The LAILAPS Search Engine: A Feature Model for Relevance Ranking in Life Science Databases

Efficient and effective information retrieval in life sciences is one of the most pressing challenge in bioinformatics. The incredible growth of life science databases to a vast network of interconnected information systems is to the same extent a big challenge and a great chance for life science research. The knowledge found in the Web, in particular in life-science databases, are a valuable major resource. In order to bring it to the scientist desktop, it is essential to have well performing search engines. Thereby, not the response time nor the number of results is important. The most crucial factor for millions of query results is the relevance ranking. In this paper, we present a feature model for relevance ranking in life science databases and its implementation in the LAILAPS search engine. Motivated by the observation of user behavior during their inspection of search engine result, we condensed a set of 9 relevance discriminating features. These features are intuitively used by scientists, who briefly screen database entries for potential relevance. The features are both sufficient to estimate the potential relevance, and efficiently quantifiable. The derivation of a relevance prediction function that computes the relevance from this features constitutes a regression problem. To solve this problem, we used artificial neural networks that have been trained with a reference set of relevant database entries for 19 protein queries. Supporting a flexible text index and a simple data import format, this concepts are implemented in the LAILAPS search engine. It can easily be used both as search engine for comprehensive integrated life science databases and for small in-house project databases. LAILAPS is publicly available for SWISSPROT data at http://lailaps.ipk-gatersleben.d

Set-Oriented Mining for Association Rules in Relational Databases

Describe set-oriented algorithms for mining association rules. Such algorithms imply performing multiple joins and may appear to be inherently less efficient than special-purpose algorithms. We develop new algorithms that can be expressed as SQL queries, and discuss the optimization of these algorithms. After analytical evaluation, an algorithm named SETM emerges as the algorithm of choice. SETM uses only simple database primitives, viz. sorting and merge-scan join. SETM is simple, fast and stable over the range of parameter values. The major contribution of this paper is that it shows that at least some aspects of data mining can be carried out by using general query languages such as SQL, rather than by developing specialized black-box algorithms. The set-oriented nature of SETM facilitates the development of extension

Set-oriented data mining in relational databases

Data mining is an important real-life application for businesses. It is critical to find efficient ways of mining large data sets. In order to benefit from the experience with relational databases, a set-oriented approach to mining data is needed. In such an approach, the data mining operations are expressed in terms of relational or set-oriented operations. Query optimization technology can then be used for efficient processing.\ud \ud In this paper, we describe set-oriented algorithms for mining association rules. Such algorithms imply performing multiple joins and thus may appear to be inherently less efficient than special-purpose algorithms. We develop new algorithms that can be expressed as SQL queries, and discuss optimization of these algorithms. After analytical evaluation, an algorithm named SETM emerges as the algorithm of choice. Algorithm SETM uses only simple database primitives, viz., sorting and merge-scan join. Algorithm SETM is simple, fast, and stable over the range of parameter values. It is easily parallelized and we suggest several additional optimizations. The set-oriented nature of Algorithm SETM makes it possible to develop extensions easily and its performance makes it feasible to build interactive data mining tools for large databases

Generic Subsequence Matching Framework: Modularity, Flexibility, Efficiency

Subsequence matching has appeared to be an ideal approach for solving many problems related to the fields of data mining and similarity retrieval. It has been shown that almost any data class (audio, image, biometrics, signals) is or can be represented by some kind of time series or string of symbols, which can be seen as an input for various subsequence matching approaches. The variety of data types, specific tasks and their partial or full solutions is so wide that the choice, implementation and parametrization of a suitable solution for a given task might be complicated and time-consuming; a possibly fruitful combination of fragments from different research areas may not be obvious nor easy to realize. The leading authors of this field also mention the implementation bias that makes difficult a proper comparison of competing approaches. Therefore we present a new generic Subsequence Matching Framework (SMF) that tries to overcome the aforementioned problems by a uniform frame that simplifies and speeds up the design, development and evaluation of subsequence matching related systems. We identify several relatively separate subtasks solved differently over the literature and SMF enables to combine them in straightforward manner achieving new quality and efficiency. This framework can be used in many application domains and its components can be reused effectively. Its strictly modular architecture and openness enables also involvement of efficient solutions from different fields, for instance efficient metric-based indexes. This is an extended version of a paper published on DEXA 2012.Comment: This is an extended version of a paper published on DEXA 201

On the Implementation of the Probabilistic Logic Programming Language ProbLog

The past few years have seen a surge of interest in the field of probabilistic logic learning and statistical relational learning. In this endeavor, many probabilistic logics have been developed. ProbLog is a recent probabilistic extension of Prolog motivated by the mining of large biological networks. In ProbLog, facts can be labeled with probabilities. These facts are treated as mutually independent random variables that indicate whether these facts belong to a randomly sampled program. Different kinds of queries can be posed to ProbLog programs. We introduce algorithms that allow the efficient execution of these queries, discuss their implementation on top of the YAP-Prolog system, and evaluate their performance in the context of large networks of biological entities.Comment: 28 pages; To appear in Theory and Practice of Logic Programming (TPLP

A storage and access architecture for efficient query processing in spatial database systems

Due to the high complexity of objects and queries and also due to extremely large data volumes, geographic database systems impose stringent requirements on their storage and access architecture with respect to efficient query processing. Performance improving concepts such as spatial storage and access structures, approximations, object decompositions and multi-phase query processing have been suggested and analyzed as single building blocks. In this paper, we describe a storage and access architecture which is composed from the above building blocks in a modular fashion. Additionally, we incorporate into our architecture a new ingredient, the scene organization, for efficiently supporting set-oriented access of large-area region queries. An experimental performance comparison demonstrates that the concept of scene organization leads to considerable performance improvements for large-area region queries by a factor of up to 150

The combination of spatial access methods and computational geometry in geographic database systems

Geographic database systems, known as geographic information systems (GISs) particularly among non-computer scientists, are one of the most important applications of the very active research area named spatial database systems. Consequently following the database approach, a GIS hag to be seamless, i.e. store the complete area of interest (e.g. the whole world) in one database map. For exhibiting acceptable performance a seamless GIS hag to use spatial access methods. Due to the complexity of query and analysis operations on geographic objects, state-of-the-art computational geomeny concepts have to be used in implementing these operations. In this paper, we present GIS operations based on the compuational geomeny technique plane sweep. Specifically, we show how the two ingredients spatial access methods and computational geomeny concepts can be combined für improving the performance of GIS operations. The fruitfulness of this combination is based on the fact that spatial access methods efficiently provide the data at the time when computational geomeny algorithms need it für processing. Additionally, this combination avoids page faults and facilitates the parallelization of the algorithms.