Chee-Ming Ting

Hwa Hui Tew, Junn Yong Loo, Fang Yu Leong et al.

Functional Magnetic Resonance Imaging (fMRI) provides non-invasive access to dynamic brain activity by measuring blood oxygen level-dependent (BOLD) signals over time. However, the resource-intensive nature of fMRI acquisition limits the availability of high-fidelity samples required for data-driven brain analysis models. While modern generative models can synthesize fMRI data, they often remain challenging in replicating their inherent non-stationarity, intricate spatiotemporal dynamics, and physiological variations of raw BOLD signals. To address these challenges, we propose Dual-Spectral Flow Matching (DSFM), a novel fMRI generative framework that cascades dual frequency representation of BOLD signals with spectral flow matching. Specifically, our framework first converts BOLD signals into a wavelet decomposition map via a discrete wavelet transform (DWT) to capture globalized transient and multi-scale variations, and projects into the discrete cosine transform (DCT) space across brain regions and time to exploit localized energy compaction of low-frequency dominant BOLD coefficients. Subsequently, a spectral flow matching model is trained to generate class-conditioned cosine-frequency representation. The generated samples are reconstructed through inverse DCT and inverse DWT operations to recover physiologically plausible time-domain BOLD signals. This dual-transform approach imposes structured frequency priors and preserves key physiological brain dynamics. Ultimately, we demonstrate the efficacy of our approach through improved downstream fMRI-based brain network classification. The code is available at https://github.com/htew0001/DSFM.git .

Ming Kang, Chee-Ming Ting, Fung Fung Ting et al.

With an excellent balance between speed and accuracy, cutting-edge YOLO frameworks have become one of the most efficient algorithms for object detection. However, the performance of using YOLO networks is scarcely investigated in brain tumor detection. We propose a novel YOLO architecture with Reparameterized Convolution based on channel Shuffle (RCS-YOLO). We present RCS and a One-Shot Aggregation of RCS (RCS-OSA), which link feature cascade and computation efficiency to extract richer information and reduce time consumption. Experimental results on the brain tumor dataset Br35H show that the proposed model surpasses YOLOv6, YOLOv7, and YOLOv8 in speed and accuracy. Notably, compared with YOLOv7, the precision of RCS-YOLO improves by 1%, and the inference speed by 60% at 114.8 images detected per second (FPS). Our proposed RCS-YOLO achieves state-of-the-art performance on the brain tumor detection task. The code is available at https://github.com/mkang315/RCS-YOLO.

Ming Kang, Chee-Ming Ting, Fung Fung Ting et al.

You Only Look Once (YOLO)-based object detectors have shown remarkable accuracy for automated brain tumor detection. In this paper, we develop a novel BGF-YOLO architecture by incorporating Bi-level routing attention, Generalized feature pyramid networks, and Fourth detecting head into YOLOv8. BGF-YOLO contains an attention mechanism to focus more on important features, and feature pyramid networks to enrich feature representation by merging high-level semantic features with spatial details. Furthermore, we investigate the effect of different attention mechanisms and feature fusions, detection head architectures on brain tumor detection accuracy. Experimental results show that BGF-YOLO gives a 4.7% absolute increase of mAP$_{50}$ compared to YOLOv8x, and achieves state-of-the-art on the brain tumor detection dataset Br35H. The code is available at https://github.com/mkang315/BGF-YOLO.

Ming Kang, Chee-Ming Ting, Fung Fung Ting et al.

Blood cell detection is a typical small-scale object detection problem in computer vision. In this paper, we propose a CST-YOLO model for blood cell detection based on YOLOv7 architecture and enhance it with the CNN-Swin Transformer (CST), which is a new attempt at CNN-Transformer fusion. We also introduce three other useful modules: Weighted Efficient Layer Aggregation Networks (W-ELAN), Multiscale Channel Split (MCS), and Concatenate Convolutional Layers (CatConv) in our CST-YOLO to improve small-scale object detection precision. Experimental results show that the proposed CST-YOLO achieves 92.7%, 95.6%, and 91.1% mAP@0.5, respectively, on three blood cell datasets, outperforming state-of-the-art object detectors, e.g., RT-DETR, YOLOv5, and YOLOv7. Our code is available at https://github.com/mkang315/CST-YOLO.

Sin-Yee Yap, Junn Yong Loo, Chee-Ming Ting et al.

Recent applications of pattern recognition techniques on brain connectome classification using functional connectivity (FC) are shifting towards acknowledging the non-Euclidean topology and dynamic aspects of brain connectivity across time. In this paper, a deep spatiotemporal variational Bayes (DSVB) framework is proposed to learn time-varying topological structures in dynamic FC networks for identifying autism spectrum disorder (ASD) in human participants. The framework incorporates a spatial-aware recurrent neural network with an attention-based message passing scheme to capture rich spatiotemporal patterns across dynamic FC networks. To overcome model overfitting on limited training datasets, an adversarial training strategy is introduced to learn graph embedding models that generalize well to unseen brain networks. Evaluation on the ABIDE resting-state functional magnetic resonance imaging dataset shows that our proposed framework substantially outperforms state-of-the-art methods in identifying patients with ASD. Dynamic FC analyses with DSVB-learned embeddings reveal apparent group differences between ASD and healthy controls in brain network connectivity patterns and switching dynamics of brain states. The code is available at https://github.com/Monash-NeuroAI/Deep-Spatiotemporal-Variational-Bayes.

Yee-Fan Tan, Chee-Ming Ting, Fuad Noman et al.

Common measures of brain functional connectivity (FC) including covariance and correlation matrices are semi-positive definite (SPD) matrices residing on a cone-shape Riemannian manifold. Despite its remarkable success for Euclidean-valued data generation, use of standard generative adversarial networks (GANs) to generate manifold-valued FC data neglects its inherent SPD structure and hence the inter-relatedness of edges in real FC. We propose a novel graph-regularized manifold-aware conditional Wasserstein GAN (GR-SPD-GAN) for FC data generation on the SPD manifold that can preserve the global FC structure. Specifically, we optimize a generalized Wasserstein distance between the real and generated SPD data under an adversarial training, conditioned on the class labels. The resulting generator can synthesize new SPD-valued FC matrices associated with different classes of brain networks, e.g., brain disorder or healthy control. Furthermore, we introduce additional population graph-based regularization terms on both the SPD manifold and its tangent space to encourage the generator to respect the inter-subject similarity of FC patterns in the real data. This also helps in avoiding mode collapse and produces more stable GAN training. Evaluated on resting-state functional magnetic resonance imaging (fMRI) data of major depressive disorder (MDD), qualitative and quantitative results show that the proposed GR-SPD-GAN clearly outperforms several state-of-the-art GANs in generating more realistic fMRI-based FC samples. When applied to FC data augmentation for MDD identification, classification models trained on augmented data generated by our approach achieved the largest margin of improvement in classification accuracy among the competing GANs over baselines without data augmentation.

Ming Kang, Chee-Ming Ting, Fung Fung Ting et al.

We propose a novel Attentional Scale Sequence Fusion based You Only Look Once (YOLO) framework (ASF-YOLO) which combines spatial and scale features for accurate and fast cell instance segmentation. Built on the YOLO segmentation framework, we employ the Scale Sequence Feature Fusion (SSFF) module to enhance the multi-scale information extraction capability of the network, and the Triple Feature Encoder (TFE) module to fuse feature maps of different scales to increase detailed information. We further introduce a Channel and Position Attention Mechanism (CPAM) to integrate both the SSFF and TPE modules, which focus on informative channels and spatial position-related small objects for improved detection and segmentation performance. Experimental validations on two cell datasets show remarkable segmentation accuracy and speed of the proposed ASF-YOLO model. It achieves a box mAP of 0.91, mask mAP of 0.887, and an inference speed of 47.3 FPS on the 2018 Data Science Bowl dataset, outperforming the state-of-the-art methods. The source code is available at https://github.com/mkang315/ASF-YOLO.

Ming Kang, Fung Fung Ting, Raphaël C. -W. Phan et al.

Nuclei panoptic segmentation supports cancer diagnostics by integrating both semantic and instance segmentation of different cell types to analyze overall tissue structure and individual nuclei in histopathology images. Major challenges include detecting small objects, handling ambiguous boundaries, and addressing class imbalance. To address these issues, we propose PanopMamba, a novel hybrid encoder-decoder architecture that integrates Mamba and Transformer with additional feature-enhanced fusion via state space modeling. We design a multiscale Mamba backbone and a State Space Model (SSM)-based fusion network to enable efficient long-range perception in pyramid features, thereby extending the pure encoder-decoder framework while facilitating information sharing across multiscale features of nuclei. The proposed SSM-based feature-enhanced fusion integrates pyramid feature networks and dynamic feature enhancement across different spatial scales, enhancing the feature representation of densely overlapping nuclei in both semantic and spatial dimensions. To the best of our knowledge, this is the first Mamba-based approach for panoptic segmentation. Additionally, we introduce alternative evaluation metrics, including image-level Panoptic Quality ($i$PQ), boundary-weighted PQ ($w$PQ), and frequency-weighted PQ ($fw$PQ), which are specifically designed to address the unique challenges of nuclei segmentation and thereby mitigate the potential bias inherent in vanilla PQ. Experimental evaluations on two multiclass nuclei segmentation benchmark datasets, MoNuSAC2020 and NuInsSeg, demonstrate the superiority of PanopMamba for nuclei panoptic segmentation over state-of-the-art methods. Consequently, the robustness of PanopMamba is validated across various metrics, while the distinctiveness of PQ variants is also demonstrated. Code is available at https://github.com/mkang315/PanopMamba.

Junn Yong Loo, Hwa Hui Tew, Fang Yu Leong et al.

Industrial soft sensing is crucial for accurate process monitoring through reliable inference of dominant sensor variables. However, developing effective data-driven soft sensor models presents challenges, such as achieving domain adaptability, addressing incomplete sensor labels, and learning stochastic data variability. To overcome these challenges, we propose a Deep Variational Potential Flow (DVPF) framework for cross-domain soft sensor modeling, taking into account the lack of sensor labels in the target domain. Our framework introduces sequential variational Bayes with recurrent neural network (RNN) parameterization to address the maximum likelihood estimation problem that characterizes cross-domain soft sensing. Central to the framework is a potential flow that performs unsupervised Bayesian inference on the RNN-extracted features to obtain an exact representation of the intractable posterior distribution. Together, these DVPF components learn domain-adaptable features that effectively capture complex cross-domain process dynamics and data variability. We validate the proposed DVPF on a real industrial multiphase flow process across varying operating modes. The results show that the DVPF demonstrates superior performance in cross-domain soft sensing compared to existing deep feature-based domain adaptation methods.

Ming Kang, Fung Fung Ting, Raphaël C. -W. Phan et al.

Existing brain tumor segmentation methods usually utilize multiple Magnetic Resonance Imaging (MRI) modalities in brain tumor images for segmentation, which can achieve better segmentation performance. However, in clinical applications, some modalities are missing due to resource constraints, leading to severe degradation in the performance of methods applying complete modality segmentation. In this paper, we propose a Multimodal feature distillation with Convolutional Neural Network (CNN)-Transformer hybrid network (MCTSeg) for accurate brain tumor segmentation with missing modalities. We first design a Multimodal Feature Distillation (MFD) module to distill feature-level multimodal knowledge into different unimodality to extract complete modality information. We further develop a Unimodal Feature Enhancement (UFE) module to model the relationship between global and local information semantically. Finally, we build a Cross-Modal Fusion (CMF) module to explicitly align the global correlations among different modalities even when some modalities are missing. Complementary features within and across different modalities are refined via the CNN-Transformer hybrid architectures in both the UFE and CMF modules, where local and global dependencies are both captured. Our ablation study demonstrates the importance of the proposed modules with CNN-Transformer networks and the convolutional blocks in Transformer for improving the performance of brain tumor segmentation with missing modalities. Extensive experiments on the BraTS2018 and BraTS2020 datasets show that the proposed MCTSeg framework outperforms the state-of-the-art methods in missing modalities cases. Our code is available at: https://github.com/mkang315/MCTSeg.

Junn Yong Loo, Michelle Adeline, Arghya Pal et al.

Energy based models (EBMs) are appealing for their generality and simplicity in data likelihood modeling, but have conventionally been difficult to train due to the unstable and time-consuming implicit MCMC sampling during contrastive divergence training. In this paper, we present a novel energy-based generative framework, Variational Potential Flow (VAPO), that entirely dispenses with implicit MCMC sampling and does not rely on complementary latent models or cooperative training. The VAPO framework aims to learn a potential energy function whose gradient (flow) guides the prior samples, so that their density evolution closely follows an approximate data likelihood homotopy. An energy loss function is then formulated to minimize the Kullback-Leibler divergence between density evolution of the flow-driven prior and the data likelihood homotopy. Images can be generated after training the potential energy, by initializing the samples from Gaussian prior and solving the ODE governing the potential flow on a fixed time interval using generic ODE solvers. Experiment results show that the proposed VAPO framework is capable of generating realistic images on various image datasets. In particular, our proposed framework achieves competitive FID scores for unconditional image generation on the CIFAR-10 and CelebA datasets.

Ming Kang, Fung Fung Ting, Raphaël C. -W. Phan et al.

Brain tumor detection in multiplane Magnetic Resonance Imaging (MRI) slices is a challenging task due to the various appearances and relationships in the structure of the multiplane images. In this paper, we propose a new You Only Look Once (YOLO)-based detection model that incorporates Pretrained Knowledge (PK), called PK-YOLO, to improve the performance for brain tumor detection in multiplane MRI slices. To our best knowledge, PK-YOLO is the first pretrained knowledge guided YOLO-based object detector. The main components of the new method are a pretrained pure lightweight convolutional neural network-based backbone via sparse masked modeling, a YOLO architecture with the pretrained backbone, and a regression loss function for improving small object detection. The pretrained backbone allows for feature transferability of object queries on individual plane MRI slices into the model encoders, and the learned domain knowledge base can improve in-domain detection. The improved loss function can further boost detection performance on small-size brain tumors in multiplanar two-dimensional MRI slices. Experimental results show that the proposed PK-YOLO achieves competitive performance on the multiplanar MRI brain tumor detection datasets compared to state-of-the-art YOLO-like and DETR-like object detectors. The code is available at https://github.com/mkang315/PK-YOLO.

Hwa Hui Tew, Fan Ding, Gaoxuan Li et al.

Higher-order sensor networks are more accurate in characterizing the nonlinear dynamics of sensory time-series data in modern industrial settings by allowing multi-node connections beyond simple pairwise graph edges. In light of this, we propose a deep spatio-temporal hypergraph convolutional neural network for soft sensing (ST-HCSS). In particular, our proposed framework is able to construct and leverage a higher-order graph (hypergraph) to model the complex multi-interactions between sensor nodes in the absence of prior structural knowledge. To capture rich spatio-temporal relationships underlying sensor data, our proposed ST-HCSS incorporates stacked gated temporal and hypergraph convolution layers to effectively aggregate and update hypergraph information across time and nodes. Our results validate the superiority of ST-HCSS compared to existing state-of-the-art soft sensors, and demonstrates that the learned hypergraph feature representations aligns well with the sensor data correlations. The code is available at https://github.com/htew0001/ST-HCSS.git

Guan Yuan Tan, Ngoc Tuan Vu, Arghya Pal et al.

We introduce FLAG-4D, a novel framework for generating novel views of dynamic scenes by reconstructing how 3D Gaussian primitives evolve through space and time. Existing methods typically rely on a single Multilayer Perceptron (MLP) to model temporal deformations, and they often struggle to capture complex point motions and fine-grained dynamic details consistently over time, especially from sparse input views. Our approach, FLAG-4D, overcomes this by employing a dual-deformation network that dynamically warps a canonical set of 3D Gaussians over time into new positions and anisotropic shapes. This dual-deformation network consists of an Instantaneous Deformation Network (IDN) for modeling fine-grained, local deformations and a Global Motion Network (GMN) for capturing long-range dynamics, refined through mutual learning. To ensure these deformations are both accurate and temporally smooth, FLAG-4D incorporates dense motion features from a pretrained optical flow backbone. We fuse these motion cues from adjacent timeframes and use a deformation-guided attention mechanism to align this flow information with the current state of each evolving 3D Gaussian. Extensive experiments demonstrate that FLAG-4D achieves higher-fidelity and more temporally coherent reconstructions with finer detail preservation than state-of-the-art methods.

Ming Kang, Chee-Ming Ting, Fung Fung Ting et al.

Medical image semantic segmentation techniques can help identify tumors automatically from computed tomography (CT) scans. In this paper, we propose a Contextual and Attentional feature Fusions enhanced Convolutional Neural Network (CNN) and Transformer hybrid network (CAFCT-Net) for liver tumor segmentation. We incorporate three novel modules in the CAFCT-Net architecture: Attentional Feature Fusion (AFF), Atrous Spatial Pyramid Pooling (ASPP) of DeepLabv3, and Attention Gates (AGs) to improve contextual information related to tumor boundaries for accurate segmentation. Experimental results show that the proposed model achieves a mean Intersection over Union (IoU) of 76.54% and Dice coefficient of 84.29%, respectively, on the Liver Tumor Segmentation Benchmark (LiTS) dataset, outperforming pure CNN or Transformer methods, e.g., Attention U-Net and PVTFormer.

Yee-Fan Tan, Jun Lin Liow, Pei-Sze Tan et al.

Modern brain imaging technologies have enabled the detailed reconstruction of human brain connectomes, capturing structural connectivity (SC) from diffusion MRI and functional connectivity (FC) from functional MRI. Understanding the intricate relationships between SC and FC is vital for gaining deeper insights into the brain's functional and organizational mechanisms. However, obtaining both SC and FC modalities simultaneously remains challenging, hindering comprehensive analyses. Existing deep generative models typically focus on synthesizing a single modality or unidirectional translation between FC and SC, thereby missing the potential benefits of bi-directional translation, especially in scenarios where only one connectome is available. Therefore, we propose Structural-Functional Connectivity GAN (SFC-GAN), a novel framework for bidirectional translation between SC and FC. This approach leverages the CycleGAN architecture, incorporating convolutional layers to effectively capture the spatial structures of brain connectomes. To preserve the topological integrity of these connectomes, we employ a structure-preserving loss that guides the model in capturing both global and local connectome patterns while maintaining symmetry. Our framework demonstrates superior performance in translating between SC and FC, outperforming baseline models in similarity and graph property evaluations compared to ground truth data, each translated modality can be effectively utilized for downstream classification.

Hwa Hui Tew, Gaoxuan Li, Fan Ding et al.

Soft sensing of hard-to-measure variables is often crucial in industrial processes. Current practices rely heavily on conventional modeling techniques that show success in improving accuracy. However, they overlook the non-linear nature, dynamics characteristics, and non-Euclidean dependencies between complex process variables. To tackle these challenges, we present a framework known as a Knowledge discovery graph Attention Network for effective Soft sensing (KANS). Unlike the existing deep learning soft sensor models, KANS can discover the intrinsic correlations and irregular relationships between the multivariate industrial processes without a predefined topology. First, an unsupervised graph structure learning method is introduced, incorporating the cosine similarity between different sensor embedding to capture the correlations between sensors. Next, we present a graph attention-based representation learning that can compute the multivariate data parallelly to enhance the model in learning complex sensor nodes and edges. To fully explore KANS, knowledge discovery analysis has also been conducted to demonstrate the interpretability of the model. Experimental results demonstrate that KANS significantly outperforms all the baselines and state-of-the-art methods in soft sensing performance. Furthermore, the analysis shows that KANS can find sensors closely related to different process variables without domain knowledge, significantly improving soft sensing accuracy.

Junn Yong Loo, Michelle Adeline, Julia Kaiwen Lau et al.

Energy-based models (EBMs) are a powerful class of probabilistic generative models due to their flexibility and interpretability. However, relationships between potential flows and explicit EBMs remain underexplored, while contrastive divergence training via implicit Markov chain Monte Carlo (MCMC) sampling is often unstable and expensive in high-dimensional settings. In this paper, we propose Variational Potential Flow Bayes (VPFB), a new energy-based generative framework that eliminates the need for implicit MCMC sampling and does not rely on auxiliary networks or cooperative training. VPFB learns an energy-parameterized potential flow by constructing a flow-driven density homotopy that is matched to the data distribution through a variational loss minimizing the Kullback-Leibler divergence between the flow-driven and marginal homotopies. This principled formulation enables robust and efficient generative modeling while preserving the interpretability of EBMs. Experimental results on image generation, interpolation, out-of-distribution detection, and compositional generation confirm the effectiveness of VPFB, showing that our method performs competitively with existing approaches in terms of sample quality and versatility across diverse generative modeling tasks.

Sin-Yee Yap, Fuad Noman, Junn Yong Loo et al.

Psychedelics, such as psilocybin, reorganise large-scale brain connectivity, yet how these changes are reflected across electrophysiological (electroencephalogram, EEG) and haemodynamic (functional magnetic resonance imaging, fMRI) networks remains unclear. We present Brain-MGF, a multimodal graph fusion network for joint EEG-fMRI connectivity analysis. For each modality, we construct graphs with partial-correlation edges and Pearson-profile node features, and learn subject-level embeddings via graph convolution. An adaptive softmax gate then fuses modalities with sample-specific weights to capture context-dependent contributions. Using the world's largest single-site psilocybin dataset, PsiConnect, Brain-MGF distinguishes psilocybin from no-psilocybin conditions in meditation and rest. Fusion improves over unimodal and non-adaptive variants, achieving 74.0% accuracy and 76.5% F1 score on meditation, and 76.0% accuracy with 85.8% ROC-AUC on rest. UMAP visualisations reveal clearer class separation for fused embeddings. These results indicate that adaptive graph fusion effectively integrates complementary EEG-fMRI information, providing an interpretable framework for characterising psilocybin-induced alterations in large-scale neural organisation.

Hwa Hui Tew, Junn Yong Loo, Yee-Fan Tan et al.

Functional Magnetic Resonance Imaging (fMRI) is an advanced neuroimaging method that enables in-depth analysis of brain activity by measuring dynamic changes in the blood oxygenation level-dependent (BOLD) signals. However, the resource-intensive nature of fMRI data acquisition limits the availability of high-fidelity samples required for data-driven brain analysis models. While modern generative models can synthesize fMRI data, they often underperform because they overlook the complex non-stationarity and nonlinear BOLD dynamics. To address these challenges, we introduce T2I-Diff, an fMRI generation framework that leverages time-frequency representation of BOLD signals and classifier-free denoising diffusion. Specifically, our framework first converts BOLD signals into windowed spectrograms via a time-dependent Fourier transform, capturing both the underlying temporal dynamics and spectral evolution. Subsequently, a classifier-free diffusion model is trained to generate class-conditioned frequency spectrograms, which are then reverted to BOLD signals via inverse Fourier transforms. Finally, we validate the efficacy of our approach by demonstrating improved accuracy and generalization in downstream fMRI-based brain network classification.

Chee-Ming Ting, Fuad Noman, Raphaël C. -W. Phan et al.

The low-rank plus sparse (L+S) decomposition model has enabled better reconstruction of dynamic magnetic resonance imaging (dMRI) with separation into background (L) and dynamic (S) component. However, use of low-rank prior alone may not fully explain the slow variations or smoothness of the background part at the local scale. In this paper, we propose a smoothness-regularized L+S (SR-L+S) model for dMRI reconstruction from highly undersampled k-t-space data. We exploit joint low-rank and smooth priors on the background component of dMRI to better capture both its global and local temporal correlated structures. Extending the L+S formulation, the low-rank property is encoded by the nuclear norm, while the smoothness by a general \ell_{p}-norm penalty on the local differences of the columns of L. The additional smoothness regularizer can promote piecewise local consistency between neighboring frames. By smoothing out the noise and dynamic activities, it allows accurate recovery of the background part, and subsequently more robust dMRI reconstruction. Extensive experiments on multi-coil cardiac and synthetic data shows that the SR-L+S model outp

Fuad Noman, Chee-Ming Ting, Hakmook Kang et al.

Brain functional connectivity (FC) reveals biomarkers for identification of various neuropsychiatric disorders. Recent application of deep neural networks (DNNs) to connectome-based classification mostly relies on traditional convolutional neural networks using input connectivity matrices on a regular Euclidean grid. We propose a graph deep learning framework to incorporate the non-Euclidean information about graph structure for classifying functional magnetic resonance imaging (fMRI)-derived brain networks in major depressive disorder (MDD). We design a novel graph autoencoder (GAE) architecture based on the graph convolutional networks (GCNs) to embed the topological structure and node content of large-sized fMRI networks into low-dimensional latent representations. In network construction, we employ the Ledoit-Wolf (LDW) shrinkage method to estimate the high-dimensional FC metrics efficiently from fMRI data. We consider both supervised and unsupervised approaches for the graph embedding learning. The learned embeddings are then used as feature inputs for a deep fully-connected neural network (FCNN) to discriminate MDD from healthy controls. Evaluated on two resting-state fMRI (rs-fMRI) MDD datasets, results show that the proposed GAE-FCNN model significantly outperforms several state-of-the-art methods for brain connectome classification, achieving the best accuracy using the LDW-FC edges as node features. The graph embeddings of fMRI FC networks learned by the GAE also reveal apparent group differences between MDD and HC. Our new framework demonstrates feasibility of learning graph embeddings on brain networks to provide discriminative information for diagnosis of brain disorders.

Chee-Ming Ting, Jeremy I. Skipper, Steven L. Small et al.

We consider the challenges in extracting stimulus-related neural dynamics from other intrinsic processes and noise in naturalistic functional magnetic resonance imaging (fMRI). Most studies rely on inter-subject correlations (ISC) of low-level regional activity and neglect varying responses in individuals. We propose a novel, data-driven approach based on low-rank plus sparse (L+S) decomposition to isolate stimulus-driven dynamic changes in brain functional connectivity (FC) from the background noise, by exploiting shared network structure among subjects receiving the same naturalistic stimuli. The time-resolved multi-subject FC matrices are modeled as a sum of a low-rank component of correlated FC patterns across subjects, and a sparse component of subject-specific, idiosyncratic background activities. To recover the shared low-rank subspace, we introduce a fused version of principal component pursuit (PCP) by adding a fusion-type penalty on the differences between the rows of the low-rank matrix. The method improves the detection of stimulus-induced group-level homogeneity in the FC profile while capturing inter-subject variability. We develop an efficient algorithm via a linearized alternating direction method of multipliers to solve the fused-PCP. Simulations show accurate recovery by the fused-PCP even when a large fraction of FC edges are severely corrupted. When applied to natural fMRI data, our method reveals FC changes that were time-locked to auditory processing during movie watching, with dynamic engagement of sensorimotor systems for speech-in-noise. It also provides a better mapping to auditory content in the movie than ISC.

Chee-Ming Ting, S. Balqis Samdin, Meini Tang et al.

We present a unified statistical framework for characterizing community structure of brain functional networks that captures variation across individuals and evolution over time. Existing methods for community detection focus only on single-subject analysis of dynamic networks; while recent extensions to multiple-subjects analysis are limited to static networks. To overcome these limitations, we propose a multi-subject, Markov-switching stochastic block model (MSS-SBM) to identify state-related changes in brain community organization over a group of individuals. We first formulate a multilayer extension of SBM to describe the time-dependent, multi-subject brain networks. We develop a novel procedure for fitting the multilayer SBM that builds on multislice modularity maximization which can uncover a common community partition of all layers (subjects) simultaneously. By augmenting with a dynamic Markov switching process, our proposed method is able to capture a set of distinct, recurring temporal states with respect to inter-community interactions over subjects and the change points between them. Simulation shows accurate community recovery and tracking of dynamic community regimes over multilayer networks by the MSS-SBM. Application to task fMRI reveals meaningful non-assortative brain community motifs, e.g., core-periphery structure at the group level, that are associated with language comprehension and motor functions suggesting their putative role in complex information integration. Our approach detected dynamic reconfiguration of modular connectivity elicited by varying task demands and identified unique profiles of intra and inter-community connectivity across different task conditions. The proposed multilayer network representation provides a principled way of detecting synchronous, dynamic modularity in brain networks across subjects.

Chun-Ren Phang, Chee-Ming Ting, Fuad Noman et al.

We exploit altered patterns in brain functional connectivity as features for automatic discriminative analysis of neuropsychiatric patients. Deep learning methods have been introduced to functional network classification only very recently for fMRI, and the proposed architectures essentially focused on a single type of connectivity measure. We propose a deep convolutional neural network (CNN) framework for classification of electroencephalogram (EEG)-derived brain connectome in schizophrenia (SZ). To capture complementary aspects of disrupted connectivity in SZ, we explore combination of various connectivity features consisting of time and frequency-domain metrics of effective connectivity based on vector autoregressive model and partial directed coherence, and complex network measures of network topology. We design a novel multi-domain connectome CNN (MDC-CNN) based on a parallel ensemble of 1D and 2D CNNs to integrate the features from various domains and dimensions using different fusion strategies. Hierarchical latent representations learned by the multiple convolutional layers from EEG connectivity reveal apparent group differences between SZ and healthy controls (HC). Results on a large resting-state EEG dataset show that the proposed CNNs significantly outperform traditional support vector machine classifiers. The MDC-CNN with combined connectivity features further improves performance over single-domain CNNs using individual features, achieving remarkable accuracy of $93.06\%$ with a decision-level fusion. The proposed MDC-CNN by integrating information from diverse brain connectivity descriptors is able to accurately discriminate SZ from HC. The new framework is potentially useful for developing diagnostic tools for SZ and other disorders.

Fuad Noman, Chee-Ming Ting, Sh-Hussain Salleh et al.

This paper proposes a framework based on deep convolutional neural networks (CNNs) for automatic heart sound classification using short-segments of individual heart beats. We design a 1D-CNN that directly learns features from raw heart-sound signals, and a 2D-CNN that takes inputs of two- dimensional time-frequency feature maps based on Mel-frequency cepstral coefficients (MFCC). We further develop a time-frequency CNN ensemble (TF-ECNN) combining the 1D-CNN and 2D-CNN based on score-level fusion of the class probabilities. On the large PhysioNet CinC challenge 2016 database, the proposed CNN models outperformed traditional classifiers based on support vector machine and hidden Markov models with various hand-crafted time- and frequency-domain features. Best classification scores with 89.22% accuracy and 89.94% sensitivity were achieved by the ECNN, and 91.55% specificity and 88.82% modified accuracy by the 2D-CNN alone on the test set.

Fuad Noman, Sh-Hussain Salleh, Chee-Ming Ting et al.

Objective: This paper considers challenges in developing algorithms for accurate segmentation and classification of heart sound (HS) signals. Methods: We propose an approach based on Markov switching autoregressive model (MSAR) to segmenting the HS into four fundamental components each with distinct second-order structure. The identified boundaries are then utilized for automated classification of pathological HS using the continuous density hidden Markov model (CD-HMM). The MSAR formulated in a state-space form is able to capture simultaneously both the continuous hidden dynamics in HS, and the regime switching in the dynamics using a discrete Markov chain. This overcomes the limitation of HMM which uses a single-layer of discrete states. We introduce three schemes for model estimation: (1.) switching Kalman filter (SKF); (2.) refined SKF; (3.) fusion of SKF and the duration-dependent Viterbi algorithm (SKF-Viterbi). Results: The proposed methods are evaluated on Physionet/CinC Challenge 2016 database. The SKF-Viterbi significantly outperforms SKF by improvement of segmentation accuracy from 71% to 84.2%. The use of CD-HMM as a classifier and Mel-frequency cepstral coefficients (MFCCs) as features can characterize not only the normal and abnormal morphologies of HS signals but also morphologies considered as unclassifiable (denoted as X-Factor). It gives classification rates with best gross F1 score of 90.19 (without X-Factor) and 82.7 (with X-Factor) for abnormal beats. Conclusion: The proposed MSAR approach for automatic localization and detection of pathological HS shows a noticeable performance on large HS dataset. Significance: It has potential applications in heart monitoring systems to assist cardiologists for pre-screening of heart pathologies.