Hi 👋, I'm Hamza (HAM-za ab-del-HE-di)

Abstract: We present Coord2Region, an open-source Python package that streamlines coordinate-based neuroimaging workflows by automatically mapping 3D brain coordinates (e.g., MNI or Talairach) to anatomical regions across multiple atlases. The package links mapped coordinates to meta-analytic resources via the Neuroimaging Meta-Analysis Research Environment (NiMARE) , providing direct integration with Neurosynth and NeuroQuery. This directly connects coordinates and regions to the broader neuroimaging literature. In addition to atlas-based labeling and literature retrieval, Coord2Region offers an optional large language model (LLM) functionality that generates text summaries of linked studies and illustrative images of queried regions. These AI-assisted features are intended to support interpretation and exploration, while remaining clearly complementary to peer-reviewed literature and established neuroimaging tools. Coord2Region provides a unified pipeline with a robust command-line interface, flexible dataset management, and provider-agnostic LLM utilities, and it supports both single-coordinate and high-throughput batch queries with nearest-region fallback for volume and surface atlases. Furthermore, Coord2Region includes a web interface for interactive configuration (via JSON Schema forms) and cloud execution (via Hugging Face), enabling users to build YAML configurations and run analyses in-browser without local installation. Together, these capabilities lower friction, reduce manual errors, and improve reproducibility in coordinate-centric neuroimaging workflows, promoting more robust and transparent research practices.

Abstract: Objective. Magnetoencephalography (MEG) is a cutting-edge neuroimaging technique that measures the intricate brain dynamics underlying cognitive processes with an unparalleled combination of high temporal and spatial precision. While MEG data analytics have traditionally relied on advanced signal processing and mathematical and statistical tools, the recent surge in artificial intelligence has led to the growing use of machine learning (ML) methods for MEG data classification. An emerging trend in this field is the use of artificial neural networks (ANNs) to address various MEG-related tasks. This review aims to provide a comprehensive overview of the state of the art in this area. Approach. This topical review included studies that applied ANNs to MEG data. Studies were sourced from PubMed, Google Scholar, arXiv, and bioRxiv using targeted search queries. The included studies were categorized into three groups: ‘Classification’, ‘Modeling’, and ‘Other’. Key findings and trends were summarized to provide a comprehensive assessment of the field. Main results. We identified 119 relevant studies, with 70 focused on ‘Classification’, 16 on ‘Modeling’, and 33 in the ‘Other’ category. ‘Classification’ studies addressed tasks such as brain decoding, clinical diagnostics, and brain–computer interfaces implementations, often achieving high predictive accuracy. ‘Modeling’ studies explored the alignment between ANN activations and brain processes, offering insights into the neural representations captured by these networks. The ‘Other’ category demonstrated innovative uses of ANNs for artifact correction, preprocessing, and neural source localization. Significance. By establishing a detailed portrait of the current state of the field, this review highlights the strengths and current limitations of ANNs in MEG research. It also provides practical recommendations for future work, offering a helpful reference for seasoned researchers and newcomers interested in using ANNs to explore the complex dynamics of the human brain with MEG.

Abstract: Machine learning (ML) is increasingly used in cognitive, computational and clinical neuroscience. The reliable and efficient application of ML requires a sound understanding of its subtleties and limitations. Training ML models on datasets with imbalanced classes is a particularly common problem, and it can have severe consequences if not adequately addressed. With the neuroscience ML user in mind, this paper provides a didactic assessment of the class imbalance problem and illustrates its impact through systematic manipulation of data imbalance ratios in (i) simulated data and (ii) brain data recorded with electroencephalography (EEG), magnetoencephalography (MEG) and functional magnetic resonance imaging (fMRI). Our results illustrate how the widely-used Accuracy (Acc) metric, which measures the overall proportion of successful predictions, yields misleadingly high performances, as class imbalance increases. Because Acc weights the per-class ratios of correct predictions proportionally to class size, it largely disregards the performance on the minority class. A binary classification model that learns to systematically vote for the majority class will yield an artificially high decoding accuracy that directly reflects the imbalance between the two classes, rather than any genuine generalizable ability to discriminate between them. We show that other evaluation metrics such as the Area Under the Curve (AUC) of the Receiver Operating Characteristic (ROC), and the less common Balanced Accuracy (BAcc) metric - defined as the arithmetic mean between sensitivity and specificity, provide more reliable performance evaluations for imbalanced data. Our findings also highlight the robustness of Random Forest (RF), and the benefits of using stratified cross-validation and hyperprameter optimization to tackle data imbalance. Critically, for neuroscience ML applications that seek to minimize overall classification error, we recommend the routine use of BAcc, which in the specific case of balanced data is equivalent to using standard Acc, and readily extends to multi-class settings. Importantly, we present a list of recommendations for dealing with imbalanced data, as well as open-source code to allow the neuroscience community to replicate and extend our observations and explore alternative approaches to coping with imbalanced data.