A Molecular Biology Database Digest

Computational Biology or Bioinformatics has been defined as the application of mathematical and Computer Science methods to solving problems in Molecular Biology that require large scale data, computation, and analysis [18]. As expected, Molecular Biology databases play an essential role in Computational Biology research and development. This paper introduces into current Molecular Biology databases, stressing data modeling, data acquisition, data retrieval, and the integration of Molecular Biology data from different sources. This paper is primarily intended for an audience of computer scientists with a limited background in Biology

Investigation of the use of navigation tools in web-based learning: A data mining approach

Web-based learning is widespread in educational settings. The popularity of Web-based learning is in great measure because of its flexibility. Multiple navigation tools provided some of this flexibility. Different navigation tools offer different functions. Therefore, it is important to understand how the navigation tools are used by learners with different backgrounds, knowledge, and skills. This article presents two empirical studies in which data-mining approaches were used to analyze learners' navigation behavior. The results indicate that prior knowledge and subject content are two potential factors influencing the use of navigation tools. In addition, the lack of appropriate use of navigation tools may adversely influence learning performance. The results have been integrated into a model that can help designers develop Web-based learning programs and other Web-based applications that can be tailored to learners' needs

An introduction to Graph Data Management

A graph database is a database where the data structures for the schema and/or instances are modeled as a (labeled)(directed) graph or generalizations of it, and where querying is expressed by graph-oriented operations and type constructors. In this article we present the basic notions of graph databases, give an historical overview of its main development, and study the main current systems that implement them

A fine grained heuristic to capture web navigation patterns

In previous work we have proposed a statistical model to capture the user behaviour when browsing the web. The user navigation information obtained from web logs is modelled as a hypertext probabilistic grammar (HPG) which is within the class of regular probabilistic grammars. The set of highest probability strings generated by the grammar corresponds to the user preferred navigation trails. We have previously conducted experiments with a Breadth-First Search algorithm (BFS) to perform the exhaustive computation of all the strings with probability above a specified cut-point, which we call the rules. Although the algorithm’s running time varies linearly with the number of grammar states, it has the drawbacks of returning a large number of rules when the cut-point is small and a small set of very short rules when the cut-point is high. In this work, we present a new heuristic that implements an iterative deepening search wherein the set of rules is incrementally augmented by first exploring trails with high probability. A stopping parameter is provided which measures the distance between the current rule-set and its corresponding maximal set obtained by the BFS algorithm. When the stopping parameter takes the value zero the heuristic corresponds to the BFS algorithm and as the parameter takes values closer to one the number of rules obtained decreases accordingly. Experiments were conducted with both real and synthetic data and the results show that for a given cut-point the number of rules induced increases smoothly with the decrease of the stopping criterion. Therefore, by setting the value of the stopping criterion the analyst can determine the number and quality of rules to be induced; the quality of a rule is measured by both its length and probability

Semantic web technology to support learning about the semantic web

This paper describes ASPL, an Advanced Semantic Platform for Learning, designed using the Magpie framework with an aim to support students learning about the Semantic Web research area. We describe the evolution of ASPL and illustrate how we used the results from a formal evaluation of the initial system to re-design the user functionalities. The second version of ASPL semantically interprets the results provided by a non-semantic web mining tool and uses them to support various forms of semantics-assisted exploration, based on pedagogical strategies such as performing later reasoning steps and problem space filtering

On the Complexity of Exact Pattern Matching in Graphs: Binary Strings and Bounded Degree

Exact pattern matching in labeled graphs is the problem of searching paths of a graph $G=(V,E)$ that spell the same string as the pattern $P[1..m]$. This basic problem can be found at the heart of more complex operations on variation graphs in computational biology, of query operations in graph databases, and of analysis operations in heterogeneous networks, where the nodes of some paths must match a sequence of labels or types. We describe a simple conditional lower bound that, for any constant $\epsilon>0$, an $O(|E|^{1 - \epsilon} \, m)$-time or an $O(|E| \, m^{1 - \epsilon})$-time algorithm for exact pattern matching on graphs, with node labels and patterns drawn from a binary alphabet, cannot be achieved unless the Strong Exponential Time Hypothesis (SETH) is false. The result holds even if restricted to undirected graphs of maximum degree three or directed acyclic graphs of maximum sum of indegree and outdegree three. Although a conditional lower bound of this kind can be somehow derived from previous results (Backurs and Indyk, FOCS'16), we give a direct reduction from SETH for dissemination purposes, as the result might interest researchers from several areas, such as computational biology, graph database, and graph mining, as mentioned before. Indeed, as approximate pattern matching on graphs can be solved in $O(|E|\,m)$ time, exact and approximate matching are thus equally hard (quadratic time) on graphs under the SETH assumption. In comparison, the same problems restricted to strings have linear time vs quadratic time solutions, respectively, where the latter ones have a matching SETH lower bound on computing the edit distance of two strings (Backurs and Indyk, STOC'15).Comment: Using Lemma 12 and Lemma 13 might to be enough to prove Lemma 14. However, the proof of Lemma 14 is correct if you assume that the graph used in the reduction is a DAG. Hence, since the problem is already quadratic for a DAG and a binary alphabet, it has to be quadratic also for a general graph and a binary alphabe

Template Mining for Information Extraction from Digital Documents

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