Using data-driven model-brain mappings to constrain formal models of cognition.
Ontology highlight
ABSTRACT:
SUBMITTER: Borst JP
PROVIDER: S-EPMC4352055 | biostudies-literature | 2015
REPOSITORIES: biostudies-literature
Publications
Using data-driven model-brain mappings to constrain formal models of cognition.
Borst Jelmer P JP Nijboer Menno M Taatgen Niels A NA van Rijn Hedderik H Anderson John R JR
PloS one 20150306 3
In this paper we propose a method to create data-driven mappings from components of cognitive models to brain regions. Cognitive models are notoriously hard to evaluate, especially based on behavioral measures alone. Neuroimaging data can provide additional constraints, but this requires a mapping from model components to brain regions. Although such mappings can be based on the experience of the modeler or on a reading of the literature, a formal method is preferred to prevent researcher-based ...[more]
Similar Datasets
Project description:The relationship between brain structure and function has been probed using a variety of approaches, but how the underlying structural connectivity of the human brain drives behavior is far from understood. To investigate the effect of anatomical brain organization on human task performance, we use a data-driven computational modeling approach and explore the functional effects of naturally occurring structural differences in brain networks. We construct personalized brain network models by combining anatomical connectivity estimated from diffusion spectrum imaging of individual subjects with a nonlinear model of brain dynamics. By performing computational experiments in which we measure the excitability of the global brain network and spread of synchronization following a targeted computational stimulation, we quantify how individual variation in the underlying connectivity impacts both local and global brain dynamics. We further relate the computational results to individual variability in the subjects' performance of three language-demanding tasks both before and after transcranial magnetic stimulation to the left-inferior frontal gyrus. Our results show that task performance correlates with either local or global measures of functional activity, depending on the complexity of the task. By emphasizing differences in the underlying structural connectivity, our model serves as a powerful tool to assess individual differences in task performances, to dissociate the effect of targeted stimulation in tasks that differ in cognitive demand, and to pave the way for the development of personalized therapeutics.
| S-EPMC6192563 | biostudies-literature
Project description:Cancer research has seen explosive development exploring deep learning (DL) techniques for analysing magnetic resonance imaging (MRI) images for predicting brain tumours. We have observed a substantial gap in explanation, interpretability, and high accuracy for DL models. Consequently, we propose an explanation-driven DL model by utilising a convolutional neural network (CNN), local interpretable model-agnostic explanation (LIME), and Shapley additive explanation (SHAP) for the prediction of discrete subtypes of brain tumours (meningioma, glioma, and pituitary) using an MRI image dataset. Unlike previous models, our model used a dual-input CNN approach to prevail over the classification challenge with images of inferior quality in terms of noise and metal artifacts by adding Gaussian noise. Our CNN training results reveal 94.64% accuracy as compared to other state-of-the-art methods. We used SHAP to ensure consistency and local accuracy for interpretation as Shapley values examine all future predictions applying all possible combinations of inputs. In contrast, LIME constructs sparse linear models around each prediction to illustrate how the model operates in the immediate area. Our emphasis for this study is interpretability and high accuracy, which is critical for realising disparities in predictive performance, helpful in developing trust, and essential in integration into clinical practice. The proposed method has a vast clinical application that could potentially be used for mass screening in resource-constraint countries.
| S-EPMC8964286 | biostudies-literature
Project description:Dynamic scene stitching still has a great challenge in maintaining the global key information without missing or deforming if multiple motion interferences exist in the image acquisition system. Object clips, motion blurs, or other synthetic defects easily occur in the final stitching image. In our research work, we proceed from human visual cognitive mechanism and construct a hybrid-saliency-based cognitive model to automatically guide the video volume stitching. The model consists of three elements of different visual stimuli, that is, intensity, edge contour, and scene depth saliencies. Combined with the manifold-based mosaicing framework, dynamic scene stitching is formulated as a cut path optimization problem in a constructed space-time graph. The cutting energy function for column width selections is defined according to the proposed visual cognition model. The optimum cut path can minimize the cognitive saliency difference throughout the whole video volume. The experimental results show that it can effectively avoid synthetic defects caused by different motion interferences and summarize the key contents of the scene without loss. The proposed method gives full play to the role of human visual cognitive mechanism for the stitching. It is of high practical value to environmental surveillance and other applications.
| S-EPMC3932260 | biostudies-other
Project description:Current limitations in quantitatively predicting biological behavior hinder our efforts to engineer biological systems to produce biofuels and other desired chemicals. Here, we present a new method for calculating metabolic fluxes, key targets in metabolic engineering, that incorporates data from 13C labeling experiments and genome-scale models. The data from 13C labeling experiments provide strong flux constraints that eliminate the need to assume an evolutionary optimization principle such as the growth rate optimization assumption used in Flux Balance Analysis (FBA). This effective constraining is achieved by making the simple but biologically relevant assumption that flux flows from core to peripheral metabolism and does not flow back. The new method is significantly more robust than FBA with respect to errors in genome-scale model reconstruction. Furthermore, it can provide a comprehensive picture of metabolite balancing and predictions for unmeasured extracellular fluxes as constrained by 13C labeling data. A comparison shows that the results of this new method are similar to those found through 13C Metabolic Flux Analysis (13C MFA) for central carbon metabolism but, additionally, it provides flux estimates for peripheral metabolism. The extra validation gained by matching 48 relative labeling measurements is used to identify where and why several existing COnstraint Based Reconstruction and Analysis (COBRA) flux prediction algorithms fail. We demonstrate how to use this knowledge to refine these methods and improve their predictive capabilities. This method provides a reliable base upon which to improve the design of biological systems.
| S-EPMC4574858 | biostudies-literature
Project description:Despite recent innovations in exoskeleton design and control, predicting subject-specific impacts of exoskeletons on gait remains challenging. We evaluated the ability of three classes of subject-specific phase-varying (PV) models to predict kinematic and myoelectric responses to ankle exoskeletons during walking, without requiring prior knowledge of specific user characteristics. Each model-PV, linear PV (LPV) and nonlinear PV (NPV)-leveraged Floquet theory to predict deviations from a nominal gait cycle due to exoskeleton torque, though the models differed in complexity and expected prediction accuracy. For 12 unimpaired adults walking with bilateral passive ankle exoskeletons, we predicted kinematics and muscle activity in response to three exoskeleton torque conditions. The LPV model's predictions were more accurate than the PV model when predicting less than 12.5% of a stride in the future and explained 49-70% of the variance in hip, knee and ankle kinematic responses to torque. The LPV model also predicted kinematic responses with similar accuracy to the more-complex NPV model. Myoelectric responses were challenging to predict with all models, explaining at most 10% of the variance in responses. This work highlights the potential of data-driven PV models to predict complex subject-specific responses to ankle exoskeletons and inform device design and control.
| S-EPMC7653383 | biostudies-literature
Project description:Producing timely, well-informed and reliable forecasts for an ongoing epidemic of an emerging infectious disease is a huge challenge. Epidemiologists and policy makers have to deal with poor data quality, limited understanding of the disease dynamics, rapidly changing social environment and the uncertainty on effects of various interventions in place. Under this setting, detailed computational models provide a comprehensive framework for integrating diverse data sources into a well-defined model of disease dynamics and social behavior, potentially leading to better understanding and actions. In this paper, we describe one such agent-based model framework developed for forecasting the 2014-2015 Ebola epidemic in Liberia, and subsequently used during the Ebola forecasting challenge. We describe the various components of the model, the calibration process and summarize the forecast performance across scenarios of the challenge. We conclude by highlighting how such a data-driven approach can be refined and adapted for future epidemics, and share the lessons learned over the course of the challenge.
| S-EPMC5568513 | biostudies-literature
Project description:Magnetic resonance electrical properties tomography (MR-EPT) is a non-invasive measurement technique that derives the electrical properties (EPs, e.g., conductivity or permittivity) of tissues in the radiofrequency range (64 MHz for 1.5 T and 128 MHz for 3 T MR systems). Clinical studies have shown the potential of tissue conductivity as a biomarker. To date, model-based conductivity reconstructions rely on numerical assumptions and approximations, leading to inaccuracies in the reconstructed maps. To address such limitations, we propose an artificial neural network (ANN)-based non-linear conductivity estimator trained on simulated data for conductivity brain imaging. Network training was performed on 201 synthesized T2-weighted spin-echo (SE) data obtained from the finite-difference time-domain (FDTD) electromagnetic (EM) simulation. The dataset was composed of an approximated T2-w SE magnitude and transceive phase information. The proposed method was tested three in-silico and in-vivo on two volunteers and three patients' data. For comparison purposes, various conventional phase-based EPT reconstruction methods were used that ignore B1+ magnitude information, such as Savitzky-Golay kernel combined with Gaussian filter (S-G Kernel), phase-based convection-reaction EPT (cr-EPT), magnitude-weighted polynomial-fitting phase-based EPT (Poly-Fit), and integral-based phase-based EPT (Integral-based). From the in-silico experiments, quantitative analysis showed that the proposed method provides more accurate and improved quality (e.g., high structural preservation) conductivity maps compared to conventional reconstruction methods. Representatively, in the healthy brain in-silico phantom experiment, the proposed method yielded mean conductivity values of 1.97 ± 0.20 S/m for CSF, 0.33 ± 0.04 S/m for WM, and 0.52 ± 0.08 S/m for GM, which were closer to the ground-truth conductivity (2.00, 0.30, 0.50 S/m) than the integral-based method (2.56 ± 2.31, 0.39 ± 0.12, 0.68 ± 0.33 S/m). In-vivo ANN-based conductivity reconstructions were also of improved quality compared to conventional reconstructions and demonstrated network generalizability and robustness to in-vivo data and pathologies. The reported in-vivo brain conductivity values were in agreement with literatures. In addition, the proposed method was observed for various SNR levels (SNR levels = 10, 20, 40, and 58) and repeatability conditions (the eight acquisitions with the number of signal averages = 1). The preliminary investigations on brain tumor patient datasets suggest that the network trained on simulated dataset can generalize to unforeseen in-vivo pathologies, thus demonstrating its potential for clinical applications.
| S-EPMC10502651 | biostudies-literature
Project description:Despite significant efforts and remarkable progress, the inference of signaling networks from experimental data remains very challenging. The problem is particularly difficult when the objective is to obtain a dynamic model capable of predicting the effect of novel perturbations not considered during model training. The problem is ill-posed due to the nonlinear nature of these systems, the fact that only a fraction of the involved proteins and their post-translational modifications can be measured, and limitations on the technologies used for growing cells in vitro, perturbing them, and measuring their variations. As a consequence, there is a pervasive lack of identifiability. To overcome these issues, we present a methodology called SELDOM (enSEmbLe of Dynamic lOgic-based Models), which builds an ensemble of logic-based dynamic models, trains them to experimental data, and combines their individual simulations into an ensemble prediction. It also includes a model reduction step to prune spurious interactions and mitigate overfitting. SELDOM is a data-driven method, in the sense that it does not require any prior knowledge of the system: the interaction networks that act as scaffolds for the dynamic models are inferred from data using mutual information. We have tested SELDOM on a number of experimental and in silico signal transduction case-studies, including the recent HPN-DREAM breast cancer challenge. We found that its performance is highly competitive compared to state-of-the-art methods for the purpose of recovering network topology. More importantly, the utility of SELDOM goes beyond basic network inference (i.e. uncovering static interaction networks): it builds dynamic (based on ordinary differential equation) models, which can be used for mechanistic interpretations and reliable dynamic predictions in new experimental conditions (i.e. not used in the training). For this task, SELDOM's ensemble prediction is not only consistently better than predictions from individual models, but also often outperforms the state of the art represented by the methods used in the HPN-DREAM challenge.
| S-EPMC5319798 | biostudies-literature
Project description:BackgroundDyslexia is a neurological disorder that affects an individual's language processing abilities. Early care and intervention can help dyslexic individuals succeed academically and socially. Recent developments in deep learning (DL) approaches motivate researchers to build dyslexia detection models (DDMs). DL approaches facilitate the integration of multi-modality data. However, there are few multi-modality-based DDMs.MethodsIn this study, the authors built a DL-based DDM using multi-modality data. A squeeze and excitation (SE) integrated MobileNet V3 model, self-attention mechanisms (SA) based EfficientNet B7 model, and early stopping and SA-based Bi-directional long short-term memory (Bi-LSTM) models were developed to extract features from magnetic resonance imaging (MRI), functional MRI, and electroencephalography (EEG) data. In addition, the authors fine-tuned the LightGBM model using the Hyperband optimization technique to detect dyslexia using the extracted features. Three datasets containing FMRI, MRI, and EEG data were used to evaluate the performance of the proposed DDM.ResultsThe findings supported the significance of the proposed DDM in detecting dyslexia with limited computational resources. The proposed model outperformed the existing DDMs by producing an optimal accuracy of 98.9%, 98.6%, and 98.8% for the FMRI, MRI, and EEG datasets, respectively. Healthcare centers and educational institutions can benefit from the proposed model to identify dyslexia in the initial stages. The interpretability of the proposed model can be improved by integrating vision transformers-based feature extraction.
| S-EPMC11232624 | biostudies-literature
Project description:The most common clinical phenotype of progressive supranuclear palsy is Richardson syndrome, characterized by levodopa unresponsive symmetric parkinsonism, with a vertical supranuclear gaze palsy, early falls and cognitive impairment. There is currently no detailed understanding of the full sequence of disease pathophysiology in progressive supranuclear palsy. Determining the sequence of brain atrophy in progressive supranuclear palsy could provide important insights into the mechanisms of disease progression, as well as guide patient stratification and monitoring for clinical trials. We used a probabilistic event-based model applied to cross-sectional structural MRI scans in a large international cohort, to determine the sequence of brain atrophy in clinically diagnosed progressive supranuclear palsy Richardson syndrome. A total of 341 people with Richardson syndrome (of whom 255 had 12-month follow-up imaging) and 260 controls were included in the study. We used a combination of 12-month follow-up MRI scans, and a validated clinical rating score (progressive supranuclear palsy rating scale) to demonstrate the longitudinal consistency and utility of the event-based model's staging system. The event-based model estimated that the earliest atrophy occurs in the brainstem and subcortical regions followed by progression caudally into the superior cerebellar peduncle and deep cerebellar nuclei, and rostrally to the cortex. The sequence of cortical atrophy progresses in an anterior to posterior direction, beginning in the insula and then the frontal lobe before spreading to the temporal, parietal and finally the occipital lobe. This in vivo ordering accords with the post-mortem neuropathological staging of progressive supranuclear palsy and was robust under cross-validation. Using longitudinal information from 12-month follow-up scans, we demonstrate that subjects consistently move to later stages over this time interval, supporting the validity of the model. In addition, both clinical severity (progressive supranuclear palsy rating scale) and disease duration were significantly correlated with the predicted subject event-based model stage (P < 0.01). Our results provide new insights into the sequence of atrophy progression in progressive supranuclear palsy and offer potential utility to stratify people with this disease on entry into clinical trials based on disease stage, as well as track disease progression.
| S-EPMC9118104 | biostudies-literature