Approximate Lifted Inference with Probabilistic Databases

This paper proposes a new approach for approximate evaluation of #P-hard queries with probabilistic databases. In our approach, every query is evaluated entirely in the database engine by evaluating a fixed number of query plans, each providing an upper bound on the true probability, then taking their minimum. We provide an algorithm that takes into account important schema information to enumerate only the minimal necessary plans among all possible plans. Importantly, this algorithm is a strict generalization of all known results of PTIME self-join-free conjunctive queries: A query is safe if and only if our algorithm returns one single plan. We also apply three relational query optimization techniques to evaluate all minimal safe plans very fast. We give a detailed experimental evaluation of our approach and, in the process, provide a new way of thinking about the value of probabilistic methods over non-probabilistic methods for ranking query answers.Comment: 12 pages, 5 figures, pre-print for a paper appearing in VLDB 2015. arXiv admin note: text overlap with arXiv:1310.625

Rankprop: a web server for protein remote homology detection

Summary: We present a large-scale implementation of the Rankprop protein homology ranking algorithm in the form of an openly accessible web server. We use the NRDB40 PSI-BLAST all-versus-all protein similarity network of 1.1 million proteins to construct the graph for the Rankprop algorithm, whereas previously, results were only reported for a database of 108 000 proteins. We also describe two algorithmic improvements to the original algorithm, including propagation from multiple homologs of the query and better normalization of ranking scores, that lead to higher accuracy and to scores with a probabilistic interpretation

Scalable Probabilistic Similarity Ranking in Uncertain Databases (Technical Report)

This paper introduces a scalable approach for probabilistic top-k similarity ranking on uncertain vector data. Each uncertain object is represented by a set of vector instances that are assumed to be mutually-exclusive. The objective is to rank the uncertain data according to their distance to a reference object. We propose a framework that incrementally computes for each object instance and ranking position, the probability of the object falling at that ranking position. The resulting rank probability distribution can serve as input for several state-of-the-art probabilistic ranking models. Existing approaches compute this probability distribution by applying a dynamic programming approach of quadratic complexity. In this paper we theoretically as well as experimentally show that our framework reduces this to a linear-time complexity while having the same memory requirements, facilitated by incremental accessing of the uncertain vector instances in increasing order of their distance to the reference object. Furthermore, we show how the output of our method can be used to apply probabilistic top-k ranking for the objects, according to different state-of-the-art definitions. We conduct an experimental evaluation on synthetic and real data, which demonstrates the efficiency of our approach

Integrating and Ranking Uncertain Scientific Data

Mediator-based data integration systems resolve exploratory queries by joining data elements across sources. In the presence of uncertainties, such multiple expansions can quickly lead to spurious connections and incorrect results. The BioRank project investigates formalisms for modeling uncertainty during scientific data integration and for ranking uncertain query results. Our motivating application is protein function prediction. In this paper we show that: (i) explicit modeling of uncertainties as probabilities increases our ability to predict less-known or previously unknown functions (though it does not improve predicting the well-known). This suggests that probabilistic uncertainty models offer utility for scientific knowledge discovery; (ii) small perturbations in the input probabilities tend to produce only minor changes in the quality of our result rankings. This suggests that our methods are robust against slight variations in the way uncertainties are transformed into probabilities; and (iii) several techniques allow us to evaluate our probabilistic rankings efficiently. This suggests that probabilistic query evaluation is not as hard for real-world problems as theory indicates

The study of probability model for compound similarity searching

Information Retrieval or IR system main task is to retrieve relevant documents according to the users query. One of IR most popular retrieval model is the Vector Space Model. This model assumes relevance based on similarity, which is defined as the distance between query and document in the concept space. All currently existing chemical compound database systems have adapt the vector space model to calculate the similarity of a database entry to a query compound. However, it assumes that fragments represented by the bits are independent of one another, which is not necessarily true. Hence, the possibility of applying another IR model is explored, which is the Probabilistic Model, for chemical compound searching. This model estimates the probabilities of a chemical structure to have the same bioactivity as a target compound. It is envisioned that by ranking chemical structures in decreasing order of their probability of relevance to the query structure, the effectiveness of a molecular similarity searching system can be increased. Both fragment dependencies and independencies assumption are taken into consideration in achieving improvement towards compound similarity searching system. After conducting a series of simulated similarity searching, it is concluded that PM approaches really did perform better than the existing similarity searching. It gave better result in all evaluation criteria to confirm this statement. In terms of which probability model performs better, the BD model shown improvement over the BIR model