353 research outputs found
Inductive queries for a drug designing robot scientist
It is increasingly clear that machine learning algorithms need to be integrated in an iterative scientific discovery loop, in which data is queried repeatedly by means of inductive queries and where the computer provides guidance to the experiments that are being performed. In this chapter, we summarise several key challenges in achieving this integration of machine learning and data mining algorithms in methods for the discovery of Quantitative Structure Activity Relationships (QSARs). We introduce the concept of a robot scientist, in which all steps of the discovery process are automated; we discuss the representation of molecular data such that knowledge discovery tools can analyse it, and we discuss the adaptation of machine learning and data mining algorithms to guide QSAR experiments
High Performance Frequent Subgraph Mining on Transactional Datasets
Graph data mining has been a crucial as well as inevitable area of research. Large amounts of graph data are produced in many areas, such as Bioinformatics, Cheminformatics, Social Networks, and Web etc. Scalable graph data mining methods are getting increasingly popular and necessary due to increased graph complexities. Frequent subgraph mining is one such area where the task is to find overly recurring patterns/subgraphs. To tackle this problem, many main memory-based methods were proposed, which proved to be inefficient as the data size grew exponentially over time. In the past few years several research groups have attempted to handle the frequent subgraph mining (FSM) problem in multiple ways. Many authors have tried to achieve better performance using Graphic Processing Units (GPUs) which has multi-fold improvement over in-memory while dealing with large datasets. Later, Google\u27s MapReduce model with the Hadoop framework proved to be a major breakthrough in high performance large batch processing. Although MapReduce came with many benefits, its disk I/O and non-iterative style model could not help much for FSM domain since subgraph mining process is an iterative approach. In recent years, Spark has emerged to be the De Facto industry standard with its distributed in-memory computing capability. This is a right fit solution for iterative style of programming as well. In this work, we cover how high-performance computing has helped in improving the performance tremendously in the transactional directed and undirected aspect of graphs and performance comparisons of various FSM techniques are done based on experimental results
Mining Frequent Neighborhood Patterns in Large Labeled Graphs
Over the years, frequent subgraphs have been an important sort of targeted
patterns in the pattern mining literatures, where most works deal with
databases holding a number of graph transactions, e.g., chemical structures of
compounds. These methods rely heavily on the downward-closure property (DCP) of
the support measure to ensure an efficient pruning of the candidate patterns.
When switching to the emerging scenario of single-graph databases such as
Google Knowledge Graph and Facebook social graph, the traditional support
measure turns out to be trivial (either 0 or 1). However, to the best of our
knowledge, all attempts to redefine a single-graph support resulted in measures
that either lose DCP, or are no longer semantically intuitive.
This paper targets mining patterns in the single-graph setting. We resolve
the "DCP-intuitiveness" dilemma by shifting the mining target from frequent
subgraphs to frequent neighborhoods. A neighborhood is a specific topological
pattern where a vertex is embedded, and the pattern is frequent if it is shared
by a large portion (above a given threshold) of vertices. We show that the new
patterns not only maintain DCP, but also have equally significant semantics as
subgraph patterns. Experiments on real-life datasets display the feasibility of
our algorithms on relatively large graphs, as well as the capability of mining
interesting knowledge that is not discovered in prior works.Comment: 9 page
Graph-based discovery of ontology change patterns
Ontologies can support a variety of purposes, ranging from capturing conceptual knowledge to the organisation of digital content and information. However, information systems are always subject to change and ontology change management can pose challenges. We investigate ontology change representation and discovery of change patterns.
Ontology changes are formalised as graph-based change logs. We use attributed graphs, which are typed over a generic graph with node and edge attribution.We analyse ontology change logs, represented as graphs, and identify frequent change sequences. Such sequences are applied as a reference in order to discover reusable, often domain-specific and usagedriven change patterns. We describe the pattern discovery algorithms and measure their performance using experimental result
A novel MapReduce-based approach for distributed frequent subgraph mining
National audienceRecently, graph mining approaches have become very popular, especially in certain domains such as bioinformatics, chemoinformatics and social networks. One of the most challenging tasks is frequent subgraph discovery. This task has been highly motivated by the tremendously increasing size of existing graph databases. Due to this fact, there is an urgent need of efficient and scaling approaches for frequent subgraph discovery. In this paper, we propose a novel approach to approximate large-scale subgraph mining by means of a density-based partitioning technique, using the MapReduce framework. Our partitioning aims to balance computational load on a collection of machines. We experimentally show that our approach decreases significantly the execution time and scales the subgraph discovery process to large graph databases
A Multiobjective Evolutionary Conceptual Clustering Methodology for Gene Annotation Within Structural Databases: A Case of Study on the Gene Ontology Database
Current tools and techniques devoted to examine the
content of large databases are often hampered by their inability
to support searches based on criteria that are meaningful to
their users. These shortcomings are particularly evident in data
banks storing representations of structural data such as biological
networks. Conceptual clustering techniques have demonstrated
to be appropriate for uncovering relationships between features
that characterize objects in structural data. However, typical con ceptual clustering approaches normally recover the most obvious
relations, but fail to discover the lessfrequent but more informative
underlying data associations. The combination of evolutionary
algorithms with multiobjective and multimodal optimization
techniques constitutes a suitable tool for solving this problem.
We propose a novel conceptual clustering methodology termed
evolutionary multiobjective conceptual clustering (EMO-CC), re lying on the NSGA-II multiobjective (MO) genetic algorithm. We
apply this methodology to identify conceptual models in struc tural databases generated from gene ontologies. These models
can explain and predict phenotypes in the immunoinflammatory
response problem, similar to those provided by gene expression or
other genetic markers. The analysis of these results reveals that
our approach uncovers cohesive clusters, even those comprising a
small number of observations explained by several features, which
allows describing objects and their interactions from different
perspectives and at different levels of detail.Ministerio de Ciencia y Tecnología TIC-2003-00877Ministerio de Ciencia y Tecnología BIO2004-0270EMinisterio de Ciencia y Tecnología TIN2006-1287
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