MaTiLDA: An Integrated Machine Learning and Topological Data Analysis Platform for Brain Network Dynamics.

Topological data analysis (TDA) combined with machine learning (ML) algorithms is a powerful approach for investigating complex brain interaction patterns in neurological disorders such as epilepsy. However, the use of ML algorithms and TDA for analysis of aberrant brain interactions requires substantial domain knowledge in computing as well as pure mathematics. To lower the threshold for clinical and computational neuroscience researchers to effectively use ML algorithms together with TDA to study neurological disorders, we introduce an integrated web platform called MaTiLDA.

Machine Learning Interpretability Methods to Characterize Brain Network Dynamics in Epilepsy.

The rapid adoption of machine learning (ML) algorithms in a wide range of biomedical applications has highlighted issues of trust and the lack of understanding regarding the results generated by ML algorithms. Recent studies have focused on developing interpretable ML models and establish guidelines for transparency and ethical use, ensuring the responsible integration of machine learning in healthcare. In this study, we demonstrate the effectiveness of ML interpretability methods to provide important insights into the dynamics of brain network interactions in epilepsy, a serious neurological disorder affecting more than 60 million persons worldwide.

NEMAR: an open access data, tools and compute resource operating on neuroelectromagnetic data.

To preserve scientific data created by publicly and/or philanthropically funded research projects and to make it ready for exploitation using recent and ongoing advances in advanced and large-scale computational modeling methods, publicly available data must use in common, now-evolving standards for formatting, identifying and annotating should share data. The OpenNeuro.org archive, built first as a repository for magnetic resonance imaging data based on the Brain Imaging Data Structure formatting standards, aims to house and share all types of human neuroimaging data.

Simulating Large-scale Models of Brain Neuronal Circuits using Google Cloud Platform.

Biophysically detailed modeling provides an unmatched method to integrate data from many disparate experimental studies, and manipulate and explore with high precision the resultin brain circuit simulation. We developed a detailed model of the brain motor cortex circuits, simulating over 10,000 biophysically detailed neurons and 30 million synaptic connections. Optimization and evaluation of the cortical model parameters and responses was achieved via parameter exploration using grid search parameter sweeps and evolutionary algorithms.

The open EEGLAB portal Interface: High-Performance computing with EEGLAB.

EEGLAB signal processing environment is currently the leading open-source software for processing electroencephalographic (EEG) data. The Neuroscience Gateway (NSG, nsgportal.org) is a web and API-based portal allowing users to easily run a variety of neuroscience-related software on high-performance computing (HPC) resources in the U.

Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits.

Computational models are powerful tools for exploring the properties of complex biological systems. In neuroscience, data-driven models of neural circuits that span multiple scales are increasingly being used to understand brain function in health and disease. But their adoption and reuse has been limited by the specialist knowledge required to evaluate and use them.

Early experiences in developing and managing the neuroscience gateway.

The last few decades have seen the emergence of computational neuroscience as a mature field where researchers are interested in modeling complex and large neuronal systems and require access to high performance computing machines and associated cyber infrastructure to manage computational workflow and data. The neuronal simulation tools, used in this research field, are also implemented for parallel computers and suitable for high performance computing machines. But using these tools on complex high performance computing machines remains a challenge because of issues with acquiring computer time on these machines located at national supercomputer centers, dealing with complex user interface of these machines, dealing with data management and retrieval.