Graph Refinement based Airway Extraction using Mean-Field Networks and Graph Neural Networks

Graph refinement, or the task of obtaining subgraphs of interest from over-complete graphs, can have many varied applications. In this work, we extract trees or collection of sub-trees from image data by, first deriving a graph-based representation of the volumetric data and then, posing the tree extraction as a graph refinement task. We present two methods to perform graph refinement. First, we use mean-field approximation (MFA) to approximate the posterior density over the subgraphs from which the optimal subgraph of interest can be estimated. Mean field networks (MFNs) are used for inference based on the interpretation that iterations of MFA can be seen as feed-forward operations in a neural network. This allows us to learn the model parameters using gradient descent. Second, we present a supervised learning approach using graph neural networks (GNNs) which can be seen as generalisations of MFNs. Subgraphs are obtained by training a GNN-based graph refinement model to directly predict edge probabilities. We discuss connections between the two classes of methods and compare them for the task of extracting airways from 3D, low-dose, chest CT data. We show that both the MFN and GNN models show significant improvement when compared to one baseline method, that is similar to a top performing method in the EXACT'09 Challenge, and a 3D U-Net based airway segmentation model, in detecting more branches with fewer false positives.Comment: Accepted for publication at Medical Image Analysis. 14 page

Algorithms of causal inference for the analysis of effective connectivity among brain regions

In recent years, powerful general algorithms of causal inference have been developed. In particular, in the framework of Pearl’s causality, algorithms of inductive causation (IC and IC*) provide a procedure to determine which causal connections among nodes in a network can be inferred from empirical observations even in the presence of latent variables, indicating the limits of what can be learned without active manipulation of the system. These algorithms can in principle become important complements to established techniques such as Granger causality and Dynamic Causal Modeling (DCM) to analyze causal influences (effective connectivity) among brain regions. However, their application to dynamic processes has not been yet examined. Here we study how to apply these algorithms to time-varying signals such as electrophysiological or neuroimaging signals. We propose a new algorithm which combines the basic principles of the previous algorithms with Granger causality to obtain a representation of the causal relations suited to dynamic processes. Furthermore, we use graphical criteria to predict dynamic statistical dependencies between the signals from the causal structure. We show how some problems for causal inference from neural signals (e.g., measurement noise, hemodynamic responses, and time aggregation) can be understood in a general graphical approach. Focusing on the effect of spatial aggregation, we show that when causal inference is performed at a coarser scale than the one at which the neural sources interact, results strongly depend on the degree of integration of the neural sources aggregated in the signals, and thus characterize more the intra-areal properties than the interactions among regions. We finally discuss how the explicit consideration of latent processes contributes to understand Granger causality and DCM as well as to distinguish functional and effective connectivity

Evaluation of Kermeta for Solving Graph-based Problems

Kermeta is a meta-language for specifying the structure and behavior of graphs of interconnected objects called models. In this paper,\ud we show that Kermeta is relatively suitable for solving three graph-based\ud problems. First, Kermeta allows the specification of generic model\ud transformations such as refactorings that we apply to different metamodels\ud including Ecore, Java, and Uml. Second, we demonstrate the extensibility\ud of Kermeta to the formal language Alloy using an inter-language model\ud transformation. Kermeta uses Alloy to generate recommendations for\ud completing partially specified models. Third, we show that the Kermeta\ud compiler achieves better execution time and memory performance compared\ud to similar graph-based approaches using a common case study. The\ud three solutions proposed for those graph-based problems and their\ud evaluation with Kermeta according to the criteria of genericity,\ud extensibility, and performance are the main contribution of the paper.\ud Another contribution is the comparison of these solutions with those\ud proposed by other graph-based tools

Planning Rural Water Services in Nicaragua: A Systems-Based Analysis of Impact Factors Using Graphical Modeling

The success or failure of rural water services in the developing world is a result of numerous factors that interact in a complex set of connections that are difficult to separate and identify. This research effort presented a novel means to empirically reveal the systemic interactions of factors that influence rural water service sustainability in the municipalities of Darío and Terrabona, Nicaragua. To accomplish this, the study employed graphical modeling to build and analyze factor networks. Influential factors were first identified by qualitatively and quantitatively analyzing transcribed interviews from community water committee members. Factor influences were then inferred by graphical modeling to create factor network diagrams that revealed the direct and indirect interaction of factors. Finally, network analysis measures were used to identify “impact factors” based on their relative influence within each factor network. Findings from this study elucidated the systematic nature of such factor interactions in both Darío and Terrabona, and highlighted key areas for programmatic impact on water service sustainability for both municipalities. Specifically, in Darío, the impact areas related to the current importance of water service management by community water committees, while in Terrabona, the impact areas related to the current importance of finances, viable water sources, and community capacity building by external support. Overall, this study presents a rigorous and useful means to identify impact factors as a way to facilitate the thoughtful planning and evaluation of sustainable rural water services in Nicaragua and beyond