Layered dynamic probabilistic networks for spatio-temporal modelling

In applications such as tracking and surveillance in large spatial environments, there is a need for representing dynamic and noisy data and at the same time dealing with them at different levels of detail. In the spatial domain, there has been work dealing with these two issues separately, however, there is no existing common framework for dealing with both of them. In this paper, we propose a new representation framework called the Layered Dynamic Probabilistic Network (LDPN), a special type of Dynamic Probabilistic Network (DPN), capable of handling uncertainty and representing spatial data at various levels of detail. The framework is thus particularly suited to applications in wide-area environments which are characterised by large region size, complex spatial layout and multiple sensors/cameras. For example, a building has three levels: entry/exit to the building, entry/exit between rooms and moving within rooms. To avoid the problem of a relatively large state space associated with a large spatial environment, the LDPN explicitly encodes the hierarchy of connected spatial locations, making it scalable to the size of the environment being modelled. There are three main advantages of the LDPN. First, the reduction in state space makes it suitable for dealing with wide area surveillance involving multiple sensors. Second, it offers a hierarchy of intervals for indexing temporal data. Lastly, the explicit representation of intermediate sub-goals allows for the extension of the framework to easily represent group interactions by allowing coupling between sub-goal layers of different individuals or objects. We describe an adaptation of the likelihood sampling inference scheme for the LDPN, and illustrate its use in a hypothetical surveillance scenario.

Dynamic decision networks for decision-making in self-adaptive systems:a case study

Bayesian decision theory is increasingly applied to support decision-making processes under environmental variability and uncertainty. Researchers from application areas like psychology and biomedicine have applied these techniques successfully. However, in the area of software engineering and speci?cally in the area of self-adaptive systems (SASs), little progress has been made in the application of Bayesian decision theory. We believe that techniques based on Bayesian Networks (BNs) are useful for systems that dynamically adapt themselves at runtime to a changing environment, which is usually uncertain. In this paper, we discuss the case for the use of BNs, speci?cally Dynamic Decision Networks (DDNs), to support the decision-making of self-adaptive systems. We present how such a probabilistic model can be used to support the decision making in SASs and justify its applicability. We have applied our DDN-based approach to the case of an adaptive remote data mirroring system. We discuss results, implications and potential bene?ts of the DDN to enhance the development and operation of self-adaptive systems, by providing mechanisms to cope with uncertainty and automatically make the best decision.

Urban maze : A typological investigation in porous morphology and dynamic pedestrian networks

Mixed use typologies and pedestrian networks are two strategies commonly applied in design of the contemporary city. These approaches, aimed towards the creation of a more sustainalble urban environment, have their roots in the traditional, pre-industrial towns; they characterize urban form, articulating the tension between privaate and public realms through a series of typological variations as well as stimulating commercial activity in the city centre. Arcades, loggias and verandas are just some of the elements which can mediate this tension. Historically they have defined physical and social spaces with particular character; in the contemporary city these features are applied to deform the urban form and create a porous, dynamic morphology. This paper, comparing case studies from Italy, Japan and Australia, investigates how the design of the transition zone can define hybrid pedestrian networks, where a clear distinction between the public and private realms is no longer applicable. Pedestrians use the city in a dynamic way, combining trajectories on the public street with ones on the fringe or inside of the private built environment. In some cases, cities offer different pedestrian network possibilities at different times, as the commercial precints are subject to variations in accessibility across various timeframes. These walkable systems have an impact on the urban form and identity of places, redefining typologies and requiring an in depth analysis through plan, section and elevation diagrams.

How long is a tweet? Mapping dynamic conversation networks on Twitter using Gawk and Gephi

Twitter is now well established as the world’s second most important social media platform, after Facebook. Its 140-character updates are designed for brief messaging, and its network structures are kept relatively flat and simple: messages from users are either public and visible to all (even to unregistered visitors using the Twitter website), or private and visible only to approved ‘followers’ of the sender; there are no more complex definitions of degrees of connection (family, friends, friends of friends) as they are available in other social networks. Over time, Twitter users have developed simple, but effective mechanisms for working around these limitations: ‘#hashtags’, which enable the manual or automatic collation of all tweets containing the same #hashtag, as well allowing users to subscribe to content feeds that contain only those tweets which feature specific #hashtags; and ‘@replies’, which allow senders to direct public messages even to users whom they do not already follow. This paper documents a methodology for extracting public Twitter activity data around specific #hashtags, and for processing these data in order to analyse and visualize the @reply networks existing between participating users – both overall, as a static network, and over time, to highlight the dynamic structure of @reply conversations. Such visualizations enable us to highlight the shifting roles played by individual participants, as well as the response of the overall #hashtag community to new stimuli – such as the entry of new participants or the availability of new information. Over longer timeframes, it is also possible to identify different phases in the overall discussion, or the formation of distinct clusters of preferentially interacting participants.

Condition deterioration prediction of bridge elements using Dynamic Bayesian Networks (DBNs)

The ability of bridge deterioration models to predict future condition provides significant advantages in improving the effectiveness of maintenance decisions. This paper proposes a novel model using Dynamic Bayesian Networks (DBNs) for predicting the condition of bridge elements. The proposed model improves prediction results by being able to handle, deterioration dependencies among different bridge elements, the lack of full inspection histories, and joint considerations of both maintenance actions and environmental effects. With Bayesian updating capability, different types of data and information can be utilised as inputs. Expert knowledge can be used to deal with insufficient data as a starting point. The proposed model established a flexible basis for bridge systems deterioration modelling so that other models and Bayesian approaches can be further developed in one platform. A steel bridge main girder was chosen to validate the proposed model.

Predicting the temporal response of seagrass meadows to dredging using Dynamic Bayesian Networks

Predicting temporal responses of ecosystems to disturbances associated with industrial activities is critical for their management and conservation. However, prediction of ecosystem responses is challenging due to the complexity and potential non-linearities stemming from interactions between system components and multiple environmental drivers. Prediction is particularly difficult for marine ecosystems due to their often highly variable and complex natures and large uncertainties surrounding their dynamic responses. Consequently, current management of such systems often rely on expert judgement and/or complex quantitative models that consider only a subset of the relevant ecological processes. Hence there exists an urgent need for the development of whole-of-systems predictive models to support decision and policy makers in managing complex marine systems in the context of industry based disturbances. This paper presents Dynamic Bayesian Networks (DBNs) for predicting the temporal response of a marine ecosystem to anthropogenic disturbances. The DBN provides a visual representation of the problem domain in terms of factors (parts of the ecosystem) and their relationships. These relationships are quantified via Conditional Probability Tables (CPTs), which estimate the variability and uncertainty in the distribution of each factor. The combination of qualitative visual and quantitative elements in a DBN facilitates the integration of a wide array of data, published and expert knowledge and other models. Such multiple sources are often essential as one single source of information is rarely sufficient to cover the diverse range of factors relevant to a management task. Here, a DBN model is developed for tropical, annual Halophila and temperate, persistent Amphibolis seagrass meadows to inform dredging management and help meet environmental guidelines. Specifically, the impacts of capital (e.g. new port development) and maintenance (e.g. maintaining channel depths in established ports) dredging is evaluated with respect to the risk of permanent loss, defined as no recovery within 5 years (Environmental Protection Agency guidelines). The model is developed using expert knowledge, existing literature, statistical models of environmental light, and experimental data. The model is then demonstrated in a case study through the analysis of a variety of dredging, environmental and seagrass ecosystem recovery scenarios. In spatial zones significantly affected by dredging, such as the zone of moderate impact, shoot density has a very high probability of being driven to zero by capital dredging due to the duration of such dredging. Here, fast growing Halophila species can recover, however, the probability of recovery depends on the presence of seed banks. On the other hand, slow growing Amphibolis meadows have a high probability of suffering permanent loss. However, in the maintenance dredging scenario, due to the shorter duration of dredging, Amphibolis is better able to resist the impacts of dredging. For both types of seagrass meadows, the probability of loss was strongly dependent on the biological and ecological status of the meadow, as well as environmental conditions post-dredging. The ability to predict the ecosystem response under cumulative, non-linear interactions across a complex ecosystem highlights the utility of DBNs for decision support and environmental management.

Programming chemical kinetics: engineering dynamic reaction networks with DNA strand displacement

Over the last century, the silicon revolution has enabled us to build faster, smaller and more sophisticated computers. Today, these computers control phones, cars, satellites, assembly lines, and other electromechanical devices. Just as electrical wiring controls electromechanical devices, living organisms employ "chemical wiring" to make decisions about their environment and control physical processes. Currently, the big difference between these two substrates is that while we have the abstractions, design principles, verification and fabrication techniques in place for programming with silicon, we have no comparable understanding or expertise for programming chemistry.

In this thesis we take a small step towards the goal of learning how to systematically engineer prescribed non-equilibrium dynamical behaviors in chemical systems. We use the formalism of chemical reaction networks (CRNs), combined with mass-action kinetics, as our programming language for specifying dynamical behaviors. Leveraging the tools of nucleic acid nanotechnology (introduced in Chapter 1), we employ synthetic DNA molecules as our molecular architecture and toehold-mediated DNA strand displacement as our reaction primitive.

Abstraction, modular design and systematic fabrication can work only with well-understood and quantitatively characterized tools. Therefore, we embark on a detailed study of the "device physics" of DNA strand displacement (Chapter 2). We present a unified view of strand displacement biophysics and kinetics by studying the process at multiple levels of detail, using an intuitive model of a random walk on a 1-dimensional energy landscape, a secondary structure kinetics model with single base-pair steps, and a coarse-grained molecular model that incorporates three-dimensional geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Our findings are consistent with previously measured or inferred rates for hybridization, fraying, and branch migration, and provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems.

In Chapters 3 and 4, we identify and overcome the crucial experimental challenges involved in using our general DNA-based technology for engineering dynamical behaviors in the test tube. In this process, we identify important design rules that inform our choice of molecular motifs and our algorithms for designing and verifying DNA sequences for our molecular implementation. We also develop flexible molecular strategies for "tuning" our reaction rates and stoichiometries in order to compensate for unavoidable non-idealities in the molecular implementation, such as imperfectly synthesized molecules and spurious "leak" pathways that compete with desired pathways.

We successfully implement three distinct autocatalytic reactions, which we then combine into a de novo chemical oscillator. Unlike biological networks, which use sophisticated evolved molecules (like proteins) to realize such behavior, our test tube realization is the first to demonstrate that Watson-Crick base pairing interactions alone suffice for oscillatory dynamics. Since our design pipeline is general and applicable to any CRN, our experimental demonstration of a de novo chemical oscillator could enable the systematic construction of CRNs with other dynamic behaviors.

Dynamic neural networks supporting memory retrieval.

How do separate neural networks interact to support complex cognitive processes such as remembrance of the personal past? Autobiographical memory (AM) retrieval recruits a consistent pattern of activation that potentially comprises multiple neural networks. However, it is unclear how such large-scale neural networks interact and are modulated by properties of the memory retrieval process. In the present functional MRI (fMRI) study, we combined independent component analysis (ICA) and dynamic causal modeling (DCM) to understand the neural networks supporting AM retrieval. ICA revealed four task-related components consistent with the previous literature: 1) medial prefrontal cortex (PFC) network, associated with self-referential processes, 2) medial temporal lobe (MTL) network, associated with memory, 3) frontoparietal network, associated with strategic search, and 4) cingulooperculum network, associated with goal maintenance. DCM analysis revealed that the medial PFC network drove activation within the system, consistent with the importance of this network to AM retrieval. Additionally, memory accessibility and recollection uniquely altered connectivity between these neural networks. Recollection modulated the influence of the medial PFC on the MTL network during elaboration, suggesting that greater connectivity among subsystems of the default network supports greater re-experience. In contrast, memory accessibility modulated the influence of frontoparietal and MTL networks on the medial PFC network, suggesting that ease of retrieval involves greater fluency among the multiple networks contributing to AM. These results show the integration between neural networks supporting AM retrieval and the modulation of network connectivity by behavior.

Complexity of Inferences in Polytree-shaped Semi-Qualitative Probabilistic Networks

Semi-qualitative probabilistic networks (SQPNs) merge two important graphical model formalisms: Bayesian networks and qualitative probabilistic networks. They provide a very general modeling framework by allowing the combination of numeric and qualitative assessments over a discrete domain, and can be compactly encoded by exploiting the same factorization of joint probability distributions that are behind the Bayesian networks. This paper explores the computational complexity of semi-qualitative probabilistic networks, and takes the polytree-shaped networks as its main target. We show that the inference problem is coNP-Complete for binary polytrees with multiple observed nodes. We also show that inferences can be performed in linear time if there is a single observed node, which is a relevant practical case. Because our proof is constructive, we obtain an efficient linear time algorithm for SQPNs under such assumptions. To the best of our knowledge, this is the first exact polynomial-time algorithm for SQPNs. Together these results provide a clear picture of the inferential complexity in polytree-shaped SQPNs.

Semi-Qualitative Probabilistic Networks in Computer Vision Problems

This paper explores the application of semi-qualitative probabilistic networks (SQPNs) that combine numeric and qualitative information to computer vision problems. Our version of SQPN allows qualitative influences and imprecise probability measures using intervals. We describe an Imprecise Dirichlet model for parameter learning and an iterative algorithm for evaluating posterior probabilities, maximum a posteriori and most probable explanations. Experiments on facial expression recognition and image segmentation problems are performed using real data.