Ontology-based protein-protein interactions extraction from literature using the hidden vector state model

This paper proposes a novel framework of incorporating protein-protein interactions (PPI) ontology knowledge into PPI extraction from biomedical literature in order to address the emerging challenges of deep natural language understanding. It is built upon the existing work on relation extraction using the Hidden Vector State (HVS) model. The HVS model belongs to the category of statistical learning methods. It can be trained directly from un-annotated data in a constrained way whilst at the same time being able to capture the underlying named entity relationships. However, it is difficult to incorporate background knowledge or non-local information into the HVS model. This paper proposes to represent the HVS model as a conditionally trained undirected graphical model in which non-local features derived from PPI ontology through inference would be easily incorporated. The seamless fusion of ontology inference with statistical learning produces a new paradigm to information extraction.

Improving envelopment in Data Envelopment Analysis under variable returns to scale

In a Data Envelopment Analysis model, some of the weights used to compute the efficiency of a unit can have zero or negligible value despite of the importance of the corresponding input or output. This paper offers an approach to preventing inputs and outputs from being ignored in the DEA assessment under the multiple input and output VRS environment, building on an approach introduced in Allen and Thanassoulis (2004) for single input multiple output CRS cases. The proposed method is based on the idea of introducing unobserved DMUs created by adjusting input and output levels of certain observed relatively efficient DMUs, in a manner which reflects a combination of technical information and the decision maker's value judgements. In contrast to many alternative techniques used to constrain weights and/or improve envelopment in DEA, this approach allows one to impose local information on production trade-offs, which are in line with the general VRS technology. The suggested procedure is illustrated using real data. © 2011 Elsevier B.V. All rights reserved.

A socio-economic approach to online vision graph generation and handover in distributed smart camera networks

In this paper we propose an approach based on self-interested autonomous cameras, which exchange responsibility for tracking objects in a market mechanism, in order to maximise their own utility. A novel ant-colony inspired mechanism is used to grow the vision graph during runtime, which may then be used to optimise communication between cameras. The key benefits of our completely decentralised approach are on the one hand generating the vision graph online which permits the addition and removal cameras to the network during runtime and on the other hand relying only on local information, increasing the robustness of the system. Since our market-based approach does not rely on a priori topology information, the need for any multi-camera calibration can be avoided. © 2011 IEEE.

Adaptive modulation scaling scheme for wireless sensor networks

Limited energy is a big challenge for large scale wireless sensor networks (WSN). Previous research works show that modulation scaling is an efficient technique to reduce energy consumption. However, the impacts of using modulation scaling on packet delivery latency and loss are not considered, which may have adverse effects on the application qualities. In this paper, we study this problem and propose control schemes to minimize energy consumption while ensuring application qualities. We first analyze the relationships of modulation scaling and energy consumption, end-to-end delivery latency and packet loss ratio. With the analytical model, we develop a centralized control scheme to adaptively adjust the modulation levels, in order to minimize energy consumption and ensure the application qualities. To improve the scalability of the centralized control scheme, we also propose a distributed control scheme. In this scheme, the sink will send the differences between the required and measured application qualities to the sensors. The sensors will update their modulation levels with the local information and feedback from the sink. Experimental results show the effectiveness of energy saving and QoS guarantee of the control schemes. The control schemes can adapt efficiently to the time-varying requirements on application qualities. Copyright © 2005 The Institute of Electronics, Information and Communication Engineers.

Measuring the spatial extent of texture pooling using reverse correlation

The local image representation produced by early stages of visual analysis is uninformative regarding spatially extensive textures and surfaces. We know little about the cortical algorithm used to combine local information over space, and still less about the area over which it can operate. But such operations are vital to support perception of real-world objects and scenes. Here, we deploy a novel reverse-correlation technique to measure the extent of spatial pooling for target regions of different areas placed either in the central visual field, or more peripherally. Stimuli were large arrays of micropatterns, with their contrasts perturbed individually on an interval-by-interval basis. By comparing trial-by-trial observer responses with the predictions of computational models, we show that substantial regions (up to 13 carrier cycles) of a stimulus can be monitored in parallel by summing contrast over area. This summing strategy is very different from the more widely assumed signal selection strategy (a MAX operation), and suggests that neural mechanisms representing extensive visual textures can be recruited by attention. We also demonstrate that template resolution is much less precise in the parafovea than in the fovea, consistent with recent accounts of crowding. © 2014 The Authors.

Socio-economic vision graph generation and handover in distributed smart camera networks

In this article we present an approach to object tracking handover in a network of smart cameras, based on self-interested autonomous agents, which exchange responsibility for tracking objects in a market mechanism, in order to maximise their own utility. A novel ant-colony inspired mechanism is used to learn the vision graph, that is, the camera neighbourhood relations, during runtime, which may then be used to optimise communication between cameras. The key benefits of our completely decentralised approach are on the one hand generating the vision graph online, enabling efficient deployment in unknown scenarios and camera network topologies, and on the other hand relying only on local information, increasing the robustness of the system. Since our market-based approach does not rely on a priori topology information, the need for any multicamera calibration can be avoided. We have evaluated our approach both in a simulation study and in network of real distributed smart cameras.

Self-organising zooms for decentralised redundancy management in visual sensor networks

When visual sensor networks are composed of cameras which can adjust the zoom factor of their own lens, one must determine the optimal zoom levels for the cameras, for a given task. This gives rise to an important trade-off between the overlap of the different cameras’ fields of view, providing redundancy, and image quality. In an object tracking task, having multiple cameras observe the same area allows for quicker recovery, when a camera fails. In contrast having narrow zooms allow for a higher pixel count on regions of interest, leading to increased tracking confidence. In this paper we propose an approach for the self-organisation of redundancy in a distributed visual sensor network, based on decentralised multi-objective online learning using only local information to approximate the global state. We explore the impact of different zoom levels on these trade-offs, when tasking omnidirectional cameras, having perfect 360-degree view, with keeping track of a varying number of moving objects. We further show how employing decentralised reinforcement learning enables zoom configurations to be achieved dynamically at runtime according to an operator’s preference for maximising either the proportion of objects tracked, confidence associated with tracking, or redundancy in expectation of camera failure. We show that explicitly taking account of the level of overlap, even based only on local knowledge, improves resilience when cameras fail. Our results illustrate the trade-off between maintaining high confidence and object coverage, and maintaining redundancy, in anticipation of future failure. Our approach provides a fully tunable decentralised method for the self-organisation of redundancy in a changing environment, according to an operator’s preferences.

The relationship between early and intermediate level spatial vision during typical development and in autism spectrum disorder

Certaines recherches ont investigué le traitement visuel de bas et de plus hauts niveaux chez des personnes neurotypiques et chez des personnes ayant un trouble du spectre de l’autisme (TSA). Cependant, l’interaction développementale entre chacun de ces niveaux du traitement visuel n’est toujours pas bien comprise. La présente thèse a donc deux objectifs principaux. Le premier objectif (Étude 1) est d’évaluer l’interaction développementale entre l’analyse visuelle de bas niveaux et de niveaux intermédiaires à travers différentes périodes développementales (âge scolaire, adolescence et âge adulte). Le second objectif (Étude 2) est d’évaluer la relation fonctionnelle entre le traitement visuel de bas niveaux et de niveaux intermédiaires chez des adolescents et des adultes ayant un TSA. Ces deux objectifs ont été évalué en utilisant les mêmes stimuli et procédures. Plus précisément, la sensibilité de formes circulaires complexes (Formes de Fréquences Radiales ou FFR), définies par de la luminance ou par de la texture, a été mesurée avec une procédure à choix forcés à deux alternatives. Les résultats de la première étude ont illustré que l’information locale des FFR sous-jacents aux processus visuels de niveaux intermédiaires, affecte différemment la sensibilité à travers des périodes développementales distinctes. Plus précisément, lorsque le contour est défini par de la luminance, la performance des enfants est plus faible comparativement à celle des adolescents et des adultes pour les FFR sollicitant la perception globale. Lorsque les FFR sont définies par la texture, la sensibilité des enfants est plus faible comparativement à celle des adolescents et des adultes pour les conditions locales et globales. Par conséquent, le type d’information locale, qui définit les éléments locaux de la forme globale, influence la période à laquelle la sensibilité visuelle atteint un niveau développemental similaire à celle identifiée chez les adultes. Il est possible qu’une faible intégration visuelle entre les mécanismes de bas et de niveaux intermédiaires explique la sensibilité réduite des FFR chez les enfants. Ceci peut être attribué à des connexions descendantes et horizontales immatures ainsi qu’au sous-développement de certaines aires cérébrales du système visuel. Les résultats de la deuxième étude ont démontré que la sensibilité visuelle en autisme est influencée par la manipulation de l’information locale. Plus précisément, en présence de luminance, la sensibilité est seulement affectée pour les conditions sollicitant un traitement local chez les personnes avec un TSA. Cependant, en présence de texture, la sensibilité est réduite pour le traitement visuel global et local. Ces résultats suggèrent que la perception de formes en autisme est reliée à l’efficacité à laquelle les éléments locaux (luminance versus texture) sont traités. Les connexions latérales et ascendantes / descendantes des aires visuelles primaires sont possiblement tributaires d’un déséquilibre entre les signaux excitateurs et inhibiteurs, influençant ainsi l’efficacité à laquelle l’information visuelle de luminance et de texture est traitée en autisme. Ces résultats supportent l’hypothèse selon laquelle les altérations de la perception visuelle de bas niveaux (local) sont à l’origine des atypies de plus hauts niveaux chez les personnes avec un TSA.

An Empirical Analysis of Performance Impacts Resulting From Conversion to Franchise Operations

Franchising is an important form of organizational control. Possible benefits of franchising include its ability to reduce agency costs that increase with costly monitoring, and provide incentives for the use of local information by onsite managers. However, these benefits may come at a cost, as franchisees may reduce quality by choosing to free ride. While many studies have investigated the reasons for franchising, few studies have documented the impacts of franchising on unit level operating performance. Using time-series data from a number of lodging properties that were converted to franchisee control from company control, this study documents the performance impacts of franchising. The analysis reveals that conversion results in a modest decline in financial performance and an immediate sharp decline in quality.

An Architecture for Proof Planning Systems

This paper presents a generic architecture for proof planning systems in terms of an interaction between a customisable proof module and search module. These refer to both global and local information contained in reasoning states.

A generic method of engagement to elicit regional coastal management options

Stakeholder engagement is important for successful management of natural resources, both to make effective decisions and to obtain support. However, in the context of coastal management, questions remain unanswered on how to effectively link decisions made at the catchment level with objectives for marine biodiversity and fisheries productivity. Moreover, there is much uncertainty on how to best elicit community input in a rigorous manner that supports management decisions. A decision support process is described that uses the adaptive management loop as its basis to elicit management objectives, priorities and management options using two case studies in the Great Barrier Reef, Australia. The approach described is then generalised for international interest. A hierarchical engagement model of local stakeholders, regional and senior managers is used. The result is a semi-quantitative generic elicitation framework that ultimately provides a prioritised list of management options in the context of clearly articulated management objectives that has widespread application for coastal communities worldwide. The case studies show that demand for local input and regional management is high, but local influences affect the relative success of both engagement processes and uptake by managers. Differences between case study outcomes highlight the importance of discussing objectives prior to suggesting management actions, and avoiding or minimising conflicts at the early stages of the process. Strong contributors to success are a) the provision of local information to the community group, and b) the early inclusion of senior managers and influencers in the group to ensure the intellectual and time investment is not compromised at the final stages of the process. The project has uncovered a conundrum in the significant gap between the way managers perceive their management actions and outcomes, and community's perception of the effectiveness (and wisdom) of these same management actions.

Modelling human behaviour and event detection from videos

Automatic analysis of human behaviour in large collections of videos is gaining interest, even more so with the advent of file sharing sites such as YouTube. However, challenges still exist owing to several factors such as inter- and intra-class variations, cluttered backgrounds, occlusion, camera motion, scale, view and illumination changes. This research focuses on modelling human behaviour for action recognition in videos. The developed techniques are validated on large scale benchmark datasets and applied on real-world scenarios such as soccer videos. Three major contributions are made. The first contribution is in the area of proper choice of a feature representation for videos. This involved a study of state-of-the-art techniques for action recognition, feature extraction processing and dimensional reduction techniques so as to yield the best performance with optimal computational requirements. Secondly, temporal modelling of human behaviour is performed. This involved frequency analysis and temporal integration of local information in the video frames to yield a temporal feature vector. Current practices mostly average the frame information over an entire video and neglect the temporal order. Lastly, the proposed framework is applied and further adapted to real-world scenario such as soccer videos. A dataset consisting of video sequences depicting events of players falling is created from actual match data to this end and used to experimentally evaluate the proposed framework.

The relationship between early and intermediate level spatial vision during typical development and in autism spectrum disorder

Certaines recherches ont investigué le traitement visuel de bas et de plus hauts niveaux chez des personnes neurotypiques et chez des personnes ayant un trouble du spectre de l’autisme (TSA). Cependant, l’interaction développementale entre chacun de ces niveaux du traitement visuel n’est toujours pas bien comprise. La présente thèse a donc deux objectifs principaux. Le premier objectif (Étude 1) est d’évaluer l’interaction développementale entre l’analyse visuelle de bas niveaux et de niveaux intermédiaires à travers différentes périodes développementales (âge scolaire, adolescence et âge adulte). Le second objectif (Étude 2) est d’évaluer la relation fonctionnelle entre le traitement visuel de bas niveaux et de niveaux intermédiaires chez des adolescents et des adultes ayant un TSA. Ces deux objectifs ont été évalué en utilisant les mêmes stimuli et procédures. Plus précisément, la sensibilité de formes circulaires complexes (Formes de Fréquences Radiales ou FFR), définies par de la luminance ou par de la texture, a été mesurée avec une procédure à choix forcés à deux alternatives. Les résultats de la première étude ont illustré que l’information locale des FFR sous-jacents aux processus visuels de niveaux intermédiaires, affecte différemment la sensibilité à travers des périodes développementales distinctes. Plus précisément, lorsque le contour est défini par de la luminance, la performance des enfants est plus faible comparativement à celle des adolescents et des adultes pour les FFR sollicitant la perception globale. Lorsque les FFR sont définies par la texture, la sensibilité des enfants est plus faible comparativement à celle des adolescents et des adultes pour les conditions locales et globales. Par conséquent, le type d’information locale, qui définit les éléments locaux de la forme globale, influence la période à laquelle la sensibilité visuelle atteint un niveau développemental similaire à celle identifiée chez les adultes. Il est possible qu’une faible intégration visuelle entre les mécanismes de bas et de niveaux intermédiaires explique la sensibilité réduite des FFR chez les enfants. Ceci peut être attribué à des connexions descendantes et horizontales immatures ainsi qu’au sous-développement de certaines aires cérébrales du système visuel. Les résultats de la deuxième étude ont démontré que la sensibilité visuelle en autisme est influencée par la manipulation de l’information locale. Plus précisément, en présence de luminance, la sensibilité est seulement affectée pour les conditions sollicitant un traitement local chez les personnes avec un TSA. Cependant, en présence de texture, la sensibilité est réduite pour le traitement visuel global et local. Ces résultats suggèrent que la perception de formes en autisme est reliée à l’efficacité à laquelle les éléments locaux (luminance versus texture) sont traités. Les connexions latérales et ascendantes / descendantes des aires visuelles primaires sont possiblement tributaires d’un déséquilibre entre les signaux excitateurs et inhibiteurs, influençant ainsi l’efficacité à laquelle l’information visuelle de luminance et de texture est traitée en autisme. Ces résultats supportent l’hypothèse selon laquelle les altérations de la perception visuelle de bas niveaux (local) sont à l’origine des atypies de plus hauts niveaux chez les personnes avec un TSA.

Retrievals of a size parameter for phytoplankton and spectral light absorption by colored detrital matter from water-leaving radiances at SeaWiFS channels in a continental shelf region off Brazil

Many efforts are currently oriented toward extracting more information from ocean color than the chlorophyll a concentration. Among biological parameters potentially accessible from space, estimates of phytoplankton cell size and light absorption by colored detrital matter (CDM) would lead to an indirect assessment of major components of the organic carbon pool in the ocean, which would benefit oceanic carbon budget models. We present here 2 procedures to retrieve simultaneously from ocean color measurements in a limited number of bands, magnitudes, and spectral shapes for both light absorption by CDM and phytoplankton, along with a size parameter for phytoplankton. The performance of the 2 procedures was evaluated using different data sets that correspond to increasing uncertainties: ( 1) measured absorption coefficients of phytoplankton, particulate detritus, and colored dissolved organic matter ( CDOM) and measured chlorophyll a concentrations and ( 2) SeaWiFS upwelling radiance measurements and chlorophyll a concentrations estimated from global algorithms. In situ data were acquired during 3 cruises, differing by their relative proportions in CDM and phytoplankton, over a continental shelf off Brazil. No local information was introduced in either procedure, to make them more generally applicable. Over the study area, the absorption coefficient of CDM at 443 nm was retrieved from SeaWiFS radiances with a relative root mean square error (RMSE) of 33%, and phytoplankton light absorption coefficients in SeaWiFS bands ( from 412 to 510 nm) were retrieved with RMSEs between 28% and 33%. These results are comparable to or better than those obtained by 3 published models. In addition, a size parameter of phytoplankton and the spectral slope of CDM absorption were retrieved with RMSEs of 17% and 22%, respectively. If these methods are applied at a regional scale, the performances could be substantially improved by locally tuning some empirical relationships.

Análisis teórico del contacto plasma-superficie y sus aplicaciones industriales

Actualmente, la física de plasmas constituye una parte importante de la investigación en física que está siendo desarrollada. Su campo de aplicación varía desde el estudio de plasmas interestelares y cósmicos, como las estrellas, las nebulosas, el medio intergaláctico, etc.; hasta aplicaciones más terrenales como la producción de microchips o los dispositivos de iluminación. Resulta particularmente interesante el estudio del contacto de una superficie metálica con un plasma. Siendo la razón que, la dinámica de la interfase formada entre un plasma imperturbado y una superficie metálica, resulta de gran importancia cuando se trata de estudiar problemas como: la implantación iónica en una oblea de silicio, el grabado por medio de plasmas, la carga de una aeronave cuando atraviesa la ionosfera y la diagnosis de plasmas mediante sondas de Langmuir. El uso de las sondas de Langmuir está extendido a través de multitud de aplicaciones tecnológicas e industriales como método de diagnosis de plasmas. Algunas de estas aplicaciones han sido mencionadas justo en el párrafo anterior. Es más, su uso también es muy popular en la investigación en física de plasmas, por ser una de las pocas técnicas de diagnosis que proporciona información local sobre el plasma. El equipamiento donde es habitualmente implementado varía desde plasmas de laboratorio de baja temperatura hasta plasmas de fusión en dispositivos como tokamaks o stellerators. La geometría más popular de este tipo de sondas es cilíndrica, y la principal magnitud que se usa para diagnosticar el plasma es la corriente recogida por la sonda cuando se encuentra polarizada a un cierto potencial. Existe un interes especial en diagnosticar por medio de la medida de la corriente iónica recogida por la sonda, puesto que produce una perturbación muy pequeña del plasma en comparación con el uso de la corriente electrónica. Dada esta popularidad, no es de extrañar que grandes esfuerzos se hayan realizado en la consecución de un modelo teórico que explique el comportamiento de una sonda de Langmuir inmersa en un plasma. Hay que remontarse a la primera mitad del siglo XX para encontrar las primeras teorías que permiten diagnosticar parámetros del plasma mediante la medida de la corriente iónica recogida por la sonda de Langmuir. Desde entonces, las mejoras en estos modelos y el desarrollo de otros nuevos ha sido una constante en la investigación en física de plasmas. No obstante, todavía no está claro como los iones se aproximan a la superficie de la sonda. Las dos principales, a la par que opuestas, aproximaciones al problema que están ampliamente aceptadas son: la radial y la orbital; siendo el problema que ambas predicen diferentes valores para la corriente iónica. Los experimentos han arrojado resultados de acuerdo con ambas teorías, la radial y la orbital; y lo que es más importante, una transición entre ambos ha sido recientemente observada. La mayoría de los logros conseguidos a la hora de comprender como los iones caen desde el plasma hacia la superficie de la sonda, han sido llevados a cabo en el campo de la dinámica de fluidos o la teoría cinética. Por otra parte, este problema puede ser abordado mediante el uso de simulaciones de partículas. La principal ventaja de las simulaciones de partículas sobre los modelos de fluidos o cinéticos es que proporcionan mucha más información sobre los detalles microscópicos del movimiento de las partículas, además es relativamente fácil introducir interacciones complejas entre las partículas. No obstante, estas ventajas no se obtienen gratuitamente, ya que las simulaciones de partículas requieren grandísimos recursos. Por esta razón, es prácticamente obligatorio el uso de técnicas de procesamiento paralelo en este tipo de simulaciones. El vacío en el conocimiento de las sondas de Langmuir, es el que motiva nuestro trabajo. Nuestra aproximación, y el principal objetivo de este trabajo, ha sido desarrollar una simulación de partículas que nos permita estudiar el problema de una sonda de Langmuir inmersa en un plasma y que está negativamente polarizada con respecto a éste. Dicha simulación nos permitiría estudiar el comportamiento de los iones en los alrededores de una sonda cilíndrica de Langmuir, así como arrojar luz sobre la transición entre las teorías radiales y orbitales que ha sido observada experimentalmente. Justo después de esta sección introductoria, el resto de la tesis está dividido en tres partes tal y como sigue: La primera parte está dedicada a establecer los fundamentos teóricos de las sondas de Langmuir. En primer lugar, se realiza una introducción general al problema y al uso de sondas de Langmuir como método de diagnosis de plasmas. A continuación, se incluye una extensiva revisión bibliográfica sobre las diferentes teorías que proporcionan la corriente iónica recogida por una sonda. La segunda parte está dedicada a explicar los detalles de las simulaciones de partículas que han sido desarrolladas a lo largo de nuestra investigación, así como los resultados obtenidos con las mismas. Esta parte incluye una introducción sobre la teoría que subyace el tipo de simulaciones de partículas y las técnicas de paralelización que han sido usadas en nuestros códigos. El resto de esta parte está dividido en dos capítulos, cada uno de los cuales se ocupa de una de las geometrías consideradas en nuestras simulaciones (plana y cilíndrica). En esta parte discutimos también los descubrimientos realizados relativos a la transición entre el comportamiento radial y orbital de los iones en los alrededores de una sonda cilíndrica de Langmuir. Finalmente, en la tercera parte de la tesis se presenta un resumen del trabajo realizado. En este resumen, se enumeran brevemente los resultados de nuestra investigación y se han incluido algunas conclusiones. Después de esto, se enumeran una serie de perspectivas futuras y extensiones para los códigos desarrollados.