Genetically Generated Neural Networks II: Searching for an Optimal Representation

Genetic Algorithms (GAs) make use of an internal representation of a given system in order to perform optimization functions. The actual structural layout of this representation, called a genome, has a crucial impact on the outcome of the optimization process. The purpose of this paper is to study the effects of different internal representations in a GA, which generates neural networks. A second GA was used to optimize the genome structure. This structure produces an optimized system within a shorter time interval.

A Spectral Network Model of Pitch Perception

A model of pitch perception, called the Spatial Pitch Network or SPINET model, is developed and analyzed. The model neurally instantiates ideas front the spectral pitch modeling literature and joins them to basic neural network signal processing designs to simulate a broader range of perceptual pitch data than previous spectral models. The components of the model arc interpreted as peripheral mechanical and neural processing stages, which arc capable of being incorporated into a larger network architecture for separating multiple sound sources in the environment. The core of the new model transforms a spectral representation of an acoustic source into a spatial distribution of pitch strengths. The SPINET model uses a weighted "harmonic sieve" whereby the strength of activation of a given pitch depends upon a weighted sum of narrow regions around the harmonics of the nominal pitch value, and higher harmonics contribute less to a pitch than lower ones. Suitably chosen harmonic weighting functions enable computer simulations of pitch perception data involving mistuned components, shifted harmonics, and various types of continuous spectra including rippled noise. It is shown how the weighting functions produce the dominance region, how they lead to octave shifts of pitch in response to ambiguous stimuli, and how they lead to a pitch region in response to the octave-spaced Shepard tone complexes and Deutsch tritones without the use of attentional mechanisms to limit pitch choices. An on-center off-surround network in the model helps to produce noise suppression, partial masking and edge pitch. Finally, it is shown how peripheral filtering and short term energy measurements produce a model pitch estimate that is sensitive to certain component phase relationships.

A Self-Organizing Neural Model of Motor Equivalent Reaching and Tool Use by a Multijoint Arm

This paper describes a self-organizing neural model for eye-hand coordination. Called the DIRECT model, it embodies a solution of the classical motor equivalence problem. Motor equivalence computations allow humans and other animals to flexibly employ an arm with more degrees of freedom than the space in which it moves to carry out spatially defined tasks under conditions that may require novel joint configurations. During a motor babbling phase, the model endogenously generates movement commands that activate the correlated visual, spatial, and motor information that are used to learn its internal coordinate transformations. After learning occurs, the model is capable of controlling reaching movements of the arm to prescribed spatial targets using many different combinations of joints. When allowed visual feedback, the model can automatically perform, without additional learning, reaches with tools of variable lengths, with clamped joints, with distortions of visual input by a prism, and with unexpected perturbations. These compensatory computations occur within a single accurate reaching movement. No corrective movements are needed. Blind reaches using internal feedback have also been simulated. The model achieves its competence by transforming visual information about target position and end effector position in 3-D space into a body-centered spatial representation of the direction in 3-D space that the end effector must move to contact the target. The spatial direction vector is adaptively transformed into a motor direction vector, which represents the joint rotations that move the end effector in the desired spatial direction from the present arm configuration. Properties of the model are compared with psychophysical data on human reaching movements, neurophysiological data on the tuning curves of neurons in the monkey motor cortex, and alternative models of movement control.

The impacts of past land-use on the ecology of an ancient woodland in south-west Ireland

A multi-disciplinary study was conducted to compare stands of ancient and secondary origin within a single wood, the Gearagh woodland, County Cork. These sites were compared with adjacent areas of grassland, which provided a reference for the former land-use (pasture) of the secondary woodland. A historical study confirmed that while the core of the Gearagh has been subject to minimal human interference, other sections have been cleared in the past for agricultural purposes. Investigations into soil structure and composition showed that soil properties in these secondary woodland areas were significantly altered by this past woodland clearance and conversion to agriculture, while the soil of the ancient woodland showed little signs of disturbance. The vegetation community also differed between the two woodland areas, partly due to altered environmental conditions. Many of the ancient woodland plant species were unable to form a persistent seed bank, while there was increased representation of species associated with more open-habitat conditions in the seed bank of the secondary woodland. While germination of woodland species was low in all sites, overall, seeds tended to germinate more successfully in the ancient woodland. The ancient woodland also provided a suitable habitat for many soil and ground detritivores, most notably enchytraeids, although earthworms were not abundant. Past agricultural use, however, changed the decomposer community considerably, with increased representation of earthworm species and a decline in the abundance of enchytraeids in the secondary stands. In conclusion, the legacies of historical agricultural activities can continue to significantly affect the structure and composition of present-day woodlands so that they may differ considerably from undisturbed ancient woodland stands, even within the same woodland. A greater understanding of the origin, development and ecological functioning of ancient woodlands should aid in determining future conservation and management requirements.

Towards a regional understanding of Irish traditional music

The geography of Irish traditional music is a complex, popular and largely unexplored element of the narrative of the tradition. Geographical concepts such as the region are recurrent in the discourse of Irish traditional music but regions and their processes are, for the most part, blurred or misunderstood. This thesis explores the geographical approach to the study of Irish traditional music focusing on the concept of the region and, in particular, the role of memory in the construction and diffusion of regional identities. This is a tripartite study considering people, place and music. Each of these elements impacts on our experience of the other. All societies have created music. Music is often associated with or derived from places. Some places construct or reinforce their identity through the music and musicians through which they are associated. The thesis challenges conventional discourse on regional styles that construct an imagined pattern of regions based on subtle musical differences that may, though are not always, shared by people in that region and focuses on the social networks through which the music is disseminated. The thesis also challenges the abandonment of regional styles and the concept of regions in understanding the complex geographies of Irish traditional music (Morton, 2001). It seeks to find a middle ground between discourse analysis, musical analysis, the experience of music and place, and the representation of music and place. The dissertation is divided into three parts. Part one considers the development of music geography, noting and critiquing the abandonment of useful paradigms in both geography and ethnomusicology in search of new ways of understanding. Of particular interest is the concept of the region but it also considers the study of landscape and the humanist approach in cultural geography. The second part focuses on the discourse and study of regions in Irish traditional music and the various agents and processes that shape the concept of the region in Irish traditional music. The final part presents a case study of the Sliabh Luachra region combining and applying the various perspectives and paradigms drawn from geographical, ethnomusicological and anthropological sources. It attempts to generate an understanding of Sliabh Luachra as a region in the Irish traditional music narrative that is based on a combination of musical, socio-cultural and locational/environmental factors.

The early years in Irish multigrade classes: trajectories of practice and identity

This study investigates how the experiences of Junior Infants are shaped in multigrade classes. Multigrade classes are composed of two or more grades within the same classroom with one teacher having responsibility for the instruction of all grades in this classroom within a time-tabled period (Little, 2001, Mason and Doepner, 1998). The overall aim of the research is to problematize the issues of early childhood pedagogy in multigrade classes in the context of children negotiating identities, positioning and power relations. A Case Study approach was employed to explore the perspectives of the teachers, children and their parents in eight multigrade schools. Concurrent with this, a nation-wide Questionnaire Survey was also conducted which gave a broader context to the case study findings. Findings from the research study suggest that institutional context is vitally important and finding the space to implement pedagogic practices is a highly complex matter for teachers. While a majority of teachers reported the benefits for younger children being in mixed-age settings alongside older children, only a minority of case study school teachers demonstrated how it is possible to promote classroom climates which were provided multiple opportunities for younger children to engage fully in classrooms. The findings reveal constraints on pedagogical practice which included: time pressures within the job, an increase in diversity in pupil population, meeting special needs, large class sizes, high pupil/teacher ratios, and planning/organisation of tasks which intensified the complexities of addressing the needs of children who differ significantly in age, cognitive, social and emotional levels. An emergent and recurrent theme of this study is the representation of Junior Infants as apprentices in their ‘communities of practice’ who contributed in peripheral ways to the practices of their groups (Lave and Wenger, 1991, Wenger, 1998). Through a continuous process of negotiation of meaning, these pupils learned the knowledge and skills within their communities of practice that empowered some to participate more fully than others. The children in their ‘figured worlds’ (Holland, Lachiotte, Skinner and Caine 1998) occupy identities which are influenced by established arrangements of resources and practices within that community as well as by their own agentive actions. Finally, the findings of the study also demonstrate how the dimension of power is central to the exercise of social relations and pedagogical practices in multigrade classes.

Manifestations of heavenly light and fire and the construction of a saint: sanctity, mission and salvation in Adomnán's Vita Columbae

This thesis examines the late seventh-century Latin Life of Columba (Vita Columbae) in a context sympathetic to the spiritual aims and formative intellectual background of its author, Adomnán of Iona. It argues that the Vita Columbae is a sophisticated work, shaped by Adomnán’s spiritual and theological concerns. This sophistication is revealed by a forensic examination of Adomnán’s representation of Columba’s sanctity through a series of miracles, in particular, miracle stories depicting divine manifestations of fire and light. This thesis considers the form and function of these miracle stories in the context of biblical, patristic and medieval interpretations of their archetypes, towards revealing the underlying influence of scriptural, hagiographical and monastic models of sanctity. Chapter one evaluates the function of the Vita Columbae, and outlines the core themes of sanctity which pervade the work, by considering the technical terminology and literary devices found in the opening prefaces in the context of the wider monastic tradition. Chapter two examines Adomnán’s use of biblical models of sanctity to establish Columba’s sanctity, and their relationship between these models and certain miraculous episodes in the Vita Columbae. Chapter three investigates Adomnán’s description of the Holy Spirit as an illuminating fire, and its significance for his portrayal of the saint, by means of a forensic examination of biblical, exegetical and hagiographical treatments of the image. Chapter four examines the missiological, soteriological and providential elements contributing to Adomnán’s portrayal of Columba’s sanctity, as conveyed through the presence of biblical models, particularly the image of the column of fire. Chapter five establishes the influence of monastic examinations of the contemplative life on Adomnán’s portrayal of Columba’s sanctity, and shows how that sanctity is confirmed in terms of his ability to contemplate divine light.

Cost savings from relaxation of operational constraints on a power system with high wind penetration

Wind energy is predominantly a nonsynchronous generation source. Large-scale integration of wind generation with existing electricity systems, therefore, presents challenges in maintaining system frequency stability and local voltage stability. Transmission system operators have implemented system operational constraints (SOCs) in order to maintain stability with high wind generation, but imposition of these constraints results in higher operating costs. A mixed integer programming tool was used to simulate generator dispatch in order to assess the impact of various SOCs on generation costs. Interleaved day-ahead scheduling and real-time dispatch models were developed to allow accurate representation of forced outages and wind forecast errors, and were applied to the proposed Irish power system of 2020 with a wind penetration of 32%. Savings of at least 7.8% in generation costs and reductions in wind curtailment of 50% were identified when the most influential SOCs were relaxed. The results also illustrate the need to relax local SOCs together with the system-wide nonsynchronous penetration limit SOC, as savings from increasing the nonsynchronous limit beyond 70% were restricted without relaxation of local SOCs. The methodology and results allow for quantification of the costs of SOCs, allowing the optimal upgrade path for generation and transmission infrastructure to be determined.

Standardizing clinical trials workflow representation in UML for international site comparison.

BACKGROUND: With the globalization of clinical trials, a growing emphasis has been placed on the standardization of the workflow in order to ensure the reproducibility and reliability of the overall trial. Despite the importance of workflow evaluation, to our knowledge no previous studies have attempted to adapt existing modeling languages to standardize the representation of clinical trials. Unified Modeling Language (UML) is a computational language that can be used to model operational workflow, and a UML profile can be developed to standardize UML models within a given domain. This paper's objective is to develop a UML profile to extend the UML Activity Diagram schema into the clinical trials domain, defining a standard representation for clinical trial workflow diagrams in UML. METHODS: Two Brazilian clinical trial sites in rheumatology and oncology were examined to model their workflow and collect time-motion data. UML modeling was conducted in Eclipse, and a UML profile was developed to incorporate information used in discrete event simulation software. RESULTS: Ethnographic observation revealed bottlenecks in workflow: these included tasks requiring full commitment of CRCs, transferring notes from paper to computers, deviations from standard operating procedures, and conflicts between different IT systems. Time-motion analysis revealed that nurses' activities took up the most time in the workflow and contained a high frequency of shorter duration activities. Administrative assistants performed more activities near the beginning and end of the workflow. Overall, clinical trial tasks had a greater frequency than clinic routines or other general activities. CONCLUSIONS: This paper describes a method for modeling clinical trial workflow in UML and standardizing these workflow diagrams through a UML profile. In the increasingly global environment of clinical trials, the standardization of workflow modeling is a necessary precursor to conducting a comparative analysis of international clinical trials workflows.

The role of tectonic uplift, climate, and vegetation in the long-term terrestrial phosphorous cycle

Phosphorus (P) is a crucial element for life and therefore for maintaining ecosystem productivity. Its local availability to the terrestrial biosphere results from the interaction between climate, tectonic uplift, atmospheric transport, and biotic cycling. Here we present a mathematical model that describes the terrestrial P-cycle in a simple but comprehensive way. The resulting dynamical system can be solved analytically for steady-state conditions, allowing us to test the sensitivity of the P-availability to the key parameters and processes. Given constant inputs, we find that humid ecosystems exhibit lower P availability due to higher runoff and losses, and that tectonic uplift is a fundamental constraint. In particular, we find that in humid ecosystems the biotic cycling seem essential to maintain long-term P-availability. The time-dependent P dynamics for the Franz Josef and Hawaii chronosequences show how tectonic uplift is an important constraint on ecosystem productivity, while hydroclimatic conditions control the P-losses and speed towards steady-state. The model also helps describe how, with limited uplift and atmospheric input, as in the case of the Amazon Basin, ecosystems must rely on mechanisms that enhance P-availability and retention. Our novel model has a limited number of parameters and can be easily integrated into global climate models to provide a representation of the response of the terrestrial biosphere to global change. © 2010 Author(s).

Economic return of clinical trials performed under the pediatric exclusivity program.

CONTEXT: In 1997, Congress authorized the US Food and Drug Administration (FDA) to grant 6-month extensions of marketing rights through the Pediatric Exclusivity Program if industry sponsors complete FDA-requested pediatric trials. The program has been praised for creating incentives for studies in children and has been criticized as a "windfall" to the innovator drug industry. This critique has been a substantial part of congressional debate on the program, which is due to expire in 2007. OBJECTIVE: To quantify the economic return to industry for completing pediatric exclusivity trials. DESIGN AND SETTING: A cohort study of programs conducted for pediatric exclusivity. Nine drugs that were granted pediatric exclusivity were selected. From the final study reports submitted to the FDA (2002-2004), key elements of the clinical trial design and study operations were obtained, and the cost of performing each study was estimated and converted into estimates of after-tax cash outflows. Three-year market sales were obtained and converted into estimates of after-tax cash inflows based on 6 months of additional market protection. Net economic return (cash inflows minus outflows) and net return-to-costs ratio (net economic return divided by cash outflows) for each product were then calculated. MAIN OUTCOME MEASURES: Net economic return and net return-to-cost ratio. RESULTS: The indications studied reflect a broad representation of the program: asthma, tumors, attention-deficit/hyperactivity disorder, hypertension, depression/generalized anxiety disorder, diabetes mellitus, gastroesophageal reflux, bacterial infection, and bone mineralization. The distribution of net economic return for 6 months of exclusivity varied substantially among products (net economic return ranged from -$8.9 million to $507.9 million and net return-to-cost ratio ranged from -0.68 to 73.63). CONCLUSIONS: The economic return for pediatric exclusivity is variable. As an incentive to complete much-needed clinical trials in children, pediatric exclusivity can generate lucrative returns or produce more modest returns on investment.

Task-driven adaptive statistical compressive sensing of gaussian mixture models

A framework for adaptive and non-adaptive statistical compressive sensing is developed, where a statistical model replaces the standard sparsity model of classical compressive sensing. We propose within this framework optimal task-specific sensing protocols specifically and jointly designed for classification and reconstruction. A two-step adaptive sensing paradigm is developed, where online sensing is applied to detect the signal class in the first step, followed by a reconstruction step adapted to the detected class and the observed samples. The approach is based on information theory, here tailored for Gaussian mixture models (GMMs), where an information-theoretic objective relationship between the sensed signals and a representation of the specific task of interest is maximized. Experimental results using synthetic signals, Landsat satellite attributes, and natural images of different sizes and with different noise levels show the improvements achieved using the proposed framework when compared to more standard sensing protocols. The underlying formulation can be applied beyond GMMs, at the price of higher mathematical and computational complexity. © 1991-2012 IEEE.

Contribution of the North Atlantic subtropical high to regional climate model (RCM) skill in simulating southeastern United States summer precipitation

© 2014, Springer-Verlag Berlin Heidelberg.This study assesses the skill of advanced regional climate models (RCMs) in simulating southeastern United States (SE US) summer precipitation and explores the physical mechanisms responsible for the simulation skill at a process level. Analysis of the RCM output for the North American Regional Climate Change Assessment Program indicates that the RCM simulations of summer precipitation show the largest biases and a remarkable spread over the SE US compared to other regions in the contiguous US. The causes of such a spread are investigated by performing simulations using the Weather Research and Forecasting (WRF) model, a next-generation RCM developed by the US National Center for Atmospheric Research. The results show that the simulated biases in SE US summer precipitation are due mainly to the misrepresentation of the modeled North Atlantic subtropical high (NASH) western ridge. In the WRF simulations, the NASH western ridge shifts 7° northwestward when compared to that in the reanalysis ensemble, leading to a dry bias in the simulated summer precipitation according to the relationship between the NASH western ridge and summer precipitation over the southeast. Experiments utilizing the four dimensional data assimilation technique further suggest that the improved representation of the circulation patterns (i.e., wind fields) associated with the NASH western ridge substantially reduces the bias in the simulated SE US summer precipitation. Our analysis of circulation dynamics indicates that the NASH western ridge in the WRF simulations is significantly influenced by the simulated planetary boundary layer (PBL) processes over the Gulf of Mexico. Specifically, a decrease (increase) in the simulated PBL height tends to stabilize (destabilize) the lower troposphere over the Gulf of Mexico, and thus inhibits (favors) the onset and/or development of convection. Such changes in tropical convection induce a tropical–extratropical teleconnection pattern, which modulates the circulation along the NASH western ridge in the WRF simulations and contributes to the modeled precipitation biases over the SE US. In conclusion, our study demonstrates that the NASH western ridge is an important factor responsible for the RCM skill in simulating SE US summer precipitation. Furthermore, the improvements in the PBL parameterizations for the Gulf of Mexico might help advance RCM skill in representing the NASH western ridge circulation and summer precipitation over the SE US.

A GLOBAL SAMPLING OF PIANO MUSIC FROM 1978 TO 2005

Pianists of the twenty-first century have a wealth of repertoire at their fingertips. They busily study music from the different periods -- Baroque, Classical, Romantic, and some of the twentieth century -- trying to understand the culture and performance practice of the time and the stylistic traits of each composer so they can communicate their music effectively. Unfortunately, this leaves little time to notice the composers who are writing music today. Whether this neglect proceeds from lack of time or lack of curiosity, I feel we should be connected to music that was written in our own lifetime, when we already understand the culture and have knowledge of the different styles that preceded us. Therefore, in an attempt to promote today’s composers, I have selected piano music written during my lifetime, to show that contemporary music is effective and worthwhile and deserves as much attention as the music that preceded it. This dissertation showcases piano music composed from 1978 to 2005. A point of departure in selecting the pieces for this recording project is to represent the major genres in the piano repertoire in order to show a variety of styles, moods, lengths, and difficulties. Therefore, from these recordings, there is enough variety to successfully program a complete contemporary recital from the selected works, and there is enough variety to meet the demands of pianists with different skill levels and recital programming needs. Since we live in an increasingly global society, music from all parts of the world is included to offer a fair representation of music being composed everywhere. Half of the music in this project comes from the United States. The other half comes from Australia, Japan, Russia, and Argentina. The composers represented in these recordings are: Lowell Liebermann, Richard Danielpour, Frederic Rzewski, Judith Lang Zaimont, Samuel Adler, Carl Vine, Nikolai Kapustin, Akira Miyoshi and Osvaldo Golijov. With the exception of one piano concerto, all the works are for solo piano. This recording project dissertation consists of two 60 minute CDs of selected repertoire, accompanied by a substantial document of in-depth program notes. The recordings are documented on compact discs that are housed within the University of Maryland Library System.

Spatial and temporal scales of neuronal correlation in visual area V4.

The spiking activity of nearby cortical neurons is correlated on both short and long time scales. Understanding this shared variability in firing patterns is critical for appreciating the representation of sensory stimuli in ensembles of neurons, the coincident influences of neurons on common targets, and the functional implications of microcircuitry. Our knowledge about neuronal correlations, however, derives largely from experiments that used different recording methods, analysis techniques, and cortical regions. Here we studied the structure of neuronal correlation in area V4 of alert macaques using recording and analysis procedures designed to match those used previously in primary visual cortex (V1), the major input to V4. We found that the spatial and temporal properties of correlations in V4 were remarkably similar to those of V1, with two notable differences: correlated variability in V4 was approximately one-third the magnitude of that in V1 and synchrony in V4 was less temporally precise than in V1. In both areas, spontaneous activity (measured during fixation while viewing a blank screen) was approximately twice as correlated as visual-evoked activity. The results provide a foundation for understanding how the structure of neuronal correlation differs among brain regions and stages in cortical processing and suggest that it is likely governed by features of neuronal circuits that are shared across the visual cortex.