LIPIcs, Volume 258, SoCG 2023, Complete Volume

LIPIcs, Volume 258, SoCG 2023, Complete Volum

LIPIcs, Volume 261, ICALP 2023, Complete Volume

LIPIcs, Volume 261, ICALP 2023, Complete Volum

Automated methods for the determination of homologous relationships and functional similarities between protein domains.

CATH is a protein database of structural domains which are assigned to superfamilies through evidence of a common evolutionary ancestor. These superfamilies are further grouped by overall structural similarity into folds. This thesis explores several automated methods for recognising homologous relationships between these domains using the structural data from the Protein Data Bank (PDB). The aim of this work was to aid the manual classification of domains into the database and provide putative functional assignments to structures solved by the structural genomics initiatives. A fast and novel algorithm, CATHEDRAL, was developed to make fold assignments to regions of polypeptide chains. By combining a fast secondary-structure method (GRATH) and a slower residue-based method (SSAP), the algorithm was able to accurately assign boundaries for distant relatives, undetectable by sequence methods. Sequence and structural conservation patterns were combined in a novel algorithm, FLORA, to develop structural templates specific to catalytic function. FLORA was able to predict the correct functional site in 80% of cases and combined with global structure comparison, it was able to assign domains to enzyme families within diverse superfamilies. Techniques in structure comparison were also applied to ab initio models of protein domains, in order to assign them to fold groups within the CATH database. A novel scoring method was developed to pre-select models that were more likely to have adopted the correct fold. A selected sample of models for each target structure was then compared against representatives from the CATH database using the MAMMOTH and SSAP algorithms. Data from these alignments were combined using a Support Vector Machine to assign the target to a fold group within CATH. This work was generously supported by the Engineering and Physical Sciences Research Council

Advances in knowledge discovery and data mining Part II

19th Pacific-Asia Conference, PAKDD 2015, Ho Chi Minh City, Vietnam, May 19-22, 2015, Proceedings, Part II</p

Generalized and efficient outlier detection for spatial, temporal, and high-dimensional data mining

Knowledge Discovery in Databases (KDD) ist der Prozess, nicht-triviale Muster aus großen Datenbanken zu extrahieren, mit dem Ziel, dass diese bisher unbekannt, potentiell nützlich, statistisch fundiert und verständlich sind. Der Prozess umfasst mehrere Schritte wie die Selektion, Vorverarbeitung, Evaluierung und den Analyseschritt, der als Data-Mining bekannt ist. Eine der zentralen Aufgabenstellungen im Data-Mining ist die Ausreißererkennung, das Identifizieren von Beobachtungen, die ungewöhnlich sind und mit der Mehrzahl der Daten inkonsistent erscheinen. Solche seltene Beobachtungen können verschiedene Ursachen haben: Messfehler, ungewöhnlich starke (aber dennoch genuine) Abweichungen, beschädigte oder auch manipulierte Daten. In den letzten Jahren wurden zahlreiche Verfahren zur Erkennung von Ausreißern vorgeschlagen, die sich oft nur geringfügig zu unterscheiden scheinen, aber in den Publikationen experimental als ``klar besser'' dargestellt sind. Ein Schwerpunkt dieser Arbeit ist es, die unterschiedlichen Verfahren zusammenzuführen und in einem gemeinsamen Formalismus zu modularisieren. Damit wird einerseits die Analyse der Unterschiede vereinfacht, andererseits aber die Flexibilität der Verfahren erhöht, indem man Module hinzufügen oder ersetzen und damit die Methode an geänderte Anforderungen und Datentypen anpassen kann. Um die Vorteile der modularisierten Struktur zu zeigen, werden (i) zahlreiche bestehende Algorithmen in dem Schema formalisiert, (ii) neue Module hinzugefügt, um die Robustheit, Effizienz, statistische Aussagekraft und Nutzbarkeit der Bewertungsfunktionen zu verbessern, mit denen die existierenden Methoden kombiniert werden können, (iii) Module modifiziert, um bestehende und neue Algorithmen auf andere, oft komplexere, Datentypen anzuwenden wie geographisch annotierte Daten, Zeitreihen und hochdimensionale Räume, (iv) mehrere Methoden in ein Verfahren kombiniert, um bessere Ergebnisse zu erzielen, (v) die Skalierbarkeit auf große Datenmengen durch approximative oder exakte Indizierung verbessert. Ausgangspunkt der Arbeit ist der Algorithmus Local Outlier Factor (LOF). Er wird zunächst mit kleinen Erweiterungen modifiziert, um die Robustheit und die Nutzbarkeit der Bewertung zu verbessern. Diese Methoden werden anschließend in einem gemeinsamen Rahmen zur Erkennung lokaler Ausreißer formalisiert, um die entsprechenden Vorteile auch in anderen Algorithmen nutzen zu können. Durch Abstraktion von einem einzelnen Vektorraum zu allgemeinen Datentypen können auch räumliche und zeitliche Beziehungen analysiert werden. Die Verwendung von Unterraum- und Korrelations-basierten Nachbarschaften ermöglicht dann, einen neue Arten von Ausreißern in beliebig orientierten Projektionen zu erkennen. Verbesserungen bei den Bewertungsfunktionen erlauben es, die Bewertung mit der statistischen Intuition einer Wahrscheinlichkeit zu interpretieren und nicht nur eine Ausreißer-Rangfolge zu erstellen wie zuvor. Verbesserte Modelle generieren auch Erklärungen, warum ein Objekt als Ausreißer bewertet wurde. Anschließend werden für verschiedene Module Verbesserungen eingeführt, die unter anderem ermöglichen, die Algorithmen auf wesentlich größere Datensätze anzuwenden -- in annähernd linearer statt in quadratischer Zeit --, indem man approximative Nachbarschaften bei geringem Verlust an Präzision und Effektivität erlaubt. Des weiteren wird gezeigt, wie mehrere solcher Algorithmen mit unterschiedlichen Intuitionen gleichzeitig benutzt und die Ergebnisse in einer Methode kombiniert werden können, die dadurch unterschiedliche Arten von Ausreißern erkennen kann. Schließlich werden für reale Datensätze neue Ausreißeralgorithmen konstruiert, die auf das spezifische Problem angepasst sind. Diese neuen Methoden erlauben es, so aufschlussreiche Ergebnisse zu erhalten, die mit den bestehenden Methoden nicht erreicht werden konnten. Da sie aus den Bausteinen der modularen Struktur entwickelt wurden, ist ein direkter Bezug zu den früheren Ansätzen gegeben. Durch Verwendung der Indexstrukturen können die Algorithmen selbst auf großen Datensätzen effizient ausgeführt werden.Knowledge Discovery in Databases (KDD) is the process of extracting non-trivial patterns in large data bases, with the focus of extracting novel, potentially useful, statistically valid and understandable patterns. The process involves multiple phases including selection, preprocessing, evaluation and the analysis step which is known as Data Mining. One of the key techniques of Data Mining is outlier detection, that is the identification of observations that are unusual and seemingly inconsistent with the majority of the data set. Such rare observations can have various reasons: they can be measurement errors, unusually extreme (but valid) measurements, data corruption or even manipulated data. Over the previous years, various outlier detection algorithms have been proposed that often appear to be only slightly different than previous but ``clearly outperform'' the others in the experiments. A key focus of this thesis is to unify and modularize the various approaches into a common formalism to make the analysis of the actual differences easier, but at the same time increase the flexibility of the approaches by allowing the addition and replacement of modules to adapt the methods to different requirements and data types. To show the benefits of the modularized structure, (i) several existing algorithms are formalized within the new framework (ii) new modules are added that improve the robustness, efficiency, statistical validity and score usability and that can be combined with existing methods (iii) modules are modified to allow existing and new algorithms to run on other, often more complex data types including spatial, temporal and high-dimensional data spaces (iv) the combination of multiple algorithm instances into an ensemble method is discussed (v) the scalability to large data sets is improved using approximate as well as exact indexing. The starting point is the Local Outlier Factor (LOF) algorithm, which is extended with slight modifications to increase robustness and the usability of the produced scores. In order to get the same benefits for other methods, these methods are abstracted to a general framework for local outlier detection. By abstracting from a single vector space, other data types that involve spatial and temporal relationships can be analyzed. The use of subspace and correlation neighborhoods allows the algorithms to detect new kinds of outliers in arbitrarily oriented subspaces. Improvements in the score normalization bring back a statistic intuition of probabilities to the outlier scores that previously were only useful for ranking objects, while improved models also offer explanations of why an object was considered to be an outlier. Subsequently, for different modules found in the framework improved modules are presented that for example allow to run the same algorithms on significantly larger data sets -- in approximately linear complexity instead of quadratic complexity -- by accepting approximated neighborhoods at little loss in precision and effectiveness. Additionally, multiple algorithms with different intuitions can be run at the same time, and the results combined into an ensemble method that is able to detect outliers of different types. Finally, new outlier detection methods are constructed; customized for the specific problems of these real data sets. The new methods allow to obtain insightful results that could not be obtained with the existing methods. Since being constructed from the same building blocks, there however exists a strong and explicit connection to the previous approaches, and by using the indexing strategies introduced earlier, the algorithms can be executed efficiently even on large data sets

Safety and Reliability - Safe Societies in a Changing World

The contributions cover a wide range of methodologies and application areas for safety and reliability that contribute to safe societies in a changing world. These methodologies and applications include: - foundations of risk and reliability assessment and management - mathematical methods in reliability and safety - risk assessment - risk management - system reliability - uncertainty analysis - digitalization and big data - prognostics and system health management - occupational safety - accident and incident modeling - maintenance modeling and applications - simulation for safety and reliability analysis - dynamic risk and barrier management - organizational factors and safety culture - human factors and human reliability - resilience engineering - structural reliability - natural hazards - security - economic analysis in risk managemen

Large bichromatic point sets admit empty monochromatic 4-gons

We consider a variation of a problem stated by Erd˝os and Szekeres in 1935 about the existence of a number fES(k) such that any set S of at least fES(k) points in general position in the plane has a subset of k points that are the vertices of a convex k-gon. In our setting the points of S are colored, and we say that a (not necessarily convex) spanned polygon is monochromatic if all its vertices have the same color. Moreover, a polygon is called empty if it does not contain any points of S in its interior. We show that any bichromatic set of n ≥ 5044 points in R2 in general position determines at least one empty, monochromatic quadrilateral (and thus linearly many).Postprint (published version