Biology subjects

Masharipov, R.

Publications and source records attributed to Masharipov, R..

5 recordsLinked to original sources

bioRxiv2025

Benchmarking resting state fMRI connectivity pipelines for classification: Robust accuracy despite processing variability in cross-site eye state prediction

The rapid evolution of machine learning (ML) methods has yielded promising results in human brain neuroscience. However, the reproducibility of ML applications in neuroimaging remains limited, challenging the generalizability of inferences to broader populations. In addition to the inherent variability of the brain activity (both in healthy and pathological states), poor reproducibility is further enhanced by inconsistencies in data preprocessing techniques and methods for calculating functional connectivity (FC), which are used as parameters for brain state classification. To systematically assess the impact of abovementioned factors on ML applications to fMRI data, we benchmarked a comprehensive set of FC analysis pipelines for the classification task between fMRI data recorded in two fundamentally different states: eyes open and eyes closed. In contrast to studies involving heterogeneous clinical populations or using complex cognitive tasks, our controlled experimental design - based on two independent datasets of healthy participants collected in different laboratories - minimizes variability related to a task design or pathological brain states. Classification accuracy and reproducibility were compared for 256 distinct FC analysis pipelines, covering common preprocessing approaches, brain parcellation schemes, and connectivity metrics. Notably, we employed two ways of validation: a direct cross-site validation strategy - when a model was trained on one site and tested on another, and few-shot domain adaptation - when a few samples of testing site were added to the train set. Despite the substantial variability in pipeline configurations, we observed consistently high classification accuracy ([~]80%), confirming that FC-based models can robustly discriminate between well-defined brain states (eye conditions) across different acquisition sites. Best results both in terms of classification accuracy and stability were observed using Pearson correlation and tangent space parametrization as FC, Brainnetome as atlas, and confound regression strategies based on the CompCor method. These findings highlight the resilience of rs-fMRI FC-derived characteristics to methodological variation and support their utility in the discovery of biomarkers, particularly in settings that involve stable and reproducible brain states.

neuroscience↗

bioRxiv2024

Comparison of whole-brain task-modulated functional connectivity methods for fMRI task connectomics

Higher brain functions require flexible integration of information across widely distributed brain regions depending on the task context. Resting-state functional magnetic resonance imaging (fMRI) has provided substantial insight into large-scale intrinsic brain network organisation, yet the principles of rapid context-dependent reconfiguration of that intrinsic network organisation are much less understood. A major challenge for task connectome mapping is the absence of a gold standard for deriving whole-brain task-modulated functional connectivity matrices. Here, we perform biophysically realistic simulations to control the ground-truth task-modulated functional connectivity over a wide range of experimental settings. We reveal the best-performing methods for different types of task designs and their fundamental limitations. Importantly, we demonstrate that rapid (100 ms) modulations of oscillatory neuronal synchronisation can be recovered from sluggish haemodynamic fluctuations even at typically low fMRI temporal resolution (2 s). Finally, we provide practical recommendations on task design and statistical analysis to foster task connectome mapping.

neuroscience↗

bioRxiv2021

Evidence for the null hypothesis in functional magnetic resonance imaging using group-level Bayesian inference

Classical null hypothesis significance testing is limited to the rejection of the point-null hypothesis; it does not allow the interpretation of non-significant results. Moreover, studies with a sufficiently large sample size will find statistically significant results even when the effect is negligible and may be considered practically equivalent to the null effect. This leads to a publication bias against the null hypothesis. There are two main approaches to assess null effects: shifting from the point-null to the interval-null hypothesis and considering the practical significance in the frequentist approach; using the Bayesian parameter inference based on posterior probabilities, or the Bayesian model inference based on Bayes factors. Herein, we discuss these statistical methods with particular focus on the application of the Bayesian parameter inference, as it is conceptually connected to both frequentist and Bayesian model inferences. Although Bayesian methods have been theoretically elaborated and implemented in commonly used neuroimaging software, they are not widely used for null effect assessment. To demonstrate the advantages of using the Bayesian parameter inference, we compared it with classical null hypothesis significance testing for fMRI data group analysis. We also consider the problem of choosing a threshold for a practically significant effect and discuss possible applications of Bayesian parameter inference in fMRI studies. We argue that Bayesian inference, which directly provides evidence for both the null and alternative hypotheses, may be more intuitive and convenient for practical use than frequentist inference, which only provides evidence against the null hypothesis. Moreover, it may indicate that the obtained data are not sufficient to make a confident inference. Because interim analysis is easy to perform using Bayesian inference, one can evaluate the data as the sample size increases and decide to terminate the experiment if the obtained data are sufficient to make a confident inference. To facilitate the application of the Bayesian parameter inference to null effect assessment, scripts with a simple GUI were developed.

neuroscience↗

bioRxiv2020

Neuroanatomical correlates of social intelligence measured by the Guilford test

Social interactions are a crucial aspect of human behaviour. Numerous neurophysiological studies have focused on socio-cognitive processes associated with the so-called theory of mind - the ability to attribute mental states to oneself and others. Theory of mind is closely related to social intelligence defined as a set of abilities that facilitate effective social interactions. Social intelligence encompasses multiple theory of mind components and can be measured by the Four Factor Test of Social Intelligence (the Guilford-Sullivan test). However, it is unclear whether the differences in social intelligence are reflected in structural brain differences. During the experiment, 48 healthy right-handed individuals completed the Guilford-Sullivan test. T1-weighted structural MRI images were obtained for all participants. Voxel-based morphometry analysis was performed to reveal grey matter volume differences between the two groups (24 subjects in each) - with high social intelligence scores and with low social intelligence scores, respectively. Participants with high social intelligence scores had larger grey matter volumes of the bilateral caudate, left insula, left inferior parietal lobule, inferior temporal gyrus, and middle occipital gyrus. Only the cluster in the caudate nuclei survived a cluster-level FWE correction for multiple comparisons. The obtained results suggest caudate nucleus involvement in the neural system of socio-cognitive processes, reflected by its structural characteristics.

neuroscience↗

bioRxiv2019

Non-selective response inhibition during an equal probability Go/NoGo task: Bayesian analysis of fMRI data

Response inhibition is typically considered a brain mechanism selectively triggered by particular "inhibitory" stimuli or events. Based on recent research, an alternative non-selective mechanism was proposed by several authors. Presumably, the inhibitory brain activity may be triggered not only by the presentation of "inhibitory" stimuli but also by any imperative stimuli, including Go stimuli, when the context is uncertain. Earlier support for this notion was mainly based on the absence of a significant difference between neural activity evoked by equiprobable Go and NoGo stimuli. Equiprobable Go/NoGo design with a simple response time task limits potential confounds between response inhibition and accompanying cognitive processes while not preventing prepotent automaticity. However, previous neuroimaging studies utilized classical null hypothesis significance testing, making it impossible to accept the null hypothesis. Therefore, the current research aimed to provide evidence for practical equivalence of neuronal activity in Go and NoGo trials using Bayesian analysis of functional magnetic resonance imaging (fMRI) data. Thirty-four healthy participants performed a cued Go/NoGo task with an equiprobable presentation of Go and NoGo stimuli. To independently localize brain areas associated with response inhibition in similar experimental conditions, we performed a meta-analysis of fMRI studies using equal probability Go/NoGo tasks. As a result, we observed overlap between response inhibition areas and areas demonstrating the practical equivalence of neuronal activity located in the right dorsolateral prefrontal cortex, parietal cortex, premotor cortex, and left inferior frontal gyrus. Thus, obtained results favour the existence of non-selective response inhibition, which can act in settings of contextual uncertainty induced by the equal probability of Go and NoGo stimuli. Highlights O_LINon-selective response inhibition was assessed by equiprobable Go/NoGo task C_LIO_LIBayesian analysis of fMRI data was combined with a meta-analysis of fMRI studies C_LIO_LISeveral nodes of response inhibition system were equally involved in Go and NoGo trials C_LIO_LIEvidence for non-selective response inhibition in uncertain context was found C_LI

neuroscience↗