QuantiMus: A Machine Learning-Based Approach for High Precision Analysis of Skeletal Muscle Morphology.

Skeletal muscle injury provokes a regenerative response, characterized by the de novo generation of myofibers that are distinguished by central nucleation and re-expression of developmentally restricted genes. In addition to these characteristics, myofiber cross-sectional area (CSA) is widely used to evaluate muscle hypertrophic and regenerative responses. Here, we introduce QuantiMus, a free software program that uses machine learning algorithms to quantify muscle morphology and molecular features with high precision and quick processing-time. The ability of QuantiMus to define and measure myofibers was compared to manual measurement or other automated software programs. QuantiMus rapidly and accurately defined total myofibers and measured CSA with comparable performance but quantified the CSA of centrally-nucleated fibers (CNFs) with greater precision compared to other software. It additionally quantified the fluorescence intensity of individual myofibers of human and mouse muscle, which was used to assess the distribution of myofiber type, based on the myosin heavy chain isoform that was expressed. Furthermore, analysis of entire quadriceps cross-sections of healthy and mdx mice showed that dystrophic muscle had an increased frequency of Evans blue dye+ injured myofibers. QuantiMus also revealed that the proportion of centrally nucleated, regenerating myofibers that express embryonic myosin heavy chain (eMyHC) or neural cell adhesion molecule (NCAM) were increased in dystrophic mice. Our findings reveal that QuantiMus has several advantages over existing software. The unique self-learning capacity of the machine learning algorithms provides superior accuracy and the ability to rapidly interrogate the complete muscle section. These qualities increase rigor and reproducibility by avoiding methods that rely on the sampling of representative areas of a section. This is of particular importance for the analysis of dystrophic muscle given the "patchy" distribution of muscle pathology. QuantiMus is an open source tool, allowing customization to meet investigator-specific needs and provides novel analytical approaches for quantifying muscle morphology

QuantiMus: A Machine Learning-Based Approach for High Precision Analysis of Skeletal Muscle Morphology

Skeletal muscle injury provokes a regenerative response, characterized by the de novo generation of myofibers that are distinguished by central nucleation and re-expression of developmentally restricted genes. In addition to these characteristics, myofiber crosssectional area (CSA) is widely used to evaluate muscle hypertrophic and regenerative responses. Here, we introduce QuantiMus, a free software program that uses machine learning algorithms to quantify muscle morphology and molecular features with high precision and quick processing-time. The ability of QuantiMus to define and measure myofibers was compared to manual measurement or other automated software programs. QuantiMus rapidly and accurately defined total myofibers and measured CSA with comparable performance but quantified the CSA of centrally-nucleated fibers (CNFs) with greater precision compared to other software. It additionally quantified the fluorescence intensity of individual myofibers of human and mouse muscle, which was used to assess the distribution of myofiber type, based on the myosin heavy chain isoform that was expressed. Furthermore, analysis of entire quadriceps cross-sections of healthy and mdx mice showed that dystrophic muscle had an increased frequency of Evans blue dye+ injured myofibers. QuantiMus also revealed that the proportion of centrally nucleated, regenerating myofibers that express embryonic myosin heavy chain (eMyHC) or neural cell adhesion molecule (NCAM) were increased in dystrophic mice. Our findings reveal that QuantiMus has several advantages over existing software. The unique self-learning capacity of the machine learning algorithms provides superior accuracy and the ability to rapidly interrogate the complete muscle section. These qualities increase rigor and reproducibility by avoiding methods that rely on the sampling of representative areas of a section. This is of particular importance for the analysis of dystrophic muscle given the “patchy” distribution of muscle pathology. QuantiMus is an open source tool, allowing customization to meet investigatorspecific needs and provides novel analytical approaches for quantifying muscle morphology

A federated learning framework for the next-generation machine learning systems

Dissertação de mestrado em Engenharia Eletrónica Industrial e Computadores (especialização em Sistemas Embebidos e Computadores)The end of Moore's Law aligned with rising concerns about data privacy is forcing machine learning (ML) to shift from the cloud to the deep edge, near to the data source. In the next-generation ML systems, the inference and part of the training process will be performed right on the edge, while the cloud will be responsible for major ML model updates. This new computing paradigm, referred to by academia and industry researchers as federated learning, alleviates the cloud and network infrastructure while increasing data privacy. Recent advances have made it possible to efficiently execute the inference pass of quantized artificial neural networks on Arm Cortex-M and RISC-V (RV32IMCXpulp) microcontroller units (MCUs). Nevertheless, the training is still confined to the cloud, imposing the transaction of high volumes of private data over a network. To tackle this issue, this MSc thesis makes the first attempt to run a decentralized training in Arm Cortex-M MCUs. To port part of the training process to the deep edge is proposed L-SGD, a lightweight version of the stochastic gradient descent optimized for maximum speed and minimal memory footprint on Arm Cortex-M MCUs. The L-SGD is 16.35x faster than the TensorFlow solution while registering a memory footprint reduction of 13.72%. This comes at the cost of a negligible accuracy drop of only 0.12%. To merge local model updates returned by edge devices this MSc thesis proposes R-FedAvg, an implementation of the FedAvg algorithm that reduces the impact of faulty model updates returned by malicious devices.O fim da Lei de Moore aliado às crescentes preocupações sobre a privacidade dos dados gerou a necessidade de migrar as aplicações de Machine Learning (ML) da cloud para o edge, perto da fonte de dados. Na próxima geração de sistemas ML, a inferência e parte do processo de treino será realizada diretamente no edge, enquanto que a cloud será responsável pelas principais atualizações do modelo ML. Este novo paradigma informático, referido pelos investigadores académicos e industriais como treino federativo, diminui a sobrecarga na cloud e na infraestrutura de rede, ao mesmo tempo que aumenta a privacidade dos dados. Avanços recentes tornaram possível a execução eficiente do processo de inferência de redes neurais artificiais quantificadas em microcontroladores Arm Cortex-M e RISC-V (RV32IMCXpulp). No entanto, o processo de treino continua confinado à cloud, impondo a transação de grandes volumes de dados privados sobre uma rede. Para abordar esta questão, esta dissertação faz a primeira tentativa de realizar um treino descentralizado em microcontroladores Arm Cortex-M. Para migrar parte do processo de treino para o edge é proposto o L-SGD, uma versão lightweight do tradicional método stochastic gradient descent (SGD), otimizada para uma redução de latência do processo de treino e uma redução de recursos de memória nos microcontroladores Arm Cortex-M. O L-SGD é 16,35x mais rápido do que a solução disponibilizada pelo TensorFlow, ao mesmo tempo que regista uma redução de utilização de memória de 13,72%. O custo desta abordagem é desprezível, sendo a perda de accuracy do modelo de apenas 0,12%. Para fundir atualizações de modelos locais devolvidas por dispositivos do edge, é proposto o RFedAvg, uma implementação do algoritmo FedAvg que reduz o impacto de atualizações de modelos não contributivos devolvidos por dispositivos maliciosos

Two and three dimensional segmentation of multimodal imagery

The role of segmentation in the realms of image understanding/analysis, computer vision, pattern recognition, remote sensing and medical imaging in recent years has been significantly augmented due to accelerated scientific advances made in the acquisition of image data. This low-level analysis protocol is critical to numerous applications, with the primary goal of expediting and improving the effectiveness of subsequent high-level operations by providing a condensed and pertinent representation of image information. In this research, we propose a novel unsupervised segmentation framework for facilitating meaningful segregation of 2-D/3-D image data across multiple modalities (color, remote-sensing and biomedical imaging) into non-overlapping partitions using several spatial-spectral attributes. Initially, our framework exploits the information obtained from detecting edges inherent in the data. To this effect, by using a vector gradient detection technique, pixels without edges are grouped and individually labeled to partition some initial portion of the input image content. Pixels that contain higher gradient densities are included by the dynamic generation of segments as the algorithm progresses to generate an initial region map. Subsequently, texture modeling is performed and the obtained gradient, texture and intensity information along with the aforementioned initial partition map are used to perform a multivariate refinement procedure, to fuse groups with similar characteristics yielding the final output segmentation. Experimental results obtained in comparison to published/state-of the-art segmentation techniques for color as well as multi/hyperspectral imagery, demonstrate the advantages of the proposed method. Furthermore, for the purpose of achieving improved computational efficiency we propose an extension of the aforestated methodology in a multi-resolution framework, demonstrated on color images. Finally, this research also encompasses a 3-D extension of the aforementioned algorithm demonstrated on medical (Magnetic Resonance Imaging / Computed Tomography) volumes