Bioconductor: open software development for computational biology and bioinformatics.

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples

Towards the development of safe, collaborative robotic freehand ultrasound

The use of robotics in medicine is of growing importance for modern health services, as robotic systems have the capacity to improve upon human tasks, thereby enhancing the treatment ability of a healthcare provider. In the medical sector, ultrasound imaging is an inexpensive approach without the high radiation emissions often associated with other modalities, especially when compared to MRI and CT imaging respectively. Over the past two decades, considerable effort has been invested into freehand ultrasound robotics research and development. However, this research has focused on the feasibility of the application, not the robotic fundamentals, such as motion control, calibration, and contextual awareness. Instead, much of the work is concentrated on custom designed robots, ultrasound image generation and visual servoing, or teleoperation. Research based on these topics often suffer from important limitations that impede their use in an adaptable, scalable, and real-world manner. Particularly, while custom robots may be designed for a specific application, commercial collaborative robots are a more robust and economical solution. Otherwise, various robotic ultrasound studies have shown the feasibility of using basic force control, but rarely explore controller tuning in the context of patient safety and deformable skin in an unstructured environment. Moreover, many studies evaluate novel visual servoing approaches, but do not consider the practicality of relying on external measurement devices for motion control. These studies neglect the importance of robot accuracy and calibration, which allow a system to safely navigate its environment while reducing the imaging errors associated with positioning. Hence, while the feasibility of robotic ultrasound has been the focal point in previous studies, there is a lack of attention to what occurs between system design and image output. This thesis addresses limitations of the current literature through three distinct contributions. Given the force-controlled nature of an ultrasound robot, the first contribution presents a closed-loop calibration approach using impedance control and low-cost equipment. Accuracy is a fundamental requirement for high-quality ultrasound image generation and targeting. This is especially true when following a specified path along a patient or synthesizing 2D slices into a 3D ultrasound image. However, even though most industrial robots are inherently precise, they are not necessarily accurate. While robot calibration itself has been extensively studied, many of the approaches rely on expensive and highly delicate equipment. Experimental testing showed that this method is comparable in quality to traditional calibration using a laser tracker. As demonstrated through an experimental study and validated with a laser tracker, the absolute accuracy of a collaborative robot was improved to a maximum error of 0.990mm, representing a 58.4% improvement when compared to the nominal model. The second contribution explores collisions and contact events, as they are a natural by-product of applications involving physical human-robot interaction (pHRI) in unstructured environments. Robot-assisted medical ultrasound is an example of a task where simply stopping the robot upon contact detection may not be an appropriate reaction strategy. Thus, the robot should have an awareness of body contact location to properly plan force-controlled trajectories along the human body using the imaging probe. This is especially true for remote ultrasound systems where safety and manipulability are important elements to consider when operating a remote medical system through a communication network. A framework is proposed for robot contact classification using the built-in sensor data of a collaborative robot. Unlike previous studies, this classification does not discern between intended vs. unintended contact scenarios, but rather classifies what was involved in the contact event. The classifier can discern different ISO/TS 15066:2016 specific body areas along a human-model leg with 89.37% accuracy. Altogether, this contact distinction framework allows for more complex reaction strategies and tailored robot behaviour during pHRI. Lastly, given that the success of an ultrasound task depends on the capability of the robot system to handle pHRI, pure motion control is insufficient. Force control techniques are necessary to achieve effective and adaptable behaviour of a robotic system in the unstructured ultrasound environment while also ensuring safe pHRI. While force control does not require explicit knowledge of the environment, to achieve an acceptable dynamic behaviour, the control parameters must be tuned. The third contribution proposes a simple and effective online tuning framework for force-based robotic freehand ultrasound motion control. Within the context of medical ultrasound, different human body locations have a different stiffness and will require unique tunings. Through real-world experiments with a collaborative robot, the framework tuned motion control for optimal and safe trajectories along a human leg phantom. The optimization process was able to successfully reduce the mean absolute error (MAE) of the motion contact force to 0.537N through the evolution of eight motion control parameters. Furthermore, contextual awareness through motion classification can offer a framework for pHRI optimization and safety through predictive motion behaviour with a future goal of autonomous pHRI. As such, a classification pipeline, trained using the tuning process motion data, was able to reliably classify the future force tracking quality of a motion session with an accuracy of 91.82 %

A new Taxonomy of Continuous Global Optimization Algorithms

Surrogate-based optimization, nature-inspired metaheuristics, and hybrid combinations have become state of the art in algorithm design for solving real-world optimization problems. Still, it is difficult for practitioners to get an overview that explains their advantages in comparison to a large number of available methods in the scope of optimization. Available taxonomies lack the embedding of current approaches in the larger context of this broad field. This article presents a taxonomy of the field, which explores and matches algorithm strategies by extracting similarities and differences in their search strategies. A particular focus lies on algorithms using surrogates, nature-inspired designs, and those created by design optimization. The extracted features of components or operators allow us to create a set of classification indicators to distinguish between a small number of classes. The features allow a deeper understanding of components of the search strategies and further indicate the close connections between the different algorithm designs. We present intuitive analogies to explain the basic principles of the search algorithms, particularly useful for novices in this research field. Furthermore, this taxonomy allows recommendations for the applicability of the corresponding algorithms.Comment: 35 pages total, 28 written pages, 4 figures, 2019 Reworked Versio

Toward a conceptual framework for designing sustainable cyber-physical system architectures: A systematic mapping study

Cyber-physical systems (CPS) represent devices whose components enable interaction between machines and processes. One of the biggest challenges of these systems today is the ability to adjust to changes at the time of execution as they are implemented in environments with a multidimensional complexity, this challenge is currently addressed from the design of the systems themselves by integrating sustainability. With this problem in mind, the present document describes a systematic mapping study of the literature with the goal of demonstrating the current panorama of the frameworks, designs, and/or models used at the time of initiating the development of a cyber-physical system. As a result, it has been concluded that there is a lack of guidelines to construct sustainable, and evolvable cyber-physical systems. To address these issues, a framework for designing sustainable CPS architectures is outlined

Multi-objective particle swarm optimization for the structural design of concentric tube continuum robots for medical applications

Concentric tube robots belong to the class of continuum robotic systems whose morphology is described by continuous tangent curvature vectors. They are composed of multiple, interacting tubes nested inside one another and are characterized by their inherent flexibility. Concentric tube continuum robots equipped with tools at their distal end have high potential in minimally invasive surgery. Their morphology enables them to reach sites within the body that are inaccessible with commercial tools or that require large incisions. Further, they can be deployed through a tight lumen or follow a nonlinear path. Fundamental research has been the focus during the last years bringing them closer to the operating room. However, there remain challenges that require attention. The structural synthesis of concentric tube continuum robots is one of these challenges, as these types of robots are characterized by their large parameter space. On the one hand, this is advantageous, as they can be deployed in different patients, anatomies, or medical applications. On the other hand, the composition of the tubes and their design is not a straightforward task but one that requires intensive knowledge of anatomy and structural behavior. Prior to the utilization of such robots, the composition of tubes (i.e. the selection of design parameters and application-specific constraints) must be solved to determine a robotic design that is specifically targeted towards an application or patient. Kinematic models that describe the change in morphology and complex motion increase the complexity of this synthesis, as their mathematical description is highly nonlinear. Thus, the state of the art is concerned with the structural design of these types of robots and proposes optimization algorithms to solve for a composition of tubes for a specific patient case or application. However, existing approaches do not consider the overall parameter space, cannot handle the nonlinearity of the model, or multiple objectives that describe most medical applications and tasks. This work aims to solve these fundamental challenges by solving the parameter optimization problem by utilizing a multi-objective optimization algorithm. The main concern of this thesis is the general methodology to solve for patient- and application-specific design of concentric tube continuum robots and presents key parameters, objectives, and constraints. The proposed optimization method is based on evolutionary concepts that can handle multiple objectives, where the set of parameters is represented by a decision vector that can be of variable dimension in multidimensional space. Global optimization algorithms specifically target the constrained search space of concentric tube continuum robots and nonlinear optimization enables to handle the highly nonlinear elasticity modeling. The proposed methodology is then evaluated based on three examples that include cooperative task deployment of two robotic arms, structural stiffness optimization under the consideration of workspace constraints and external forces, and laser-induced thermal therapy in the brain using a concentric tube continuum robot. In summary, the main contributions are 1) the development of an optimization methodology that describes the key parameters, objectives, and constraints of the parameter optimization problem of concentric tube continuum robots, 2) the selection of an appropriate optimization algorithm that can handle the multidimensional search space and diversity of the optimization problem with multiple objectives, and 3) the evaluation of the proposed optimization methodology and structural synthesis based on three real applications

Performance Problem Diagnostics by Systematic Experimentation

Diagnostics of performance problems requires deep expertise in performance engineering and entails a high manual effort. As a consequence, performance evaluations are postponed to the last minute of the development process. In this thesis, we introduce an automatic, experiment-based approach for performance problem diagnostics in enterprise software systems. With this approach, performance engineers can concentrate on their core competences instead of conducting repeating tasks

Concepção e realização de um framework para sistemas embarcados baseados em FPGA aplicado a um classificador Floresta de Caminhos Ótimos

Orientadores: Eurípedes Guilherme de Oliveira Nóbrega, Isabelle Fantoni-Coichot, Vincent FrémontTese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia Mecânica, Université de Technologie de CompiègneResumo: Muitas aplicações modernas dependem de métodos de Inteligência Artificial, tais como classificação automática. Entretanto, o alto custo computacional associado a essas técnicas limita seu uso em plataformas embarcadas com recursos restritos. Grandes quantidades de dados podem superar o poder computacional disponível em tais ambientes, o que torna o processo de projetá-los uma tarefa desafiadora. As condutas de processamento mais comuns usam muitas funções de custo computacional elevadas, o que traz a necessidade de combinar alta capacidade computacional com eficiência energética. Uma possível estratégia para superar essas limitações e prover poder computacional suficiente aliado ao baixo consumo de energia é o uso de hardware especializado como, por exemplo, FPGA. Esta classe de dispositivos é amplamente conhecida por sua boa relação desempenho/consumo, sendo uma alternativa interessante para a construção de sistemas embarcados eficazes e eficientes. Esta tese propõe um framework baseado em FPGA para a aceleração de desempenho de um algoritmo de classificação a ser implementado em um sistema embarcado. A aceleração do desempenho foi atingida usando o esquema de paralelização SIMD, aproveitando as características de paralelismo de grão fino dos FPGA. O sistema proposto foi implementado e testado em hardware FPGA real. Para a validação da arquitetura, um classificador baseado em Teoria dos Grafos, o OPF, foi avaliado em uma proposta de aplicação e posteriormente implementado na arquitetura proposta. O estudo do OPF levou à proposição de um novo algoritmo de aprendizagem para o mesmo, usando conceitos de Computação Evolutiva, visando a redução do tempo de processamento de classificação, que, combinada à implementação em hardware, oferece uma aceleração de desempenho suficiente para ser aplicada em uma variedade de sistemas embarcadosAbstract: Many modern applications rely on Artificial Intelligence methods such as automatic classification. However, the computational cost associated with these techniques limit their use in resource constrained embedded platforms. A high amount of data may overcome the computational power available in such embedded environments while turning the process of designing them a challenging task. Common processing pipelines use many high computational cost functions, which brings the necessity of combining high computational capacity with energy efficiency. One of the strategies to overcome this limitation and provide sufficient computational power allied with low energy consumption is the use of specialized hardware such as FPGA. This class of devices is widely known for their performance to consumption ratio, being an interesting alternative to building capable embedded systems. This thesis proposes an FPGA-based framework for performance acceleration of a classification algorithm to be implemented in an embedded system. Acceleration is achieved using SIMD-based parallelization scheme, taking advantage of FPGA characteristics of fine-grain parallelism. The proposed system is implemented and tested in actual FPGA hardware. For the architecture validation, a graph-based classifier, the OPF, is evaluated in an application proposition and afterward applied to the proposed architecture. The OPF study led to a proposition of a new learning algorithm using evolutionary computation concepts, aiming at classification processing time reduction, which combined to the hardware implementation offers sufficient performance acceleration to be applied in a variety of embedded systemsDoutoradoMecanica dos Sólidos e Projeto MecanicoDoutor em Engenharia Mecânica3077/2013-09CAPE

On microelectronic self-learning cognitive chip systems

After a brief review of machine learning techniques and applications, this Ph.D. thesis examines several approaches for implementing machine learning architectures and algorithms into hardware within our laboratory. From this interdisciplinary background support, we have motivations for novel approaches that we intend to follow as an objective of innovative hardware implementations of dynamically self-reconfigurable logic for enhanced self-adaptive, self-(re)organizing and eventually self-assembling machine learning systems, while developing this new particular area of research. And after reviewing some relevant background of robotic control methods followed by most recent advanced cognitive controllers, this Ph.D. thesis suggests that amongst many well-known ways of designing operational technologies, the design methodologies of those leading-edge high-tech devices such as cognitive chips that may well lead to intelligent machines exhibiting conscious phenomena should crucially be restricted to extremely well defined constraints. Roboticists also need those as specifications to help decide upfront on otherwise infinitely free hardware/software design details. In addition and most importantly, we propose these specifications as methodological guidelines tightly related to ethics and the nowadays well-identified workings of the human body and of its psyche

Evolutionary design assistants for architecture

In its parallel pursuit of an increased competitivity for design offices and more pleasurable and easier workflows for designers, artificial design intelligence is a technical, intellectual, and political challenge. While human-machine cooperation has become commonplace through Computer Aided Design (CAD) tools, a more improved collaboration and better support appear possible only through an endeavor into a kind of artificial design intelligence, which is more sensitive to the human perception of affairs. Considered as part of the broader Computational Design studies, the research program of this quest can be called Artificial / Autonomous / Automated Design (AD). The current available level of Artificial Intelligence (AI) for design is limited and a viable aim for current AD would be to develop design assistants that are capable of producing drafts for various design tasks. Thus, the overall aim of this thesis is the development of approaches, techniques, and tools towards artificial design assistants that offer a capability for generating drafts for sub-tasks within design processes. The main technology explored for this aim is Evolutionary Computation (EC), and the target design domain is architecture. The two connected research questions of the study concern, first, the investigation of the ways to develop an architectural design assistant, and secondly, the utilization of EC for the development of such assistants. While developing approaches, techniques, and computational tools for such an assistant, the study also carries out a broad theoretical investigation into the main problems, challenges, and requirements towards such assistants on a rather overall level. Therefore, the research is shaped as a parallel investigation of three main threads interwoven along several levels, moving from a more general level to specific applications. The three research threads comprise, first, theoretical discussions and speculations with regard to both existing literature and the proposals and applications of the thesis; secondly, proposals for descriptive and prescriptive models, mappings, summary illustrations, task structures, decomposition schemes, and integratory frameworks; and finally, experimental applications of these proposals. This tripartite progression allows an evaluation of each proposal both conceptually and practically; thereby, enabling a progressive improvement of the understanding regarding the research question, while producing concrete outputs on the way. Besides theoretical and interpretative examinations, the thesis investigates its subject through a set of practical and speculative proposals, which function as both research instruments and the outputs of the study. The first main output of the study is the “design_proxy” approach (d_p), which is an integrated approach for draft making design assistants. It is an outcome of both theoretical examinations and experimental applications, and proposes an integration of, (1) flexible and relaxed task definitions and representations (instead of strict formalisms), (2) intuitive interfaces that make use of usual design media, (3) evaluation of solution proposals through their similarity to given examples, and (4) a dynamic evolutionary approach for solution generation. The design_proxy approach may be useful for AD researchers that aim at developing practical design assistants, as has been examined and demonstrated with the two applications, i.e., design_proxy.graphics and design_proxy.layout. The second main output, the “Interleaved Evolutionary Algorithm” (IEA, or Interleaved EA) is a novel evolutionary algorithm proposed and used as the underlying generative mechanism of design_proxybased design assistants. The Interleaved EA is a dynamic, adaptive, and multi-objective EA, in which one of the objectives leads the evolution until its fitness progression stagnates; in the sense that the settings and fitness values of this objective is used for most evolutionary decisions. In this way, the Interleaved EA enables the use of different settings and operators for each of the objectives within an overall task, which would be the same for all objectives in a regular multi-objective EA. This property gives the algorithm a modular structure, which offers an improvable method for the utilization of domain-specific knowledge for each sub-task, i.e., objective. The Interleaved EA can be used by Evolutionary Computation (EC) researchers and by practitioners who employ EC for their tasks. As a third main output, the “Architectural Stem Cells Framework” is a conceptual framework for architectural design assistants. It proposes a dynamic and multi-layered method for combining a set of design assistants for larger tasks in architectural design. The first component of the framework is a layer-based, parallel task decomposition approach, which aims at obtaining a dynamic parallelization of sub-tasks within a more complicated problem. The second component of the framework is a conception for the development mechanisms for building drafts, i.e., Architectural Stem Cells (ASC). An ASC can be conceived as a semantically marked geometric structure, which contains the information that specifies the possibilities and constraints for how an abstract building may develop from an undetailed stage to a fully developed building draft. ASCs are required for re-integrating the separated task layers of an architectural problem through solution-based development. The ASC Framework brings together many of the ideas of this thesis for a practical research agenda and it is presented to the AD researchers in architecture. Finally, the “design_proxy.layout” (d_p.layout) is an architectural layout design assistant based on the design_proxy approach and the IEA. The system uses a relaxed problem definition (producing draft layouts) and a flexible layout representation that permits the overlapping of design units and boundaries. User interaction with the system is carried out through intuitive 2D graphics and the functional evaluations are performed by measuring the similarity of a proposal to existing layouts. Functioning in an integrated manner, these properties make the system a practicable and enjoying design assistant, which was demonstrated through two workshop cases. The d_p.layout is a versatile and robust layout design assistant that can be used by architects in their design processes

Handling minority class problem in threats detection based on heterogeneous ensemble learning approach.

Multiclass problem, such as detecting multi-steps behaviour of Advanced Persistent Threats (APTs) have been a major global challenge, due to their capability to navigates around defenses and to evade detection for a prolonged period of time. Targeted APT attacks present an increasing concern for both cyber security and business continuity. Detecting the rare attack is a classification problem with data imbalance. This paper explores the applications of data resampling techniques, together with heterogeneous ensemble approach for dealing with data imbalance caused by unevenly distributed data elements among classes with our focus on capturing the rare attack. It has been shown that the suggested algorithms provide not only detection capability, but can also classify malicious data traffic corresponding to rare APT attacks