Complex network analysis using modulus of families of walks

Doctor of PhilosophyDepartment of Electrical and Computer EngineeringPietro Poggi-CorradiniCaterina M. ScoglioThe modulus of a family of walks quantifies the richness of the family by favoring having many short walks over a few longer ones. In this dissertation, we investigate various families of walks to study new measures for quantifying network properties using modulus. The proposed new measures are compared to other known quantities. Our proposed method is based on walks on a network, and therefore will work in great generality. For instance, the networks we consider can be directed, multi-edged, weighted, and even contain disconnected parts. We study the popular centrality measure known in some circles as information centrality, also known as effective conductance centrality. After reinterpreting this measure in terms of modulus of families of walks, we introduce a modification called shell modulus centrality, that relies on the egocentric structure of the graph. Ego networks are networks formed around egos with a specific order of neighborhoods. We then propose efficient analytical and approximate methods for computing these measures on both directed and undirected networks. Finally, we describe a simple method inspired by shell modulus centrality, called general degree, which improves simple degree centrality and could prove to be a useful tool for practitioners in the applied sciences. General degree is useful for detecting the best set of nodes for immunization. We also study the structure of loops in networks using the notion of modulus of loop families. We introduce a new measure of network clustering by quantifying the richness of families of (simple) loops. Modulus tries to minimize the expected overlap among loops by spreading the expected link-usage optimally. We propose weighting networks using these expected link-usages to improve classical community detection algorithms. We show that the proposed method enhances the performance of certain algorithms, such as spectral partitioning and modularity maximization heuristics, on standard benchmarks. Computing loop modulus benefits from efficient algorithms for finding shortest loops, thus we propose a deterministic combinatorial algorithm that finds a shortest cycle in graphs. The proposed algorithm reduces the worst case time complexity of the existing combinatorial algorithms while visiting at most the cycle basis. For most empirical networks with sublinear average degree our algorithm is subcubic

Computational Labeling, Partitioning, and Balancing of Molecular Networks

Recent advances in high throughput techniques enable large-scale molecular quantification with high accuracy, including mRNAs, proteins and metabolites. Differential expression of these molecules in case and control samples provides a way to select phenotype-associated molecules with statistically significant changes. However, given the significance ranking list of molecular changes, how those molecules work together to drive phenotype formation is still unclear. In particular, the changes in molecular quantities are insufficient to interpret the changes in their functional behavior. My study is aimed at answering this question by integrating molecular network data to systematically model and estimate the changes of molecular functional behaviors. We build three computational models to label, partition, and balance molecular networks using modern machine learning techniques. (1) Due to the incompleteness of protein functional annotation, we develop AptRank, an adaptive PageRank model for protein function prediction on bilayer networks. By integrating Gene Ontology (GO) hierarchy with protein-protein interaction network, our AptRank outperforms four state-of-the-art methods in a comprehensive evaluation using benchmark datasets. (2) We next extend our AptRank into a network partitioning method, BioSweeper, to identify functional network modules in which molecules share similar functions and also densely connect to each other. Compared to traditional network partitioning methods using only network connections, BioSweeper, which integrates the GO hierarchy, can automatically identify functionally enriched network modules. (3) Finally, we conduct a differential interaction analysis, namely difFBA, on protein-protein interaction networks by simulating protein fluxes using flux balance analysis (FBA). We test difFBA using quantitative proteomic data from colon cancer, and demonstrate that difFBA offers more insights into functional changes in molecular behavior than does protein quantity changes alone. We conclude that our integrative network model increases the observational dimensions of complex biological systems, and enables us to more deeply understand the causal relationships between genotypes and phenotypes

Think locally, act locally: Detection of small, medium-sized, and large communities in large networks

It is common in the study of networks to investigate intermediate-sized (or “meso-scale”) features to try to gain an understanding of network structure and function. For example, numerous algorithms have been developed to try to identify “communities,” which are typically construed as sets of nodes with denser connections internally than with the remainder of a network. In this paper, we adopt a complementary perspective that “communities” are associated with bottlenecks of locally-biased dynamical processes that begin at seed sets of nodes, and we employ several different community-identification procedures (using diffusion-based and geodesic-based dynamics) to investigate community quality as a function of community size. Using several empirical and synthetic networks, we identify several distinct scenarios for “size-resolved community structure” that can arise in real (and realistic) networks: (i) the best small groups of nodes can be better than the best large groups (for a given formulation of the idea of a good community); (ii) the best small groups can have a quality that is comparable to the best medium-sized and large groups; and (iii) the best small groups of nodes can be worse than the best large groups. As we discuss in detail, which of these three cases holds for a given network can make an enormous difference when investigating and making claims about network community structure, and it is important to take this into account to obtain reliable downstream conclusions. Depending on which scenario holds, one may or may not be able to successfully identify “good” communities in a given network (and good communities might not even exist for a given community quality measure), the manner in which different small communities fit together to form meso-scale network structures can be very different, and processes such as viral propagation and information diffusion can exhibit very different dynamics. In addition, our results suggest that, for many large realistic networks, the output of locally-biased methods that focus on communities that are centered around a given seed node might have better conceptual grounding and greater practical utility than the output of global community-detection methods. They also illustrate subtler structural properties that are important to consider in the development of better benchmark networks to test methods for community detection

The Exchange of Social Support via Social Networks of Maternal Caregivers for Children with Autism Spectrum Disorders

The role of social support in the lives of the 16.8 million caregivers for children with special needs in the U.S. is not adequately understood. Many studies have explored seeking health information online, but failed to consider information exchanged through social networks (i.e., family, friends, colleagues, neighbors, etc.). Caregivers of children with special needs spend on average 30 hours per week providing such care. The burden of caregiving can negatively affect caregivers physically, mentally and emotionally, socially, and financially. Social support is one potential mediator for the effects of caregiver burden. The objective of this study was to explore the flow of four dimensions of social support within the social networks of maternal caregivers for children diagnosed with an autism spectrum disorder (ASD). A convenience sample was gathered via electronic distribution lists for Indiana parents of children with special needs. Participants could elect to complete a face-to-face interview or an anonymous online survey. The typical participant was Caucasian, married, college-educated, and located in Central Indiana. Respondent social networks are composed of multiplex relations, indicating strong ties. Significant correlations were found for participant age, child age, and the age of diagnosis, and network members for various networks. Specifically, a later age of child diagnosis is associated with fewer network members for the caregiver. Correlational analyses between dimensions of social support and network characteristics suggest options for further study. Overall, the results of this exploratory study are inconclusive, but can provide direction for future research

Episodic memory, perceptual memory, and their interaction: foundations for a theory of posttraumatic stress disorder

A number of autobiographical memory theories and clinical theories of posttraumatic stress disorder (PTSD) make claims that are different from standard views of memory and have been the subject of controversy. These claims include the existence of a long-term perceptual memory system supporting conscious experience separate to episodic memory; greater involvement of perceptual memory in the response to emotion-laden and personally meaningful events; increased perceptual memory intrusions accompanied by impaired episodic memory for the traumatic event among PTSD patients; and a lack of association, or inverse association, between indices of voluntary recall and involuntary images relating to the same traumatic materials. In this article I review current research on perceptual memory, which supports the presence of long-term representations that are selective or incomplete reflections of sensory input. The functional independence of perceptual and episodic memory is illustrated by research on verbal overshadowing but is most clearly exemplified by the strong evidence in favor of enhanced perceptual memory and impaired episodic memory in PTSD. Theoretical predictions concerning the relation between perceptual priming and the development of intrusive images, the effect of verbal versus visuospatial secondary tasks on intrusive trauma images, and the independence of voluntary and involuntary memory for the same materials have garnered widespread support. Reasons for the continuing controversy over traumatic memory are discussed, and some implications of the review for general theories of recall and recognition, clinical theories of PTSD, and "special mechanism" views of memory are set out

Novel supports to the assessment of cognitive functions through the combined use of technologies and subjective and objective measurements

Tesis por compendio[ES] Las funciones cognitivas incluyen todos los procesos a través de los cuales un individuo percibe, registra, mantiene, manipula, usa y expresa información que está involucrada en cualquier actividad cotidiana. Las principales herramientas estandarizadas se pueden dividir en tres grupos principales: escalas cortas de pruebas de seguimiento cognitivo: cuestionarios, baterías neuropsicológicas generales y pruebas específicas. Estas herramientas están bien validadas y son confiables, pero, en la última década, varias investigaciones han demostrado que algunos pacientes pueden realizar bien estas pruebas neuropsicológicas, incluso cuando tienen dificultades significativas para adaptar sus comportamientos a las actividades de la vida diaria. De acuerdo con esto, más recientemente, un nuevo enfoque ha aumentado sustancialmente, lo que podría proporcionar una mayor validez ecológica en la evaluación de las capacidades cognitivas funcionales que el enfoque estandarizado: el uso de sistemas tecnológicos avanzados para la evaluación neuropsicológica (STAEN). STAEN se refiere a un conjunto de dispositivos y aplicaciones de software tales como pruebas computarizadas, juegos divertidos e interactivos de fantasía (JS) y / o sistemas de realidad virtual simulada (RV) y / o aumentada (RA) que van más allá de las pruebas de evaluación tradicionales y que Brindar la posibilidad de entregar estímulos controlados y dinámicos, en entornos ecológicamente válidos y seguros. Partiendo de estas premisas, el objetivo principal de la tesis era diseñar, desarrollar y validar un SG 2D no inmersivo versus un JS 3D inmersivo y una actividad de la vida diaria en un entorno 3D RV inmersivo versus un RA para la evaluación de funciones cognitivas, comparando la eficacia y efectividad de ellos. El primer estudio 2D incluyó 354 sujetos sanos y se encontraron correlaciones entre el juego y los métodos tradicionales, lo que sugiere que el juego podría ser una herramienta válida para evaluar las funciones cognitivas en adultos. El segundo estudio, comparó la versión 2D versus una versión 3D STAEN, involucró a 94 sujetos sanos y mostró que la versión 3D fue capaz de generar tiempos más bajos y respuestas correctas más altas que la 2D, lo que sugiere evidencia inicial de la eficacia de un sistema más inmersivo en comparación con un sistema no-inmersivo. Aunque este resultado destaca una posible limitación en el uso de diferentes sistemas tecnológicos debido a las diferencias en los dos métodos de interacción (el sistema 2D aplicó el mouse y el teclado; los controladores de dos manos virtuales 3D) y el registro de datos de latencia de hardware y software. Con respecto a la variabilidad individual en edad, género y educación, los hallazgos mostraron consistencia con la literatura de referencia. Específicamente, los más jóvenes mostraron un mayor rendimiento que los mayores; niveles educativos más altos reflejados en una mejor puntuación y sobre género, los resultados mostraron un panorama más compuesto. Además, para mejorar la validez ecológica de la evaluación, el último estudio de esta tesis comparó el rendimiento conductual y las respuestas fisiológicas, durante una tarea de cocina ecológica, entre un sistema virtual y un sistema aumentado en 50 sujetos sanos. La tarea de cocinar consistió en 4 niveles que aumentaron en dificultad. A medida que el nivel aumentó, aparecieron actividades adicionales. Los resultados de comportamiento mostraron que los tiempos son siempre más bajos en realidad virtual que en RA, aumentando constantemente de acuerdo con la dificultad de las tareas. Con respecto a las respuestas fisiológicas, los hallazgos mostraron que la condición RA produjo más excitación y activación individual que la realidad virtual. Para concluir, STAEN está demostrando ser herramientas confiables y efectivas para la evaluación de las funciones cognitivas en adultos, proporcionando más validez ec[CA] Les funcions cognitives inclouen tots els processos a través dels quals un individu percep, registra, manté, manipula, usa i expressa informació que està involucrada en qualsevol activitat quotidiana. Les principals ferramentes estandarditzades es poden dividir en tres grups principals: escales curtes de proves de seguiment cognitiu: qüestionaris, bateries neuropsicológiques generals i proves específiques. Estes ferramentes estan ben validades i són confiables, però, en l'última dècada, diverses investigacions han demostrat que alguns pacients poden realitzar bé estes proves neuropsicológiques, inclús quan tenen dificultats significatives per a adaptar els seus comportaments a les activitats de la vida diària. D'acord amb açò, més recentment, un nou enfocament ha augmentat substancialment, la qual cosa podria proporcionar una major validesa ecològica en l'avaluació de les capacitats cognitives funcionals que l'enfocament estandarditzat: l'ús de sistemes tecnològics avançats per a l'avaluació neuropsicológica (STAEN). STAEN es referix a un conjunt de dispositius i aplicacions de software com ara proves computaritzades, jocs divertits i interactius de fantasia (JS) i / o sistemes de realitat virtual simulada (RV) i / o augmentada (RA) que van més enllà de les proves d'avaluació tradicionals i que brinden la possibilitat de presentar estímuls controlats i dinàmics, en entorns ecològicament vàlids i segurs. Partint d'estes premisses, l'objectiu principal de la tesi era dissenyar, desenrotllar i validar un SG 2D no inmersiu versus un JS 3D inmersiu i una activitat de la vida diària en un entorn 3D RV inmersiu versus un RA per a l'avaluació de funcions cognitives, comparant l'eficàcia i efectivitat d'ells. El primer estudi 2D va incloure 354 subjectes sans i es van trobar correlacions entre el joc i els mètodes tradicionals, la qual cosa suggerix que el joc podria ser una ferramenta vàlida per a avaluar les funcions cognitives en adults. El segon estudi, va comparar la versió 2D versus una versió 3D STAEN, va involucrar a 94 subjectes sans i va mostrar que la versió 3D va ser capaç de generar temps més baixos i respostes correctes més altes que la 2D, la qual cosa suggerix evidència inicial de l'eficàcia d'un sistema més inmersiu en comparació amb un sistema no-inmersiu. Encara que este resultat destaca una possible limitació en l'ús de diferents sistemes tecnològics a causa de les diferències en els dos mètodes d'interacció (el sistema 2D va aplicar el ratolí i el teclat; els controladors de dos mans virtuals 3D) i el registre de dades de latència de hardware i software. Respecte a la variabilitat individual en edat, gènere i educació, les troballes van mostrar consistència amb la literatura de referència. Específicament, els més jóvens van mostrar un major rendiment que els majors; nivells educatius més alts reflectits en una millor puntuació i sobre gènere, els resultats van mostrar un panorama més compost. A més, per a millorar la validesa ecològica de l'avaluació, l'últim estudi d'esta tesi va comparar el rendiment conductual i les respostes fisiològiques, durant una tasca de cuina ecològica, entre un sistema virtual i un sistema augmentat en 50 subjectes sans. La tasca de cuinar va consistir en 4 nivells que van augmentar en dificultat. A mesura que el nivell va augmentar, van aparéixer activitats addicionals. Els resultats de comportament van mostrar que els temps són sempre més baixos en realitat virtual que en RA, augmentant constantment d'acord amb la dificultat de les tasques. Respecte a les respostes fisiològiques, les troballes van mostrar que la condició RA va produir més excitació i activació individual que la realitat virtual. Per a concloure, STAEN està demostrant ser ferramentes confiables i efectives per a l'avaluació de les funcions cognitives en adults, proporcionant més validesa ecològica i objectivitat que els mètodes tradicio[EN] Cognitive functions include all the processes through which an individual perceives, records, maintains, manipulates, uses and expresses information that are involved in any everyday activity. The main standardized tools can be divided in three main groups: short scales of cognitive tracking tests - questionnaires, general neuropsychological batteries, and specific tests. These tools are well-validated and reliable but, in the last decade, several research have shown that some patients can perform these neuropsychological tests well, even when they have significant difficulties in adapting their behaviours to daily life activities. According to this, more recently, a new approach has substantially increased, potentially providing a higher ecological validity in functional cognitive abilities assessment than standardized approach: the use of advanced technological systems for neuropsychological assessment (ATSNA). ATSNA refer to a set of devices and software applications such as computerized tests, fun and interactive fantasy serious games (SG), and/or simulated virtual (VR) and/or augmented (AR) reality systems that go beyond traditional assessment tests and that supply the possibility to deliver controlled and dynamic stimuli, in ecologically valid, and secure environments. Starting from these premises, the main objective of the thesis was to design, develop, and validate a non-immersive 2D SG versus an immersive 3D SG and a daily life activity in an immersive 3D VR environment versus an AR for the assessment of cognitive functions, comparing the efficacy and effectiveness of them. The first 2D study involved 354 healthy subjects and correlations were found between the game and traditional methods, suggesting that the game could be a valid tool for assessing cognitive functions in adults. The second study, compared 2D versus a 3D ATSNA version, it involved 94 healthy subjects and showed that 3D version was able to generate lower times and higher correct answers that the 2D, suggesting initial evidence of efficacy of a more immersive system compared to a non-immersive system. Although this result highlights a potential limitation on using different technological systems due to the differences on the two interaction methods (the 2D system applied mouse and keyboard; the 3D two virtual hands' controllers) and hardware and software latency data recording. Regarding individual variability on age, gender, and education, the findings showed consistency with the reference literature. Specifically, younger showed higher performance that older; higher educational levels reflected on a better score and about gender, results showed a more composite panorama. Furthermore, to enhance the ecological validity of assessment, the last study of this thesis compared the behavioural performance and physiological responses, during an ecological cooking task, between a virtual and an augmented system on 50 healthy subjects. The cooking task consisted of 4 levels that increased in difficulty. As the level increased, additional activities appeared. The behavioural results showed that times are always lower in VR than in AR, increasing constantly in accordance with the difficulty of the tasks. Regarding physiological responses, the findings showed that AR condition produced more individual excitement and activation than VR. To conclude, ATSNA are proving to be reliable and effective tools for the assessment of cognitive functions in adults, providing more ecological validity and objectivity than traditional methods of assessment.Chicchi Giglioli, IAM. (2020). Novel supports to the assessment of cognitive functions through the combined use of technologies and subjective and objective measurements [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/139075TESISCompendi