Investigating biocomplexity through the agent-based paradigm.

Capturing the dynamism that pervades biological systems requires a computational approach that can accommodate both the continuous features of the system environment as well as the flexible and heterogeneous nature of component interactions. This presents a serious challenge for the more traditional mathematical approaches that assume component homogeneity to relate system observables using mathematical equations. While the homogeneity condition does not lead to loss of accuracy while simulating various continua, it fails to offer detailed solutions when applied to systems with dynamically interacting heterogeneous components. As the functionality and architecture of most biological systems is a product of multi-faceted individual interactions at the sub-system level, continuum models rarely offer much beyond qualitative similarity. Agent-based modelling is a class of algorithmic computational approaches that rely on interactions between Turing-complete finite-state machines--or agents--to simulate, from the bottom-up, macroscopic properties of a system. In recognizing the heterogeneity condition, they offer suitable ontologies to the system components being modelled, thereby succeeding where their continuum counterparts tend to struggle. Furthermore, being inherently hierarchical, they are quite amenable to coupling with other computational paradigms. The integration of any agent-based framework with continuum models is arguably the most elegant and precise way of representing biological systems. Although in its nascence, agent-based modelling has been utilized to model biological complexity across a broad range of biological scales (from cells to societies). In this article, we explore the reasons that make agent-based modelling the most precise approach to model biological systems that tend to be non-linear and complex

Mobile Robots

The objective of this book is to cover advances of mobile robotics and related technologies applied for multi robot systems' design and development. Design of control system is a complex issue, requiring the application of information technologies to link the robots into a single network. Human robot interface becomes a demanding task, especially when we try to use sophisticated methods for brain signal processing. Generated electrophysiological signals can be used to command different devices, such as cars, wheelchair or even video games. A number of developments in navigation and path planning, including parallel programming, can be observed. Cooperative path planning, formation control of multi robotic agents, communication and distance measurement between agents are shown. Training of the mobile robot operators is very difficult task also because of several factors related to different task execution. The presented improvement is related to environment model generation based on autonomous mobile robot observations

NON-RIGID BODY MECHANICAL PROPERTY RECOVERY FROM IMAGES AND VIDEOS

Material property has great importance in surgical simulation and virtual reality. The mechanical properties of the human soft tissue are critical to characterize the tissue deformation of each patient. Studies have shown that the tissue stiffness described by the tissue properties may indicate abnormal pathological process. The (recovered) elasticity parameters can assist surgeons to perform better pre-op surgical planning and enable medical robots to carry out personalized surgical procedures. Traditional elasticity parameters estimation methods rely largely on known external forces measured by special devices and strain field estimated by landmarks on the deformable bodies. Or they are limited to mechanical property estimation for quasi-static deformation. For virtual reality applications such as virtual try-on, garment material capturing is of equal significance as the geometry reconstruction. In this thesis, I present novel approaches for automatically estimating the material properties of soft bodies from images or from a video capturing the motion of the deformable body. I use a coupled simulation-optimization-identification framework to deform one soft body at its original, non-deformed state to match the deformed geometry of the same object in its deformed state. The optimal set of material parameters is thereby determined by minimizing the error metric function. This method can simultaneously recover the elasticity parameters of multiple regions of soft bodies using Finite Element Method-based simulation (of either linear or nonlinear materials undergoing large deformation) and particle-swarm optimization methods. I demonstrate the effectiveness of this approach on real-time interaction with virtual organs in patient-specific surgical simulation, using parameters acquired from low-resolution medical images. With the recovered elasticity parameters and the age of the prostate cancer patients as features, I build a cancer grading and staging classifier. The classifier achieves up to 91% for predicting cancer T-Stage and 88% for predicting Gleason score. To recover the mechanical properties of soft bodies from a video, I propose a method which couples statistical graphical model with FEM simulation. Using this method, I can recover the material properties of a soft ball from a high-speed camera video that captures the motion of the ball. Furthermore, I extend the material recovery framework to fabric material identification. I propose a novel method for garment material extraction from a single-view image and a learning based cloth material recovery method from a video recording the motion of the cloth. Most recent garment capturing techniques rely on acquiring multiple views of clothing, which may not always be readily available, especially in the case of pre-existing photographs from the web. As an alternative, I propose a method that can compute a 3D model of a human body and its outfit from a single photograph with little human interaction. My proposed learning-based cloth material type recovery method exploits simulated data-set and deep neural network. I demonstrate the effectiveness of my algorithms by re-purposing the reconstructed garments for virtual try-on, garment transfer, and cloth animation on digital characters. With the recovered mechanical properties, one can construct a virtual world with soft objects exhibiting real-world behaviors.Doctor of Philosoph

Planning for steerable needles in neurosurgery

The increasing adoption of robotic-assisted surgery has opened up the possibility to control innovative dexterous tools to improve patient outcomes in a minimally invasive way. Steerable needles belong to this category, and their potential has been recognised in various surgical fields, including neurosurgery. However, planning for steerable catheters' insertions might appear counterintuitive even for expert clinicians. Strategies and tools to aid the surgeon in selecting a feasible trajectory to follow and methods to assist them intra-operatively during the insertion process are currently of great interest as they could accelerate steerable needles' translation from research to practical use. However, existing computer-assisted planning (CAP) algorithms are often limited in their ability to meet both operational and kinematic constraints in the context of precise neurosurgery, due to its demanding surgical conditions and highly complex environment. The research contributions in this thesis relate to understanding the existing gap in planning curved insertions for steerable needles and implementing intelligent CAP techniques to use in the context of neurosurgery. Among this thesis contributions showcase (i) the development of a pre-operative CAP for precise neurosurgery applications able to generate optimised paths at a safe distance from brain sensitive structures while meeting steerable needles kinematic constraints; (ii) the development of an intra-operative CAP able to adjust the current insertion path with high stability while compensating for online tissue deformation; (iii) the integration of both methods into a commercial user front-end interface (NeuroInspire, Renishaw plc.) tested during a series of user-controlled needle steering animal trials, demonstrating successful targeting performances. (iv) investigating the use of steerable needles in the context of laser interstitial thermal therapy (LiTT) for maesial temporal lobe epilepsy patients and proposing the first LiTT CAP for steerable needles within this context. The thesis concludes with a discussion of these contributions and suggestions for future work.Open Acces

Image-Based Force Estimation and Haptic Rendering For Robot-Assisted Cardiovascular Intervention

Clinical studies have indicated that the loss of haptic perception is the prime limitation of robot-assisted cardiovascular intervention technology, hindering its global adoption. It causes compromised situational awareness for the surgeon during the intervention and may lead to health risks for the patients. This doctoral research was aimed at developing technology for addressing the limitation of the robot-assisted intervention technology in the provision of haptic feedback. The literature review showed that sensor-free force estimation (haptic cue) on endovascular devices, intuitive surgeon interface design, and haptic rendering within the surgeon interface were the major knowledge gaps. For sensor-free force estimation, first, an image-based force estimation methods based on inverse finite-element methods (iFEM) was developed and validated. Next, to address the limitation of the iFEM method in real-time performance, an inverse Cosserat rod model (iCORD) with a computationally efficient solution for endovascular devices was developed and validated. Afterward, the iCORD was adopted for analytical tip force estimation on steerable catheters. The experimental studies confirmed the accuracy and real-time performance of the iCORD for sensor-free force estimation. Afterward, a wearable drift-free rotation measurement device (MiCarp) was developed to facilitate the design of an intuitive surgeon interface by decoupling the rotation measurement from the insertion measurement. The validation studies showed that MiCarp had a superior performance for spatial rotation measurement compared to other modalities. In the end, a novel haptic feedback system based on smart magnetoelastic elastomers was developed, analytically modeled, and experimentally validated. The proposed haptics-enabled surgeon module had an unbounded workspace for interventional tasks and provided an intuitive interface. Experimental validation, at component and system levels, confirmed the usability of the proposed methods for robot-assisted intervention systems

High-Performance Modelling and Simulation for Big Data Applications

This open access book was prepared as a Final Publication of the COST Action IC1406 “High-Performance Modelling and Simulation for Big Data Applications (cHiPSet)“ project. Long considered important pillars of the scientific method, Modelling and Simulation have evolved from traditional discrete numerical methods to complex data-intensive continuous analytical optimisations. Resolution, scale, and accuracy have become essential to predict and analyse natural and complex systems in science and engineering. When their level of abstraction raises to have a better discernment of the domain at hand, their representation gets increasingly demanding for computational and data resources. On the other hand, High Performance Computing typically entails the effective use of parallel and distributed processing units coupled with efficient storage, communication and visualisation systems to underpin complex data-intensive applications in distinct scientific and technical domains. It is then arguably required to have a seamless interaction of High Performance Computing with Modelling and Simulation in order to store, compute, analyse, and visualise large data sets in science and engineering. Funded by the European Commission, cHiPSet has provided a dynamic trans-European forum for their members and distinguished guests to openly discuss novel perspectives and topics of interests for these two communities. This cHiPSet compendium presents a set of selected case studies related to healthcare, biological data, computational advertising, multimedia, finance, bioinformatics, and telecommunications

High-Performance Modelling and Simulation for Big Data Applications

This open access book was prepared as a Final Publication of the COST Action IC1406 “High-Performance Modelling and Simulation for Big Data Applications (cHiPSet)“ project. Long considered important pillars of the scientific method, Modelling and Simulation have evolved from traditional discrete numerical methods to complex data-intensive continuous analytical optimisations. Resolution, scale, and accuracy have become essential to predict and analyse natural and complex systems in science and engineering. When their level of abstraction raises to have a better discernment of the domain at hand, their representation gets increasingly demanding for computational and data resources. On the other hand, High Performance Computing typically entails the effective use of parallel and distributed processing units coupled with efficient storage, communication and visualisation systems to underpin complex data-intensive applications in distinct scientific and technical domains. It is then arguably required to have a seamless interaction of High Performance Computing with Modelling and Simulation in order to store, compute, analyse, and visualise large data sets in science and engineering. Funded by the European Commission, cHiPSet has provided a dynamic trans-European forum for their members and distinguished guests to openly discuss novel perspectives and topics of interests for these two communities. This cHiPSet compendium presents a set of selected case studies related to healthcare, biological data, computational advertising, multimedia, finance, bioinformatics, and telecommunications