Bayesian stochastic blockmodeling

This chapter provides a self-contained introduction to the use of Bayesian inference to extract large-scale modular structures from network data, based on the stochastic blockmodel (SBM), as well as its degree-corrected and overlapping generalizations. We focus on nonparametric formulations that allow their inference in a manner that prevents overfitting, and enables model selection. We discuss aspects of the choice of priors, in particular how to avoid underfitting via increased Bayesian hierarchies, and we contrast the task of sampling network partitions from the posterior distribution with finding the single point estimate that maximizes it, while describing efficient algorithms to perform either one. We also show how inferring the SBM can be used to predict missing and spurious links, and shed light on the fundamental limitations of the detectability of modular structures in networks.Comment: 44 pages, 16 figures. Code is freely available as part of graph-tool at https://graph-tool.skewed.de . See also the HOWTO at https://graph-tool.skewed.de/static/doc/demos/inference/inference.htm

Data challenges of time domain astronomy

Astronomy has been at the forefront of the development of the techniques and methodologies of data intensive science for over a decade with large sky surveys and distributed efforts such as the Virtual Observatory. However, it faces a new data deluge with the next generation of synoptic sky surveys which are opening up the time domain for discovery and exploration. This brings both new scientific opportunities and fresh challenges, in terms of data rates from robotic telescopes and exponential complexity in linked data, but also for data mining algorithms used in classification and decision making. In this paper, we describe how an informatics-based approach-part of the so-called "fourth paradigm" of scientific discovery-is emerging to deal with these. We review our experiences with the Palomar-Quest and Catalina Real-Time Transient Sky Surveys; in particular, addressing the issue of the heterogeneity of data associated with transient astronomical events (and other sensor networks) and how to manage and analyze it.Comment: 15 pages, 3 figures, to appear in special issue of Distributed and Parallel Databases on Data Intensive eScienc

Optimization of Automatic Target Recognition with a Reject Option Using Fusion and Correlated Sensor Data

This dissertation examines the optimization of automatic target recognition (ATR) systems when a rejection option is included. First, a comprehensive review of the literature inclusive of ATR assessment, fusion, correlated sensor data, and classifier rejection is presented. An optimization framework for the fusion of multiple sensors is then developed. This framework identifies preferred fusion rules and sensors along with rejection and receiver operating characteristic (ROC) curve thresholds without the use of explicit misclassification costs as required by a Bayes\u27 loss function. This optimization framework is the first to integrate both vertical warfighter output label analysis and horizontal engineering confusion matrix analysis. In addition, optimization is performed for the true positive rate, which incorporates the time required by classification systems. The mathematical programming framework is used to assess different fusion methods and to characterize correlation effects both within and across sensors. A synthetic classifier fusion-testing environment is developed by controlling the correlation levels of generated multivariate Gaussian data. This synthetic environment is used to demonstrate the utility of the optimization framework and to assess the performance of fusion algorithms as correlation varies. The mathematical programming framework is then applied to collected radar data. This radar fusion experiment optimizes Boolean and neural network fusion rules across four levels of sensor correlation. Comparisons are presented for the maximum true positive rate and the percentage of feasible thresholds to assess system robustness. Empirical evidence suggests ATR performance may improve by reducing the correlation within and across polarimetric radar sensors. Sensitivity analysis shows ATR performance is affected by the number of forced looks, prior probabilities, the maximum allowable rejection level, and the acceptable error rates

Transforming Graph Representations for Statistical Relational Learning

Relational data representations have become an increasingly important topic due to the recent proliferation of network datasets (e.g., social, biological, information networks) and a corresponding increase in the application of statistical relational learning (SRL) algorithms to these domains. In this article, we examine a range of representation issues for graph-based relational data. Since the choice of relational data representation for the nodes, links, and features can dramatically affect the capabilities of SRL algorithms, we survey approaches and opportunities for relational representation transformation designed to improve the performance of these algorithms. This leads us to introduce an intuitive taxonomy for data representation transformations in relational domains that incorporates link transformation and node transformation as symmetric representation tasks. In particular, the transformation tasks for both nodes and links include (i) predicting their existence, (ii) predicting their label or type, (iii) estimating their weight or importance, and (iv) systematically constructing their relevant features. We motivate our taxonomy through detailed examples and use it to survey and compare competing approaches for each of these tasks. We also discuss general conditions for transforming links, nodes, and features. Finally, we highlight challenges that remain to be addressed

Visual Place Recognition in Changing Environments

Localization is an essential capability of mobile robots and place recognition is an important component of localization. Only having precise localization, robots can reliably plan, navigate and understand the environment around them. The main task of visual place recognition algorithms is to recognize based on the visual input if the robot has seen previously a given place in the environment. Cameras are one of the popular sensors robots get information from. They are lightweight, affordable, and provide detailed descriptions of the environment in the form of images. Cameras are shown to be useful for the vast variety of emerging applications, from virtual and augmented reality applications to autonomous cars or even fleets of autonomous cars. All these applications need precise localization. Nowadays, the state-of-the-art methods are able to reliably estimate the position of the robots using image streams. One of the big challenges still is the ability to localize a camera given an image stream in the presence of drastic visual appearance changes in the environment. Visual appearance changes may be caused by a variety of different reasons, starting from camera-related factors, such as changes in exposure time, camera position-related factors, e.g. the scene is observed from a different position or viewing angle, occlusions, as well as factors that stem from natural sources, for example seasonal changes, different weather conditions, illumination changes, etc. These effects change the way the same place in the environments appears in the image and can lead to situations where it becomes hard even for humans to recognize the places. Also, the performance of the traditional visual localization approaches, such as FABMAP or DBow, decreases dramatically in the presence of strong visual appearance changes. The techniques presented in this thesis aim at improving visual place recognition capabilities for robotic systems in the presence of dramatic visual appearance changes. To reduce the effect of visual changes on image matching performance, we exploit sequences of images rather than individual images. This becomes possible as robotic systems collect data sequentially and not in random order. We formulate the visual place recognition problem under strong appearance changes as a problem of matching image sequences collected by a robotic system at different points in time. A key insight here is the fact that matching sequences reduces the ambiguities in the data associations. This allows us to establish image correspondences between different sequences and thus recognize if two images represent the same place in the environment. To perform a search for image correspondences, we construct a graph that encodes the potential matches between the sequences and at the same time preserves the sequentiality of the data. The shortest path through such a data association graph provides the valid image correspondences between the sequences. Robots operating reliably in an environment should be able to recognize a place in an online manner and not after having recorded all data beforehand. As opposed to collecting image sequences and then determining the associations between the sequences offline, a real-world system should be able to make a decision for every incoming image. In this thesis, we therefore propose an algorithm that is able to perform visual place recognition in changing environments in an online fashion between the query and the previously recorded reference sequences. Then, for every incoming query image, our algorithm checks if the robot is in the previously seen environment, i.e. there exists a matching image in the reference sequence, as well as if the current measurement is consistent with previously obtained query images. Additionally, to be able to recognize places in an online manner, a robot needs to recognize the fact that it has left the previously mapped area as well as relocalize when it re-enters environment covered by the reference sequence. Thus, we relax the assumption that the robot should always travel within the previously mapped area and propose an improved graph-based matching procedure that allows for visual place recognition in case of partially overlapping image sequences. To achieve a long-term autonomy, we further increase the robustness of our place recognition algorithm by incorporating information from multiple image sequences, collected along different overlapping and non-overlapping routes. This allows us to grow the coverage of the environment in terms of area as well as various scene appearances. The reference dataset then contains more images to match against and this increases the probability of finding a matching image, which can lead to improved localization. To be able to deploy a robot that performs localization in large scaled environments over extended periods of time, however, collecting a reference dataset may be a tedious, resource consuming and in some cases intractable task. Avoiding an explicit map collection stage fosters faster deployment of robotic systems in the real world since no map has to be collected beforehand. By using our visual place recognition approach the map collection stage can be skipped, as we are able to incorporate the information from a publicly available source, e.g., from Google Street View, into our framework due to its general formulation. This automatically enables us to perform place recognition on already existing publicly available data and thus avoid costly mapping phase. In this thesis, we additionally show how to organize the images from the publicly available source into the sequences to perform out-of-the-box visual place recognition without previously collecting the otherwise required reference image sequences at city scale. All approaches described in this thesis have been published in peer-reviewed conference papers and journal articles. In addition to that, most of the presented contributions have been released publicly as open source software

Quantifying spatio-temporal variation in malaria transmission in near elimination settings using individual level surveillance data

As countries move towards malaria elimination, tracking progress through quantifying changes in transmission over space and time is key. This information is necessary to effectively target resources to remaining ‘hotspots’ (high-risk locations) and ‘hotpops’ (high-risk populations) where transmission remains, decide if and when it is appropriate to scale back interventions, and to evaluate the success of existing interventions. However, as countries approach zero cases, it becomes difficult to measure transmission. Traditional metrics, such as the prevalence of parasites in the population, are no longer appropriate due to small numbers and increasingly focal distributions of cases over space and time. In order to address this, this thesis developed Bayesian network inference approaches to utilise information about the time and location of cases showing symptoms of malaria to jointly infer the likelihood that a) each observed case was linked to another by transmission and b) that a case was infected by an external, unobserved source. This information was used to calculate individual reproduction numbers for each reported case, or how many new cases of malaria are expected to have resulted from each case. In elimination settings, quantifying the distribution of individual reproduction numbers provides useful information about how quickly a disease may die out, and how the introduction of new cases through importation may affect ongoing transmission. These estimates were incorporated into additive regression models as well as geostatistical models to map how malaria transmission varied over space and time as well as considering timelines to elimination and the likelihood of resurgence of transmission once zero cases is achieved. This approach was applied to previously unanalysed individual-level datasets of malaria cases from China and El Salvador.Open Acces

Towards a Visipedia: Combining Computer Vision and Communities of Experts

Motivated by the idea of a Visipedia, where users can search and explore by image, this thesis presents tools and techniques for empowering expert communities through computer vision. The collective aim of this work is to provide a scalable foundation upon which an application like Visipedia can be built. We conduct experiments using two highly motivated communities, the birding community and the naturalist community, and report results and lessons on how to build the necessary components of a Visipedia. First, we conduct experiments analyzing the behavior of state-of-the-art computer vision classifiers on long tailed datasets. We find poor feature sharing between classes, potentially limiting the applicability of these models and emphasizing the ability to intelligently direct data collection resources. Second, we devise online crowdsourcing algorithms to make dataset collection for binary labels, multiclass labels, keypoints, and mulit-instance bounding boxes faster, cheaper, and more accurate. These methods jointly estimate labels, worker skills, and train computer vision models for these tasks. Experiments show that we can achieve significant cost savings compared to traditional data collection techniques, and that we can produce a more accurate dataset compared to traditional data collection techniques. Third, we present two fine-grained datasets, detail how they were constructed, and analyze the test accuracy of state-of-the-art methods. These datasets are then used to create applications that help users identify species in their photographs: Merlin, an app assisting users in identifying birds species, and iNaturalist, an app that assists users in identifying a broad variety of species. Finally, we present work aimed at reducing the computational burden of large scale classification with the goal of creating an application that allows users to classify tens of thousands of species in real time on their mobile device. As a whole, the lessons learned and the techniques presented in this thesis bring us closer to the realization of a Visipedia.</p