Tri-Clustering Dynamic Functional Network Connectivity Identifies Significant Schizophrenia Effects Across Multiple States in Distinct Subgroups of Individuals

A survey of brain functional network extraction methods using fMRI data

Functional network (FN) analyses play a pivotal role in uncovering insights into brain function and understanding the pathophysiology of various brain disorders. This paper focuses on classical and advanced methods for deriving brain FNs from functional magnetic resonance imaging (fMRI) data. We systematically review their foundational principles, advantages, shortcomings, and interrelations, encompassing both static and dynamic FN extraction approaches. In the context of static FN extraction, we present hypothesis-driven methods such as region of interest (ROI)-based approaches as well as data-driven methods including matrix decomposition, clustering, and deep learning. For dynamic FN extraction, both window-based and windowless methods are surveyed with respect to the estimation of time-varying FN and the subsequent computation of FN states. We also discuss the scope of application of the various methods and avenues for future improvements.

Elucidating salient site-specific functional connectivity features and site-invariant biomarkers in schizophrenia via deep neural networks

Schizophrenia is a highly heterogeneous disorder and salient functional connectivity (FC) features have been observed to vary across study sites, warranting the need for methods that can differentiate between site-invariant FC biomarkers and site-specific salient FC features. We propose a technique named Semi-supervised learning with data HaRmonisation via Encoder-Decoder-classifier (SHRED) to examine these features from resting state functional magnetic resonance imaging scans gathered from four sites. Our approach involves an encoder-decoder-classifier architecture that simultaneously performs data harmonisation and semi-supervised learning (SSL) to deal with site differences and labelling inconsistencies across sites respectively. The minimisation of reconstruction loss from SSL was shown to improve model performance even within small datasets whilst data harmonisation often led to lower model generalisability, which was unaffected using the SHRED technique. We show that our proposed model produces site-invariant biomarkers, most notably the connection between transverse temporal gyrus and paracentral lobule. Site-specific salient FC features were also elucidated, especially implicating the paracentral lobule for our local dataset. Our examination of these salient FC features demonstrates how site-specific features and site-invariant biomarkers can be differentiated, which can deepen our understanding of the neurobiology of schizophrenia.

Auto-Classification of Parkinson's Disease with Different Motor Subtypes Using Arterial Spin Labelling MRI Based on Machine Learning

The purpose of this study was to automatically classify different motor subtypes of Parkinson's disease (PD) on arterial spin labelling magnetic resonance imaging (ASL-MRI) data using support vector machine (SVM). This study included 38 subjects: 21 PD patients and 17 normal controls (NCs). Based on the Unified Parkinson's Disease Rating Scale (UPDRS) subscores, patients were divided into the tremor-dominant (TD) subtype and the postural instability gait difficulty (PIGD) subtype. The subjects were in a resting state during the acquisition of ASL-MRI data. The automated anatomical atlas 3 (AAL3) template was registered to obtain an ASL image of the same size and shape. We obtained the voxel values of 170 brain regions by considering the location coordinates of these regions and then normalized the data. The length of the feature vector depended on the number of voxel values in each brain region. Three binary classification models were utilized for classifying subjects' data, and we applied SVM to classify voxels in the brain regions. The left subgenual anterior cingulate cortex (ACC_sub_L) was clearly distinguished in both NCs and PD patients using SVM, and we obtained satisfactory diagnostic rates (accuracy = 92.31%, specificity = 96.97%, sensitivity = 84.21%, and AUCmax = 0.9585). For the right supramarginal gyrus (SupraMarginal_R), SVM distinguished the TD group from the other groups with satisfactory diagnostic rates (accuracy = 84.21%, sensitivity = 63.64%, specificity = 92.59%, and AUCmax = 0.9192). For the right intralaminar of thalamus (Thal_IL_R), SVM distinguished the PIGD group from the other groups with satisfactory diagnostic rates (accuracy = 89.47%, sensitivity = 70.00%, specificity = 6.43%, and AUCmax = 0.9464). These results are consistent with the changes in blood perfusion related to PD subtypes. In addition, the sensitive brain regions of the TD group and PIGD group involve the brain regions where the cerebellothalamocortical (CTC) and the striatal thalamocortical (STC) loops are located. Therefore, it is suggested that the blood perfusion patterns of the two loops may be different. These characteristic brain regions could become potential imaging markers of cerebral blood flow to distinguish TD from PIGD. Meanwhile, our findings provide an imaging basis for personalised treatment, thereby optimising clinical diagnostic and treatment approaches.

Current Approaches in Computational Psychiatry for the Data-Driven Identification of Brain-Based Subtypes

The ability of our current psychiatric nosology to accurately delineate clinical populations and inform effective treatment plans has reached a critical point with only moderately successful interventions and high relapse rates. These challenges continue to motivate the search for approaches to better stratify clinical populations into more homogeneous delineations, to better inform diagnosis and disease evaluation, and prescribe and develop more precise treatment plans. The promise of brain-based subtyping based on neuroimaging data is that finding subgroups of individuals with a common biological signature will facilitate the development of biologically grounded, targeted treatments. This review provides a snapshot of the current state of the field in empirical brain-based subtyping studies in child, adolescent, and adult psychiatric populations published between 2019 and March 2022. We found that there is vast methodological exploration and a surprising number of new methods being created for the specific purpose of brain-based subtyping. However, this methodological exploration and advancement is not being met with rigorous validation approaches that assess both reproducibility and clinical utility of the discovered brain-based subtypes. We also found evidence for a collaboration crisis, in which methodological exploration and advancements are not clearly grounded in clinical goals. We propose several steps that we believe are crucial to address these shortcomings in the field. We conclude, and agree with the authors of the reviewed studies, that the discovery of biologically grounded subtypes would be a significant advancement for treatment development in psychiatry.

Abnormal dynamic functional network connectivity in first-episode, drug-naïve patients with major depressive disorder

Dynamic functional network connectivity (dFNC) could capture temporal features of spontaneous brain activity during MRI scanning, and it might be a powerful tool to examine functional brain network alters in major depressive disorder (MDD). Therefore, this study investigated the changes in temporal properties of dFNC of first-episode, drug-naïve patients with MDD. A total of 48 first-episode, drug-naïve MDD patients and 46 age- and gender-matched healthy controls were recruited in this study. Sliding windows were implied to construct dFNC. We assessed the relationships between altered dFNC temporal properties and depressive symptoms. Receiver operating characteristic (ROC) curve analyses were used to examine the diagnostic performance of these altered temporal properties. The results showed that patients with MDD have more occurrences and spent more time in a weak connection state, but with fewer occurrences and shorter dwell time in a strong connection state. Importantly, the fractional time and mean dwell time of state 2 was negatively correlated with Hamilton Depression Rating Scale (HDRS) scores. ROC curve analysis demonstrated that these temporal properties have great identified power including the fractional time and mean dwell time in state 2, and the AUC is 0.872, 0.837, respectively. The AUC of the combination of fractional time and mean dwell time in state 2 with age, gender is 0.881. Our results indicated the temporal properties of dFNC are altered in first-episode, drug-naïve patients with MDD, and these changes' properties could serve as a potential biomarker in MDD.

Neuroimaging biomarkers for detecting schizophrenia: A resting-state functional MRI-based radiomics analysis

Schizophrenia (SZ) is a common psychiatric disorder that is difficult to accurately diagnose in clinical practice. Quantifiable biomarkers are urgently required to explore the potential physiological mechanism of SZ and improve its diagnostic accuracy. Thus, this study aimed to identify biomarkers that classify SZ patients and healthy control subjects and investigate the potential neural mechanisms of SZ using degree centrality (DC)- and voxel-mirrored homotopic connectivity (VMHC)-based radiomics. Radiomics features were extracted from DC and VMHC metrics generated via resting-state functional magnetic resonance imaging, and significant features were selected and dimensionality was reduced using t-tests and least absolute shrinkage and selection operator. Subsequently, we built our model using a support vector machine classifier. We observed that our method obtained great classification performance (area under the curve, 0.808; accuracy, 74.02%), and it could be generalized to different brain atlases. The regions that we identified as discriminative features mainly included bilateral dorsal caudate and front-parietal, somatomotor, limbic, and default mode networks. Our findings showed that the radiomics-based machine learning method could facilitate us to understand the potential pathological mechanism of SZ more comprehensively and contribute to the accurate diagnosis of patients with SZ.

Statelets: Capturing recurrent transient variations in dynamic functional network connectivity

Dynamic functional network connectivity (dFNC) analysis is a widely used approach for capturing brain activation patterns, connectivity states, and network organization. However, a typical sliding window plus clustering (SWC) approach for analyzing dFNC models the system through a fixed sequence of connectivity states. SWC assumes connectivity patterns span throughout the brain, but they are relatively spatially constrained and temporally short‐lived in practice. Thus, SWC is neither designed to capture transient dynamic changes nor heterogeneity across subjects/time. We propose a state‐space time series summarization framework called “statelets” to address these shortcomings. It models functional connectivity dynamics at fine‐grained timescales, adapting time series motifs to changes in connectivity strength, and constructs a concise yet informative representation of the original data that conveys easily comprehensible information about the phenotypes. We leverage the earth mover distance in a nonstandard way to handle scale differences and utilize kernel density estimation to build a probability density profile for local motifs. We apply the framework to study dFNC of patients with schizophrenia (SZ) and healthy control (HC). Results demonstrate SZ subjects exhibit reduced modularity in their brain network organization relative to HC. Statelets in the HC group show an increased recurrence across the dFNC time‐course compared to the SZ. Analyzing the consistency of the connections across time reveals significant differences within visual, sensorimotor, and default mode regions where HC subjects show higher consistency than SZ. The introduced approach also enables handling dynamic information in cross‐modal and multimodal applications to study healthy and disordered brains.