Multi-level models and infrastructures for simulating biological system development

The hierarchical organisation of biological systems plays a crucial role in the pattern formation of gene expression resulting from the morphogenetic processes, where autonomous internal dynamics of cells, as well as cell-to-cell interactions through membranes, are responsible for the emergent peculiar structures of the individual phenotype. Being able to reproduce the systems dynamics at different levels of such a hierarchy might be very useful for studying such a complex phenomenon of self-organisation. The idea is to model the phenomenon in terms of a large and dynamic network of compartments, where the interplay between inter-compartment and intra-compartment events determines the emergent behaviour resulting in the formation of spatial patterns. According to these premises the thesis proposes a review of the different approaches already developed in modelling developmental biology problems, as well as the main models and infrastructures available in literature for modelling biological systems, analysing their capabilities in tackling multi-compartment / multi-level models. The thesis then introduces a practical framework, MS-BioNET, for modelling and simulating these scenarios exploiting the potential of multi-level dynamics. This is based on (i) a computational model featuring networks of compartments and an enhanced model of chemical reaction addressing molecule transfer, (ii) a logic-oriented language to flexibly specify complex simulation scenarios, and (iii) a simulation engine based on the many-species/many-channels optimised version of Gillespie’s direct method. The thesis finally proposes the adoption of the agent-based model as an approach capable of capture multi-level dynamics. To overcome the problem of parameter tuning in the model, the simulators are supplied with a module for parameter optimisation. The task is defined as an optimisation problem over the parameter space in which the objective function to be minimised is the distance between the output of the simulator and a target one. The problem is tackled with a metaheuristic algorithm. As an example of application of the MS-BioNET framework and of the agent-based model, a model of the first stages of Drosophila Melanogaster development is realised. The model goal is to generate the early spatial pattern of gap gene expression. The correctness of the models is shown comparing the simulation results with real data of gene expression with spatial and temporal resolution, acquired in free on-line sources.

Reuse Mechanisms and Concurrency: From Actors to Agent-Oriented Programming

La presente tesi è dedicata al riuso nel software. Eccettuata un'introduzione organica al tema, l'analisi è a livello dei meccanismi offerti dai linguaggi di programmazione e delle tecniche di sviluppo, con speciale attenzione rivolta al tema della concorrenza. Il primo capitolo fornisce un quadro generale nel quale il riuso del software è descritto, assieme alle ragioni che ne determinano l'importanza e ai punti cruciali relativi alla sua attuazione. Si individuano diversi livelli di riuso sulla base dell'astrazione e degli artefatti in gioco, e si sottolinea come i linguaggi contribuiscano alla riusabilità e alla realizzazione del riuso. In seguito, viene esplorato, con esempi di codice, il supporto al riuso da parte del paradigma ad oggetti, in termini di incapsulamento, ereditarietà, polimorfismo, composizione. La trattazione prosegue analizzando differenti feature – tipizzazione, interfacce, mixin, generics – offerte da vari linguaggi di programmazione, mostrando come esse intervengano sulla riusabilità dei componenti software. A chiudere il capitolo, qualche parola contestualizzata sull'inversione di controllo, la programmazione orientata agli aspetti, e il meccanismo della delega. Il secondo capitolo abbraccia il tema della concorrenza. Dopo aver introdotto l'argomento, vengono approfonditi alcuni significativi modelli di concorrenza: programmazione multi-threaded, task nel linguaggio Ada, SCOOP, modello ad Attori. Essi vengono descritti negli elementi fondamentali e ne vengono evidenziati gli aspetti cruciali in termini di contributo al riuso, con esempi di codice. Relativamente al modello ad Attori, viene presentata la sua implementazione in Scala/Akka come caso studio. Infine, viene esaminato il problema dell'inheritance anomaly, sulla base di esempi e delle tre classi principali di anomalia, e si analizza la suscettibilità del supporto di concorrenza di Scala/Akka a riscontrare tali problemi. Inoltre, in questo capitolo si nota come alcuni aspetti relativi al binomio riuso/concorrenza, tra cui il significato profondo dello stesso, non siano ancora stati adeguatamente affrontati dalla comunità informatica. Il terzo e ultimo capitolo esordisce con una panoramica dell'agent-oriented programming, prendendo il linguaggio simpAL come riferimento. In seguito, si prova ad estendere al caso degli agenti la nozione di riuso approfondita nei capitoli precedenti.

Groupme: city data and multi-preference activity allocation

Classic group recommender systems focus on providing suggestions for a fixed group of people. Our work tries to give an inside look at design- ing a new recommender system that is capable of making suggestions for a sequence of activities, dividing people in subgroups, in order to boost over- all group satisfaction. However, this idea increases problem complexity in more dimensions and creates great challenge to the algorithm’s performance. To understand the e↵ectiveness, due to the enhanced complexity and pre- cise problem solving, we implemented an experimental system from data collected from a variety of web services concerning the city of Paris. The sys- tem recommends activities to a group of users from two di↵erent approaches: Local Search and Constraint Programming. The general results show that the number of subgroups can significantly influence the Constraint Program- ming Approaches’s computational time and e�cacy. Generally, Local Search can find results much quicker than Constraint Programming. Over a lengthy period of time, Local Search performs better than Constraint Programming, with similar final results.

DESIGN AND IMPLEMENT DYNAMIC PROGRAMMING BASED DISCRETE POWER LEVEL SMART HOME SCHEDULING USING FPGA

With the development and capabilities of the Smart Home system, people today are entering an era in which household appliances are no longer just controlled by people, but also operated by a Smart System. This results in a more efficient, convenient, comfortable, and environmentally friendly living environment. A critical part of the Smart Home system is Home Automation, which means that there is a Micro-Controller Unit (MCU) to control all the household appliances and schedule their operating times. This reduces electricity bills by shifting amounts of power consumption from the on-peak hour consumption to the off-peak hour consumption, in terms of different “hour price”. In this paper, we propose an algorithm for scheduling multi-user power consumption and implement it on an FPGA board, using it as the MCU. This algorithm for discrete power level tasks scheduling is based on dynamic programming, which could find a scheduling solution close to the optimal one. We chose FPGA as our system’s controller because FPGA has low complexity, parallel processing capability, a large amount of I/O interface for further development and is programmable on both software and hardware. In conclusion, it costs little time running on FPGA board and the solution obtained is good enough for the consumers.

Context-Oriented Programming

Context-dependent behavior is becoming increasingly important for a wide range of application domains, from pervasive computing to common business applications. Unfortunately, mainstream programming languages do not provide mechanisms that enable software entities to adapt their behavior dynamically to the current execution context. This leads developers to adopt convoluted designs to achieve the necessary runtime flexibility. We propose a new programming technique called Context-oriented Programming (COP) which addresses this problem. COP treats context explicitly, and provides mechanisms to dynamically adapt behavior in reaction to changes in context, even after system deployment at runtime. In this paper we lay the foundations of COP, show how dynamic layer activation enables multi-dimensional dispatch, illustrate the application of COP by examples in several language extensions, and demonstrate that COP is largely independent of other commitments to programming style.

Gesture-Based, Touch-Free Multi-User Gaming on Wall-Sized, High-Resolution Tiled Displays

Having to carry input devices can be inconvenient when interacting with wall-sized, high-resolution tiled displays. Such displays are typically driven by a cluster of computers. Running existing games on a cluster is non-trivial, and the performance attained using software solutions like Chromium is not good enough. This paper presents a touch-free, multi-user, humancomputer interface for wall-sized displays that enables completely device-free interaction. The interface is built using 16 cameras and a cluster of computers, and is integrated with the games Quake 3 Arena (Q3A) and Homeworld. The two games were parallelized using two different approaches in order to run on a 7x4 tile, 21 megapixel display wall with good performance. The touch-free interface enables interaction with a latency of 116 ms, where 81 ms are due to the camera hardware. The rendering performance of the games is compared to their sequential counterparts running on the display wall using Chromium. Parallel Q3A’s framerate is an order of magnitude higher compared to using Chromium. The parallel version of Homeworld performed on par with the sequential, which did not run at all using Chromium. Informal use of the touch-free interface indicates that it works better for controlling Q3A than Homeworld.

Collision Detection: Broad Phase Adaptation from Multi-Core to Multi-GPU Architecture

We present in this paper several contributions on the collision detection optimization centered on hardware performance. We focus on the broad phase which is the first step of the collision detection process and propose three new ways of parallelization of the well-known Sweep and Prune algorithm. We first developed a multi-core model takes into account the number of available cores. Multi-core architecture enables us to distribute geometric computations with use of multi-threading. Critical writing section and threads idling have been minimized by introducing new data structures for each thread. Programming with directives, like OpenMP, appears to be a good compromise for code portability. We then proposed a new GPU-based algorithm also based on the "Sweep and Prune" that has been adapted to multi-GPU architectures. Our technique is based on a spatial subdivision method used to distribute computations among GPUs. Results show that significant speed-up can be obtained by passing from 1 to 4 GPUs in a large-scale environment.

An optimized multi-proxy, multi-site Antarctic ice and gas orbital chronology (AICC2012): 120--800 ka

An accurate and coherent chronological framework is essential for the interpretation of climatic and environmental records obtained from deep polar ice cores. Until now, one common ice core age scale had been developed based on an inverse dating method (Datice), combining glaciological modelling with absolute and stratigraphic markers between 4 ice cores covering the last 50 ka (thousands of years before present) (Lemieux-Dudon et al., 2010). In this paper, together with the companion paper of Veres et al. (2013), we present an extension of this work back to 800 ka for the NGRIP, TALDICE, EDML, Vostok and EDC ice cores using an improved version of the Datice tool. The AICC2012 (Antarctic Ice Core Chronology 2012) chronology includes numerous new gas and ice stratigraphic links as well as improved evaluation of background and associated variance scenarios. This paper concentrates on the long timescales between 120–800 ka. In this framework, new measurements of δ18Oatm over Marine Isotope Stage (MIS) 11–12 on EDC and a complete δ18Oatm record of the TALDICE ice cores permit us to derive additional orbital gas age constraints. The coherency of the different orbitally deduced ages (from δ18Oatm, δO2/N2 and air content) has been verified before implementation in AICC2012. The new chronology is now independent of other archives and shows only small differences, most of the time within the original uncertainty range calculated by Datice, when compared with the previous ice core reference age scale EDC3, the Dome F chronology, or using a comparison between speleothems and methane. For instance, the largest deviation between AICC2012 and EDC3 (5.4 ka) is obtained around MIS 12. Despite significant modifications of the chronological constraints around MIS 5, now independent of speleothem records in AICC2012, the date of Termination II is very close to the EDC3 one.

Segmentation and Recognition of Multi-Food Meal Images for Carbohydrate Counting

In this paper, we propose novel methodologies for the automatic segmentation and recognition of multi-food images. The proposed methods implement the first modules of a carbohydrate counting and insulin advisory system for type 1 diabetic patients. Initially the plate is segmented using pyramidal mean-shift filtering and a region growing algorithm. Then each of the resulted segments is described by both color and texture features and classified by a support vector machine into one of six different major food classes. Finally, a modified version of the Huang and Dom evaluation index was proposed, addressing the particular needs of the food segmentation problem. The experimental results prove the effectiveness of the proposed method achieving a segmentation accuracy of 88.5% and recognition rate equal to 87%

Multi-Model Data Fusion to Improve an Early Warning System for Hypo-/Hyperglycemic Events

Correct predictions of future blood glucose levels in individuals with Type 1 Diabetes (T1D) can be used to provide early warning of upcoming hypo-/hyperglycemic events and thus to improve the patient's safety. To increase prediction accuracy and efficiency, various approaches have been proposed which combine multiple predictors to produce superior results compared to single predictors. Three methods for model fusion are presented and comparatively assessed. Data from 23 T1D subjects under sensor-augmented pump (SAP) therapy were used in two adaptive data-driven models (an autoregressive model with output correction - cARX, and a recurrent neural network - RNN). Data fusion techniques based on i) Dempster-Shafer Evidential Theory (DST), ii) Genetic Algorithms (GA), and iii) Genetic Programming (GP) were used to merge the complimentary performances of the prediction models. The fused output is used in a warning algorithm to issue alarms of upcoming hypo-/hyperglycemic events. The fusion schemes showed improved performance with lower root mean square errors, lower time lags, and higher correlation. In the warning algorithm, median daily false alarms (DFA) of 0.25%, and 100% correct alarms (CA) were obtained for both event types. The detection times (DT) before occurrence of events were 13.0 and 12.1 min respectively for hypo-/hyperglycemic events. Compared to the cARX and RNN models, and a linear fusion of the two, the proposed fusion schemes represents a significant improvement.

SOMS: SurrOgate MultiStart algorithm for use with nonlinear programming for global optimization

SOMS is a general surrogate-based multistart algorithm, which is used in combination with any local optimizer to find global optima for computationally expensive functions with multiple local minima. SOMS differs from previous multistart methods in that a surrogate approximation is used by the multistart algorithm to help reduce the number of function evaluations necessary to identify the most promising points from which to start each nonlinear programming local search. SOMS’s numerical results are compared with four well-known methods, namely, Multi-Level Single Linkage (MLSL), MATLAB’s MultiStart, MATLAB’s GlobalSearch, and GLOBAL. In addition, we propose a class of wavy test functions that mimic the wavy nature of objective functions arising in many black-box simulations. Extensive comparisons of algorithms on the wavy testfunctions and on earlier standard global-optimization test functions are done for a total of 19 different test problems. The numerical results indicate that SOMS performs favorably in comparison to alternative methods and does especially well on wavy functions when the number of function evaluations allowed is limited.

Youth empowerment evaluation to improve afterschool programming

Community-based participatory research necessitates that community members act as partners in decision making and mutual learning and discovery. In the same light, for programs/issues involving youth, youth should be partners in knowledge sharing and evaluation (Checkoway & Richards-Schuster, 2004). This study is a youth-focused empowerment evaluation for the Successful Youth program. Successful Youth is a multi-component youth development after-school program for Latino middle school youth, created with the goal of reducing teen pregnancy. An empowerment evaluation is collaborative and participatory (Balcazar and Harper 2003). The three steps of an empowerment evaluation are: (1) defining mission, (2) taking stock, and (3) planning for the future (Fetterman 2001).^ In a program where youth are developing leadership skills, making choices, and learning how to self reflect and evaluate, the empowerment evaluation could not be more aligned with promoting and enhancing these skills. In addition, an empowerment evaluation is designed to "foster improvement and self-determination" and "build capacity" (Fetterman 2001). Four empowerment groups were conducted with approximately 6-9 Latino 7th grade students per group. All participants were enrolled in the Successful Youth program. Results indicate points where students' perceptions of the program were aligned with the program's mission and where gaps were identified. Students offered recommendations for program improvements. Additionally, students enjoyed expressing their feelings about the program and appreciated that their opinions were valued. Youth recommendations will be brought to program staff; and, where possible, gaps will be addressed. Empowerment evaluations with youth will continue during the duration of the program so that youth involvement and input remains integral in the evaluation and to ascertain whether the program's goals are being met. ^

Engaging stakeholders in community-level obesity prevention programming: Evaluation of the Fit Family Challenge

Introduction: Both a systems approach to change and a focus on multi-sector interventions ensures obesity prevention programming within the community is equitable, sustainable, and cost-effective. An authentic community engagement approach is required to implement interventions guided by best-evidence research and practice. Although there are examples illustrating the benefits of community engagement, there is no standardized method to implement it. The San Antonio Sports Foundation (SA Sports), a non-profit community-based organization, implements a variety of free events and programs promoting active life styles. One such program is the Fit Family Challenge which is a summer-long program implemented at the school level targeted at families. ^ Aims: This thesis was a culmination of the experience from the student collaborating with SA Sports as part of a practicum opportunity. Using secondary data collected by the Fit Family Challenge during the 2011 year, the goals of this thesis were: to assess individual changes; evaluate short-term impact; and describe the community engagement process. ^ Methods: SA Sports collected quantitative and qualitative data during the implementation and evaluation of the FFC program. SA Sports allowed the used of de-identified data to be analyzed to study the aims of this thesis. ^ Results: The program was able to provide families with the knowledge, information, and opportunity to exercise as a family and cook healthier meals. School district coordinators were generally satisfied and illustrated the benefits of a community partnership. An authentic community engagement was present highlighting the importance of communication, collaboration and the sustainability of such partnerships in the community. ^ Conclusion: The success of an obesity program should focus on triggers that initiate behavioral change rather than physiological changes. The evaluation was guided by a community engagement approach, which illustrated the development of new partnerships and the strengthening of other collaborations. Ultimately, the engagement approach empowered the community to identify their own problems and build collaboration, rather than tackling obesity prevention alone. ^