutoTune, which learns and refines the association between a face and wireless identifier over time, by increasing the inter-cluster separation and minimizing the intra-cluster distance. Through extensive experiments with multiple users on two sites, we demonstrate the ability of AutoTune to design an environment-specific, continually evolving facial recognition system with entirely no user effort.