Enlarging a training set for genomic selction by imputation of un-genotyped animals in populations of varying genetic architecture

Background: The most common application of imputation is to infer genotypes of a high-density panel of markers on animals that are genotyped for a low-density panel. However, the increase in accuracy of genomic predictions resulting from an increase in the number of markers tends to reach a plateau beyond a certain density. Another application of imputation is to increase the size of the training set with un-genotyped animals. This strategy can be particularly successful when a set of closely related individuals are genotyped. ----- Methods: Imputation on completely un-genotyped dams was performed using known genotypes from the sire of each dam, one offspring and the offspring’s sire. Two methods were applied based on either allele or haplotype frequencies to infer genotypes at ambiguous loci. Results of these methods and of two available software packages were compared. Quality of imputation under different population structures was assessed. The impact of using imputed dams to enlarge training sets on the accuracy of genomic predictions was evaluated for different populations, heritabilities and sizes of training sets. ----- Results: Imputation accuracy ranged from 0.52 to 0.93 depending on the population structure and the method used. The method that used allele frequencies performed better than the method based on haplotype frequencies. Accuracy of imputation was higher for populations with higher levels of linkage disequilibrium and with larger proportions of markers with more extreme allele frequencies. Inclusion of imputed dams in the training set increased the accuracy of genomic predictions. Gains in accuracy ranged from close to zero to 37.14%, depending on the simulated scenario. Generally, the larger the accuracy already obtained with the genotyped training set, the lower the increase in accuracy achieved by adding imputed dams. ----- Conclusions: Whenever a reference population resembling the family configuration considered here is available, imputation can be used to achieve an extra increase in accuracy of genomic predictions by enlarging the training set with completely un-genotyped dams. This strategy was shown to be particularly useful for populations with lower levels of linkage disequilibrium, for genomic selection on traits with low heritability, and for species or breeds for which the size of the reference population is limited.

Knowledge Building in Landscape Architecture

The objective of this study was to develop an internet-based seminar framework applicable for landscape architecture education. This process was accompanied by various aims. The basic expectation was to keep the main characteristics of landscape architecture education also in the online format. On top of that, four further objectives were anticipated: (1) training of competences for virtual team work, (2) fostering intercultural competence, (3) creation of equal opportunities for education through internet-based open access and (4) synergy effects and learning processes across institutional boundaries. This work started with the hypothesis that these four expected advantages would compensate for additional organisational efforts caused by the online delivery of the seminars and thus lead to a sustainable integration of this new learning mode into landscape architecture curricula. This rationale was followed by a presentation of four areas of knowledge to which the seminar development was directly related (1) landscape architecture as a subject and its pedagogy, (2) general learning theories, (3) developments in the ICT sector and (4) wider societal driving forces such as global citizenship and the increase of open educational resources. The research design took the shape of a pedagogical action research cycle. This approach was constructive: The author herself is teaching international landscape architecture students so that the model could directly be applied in practice. Seven online seminars were implemented in the period from 2008 to 2013 and this experience represents the core of this study. The seminars were conducted with varying themes while its pedagogy, organisation and the technological tools remained widely identical. The research design is further based on three levels of observation: (1) the seminar design on the basis of theory and methods from the learning sciences, in particular educational constructivism, (2) the seminar evaluation and (3) the evaluation of the seminars’ long term impact. The seminar model itself basically consists of four elements: (1) the taxonomy of learning objectives, (2) ICT tools and their application and pedagogy, (3) process models and (4) the case study framework. The seminar framework was followed by the presentation of the evaluation findings. The major findings of this study can be summed up as follows: Implementing online seminars across educational and national boundaries was possible both in term of organisation and technology. In particular, a high level of cultural diversity among the seminar participants has definitively been achieved. However, there were also obvious obstacles. These were primarily competing study commitments and incompatible schedules among the students attending from different academic programmes, partly even in different time zones. Both factors had negative impact on the individual and working group performances. With respect to the technical framework it can be concluded that the majority of the participants were able to use the tools either directly without any problem or after overcoming some smaller problems. Also the seminar wiki was intensively used for completing the seminar assignments. However, too less truly collaborative text production was observed which could be improved by changing the requirements for the collaborative task. Two different process models have been applied for guiding the collaboration of the small groups and both were in general successful. However, it needs to be said that even if the students were able to follow the collaborative task and to co-construct and compare case studies, most of them were not able to synthesize the knowledge they had compiled. This means that the area of consideration often remained on the level of the case and further reflections, generalisations and critique were largely missing. This shows that the seminar model needs to find better ways for triggering knowledge building and critical reflection. It was also suggested to have a more differentiated group building strategy in future seminars. A comparison of pre- and post seminar concept maps showed that an increase of factual and conceptual knowledge on the individual level was widely recognizable. Also the evaluation of the case studies (the major seminar output) revealed that the students have undergone developments of both the factual and the conceptual knowledge domain. Also their self-assessment with respect to individual learning development showed that the highest consensus was achieved in the field of subject-specific knowledge. The participants were much more doubtful with regard to the progress of generic competences such as analysis, communication and organisation. However, 50% of the participants confirmed that they perceived individual development on all competence areas the survey had asked for. Have the additional four targets been met? Concerning the competences for working in a virtual team it can be concluded that the vast majority was able to use the internet-based tools and to work with them in a target-oriented way. However, there were obvious differences regarding the intensity and activity of participation, both because of external and personal factors. A very positive aspect is the achievement of a high cultural diversity supporting the participants’ intercultural competence. Learning from group members was obviously a success factor for the working groups. Regarding the possibilities for better accessibility of educational opportunities it became clear that a significant number of participants were not able to go abroad during their studies because of financial or personal reasons. They confirmed that the online seminar was to some extent a compensation for not having been abroad for studying. Inter-institutional learning and synergy was achieved in so far that many teachers from different countries contributed with individual lectures. However, those teachers hardly ever followed more than one session. Therefore, the learning effect remained largely within the seminar learning group. Looking back at the research design it can be said that the pedagogical action research cycle was an appropriate and valuable approach allowing for strong interaction between theory and practice. However, some more external evaluation from peers in particular regarding the participants’ products would have been valuable.

Performance Evaluation of the Scheme 86 and HP Precision Architecture

The Scheme86 and the HP Precision Architectures represent different trends in computer processor design. The former uses wide micro-instructions, parallel hardware, and a low latency memory interface. The latter encourages pipelined implementation and visible interlocks. To compare the merits of these approaches, algorithms frequently encountered in numerical and symbolic computation were hand-coded for each architecture. Timings were done in simulators and the results were evaluated to determine the speed of each design. Based on these measurements, conclusions were drawn as to which aspects of each architecture are suitable for a high- performance computer.

A Colony Architecture for an Artificial Creature

This report describes a working autonomous mobile robot whose only goal is to collect and return empty soda cans. It operates in an unmodified office environment occupied by moving people. The robot is controlled by a collection of over 40 independent "behaviors'' distributed over a loosely coupled network of 24 processors. Together this ensemble helps the robot locate cans with its laser rangefinder, collect them with its on-board manipulator, and bring them home using a compass and an array of proximity sensors. We discuss the advantages of using such a multi-agent control system and show how to decompose the required tasks into component activities. We also examine the benefits and limitations of spatially local, stateless, and independent computation by the agents.

Pi: A Parallel Architecture Interface for Multi-Model Execution

This thesis defines Pi, a parallel architecture interface that separates model and machine issues, allowing them to be addressed independently. This provides greater flexibility for both the model and machine builder. Pi addresses a set of common parallel model requirements including low latency communication, fast task switching, low cost synchronization, efficient storage management, the ability to exploit locality, and efficient support for sequential code. Since Pi provides generic parallel operations, it can efficiently support many parallel programming models including hybrids of existing models. Pi also forms a basis of comparison for architectural components.

ADAM: A Decentralized Parallel Computer Architecture Featuring Fast Thread and Data Migration and a Uniform Hardware Abstraction

The furious pace of Moore's Law is driving computer architecture into a realm where the the speed of light is the dominant factor in system latencies. The number of clock cycles to span a chip are increasing, while the number of bits that can be accessed within a clock cycle is decreasing. Hence, it is becoming more difficult to hide latency. One alternative solution is to reduce latency by migrating threads and data, but the overhead of existing implementations has previously made migration an unserviceable solution so far. I present an architecture, implementation, and mechanisms that reduces the overhead of migration to the point where migration is a viable supplement to other latency hiding mechanisms, such as multithreading. The architecture is abstract, and presents programmers with a simple, uniform fine-grained multithreaded parallel programming model with implicit memory management. In other words, the spatial nature and implementation details (such as the number of processors) of a parallel machine are entirely hidden from the programmer. Compiler writers are encouraged to devise programming languages for the machine that guide a programmer to express their ideas in terms of objects, since objects exhibit an inherent physical locality of data and code. The machine implementation can then leverage this locality to automatically distribute data and threads across the physical machine by using a set of high performance migration mechanisms. An implementation of this architecture could migrate a null thread in 66 cycles -- over a factor of 1000 improvement over previous work. Performance also scales well; the time required to move a typical thread is only 4 to 5 times that of a null thread. Data migration performance is similar, and scales linearly with data block size. Since the performance of the migration mechanism is on par with that of an L2 cache, the implementation simulated in my work has no data caches and relies instead on multithreading and the migration mechanism to hide and reduce access latencies.

Space System Architecture: Final Report of SSPARC: the Space Systems, Policy, and Architecture Research Consortium (Thrust I and II)

The Space Systems, Policy and Architecture Research Consortium (SSPARC) was formed to make substantial progress on problems of national importance. The goals of SSPARC were to: • Provide technologies and methods that will allow the creation of flexible, upgradable space systems, • Create a “clean sheet” approach to space systems architecture determination and design, including the incorporation of risk, uncertainty, and flexibility issues, and • Consider the impact of national space policy on the above. This report covers the last two goals, and demonstrates that the effort was largely successful.

Fast Sorting on a Distributed-Memory Architecture

We consider the often-studied problem of sorting, for a parallel computer. Given an input array distributed evenly over p processors, the task is to compute the sorted output array, also distributed over the p processors. Many existing algorithms take the approach of approximately load-balancing the output, leaving each processor with Θ(n/p) elements. However, in many cases, approximate load-balancing leads to inefficiencies in both the sorting itself and in further uses of the data after sorting. We provide a deterministic parallel sorting algorithm that uses parallel selection to produce any output distribution exactly, particularly one that is perfectly load-balanced. Furthermore, when using a comparison sort, this algorithm is 1-optimal in both computation and communication. We provide an empirical study that illustrates the efficiency of exact data splitting, and shows an improvement over two sample sort algorithms.

VLSI architecture for an Underwater Robot Vision System

It is well known that image processing requires a huge amount of computation, mainly at low level processing where the algorithms are dealing with a great number of data-pixel. One of the solutions to estimate motions involves detection of the correspondences between two images. For normalised correlation criteria, previous experiments shown that the result is not altered in presence of nonuniform illumination. Usually, hardware for motion estimation has been limited to simple correlation criteria. The main goal of this paper is to propose a VLSI architecture for motion estimation using a matching criteria more complex than Sum of Absolute Differences (SAD) criteria. Today hardware devices provide many facilities for the integration of more and more complex designs as well as the possibility to easily communicate with general purpose processors

Proposal of a parallel architecture for a motion detection algorithm

This paper proposes a parallel architecture for estimation of the motion of an underwater robot. It is well known that image processing requires a huge amount of computation, mainly at low-level processing where the algorithms are dealing with a great number of data. In a motion estimation algorithm, correspondences between two images have to be solved at the low level. In the underwater imaging, normalised correlation can be a solution in the presence of non-uniform illumination. Due to its regular processing scheme, parallel implementation of the correspondence problem can be an adequate approach to reduce the computation time. Taking into consideration the complexity of the normalised correlation criteria, a new approach using parallel organisation of every processor from the architecture is proposed

On AUV control architecture

This paper surveys control architectures proposed in the literature and describes a control architecture that is being developed for a semi-autonomous underwater vehicle for intervention missions (SAUVIM) at the University of Hawaii. Conceived as hybrid, this architecture has been organized in three layers: planning, control and execution. The mission is planned with a sequence of subgoals. Each subgoal has a related task supervisor responsible for arranging a set of pre-programmed task modules in order to achieve the subgoal. Task modules are the key concept of the architecture. They are the main building blocks and can be dynamically re-arranged by the task supervisor. In our architecture, deliberation takes place at the planning layer while reaction is dealt through the parallel execution of the task modules. Hence, the system presents both a hierarchical and an heterarchical decomposition, being able to show a predictable response while keeping rapid reactivity to the dynamic environment

All-Optical Label Stacking: Easing the Trade-offs Between Routing and Architecture Cost in All-Optical Packet Switching

All-optical label swapping (AOLS) forms a key technology towards the implementation of all-optical packet switching nodes (AOPS) for the future optical Internet. The capital expenditures of the deployment of AOLS increases with the size of the label spaces (i.e. the number of used labels), since a special optical device is needed for each recognized label on every node. Label space sizes are affected by the way in which demands are routed. For instance, while shortest-path routing leads to the usage of fewer labels but high link utilization, minimum interference routing leads to the opposite. This paper studies all-optical label stacking (AOLStack), which is an extension of the AOLS architecture. AOLStack aims at reducing label spaces while easing the compromise with link utilization. In this paper, an integer lineal program is proposed with the objective of analyzing the softening of the aforementioned trade-off due to AOLStack. Furthermore, a heuristic aiming at finding good solutions in polynomial-time is proposed as well. Simulation results show that AOLStack either a) reduces the label spaces with a low increase in the link utilization or, similarly, b) uses better the residual bandwidth to decrease the number of labels even more

What is the Web? The Web Architecture

The Introductory Lecture is a discussion about "What is the Web". It involves lots of calling out TLAs and writing them on the blackboard, dividing things into servers, clients, protocols, formats, and the punchline is that the one unique and novel thing about the web is the hypertext link. This follows naturally into the Web architecture - the answer to the question "what is the web".