Towards a Reference Architecture with Modular Design for Large-scale Genotyping and Phenotyping Data Analysis: A Case Study with Image Data

With the rapid advancement of computing technologies, various scientific research communities have been extensively using cloud-based software tools or applications. Cloud-based applications allow users to access software applications from web browsers while relieving them from the installation of any software applications in their desktop environment. For example, Galaxy, GenAP, and iPlant Colaborative are popular cloud-based systems for scientific workflow analysis in the domain of plant Genotyping and Phenotyping. These systems are being used for conducting research, devising new techniques, and sharing the computer assisted analysis results among collaborators. Researchers need to integrate their new workflows/pipelines, tools or techniques with the base system over time. Moreover, large scale data need to be processed within the time-line for more effective analysis. Recently, Big Data technologies are emerging for facilitating large scale data processing with commodity hardware. Among the above-mentioned systems, GenAp is utilizing the Big Data technologies for specific cases only. The structure of such a cloud-based system is highly variable and complex in nature. Software architects and developers need to consider totally different properties and challenges during the development and maintenance phases compared to the traditional business/service oriented systems. Recent studies report that software engineers and data engineers confront challenges to develop analytic tools for supporting large scale and heterogeneous data analysis. Unfortunately, less focus has been given by the software researchers to devise a well-defined methodology and frameworks for flexible design of a cloud system for the Genotyping and Phenotyping domain. To that end, more effective design methodologies and frameworks are an urgent need for cloud based Genotyping and Phenotyping analysis system development that also supports large scale data processing. In our thesis, we conduct a few studies in order to devise a stable reference architecture and modularity model for the software developers and data engineers in the domain of Genotyping and Phenotyping. In the first study, we analyze the architectural changes of existing candidate systems to find out the stability issues. Then, we extract architectural patterns of the candidate systems and propose a conceptual reference architectural model. Finally, we present a case study on the modularity of computation-intensive tasks as an extension of the data-centric development. We show that the data-centric modularity model is at the core of the flexible development of a Genotyping and Phenotyping analysis system. Our proposed model and case study with thousands of images provide a useful knowledge-base for software researchers, developers, and data engineers for cloud based Genotyping and Phenotyping analysis system development

Artificial Intelligence Applied to Conceptual Design. A Review of Its Use in Architecture

Financiado para publicación en acceso aberto: Universidade da Coruña/CISUG[Abstract] Conceptual architectural design is a complex process that draws on past experience and creativity to generate new designs. The application of artificial intelligence to this process should not be oriented toward finding a solution in a defined search space since the design requirements are not yet well defined in the conceptual stage. Instead, this process should be considered as an exploration of the requirements, as well as of possible solutions to meet those requirements. This work offers a tour of major research projects that apply artificial intelligence solutions to architectural conceptual design. We examine several approaches, but most of the work focuses on the use of evolutionary computing to perform these tasks. We note a marked increase in the number of papers in recent years, especially since 2015. Most employ evolutionary computing techniques, including cellular automata. Most initial approaches were oriented toward finding innovative and creative forms, while the latest research focuses on optimizing architectural form.This project was supported by the General Directorate of Culture, Education and University Management of Xunta de Galicia (Ref. ED431G/01, ED431D 2017/16), and the Spanish Ministry of Economy and Competitiveness via funding of the unique installation BIOCAI (UNLC08-1E-002, UNLC13-13-3503) and the European Regional Development Funds (FEDER)Xunta de Galicia; ED431G/01Xunta de Galicia; ED431D 2017/1

The diversity-accuracy duality in ensembles of classifiersd

Horizontal scaling of Machine Learning algorithms has the potential to tackle concerns over the scalability and sustainability of Deep Learning methods, viz. their consumption of energy and computational resources, as well their increasing inaccessibility to researchers. One way to enact horizontal scaling is by employing ensemble learning methods, since they enable distribution. There is a consensus on the point that diversity between individual learners leads to better performance, which is why we have focused on it as the criterion for distributing the base models of an ensemble. However, there is no standard agreement on how diversity should be defined and thus how to exploit it to construct a high-performing classifier. Therefore, we have proposed different definitions of diversity and innovative algorithms which promote it in a systematic way. We have first considered architectural diversity with an algorithm called WILDA: Wide Learning of Diverse Architectures. In a distributed fashion, this algorithm evolves a set of neural networks that are pretrained on the target task and diverse w.r.t. architectural feature descriptors. We have then generalised this notion by defining behavioural diversity on the basis of the divergence between the errors made by different models on a dataset. We have defined several diversity metrics and used them to guide a novelty search algorithm which builds an ensemble of behaviourally diverse classifiers. The algorithm promotes diversity in ensembles by explicitly searching for it, without selecting for accuracy. We have then extended this approach with a surrogate diversity model, which reduces the computational burden of this search by eliminating the need to train each network in the population with stochastic gradient descent at each step. These methods have enabled us to investigate the role that both architectural and behavioural diversity play in contributing to the performance of an ensemble. In order to study the relationship between diversity and accuracy in classifier ensembles, we have then proposed several methods that extend the novelty search with accuracy objectives. Surprisingly, we have observed that, with the highest-performing diversity metrics, there is an equivalence between searching for diversity objectives and searching for accuracy objectives. This contradicts widespread assumptions that a trade-off must be found by balancing diversity and accuracy objectives. We therefore posit the existence of a diversity-accuracy duality in ensembles of classifiers. An implication of this is the possibility of evolving diverse ensembles without detriment to their accuracy, since it is implicitly ensured.Open Acces

Memory Hierarchy Hardware-Software Co-design in Embedded Systems

The memory hierarchy is the main bottleneck in modern computer systems as the gap between the speed of the processor and the memory continues to grow larger. The situation in embedded systems is even worse. The memory hierarchy consumes a large amount of chip area and energy, which are precious resources in embedded systems. Moreover, embedded systems have multiple design objectives such as performance, energy consumption, and area, etc. Customizing the memory hierarchy for specific applications is a very important way to take full advantage of limited resources to maximize the performance. However, the traditional custom memory hierarchy design methodologies are phase-ordered. They separate the application optimization from the memory hierarchy architecture design, which tend to result in local-optimal solutions. In traditional Hardware-Software co-design methodologies, much of the work has focused on utilizing reconfigurable logic to partition the computation. However, utilizing reconfigurable logic to perform the memory hierarchy design is seldom addressed. In this paper, we propose a new framework for designing memory hierarchy for embedded systems. The framework will take advantage of the flexible reconfigurable logic to customize the memory hierarchy for specific applications. It combines the application optimization and memory hierarchy design together to obtain a global-optimal solution. Using the framework, we performed a case study to design a new software-controlled instruction memory that showed promising potential.Singapore-MIT Alliance (SMA

Browser-based Data Annotation, Active Learning, and Real-Time Distribution of Artificial Intelligence Models: From Tumor Tissue Microarrays to COVID-19 Radiology.

BACKGROUND: Artificial intelligence (AI) is fast becoming the tool of choice for scalable and reliable analysis of medical images. However, constraints in sharing medical data outside the institutional or geographical space, as well as difficulties in getting AI models and modeling platforms to work across different environments, have led to a "reproducibility crisis" in digital medicine. METHODS: This study details the implementation of a web platform that can be used to mitigate these challenges by orchestrating a digital pathology AI pipeline, from raw data to model inference, entirely on the local machine. We discuss how this federated platform provides governed access to data by consuming the Application Program Interfaces exposed by cloud storage services, allows the addition of user-defined annotations, facilitates active learning for training models iteratively, and provides model inference computed directly in the web browser at practically zero cost. The latter is of particular relevance to clinical workflows because the code, including the AI model, travels to the user's data, which stays private to the governance domain where it was acquired. RESULTS: We demonstrate that the web browser can be a means of democratizing AI and advancing data socialization in medical imaging backed by consumer-facing cloud infrastructure such as Box.com. As a case study, we test the accompanying platform end-to-end on a large dataset of digital breast cancer tissue microarray core images. We also showcase how it can be applied in contexts separate from digital pathology by applying it to a radiology dataset containing COVID-19 computed tomography images. CONCLUSIONS: The platform described in this report resolves the challenges to the findable, accessible, interoperable, reusable stewardship of data and AI models by integrating with cloud storage to maintain user-centric governance over the data. It also enables distributed, federated computation for AI inference over those data and proves the viability of client-side AI in medical imaging. AVAILABILITY: The open-source application is publicly available at , with a short video demonstration at

A Computational Design System for Environmentally Responsive Urban Design

This thesis introduces a design tool that attempts to optimize urban energy needs through the mass-customization of urban typology. Developing low-energy, high-density urban typology is a critical goal for cities given current energy consumption and urban growth trajectories. This target is contradicted in part by the increase of building energy per square meter, required by dense urban typologies. Studies have shown that the energy impact of urban typology design is significant, due to city microclimates, and increased structural and mechanical inputs, and thus justifies coordinating building energy needs in urban neighborhoods. Despite this, current urban energy modeling tools do not account for the consequences of different typology choices and urban modeling tools do not integrate state-of-the-art environmental and energy simulation methods. Recent advances in computational tools can be used to efficiently generate a solution space of potential typologies to fill this gap in current urban design and analysis software. As such the broader goal of this research is to develop a design system that derives high density urban fabric according to a nuanced simulation of urban energy demand. Daylighting, out of the multiple energy reduction strategies available, offers significant opportunity for architectural optimization. Daylighting varies greatly, even at relatively high densities, due to the effects of ambient light, surface reflectance, and building geometry. In conjunction with the decreasing contribution of heating demand in the overall building energy budget this indicates that gains in urban energy efficiency today can be made by focusing on reducing lighting energy demand. Therefore the current goal of this research is to develop a proof-of-concept that generates and optimizes city fabric according to the conflicting objectives of building daylighting potential and urban densification. The proof-of-concept will consist of a parametric set shape grammar that is extended with existing software or algorithmic models to achieve the current goal. The tool consists of four parts: algorithmic city simulation to derive density targets, a generative rule set to encode building typology, a performance simulator to derive solar zoning boundaries and interior illuminance metrics, and finally an optimization method to identify the typology solutions that best match the current thesis goal. Daylighting metrics and material simulation is achieved with the RADIANCE/DAYSIM modeler. Existing urban modeling algorithms will be translated within the shape grammar system to map the dynamics of non-uniform urban densities. Optimization is implemented through the Galapagos evolutionary computing plug-in for Grasshopper3D. The thesis design system integrates research from two domains through computational methods: urban modeling and building performance simulation. The synthesis of this existing research and work thus puts forward a model of integrated city design via generative design systems. The contribution of the synthesis lies in the development of the urban energy-centric form generator, which extends procedural type generation of cities to simulated environmental and material data. The proof-of-concept is licensed under the open-source GNU General Public License, and packaged as a Python-based plug-in for Grasshopper3D, the visual scripting interface for the Rhinoceros3D CAD modeler