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

Efficient Hill Climber for Constrained Pseudo-Boolean Optimization Problems

Efficient hill climbers have been recently proposed for single- and multi-objective pseudo-Boolean optimization problems. For $k$-bounded pseudo-Boolean functions where each variable appears in at most a constant number of subfunctions, it has been theoretically proven that the neighborhood of a solution can be explored in constant time. These hill climbers, combined with a high-level exploration strategy, have shown to improve state of the art methods in experimental studies and open the door to the so-called Gray Box Optimization, where part, but not all, of the details of the objective functions are used to better explore the search space. One important limitation of all the previous proposals is that they can only be applied to unconstrained pseudo-Boolean optimization problems. In this work, we address the constrained case for multi-objective $k$-bounded pseudo-Boolean optimization problems. We find that adding constraints to the pseudo-Boolean problem has a linear computational cost in the hill climber.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Solving finite-domain linear constraints in presence of the alldifferent\texttt{alldifferent}

In this paper, we investigate the possibility of improvement of the widely-used filtering algorithm for the linear constraints in constraint satisfaction problems in the presence of the alldifferent constraints. In many cases, the fact that the variables in a linear constraint are also constrained by some alldifferent constraints may help us to calculate stronger bounds of the variables, leading to a stronger constraint propagation. We propose an improved filtering algorithm that targets such cases. We provide a detailed description of the proposed algorithm and prove its correctness. We evaluate the approach on five different problems that involve combinations of the linear and the alldifferent constraints. We also compare our algorithm to other relevant approaches. The experimental results show a great potential of the proposed improvement.Comment: 28 pages, 2 figure

Informed RRT*: Optimal Sampling-based Path Planning Focused via Direct Sampling of an Admissible Ellipsoidal Heuristic

Rapidly-exploring random trees (RRTs) are popular in motion planning because they find solutions efficiently to single-query problems. Optimal RRTs (RRT*s) extend RRTs to the problem of finding the optimal solution, but in doing so asymptotically find the optimal path from the initial state to every state in the planning domain. This behaviour is not only inefficient but also inconsistent with their single-query nature. For problems seeking to minimize path length, the subset of states that can improve a solution can be described by a prolate hyperspheroid. We show that unless this subset is sampled directly, the probability of improving a solution becomes arbitrarily small in large worlds or high state dimensions. In this paper, we present an exact method to focus the search by directly sampling this subset. The advantages of the presented sampling technique are demonstrated with a new algorithm, Informed RRT*. This method retains the same probabilistic guarantees on completeness and optimality as RRT* while improving the convergence rate and final solution quality. We present the algorithm as a simple modification to RRT* that could be further extended by more advanced path-planning algorithms. We show experimentally that it outperforms RRT* in rate of convergence, final solution cost, and ability to find difficult passages while demonstrating less dependence on the state dimension and range of the planning problem.Comment: 8 pages, 11 figures. Videos available at https://www.youtube.com/watch?v=d7dX5MvDYTc and https://www.youtube.com/watch?v=nsl-5MZfwu

The application of user log for online business environment using content-based Image retrieval system

Over the past few years, inter-query learning has gained much attention in the research and development of content-based image retrieval (CBIR) systems. This is largely due to the capability of inter-query approach to enable learning from the retrieval patterns of previous query sessions. However, much of the research works in this field have been focusing on analyzing image retrieval patterns stored in the database. This is not suitable for a dynamic environment such as the World Wide Web (WWW) where images are constantly added or removed. A better alternative is to use an image's visual features to capture the knowledge gained from the previous query sessions. Based on the previous work (Chung et al., 2006), the aim of this paper is to propose a framework of inter-query learning for the WWW-CBIR systems. Such framework can be extremely useful for those online companies whose core business involves providing multimedia content-based services and products to their customers