搜索结果：IBRO neuroscience reports

Neuroscience research publications encompass a vast wealth of knowledge. Accurately retrieving existing information and discovering new insights from this extensive literature is essential for advancing the field. However, when knowledge is dispersed across multiple sources, current state-of-the-art retrieval methods often struggle to extract the necessary information. A knowledge graph (KG) can integrate and link knowledge from multiple sources. However, existing methods for constructing KGs in neuroscience often rely on labeled data and require domain expertise. Acquiring large-scale, labeled data for a specialized area like neuroscience presents significant challenges. This work proposes novel methods for constructing KG from unlabeled large-scale neuroscience research corpus utilizing large language models (LLM), neuroscience ontology, and text embeddings. We analyze the semantic relevance of neuroscience text segments identified by LLM for building the knowledge graph. We also introduce an entity-augmented information retrieval algorithm to extract knowledge from the KG. Several experiments were conducted to evaluate the proposed approaches. The results demonstrate that our me

Modern scientific fields face the challenge of integrating a wealth of data, analyses, and results. We recently showed that a neglect of this integration can lead to circular analyses and redundant explanations. Here, we help advance scientific integration by describing equivalences that unify diverse analyses of datasets and networks. We describe equivalences across analyses of clustering and dimensionality reduction, network centrality and dynamics, and popular models in imaging and network neuroscience. First, we equate foundational objectives across unsupervised learning and network science (from k means to modularity to UMAP), fuse classic algorithms for optimizing these objectives, and extend these objectives to simplify interpretations of popular dimensionality reduction methods. Second, we equate basic measures of connectional magnitude and dispersion with six measures of communication, control, and diversity in network science and network neuroscience. Third, we describe three semi-analytical vignettes that clarify and simplify the interpretation of structural and dynamical analyses in imaging and network neuroscience. We illustrate our results on example brain-imaging dat

Purpose: We investigated the utilization of privacy-preserving, locally-deployed, open-source Large Language Models (LLMs) to extract diagnostic information from free-text cardiovascular magnetic resonance (CMR) reports. Materials and Methods: We evaluated nine open-source LLMs on their ability to identify diagnoses and classify patients into various cardiac diagnostic categories based on descriptive findings in 109 clinical CMR reports. Performance was quantified using standard classification metrics including accuracy, precision, recall, and F1 score. We also employed confusion matrices to examine patterns of misclassification across models. Results: Most open-source LLMs demonstrated exceptional performance in classifying reports into different diagnostic categories. Google's Gemma2 model achieved the highest average F1 score of 0.98, followed by Qwen2.5:32B and DeepseekR1-32B with F1 scores of 0.96 and 0.95, respectively. All other evaluated models attained average scores above 0.93, with Mistral and DeepseekR1-7B being the only exceptions. The top four LLMs outperformed our board-certified cardiologist (F1 score of 0.94) across all evaluation metrics in analyzing CMR reports.

With the growth of global maritime transportation, energy optimization has become crucial for reducing costs and ensuring operational efficiency. Shaft power is the mechanical power transmitted from the engine to the shaft and directly impacts fuel consumption, making its accurate prediction a paramount step in optimizing vessel performance. Power consumption is highly correlated with ship parameters such as speed and shaft rotation per minute, as well as weather and sea conditions. Frequent access to this operational data can improve prediction accuracy. However, obtaining high-quality sensor data is often infeasible and costly, making alternative sources such as noon reports a viable option. In this paper, we propose a transfer learning-based approach for predicting vessels shaft power, where a model is initially trained on high-frequency data from a vessel and then fine-tuned with low-frequency daily noon reports from other vessels. We tested our approach on sister vessels (identical dimensions and configurations), a similar vessel (slightly larger with a different engine), and a different vessel (distinct dimensions and configurations). The experiments showed that the mean abso

Neuroscience and AI have an intertwined history, largely relayed in the literature of both fields. In recent years, due to the engineering orientations of AI research and the monopoly of industry for its large-scale applications, the mutual expansion of neuroscience and AI in fundamental research seems challenged. In this paper, we bring some empirical evidences that, on the contrary, AI and neuroscience are continuing to grow together, but with a pronounced interest in the fields of study related to neurodegenerative diseases since the 1990s. With a temporal knowledge cartography of neuroscience drawn with advanced document embedding techniques, we draw the dynamical shaping of the discipline since the 1970s and identified the conceptual articulation of AI with this particular subfield mentioned before. However, a further analysis of the underlying citation network of the studied corpus shows that the produced AI technologies remain confined in the different subfields and are not transferred from one subfield to another. This invites us to discuss the genericity capability of AI in the context of an intradisciplinary development, especially in the diffusion of its associated metro

The development of large-scale artificial intelligence (AI) models is influencing neuroscience research by enabling end-to-end learning from raw brain signals and neural data. In this paper, we review applications of large-scale AI models across four major neuroscience domains: neuroimaging and data processing, brain-computer interfaces and neural decoding, clinical decision support and translational frameworks, and disease-specific applications across neurological and psychiatric disorders. These models show potential to address major computational neuroscience challenges, including multimodal neural data integration, spatiotemporal pattern interpretation, and the development of translational frameworks for clinical research. Moreover, the interaction between neuroscience and AI has become increasingly reciprocal, as biologically informed architectural constraints are now incorporated to develop more interpretable and computationally efficient models. This review highlights both the promise of such technologies and critical implementation considerations, with particular emphasis on rigorous evaluation frameworks, effective integration of domain knowledge, prospective clinical vali

In cognitive neuroscience research, Representational Dissimilarity Matrices (RDMs) are often incomplete because pairwise similarity judgments cannot always be exhaustively collected as the number of pairs rapidly increases with the number of conditions. Existing methods to fill these missing values, such as deep neural network imputation, are powerful but computationally demanding and relatively opaque. We introduce a simple algorithm based on geometric inference that fills missing dissimilarity matrix entries using known distances. We use tests on publicly available empirical cognitive neuroscience datasets, as well as simulations, to demonstrate the method's effectiveness and robustness across varying sparsity and matrix sizes. We have made this geometric reconstruction algorithm, implemented in Python and MATLAB, publicly available. This method provides a fast and accurate solution for completing partial dissimilarity matrices in the cognitive neurosciences.

The exponential growth of neuroscience literature presents a significant challenge for researchers seeking to efficiently access and utilize relevant information. To address this issue, we introduce the Brain Knowledge Engine (BrainKnow), an automated system designed to extract, link, and synthesize neuroscience knowledge from scientific publications. BrainKnow constructs a comprehensive knowledge graph encompassing 3,626,931 relationships across 37,011 neuroscience concepts, derived from 1,817,744 articles. This vast repository of knowledge is accessible through a user-friendly web interface, facilitating efficient navigation and data retrieval. BrainKnow employs advanced graph network algorithms, specifically Node2Vec, to enhance knowledge recommendation and visualization. This enables users to explore semantic relationships between concepts, predict potential new relationships, and gain a deeper understanding of the interconnectedness within neuroscience. Additionally, BrainKnow ensures real-time updates by synchronizing with PubMed, providing researchers with access to the most current information. BrainKnow serves as a valuable resource for neuroscience researchers, offering a

Endowing brain anatomy, dynamics, and function with a network structure is becoming standard in neuroscience. In its simplest form, a network is a collection of units and relationships between them. The pattern of relations among the units encodes numerous properties which have been shown to have a profound effect on networked systems' dynamics and function. In an effort to strike a balance between idealization and detail, network neuroscience studies typically involve simplifying assumptions at both neural and network modeling levels. However, the extent to which existing neural models depend on such approximations is as yet poorly understood. Here, we discuss whether and how increasing neurophysiological detail and generalizing the basic simple network structure often adopted in network neuroscience may help improve our understanding of brain phenomenology and function.

Neuroscience has long informed the development of artificial neural networks, but the success of modern architectures invites, in turn, the converse: can modern networks teach us lessons about brain function? Here, we examine the structure of the cortical column and propose that the transformer provides a natural computational analogy for multiple elements of cortical microcircuit organization. Rather than claiming a literal implementation of transformer equations in cortex, we develop a hypothetical mapping between transformer operations and laminar cortical features, using the analogy as an orienting framework for analysis and discussion. This mapping allows us to examine in greater depth how contextual selection, content routing, recurrent integration, and interlaminar transformations may be distributed across cortical circuitry. In doing so, we generate a broad set of predictions and experimentally testable hypotheses concerning laminar specialization, contextual modulation, dendritic integration, oscillatory coordination, and the effective connectivity of cortical columns. This proposal is intended as a structured hypothesis rather than a definitive account of cortical computa

Videogames have been a catalyst for advances in many research fields, such as artificial intelligence, human-computer interaction or virtual reality. Over the years, research in fields such as artificial intelligence has enabled the design of new types of games, while games have often served as a powerful tool for testing and simulation. Can this also happen with neuroscience? What is the current relationship between neuroscience and games research? what can we expect from the future? In this article, we'll try to answer these questions, analysing the current state-of-the-art at the crossroads between neuroscience and games and envisioning future directions.

The unprecedented availability of large-scale datasets in neuroscience has spurred the exploration of artificial deep neural networks (DNNs) both as empirical tools and as models of natural neural systems. Their appeal lies in their ability to approximate arbitrary functions directly from observations, circumventing the need for cumbersome mechanistic modeling. However, without appropriate constraints, DNNs risk producing implausible models, diminishing their scientific value. Moreover, the interpretability of DNNs poses a significant challenge, particularly with the adoption of more complex expressive architectures. In this perspective, we argue for universal differential equations (UDEs) as a unifying approach for model development and validation in neuroscience. UDEs view differential equations as parameterizable, differentiable mathematical objects that can be augmented and trained with scalable deep learning techniques. This synergy facilitates the integration of decades of extensive literature in calculus, numerical analysis, and neural modeling with emerging advancements in AI into a potent framework. We provide a primer on this burgeoning topic in scientific machine learnin

Despite the centrality of the notion of representation in neuroscience, the field lacks a unified framework for the concepts used to characterize representation, leading to disparate use of both terminology and measures associated with it. To offer clarification, we propose a core set of conceptual dimensions that characterize representations in neuroscience. These dimensions describe relations between a neural response, features that may be represented, and downstream effects of the neural response. A neural response may be shown to be sensitive or specific to a feature, invariant to other features, or functional (it is used downstream in the brain). We use information-theoretic measures to illustrate these conceptual dimensions and explain how they relate to data analysis methods such as correlational analyses, decoding and encoding models, representational similarity analysis, and tests of statistical dependence or adaptation. We consider several canonical examples, including models of the representation of orientation, numerosity, and spatial location, which illustrate how the evidence put forth in support or criticism of these models is systematized by our framework. By offeri

Timely identification of issue reports reflecting software vulnerabilities is crucial, particularly for Internet-of-Things (IoT) where analysis is slower than non-IoT systems. While Machine Learning (ML) and Large Language Models (LLMs) detect vulnerability-indicating issues in non-IoT systems, their IoT use remains unexplored. We are the first to tackle this problem by proposing two approaches: (1) combining ML and LLMs with Natural Language Processing (NLP) techniques to detect vulnerability-indicating issues of 21 Eclipse IoT projects and (2) fine-tuning a pre-trained BERT Masked Language Model (MLM) on 11,000 GitHub issues for classifying \vul. Our best performance belongs to a Support Vector Machine (SVM) trained on BERT NLP features, achieving an Area Under the receiver operator characteristic Curve (AUC) of 0.65. The fine-tuned BERT achieves 0.26 accuracy, emphasizing the importance of exposing all data during training. Our contributions set the stage for accurately detecting IoT vulnerabilities from issue reports, similar to non-IoT systems.

A new scientific field is introduced and discussed, named cybernetical neuroscience, which studies mathematical models adopted in computational neuroscience by methods of cybernetics -- the science of control and communication in a living organism, machine and society. It also considers the practical application of the results obtained when studying mathematical models. The main tasks and methods, as well as some results of cybernetic neuroscience are considered.

In recent years, Artificial Intelligence (AI) shows a spectacular ability of insertion inside a variety of disciplines which use it for scientific advancements and which sometimes improve it for their conceptual and methodological needs. According to the transverse science framework originally conceived by Shinn and Joerges, AI can be seen as an instrument which is progressively acquiring a universal character through its diffusion across science. In this paper we address empirically one aspect of this diffusion, namely the penetration of AI into a specific field of research. Taking neuroscience as a case study, we conduct a scientometric analysis of the development of AI in this field. We especially study the temporal egocentric citation network around the articles included in this literature, their represented journals and their authors linked together by a temporal collaboration network. We find that AI is driving the constitution of a particular disciplinary ecosystem in neuroscience which is distinct from other subfields, and which is gathering atypical scientific profiles who are coming from neuroscience or outside it. Moreover we observe that this AI community in neuroscienc

Recent advances and reflections on reproducible human neuroscience, especially brain-wide association studies (BWAS) leveraging large datasets, have led to divergent and sometimes opposing views on research practices and priorities. The debates span multiple dimensions. Shifts along these axes have fractured consensus and further fragmented an already heterogeneous field of cognitive neuroscience. Here, we sketch a holistic and integrative response grounded in population neuroscience, organized around a closed-loop "design-analysis-interpretation" research cycle that aims to build consensus while bridging these divides. Our central claim is that population neuroscience offers a unique population-level vantage point for identifying general principles, characterizing inter-individual variabilities, and benchmarking intra-individual changes, thereby providing a supportive framework for small-scale, mechanism-focused studies at the individual level and allowing them to co-evolve with population-level studies. Population neuroscience is not simply about providing larger N for BWAS; its deeper goal is to accumulate a family of cross-scale priors and shared infrastructures that can suppor

In recent years, deep learning revolutionized machine learning and its applications, producing results comparable to human experts in several domains, including neuroscience. Each year, hundreds of scientific publications present applications of deep neural networks for biomedical data analysis. Due to the fast growth of the domain, it could be a complicated and extremely time-consuming task for worldwide researchers to have a clear perspective of the most recent and advanced software libraries. This work contributes to clarify the current situation in the domain, outlining the most useful libraries that implement and facilitate deep learning application to neuroscience, allowing scientists to identify the most suitable options for their research or clinical projects. This paper summarizes the main developments in Deep Learning and their relevance to Neuroscience; it then reviews neuroinformatic toolboxes and libraries, collected from the literature and from specific hubs of software projects oriented to neuroscience research. The selected tools are presented in tables detailing key features grouped by domain of application (e.g. data type, neuroscience area, task), model engineeri

Neuroscience research has evolved to generate increasingly large and complex experimental data sets, and advanced data science tools are taking on central roles in neuroscience research. Neurodata Without Borders (NWB), a standard language for neurophysiology data, has recently emerged as a powerful solution for data management, analysis, and sharing. We here discuss our efforts to implement NWB data science pipelines. We describe general principles and specific use cases that illustrate successes, challenges, and non-trivial decisions in software engineering. We hope that our experience can provide guidance for the neuroscience community and help bridge the gap between experimental neuroscience and data science.