981 research outputs found
Unified Framework for Development, Deployment and Robust Testing of Neuroimaging Algorithms
Developing both graphical and commandline user interfaces for neuroimaging algorithms requires considerable effort. Neuroimaging algorithms can meet their potential only if they can be easily and frequently used by their intended users. Deployment of a large suite of such algorithms on multiple platforms requires consistency of user interface controls, consistent results across various platforms and thorough testing.
We present the design and implementation of a novel object-oriented framework that allows for rapid development of complex image analysis algorithms with many reusable components and the ability to easily add graphical user interface controls. Our framework also allows for simplified yet robust nightly testing of the algorithms to ensure stability and cross platform interoperability. All of the functionality is encapsulated into a software object requiring no separate source code for user interfaces, testing or deployment. This formulation makes our framework ideal for developing novel, stable and easy-to-use algorithms for medical image analysis and computer assisted interventions. The technological The framework has been both deployed at Yale and released for public use in the open source multi-platform image analysis software - BioImage Suite (bioimagesuite.org)
A Maturity Model for Operations in Neuroscience Research
Scientists are adopting new approaches to scale up their activities and
goals. Progress in neurotechnologies, artificial intelligence, automation, and
tools for collaboration promises new bursts of discoveries. However, compared
to other disciplines and the industry, neuroscience laboratories have been slow
to adopt key technologies to support collaboration, reproducibility, and
automation. Drawing on progress in other fields, we define a roadmap for
implementing automated research workflows for diverse research teams. We
propose establishing a five-level capability maturity model for operations in
neuroscience research. Achieving higher levels of operational maturity requires
new technology-enabled methodologies, which we describe as ``SciOps''. The
maturity model provides guidelines for evaluating and upgrading operations in
multidisciplinary neuroscience teams.Comment: 10 pages, one figur
An Automated Images-to-Graphs Framework for High Resolution Connectomics
Reconstructing a map of neuronal connectivity is a critical challenge in
contemporary neuroscience. Recent advances in high-throughput serial section
electron microscopy (EM) have produced massive 3D image volumes of nanoscale
brain tissue for the first time. The resolution of EM allows for individual
neurons and their synaptic connections to be directly observed. Recovering
neuronal networks by manually tracing each neuronal process at this scale is
unmanageable, and therefore researchers are developing automated image
processing modules. Thus far, state-of-the-art algorithms focus only on the
solution to a particular task (e.g., neuron segmentation or synapse
identification).
In this manuscript we present the first fully automated images-to-graphs
pipeline (i.e., a pipeline that begins with an imaged volume of neural tissue
and produces a brain graph without any human interaction). To evaluate overall
performance and select the best parameters and methods, we also develop a
metric to assess the quality of the output graphs. We evaluate a set of
algorithms and parameters, searching possible operating points to identify the
best available brain graph for our assessment metric. Finally, we deploy a
reference end-to-end version of the pipeline on a large, publicly available
data set. This provides a baseline result and framework for community analysis
and future algorithm development and testing. All code and data derivatives
have been made publicly available toward eventually unlocking new biofidelic
computational primitives and understanding of neuropathologies.Comment: 13 pages, first two authors contributed equally V2: Added additional
experiments and clarifications; added information on infrastructure and
pipeline environmen
DEEP-AD: The deep learning model for diagnostic classification and prognostic prediction of alzheimer's disease
In terms of context, the aim of this dissertation is to aid neuroradiologists in their clinical judgment regarding the early detection of AD by using DL. To that aim, the system design research methodology is suggested in this dissertation for achieving three goals.
The first goal is to investigate the DL models that have performed well at identifying patterns associated with AD, as well as the accuracy so far attained, limitations, and gaps. A systematic review of the literature (SLR) revealed a shortage of empirical studies on the early identification of AD through DL. In this regard, thirteen empirical studies were identified and examined. We concluded that three-dimensional (3D) DL models have been generated far less often and that their performance is also inadequate to qualify them for clinical trials.
The second goal is to provide the neuroradiologist with the computer-interpretable information they need to analyze neuroimaging biomarkers. Given this context, the next step in this dissertation is to find the optimum DL model to analyze neuroimaging biomarkers. It has been achieved in
two steps. In the first step, eight state-of-the-art DL models have been implemented by training from scratch using end-to-end learning (E2EL) for two binary classification tasks (AD vs. CN and AD vs. stable MCI) and compared by utilizing MRI scans from the publicly accessible datasets of neuroimaging biomarkers. Comparative analysis is carried out by utilizing efficiency-effects graphs, comprehensive indicators, and ranking mechanisms. For the training of the AD vs. sMCI task, the EfficientNet-B0 model gets the highest value for the comprehensive indicator and has the fewest parameters. DenseNet264 performed better than the others in terms of evaluation matrices, but since it has the most parameters, it costs more to train. For the AD vs. CN task by DenseNet264, we achieved 100% accuracy for training and 99.56% accuracy for testing. However, the classification accuracy was still only 82.5% for the AD vs. sMCI task. In the second step, fusion of transfer learning (TL) with E2EL is applied to train the EfficientNet-B0 for the AD vs. sMCI task, which achieved 95.29% accuracy for training and 93.10% accuracy for testing. Additionally, we have also implemented EfficientNet-B0 for the multiclass AD vs. CN vs. sMCI classification task with E2EL to be used in ensemble of models and achieved 85.66% training accuracy and 87.38% testing accuracy.
To evaluate the model’s robustness, neuroradiologists must validate the implemented model. As a result, the third goal of this dissertation is to create a tool that neuroradiologists may use at their convenience. To achieve this objective, this dissertation proposes a web-based application (DEEP-AD) that has been created by making an ensemble of Efficient-Net B0 and DenseNet 264 (based on the contribution of goal 2).
The accuracy of a DEEP-AD prototype has undergone repeated evaluation and improvement. First, we validated 41 subjects of Spanish MRI datasets (acquired from HT Medica, Madrid, Spain), achieving an accuracy of 82.90%, which was later verified by neuroradiologists. The results of these evaluation studies showed the accomplishment of such goals and relevant directions for future research in applied DL for the early detection of AD in clinical settings.En términos de contexto, el objetivo de esta tesis es ayudar a los neurorradiólogos en su juicio clínico sobre la detección precoz de la AD mediante el uso de DL. Para ello, en esta tesis se propone la metodología de investigación de diseño de sistemas para lograr tres objetivos.
El segundo objetivo es proporcionar al neurorradiólogo la información interpretable por ordenador que necesita para analizar los biomarcadores de neuroimagen. Dado este contexto, el siguiente paso en esta tesis es encontrar el modelo DL óptimo para analizar biomarcadores de neuroimagen. Esto se ha logrado en dos pasos. En el primer paso, se han implementado ocho modelos DL de última generación mediante entrenamiento desde cero utilizando aprendizaje de extremo a extremo (E2EL) para dos tareas de clasificación binarias (AD vs. CN y AD vs. MCI estable) y se han comparado utilizando escaneos MRI de los conjuntos de datos de biomarcadores de neuroimagen de acceso público. El análisis comparativo se lleva a cabo utilizando gráficos de efecto-eficacia, indicadores exhaustivos y mecanismos de clasificación. Para el entrenamiento de la tarea AD vs. sMCI, el modelo EfficientNet-B0 obtiene el valor más alto para el indicador exhaustivo y tiene el menor número de parámetros. DenseNet264 obtuvo mejores resultados que los demás en términos de matrices de evaluación, pero al ser el que tiene más parámetros, su entrenamiento es más costoso. Para la tarea AD vs. CN de DenseNet264, conseguimos una accuracy del 100% en el entrenamiento y del 99,56% en las pruebas. Sin embargo, la accuracy de la clasificación fue sólo del 82,5% para la tarea AD vs. sMCI. En el segundo paso, se aplica la fusión del aprendizaje por transferencia (TL) con E2EL para entrenar la EfficientNet-B0 para la tarea AD vs. sMCI, que alcanzó una accuracy del 95,29% en el entrenamiento y del 93,10% en las pruebas. Además, también hemos implementado EfficientNet-B0 para la tarea de clasificación multiclase AD vs. CN vs. sMCI con E2EL para su uso en conjuntos de modelos y hemos obtenido una accuracy de entrenamiento del 85,66% y una precisión de prueba del 87,38%.
Para evaluar la solidez del modelo, los neurorradiólogos deben validar el modelo implementado. Como resultado, el tercer objetivo de esta disertación es crear una herramienta que los neurorradiólogos puedan utilizar a su conveniencia. Para lograr este objetivo, esta disertación propone una aplicación basada en web (DEEP-AD) que ha sido creada haciendo un ensemble de Efficient-Net B0 y DenseNet 264 (basado en la contribución del objetivo 2).
La accuracy del prototipo DEEP-AD ha sido sometida a repetidas evaluaciones y mejoras. En primer lugar, validamos 41 sujetos de conjuntos de datos de MRI españoles (adquiridos de HT Medica, Madrid, España), logrando una accuracy del 82,90%, que posteriormente fue verificada por neurorradiólogos. Los resultados de estos estudios de evaluación mostraron el cumplimiento de dichos objetivos y las direcciones relevantes para futuras investigaciones en DL, aplicada en la detección precoz de la AD en entornos clínicos.Escuela de DoctoradoDoctorado en Tecnologías de la Información y las Telecomunicacione
A Review on the Role of Nano-Communication in Future Healthcare Systems: A Big Data Analytics Perspective
This paper presents a first-time review of the open literature focused on the significance of big data generated within nano-sensors and nano-communication networks intended for future healthcare and biomedical applications. It is aimed towards the development of modern smart healthcare systems enabled with P4, i.e. predictive, preventive, personalized and participatory capabilities to perform diagnostics, monitoring, and treatment. The analytical capabilities that can be produced from the substantial amount of data gathered in such networks will aid in exploiting the practical intelligence and learning capabilities that could be further integrated with conventional medical and health data leading to more efficient decision making. We have also proposed a big data analytics framework for gathering intelligence, form the healthcare big data, required by futuristic smart healthcare to address relevant problems and exploit possible opportunities in future applications. Finally, the open challenges, future directions for researchers in the evolving healthcare domain, are presented
A Review of the Role of Causality in Developing Trustworthy AI Systems
State-of-the-art AI models largely lack an understanding of the cause-effect
relationship that governs human understanding of the real world. Consequently,
these models do not generalize to unseen data, often produce unfair results,
and are difficult to interpret. This has led to efforts to improve the
trustworthiness aspects of AI models. Recently, causal modeling and inference
methods have emerged as powerful tools. This review aims to provide the reader
with an overview of causal methods that have been developed to improve the
trustworthiness of AI models. We hope that our contribution will motivate
future research on causality-based solutions for trustworthy AI.Comment: 55 pages, 8 figures. Under revie
A Survey of Multimodal Information Fusion for Smart Healthcare: Mapping the Journey from Data to Wisdom
Multimodal medical data fusion has emerged as a transformative approach in
smart healthcare, enabling a comprehensive understanding of patient health and
personalized treatment plans. In this paper, a journey from data to information
to knowledge to wisdom (DIKW) is explored through multimodal fusion for smart
healthcare. We present a comprehensive review of multimodal medical data fusion
focused on the integration of various data modalities. The review explores
different approaches such as feature selection, rule-based systems, machine
learning, deep learning, and natural language processing, for fusing and
analyzing multimodal data. This paper also highlights the challenges associated
with multimodal fusion in healthcare. By synthesizing the reviewed frameworks
and theories, it proposes a generic framework for multimodal medical data
fusion that aligns with the DIKW model. Moreover, it discusses future
directions related to the four pillars of healthcare: Predictive, Preventive,
Personalized, and Participatory approaches. The components of the comprehensive
survey presented in this paper form the foundation for more successful
implementation of multimodal fusion in smart healthcare. Our findings can guide
researchers and practitioners in leveraging the power of multimodal fusion with
the state-of-the-art approaches to revolutionize healthcare and improve patient
outcomes.Comment: This work has been submitted to the ELSEVIER for possible
publication. Copyright may be transferred without notice, after which this
version may no longer be accessibl
A formal architecture-centric and model driven approach for the engineering of science gateways
From n-Tier client/server applications, to more complex academic Grids, or even the most recent and promising industrial Clouds, the last decade has witnessed significant developments in distributed computing. In spite of this conceptual heterogeneity, Service-Oriented Architecture (SOA) seems to have emerged as the common and underlying abstraction paradigm, even though different standards and technologies are applied across application domains. Suitable access to data and algorithms resident in SOAs via so-called ‘Science Gateways’ has thus become a pressing need in order to realize the benefits of distributed computing infrastructures.In an attempt to inform service-oriented systems design and developments in Grid-based biomedical research infrastructures, the applicant has consolidated work from three complementary experiences in European projects, which have developed and deployed large-scale production quality infrastructures and more recently Science Gateways to support research in breast cancer, pediatric diseases and neurodegenerative pathologies respectively. In analyzing the requirements from these biomedical applications the applicant was able to elaborate on commonly faced issues in Grid development and deployment, while proposing an adapted and extensible engineering framework. Grids implement a number of protocols, applications, standards and attempt to virtualize and harmonize accesses to them. Most Grid implementations therefore are instantiated as superposed software layers, often resulting in a low quality of services and quality of applications, thus making design and development increasingly complex, and rendering classical software engineering approaches unsuitable for Grid developments.The applicant proposes the application of a formal Model-Driven Engineering (MDE) approach to service-oriented developments, making it possible to define Grid-based architectures and Science Gateways that satisfy quality of service requirements, execution platform and distribution criteria at design time. An novel investigation is thus presented on the applicability of the resulting grid MDE (gMDE) to specific examples and conclusions are drawn on the benefits of this approach and its possible application to other areas, in particular that of Distributed Computing Infrastructures (DCI) interoperability, Science Gateways and Cloud architectures developments
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