Improving average ranking precision in user searches for biomedical research datasets

Availability of research datasets is keystone for health and life science study reproducibility and scientific progress. Due to the heterogeneity and complexity of these data, a main challenge to be overcome by research data management systems is to provide users with the best answers for their search queries. In the context of the 2016 bioCADDIE Dataset Retrieval Challenge, we investigate a novel ranking pipeline to improve the search of datasets used in biomedical experiments. Our system comprises a query expansion model based on word embeddings, a similarity measure algorithm that takes into consideration the relevance of the query terms, and a dataset categorisation method that boosts the rank of datasets matching query constraints. The system was evaluated using a corpus with 800k datasets and 21 annotated user queries. Our system provides competitive results when compared to the other challenge participants. In the official run, it achieved the highest infAP among the participants, being +22.3% higher than the median infAP of the participant's best submissions. Overall, it is ranked at top 2 if an aggregated metric using the best official measures per participant is considered. The query expansion method showed positive impact on the system's performance increasing our baseline up to +5.0% and +3.4% for the infAP and infNDCG metrics, respectively. Our similarity measure algorithm seems to be robust, in particular compared to Divergence From Randomness framework, having smaller performance variations under different training conditions. Finally, the result categorization did not have significant impact on the system's performance. We believe that our solution could be used to enhance biomedical dataset management systems. In particular, the use of data driven query expansion methods could be an alternative to the complexity of biomedical terminologies

Term-Specific Eigenvector-Centrality in Multi-Relation Networks

Fuzzy matching and ranking are two information retrieval techniques widely used in web search. Their application to structured data, however, remains an open problem. This article investigates how eigenvector-centrality can be used for approximate matching in multi-relation graphs, that is, graphs where connections of many different types may exist. Based on an extension of the PageRank matrix, eigenvectors representing the distribution of a term after propagating term weights between related data items are computed. The result is an index which takes the document structure into account and can be used with standard document retrieval techniques. As the scheme takes the shape of an index transformation, all necessary calculations are performed during index tim

Using COTS Search Engines and Custom Query Strategies at CLEF

This paper presents a system for bilingual information retrieval using commercial off-the-shelf search engines (COTS). Several custom query construction, expansion and translation strategies are compared. We present the experiments and the corresponding results for the CLEF 2004 event

Flexible information retrieval: some research trends

In this paper some research trends in the field of Information Retrieval are presented. The focus is on the definition of flexible systems, i.e. systems that can represent and manage the vagueness and uncertainty which is characteristic of the process of information searching and retrieval. In this paper the application of soft computing techniques is considered, in particular fuzzy set theory

Local search: A guide for the information retrieval practitioner

There are a number of combinatorial optimisation problems in information retrieval in which the use of local search methods are worthwhile. The purpose of this paper is to show how local search can be used to solve some well known tasks in information retrieval (IR), how previous research in the field is piecemeal, bereft of a structure and methodologically flawed, and to suggest more rigorous ways of applying local search methods to solve IR problems. We provide a query based taxonomy for analysing the use of local search in IR tasks and an overview of issues such as fitness functions, statistical significance and test collections when conducting experiments on combinatorial optimisation problems. The paper gives a guide on the pitfalls and problems for IR practitioners who wish to use local search to solve their research issues, and gives practical advice on the use of such methods. The query based taxonomy is a novel structure which can be used by the IR practitioner in order to examine the use of local search in IR

CBR and MBR techniques: review for an application in the emergencies domain

The purpose of this document is to provide an in-depth analysis of current reasoning engine practice and the integration strategies of Case Based Reasoning and Model Based Reasoning that will be used in the design and development of the RIMSAT system. RIMSAT (Remote Intelligent Management Support and Training) is a European Commission funded project designed to: a.. Provide an innovative, 'intelligent', knowledge based solution aimed at improving the quality of critical decisions b.. Enhance the competencies and responsiveness of individuals and organisations involved in highly complex, safety critical incidents - irrespective of their location. In other words, RIMSAT aims to design and implement a decision support system that using Case Base Reasoning as well as Model Base Reasoning technology is applied in the management of emergency situations. This document is part of a deliverable for RIMSAT project, and although it has been done in close contact with the requirements of the project, it provides an overview wide enough for providing a state of the art in integration strategies between CBR and MBR technologies.Postprint (published version

Effective retrieval and new indexing method for case based reasoning: Application in chemical process design

In this paper we try to improve the retrieval step for case based reasoning for preliminary design. This improvement deals with three major parts of our CBR system. First, in the preliminary design step, some uncertainties like imprecise or unknown values remain in the description of the problem, because they need a deeper analysis to be withdrawn. To deal with this issue, the faced problem description is soften with the fuzzy sets theory. Features are described with a central value, a percentage of imprecision and a relation with respect to the central value. These additional data allow us to build a domain of possible values for each attributes. With this representation, the calculation of the similarity function is impacted, thus the characteristic function is used to calculate the local similarity between two features. Second, we focus our attention on the main goal of the retrieve step in CBR to find relevant cases for adaptation. In this second part, we discuss the assumption of similarity to find the more appropriated case. We put in highlight that in some situations this classical similarity must be improved with further knowledge to facilitate case adaptation. To avoid failure during the adaptation step, we implement a method that couples similarity measurement with adaptability one, in order to approximate the cases utility more accurately. The latter gives deeper information for the reusing of cases. In a last part, we present a generic indexing technique for the base, and a new algorithm for the research of relevant cases in the memory. The sphere indexing algorithm is a domain independent index that has performances equivalent to the decision tree ones. But its main strength is that it puts the current problem in the center of the research area avoiding boundaries issues. All these points are discussed and exemplified through the preliminary design of a chemical engineering unit operation

Bridging the semantic gap in content-based image retrieval.

To manage large image databases, Content-Based Image Retrieval (CBIR) emerged as a new research subject. CBIR involves the development of automated methods to use visual features in searching and retrieving. Unfortunately, the performance of most CBIR systems is inherently constrained by the low-level visual features because they cannot adequately express the user\u27s high-level concepts. This is known as the semantic gap problem. This dissertation introduces a new approach to CBIR that attempts to bridge the semantic gap. Our approach includes four components. The first one learns a multi-modal thesaurus that associates low-level visual profiles with high-level keywords. This is accomplished through image segmentation, feature extraction, and clustering of image regions. The second component uses the thesaurus to annotate images in an unsupervised way. This is accomplished through fuzzy membership functions to label new regions based on their proximity to the profiles in the thesaurus. The third component consists of an efficient and effective method for fusing the retrieval results from the multi-modal features. Our method is based on learning and adapting fuzzy membership functions to the distribution of the features\u27 distances and assigning a degree of worthiness to each feature. The fourth component provides the user with the option to perform hybrid querying and query expansion. This allows the enrichment of a visual query with textual data extracted from the automatically labeled images in the database. The four components are integrated into a complete CBIR system that can run in three different and complementary modes. The first mode allows the user to query using an example image. The second mode allows the user to specify positive and/or negative sample regions that should or should not be included in the retrieved images. The third mode uses a Graphical Text Interface to allow the user to browse the database interactively using a combination of low-level features and high-level concepts. The proposed system and ail of its components and modes are implemented and validated using a large data collection for accuracy, performance, and improvement over traditional CBIR techniques

A novel approach integrating ranking functions discovery, optimization and infernce to improve retrieval performance

The significant roles play by ranking function in the performance and success of Information Retrieval (IR) systems and search engines cannot be underestimated. Diverse ranking functions are available in IR literature. However, empirical studies show that ranking functions do not perform constantly well across different contexts (queries, collections, users). In this study, a novel three-stage integrated ranking framework is proposed for implementing discovering, optimizing and inference rankings used in IR systems. The first phase, discovery process is based on Genetic Programming (GP) approach which smartly combines structural and contents features in the documents while the second phase, optimization process is based on Genetic Algorithm (GA) which combines document retrieval scores of various well-known ranking functions. In the 3rd phase, Fuzzy inference proves as soft search constraints to be applied on documents. We demonstrate how these two features are combined to bring new tasks and processes within the three concept stages of integrated framework for effective IR