Searching for optimal machine learning model to classify mild cognitive impairment (MCI) subtypes using multimodal MRI data

Exploring intricate connectivity patterns for cognitive functioning and neurological disorders: incorporating frequency-domain NC method into fMRI analysis

This study extends the application of the frequency-domain new causality method to functional magnetic resonance imaging analysis. Strong causality, weak causality, balanced causality, cyclic causality, and transitivity causality were constructed to simulate varying degrees of causal associations among multivariate functional-magnetic-resonance-imaging blood-oxygen-level-dependent signals. Data from 1,252 groups of individuals with different degrees of cognitive impairment were collected. The frequency-domain new causality method was employed to construct directed efficient connectivity networks of the brain, analyze the statistical characteristics of topological variations in brain regions related to cognitive impairment, and utilize these characteristics as features for training a deep learning model. The results demonstrated that the frequency-domain new causality method accurately detected causal associations among simulated signals of different degrees. The deep learning tests also confirmed the superior performance of new causality, surpassing the other three methods in terms of accuracy, precision, and recall rates. Furthermore, consistent significant differences were observed in the brain efficiency networks, where several subregions defined by the multimodal parcellation method of Human Connectome Project simultaneously appeared in the topological statistical results of different patient groups. This suggests a significant association between these fine-grained cortical subregions, driven by multimodal data segmentation, and human cognitive function, making them potential biomarkers for further analysis of Alzheimer's disease.

Clinical variables contributing to the identification of biologically defined subgroups within cognitively unimpaired and mild cognitive impairment individuals

BACKGROUND

A lack of consensus exists in linking demographic, behavioral, and cognitive characteristics to biological stages of dementia, defined by the ATN (amyloid, tau, neurodegeneration) classification incorporating amyloid, tau, and neuronal injury biomarkers.

METHODS

Using a random forest classifier we investigated whether 27 demographic, behavioral, and cognitive characteristics allowed distinction between ATN-defined groups with the same cognitive profile. This was done separately for three cognitively unimpaired (CU) (112 A-T-N-; 46 A+T+N+/-; 65 A-T+/-N+/-) and three mild cognitive impairment (MCI) (128 A-T-N-; 223 A+T+N+/-; 94 A-T+/-N+/-) subgroups.

RESULTS

Classification-balanced accuracy reached 39% for the CU and 52% for the MCI subgroups. Logical Delayed Recall (explaining 16% of the variance), followed by the Alzheimer's Disease Assessment Scale 13 (14%) and Everyday Cognition Informant (10%), were the most relevant characteristics for classification of the MCI subgroups. Race and ethnicity, marital status, and Everyday Cognition Patient were not relevant (0%).

CONCLUSIONS

The demographic, behavioral, and cognitive measures used in our model were not informative in differentiating ATN-defined CU profiles. Measures of delayed memory, general cognition, and activities of daily living were the most informative in differentiating ATN-defined MCI profiles; however, these measures alone were not sufficient to reach high classification performance.

Atrophy of the cholinergic regions advances from early to late mild cognitive impairment

PURPOSE

We investigated the volumetric changes in the components of the cholinergic pathway for patients with early mild cognitive impairment (EMCI) and those with late mild cognitive impairment (LMCI). The effect of patients' apolipoprotein 4 (APOE-ε4) allele status on the structural changes were analyzed.

METHODS

Structural magnetic resonance imaging data were collected. Patients' demographic information, plasma data, and validated global cognitive composite scores were included. Relevant features were extracted for constructing machine learning models to differentiate between EMCI (n = 312) and LMCI (n = 541) and predict patients' neurocognitive function. The data were analyzed primarily through one-way analysis of variance and two-way analysis of covariance.

RESULTS

Considerable differences were observed in cholinergic structural changes between patients with EMCI and LMCI. Cholinergic atrophy was more prominent in the LMCI cohort than in the EMCI cohort (P < 0.05 family-wise error corrected). APOE-ε4 differentially affected cholinergic atrophy in the LMCI and EMCI cohorts. For LMCI cohort, APOE-ε4 carriers exhibited increased brain atrophy (left amygdala: P = 0.001; right amygdala: P = 0.006, and right Ch123, P = 0.032). EMCI and LCMI patients showed distinctive associations of gray matter volumes in cholinergic regions with executive (R2 = 0.063 and 0.030 for EMCI and LMCI, respectively) and language (R2 = 0.095 and 0.042 for EMCI and LMCI, respectively) function.

CONCLUSIONS

Our data confirmed significant cholinergic atrophy differences between early and late stages of mild cognitive impairment. The impact of the APOE-ε4 allele on cholinergic atrophy varied between the LMCI and EMCI groups.

Exploring brain effective connectivity of early MCI with GRU_GC model on resting-state fMRI

BACKGROUND

Investigating the functional interactions between different brain regions and revealing the transmission of information by computing brain connectivity have great potential and significance in the diagnosis of early Mild Cognitive Impairment (EMCI).

METHODS

The Granger causality with Gate Recurrent Unit (GRU_GC) model is a suitable method that allows the detection of a nonlinear causal relationship and solves the limitation of fixed time lag, which cannot be detected by the classical Granger method. The model can transmit time series signals with any transmission delay length, and the time series can be screened and learned through the gate model.

RESULTS

The classification experiment of 89 EMCI and 73 neurologically healthy controls (HC) shows that the accuracy reached 87.88%. Compared with multivariate variables GC (MVGC) and Long Short-Term Memory-based GC (LSTM_GC), the GRU_GC significantly improved the estimation of brain connectivity communication. Constructing a difference network to explore the brain effective connectivity between EMCI and HC.

CONCLUSIONS

The GRU_GC can discover the abnormal brain regions, including the parahippocampal gyrus, the posterior cingulate gyrus. The method can be used in clinical applications as an effective brain connectivity analysis tool and provides auxiliary means for the medical diagnosis of EMCI.

Subject classification and cross-time prediction based on functional connectivity and white matter microstructure features in a rat model of Alzheimer's using machine learning

BACKGROUND

The pathological process of Alzheimer's disease (AD) typically takes decades from onset to clinical symptoms. Early brain changes in AD include MRI-measurable features such as altered functional connectivity (FC) and white matter degeneration. The ability of these features to discriminate between subjects without a diagnosis, or their prognostic value, is however not established.

METHODS

The main trigger mechanism of AD is still debated, although impaired brain glucose metabolism is taking an increasingly central role. Here, we used a rat model of sporadic AD, based on impaired brain glucose metabolism induced by an intracerebroventricular injection of streptozotocin (STZ). We characterized alterations in FC and white matter microstructure longitudinally using functional and diffusion MRI. Those MRI-derived measures were used to classify STZ from control rats using machine learning, and the importance of each individual measure was quantified using explainable artificial intelligence methods.

RESULTS

Overall, combining all the FC and white matter metrics in an ensemble way was the best strategy to discriminate STZ rats, with a consistent accuracy over 0.85. However, the best accuracy early on was achieved using white matter microstructure features, and later on using FC. This suggests that consistent damage in white matter in the STZ group might precede FC. For cross-timepoint prediction, microstructure features also had the highest performance while, in contrast, that of FC was reduced by its dynamic pattern which shifted from early hyperconnectivity to late hypoconnectivity.

CONCLUSIONS

Our study highlights the MRI-derived measures that best discriminate STZ vs control rats early in the course of the disease, with potential translation to humans.

Identification of Mild Cognitive Impairment Subtypes using an Interpretable Neural Network based Clustering of Gene Expression Data and Neuroimaging Markers

In this study, an attempt is made to cluster the gene expression data and neuroimaging markers using an interpretable neural network model to identify Mild Cognitive Impairment (MCI) subtypes. For this, structural Magnetic Resonance (MR) brain images and gene expression data of early and late MCI subjects are considered from a public database. A neural network model is employed to cluster the gene expression data and regional MR volumes. To evaluate the performance of model, clustering metrics are employed and model is explained using perturbation-based method. Results indicate that the developed model is able to identify MCI subtypes. The network learns latent embeddings of disease-specific genes and MR images markers. The clustering metrics are found to be highest when both the imaging and genetic markers are employed. Volumes of lateral ventricles, hippocampus, amygdala and thalamus are found to be associated with late MCI. Significant scores suggest that genes such as StAR, CCDC108, APOO, TRMT13, RASAL2 and ZNF43 play a key role in identifying the MCI subtypes.Clinical Relevance-Identifying distinct MCI subtypes offer potential for precision diagnostics and targeted clinical recruitment.

Identification of Resting-State Network Functional Connectivity and Brain Structural Signatures in Fibromyalgia Using a Machine Learning Approach

Abnormal resting-state functional connectivity (rs-FC) and brain structure have emerged as pathological hallmarks of fibromyalgia (FM). This study investigated and compared the accuracy of network rs-FC and brain structural features in identifying FM with a machine learning (ML) approach. Twenty-six FM patients and thirty healthy controls were recruited. Clinical presentation was measured by questionnaires. After MRI acquisitions, network rs-FC z-score and network-based gray matter volume matrices were exacted and preprocessed. The performance of feature selection and classification methods was measured. Correlation analyses between predictive features in final models and clinical data were performed. The combination of the recursive feature elimination (RFE) selection method and support vector machine (rs-FC data) or logistic regression (structural data), after permutation importance feature selection, showed high performance in distinguishing FM patients from pain-free controls, in which the rs-FC ML model outperformed the structural ML model (accuracy: 0.91 vs. 0.86, AUC: 0.93 vs. 0.88). The combined rs-FC and structural ML model showed the best performance (accuracy: 0.95, AUC: 0.95). Additionally, several rs-FC features in the final ML model correlated with FM's clinical data. In conclusion, ML models based on rs-FC and brain structural MRI features could effectively differentiate FM patients from pain-free subjects.

Zoom-In Neural Network Deep-Learning Model for Alzheimer's Disease Assessments

Deep neural networks have been successfully applied to generate predictive patterns from medical and diagnostic data. This paper presents an approach for assessing persons with Alzheimer's disease (AD) mild cognitive impairment (MCI), compared with normal control (NC) persons, using the zoom-in neural network (ZNN) deep-learning algorithm. ZNN stacks a set of zoom-in learning units (ZLUs) in a feedforward hierarchy without backpropagation. The resting-state fMRI (rs-fMRI) dataset for AD assessments was obtained from the Alzheimer's Disease Neuroimaging Initiative (ADNI). The Automated Anatomical Labeling (AAL-90) atlas, which provides 90 neuroanatomical functional regions, was used to assess and detect the implicated regions in the course of AD. The features of the ZNN are extracted from the 140-time series rs-fMRI voxel values in a region of the brain. ZNN yields the three classification accuracies of AD versus MCI and NC, NC versus AD and MCI, and MCI versus AD and NC of 97.7%, 84.8%, and 72.7%, respectively, with the seven discriminative regions of interest (ROIs) in the AAL-90.

Classification and Interpretability of Mild Cognitive Impairment Based on Resting-State Functional Magnetic Resonance and Ensemble Learning

The combination and integration of multimodal imaging and clinical markers have introduced numerous classifiers to improve diagnostic accuracy in detecting and predicting AD; however, many studies cannot ensure the homogeneity of data sets and consistency of results. In our study, the XGBoost algorithm was used to classify mild cognitive impairment (MCI) and normal control (NC) populations through five rs-fMRI analysis datasets. Shapley Additive exPlanations (SHAP) is used to analyze the interpretability of the model. The highest accuracy for diagnosing MCI was 65.14% (using the mPerAF dataset). The characteristics of the left insula, right middle frontal gyrus, and right cuneus correlated positively with the output value using DC datasets. The characteristics of left cerebellum 6, right inferior frontal gyrus, opercular part, and vermis 6 correlated positively with the output value using fALFF datasets. The characteristics of the right middle temporal gyrus, left middle temporal gyrus, left temporal pole, and middle temporal gyrus correlated positively with the output value using mPerAF datasets. The characteristics of the right middle temporal gyrus, left middle temporal gyrus, and left hippocampus correlated positively with the output value using PerAF datasets. The characteristics of left cerebellum 9, vermis 9, and right precentral gyrus, right amygdala, and left middle occipital gyrus correlated positively with the output value using Wavelet-ALFF datasets. We found that the XGBoost algorithm constructed from rs-fMRI data is effective for the diagnosis and classification of MCI. The accuracy rates obtained by different rs-fMRI data analysis methods are similar, but the important features are different and involve multiple brain regions, which suggests that MCI may have a negative impact on brain function.

Machine Learning Decomposition of the Anatomy of Neuropsychological Deficit in Alzheimer’s Disease and Mild Cognitive Impairment

Objective

Alzheimer’s Disease (AD) is a progressive condition characterized by cognitive decline. AD is often preceded by mild cognitive impairment (MCI), though the diagnosis of both conditions remains a challenge. Early diagnosis of AD, and prediction of MCI progression require data-driven approaches to improve patient selection for treatment. We used a machine learning tool to predict performance in neuropsychological tests in AD and MCI based on functional connectivity using a whole-brain connectome, in an attempt to identify network substrates of cognitive deficits in AD.

Methods

Neuropsychological tests, baseline anatomical T1 magnetic resonance imaging (MRI), resting-state functional MRI, and diffusion weighted imaging scans were obtained from 149 MCI, and 85 AD patients; and 140 cognitively unimpaired geriatric participants. A novel machine learning tool, Hollow Tree Super (HoTS) was utilized to extract feature importance from each machine learning model to identify brain regions that were associated with deficit and absence of deficit for 11 neuropsychological tests.

Results

11 models attained an area under the receiver operating curve (AUC-ROC) greater than 0.65, while five models had an AUC-ROC ≥ 0.7. 20 parcels of the Human Connectome Project Multimodal Parcelation Atlas matched to poor performance in at least two neuropsychological tests, while 14 parcels were associated with good performance in at least two tests. At a network level, most parcels predictive of both presence and absence of deficit were affiliated with the Central Executive Network, Default Mode Network, and the Sensorimotor Networks. Segregating predictors by the cognitive domain associated with each test revealed areas of coherent overlap between cognitive domains, with the parcels providing possible markers to screen for cognitive impairment.

Conclusion

Approaches such as ours which incorporate whole-brain functional connectivity and harness feature importance in machine learning models may aid in identifying diagnostic and therapeutic targets in AD.