Document re-ranking by generality in bio-medical information retrieval

Document ranking is an important process in information retrieval (IR). It presents retrieved documents in an order of their estimated degrees of relevance to query. Traditional document ranking methods are mostly based on the similarity computations between documents and query. In this paper we argue that the similarity-based document ranking is insufficient in some cases. There are two reasons. Firstly it is about the increased information variety. There are far too many different types documents available now for user to search. The second is about the users variety. In many cases user may want to retrieve documents that are not only similar but also general or broad regarding a certain topic. This is particularly the case in some domains such as bio-medical IR. In this paper we propose a novel approach to re-rank the retrieved documents by incorporating the similarity with their generality. By an ontology-based analysis on the semantic cohesion of text, document generality can be quantified. The retrieved documents are then re-ranked by their combined scores of similarity and the closeness of documents’ generality to the query’s. Our experiments have shown an encouraging performance on a large bio-medical document collection, OHSUMED, containing 348,566 medical journal references and 101 test queries.

Concept-based document readability in domain specific information retrieval

Domain specific information retrieval has become in demand. Not only domain experts, but also average non-expert users are interested in searching domain specific (e.g., medical and health) information from online resources. However, a typical problem to average users is that the search results are always a mixture of documents with different levels of readability. Non-expert users may want to see documents with higher readability on the top of the list. Consequently the search results need to be re-ranked in a descending order of readability. It is often not practical for domain experts to manually label the readability of documents for large databases. Computational models of readability needs to be investigated. However, traditional readability formulas are designed for general purpose text and insufficient to deal with technical materials for domain specific information retrieval. More advanced algorithms such as textual coherence model are computationally expensive for re-ranking a large number of retrieved documents. In this paper, we propose an effective and computationally tractable concept-based model of text readability. In addition to textual genres of a document, our model also takes into account domain specific knowledge, i.e., how the domain-specific concepts contained in the document affect the document’s readability. Three major readability formulas are proposed and applied to health and medical information retrieval. Experimental results show that our proposed readability formulas lead to remarkable improvements in terms of correlation with users’ readability ratings over four traditional readability measures.

Structured ontology and information retrieval for email search and discovery

This paper discusses an document discovery tool based on formal concept analysis. The program allows users to navigate email using a visual lattice metaphor rather than a tree. It implements a virtual file structure over email where files and entire directories can appear in multiple positions. The content and shape of the lattice formed by the conceptual ontology can assist in email discovery. The system described provides more flexibility in retrieving stored emails than what is normally available in email clients. The paper discusses how conceptual ontologies can leverage traditional document retrieval systems.

Fitness assessment of document model

Document classification is a supervised machine learning process, where predefined category labels are assigned to documents based on the hypothesis derived from training set of labelled documents. Documents cannot be directly interpreted by a computer system unless they have been modelled as a collection of computable features. Rogati and Yang [M. Rogati and Y. Yang, Resource selection for domain-specific cross-lingual IR, in SIGIR 2004: Proceedings of the 27th annual international conference on Research and Development in Information Retrieval, ACM Press, Sheffied: United Kingdom, pp. 154-161.] pointed out that the effectiveness of document classification system may vary in different domains. This implies that the quality of document model contributes to the effectiveness of document classification. Conventionally, model evaluation is accomplished by comparing the effectiveness scores of classifiers on model candidates. However, this kind of evaluation methods may encounter either under-fitting or over-fitting problems, because the effectiveness scores are restricted by the learning capacities of classifiers. We propose a model fitness evaluation method to determine whether a model is sufficient to distinguish positive and negative instances while still competent to provide satisfactory effectiveness with a small feature subset. Our experiments demonstrated how the fitness of models are assessed. The results of our work contribute to the researches of feature selection, dimensionality reduction and document classification.

A Correlation Analysis on LSA and HAL Semantic Space Models

In this paper, we compare a well-known semantic spacemodel, Latent Semantic Analysis (LSA) with another model, Hyperspace Analogue to Language (HAL) which is widely used in different area, especially in automatic query refinement. We conduct this comparative analysis to prove our hypothesis that with respect to ability of extracting the lexical information from a corpus of text, LSA is quite similar to HAL. We regard HAL and LSA as black boxes. Through a Pearsonrsquos correlation analysis to the outputs of these two black boxes, we conclude that LSA highly co-relates with HAL and thus there is a justification that LSA and HAL can potentially play a similar role in the area of facilitating automatic query refinement. This paper evaluates LSA in a new application area and contributes an effective way to compare different semantic space models.

How does your model grow? An empirical investigation of the effects of ontological clarity and application domain size on query performance

Semantic data models provide a map of the components of an information system. The characteristics of these models affect their usefulness for various tasks (e.g., information retrieval). The quality of information retrieval has obvious important consequences, both economic and otherwise. Traditionally, data base designers have produced parsimonious logical data models. In spite of their increased size, ontologically clearer conceptual models have been shown to facilitate better performance for both problem solving and information retrieval tasks in experimental settings. The experiments producing evidence of enhanced performance for ontologically clearer models have, however, used application domains of modest size. Data models in organizational settings are likely to be substantially larger than those used in these experiments. This research used an experiment to investigate whether the benefits of improved information retrieval performance associated with ontologically clearer models are robust as the size of the application domains increase. The experiment used an application domain of approximately twice the size as tested in prior experiments. The results indicate that, relative to the users of the parsimonious implementation, end users of the ontologically clearer implementation made significantly more semantic errors, took significantly more time to compose their queries, and were significantly less confident in the accuracy of their queries.

Dissecting query performance in logical data models: Parsimony vs. greater ontological clarity

Even when data repositories exhibit near perfect data quality, users may formulate queries that do not correspond to the information requested. Users’ poor information retrieval performance may arise from either problems understanding of the data models that represent the real world systems, or their query skills. This research focuses on users’ understanding of the data structures, i.e., their ability to map the information request and the data model. The Bunge-Wand-Weber ontology was used to formulate three sets of hypotheses. Two laboratory experiments (one using a small data model and one using a larger data model) tested the effect of ontological clarity on users’ performance when undertaking component, record, and aggregate level tasks. The results indicate for the hypotheses associated with different representations but equivalent semantics that parsimonious data model participants performed better for component level tasks but that ontologically clearer data model participants performed better for record and aggregate level tasks.

A hybrid probabilistic criterion for market-based transmission expansion planning

Market-based transmission expansion planning gives information to investors on where is the most cost efficient place to invest and brings benefits to those who invest in this grid. However, both market issue and power system adequacy problems are system planers’ concern. In this paper, a hybrid probabilistic criterion of Expected Economical Loss (EEL) is proposed as an index to evaluate the systems’ overall expected economical losses during system operation in a competitive market. It stands on both investors’ and planner’s point of view and will further improves the traditional reliability cost. By applying EEL, it is possible for system planners to obtain a clear idea regarding the transmission network’s bottleneck and the amount of losses arises from this weak point. Sequentially, it enables planners to assess the worth of providing reliable services. Also, the EEL will contain valuable information for moneymen to undertake their investment. This index could truly reflect the random behaviors of power systems and uncertainties from electricity market. The performance of the EEL index is enhanced by applying Normalized Coefficient of Probability (NCP), so it can be utilized in large real power systems. A numerical example is carried out on IEEE Reliability Test System (RTS), which will show how the EEL can predict the current system bottleneck under future operational conditions and how to use EEL as one of planning objectives to determine future optimal plans. A well-known simulation method, Monte Carlo simulation, is employed to achieve the probabilistic characteristic of electricity market and Genetic Algorithms (GAs) is used as a multi-objective optimization tool.

Extracting ontological concepts for tendering conceptual structures

It has been argued that beyond software engineering and process engineering, ontological engineering is the third capability needed if successful e-commerce is to be realized. In our experience of building an ontological-based tendering system, we face the problem of building an ontology. In this paper, we demonstrate how to build ontologies in the tendering domain. The ontology life cycle is identified. Extracting concepts from existing resources like on-line catalogs is described. We have reused electronic data interchange (EDI) to build conceptual structures in the tendering domain. An algorithm to extract abstract ontological concepts from these structures is proposed.

Authorship Attribution with Support Vector Machines

In this paper we explore the use of text-mining methods for the identification of the author of a text. We apply the support vector machine (SVM) to this problem, as it is able to cope with half a million of inputs it requires no feature selection and can process the frequency vector of all words of a text. We performed a number of experiments with texts from a German newspaper. With nearly perfect reliability the SVM was able to reject other authors and detected the target author in 60–80% of the cases. In a second experiment, we ignored nouns, verbs and adjectives and replaced them by grammatical tags and bigrams. This resulted in slightly reduced performance. Author detection with SVMs on full word forms was remarkably robust even if the author wrote about different topics.

Efficiently computing weighted proximity relationships in spatial databases

Spatial data mining recently emerges from a number of real applications, such as real-estate marketing, urban planning, weather forecasting, medical image analysis, road traffic accident analysis, etc. It demands for efficient solutions for many new, expensive, and complicated problems. In this paper, we investigate the problem of evaluating the top k distinguished “features” for a “cluster” based on weighted proximity relationships between the cluster and features. We measure proximity in an average fashion to address possible nonuniform data distribution in a cluster. Combining a standard multi-step paradigm with new lower and upper proximity bounds, we presented an efficient algorithm to solve the problem. The algorithm is implemented in several different modes. Our experiment results not only give a comparison among them but also illustrate the efficiency of the algorithm.