Frontiers in Neuroinformatics最新文献

{"title":"Decoupling model descriptions from execution: a modular paradigm for extensible neurosimulation with EDEN.","authors":"Sotirios Panagiotou, Rene Miedema, Dimitrios Soudris, Christos Strydis","doi":"10.3389/fninf.2025.1572782","DOIUrl":"10.3389/fninf.2025.1572782","url":null,"abstract":"<p><p>Computational-neuroscience simulators have traditionally been constrained by tightly coupled simulation engines and modeling languages, limiting their flexibility and scalability. Retrofitting these platforms to accommodate new backends is often costly, and sharing models across simulators remains cumbersome. This paper puts forward an alternative approach based on the EDEN neural simulator, which introduces a modular stack that decouples abstract model descriptions from execution. This architecture enhances flexibility and extensibility by enabling seamless integration of multiple backends, including hardware accelerators, without extensive reprogramming. Through the use of NeuroML, simulation developers can focus on high-performance execution, while model users benefit from improved portability without the need to implement custom simulation engines. Additionally, the proposed method for incorporating arbitrary simulation platforms-from model-optimized code kernels to custom hardware devices-as backends offers a more sustainable and adaptable framework for the computational-neuroscience community. The effectiveness of EDEN's approach is demonstrated by integrating two distinct backends: flexHH, an FPGA-based accelerator for extended Hodgkin-Huxley networks, and SpiNNaker, the well-known, neuromorphic platform for large-scale spiking neural networks. Experimental results show that EDEN integrates the different backends with minimal effort while maintaining competitive performance, reaffirming it as a robust, extensible platform that advances the design paradigm for neural simulators by achieving high generality, performance, and usability.</p>","PeriodicalId":12462,"journal":{"name":"Frontiers in Neuroinformatics","volume":"19 ","pages":"1572782"},"PeriodicalIF":2.5,"publicationDate":"2025-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12367680/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144949023","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A neuronal imaging dataset for deep learning in the reconstruction of single-neuron axons.","authors":"Liya Li, Ying Hu, Xiaojun Wang, Pei Sun, Tingwei Quan","doi":"10.3389/fninf.2025.1628030","DOIUrl":"10.3389/fninf.2025.1628030","url":null,"abstract":"<p><p>Neuron reconstruction is a critical step in quantifying neuronal structures from imaging data. Advances in molecular labeling techniques and optical imaging technologies have spurred extensive research into the patterns of long-range neuronal projections. However, mapping these projections incurs significant costs, as large-scale reconstruction of individual axonal arbors remains time-consuming. In this study, we present a dataset comprising axon imaging volumes along with corresponding annotations to facilitate the evaluation and development of axon reconstruction algorithms. This dataset, derived from 11 mouse brain samples imaged using fluorescence micro-optical sectioning tomography, contains carefully selected 852 volume images sized at 192 × 192 × 192 voxels. These images exhibit substantial variations in terms of axon density, image intensity, and signal-to-noise ratios, even within localized regions. Conventional methods often struggle when processing such complex data. To address these challenges, we propose a distance field-supervised segmentation network designed to enhance image signals effectively. Our results demonstrate significantly improved axon detection rates across both state-of-the-art and traditional methodologies. The released dataset and benchmark algorithm provide a data foundation for advancing novel axon reconstruction methods and are valuable for accelerating the reconstruction of long-range axonal projections.</p>","PeriodicalId":12462,"journal":{"name":"Frontiers in Neuroinformatics","volume":"19 ","pages":"1628030"},"PeriodicalIF":2.5,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12361129/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144949067","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: Transdiagnostic clustering of self-schema from self-referential judgements identifies subtypes of healthy personality and depression.","authors":"Geoffrey Chern-Yee Tan, Ziying Wang, Ethel Siew Ee Tan, Rachel Jing Min Ong, Pei En Ooi, Danan Lee, Nikita Rane, Sheryl Yu Xuan Tey, Si Ying Chua, Nicole Goh, Glynis Weibin Lam, Atlanta Chakraborty, Anthony Khye Loong Yew, Sin Kee Ong, Jin Lin Kee, Xin Ying Lim, Nawal Hashim, Sharon Huixian Lu, Michael Meany, Serenella Tolomeo, Christopher Lee Asplund, Hong Ming Tan, Jussi Keppo","doi":"10.3389/fninf.2025.1633196","DOIUrl":"10.3389/fninf.2025.1633196","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.3389/fninf.2023.1244347.].</p>","PeriodicalId":12462,"journal":{"name":"Frontiers in Neuroinformatics","volume":"19 ","pages":"1633196"},"PeriodicalIF":2.5,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12351648/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144872317","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sensitivity analysis of a mathematical model of Alzheimer's disease progression unveils important causal pathways.","authors":"Seyedadel Moravveji, Halima Sadia, Nicolas Doyon, Simon Duchesne","doi":"10.3389/fninf.2025.1590968","DOIUrl":"10.3389/fninf.2025.1590968","url":null,"abstract":"<p><strong>Introduction: </strong>Mathematical models serve as essential tools to investigate brain aging, the onset of Alzheimer's disease (AD) and its progression. By studying the representation of the complex dynamics of brain aging processes, such as amyloid beta (Aβ) deposition, tau tangles, neuro-inflammation, and neuronal death. Sensitivity analyses provide a powerful framework for identifying the underlying mechanisms that drive disease progression. In this study, we present the first local sensitivity analysis of a recent and comprehensive multiscale ODE-based model of Alzheimer's Disease (AD) that originates from our group. As such, it is one of the most complex model that captures the multifactorial nature of AD, incorporating neuronal, pathological, and inflammatory processes at the nano, micro and macro scales. This detailed framework enables realistic simulation of disease progression and identification of key biological parameters that influence system behavior. Our analysis identifies the key drivers of disease progression across patient profiles, providing insight into targeted therapeutic strategies.</p><p><strong>Methods: </strong>We investigated a recent ODE-based model composed of 19 variables and 75 parameters, developed by our group, to study Alzheimer's disease dynamics. We performed single- and paired-parameter sensitivity analyses, focusing on three key outcomes: neural density, amyloid beta plaques, and tau proteins.</p><p><strong>Results: </strong>Our findings suggest that the parameters related to glucose and insulin regulation could play an important role in neurodegeneration and cognitive decline. Second, the parameters that have the most important impact on cognitive decline are not completely the same depending on sex and APOE status.</p><p><strong>Discussion: </strong>These results underscore the importance of incorporating a multifactorial approach tailored to demographic characteristics when considering strategies for AD treatment. This approach is essential to identify the factors that contribute significantly to neural loss and AD progression.</p>","PeriodicalId":12462,"journal":{"name":"Frontiers in Neuroinformatics","volume":"19 ","pages":"1590968"},"PeriodicalIF":2.5,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12325246/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144793928","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Breaking barriers: broadening neuroscience education via cloud platforms and course-based undergraduate research.","authors":"Franco Delogu, Chantol Aspinall, Kimberly Ray, Anibal Solon Heinsfeld, Conner Victory, Franco Pestilli","doi":"10.3389/fninf.2025.1608900","DOIUrl":"10.3389/fninf.2025.1608900","url":null,"abstract":"<p><p>This study demonstrates the effectiveness of integrating cloud computing platforms with Course-based Undergraduate Research Experiences (CUREs) to broaden access to neuroscience education. Over four consecutive spring semesters (2021-2024), a total of 42 undergraduate students at Lawrence Technological University participated in computational neuroscience CUREs using brainlife.io, a cloud-computing platform. Students conducted anatomical and functional brain imaging analyses on openly available datasets, testing original hypotheses about brain structure variations. The program evolved from initial data processing to hypothesis-driven research exploring the influence of age, gender, and pathology on brain structures. By combining open science and big data within a user-friendly cloud environment, the CURE model provided hands-on, problem-based learning to students with limited prior knowledge. This approach addressed key limitations of traditional undergraduate research experiences, including scalability, early exposure, and inclusivity. Students consistently worked with MRI datasets, focusing on volumetric analysis of brain structures, and developed scientific communication skills by presenting findings at annual research days. The success of this program demonstrates its potential to democratize neuroscience education, enabling advanced research without extensive laboratory facilities or prior experience, and promoting original undergraduate research using real-world datasets.</p>","PeriodicalId":12462,"journal":{"name":"Frontiers in Neuroinformatics","volume":"19 ","pages":"1608900"},"PeriodicalIF":2.5,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12307389/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144752882","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Decoding event-related potentials: single-dose energy dietary supplement acts on earlier brain processes than we thought.","authors":"Karina J Maciejewska","doi":"10.3389/fninf.2025.1563893","DOIUrl":"10.3389/fninf.2025.1563893","url":null,"abstract":"<p><strong>Introduction: </strong>This paper describes an experimental work using machine learning (ML) as a \"decoding for interpretation\" to understand the brain's physiology better.</p><p><strong>Methods: </strong>Multivariate pattern analysis (MVPA) was used to decode the patterns of event-related potentials (ERPs, brain responses to stimuli) in a visual oddball task. The ERPs were measured before (run 1) and after (30 min-run 2, 90 min-run 3) a single dose of an energy dietary supplement with only a small amount of caffeine.</p><p><strong>Results: </strong>Its effect on ERPs was successfully decoded. Above-chance decoding accuracies were obtained between ∼350 and 450 ms (corresponds to P3 peak) after stimulus onset for both the placebo and study groups, whereas between ∼200 and 260 ms (corresponds to P2 waveform) only in the placebo group. Moreover, the decoding accuracies were significantly higher in the placebo than in the study group in the 200-250 ms and 450-500 ms time bins. Our previously reported findings showed an increase in P3 amplitude among the runs only in the placebo group, indicating a reduction of mental fatigue caused by the supplementation.</p><p><strong>Discussion: </strong>Thus, this paper extends these results, showing that the dietary supplement affected the brain's neural activity related to the attention-related processing of the visual stimuli in the oddball task already at the early processing stage. This implies that inhibiting the fatigue-related brain changes after only a single dose of a dietary neurostimulant acts on early and late processing stages. This emphasizes the value of decoding for interpretation in ERP research. The results also point out the necessity of controlling the uptake of dietary supplements before the neurophysiological examinations.</p>","PeriodicalId":12462,"journal":{"name":"Frontiers in Neuroinformatics","volume":"19 ","pages":"1563893"},"PeriodicalIF":2.5,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12279804/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144689712","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Digitoids: a novel computational platform for mimicking oxygen-dependent firing of neurons <i>in vitro</i>.","authors":"Rachele Fabbri, Ermes Botte, Arti Ahluwalia, Chiara Magliaro","doi":"10.3389/fninf.2025.1549916","DOIUrl":"10.3389/fninf.2025.1549916","url":null,"abstract":"<p><strong>Introduction: </strong>Computational models are valuable tools for understanding and studying a wide range of characteristics and mechanisms of the brain. Furthermore, they can also be exploited to explore biological neural networks from neuronal cultures. However, few of the current in silico approaches consider the energetic demand of neurons to sustain their electrophysiological functions, specifically their well-known oxygen-dependent firing.</p><p><strong>Methods: </strong>In this work, we introduce Digitoids, a computational platform which integrates a Hodgkin-Huxley-like model to describe the time-dependent oscillations of the neuronal membrane potential with oxygen dynamics in the culture environment. In Digitoids, neurons are connected to each other according to Small-World topologies observed in cell cultures, and oxygen consumption by cells is modeled as limited by diffusion through the culture medium. The oxygen consumed is used to fuel their basal metabolism and the activity of Na⁺-K⁺-ATP membrane pumps, thus it modulates neuronal firing.</p><p><strong>Results: </strong>Our simulations show that the characteristics of neuronal firing predicted throughout the network are related to oxygen availability. In addition, the average firing rate predicted by Digitoids is statistically similar to that measured in neuronal networks <i>in vitro</i>, further proving the relevance of this platform.</p><p><strong>Dicussion: </strong>Digitoids paves the way for a new generation of <i>in silico</i> models of neuronal networks, establishing the oxygen dependence of electrophysiological dynamics as a fundamental requirement to improve their physiological relevance.</p>","PeriodicalId":12462,"journal":{"name":"Frontiers in Neuroinformatics","volume":"19 ","pages":"1549916"},"PeriodicalIF":2.5,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12259620/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144642248","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"From pronounced to imagined: improving speech decoding with multi-condition EEG data.","authors":"Denise Alonso-Vázquez, Omar Mendoza-Montoya, Ricardo Caraza, Hector R Martinez, Javier M Antelis","doi":"10.3389/fninf.2025.1583428","DOIUrl":"10.3389/fninf.2025.1583428","url":null,"abstract":"<p><strong>Introduction: </strong><i>Imagined speech</i> decoding using EEG holds promising applications for individuals with motor neuron diseases, although its performance remains limited due to small dataset sizes and the absence of sensory feedback. Here, we investigated whether incorporating EEG data from <i>overt</i> (pronounced) speech could enhance <i>imagined speech</i> classification.</p><p><strong>Methods: </strong>Our approach systematically compares four classification scenarios by modifying the training dataset: intra-subject (using only <i>imagined speech</i>, combining <i>overt</i> and <i>imagined speech</i>, and using only <i>overt speech</i>) and multi-subject (combining <i>overt speech</i> data from different participants with the <i>imagined speech</i> of the target participant). We implemented all scenarios using the convolutional neural network EEGNet. To this end, twenty-four healthy participants pronounced and imagined five Spanish words.</p><p><strong>Results: </strong>In binary word-pair classifications, combining <i>overt</i> and <i>imagined speech</i> data in the intra-subject scenario led to accuracy improvements of 3%-5.17% in four out of 10 word pairs, compared to training with <i>imagined speech</i> only. Although the highest individual accuracy (95%) was achieved with <i>imagined speech</i> alone, the inclusion of <i>overt speech</i> data allowed more participants to surpass 70% accuracy, increasing from 10 (<i>imagined only</i>) to 15 participants. In the intra-subject multi-class scenario, combining <i>overt</i> and <i>imagined speech</i> did not yield statistically significant improvements over using <i>imagined speech</i> exclusively.</p><p><strong>Discussion: </strong>Finally, we observed that features such as word length, phonological complexity, and frequency of use contributed to higher discriminability between certain <i>imagined</i> word pairs. These findings suggest that incorporating <i>overt speech</i> data can improve <i>imagined speech</i> decoding in individualized models, offering a feasible strategy to support the early adoption of brain-computer interfaces before speech deterioration occurs in individuals with motor neuron diseases.</p>","PeriodicalId":12462,"journal":{"name":"Frontiers in Neuroinformatics","volume":"19 ","pages":"1583428"},"PeriodicalIF":2.5,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12245923/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144625885","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editorial: Advanced EEG analysis techniques for neurological disorders.","authors":"Jisu Elsa Jacob, Sreejith Chandrasekharan","doi":"10.3389/fninf.2025.1637890","DOIUrl":"https://doi.org/10.3389/fninf.2025.1637890","url":null,"abstract":"","PeriodicalId":12462,"journal":{"name":"Frontiers in Neuroinformatics","volume":"19 ","pages":"1637890"},"PeriodicalIF":2.5,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12213536/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144552891","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bridging neuroscience and AI: a survey on large language models for neurological signal interpretation.","authors":"Sreejith Chandrasekharan, Jisu Elsa Jacob","doi":"10.3389/fninf.2025.1561401","DOIUrl":"10.3389/fninf.2025.1561401","url":null,"abstract":"<p><p>Electroencephalogram (EEG) signal analysis is important for the diagnosis of various neurological conditions. Traditional deep neural networks, such as convolutional networks, sequence-to-sequence networks, and hybrids of such neural networks were proven to be effective for a wide range of neurological disease classifications. However, these are limited by the requirement of a large dataset, extensive training, and hyperparameter tuning, which require expert-level machine learning knowledge. This survey paper aims to explore the ability of Large Language Models (LLMs) to transform existing systems of EEG-based disease diagnostics. LLMs have a vast background knowledge in neuroscience, disease diagnostics, and EEG signal processing techniques. Thus, these models are capable of achieving expert-level performance with minimal training data, nominal fine-tuning, and less computational overhead, leading to a shorter time to find effective solutions for diagnostics. Further, in comparison with traditional methods, LLM's capability to generate intermediate results and meaningful reasoning makes it more reliable and transparent. This paper delves into several use cases of LLM in EEG signal analysis and attempts to provide a comprehensive understanding of techniques in the domain that can be applied to different disease diagnostics. The study also strives to highlight challenges in the deployment of LLM models, ethical considerations, and bottlenecks in optimizing models due to requirements of specialized methods such as Low-Rank Adapation. In general, this survey aims to stimulate research in the area of EEG disease diagnostics by effectively using LLMs and associated techniques in machine learning pipelines.</p>","PeriodicalId":12462,"journal":{"name":"Frontiers in Neuroinformatics","volume":"19 ","pages":"1561401"},"PeriodicalIF":2.5,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12213581/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144552890","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}