Lack Of Ground Truth Information Research Articles

Kinetics-based inference of environment-dependent microbial interactions and their dynamic variation.

Microbial communities in nature are dynamically evolving as member species change their interactions subject to environmental variations. Accounting for such context-dependent dynamic variations in interspecies interactions is critical for predictive ecological modeling. In the absence of generalizable theoretical foundations, we lack a fundamental understanding of how microbial interactions are driven by environmental factors, significantly limiting our capability to predict and engineer community dynamics and function. To address this issue, we propose a novel theoretical framework that allows us to represent interspecies interactions as an explicit function of environmental variables (such as substrate concentrations) by combining growth kinetics and a generalized Lotka-Volterra model. A synergistic integration of these two complementary models leads to the prediction of alterations in interspecies interactions as the outcome of dynamic balances between positive and negative influences of microbial species in mixed relationships. The effectiveness of our method was experimentally demonstrated using a synthetic consortium of two Escherichia coli mutants that are metabolically dependent (due to an inability to synthesize essential amino acids) but competitively grow on a shared substrate. The analysis of the E. coli binary consortium using our model not only showed how interactions between the two amino acid auxotrophic mutants are controlled by the dynamic shifts in limiting substrates but also enabled quantifying previously uncharacterizable complex aspects of microbial interactions, such as asymmetry in interactions. Our approach can be extended to other ecological systems to model their environment-dependent interspecies interactions from growth kinetics.IMPORTANCEModeling environment-controlled interspecies interactions through separate identification of positive and negative influences of microbes in mixed relationships is a new capability that can significantly improve our ability to understand, predict, and engineer the complex dynamics of microbial communities. Moreover, the prediction of microbial interactions as a function of environmental variables can serve as valuable benchmark data to validate modeling and network inference tools in microbial ecology, the development of which has often been impeded due to the lack of ground truth information on interactions. While demonstrated against microbial data, the theory developed in this work is readily applicable to general community ecology to predict interactions among macroorganisms, such as plants and animals, as well as microorganisms.

Residency and worker status identification based on mobile device location data

Mobile device location data (MDLD) have been widely recognized for their rich human mobility information and thus considered as a supplementary data source for the current travel data bank consisting of travel survey data and traffic monitoring data. However, the lack of ground truth information about the device owners raises concern about the biases and representativeness of the nonprobability MDLD sample and significantly limits the applications of MDLD. This paper focuses on identifying two important socio-demographic characteristics for the MDLD sample devices: residency and worker status, including four worker types (normal commuters, professional drivers, mobility-for-work workers, and nonworkers/home-based workers). Based on the spatial–temporal patterns of location sightings and derived trips from MDLD, a comprehensive imputation framework is proposed with parameters calibrated against public domain ground truth data. A national-level case study in the U.S. based on a commercial MDLD dataset further evaluates the performances of the proposed heuristic rules. The multi-level validation results indicate a satisfying match against the ground truth data and prove the effectiveness of the proposed methods. As one of the earliest efforts to identify the residency and worker status information for a large-scale national-level MDLD dataset, mobile workers—including professional drivers and mobility-for-work workers—are also identified from MDLD for the first time.

Community Detection Based on a Preferential Decision Model

The research on complex networks is a hot topic in many fields, among which community detection is a complex and meaningful process, which plays an important role in researching the characteristics of complex networks. Community structure is a common feature in the network. Given a graph, the process of uncovering its community structure is called community detection. Many community detection algorithms from different perspectives have been proposed. Achieving stable and accurate community division is still a non-trivial task due to the difficulty of setting specific parameters, high randomness and lack of ground-truth information. In this paper, we explore a new decision-making method through real-life communication and propose a preferential decision model based on dynamic relationships applied to dynamic systems. We apply this model to the label propagation algorithm and present a Community Detection based on Preferential Decision Model, called CDPD. This model intuitively aims to reveal the topological structure and the hierarchical structure between networks. By analyzing the structural characteristics of complex networks and mining the tightness between nodes, the priority of neighbor nodes is chosen to perform the required preferential decision, and finally the information in the system reaches a stable state. In the experiments, through the comparison of eight comparison algorithms, we verified the performance of CDPD in real-world networks and synthetic networks. The results show that CDPD not only has better performance than most recent algorithms on most datasets, but it is also more suitable for many community networks with ambiguous structure, especially sparse networks.

Community detection based on information dynamics

Community detection, as the primary task of network analysis, provides a promising way to summarize the network structure, study the interactions of groups and obtain insight into the potential network functions. Many community detection algorithms have been proposed from different viewpoints. However, uncovering the intrinsic communities in networks is still a non-trivial task due to the difficulty of parameter tuning, user-bias criteria and the lack of ground-truth information. In this paper, we propose a new dynamic model that aims to uncover the communities in networks in a more intuitive and topologically driven way. The basic idea is to explore the community structure by simulating the information exchange in a given network. The information that is flowing on a given network is governed by the underlying network community structure. The community structure, in turn, is reflected by the information dynamics. To prove the convergence of the information dynamic model, the monotone convergence theorem is employed. In the experiments, we have demonstrated that our proposed approach is superior to many representative algorithms on both synthetic and real-world networks.

User guidance for efficient fact checking

The Web constitutes a valuable source of information. In recent years, it fostered the construction of large-scale knowledge bases, such as Freebase, YAGO, and DBpedia. The open nature of the Web, with content potentially being generated by everyone, however, leads to inaccuracies and misinformation. Construction and maintenance of a knowledge base thus has to rely on fact checking, an assessment of the credibility of facts. Due to an inherent lack of ground truth information, such fact checking cannot be done in a purely automated manner, but requires human involvement. In this paper, we propose a comprehensive framework to guide users in the validation of facts, striving for a minimisation of the invested effort. Our framework is grounded in a novel probabilistic model that combines user input with automated credibility inference. Based thereon, we show how to guide users in fact checking by identifying the facts for which validation is most beneficial. Moreover, our framework includes techniques to reduce the manual effort invested in fact checking by determining when to stop the validation and by supporting efficient batching strategies. We further show how to handle fact checking in a streaming setting. Our experiments with three real-world datasets demonstrate the efficiency and effectiveness of our framework: A knowledge base of high quality, with a precision of above 90%, is constructed with only a half of the validation effort required by baseline techniques.

Overlapping Community Detection Based on Information Dynamics

Identifying overlapping communities is essential for analyzing network structures, exploring the interactions of groups, studying network functions, and obtaining insight into the dynamics of networks. Many algorithms have been proposed for detecting overlapping communities but identifying the intrinsic communities is still a non-trivial problem because of the difficulties with parameter tuning, user bias criteria, and the lack of ground truth information. In this paper, we propose a new model called OCDID (Overlapping Community Detection based on Information Dynamics) to uncover the overlapping communities, which treats the network as a dynamical system that allows an individual to communicate and share information with its neighbors. The information flow in the network is controlled by the underlying topology structure (e.g., the community structure), and the community structure is also reflected by the information dynamics. Overlapping nodes act as bridges between multiple communities and the information from multiple communities flows through these nodes. Thus, the overlapping nodes can be identified by analyzing the information flow among communities. In addition, we use the monotone convergence theorem to confirm the convergence of our model. Experiments based on synthetic and real-world networks demonstrate that in most cases, our proposed approach is superior to other representative algorithms in terms of the quality of overlapping community detection.

Using remote sensing to assess tsunami-induced impacts on coastal forest ecosystems at the Andaman Sea coast of Thailand

Abstract. The December 2004 tsunami strongly impacted coastal ecosystems along the Andaman Sea coast of Thailand. In this paper tsunami-induced damage of five different coastal forest ecosystems at the Phang-Nga province coast is analysed with a remote sensing driven approach based on multi-date IKONOS imagery. Two change detection algorithms, change vector analysis (CVA) and direct multi-date classification (DMC), are applied and compared regarding their applicability to assess tsunami impacts. The analysis shows that DMC outperforms CVA in terms of accuracy (Kappa values for DMC ranging between 0.947 and 0.950 and between 0.610–0.730 for CVA respectively) and the degree of detail of the created change classes. Results from DMC show that mangroves were the worst damaged among the five forests, with a 55% of directly damaged forest in the study area, followed by casuarina forest and coconut plantation. Additionally this study points out the uncertainties in both methods which are mainly due to a lack of ground truth information for the time between the two acquisition dates of satellite images. The created damage maps help to better understand the way the tsunami impacted coastal forests and give basic information for estimating tsunami sensitivity of coastal forests.

Evaluating the performance of microarray segmentation algorithms

Although numerous algorithms have been developed for microarray segmentation, extensive comparisons between the algorithms have acquired far less attention. In this study, we evaluate the performance of nine microarray segmentation algorithms. Using both simulated and real microarray experiments, we overcome the challenges in performance evaluation, arising from the lack of ground-truth information. The usage of simulated experiments allows us to analyze the segmentation accuracy on a single pixel level as is commonly done in traditional image processing studies. With real experiments, we indirectly measure the segmentation performance, identify significant differences between the algorithms, and study the characteristics of the resulting gene expression data. Overall, our results show clear differences between the algorithms. The results demonstrate how the segmentation performance depends on the image quality, which algorithms operate on significantly different performance levels, and how the selection of a segmentation algorithm affects the identification of differentially expressed genes. Supplementary results and the microarray images used in this study are available at the companion web site http://www.cs.tut.fi/sgn/csb/spotseg/