Expert System for Crop Disease based on Graph Pattern Matching: A proposal

Para la agroindustria, las enfermedades en cultivos constituyen uno de los problemas más frecuentes que generan grandes pérdidas económicas y baja calidad en la producción. Por otro lado, desde las ciencias de la computación, han surgido diferentes herramientas cuya finalidad es mejorar la prevención y el tratamiento de estas enfermedades. En este sentido, investigaciones recientes proponen el desarrollo de sistemas expertos para resolver este problema haciendo uso de técnicas de minería de datos e inteligencia artificial, como inferencia basada en reglas, árboles de decisión, redes bayesianas, entre otras. Además, los grafos pueden ser usados para el almacenamiento de los diferentes tipos de variables que se encuentran presentes en un ambiente de cultivos, permitiendo la aplicación de técnicas de minería de datos en grafos, como el emparejamiento de patrones en los mismos. En este artículo presentamos una visión general de las temáticas mencionadas y una propuesta de un sistema experto para enfermedades en cultivos, basado en emparejamiento de patrones en grafos.For agroindustry, crop diseases constitute one of the most common problems that generate large economic losses and low production quality. On the other hand, from computer science, several tools have emerged in order to improve the prevention and treatment of these diseases. In this sense, recent research proposes the development of expert systems to solve this problem, making use of data mining and artificial intelligence techniques like rule-based inference, decision trees, Bayesian network, among others. Furthermore, graphs can be used for storage of different types of variables that are present in an environment of crops, allowing the application of graph data mining techniques like graph pattern matching. Therefore, in this paper we present an overview of the above issues and a proposal of an expert system for crop disease based on graph pattern matching

Differential analysis of biological networks

In cancer research, the comparison of gene expression or DNA methylation networks inferred from healthy controls and patients can lead to the discovery of biological pathways associated to the disease. As a cancer progresses, its signalling and control networks are subject to some degree of localised re-wiring. Being able to detect disrupted interaction patterns induced by the presence or progression of the disease can lead to the discovery of novel molecular diagnostic and prognostic signatures. Currently there is a lack of scalable statistical procedures for two-network comparisons aimed at detecting localised topological differences. We propose the dGHD algorithm, a methodology for detecting differential interaction patterns in two-network comparisons. The algorithm relies on a statistic, the Generalised Hamming Distance (GHD), for assessing the degree of topological difference between networks and evaluating its statistical significance. dGHD builds on a non-parametric permutation testing framework but achieves computationally efficiency through an asymptotic normal approximation. We show that the GHD is able to detect more subtle topological differences compared to a standard Hamming distance between networks. This results in the dGHD algorithm achieving high performance in simulation studies as measured by sensitivity and specificity. An application to the problem of detecting differential DNA co-methylation subnetworks associated to ovarian cancer demonstrates the potential benefits of the proposed methodology for discovering network-derived biomarkers associated with a trait of interest

Any-k: Anytime Top-k Tree Pattern Retrieval in Labeled Graphs

Many problems in areas as diverse as recommendation systems, social network analysis, semantic search, and distributed root cause analysis can be modeled as pattern search on labeled graphs (also called "heterogeneous information networks" or HINs). Given a large graph and a query pattern with node and edge label constraints, a fundamental challenge is to nd the top-k matches ac- cording to a ranking function over edge and node weights. For users, it is di cult to select value k . We therefore propose the novel notion of an any-k ranking algorithm: for a given time budget, re- turn as many of the top-ranked results as possible. Then, given additional time, produce the next lower-ranked results quickly as well. It can be stopped anytime, but may have to continues until all results are returned. This paper focuses on acyclic patterns over arbitrary labeled graphs. We are interested in practical algorithms that effectively exploit (1) properties of heterogeneous networks, in particular selective constraints on labels, and (2) that the users often explore only a fraction of the top-ranked results. Our solution, KARPET, carefully integrates aggressive pruning that leverages the acyclic nature of the query, and incremental guided search. It enables us to prove strong non-trivial time and space guarantees, which is generally considered very hard for this type of graph search problem. Through experimental studies we show that KARPET achieves running times in the order of milliseconds for tree patterns on large networks with millions of nodes and edges.Comment: To appear in WWW 201