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Ting Xu

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25 papers
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25

ECAI Conference 2025 Conference Paper

Cross-Modality Disentanglement and Fusion via Hyperedge-Centric Graph Learning for Brain Network Connectivity Analysis

  • Manman Yuan
  • Jiapei Li
  • Junlin Li
  • Jiacheng Wang
  • Ting Xu
  • Can Yin

Analyzing brain network connectivity (BNC) using multimodal neuroimaging to identify neurodegenerative diseases has attracted increasing attention. However, current methods largely rely on node-centric graphs and assume structural or semantic alignment across modalities, limiting the capture of high-order interactions and modality-specific patterns critical for accurate disease identification. In this paper, we propose a novel Hyperedge-Centric Graph Learning Network (HCGLNet) to address these limitations. Specifically, we present a hyperedge-centric graph construction strategy (HGC) that represents each modality as a hyperedge-centric graph, explicitly modelling high-order connectivity unique to each modality. Moreover, we design a disentangled latent learning module (DLM) that factorize shared and specific representations, preserving modality-specific features from dilution while enabling the extraction of shared cross-modal representations. Finally, we develop a representation-aware routing (RAR) algorithm to adaptively fuse modality-specific and shared features based on learned weights, enhancing discriminability for downstream tasks. Experiments on three real-world datasets show that our HCGLNet abstraction reduces graph size by over 80%, lowers computation, and achieves state-of-the-art performance in neurodegenerative disease classification.

YNIMG Journal 2025 Journal Article

Early wounds, delayed consequences: Brain-behavior modeling reveals neural pathways linking childhood trauma to procrastination

  • Luo Xu
  • Yao Yin
  • Xueke Wang
  • Ting Xu
  • Xi Zhang
  • Tingyong Feng

Childhood trauma has enduring effects on emotional and cognitive functioning, yet its impact on procrastination, particularly from a neurodevelopmental perspective, remains poorly understood. To achieve this, we employed resting-state functional MRI in conjunction with standardized behavioral assessments of childhood trauma, trait anxiety, self-control, and procrastination across two datasets (discovery dataset: n = 760; validation dataset: n = 429). By leveraging the advanced predictive analytics-including connectome-based predictive modeling (CPM) and least absolute shrinkage and selection operator (LASSO) regression-we aimed to elucidate the neural basis linking childhood trauma to procrastination. Our behavioral results revealed that childhood trauma was a significant predictor of elevated procrastination tendencies, with this association mediated by increased trait anxiety and reduced self-control. At the neural level, the predictive modeling using CPM and LASSO regression demonstrated that functional connectivity within and between the frontoparietal network (FPN), salience network (SAN), visual network (VN), and cerebellum significantly predicted childhood trauma. These patterns likely reflect trauma-related disruptions in higher-order cognitive control (e.g., self-control) and increased affective reactivity (e.g., trait anxiety). More importantly, the mediation analyses further confirmed that trait anxiety and self-control jointly mediate the relationship between trauma-related neural network connectivity and procrastination. These findings presented novel evidence that childhood trauma is associated with procrastination via functional alterations in large-scale neural networks implicated in self-control and emotion regulation, providing critical insights into the long-term behavioral consequences of early-life adversity, and informing the development of targeted interventions to reduce procrastination in trauma-exposed individuals.

EAAI Journal 2025 Journal Article

Reshaping the future of sports with artificial intelligence: Challenges and opportunities in performance enhancement, fan engagement, and strategic decision-making

  • Ting Xu
  • S. Baghaei

The rapid advancement of artificial intelligence has significantly transformed the sports industry over the past decade. In sports performance, artificial intelligence-driven analytics has become essential for optimizing athlete training, injury prevention, and performance enhancement, with sophisticated algorithms analyzing player data to develop personalized training programs and identify areas for improvement. The impact of artificial intelligence on fan engagement has been profound, enabling the delivery of highly personalized content and recommendations that foster stronger connections between fans and their favorite teams or athletes. Leveraging artificial intelligence-powered algorithms, ticket pricing strategies are optimized, resulting in increased ticket sales and revenue. Artificial intelligence-based performance evaluation tools assist sports managers in making well-informed decisions regarding team composition and tactics. This study shows the use of an artificial neural network with artificial intelligence technologies, including data analysis, to improve sports performance, management, and decision-making. Data-driven insights aid in talent scouting and recruitment, allowing managers to identify promising athletes with precision. Issues about data privacy, algorithmic bias, and fair competition need to be addressed to ensure responsible and equitable utilization of artificial intelligence in augmenting the sports industry. The integration of artificial intelligence technologies has profoundly transformed both sports and sports management. From enhancing athlete performance and fan engagement to optimizing administrative tasks and strategic decision-making, the impact of artificial intelligence on the sports domain continues to expand. Results show significant enhancements in all areas, with artificial intelligence outperforming data analysis alone. Prediction errors of the artificial neural network model align well with experimental targets.

TMLR Journal 2024 Journal Article

Independence Testing for Temporal Data

  • Cencheng Shen
  • Jaewon Chung
  • Ronak Mehta
  • Ting Xu
  • Joshua T Vogelstein

Temporal data are increasingly prevalent in modern data science. A fundamental question is whether two time series are related or not. Existing approaches often have limitations, such as relying on parametric assumptions, detecting only linear associations, and requiring multiple tests and corrections. While many non-parametric and universally consistent dependence measures have recently been proposed, directly applying them to temporal data can inflate the p-value and result in an invalid test. To address these challenges, this paper introduces the temporal dependence statistic with block permutation to test independence between temporal data. Under proper assumptions, the proposed procedure is asymptotically valid and universally consistent for testing independence between stationary time series, and capable of estimating the optimal dependence lag that maximizes the dependence. Moreover, it is compatible with a rich family of distance and kernel based dependence measures, eliminates the need for multiple testing, and exhibits excellent testing power in various simulation settings.

IS Journal 2023 Journal Article

A Fault Diagnosis of Rotating Machinery Based on a Mutual Dimensionless Index and a Convolution Neural Network

  • Naiquan Su
  • Qinghua Zhang
  • Lingmeng Zhou
  • Xiaoxiao Chang
  • Ting Xu

For the fault diagnosis process of petrochemical rotating machinery, it is difficult to accurately identify faults by relying only on dimensionless index methods. Therefore, a fault diagnosis of rotating machinery based on mutual dimensionless index and a convolution neural network is proposed. First, it collects the rotating machinery fault signal of the petrochemical large unit and mutual dimensionless index. Then the sensitivity analysis of mutual dimensionless index is carried out to extract the sensitive features. And then, the sensitive feature samples are mapped to the common subspace of the adversarial network for capacity augmentation. Finally, the sensitive features sample after capacity is input to the convolutional neural network for recognition. Through the verification of the petrochemical experimental platform fault and the wind turbine blade fault, The proposed method has a good diagnosis effect and can adapt to complex on-site conditions.

YNIMG Journal 2023 Journal Article

Anatomical details affect electric field predictions for non-invasive brain stimulation in non-human primates

  • Kathleen E. Mantell
  • Nipun D. Perera
  • Sina Shirinpour
  • Oula Puonti
  • Ting Xu
  • Jan Zimmermann
  • Arnaud Falchier
  • Sarah R. Heilbronner

Non-human primates (NHPs) have become key for translational research in noninvasive brain stimulation (NIBS). However, in order to create comparable stimulation conditions for humans it is vital to study the accuracy of current modeling practices across species. Numerical models to simulate electric fields are an important tool for experimental planning in NHPs and translation to human studies. It is thus essential whether and to what extent the anatomical details of NHP models agree with current modeling practices when calculating NIBS electric fields. Here, we create highly accurate head models of two non-human primates (NHP) MR data. We evaluate how muscle tissue and head field of view (depending on MRI parameters) affect simulation results in transcranial electric and magnetic stimulation (TES and TMS). Our findings indicate that the inclusion of anisotropic muscle can affect TES electric field strength up to 22% while TMS is largely unaffected. Additionally, comparing a full head model to a cropped head model illustrates the impact of head field of view on electric fields for both TES and TMS. We find opposing effects between TES and TMS with an increase up to 24.8% for TES and a decrease up to 24.6% for TMS for the cropped head model compared to the full head model. Our results provide important insights into the level of anatomical detail needed for NHP head models and can inform future translational efforts for NIBS studies.

YNIMG Journal 2023 Journal Article

Cortical gradients during naturalistic processing are hierarchical and modality-specific

  • Ahmad Samara
  • Jeffrey Eilbott
  • Daniel S. Margulies
  • Ting Xu
  • Tamara Vanderwal

Understanding cortical topographic organization and how it supports complex perceptual and cognitive processes is a fundamental question in neuroscience. Previous work has characterized functional gradients that demonstrate large-scale principles of cortical organization. How these gradients are modulated by rich ecological stimuli remains unknown. Here, we utilize naturalistic stimuli via movie-fMRI to assess macroscale functional organization. We identify principal movie gradients that delineate separate hierarchies anchored in sensorimotor, visual, and auditory/language areas. At the opposite/heteromodal end of these perception-to-cognition axes, we find a more central role for the frontoparietal network along with the default network. Even across different movie stimuli, movie gradients demonstrated good reliability, suggesting that these hierarchies reflect a brain state common across different naturalistic conditions. The relative position of brain areas within movie gradients showed stronger and more numerous correlations with cognitive behavioral scores compared to resting state gradients. Together, these findings provide an ecologically valid representation of the principles underlying cortical organization while the brain is active and engaged in multimodal, dynamic perceptual and cognitive processing.

EAAI Journal 2023 Journal Article

Mixed local channel attention for object detection

  • Dahang Wan
  • Rongsheng Lu
  • Siyuan Shen
  • Ting Xu
  • Xianli Lang
  • Zhijie Ren

Attention mechanism, one of the most extensively utilized components in computer vision, can assist neural networks in emphasizing significant elements and suppressing irrelevant ones. However, the vast majority of channel attention mechanisms only contain channel feature information and ignore spatial feature information, resulting in poor model representation effect or object detection performance, and the spatial attention modules were often complex and expensive. In order to strike a balance between performance and complexity, this paper proposes a lightweight Mixed Local Channel Attention (MLCA) module to improve the performance of the object detection network, and it can simultaneously incorporate both channel information and spatial information, as well as local information and global information to improve the expression effect of the network. On this basis, the MobileNet-Attention-YOLO(MAY) algorithm for comparing the performance of various attention modules is presented. On the Pascal VOC and SMID datasets, MLCA achieves a better balance between model representation efficacy, performance, and complexity than alternative attention techniques. Against the Squeeze-and-Excitation(SE) attention mechanism on the PASCAL VOC dataset and the Coordinate Attention(CA) method on the SIMD dataset, the mAP is enhanced by 1. 0 % and 1. 5 %, respectively.

YNIMG Journal 2023 Journal Article

Omnipresence of the sensorimotor-association axis topography in the human connectome

  • Karl-Heinz Nenning
  • Ting Xu
  • Alexandre R. Franco
  • Khena M. Swallow
  • Arielle Tambini
  • Daniel S. Margulies
  • Jonathan Smallwood
  • Stanley J. Colcombe

Low-dimensional representations are increasingly used to study meaningful organizational principles within the human brain. Most notably, the sensorimotor-association axis consistently explains the most variance in the human connectome as its so-called principal gradient, suggesting that it represents a fundamental organizational principle. While recent work indicates these low dimensional representations are relatively robust, they are limited by modeling only certain aspects of the functional connectivity structure. To date, the majority of studies have restricted these approaches to the strongest connections in the brain, treating weaker or negative connections as noise despite evidence of meaningful structure among them. The present work examines connectivity gradients of the human connectome across a full range of connectivity strengths and explores the implications for outcomes of individual differences, identifying potential dependencies on thresholds and opportunities to improve prediction tasks. Interestingly, the sensorimotor-association axis emerged as the principal gradient of the human connectome across the entire range of connectivity levels. Moreover, the principal gradient of connections at intermediate strengths encoded individual differences, better followed individual-specific anatomical features, and was also more predictive of intelligence. Taken together, our results add to evidence of the sensorimotor-association axis as a fundamental principle of the brain's functional organization, since it is evident even in the connectivity structure of more lenient connectivity thresholds. These more loosely coupled connections further appear to contain valuable and potentially important information that could be used to improve our understanding of individual differences, diagnosis, and the prediction of treatment outcomes.

YNIMG Journal 2022 Journal Article

Brain intrinsic connection patterns underlying tool processing in human adults are present in neonates and not in macaques

  • Haojie Wen
  • Ting Xu
  • Xiaoying Wang
  • Xi Yu
  • Yanchao Bi

Tool understanding and use are supported by a dedicated left-lateralized, intrinsically connected network in the human adult brain. To examine this network's phylogenetic and ontogenetic origins, we compared resting-state functional connectivity (rsFC) among regions subserving tool processing in human adults to rsFC among homologous regions in human neonates and macaque monkeys (adolescent and mature). These homologous regions formed an intrinsic network in human neonates, but not in macaques. Network topological patterns were highly similar between human adults and neonates, and significantly less so between humans and macaques. The premotor-parietal rsFC had most significant contribution to the formation of the neonatal tool network. These results suggest that an intrinsic brain network potentially supporting tool processing exists in the human brain prior to individual tool use experiences, and that the premotor-parietal functional connection in particular offers a brain basis for complex tool behaviors specific to humans.

YNIMG Journal 2021 Journal Article

A collaborative resource platform for non-human primate neuroimaging

  • Adam Messinger
  • Nikoloz Sirmpilatze
  • Katja Heuer
  • Kep Kee Loh
  • Rogier B. Mars
  • Julien Sein
  • Ting Xu
  • Daniel Glen

Neuroimaging non-human primates (NHPs) is a growing, yet highly specialized field of neuroscience. Resources that were primarily developed for human neuroimaging often need to be significantly adapted for use with NHPs or other animals, which has led to an abundance of custom, in-house solutions. In recent years, the global NHP neuroimaging community has made significant efforts to transform the field towards more open and collaborative practices. Here we present the PRIMatE Resource Exchange (PRIME-RE), a new collaborative online platform for NHP neuroimaging. PRIME-RE is a dynamic community-driven hub for the exchange of practical knowledge, specialized analytical tools, and open data repositories, specifically related to NHP neuroimaging. PRIME-RE caters to both researchers and developers who are either new to the field, looking to stay abreast of the latest developments, or seeking to collaboratively advance the field .

YNIMG Journal 2021 Journal Article

Imaging evolution of the primate brain: the next frontier?

  • Patrick Friedrich
  • Stephanie J. Forkel
  • Céline Amiez
  • Joshua H. Balsters
  • Olivier Coulon
  • Lingzhong Fan
  • Alexandros Goulas
  • Fadila Hadj-Bouziane

Evolution, as we currently understand it, strikes a delicate balance between animals' ancestral history and adaptations to their current niche. Similarities between species are generally considered inherited from a common ancestor whereas observed differences are considered as more recent evolution. Hence comparing species can provide insights into the evolutionary history. Comparative neuroimaging has recently emerged as a novel subdiscipline, which uses magnetic resonance imaging (MRI) to identify similarities and differences in brain structure and function across species. Whereas invasive histological and molecular techniques are superior in spatial resolution, they are laborious, post-mortem, and oftentimes limited to specific species. Neuroimaging, by comparison, has the advantages of being applicable across species and allows for fast, whole-brain, repeatable, and multi-modal measurements of the structure and function in living brains and post-mortem tissue. In this review, we summarise the current state of the art in comparative anatomy and function of the brain and gather together the main scientific questions to be explored in the future of the fascinating new field of brain evolution derived from comparative neuroimaging.

YNIMG Journal 2021 Journal Article

Impact of concatenating fMRI data on reliability for functional connectomics

  • Jae Wook Cho
  • Annachiara Korchmaros
  • Joshua T Vogelstein
  • Michael P Milham
  • Ting Xu

Compelling evidence suggests the need for more data per individual to reliably map the functional organization of the human connectome. As the notion that ‘more data is better’ emerges as a golden rule for functional connectomics, researchers find themselves grappling with the challenges of how to obtain the desired amounts of data per participant in a practical manner, particularly for retrospective data aggregation. Increasingly, the aggregation of data across all fMRI scans available for an individual is being viewed as a solution, regardless of scan condition (e.g., rest, task, movie). A number of open questions exist regarding the aggregation process and the impact of different decisions on the reliability of resultant aggregate data. We leveraged the availability of highly sampled test-retest datasets to systematically examine the impact of data aggregation strategies on the reliability of cortical functional connectomics. Specifically, we compared functional connectivity estimates derived after concatenating from: 1) multiple scans under the same state, 2) multiple scans under different states (i.e. hybrid or general functional connectivity), and 3) subsets of one long scan. We also varied connectivity processing (i.e. global signal regression, ICA-FIX, and task regression) and estimation procedures. When the total number of time points is equal, and the scan state held constant, concatenating multiple shorter scans had a clear advantage over a single long scan. However, this was not necessarily true when concatenating across different fMRI states (i.e. task conditions), where the reliability from the aggregate data varied across states. Concatenating fewer numbers of states that are more reliable tends to yield higher reliability. Our findings provide an overview of multiple dependencies of data concatenation that should be considered to optimize reliability in analysis of functional connectivity data.

TCS Journal 2021 Journal Article

Injective coloring of planar graphs

  • Yuehua Bu
  • Chentao Qi
  • Junlei Zhu
  • Ting Xu

An injective k-coloring of a graph G is a mapping f: V ( G ) → { 1, 2, …, k } such that for any two vertices v 1, v 2 ∈ V ( G ), f ( v 1 ) ≠ f ( v 2 ) if N ( v 1 ) ∩ N ( v 2 ) ≠ ∅. The injective chromatic number of a graph G, denoted by χ i ( G ), is the smallest integer k such that G has an injective k-coloring. In this paper, we prove that for a Halin graph G, χ i ( G ) ≤ Δ ( G ) + 2. Moreover, χ i ( G ) ≤ Δ ( G ) + 1 if Δ ( G ) ≥ 6. Also, we show that for a triangle-free planar graph G without intersecting 4-cycles, χ i ( G ) ≤ Δ ( G ) + 6 if Δ ( G ) ≥ 20.

YNIMG Journal 2021 Journal Article

Measurement reliability for individual differences in multilayer network dynamics: Cautions and considerations

  • Zhen Yang
  • Qawi K. Telesford
  • Alexandre R. Franco
  • Ryan Lim
  • Shi Gu
  • Ting Xu
  • Lei Ai
  • Francisco X. Castellanos

Multilayer network models have been proposed as an effective means of capturing the dynamic configuration of distributed neural circuits and quantitatively describing how communities vary over time. Beyond general insights into brain function, a growing number of studies have begun to employ these methods for the study of individual differences. However, test-retest reliabilities for multilayer network measures have yet to be fully quantified or optimized, potentially limiting their utility for individual difference studies. Here, we systematically evaluated the impact of multilayer community detection algorithms, selection of network parameters, scan duration, and task condition on test-retest reliabilities of multilayer network measures (i.e., flexibility, integration, and recruitment). A key finding was that the default method used for community detection by the popular generalized Louvain algorithm can generate erroneous results. Although available, an updated algorithm addressing this issue is yet to be broadly adopted in the neuroimaging literature. Beyond the algorithm, the present work identified parameter selection as a key determinant of test-retest reliability; however, optimization of these parameters and expected reliabilities appeared to be dataset-specific. Once parameters were optimized, consistent with findings from the static functional connectivity literature, scan duration was a much stronger determinant of reliability than scan condition. When the parameters were optimized and scan duration was sufficient, both passive (i.e., resting state, Inscapes, and movie) and active (i.e., flanker) tasks were reliable, although reliability in the movie watching condition was significantly higher than in the other three tasks. The minimal data requirement for achieving reliable measures for the movie watching condition was 20 min, and 30 min for the other three tasks. Our results caution the field against the use of default parameters without optimization based on the specific datasets to be employed - a process likely to be limited for most due to the lack of test-retest samples to enable parameter optimization.

YNIMG Journal 2021 Journal Article

Multimodal 3D atlas of the macaque monkey motor and premotor cortex

  • Lucija Rapan
  • Sean Froudist-Walsh
  • Meiqi Niu
  • Ting Xu
  • Thomas Funck
  • Karl Zilles
  • Nicola Palomero-Gallagher

In the present study we reevaluated the parcellation scheme of the macaque frontal agranular cortex by implementing quantitative cytoarchitectonic and multireceptor analyses, with the purpose to integrate and reconcile the discrepancies between previously published maps of this region. We applied an observer-independent and statistically testable approach to determine the position of cytoarchitectonic borders. Analysis of the regional and laminar distribution patterns of 13 different transmitter receptors confirmed the position of cytoarchitectonically identified borders. Receptor densities were extracted from each area and visualized as its "receptor fingerprint". Hierarchical and principal components analyses were conducted to detect clusters of areas according to the degree of (dis)similarity of their fingerprints. Finally, functional connectivity pattern of each identified area was analyzed with areas of prefrontal, cingulate, somatosensory and lateral parietal cortex and the results were depicted as "connectivity fingerprints" and seed-to-vertex connectivity maps. We identified 16 cyto- and receptor architectonically distinct areas, including novel subdivisions of the primary motor area 4 (i.e. 4a, 4p, 4m) and of premotor areas F4 (i.e. F4s, F4d, F4v), F5 (i.e. F5s, F5d, F5v) and F7 (i.e. F7d, F7i, F7s). Multivariate analyses of receptor fingerprints revealed three clusters, which first segregated the subdivisions of area 4 with F4d and F4s from the remaining premotor areas, then separated ventrolateral from dorsolateral and medial premotor areas. The functional connectivity analysis revealed that medial and dorsolateral premotor and motor areas show stronger functional connectivity with areas involved in visual processing, whereas 4p and ventrolateral premotor areas presented a stronger functional connectivity with areas involved in somatomotor responses. For the first time, we provide a 3D atlas integrating cyto- and multi-receptor architectonic features of the macaque motor and premotor cortex. This atlas constitutes a valuable resource for the analysis of functional experiments carried out with non-human primates, for modeling approaches with realistic synaptic dynamics, as well as to provide insights into how brain functions have developed by changes in the underlying microstructure and encoding strategies during evolution.

YNIMG Journal 2021 Journal Article

U-net model for brain extraction: Trained on humans for transfer to non-human primates

  • Xindi Wang
  • Xin-Hui Li
  • Jae Wook Cho
  • Brian E. Russ
  • Nanditha Rajamani
  • Alisa Omelchenko
  • Lei Ai
  • Annachiara Korchmaros

Brain extraction (a.k.a. skull stripping) is a fundamental step in the neuroimaging pipeline as it can affect the accuracy of downstream preprocess such as image registration, tissue classification, etc. Most brain extraction tools have been designed for and applied to human data and are often challenged by non-human primates (NHP) data. Amongst recent attempts to improve performance on NHP data, deep learning models appear to outperform the traditional tools. However, given the minimal sample size of most NHP studies and notable variations in data quality, the deep learning models are very rarely applied to multi-site samples in NHP imaging. To overcome this challenge, we used a transfer-learning framework that leverages a large human imaging dataset to pretrain a convolutional neural network (i.e. U-Net Model), and then transferred this to NHP data using a small NHP training sample. The resulting transfer-learning model converged faster and achieved more accurate performance than a similar U-Net Model trained exclusively on NHP samples. We improved the generalizability of the model by upgrading the transfer-learned model using additional training datasets from multiple research sites in the Primate Data-Exchange (PRIME-DE) consortium. Our final model outperformed brain extraction routines from popular MRI packages (AFNI, FSL, and FreeSurfer) across a heterogeneous sample from multiple sites in the PRIME-DE with less computational cost (20 s~10 min). We also demonstrated the transfer-learning process enables the macaque model to be updated for use with scans from chimpanzees, marmosets, and other mammals (e.g. pig). Our model, code, and the skull-stripped mask repository of 136 macaque monkeys are publicly available for unrestricted use by the neuroimaging community at https://github.com/HumanBrainED/NHP-BrainExtraction.

YNIMG Journal 2020 Journal Article

Bagging improves reproducibility of functional parcellation of the human brain

  • Aki Nikolaidis
  • Anibal Solon Heinsfeld
  • Ting Xu
  • Pierre Bellec
  • Joshua Vogelstein
  • Michael Milham

Increasing the reproducibility of neuroimaging measurement addresses a central impediment to the advancement of human neuroscience and its clinical applications. Recent efforts demonstrating variance in functional brain organization within and between individuals shows a need for improving reproducibility of functional parcellations without long scan times. We apply bootstrap aggregation, or bagging, to the problem of improving reproducibility in functional parcellation. We use two large datasets to demonstrate that compared to a standard clustering framework, bagging improves the reproducibility and test-retest reliability of both cortical and subcortical functional parcellations across a range of sites, scanners, samples, scan lengths, clustering algorithms, and clustering parameters (e.g., number of clusters, spatial constraints). With as little as 6 ​min of scan time, bagging creates more reproducible group and individual level parcellations than standard approaches with twice as much data. This suggests that regardless of the specific parcellation strategy employed, bagging may be a key method for improving functional parcellation and bringing functional neuroimaging-based measurement closer to clinical impact.

YNIMG Journal 2020 Journal Article

Cross-species functional alignment reveals evolutionary hierarchy within the connectome

  • Ting Xu
  • Karl-Heinz Nenning
  • Ernst Schwartz
  • Seok-Jun Hong
  • Joshua T. Vogelstein
  • Alexandros Goulas
  • Damien A. Fair
  • Charles E. Schroeder

Evolution provides an important window into how cortical organization shapes function and vice versa. The complex mosaic of changes in brain morphology and functional organization that have shaped the mammalian cortex during evolution, complicates attempts to chart cortical differences across species. It limits our ability to fully appreciate how evolution has shaped our brain, especially in systems associated with unique human cognitive capabilities that lack anatomical homologues in other species. Here, we develop a function-based method for cross-species alignment that enables the quantification of homologous regions between humans and rhesus macaques, even when their location is decoupled from anatomical landmarks. Critically, we find cross-species similarity in functional organization reflects a gradient of evolutionary change that decreases from unimodal systems and culminates with the most pronounced changes in posterior regions of the default mode network (angular gyrus, posterior cingulate and middle temporal cortices). Our findings suggest that the establishment of the default mode network, as the apex of a cognitive hierarchy, has changed in a complex manner during human evolution - even within subnetworks.

YNIMG Journal 2020 Journal Article

Joint embedding: A scalable alignment to compare individuals in a connectivity space

  • Karl-Heinz Nenning
  • Ting Xu
  • Ernst Schwartz
  • Jesus Arroyo
  • Adelheid Woehrer
  • Alexandre R. Franco
  • Joshua T. Vogelstein
  • Daniel S. Margulies

A common coordinate space enabling comparison across individuals is vital to understanding human brain organization and individual differences. By leveraging dimensionality reduction algorithms, high-dimensional fMRI data can be represented in a low-dimensional space to characterize individual features. Such a representative space encodes the functional architecture of individuals and enables the observation of functional changes across time. However, determining comparable functional features across individuals in resting-state fMRI in a way that simultaneously preserves individual-specific connectivity structure can be challenging. In this work we propose scalable joint embedding to simultaneously embed multiple individual brain connectomes within a common space that allows individual representations across datasets to be aligned. Using Human Connectome Project data, we evaluated the joint embedding approach by comparing it to the previously established orthonormal alignment model. Alignment using joint embedding substantially increased the similarity of functional representations across individuals while simultaneously capturing their distinct profiles, allowing individuals to be more discriminable from each other. Additionally, we demonstrated that the common space established using resting-state fMRI provides a better overlap of task-activation across participants. Finally, in a more challenging scenario - alignment across a lifespan cohort aged from 6 to 85 - joint embedding provided a better prediction of age (r2 = 0. 65) than the prior alignment model. It facilitated the characterization of functional trajectories across lifespan. Overall, these analyses establish that joint embedding can simultaneously capture individual neural representations in a common connectivity space aligning functional data across participants and populations and preserve individual specificity.

YNIMG Journal 2020 Journal Article

Reliability map of individual differences reflected in inter-subject correlation in naturalistic imaging

  • Jiaqi Gao
  • Gang Chen
  • Jinfeng Wu
  • YinShan Wang
  • Yang Hu
  • Ting Xu
  • Xi-Nian Zuo
  • Zhi Yang

Understanding individual differences in brain function is an essential aim of neuroscience. Naturalistic imaging links neural activity to real-life contexts and reflects individual differences in brain response. These unique features make it a promising tool for individualized psychiatry. An essential prerequisite for the extensive use of this paradigm is the reliable representation of inter-individual relationships. We used a test–retest approach to examine whether the naturalistic paradigm reliably represents inter-individual differences, which brain regions have the superior capability, and whether the ability alters with the contents of the stimuli. We quantified the reliability of the inter-subject relationships in repeated scans of two movie clips: a natural sight view and an emotion-evoking story. Besides statistical inference, we included resting-state scans, behavioral tests, and questionnaires as references for the comparison. The results showed that over one-third area of the brain could reliably characterize the inter-individual relationship, and the superior temporal lobe demonstrated comparable reliability representation with the State and Trait Anxiety Inventory. Furthermore, the temporal lobe regions could retain this capability across emotional movies with different contents. This study provides a base for pushing the naturalistic imaging paradigm towards clinical applications and proposes reliable target brain regions for future studies.

YNIMG Journal 2020 Journal Article

Toward a connectivity gradient-based framework for reproducible biomarker discovery

  • Seok-Jun Hong
  • Ting Xu
  • Aki Nikolaidis
  • Jonathan Smallwood
  • Daniel S. Margulies
  • Boris Bernhardt
  • Joshua Vogelstein
  • Michael P. Milham

Despite myriad demonstrations of feasibility, the high dimensionality of fMRI data remains a critical barrier to its utility for reproducible biomarker discovery. Recent efforts to address this challenge have capitalized on dimensionality reduction techniques applied to resting-state fMRI, identifying principal components of intrinsic connectivity which describe smooth transitions across different cortical systems, so called “connectivity gradients”. These gradients recapitulate neurocognitively meaningful organizational principles that are present in both human and primate brains, and also appear to differ among individuals and clinical populations. Here, we provide a critical assessment of the suitability of connectivity gradients for biomarker discovery. Using the Human Connectome Project (discovery subsample=209; two replication subsamples= 209 × 2) and the Midnight scan club (n = 9), we tested the following key biomarker traits – reliability, reproducibility and predictive validity – of functional gradients. In doing so, we systematically assessed the effects of three analytical settings, including i) dimensionality reduction algorithms (i. e. , linear vs. non-linear methods), ii) input data types (i. e. , raw time series, [un-]thresholded functional connectivity), and iii) amount of the data (resting-state fMRI time-series lengths). We found that the reproducibility of functional gradients across algorithms and subsamples is generally higher for those explaining more variances of whole-brain connectivity data, as well as those having higher reliability. Notably, among different analytical settings, a linear dimensionality reduction (principal component analysis in our study), more conservatively thresholded functional connectivity (e. g. , 95–97%) and longer time-series data (at least ≥20mins) was found to be preferential conditions to obtain higher reliability. Those gradients with higher reliability were able to predict unseen phenotypic scores with a higher accuracy, highlighting reliability as a critical prerequisite for validity. Importantly, prediction accuracy with connectivity gradients exceeded that observed with more traditional edge-based connectivity measures, suggesting the added value of a low-dimensional and multivariate gradient approach. Finally, the present work highlights the importance and benefits of systematically exploring the parameter space for new imaging methods before widespread deployment.

YNIMG Journal 2014 Journal Article

Connectivity trajectory across lifespan differentiates the precuneus from the default network

  • Zhi Yang
  • Catie Chang
  • Ting Xu
  • Lili Jiang
  • Daniel A. Handwerker
  • F. Xavier Castellanos
  • Michael P. Milham
  • Peter A. Bandettini

The default network of the human brain has drawn much attention due to its relevance to various brain disorders, cognition, and behavior. However, its functional components and boundaries have not been precisely defined. There is no consensus as to whether the precuneus, a hub in the functional connectome, acts as part of the default network. This discrepancy is more critical for brain development and aging studies: it is not clear whether age has a stronger impact on the default network or precuneus, or both. We used Generalized Ranking and Averaging Independent Component Analysis by Reproducibility (gRAICAR) to investigate the lifespan trajectories of intrinsic functional networks. By estimating individual-specific spatial components and aligning them across subjects, gRAICAR measures the spatial variation of component maps across a population without constraining the same components to appear in every subject. In a cross-lifespan fMRI dataset (N=126, 7–85years old), we observed stronger age dependence in the spatial pattern of a precuneus–dorsal posterior cingulate cortex network compared to the default network, despite the fact that the two networks exhibit considerable spatial overlap and temporal correlation. These results remained even when analyses were restricted to a subpopulation with very similar head motion across age. Our analyses further showed that the two networks tend to merge with increasing age. Post-hoc analyses of functional connectivity confirmed the distinguishable cross-lifespan trajectories between the two networks. Based on these observations, we proposed a dynamic model of cross-lifespan functional segregation and integration between the two networks, suggesting that the precuneus network may have a different functional role than the default network, which declines with age. These findings have implications for understanding the functional roles of the default network, gaining insight into its dynamics throughout life, and guiding interpretation of alterations in brain disorders.

YNIMG Journal 2013 Journal Article

Functional brain hubs and their test–retest reliability: A multiband resting-state functional MRI study

  • Xu-Hong Liao
  • Ming-Rui Xia
  • Ting Xu
  • Zheng-Jia Dai
  • Xiao-Yan Cao
  • Hai-Jing Niu
  • Xi-Nian Zuo
  • Yu-Feng Zang

Resting-state functional MRI (R-fMRI) has emerged as a promising neuroimaging technique used to identify global hubs of the human brain functional connectome. However, most R-fMRI studies on functional hubs mainly utilize traditional R-fMRI data with relatively low sampling rates (e. g. , repetition time [TR]=2s). R-fMRI data scanned with higher sampling rates are important for the characterization of reliable functional connectomes because they can provide temporally complementary information about functional integration among brain regions and simultaneously reduce the effects of high frequency physiological noise. Here, we employed a publicly available multiband R-fMRI dataset with a sub-second sampling rate (TR=645ms) to identify global hubs in the human voxel-wise functional networks, and further examined their test–retest (TRT) reliability over scanning time. We showed that the functional hubs of human brain networks were mainly located at the default-mode regions (e. g. , medial prefrontal and parietal cortex as well as the lateral parietal and temporal cortex) and the sensorimotor and visual cortex. These hub regions were highly anatomically distance-dependent, where short-range and long-range hubs were primarily located at the primary cortex and the multimodal association cortex, respectively. We found that most functional hubs exhibited fair to good TRT reliability using intraclass correlation coefficients. Interestingly, our analysis suggested that a 6-minute scan duration was able to reliably detect these functional hubs. Further comparison analysis revealed that these results were approximately consistent with those obtained using traditional R-fMRI scans of the same subjects with TR=2500ms, but several regions (e. g. , lateral frontal cortex, paracentral lobule and anterior temporal lobe) exhibited different TRT reliability. Finally, we showed that several regions (including the medial/lateral prefrontal cortex and lateral temporal cortex) were identified as brain hubs in a high frequency band (0. 2–0. 3Hz), which is beyond the frequency scope of traditional R-fMRI scans. Our results demonstrated the validity of multiband R-fMRI data to reliably detect functional hubs in the voxel-wise whole-brain networks, which motivated the acquisition of high temporal resolution R-fMRI data for the studies of human brain functional connectomes in healthy and diseased conditions.

YNIMG Journal 2013 Journal Article

Toward reliable characterization of functional homogeneity in the human brain: Preprocessing, scan duration, imaging resolution and computational space

  • Xi-Nian Zuo
  • Ting Xu
  • Lili Jiang
  • Zhi Yang
  • Xiao-Yan Cao
  • Yong He
  • Yu-Feng Zang
  • F. Xavier Castellanos

While researchers have extensively characterized functional connectivity between brain regions, the characterization of functional homogeneity within a region of the brain connectome is in early stages of development. Several functional homogeneity measures were proposed previously, among which regional homogeneity (ReHo) was most widely used as a measure to characterize functional homogeneity of resting state fMRI (R-fMRI) signals within a small region (Zang et al. , 2004). Despite a burgeoning literature on ReHo in the field of neuroimaging brain disorders, its test–retest (TRT) reliability remains unestablished. Using two sets of public R-fMRI TRT data, we systematically evaluated the ReHo's TRT reliability and further investigated the various factors influencing its reliability and found: 1) nuisance (head motion, white matter, and cerebrospinal fluid) correction of R-fMRI time series can significantly improve the TRT reliability of ReHo while additional removal of global brain signal reduces its reliability, 2) spatial smoothing of R-fMRI time series artificially enhances ReHo intensity and influences its reliability, 3) surface-based R-fMRI computation largely improves the TRT reliability of ReHo, 4) a scan duration of 5min can achieve reliable estimates of ReHo, and 5) fast sampling rates of R-fMRI dramatically increase the reliability of ReHo. Inspired by these findings and seeking a highly reliable approach to exploratory analysis of the human functional connectome, we established an R-fMRI pipeline to conduct ReHo computations in both 3-dimensions (volume) and 2-dimensions (surface).

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