MULTIVARIATE MODELING OF COGNITIVE PERFORMANCE AND CATEGORICAL PERCEPTION FROM NEUROIMAGING DATA

State-of-the-art cognitive-neuroscience mainly uses hypothesis-driven statistical testing to characterize and model neural disorders and diseases. While such techniques have proven to be powerful in understanding diseases and disorders, they are inadequate in explaining causal relationships as well as individuality and variations. In this study, we proposed multivariate data-driven approaches for predictive modeling of cognitive events and disorders. We developed network descriptions of both structural and functional connectivities that are critical in multivariate modeling of cognitive performance (i.e., fluency, attention, and working memory) and categorical perceptions (i.e., emotion, speech perception). We also performed dynamic network analysis on brain connectivity measures to determine the role of different functional areas in relation to categorical perceptions and cognitive events. Our empirical studies of structural connectivity were performed using Diffusion Tensor Imaging (DTI). The main objective was to discover the role of structural connectivity in selecting clinically interpretable features that are consistent over a large range of model parameters in classifying cognitive performances in relation to Acute Lymphoblastic Leukemia (ALL). The proposed approach substantially improved accuracy (13% - 26%) over existing models and also selected a relevant, small subset of features that were verified by domain experts. In summary, the proposed approach produced interpretable models with better generalization.Functional connectivity is related to similar patterns of activation in different brain regions regardless of the apparent physical connectedness of the regions. The proposed data-driven approach to the source localized electroencephalogram (EEG) data includes an array of tools such as graph mining, feature selection, and multivariate analysis to determine the functional connectivity in categorical perceptions. We used the network description to correctly classify listeners behavioral responses with an accuracy over 92% on 35 participants. State-of-the-art network description of human brain assumes static connectivities. However, brain networks in relation to perception and cognition are complex and dynamic. Analysis of transient functional networks with spatiotemporal variations to understand cognitive functions remains challenging. One of the critical missing links is the lack of sophisticated methodologies in understanding dynamics neural activity patterns. We proposed a clustering-based complex dynamic network analysis on source localized EEG data to understand the commonality and differences in gender-specific emotion processing. Besides, we also adopted Bayesian nonparametric framework for segmentation neural activity with a finite number of microstates. This approach enabled us to find the default network and transient pattern of the underlying neural mechanism in relation to categorical perception. In summary, multivariate and dynamic network analysis methods developed in this dissertation to analyze structural and functional connectivities will have a far-reaching impact on computational neuroscience to identify meaningful changes in spatiotemporal brain activities

Linear and nonlinear approaches to unravel dynamics and connectivity in neuronal cultures

[eng] In the present thesis, we propose to explore neuronal circuits at the mesoscale, an approach in which one monitors small populations of few thousand neurons and concentrates in the emergence of collective behavior. In our case, we carried out such an exploration both experimentally and numerically, and by adopting an analysis perspective centered on time series analysis and dynamical systems. Experimentally, we used neuronal cultures and prepared more than 200 of them, which were monitored using fluorescence calcium imaging. By adjusting the experimental conditions, we could set two basic arrangements of neurons, namely homogeneous and aggregated. In the experiments, we carried out two major explorations, namely development and disintegration. In the former we investigated changes in network behavior as it matured; in the latter we applied a drug that reduced neuronal interconnectivity. All the subsequent analyses and modeling along the thesis are based on these experimental data. Numerically, the thesis comprised two aspects. The first one was oriented towards a simulation of neuronal connectivity and dynamics. The second one was oriented towards the development of linear and nonlinear analysis tools to unravel dynamic and connectivity aspects of the measured experimental networks. For the first aspect, we developed a sophisticated software package to simulate single neuronal dynamics using a quadratic integrate–and–fire model with adaptation and depression. This model was plug into a synthetic graph in which the nodes of the network are neurons, and the edges connections. The graph was created using spatial embedding and realistic biology. We carried out hundreds of simulations in which we tuned the density of neurons, their spatial arrangement and the characteristics of the fluorescence signal. As a key result, we observed that homogeneous networks required a substantial number of neurons to fire and exhibit collective dynamics, and that the presence of aggregation significantly reduced the number of required neurons. For the second aspect, data analysis, we analyzed experiments and simulations to tackle three major aspects: network dynamics reconstruction using linear descriptions, dynamics reconstruction using nonlinear descriptors, and the assessment of neuronal connectivity from solely activity data. For the linear study, we analyzed all experiments using the power spectrum density (PSD), and observed that it was sufficiently good to describe the development of the network or its disintegration. PSD also allowed us to distinguish between healthy and unhealthy networks, and revealed dynamical heterogeneities across the network. For the nonlinear study, we used techniques in the context of recurrence plots. We first characterized the embedding dimension m and the time delay δ for each experiment, built the respective recurrence plots, and extracted key information of the dynamics of the system through different descriptors. Experimental results were contrasted with numerical simulations. After analyzing about 400 time series, we concluded that the degree of dynamical complexity in neuronal cultures changes both during development and disintegration. We also observed that the healthier the culture, the higher its dynamic complexity. Finally, for the reconstruction study, we first used numerical simulations to determine the best measure of ‘statistical interdependence’ among any two neurons, and took Generalized Transfer Entropy. We then analyzed the experimental data. We concluded that young cultures have a weak connectivity that increases along maturation. Aggregation increases average connectivity, and more interesting, also the assortativity, i.e. the tendency of highly connected nodes to connect with other highly connected node. In turn, this assortativity may delineates important aspects of the dynamics of the network. Overall, the results show that spatial arrangement and neuronal dynamics are able to shape a very rich repertoire of dynamical states of varying complexity.[cat] L’habilitat dels teixits neuronals de processar i transmetre informació de forma eficient depèn de les propietats dinàmiques intrínseques de les neurones i de la connectivitat entre elles. La present tesi proposa explorar diferents tècniques experimentals i de simulació per analitzar la dinàmica i connectivitat de xarxes neuronals corticals de rata embrionària. Experimentalment, la gravació de l’activitat espontània d’una població de neurones en cultiu, mitjançant una càmera ràpida i tècniques de fluorescència, possibilita el seguiment de forma controlada de l’activitat individual de cada neurona, així com la modificació de la seva connectivitat. En conjunt, aquestes eines permeten estudiar el comportament col.lectiu emergent de la població neuronal. Amb l’objectiu de simular els patrons observats en el laboratori, hem implementat un model mètric aleatori de creixement neuronal per simular la xarxa física de connexions entre neurones, i un model quadràtic d’integració i dispar amb adaptació i depressió per modelar l’ampli espectre de dinàmiques neuronals amb un cost computacional reduït. Hem caracteritzat la dinàmica global i individual de les neurones i l’hem correlacionat amb la seva estructura subjacent mitjançant tècniques lineals i no–lineals de series temporals. L’anàlisi espectral ens ha possibilitat la descripció del desenvolupament i els canvis en connectivitat en els cultius, així com la diferenciació entre cultius sans dels patològics. La reconstrucció de la dinàmica subjacent mitjançant mètodes d’incrustació i l’ús de gràfics de recurrència ens ha permès detectar diferents transicions dinàmiques amb el corresponent guany o pèrdua de la complexitat i riquesa dinàmica del cultiu durant els diferents estudis experimentals. Finalment, a fi de reconstruir la connectivitat interna hem testejat, mitjançant simulacions, diferents quantificadors per mesurar la dependència estadística entre neurona i neurona, seleccionant finalment el mètode de transferència d’entropia gereralitzada. Seguidament, hem procedit a caracteritzar les xarxes amb diferents paràmetres. Malgrat presentar certs tres de xarxes tipus ‘petit món’, els nostres cultius mostren una distribució de grau ‘exponencial’ o ‘esbiaixada’ per, respectivament, cultius joves i madurs. Addicionalment, hem observat que les xarxes homogènies presenten la propietat de disassortativitat, mentre que xarxes amb un creixent nivell d’agregació espaial presenten assortativitat. Aquesta propietat impacta fortament en la transmissió, resistència i sincronització de la xarxa

A multi-armed bandit approach for batch mode active learning on information networks

We propose an adaptive batch mode active learning algorithm, MABAL (Multi-Armed Bandit for Active Learning), for classification on heterogeneous information networks. Observing the parallels between active learning and multi-armed bandit (MAB), we base MABAL on an existing combinatorial MAB algorithm to combine simple strategies to generate query batches. MABAL employs a novel error expectation measure for network classification that does not assume assortativity as MAB reward feedback to determine the most fit strategy for the given task. We provide a preliminary optimality analysis of MABAL based on performance bounds for combinatorial MAB. A case study illustrates that MABAL not only converges quickly to the optimal strategy but also provides insight into the functional roles of the different node types. Evaluations of MABAL on real world network classification tasks demonstrate that it achieves performance gains over existing methods independent of the underlying classification model

Mining Butterflies in Streaming Graphs

This thesis introduces two main-memory systems sGrapp and sGradd for performing the fundamental analytic tasks of biclique counting and concept drift detection over a streaming graph. A data-driven heuristic is used to architect the systems. To this end, initially, the growth patterns of bipartite streaming graphs are mined and the emergence principles of streaming motifs are discovered. Next, the discovered principles are (a) explained by a graph generator called sGrow; and (b) utilized to establish the requirements for efficient, effective, explainable, and interpretable management and processing of streams. sGrow is used to benchmark stream analytics, particularly in the case of concept drift detection. sGrow displays robust realization of streaming growth patterns independent of initial conditions, scale and temporal characteristics, and model configurations. Extensive evaluations confirm the simultaneous effectiveness and efficiency of sGrapp and sGradd. sGrapp achieves mean absolute percentage error up to 0.05/0.14 for the cumulative butterfly count in streaming graphs with uniform/non-uniform temporal distribution and a processing throughput of 1.5 million data records per second. The throughput and estimation error of sGrapp are 160x higher and 0.02x lower than baselines. sGradd demonstrates an improving performance over time, achieves zero false detection rates when there is not any drift and when drift is already detected, and detects sequential drifts in zero to a few seconds after their occurrence regardless of drift intervals

Dealings on the Dark Web: An Examination of the Trust, Consumer Satisfaction, and the Efficacy of Interventions Against a Dark Web Cryptomarket

Abstract Objective. The overarching goal of this thesis is to better understand not only the network dynamics which undergird the function and operation of cryptomarkets but the nature of consumer satisfaction and trust on these platforms. More specifically, I endeavour to push the cryptomarket literature beyond its current theoretical and methodological limits by documenting the network structure of a cryptomarket, the factors which predicts for vendor trust, the efficacy of targeted strategies on the transactional network of a cryptomarket, and the dynamics which facilitate consumer satisfaction despite information asymmetry. Moreover, we also aim to test the generalizability of findings made in prior cryptomarket studies (Duxbury and Haynie, 2017; 2020; Norbutas, 2018). Methods. I realize the aims of this research by using a buyer-seller dataset from the Abraxas cryptomarket (Branwen et al., 2015). Given the differences between the topics and the research questions featured, this thesis employs a variety of methodological techniques. Chapter two uses a combination of descriptive network analysis, community detection analysis, statistical modelling, and trajectory modelling. Chapter three utilizes three text analytic strategies: descriptive text analysis, sentiment analysis, and textual feature extraction. Finally, chapter four employs sequential node deletion pursuant to six law enforcement strategies: lead k (degree centrality), eccentricity, unique items bought/sold, cumulative reputation score, total purchase price, and random targeting. Results. Social network analysis of the Abraxas cryptomarket revealed a large and diffuse network where the majority of buyers purchased from a small cohort of vendors. This theme of preferential selection of vendors on the part of buyers is repeated in other findings within this study. More generally, the Abraxas transactional network can then be viewed as set of transactional islands as opposed to a large, densely connected conglomeration of vendors and buyers. With regard buyer feedback, buyers are generally pleased with their transactions on Abraxas as long as the product arrives on time and is as advertised. In general, vendors have a relatively low bar to achieve when it comes to satisfying their customers. Based on the results of the sequential node deletion, random targeting was found to be ineffective across the five outcome measures, producing minimal and a slow disruptive effect. Finally, these strategies are based on a power law where a small percentage of deleted nodes is responsible for an outsized proportion of the disruptive impact. Conclusion. As with all applied research examining emergent phenomena, this thesis lends itself to a more refined understanding of dark web cryptomarkets. While the results and conclusions drawn from these results are not perfectly generalizable to all cryptomarkets, they should serve to inform law enforcement on the dynamics which undergird these markets. To this extent, a sombre consideration of trust, consumer satisfaction, and tactical effectiveness of interventions is a necessary step towards the development of more effective countermeasures against these illicit online marketplaces. For law enforcement to be more effective against cryptomarkets, it is advised that an evidence-based approach be taken

Epizoological Tools for Acute Hepatopancreatic Necrosis Disease (AHPND) in Thai Shrimp Farming

Acute hepatopancreatic necrosis disease (AHPND) is an emerging bacterial infection in shrimp that has been widespread across the major world shrimp producing countries since 2009. AHPND epizootics have resulted in a huge loss of global shrimp production, similar to that caused by white spot disease in the 1990’s. The epizootiological understanding of the spread of AHPND is still in its early stages, however, and most of the currently published research findings are based on experimental studies that may struggle to capture the potential for disease transmission at the country scale. The main aim of this research, therefore, is to develop epizootiological tools to study AHPND transmission between shrimp farming sites. Some tools used in this research have already been applied to shrimp epizoology, but others are used here for the first time to evaluate the spread of shrimp diseases. According to an epizootiological survey of AHPND in Thailand (Chapter 3), the first case of AHPND in the country was in eastern shrimp farms in January 2012. The disease was then transmitted to the south in December 2012. The results obtained from interviews, undertaken with 143 sample farms were stratified by three farm-scales (large, medium and small) and two locations (east and south). Both the southern location and large-scale farming were associated with a delay in AHPND onset compared with the eastern location and small- and medium-scale farming. The 24 risk factors (mostly related to farming management practices) for AHPND were investigated in a cross-sectional study (Chapter 3). This allowed the development of an AHPND decision tree for defining cases (diseased farms) and controls (non-diseased farms) because at the time of the study AHPND was a disease of unknown etiology. Results of univariate and unconditional logistic regression models indicated that two farming management practices related to the onset of AHPND. First, the absence of pond harrowing before shrimp stocking increased the risk of AHPND occurrence with an odds ratio () of 3.9 (95 % CI 1.3–12.6; P‑value = 0.01), whereas earthen ponds decreased the risk of AHPND with an of 0.25 (95 % CI 0.06–0.8; P‑value = 0.02). These findings imply that good farming management practices, such as pond-bottom harrowing, which are a common practice of shrimp farming in earthen ponds, may contribute to overcoming AHPND infection at farm level. For the purposes of disease surveillance and control, the structure of the live shrimp movement network within Thailand (LSMN) was modelled, which demonstrated the high potential for site-to-site disease spread (Chapter 4). Real network data was recorded over a 13-month period from March 2013 to March 2014 by the Thailand Department of Fisheries. After data validation, c. 74 400 repeated connections between 13 801 shrimp farming sites were retained. 77 % of the total connections were inter-province movements; the remaining connections were intra-province movements (23 %). The results demonstrated that the LSMN had properties that both aided and hindered disease spread (Chapter 4). For hindering transmission, the correlation between and degrees was weakly positive, i.e. it suggests that sites with a high risk of catching disease posed a low risk for transmitting the disease (assuming solely network spread), and the LSMN showed disassortative mixing, i.e. a low preference for connections joining sites with high degree linked to connections with high degree. However, there were low values for mean shortest path length and clustering. The latter characteristics tend to be associated with the potential for disease epidemics. Moreover, the LSMN displayed the power-law in both and degree distributions with the exponents 2.87 and 2.17, respectively. The presence of power-law distributions indicates that most sites in the LSMN have a small number of connections, while a few sites have large numbers of connections. These findings not only contribute to a better understanding of disease spread between sites, therefore, but also reveal the importance of targeted disease surveillance and control, due to the detection of scale-free properties in the LSMN. Chapter 5, therefore, examined the effectiveness of targeted disease surveillance and control in respect to reducing the potential size of epizootics in the LSMN. The study untilised network approaches to identify high-risk connections, whose removal from the network could reduce epizootics. Five disease-control algorithms were developed for the comparison: four of these algorithms were based on centrality measures to represent targeted approaches, with a non-targeted approach as a control. With the targeted approaches, technically admissible centrality measures were considered: the betweenness (the number of shortest paths that go through connections in a network), connection weight (the frequency of repeated connections between a site pair), eigenvector (considering the degree centralities of all neighbouring sites connected to a specified site), and subnet-crossing (prioritising connections that links two different subnetworks). The results showed that the estimated epizootic sizes were smaller when an optimal targeted approach was applied, compared with the random targeting of high-risk connections. This optimal targeted approach can be used to prioritise targets in the context of establishing disease surveillance and control programmes. With complex modes of disease transmission (i.e. long-distance transmission like via live shrimp movement, and local transmission), an compartmental, individual-based epizootic model was constructed for AHPND (Chapter 6). The modelling uncovered the seasonality of AHPND epizootics in Thailand, which were found likely to occur between April and August (during the hot and rainy seasons of Thailand). Based on two movement types, intra-province movements were a small proportion of connections, and they alone could cause a small AHPND epizootic. The main pathway for AHPND spread is therefore long-distance transmission and regulators need to increase the efficacy of testing for diseases in farmed shrimp before movements and improve the conduct of routine monitoring for diseases. The implementation of these biosecurity practices was modelled by changing the values of the long-distance transmission rate. The model demonstrated that high levels of biosecurity on live shrimp movements (1) led to a decrease in the potential size of epizootics in Thai shrimp farming. Moreover, the potential size of epizootics was also decreased when AHPND spread was modelled with a decreased value for the local transmission rate. Hence, not only did the model predict AHPND epizootic dynamics stochastically, but it also assessed biosecurity enhancement, allowing the design of effective prevention programmes. In brief, this thesis develops tools for the systematic epizootiological study of AHPND transmission in Thai shrimp farming and demonstrates that: (1) at farm level, current Thai shrimp farming should enhance biosecurity systems even in larger businesses, (2) at country level, targeted disease control strategies are required to establish disease surveillance and control measures. Although the epizootiological tools used here mainly evaluate the spread of AHPND in shrimp farming sites, they could be adapted to other infectious diseases or other farming sectors, such as the current spread of tilapia lake virus in Nile tilapia farms

Topology Reconstruction of Dynamical Networks via Constrained Lyapunov Equations

The network structure (or topology) of a dynamical network is often unavailable or uncertain. Hence, we consider the problem of network reconstruction. Network reconstruction aims at inferring the topology of a dynamical network using measurements obtained from the network. In this technical note we define the notion of solvability of the network reconstruction problem. Subsequently, we provide necessary and sufficient conditions under which the network reconstruction problem is solvable. Finally, using constrained Lyapunov equations, we establish novel network reconstruction algorithms, applicable to general dynamical networks. We also provide specialized algorithms for specific network dynamics, such as the well-known consensus and adjacency dynamics.Comment: 8 page

COMMUNITY DETECTION IN GRAPHS

Thesis (Ph.D.) - Indiana University, Luddy School of Informatics, Computing, and Engineering/University Graduate School, 2020Community detection has always been one of the fundamental research topics in graph mining. As a type of unsupervised or semi-supervised approach, community detection aims to explore node high-order closeness by leveraging graph topological structure. By grouping similar nodes or edges into the same community while separating dissimilar ones apart into different communities, graph structure can be revealed in a coarser resolution. It can be beneficial for numerous applications such as user shopping recommendation and advertisement in e-commerce, protein-protein interaction prediction in the bioinformatics, and literature recommendation or scholar collaboration in citation analysis. However, identifying communities is an ill-defined problem. Due to the No Free Lunch theorem [1], there is neither gold standard to represent perfect community partition nor universal methods that are able to detect satisfied communities for all tasks under various types of graphs. To have a global view of this research topic, I summarize state-of-art community detection methods by categorizing them based on graph types, research tasks and methodology frameworks. As academic exploration on community detection grows rapidly in recent years, I hereby particularly focus on the state-of-art works published in the latest decade, which may leave out some classic models published decades ago. Meanwhile, three subtle community detection tasks are proposed and assessed in this dissertation as well. First, apart from general models which consider only graph structures, personalized community detection considers user need as auxiliary information to guide community detection. In the end, there will be fine-grained communities for nodes better matching user needs while coarser-resolution communities for the rest of less relevant nodes. Second, graphs always suffer from the sparse connectivity issue. Leveraging conventional models directly on such graphs may hugely distort the quality of generate communities. To tackle such a problem, cross-graph techniques are involved to propagate external graph information as a support for target graph community detection. Third, graph community structure supports a natural language processing (NLP) task to depict node intrinsic characteristics by generating node summarizations via a text generative model. The contribution of this dissertation is threefold. First, a decent amount of researches are reviewed and summarized under a well-defined taxonomy. Existing works about methods, evaluation and applications are all addressed in the literature review. Second, three novel community detection tasks are demonstrated and associated models are proposed and evaluated by comparing with state-of-art baselines under various datasets. Third, the limitations of current works are pointed out and future research tracks with potentials are discussed as well