Biology subjects

Sendi, M. S. E.

Publications and source records attributed to Sendi, M. S. E..

15 recordsLinked to original sources

bioRxiv2026

From micro-architecture to networks: canonical neurobiological architecture of functional brain organization across the lifespan and in psychopathology

Understanding how macroscale functional network connectivity (FNC) across the lifespan and in psychopathology is spatially organized with respect to microscale neurobiological architecture remains a challenge. Here, we constructed a cross-omics mapping framework by linking resting-state fMRI data (5,349 individuals, 6-80 years) with 49 neurobiological markers (24 cell types, 19 neurotransmitters, 6 mitochondria). We show that FNC development and aging unfold along cellular and molecular gradients. Specifically, spatial correspondence between age-related FNC changes and neurobiological microprofile networks varied by life stage, peaking for cell types in adolescence, neurotransmitter systems in mid-young adulthood and mitochondrial phenotypes in early adulthood. Applying normative modeling to 5 psychiatric disorders (schizophrenia, bipolar disorder, major depressive disorder, autism, and attention-deficit/hyperactivity disorder), we identified disorder-specific and cross-disorder FNC phenotypes spatially associated with neurobiological architecture. Together, these findings provide a hypothesis-generating framework linking functional brain organization and dysfunction to canonical neurobiological architecture across the lifespan and psychiatric disorders.

neuroscience↗

bioRxiv2025

Diagnosis-Optimized Dynamic Feature Learning Reveals Altered Default Mode Network Connectivity in Schizophrenia

Schizophrenia (SZ) is characterized by widespread neural dysconnectivity, with particularly pronounced alterations in the default mode network (DMN)--a set of brain regions involved in self-referential thought and mind-wandering. We investigated dynamic functional connectivity within the DMN in SZ by analyzing resting-state fMRI data from two independent cohorts (FBIRN and COBRE). Using a novel iterative feature-removal clustering approach focusing on DMN independent components, we identified distinct recurring connectivity states while iteratively removing dominant connectivity features to reveal subtler network patterns. This approach iteratively refines the set of features considered, ensuring a more balanced representation and facilitating the identification of significant interactions that would otherwise be overlooked. Cluster centroids for the four connectivity states were highly similar across both datasets, reflecting stable shared DMN patterns. State occupancy was compared between participants with SZ and healthy controls, and associations with clinical symptom severity were examined. The SZ group exhibited significant alterations in DMN connectivity dynamics, spending more time than controls in certain connectivity states characterized by atypical DMN coupling and less time in a state reflecting a normative DMN configuration. A comparison between the FBIRN and COBRE datasets reveals both similarities and differences in occupancy rate (OCR) states. Overall, the pattern of group effects converged while state-specific divergences likely reflected protocol/sample differences rather than conflicting biology. Crucially, the explainability pipeline yielded a highly similar feature-removal order across datasets, indicating that the same DMN edges drive the diagnostic signal in both cohorts. Several OCR effects also tracked symptom ratings, linking abnormal DMN dynamics to clinical expression. Our findings suggest that SZ is characterized by reproducible disturbances in the temporal organization of DMN connectivity. These dynamic DMN features may serve as potential biomarkers for SZ, offering diagnostic and clinical utility by capturing network dysfunction that static connectivity measures could overlook.

neuroscience↗

bioRxiv2024

Visualizing Functional Network Connectivity Differences Using an Explainable Machine-learning Method

Functional network connectivity (FNC) estimated from resting-state functional magnetic resonance imaging showed great information about the neural mechanism in different brain disorders. But previous research has mainly focused on standard statistical learning approaches to find FNC features separating patients from control. Although machine learning approaches provide better models separating controls from patients, it is not straightforward for these approaches to provide intuition on the model and the underlying neural process of each disorder. Explainable machine learning offers a solution to this problem by applying machine learning to understand the neural process behind brain disorders. In this study, we introduce a novel framework leveraging SHapley Additive exPlanations (SHAP) to identify crucial Functional Network Connectivity (FNC) features distinguishing between two distinct population classes. Initially, we validate our approach using synthetic data. Subsequently, applying our framework, we ascertain FNC biomarkers distinguishing between, controls and schizophrenia patients with accuracy of 81.04% as well as middle aged adults and old aged adults with accuracy 71.38%, respectively, employing Random Forest (RF), XGBoost, and CATBoost models. Our analysis underscores the pivotal role of the cognitive control network (CCN), subcortical network (SCN), and somatomotor network (SMN) in discerning individuals with schizophrenia from controls. In addition, our platform found CCN and SCN as the most important networks separating young adults from older.

neuroscience↗

bioRxiv2024

Uncovering Effects of Schizophrenia upon a Maximally Significant, Minimally Complex Subset of Default Mode Network Connectivity Features

A common analysis approach for resting state functional magnetic resonance imaging (rs-fMRI) dynamic functional network connectivity (dFNC) data involves clustering windowed correlation time-series and assigning time windows to clusters (i.e., states) that can be quantified to summarize aspects of the dFNC dynamics. However, those methods can be dominated by a select few features and obscure key dynamics related to less dominant features. This study presents an iterative feature learning approach to identify a maximally significant and minimally complex subset of dFNC features within the default mode network (DMN) in schizophrenia (SZ). Utilizing dFNC data from individuals with SZ and healthy controls (HC), our approach uncovers a subset of features that has a greater number of dFNC states with disorder-related dynamics than is found when all features are present in the clustering. We find that anterior cingulate cortex/posterior cingulate cortex (ACC/PCC) interactions are consistently related to SZ across the most significant iterations of the feature learning analysis and that individuals with SZ tend to spend more time in states with greater intra-ACC anticorrelation and almost no time in a state of high intra-ACC correlation that HCs periodically enter. Our findings highlight the need for nuanced analyses to reveal disorder-related dynamics and advance our understanding of neuropsychiatric disorders.

neuroscience↗

bioRxiv2022

iSparse kmeans: a two-step clustering approach for big dynamic functional network connectivity data

BackgroundDynamic functional network connectivity (dFNC) estimated from resting-state functional magnetic imaging (rs-fMRI) studies the temporally varying of functional integration between brain networks. In a typical dFNC pipeline, a clustering stage to summarize the connectivity patterns that are transiently but reliably realized over the course of a scanning session. However, identifying the right number of clusters through a conventional clustering criterion computed by running the algorithm repeatedly, over a large range of cluster numbers is time-consuming and requires substantial computational power even for typical dFNC datasets, and the computational demands become prohibitive as datasets become larger and scans longer. Here we developed a new dFNC pipeline, called iterative sparse kmeans or iSparse kmeans, to analyze large dFNC data without having access to huge computational power. MethodIn iSparse kmeans, we implement two-step clustering. In the first step, we randomly use a sub-sample dFNC data and identify several sets of states at different model orders. In the second step, we aggregate all dFNC states estimated from all iterations in the first step and use this to identify the optimum number of clusters using the elbow criteria. Additionally, we use this new reduced dataset and estimate a final set of states by performing a second kmeans clustering on the aggregated dFNC states from the first k-means clustering. To validate the reproducibility of iSparse kmeans, we analyzed four dFNC datasets from the human connectome project (HCP). ResultsWe found that both conventional kmeans and iSparse kmeans generate similar brain dFNC states while iSparse kmeans is 27 times faster than the traditional method in finding the optimum number of clusters. We show that the results are replicated across four different datasets from HCP. ConclusionWe developed a new analytic pipeline which facilitates analysis of large dFNC datasets without having access to a huge computational power source. We validated the reproducibility of the result across multiple datasets.

bioinformatics↗

bioRxiv2022

Overlap across psychotic disorders: A functional network connectivity analysis

Functional network connectivity has previously been shown to distinguish patient groups from healthy controls (HC). However, the overlap across schizophrenia (SZ), bipolar (BP), and schizoaffective disorder (SAD) is not clear yet. This study focuses on finding overlap across these three psychotic disorders using dynamic FNC (dFNC) and compares it with static FNC (sFNC). We used resting-state fMRI, demographics, and clinical information from the Bipolar- Schizophrenia Network on Intermediate Phenotypes cohort. The data includes three groups of patients with schizophrenia (SZP, N=102), bipolar (BPP, N=102), and schizoaffective (SADP, N=102), their relatives SZR (N=102), BPR (N=102), SADR (N=102), and HC (N=118) groups. After estimating each individuals dFNC, we put them into three identical states. We estimated five different features, including occupancy rate (OCR), number of transitions, the total number of transitions, and the total distance traveled. Finally, the extracted features are tested statistically across patients and HC groups. In addition, we explored the link between the clinical scores and the extracted features. We found that the OCR difference between SZP and SZR in state2, between BPP and HC in state1, and between SADP and HC in state2. Also, state2 OCR separates SZP from BPP, state 3 OCR separates BPP from SZP and SADP. Moreover, the OCR and traveled distance feature extracted from SZ and BP could significantly predict PANSS Total and PANSS General scores. Finally, combined distance features of all disorders showed a significant relationship to PANSS Total and PANSS General scores.

neuroscience↗

bioRxiv2021

A Novel Activation Maximization-based Approach for Insight into Electrophysiology Classifiers

Spectral analysis remains a hallmark approach for gaining insight into electrophysiology modalities like electroencephalography (EEG). As the field of deep learning has progressed, more studies have begun to train deep learning classifiers on raw EEG data, which presents unique problems for explainability. A growing number of studies have presented explainability approaches that provide insight into the spectral features learned by deep learning classifiers. However, existing approaches only attribute importance to different frequency bands. Most of the methods cannot provide insight into the actual spectral values or the relationship between spectral features that models have learned. Here, we present a novel adaptation of activation maximization for electrophysiology time-series that generates samples that indicate the features learned by classifiers by optimizing their spectral content. We evaluate our approach within the context of EEG sleep stage classification with a convolutional neural network, and we find that our approach is able to identify spectral patterns known to be associated with each sleep stage. We also find surprising results suggesting that our classifier may have prioritized the use of eye and motion artifact when identifying Awake samples. Our approach is the first adaptation of activation maximization to the domain of raw electrophysiology classification. Additionally, our approach has implications for explaining any classifier trained on highly dynamic, long time-series.

bioinformatics↗

bioRxiv2021

A Gradient-based Spectral Explainability Method for EEG Deep Learning Classifiers

The automated feature extraction capabilities of deep learning classifiers have promoted their broader application to EEG analysis. In contrast to earlier machine learning studies that used extracted features and traditional explainability approaches, explainability for classifiers trained on raw data is particularly challenging. As such, studies have begun to present methods that provide insight into the spectral features learned by deep learning classifiers trained on raw EEG. These approaches have two key shortcomings. (1) They involve perturbation, which can create out-of-distribution samples that cause inaccurate explanations. (2) They are global, not local. Local explainability approaches can be used to examine how demographic and clinical variables affected the patterns learned by the classifier. In our study, we present a novel local spectral explainability approach. We apply it to a convolutional neural network trained for automated sleep stage classification. We apply layer-wise relevance propagation to identify the relative importance of the features in the raw EEG and subsequently examine the frequency domain of the explanations to determine the importance of each canonical frequency band locally and globally. We then perform a statistical analysis to determine whether age and sex affected the patterns learned by the classifier for each frequency band and sleep stage. Results showed that {delta}, {beta}, and {gamma} were the overall most important frequency bands. In addition, age and sex significantly affected the patterns learned by the classifier for most sleep stages and frequency bands. Our study presents a novel spectral explainability approach that could substantially increase the level of insight into classifiers trained on raw EEG.

bioinformatics↗

bioRxiv2021

A Novel Local Ablation Approach for Explaining Multimodal Classifiers

With the growing use of multimodal data for deep learning classification in healthcare research, more studies have begun to present explainability methods for insight into multimodal classifiers. Among these studies, few have utilized local explainability methods, which could provide (1) insight into the classification of each sample and (2) an opportunity to better understand the effects of demographic and clinical variables within datasets (e.g., medication of subjects in electrophysiology data). To the best of our knowledge, this opportunity has not yet been explored within multimodal classification. We present a novel local ablation approach that shows the importance of each modality to the correct classification of each class and explore the effects of demographic and clinical variables upon the classifier. As a use-case, we train a convolutional neural network for automated sleep staging with electroencephalogram (EEG), electrooculogram (EOG), and electromyogram (EMG) data. We find that EEG is the most important modality across most stages, though EOG is particular important for non-rapid eye movement stage 1. Further, we identify significant relationships between the local explanations and subject age, sex, and state of medication which suggest that the classifier learned specific features associated with these variables across multiple modalities and correctly classified samples. Our novel explainability approach has implications for many fields involving multimodal classification. Moreover, our examination of the degree to which demographic and clinical variables may affect classifiers could provide direction for future studies in automated biomarker discovery.

bioinformatics↗

bioRxiv2021

Dynamic functional connectivity links with treatment response of electroconvulsive therapy in major depressive disorder

BackgroundElectroconvulsive Therapy (ECT) is one of the most effective treatments for major depressive disorder (DEP). There is recently increasing attention to evaluate ECTs effect on resting-state functional magnetic resonance imaging (rs-fMRI). This study aims to compare rs-fMRI of DEP patients with healthy participants, investigate whether dynamic functional network connectivity network (dFNC) estimated from rs-fMRI predicts the ECT outcome, and explore the effect of ECT on brain network states. MethodResting-state fMRI data were collected from 119 patients with depression or DEP (76 females), and 61 Healthy (HC) participants (34 females) with an age mean of 52.25 (N=180) years old. The pre-ECT and post-ECT Hamilton Depression Rating Scale (HDRS) were 25.59{+/-}6.14 and 11.48{+/-}9.07, respectively. Twenty-four independent components from default mode (DMN) and cognitive control network (CCN) were extracted using group-independent component analysis from pre-ECT and post-ECT rs-fMRI. Then, the sliding window approach was used to estimate the pre-and post-ECT dFNC of each participant. Next, k-means clustering was separately applied to pre-ECT dFNC and post-ECT dFNC to assess three distinct states from each participant. We calculated the amount of time each individual spends in each state, called occupancy rate or OCR. Next, we compared OCR values between HC and DEP participants. We also calculated the partial correlation between pre-ECT OCRs and HDRS change while controlling for age, gender, number of treatment, and site. Finally, we evaluated the effectiveness of ECT by comparing pre-and post-ECT OCR of DEP and HC participants. ResultsThe main findings include: 1) DEP patients had significantly lower OCR values than the HC group in a state, where connectivity between CCN and DMN was relatively higher than other states (corrected p= 0.015), 2) Pre-ECT OCR of state, with more negative connectivity between CCN and DMN components, predicted the HDRS changes (R=0.23 corrected p=0.03). This means that those DEP patients who spend less time in this state showed more HDRS change, and 3) The post-ECT OCR analysis suggested that ECT increased the amount of time DEP patients spend in state 2 (corrected p=0.03). Finally, we found ECT increases the total traveled distance in DEP. ConclusionOur finding suggests that dFNC features, estimated from CCN and DMN, show promise as a predictive biomarker of the ECT outcome of DEP patients. Also, this study identified a possible underlying mechanism associated with the ECT effect in DEP patients.

neuroscience↗

bioRxiv2021

The link between static and dynamic brain functional network connectivity and genetic risk of Alzheimer's disease

Apolipoprotein E (APOE) polymorphic alleles are genetic factors associated with Alzheimers disease (AD) risk. Although previous studies have explored the link between AD genetic risk and static functional network connectivity (sFNC), to the best of our knowledge, no previous studies have evaluated the association between dynamic FNC (dFNC) and AD genetic risk. Here, we examined the link between sFNC, dFNC, and AD genetic risk with a reproducible, data-driven approach. We used rs-fMRI, demographic, and APOE data from cognitively normal individuals (N=894) between 42 to 95 years of age (mean = 70 years). We divided individuals into low, moderate, and high-risk groups. Using Pearson correlation, we calculated sFNC across seven brain networks. We also calculated dFNC with a sliding window and Pearson correlation. The dFNC windows were partitioned into three distinct states with k-means clustering. Next, we calculated the amount of time each subject spent in each state, called occupancy rate or OCR. We compared both sFNC and OCR, estimated from dFNC, across individuals with different genetic risk and found that both sFNC and dFNC are related to AD genetic risk. We found that higher AD risk reduces within-visual sensory network (VSN) sFNC and that individuals with higher AD risk spend more time in a state with lower within-VSN dFNC. Additionally, we found that AD genetic risk affects whole-brain sFNC and dFNC in women but not in men. In conclusion, we presented novel insights into the links between sFNC, dFNC, and AD genetic risk.

neuroscience↗

bioRxiv2021

The relationship between dynamic functional network connectivity and spatial orientation in healthy young adults

Spatial orientation is essential to interacting with a physical environment, and better understanding it could contribute to a better understanding of a variety of diseases and disorders that are characterized by deficits in spatial orientation. Many previous studies have focused on the relationship between spatial orientation and individual brain regions, though in recent years studies have begun to examine spatial orientation from a network perspective. This study analyzes dynamic functional network connectivity (dFNC) values extracted from over 800 resting-state fMRI recordings of healthy young adults (age 22-37 years) and applies unsupervised machine learning methods to identify neural brain states that occur across all subjects. We estimated the occupancy rate (OCR) for each subject, which was proportional to the amount of time that they spent in each state, and investigated the link between the OCR and spatial orientation and the state-specific FNC values and spatial orientation controlling for age and sex. Our findings showed that the amount of time subjects spent in a state characterized by increased connectivity within and between visual, auditory, and sensorimotor networks and within the default mode network while at rest corresponded to their performance on tests of spatial orientation. We also found that increased sensorimotor network connectivity in two of the identified states negatively correlated with decreased spatial orientation, further highlighting the relationship between the sensorimotor network and spatial orientation. This study provides insight into how the temporal properties of the functional brain connectivity within and between key brain networks may influence spatial orientation.

neuroscience↗

bioRxiv2021

Aberrant Dynamic Functional Connectivity of Default Mode Network in Schizophrenia and Links to Symptom Severity

BackgroundSchizophrenia affects around 1% of the global population. Functional connectivity extracted from resting-state functional magnetic resonance imaging (rs-fMRI) has previously been used to study schizophrenia and has great potential to provide novel insights into the disorder. Some studies have shown abnormal functional connectivity in the default mode network of individuals with schizophrenia, and more recent studies have shown abnormal dynamic functional connectivity (dFC) in individuals with schizophrenia. However, DMN dFC and the link between abnormal DMN dFC and symptom severity have not been well characterized. MethodResting-state fMRI data from subjects with schizophrenia (SZ) and healthy controls (HC) across two datasets were analyzed independently. We captured seven maximally independent subnodes in the DMN by applying group independent component analysis and estimated dFC between subnode time courses using a sliding window approach. A clustering method separated the dFCs into five reoccurring brain states. A feature selection method modeled the difference between SZs and HCs using the state-specific FC features. Finally, we used the transition probability of a hidden Markov model to characterize the link between symptom severity and dFC in SZ subjects. ResultsWe found decreases in the connectivity of the anterior cingulate cortex (ACC) and increases in the connectivity between the precuneus (PCu) and the posterior cingulate cortex (PCC) (i.e., PCu/PCC) of SZ subjects. In SZ, the transition probability from a state with weaker PCu/PCC and stronger ACC connectivity to a state with stronger PCu/PCC and weaker ACC connectivity increased with symptom severity. ConclusionsTo our knowledge, this was the first study to investigate DMN dFC and its link to schizophrenia symptom severity. We identified reproducible neural states in a data-driven manner and demonstrated that the strength of connectivity within those states differed between SZs and HCs. Additionally, we identified a relationship between SZ symptom severity and the dynamics of DMN functional connectivity. We validated our results across two datasets. These results support the potential of dFC for use as a biomarker of schizophrenia and shed new light upon the relationship between schizophrenia and DMN dynamics.

neuroscience↗

bioRxiv2021

Disrupted dynamic functional network connectivity among cognitive control networks in the progression of Alzheimer's disease

BackgroundAlzheimers disease (AD) is the most common age-related dementia that promotes a decline in memory, thinking, and social skills. The initial stages of dementia can be associated with mild symptoms, and symptom progression to a more severe state is heterogeneous across patients. Recent work has demonstrated the potential for functional network mapping to assist in the prediction of symptomatic progression. However, this work has primarily used static functional connectivity (sFC) from rs-fMRI. Recently, dynamic functional connectivity (dFC) has been recognized as a powerful advance in functional connectivity methodology to differentiate brain network dynamics between healthy and diseased populations. MethodsGroup independent component analysis was applied to extract 17 components within the cognitive control network (CCN) from 1385 individuals across varying stages of AD symptomology. We estimated dFC among 17 components within the CCN, followed by clustering the dFCs into 3 recurring brain states and then estimated a hidden Markov model and the occupancy rate for each subject. Finally, we investigated the link between CCN dFC connectivity features with AD progression. ResultsProgression of AD symptoms were associated with increases in connectivity within the middle frontal gyrus. Also, the AD with mild and severer symptoms showed less connectivity within the inferior parietal lobule and between this region with the rest of CCN. Finally, comparing with mild dementia, we found that the normal brain spends significantly more time in a state with lower within middle frontal gyrus connectivity and higher connectivity between the hippocampus and the rest of CCN, highlighting the importance of assessing the dynamics of brain connectivity in this disease. ConclusionOur results suggest that AD progress not only alters the CCN connectivity strength but also changes the temporal properties in this brain network. This suggests the temporal and spatial pattern of CCN as a biomarker that differentiates different stages of AD. Impact StatementBy assuming that functional connectivity is static over time, many of previous studies have ignored the brain dynamic in Alzheimers disease progression. Here, a longitudinal resting-state functional magnetic resonance imaging data are used to explore the temporal changes of functional connectivity in the cognitive control network in Alzheimers disease progression. The result of this study would increase our understanding about the underlying mechanisms of Alzheimers Disease and help in finding future treatment of this neurological disorder.

neuroscience↗

bioRxiv2020

Multiple overlapping dynamic patterns of the visual sensory network in schizophrenia

Although visual processing impairments have been explored in schizophrenia (SZ), their underlying neurobiology of the visual processing impairments has not been widely studied. Also, while some research has hinted at differences in information transfer and flow in SZ, there are few investigations of the dynamics of functional connectivity within visual networks. In this study, we analyzed resting-state fMRI data of the visual sensory network (VSN) in 160 healthy control (HC) subjects and 151 SZ subjects. We estimated 9 independent components within the VSN. Then, we calculated the dynamic functional network connectivity (dFNC) using the Pearson correlation. Next, using k-means clustering, we partitioned the dFNCs into five distinct states, and then we calculated the portion of time each subject spent in each state, that we termed the occupancy rate (OCR). Using OCR, we compared HC with SZ subjects and investigated the link between OCR and visual learning in SZ subjects. Besides, we compared the VSN functional connectivity of SZ and HC subjects in each state. We found that this network is indeed highly dynamic. Each state represents a unique connectivity pattern of fluctuations in VSN FNC, and all states showed significant disruption in SZ. Overall, HC showed stronger connectivity within the VSN in states. SZ subjects spent more time in a state in which the connectivity between the middle temporal gyrus and other regions of VNS is highly negative. Besides, OCR in a state with strong positive connectivity between middle temporal gyrus and other regions correlated significantly with visual learning scores in SZ.

neuroscience↗