Evaluation of a Bayesian inference network for ligand-based virtual screening

Background Bayesian inference networks enable the computation of the probability that an event will occur. They have been used previously to rank textual documents in order of decreasing relevance to a user-defined query. Here, we modify the approach to enable a Bayesian inference network to be used for chemical similarity searching, where a database is ranked in order of decreasing probability of bioactivity. Results Bayesian inference networks were implemented using two different types of network and four different types of belief function. Experiments with the MDDR and WOMBAT databases show that a Bayesian inference network can be used to provide effective ligand-based screening, especially when the active molecules being sought have a high degree of structural homogeneity; in such cases, the network substantially out-performs a conventional, Tanimoto-based similarity searching system. However, the effectiveness of the network is much less when structurally heterogeneous sets of actives are being sought. Conclusion A Bayesian inference network provides an interesting alternative to existing tools for ligand-based virtual screening

Rhetorical relations for information retrieval

Typically, every part in most coherent text has some plausible reason for its presence, some function that it performs to the overall semantics of the text. Rhetorical relations, e.g. contrast, cause, explanation, describe how the parts of a text are linked to each other. Knowledge about this socalled discourse structure has been applied successfully to several natural language processing tasks. This work studies the use of rhetorical relations for Information Retrieval (IR): Is there a correlation between certain rhetorical relations and retrieval performance? Can knowledge about a document's rhetorical relations be useful to IR? We present a language model modification that considers rhetorical relations when estimating the relevance of a document to a query. Empirical evaluation of different versions of our model on TREC settings shows that certain rhetorical relations can benefit retrieval effectiveness notably (> 10% in mean average precision over a state-of-the-art baseline)

A survey on the use of relevance feedback for information access systems

Users of online search engines often find it difficult to express their need for information in the form of a query. However, if the user can identify examples of the kind of documents they require then they can employ a technique known as relevance feedback. Relevance feedback covers a range of techniques intended to improve a user's query and facilitate retrieval of information relevant to a user's information need. In this paper we survey relevance feedback techniques. We study both automatic techniques, in which the system modifies the user's query, and interactive techniques, in which the user has control over query modification. We also consider specific interfaces to relevance feedback systems and characteristics of searchers that can affect the use and success of relevance feedback systems

Statistical Significance Testing in Information Retrieval: An Empirical Analysis of Type I, Type II and Type III Errors

Statistical significance testing is widely accepted as a means to assess how well a difference in effectiveness reflects an actual difference between systems, as opposed to random noise because of the selection of topics. According to recent surveys on SIGIR, CIKM, ECIR and TOIS papers, the t-test is the most popular choice among IR researchers. However, previous work has suggested computer intensive tests like the bootstrap or the permutation test, based mainly on theoretical arguments. On empirical grounds, others have suggested non-parametric alternatives such as the Wilcoxon test. Indeed, the question of which tests we should use has accompanied IR and related fields for decades now. Previous theoretical studies on this matter were limited in that we know that test assumptions are not met in IR experiments, and empirical studies were limited in that we do not have the necessary control over the null hypotheses to compute actual Type I and Type II error rates under realistic conditions. Therefore, not only is it unclear which test to use, but also how much trust we should put in them. In contrast to past studies, in this paper we employ a recent simulation methodology from TREC data to go around these limitations. Our study comprises over 500 million p-values computed for a range of tests, systems, effectiveness measures, topic set sizes and effect sizes, and for both the 2-tail and 1-tail cases. Having such a large supply of IR evaluation data with full knowledge of the null hypotheses, we are finally in a position to evaluate how well statistical significance tests really behave with IR data, and make sound recommendations for practitioners.Comment: 10 pages, 6 figures, SIGIR 201

Evaluating effectiveness of linguistic technologies of knowledge identification in text collections

The possibility of using integral coefficients of recall and precision to evaluate effectiveness of linguistic technologies of knowledge identification in texts is analyzed in the paper. An approach is based on the method of test collections, which is used for experimental validation of received effectiveness coefficients, and on methods of mathematical statistics. The problem of maximizing the reliability of sample results in their propagation on the general population of the tested text collection is studied. The method for determining the confidence interval for the attribute proportion, which is based on Wilson’s formula, and the method for determining the required size of the relevant sample under specified relative error and confidence probability, are considered

Evaluating effectiveness of linguistic technologies of knowledge identification in text collections

The possibility of using integral coefficients of recall and precision to evaluate effectiveness of linguistic technologies of knowledge identification in texts is analyzed in the paper. An approach is based on the method of test collections, which is used for experimental validation of received effectiveness coefficients, and on methods of mathematical statistics. The problem of maximizing the reliability of sample results in their propagation on the general population of the tested text collection is studied. The method for determining the confidence interval for the attribute proportion, which is based on Wilson’s formula, and the method for determining the required size of the relevant sample under specified relative error and confidence probability, are considered