Matti Nykänen

Efficient Discovery of Statistically Significant Association Rules

Searching statistically significant association rules is an important but neglected problem. Traditional association rules do not capture the idea of statistical dependence and the resulting rules can be spurious, while the most significant rules may be missing. This leads to erroneous models and predictions which often become expensive.The problem is computationally very difficult, because the significance is not a monotonic property. However, in this paper we prove several other properties, which can be used for pruning the search space. The properties are implemented in the StatApriori algorithm, which searches statistically significant, non-redundant association rules. Based on both theoretical and empirical observations, the resulting rules are very accurate compared to traditional association rules. In addition, StatApriori can work with extremely low frequencies, thus finding new interesting rules.

Reasoning about strings in databases

In order to enable the database programmer to reason about relations over strings of arbitrary length we introduce alignment logic, a modal extension of relational calculus. In addition to relations, a state in the model consists of a two-dimensional array where the strings are aligned on top of each other. The basic modality in the language (a transpose, or “slide”) allows for a rearrangement of the alignment, and more complex formulas can be formed using a syntax reminiscent of regular expressions, in addition to the usual connectives and quantifiers. It turns out that the computational counterpart of the string-based portion of the logic is the class of multitape two-way finite state automata, which are devices particularly well suited for the implementation of string matching. A computational counterpart of the full logic is obtained from relational algebra by extending the selection operator into filters based on these multitape machines. Safety of formulas in alignment logic implies that new strings generated from old ones have to be of bounded length. While an undecidable property in general, this boundedness is decidable for an important subclass of formulas. As far as expressive power is concerned, alignment logic includes previous proposals for querying string databases, and gives full Turing computability. The language can be restricted to define exactly regular sets and sets in the polynomial hierarchy.

Fine structure of the transitional zone of the rat seminiferous tubule

SummaryAn electron microscopic study was made on the structure of the testicular transitional zone (TZ) in the adult rat.The TZ proper consists of modified Sertoli cells, with only a few spermatogonia and macrophages, surrounding distally a very narrow lumen. The TZ Sertoli cells have nuclei with a somewhat coarser matrix and more peripheral heterochromatin than Sertoli cell nuclei of the nearby seminiferous tubules, and the electron density of the cytoplasm varies from cell to cell. Smooth endoplasmic reticulum is abundant, but usually there are also scattered ribosomal rosettes and an occasional profile of rough endoplasmic reticulum. Microtubules are very numerous in the columnar portion of the cell, and laminar structures seemingly joining the cell surfaces are sometimes seen. Lipid droplets and lysosomal structures are frequent cellular components in proximal TZ Sertoli cells. Empty intracellular vacuoles are abundant, sometimes arranged around areas of smooth endoplasmic reticulum. Occasionally, membrane-limited fine granules and vacuoles are seen within Sertoli cells and also in the TZ lumen, suggesting a possible secretory activity by these cells. The apical processes of the Sertoli cells form large vacuolar structures, and in the basal parts of the epithelium vacuoles with capillary-like appearance are frequently seen. Phagocytosis of germinal cells by the Sertoli cells occurs in the proximal region of the TZ. Round waste bodies in contact with the Sertoli cell apices protruding into the tubulus rectus, are also common.The tunica propria of the TZ is thickened and somewhat wrinkled, and in the proximal region the myoid cell layer loses its continuity and is replaced by fibroblasts. The epithelium of the tubulus rectus adjacent to the TZ consists of several overlapping epithelial cells.The typical junctional complexes between TZ Sertoli cells appear to be impermeable to the lanthanum tracer.

The Exact Path Length Problem

We study a problem related to finding shortest paths in weighted graphs. We ask whether or not there is a path between two nodes that has a given total cost k. The edge weights of the graph can be both positive and negative integers or even integer vectors. We show that many variants of this problem are NP-complete. We develop a pseudo-polynomial algorithm for (both positive and negative) integer weights. The running time of this algorithm is O(W2n3+|k| min(|k|,W)n2), where n is the number of nodes in the graph, W is the largest absolute value of any edge weight, and k is the target cost. The algorithm is based on preprocessing the graph with a relaxation algorithm to eliminate the effects of weight sign alternations along a path. This preprocessing stage is applicable to other problems as well. For example, we show how to find the minimum absolute cost of any path between two given nodes in a graph with integer weights in O(W2n3) time.

Finding lowest common ancestors in arbitrarily directed trees

Abstract It is well known how to preprocess a rooted tree in linear time to yield the lowest common ancestor of any given pair of nodes in constant time. We generalize these algorithms for graphs called Arbitrarily Directed Trees, or ADTs. Such trees are obtained by reversing the directions of some edges in trees with the customary “root-to-leaf” orientation of edges.

Reasoning about Strings in Databases

In order to enable the database programmer to reason about relations over strings of arbitrary length, we introduce alignment calculus, a modal extension of the relational calculus. In addition to relations, a state in the model consists of a two-dimensional array where the strings are aligned on top of each other. The basic modality in the language (a transpose, or “slide”) rearranges this alignment, and more complex formulae can be formed using a syntax reminiscent of regular expressions, in addition to the usual connectives and quantifiers. It turns out that the computational counterpart of the string-based portion of the logic is the class of multitape two-way finite state automata, which are devices particularly well suited for the implementation of string matching. A computational counterpart of the full logic is obtained from relational algebra by performing selection with these devices. Safety of formulae in alignment calculus implies that new strings generated from old ones have to be of bounded length. While an undecidable property in general, this boundedness is decidable for an important subclass of formulae. As far as expressive power is concerned, alignment calculus includes previous proposals for querying string databases and gives full Turing computability. The language can be restricted to define exactly the regular sets and the sets in each level of the polynomial-time hierarchy above P.

Implementing a Declarative String Query Language with String Restructuring

We describe the design and implementation of a declarative database query language for manipulating character strings. The language can be used to create logical predicates expressing structural properties of strings and relations between several strings. The predicates can be used to query strings in databases, and by leaving variables uninstantiated, also to generate new strings not contained in the database. A full working system was implemented as an extension of an object-oriented database management system and its query language. The declarative expressions are evaluated by first performing a compilation transforming them to nondeterministic finite state automata and then by simulating these automata using a depth-first search engine. The system checks the safety of each string-manipulation query in advance to preclude infinite ones. This safety checking provides also a compile-time loop-checking mechanism for the search engine, improving its eficiency.

Design and implementation of a string database query language

Current data management and information retrieval systems lack advanced string processing capabilities needed in string-oriented application areas like computational molecular biology. Several theoretical models for string processing have been proposed but they either have not been implemented in practice or the implementations are too restricted or platform-dependent to be generally useful. In this article, we introduce the language Alignment Declarations designed for string querying and restructuring. The language extends the capabilities of existing database query languages by allowing the user to define database predicates that express structural properties of strings (e.g. containment of certain patterns) or relations between several strings (e.g. similarity measures). These predicates can be created and executed within the same database session and also stored for later sessions. We also describe the design and implementation of a working system.

Morphology of the rat rete testis in experimental autoimmune orchids

SummaryThe role of the rete testis and related structures in the development of experimental autoimmune orchitis (EAO) was studied in adult inbred Sprague-Dawley rats. Histology and electron microscopy showed focal perivascular infiltration and an increase in the number of mast cells and polymorphonuclears. Often there were vacuolated macrophages. These changes were first observed two weeks after the beginning of immunization, but they did not clearly precede lesions in seminiferous tubules. Increased amounts of cellular debris appeared in rete cavities, suggesting damage to germinal epithelium. Lanthanum tracer studies of immunized rats showed local lesions in the blood-testis barrier of the seminiferous tubules but did not indicate spreading of lesions from the rete testis. Efferent duct ligation of immunized rats for 24 h did not increase the frequency of lesions. The present observations do not support the theory that the rete testis is the route of spreading of EAO.

Accommodative Belief Revision

Accommodative revision is a novel method of non-prioritized belief revision. The epistemic state of an agent contains both knowledge that is immune to revision and beliefs that are allowed to change. Incoming information is first revised by the knowledge of the agent, and then the epistemic state of the agent is revised using this modified input. The properties of the method are studied and examples of its use are given.