Evolutionary genomics : statistical and computational methods

This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward

Exploring the adaptive structure of the mental lexicon

The mental lexicon is a complex structure organised in terms of phonology, semantics and syntax, among other levels. In this thesis I propose that this structure can be explained in terms of the pressures acting on it: every aspect of the organisation of the lexicon is an adaptation ultimately related to the function of language as a tool for human communication, or to the fact that language has to be learned by subsequent generations of people. A collection of methods, most of which are applied to a Spanish speech corpus, reveal structure at different levels of the lexicon.• The patterns of intra-word distribution of phonological information may be a consequence of pressures for optimal representation of the lexicon in the brain, and of the pressure to facilitate speech segmentation.• An analysis of perceived phonological similarity between words shows that the sharing of different aspects of phonological similarity is related to different functions. Phonological similarity perception sometimes relates to morphology (the stressed final vowel determines verb tense and person) and at other times shows processing biases (similarity in the word initial and final segments is more readily perceived than in word-internal segments).• Another similarity analysis focuses on cooccurrence in speech to create a representation of the lexicon where the position of a word is determined by the words that tend to occur in its close vicinity. Variations of context-based lexical space naturally categorise words syntactically and semantically.• A higher level of lexicon structure is revealed by examining the relationships between the phonological and the cooccurrence similarity spaces. A study in Spanish supports the universality of the small but significant correlation between these two spaces found in English by Shillcock, Kirby, McDonald and Brew (2001). This systematicity across levels of representation adds an extra layer of structure that may help lexical acquisition and recognition. I apply it to a new paradigm to determine the function of parameters of phonological similarity based on their relationships with the syntacticsemantic level. I find that while some aspects of a language's phonology maintain systematicity, others work against it, perhaps responding to the opposed pressure for word identification.This thesis is an exploratory approach to the study of the mental lexicon structure that uses existing and new methodology to deepen our understanding of the relationships between language use and language structure

Evolutionary Genomics

This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward

Theoretical and Practical Advances in Computer-based Educational Measurement

This open access book presents a large number of innovations in the world of operational testing. It brings together different but related areas and provides insight in their possibilities, their advantages and drawbacks. The book not only addresses improvements in the quality of educational measurement, innovations in (inter)national large scale assessments, but also several advances in psychometrics and improvements in computerized adaptive testing, and it also offers examples on the impact of new technology in assessment. Due to its nature, the book will appeal to a broad audience within the educational measurement community. It contributes to both theoretical knowledge and also pays attention to practical implementation of innovations in testing technology

Uncertain Multi-Criteria Optimization Problems

Most real-world search and optimization problems naturally involve multiple criteria as objectives. Generally, symmetry, asymmetry, and anti-symmetry are basic characteristics of binary relationships used when modeling optimization problems. Moreover, the notion of symmetry has appeared in many articles about uncertainty theories that are employed in multi-criteria problems. Different solutions may produce trade-offs (conflicting scenarios) among different objectives. A better solution with respect to one objective may compromise other objectives. There are various factors that need to be considered to address the problems in multidisciplinary research, which is critical for the overall sustainability of human development and activity. In this regard, in recent decades, decision-making theory has been the subject of intense research activities due to its wide applications in different areas. The decision-making theory approach has become an important means to provide real-time solutions to uncertainty problems. Theories such as probability theory, fuzzy set theory, type-2 fuzzy set theory, rough set, and uncertainty theory, available in the existing literature, deal with such uncertainties. Nevertheless, the uncertain multi-criteria characteristics in such problems have not yet been explored in depth, and there is much left to be achieved in this direction. Hence, different mathematical models of real-life multi-criteria optimization problems can be developed in various uncertain frameworks with special emphasis on optimization problems

LIPIcs, Volume 274, ESA 2023, Complete Volume

LIPIcs, Volume 274, ESA 2023, Complete Volum

Subgroup discovery for structured target concepts

The main object of study in this thesis is subgroup discovery, a theoretical framework for finding subgroups in data—i.e., named sub-populations— whose behaviour with respect to a specified target concept is exceptional when compared to the rest of the dataset. This is a powerful tool that conveys crucial information to a human audience, but despite past advances has been limited to simple target concepts. In this work we propose algorithms that bring this framework to novel application domains. We introduce the concept of representative subgroups, which we use not only to ensure the fairness of a sub-population with regard to a sensitive trait, such as race or gender, but also to go beyond known trends in the data. For entities with additional relational information that can be encoded as a graph, we introduce a novel measure of robust connectedness which improves on established alternative measures of density; we then provide a method that uses this measure to discover which named sub-populations are more well-connected. Our contributions within subgroup discovery crescent with the introduction of kernelised subgroup discovery: a novel framework that enables the discovery of subgroups on i.i.d. target concepts with virtually any kind of structure. Importantly, our framework additionally provides a concrete and efficient tool that works out-of-the-box without any modification, apart from specifying the Gramian of a positive definite kernel. To use within kernelised subgroup discovery, but also on any other kind of kernel method, we additionally introduce a novel random walk graph kernel. Our kernel allows the fine tuning of the alignment between the vertices of the two compared graphs, during the count of the random walks, while we also propose meaningful structure-aware vertex labels to utilise this new capability. With these contributions we thoroughly extend the applicability of subgroup discovery and ultimately re-define it as a kernel method.Der Hauptgegenstand dieser Arbeit ist die Subgruppenentdeckung (Subgroup Discovery), ein theoretischer Rahmen für das Auffinden von Subgruppen in Daten—d. h. benannte Teilpopulationen—deren Verhalten in Bezug auf ein bestimmtes Targetkonzept im Vergleich zum Rest des Datensatzes außergewöhnlich ist. Es handelt sich hierbei um ein leistungsfähiges Instrument, das einem menschlichen Publikum wichtige Informationen vermittelt. Allerdings ist es trotz bisherigen Fortschritte auf einfache Targetkonzepte beschränkt. In dieser Arbeit schlagen wir Algorithmen vor, die diesen Rahmen auf neuartige Anwendungsbereiche übertragen. Wir führen das Konzept der repräsentativen Untergruppen ein, mit dem wir nicht nur die Fairness einer Teilpopulation in Bezug auf ein sensibles Merkmal wie Rasse oder Geschlecht sicherstellen, sondern auch über bekannte Trends in den Daten hinausgehen können. Für Entitäten mit zusätzlicher relationalen Information, die als Graph kodiert werden kann, führen wir ein neuartiges Maß für robuste Verbundenheit ein, das die etablierten alternativen Dichtemaße verbessert; anschließend stellen wir eine Methode bereit, die dieses Maß verwendet, um herauszufinden, welche benannte Teilpopulationen besser verbunden sind. Unsere Beiträge in diesem Rahmen gipfeln in der Einführung der kernelisierten Subgruppenentdeckung: ein neuartiger Rahmen, der die Entdeckung von Subgruppen für u.i.v. Targetkonzepten mit praktisch jeder Art von Struktur ermöglicht. Wichtigerweise, unser Rahmen bereitstellt zusätzlich ein konkretes und effizientes Werkzeug, das ohne jegliche Modifikation funktioniert, abgesehen von der Angabe des Gramian eines positiv definitiven Kernels. Für den Einsatz innerhalb der kernelisierten Subgruppentdeckung, aber auch für jede andere Art von Kernel-Methode, führen wir zusätzlich einen neuartigen Random-Walk-Graph-Kernel ein. Unser Kernel ermöglicht die Feinabstimmung der Ausrichtung zwischen den Eckpunkten der beiden unter-Vergleich-gestelltenen Graphen während der Zählung der Random Walks, während wir auch sinnvolle strukturbewusste Vertex-Labels vorschlagen, um diese neue Fähigkeit zu nutzen. Mit diesen Beiträgen erweitern wir die Anwendbarkeit der Subgruppentdeckung gründlich und definieren wir sie im Endeffekt als Kernel-Methode neu

From Hesiod to Saussure, from Hippocrates to Jevons: An Introduction to the History of Scientific Thought between Iran and the Atlantic

This work offers an introduction to the history of scientific thought in the region between Iran and the Atlantic from the beginnings of the Bronze Age until 1900 CE—a “science” that can be understood more or less as a German Wissenschaft: a coherent body of knowledge carried by a socially organized group or profession. It thus deals with the social and human as well as medical and natural sciences and, in earlier times, even such topics as astrology and exorcism. It discusses eight periods or knowledge cultures: Ancient Mesopotamia – classical Antiquity – Islamic Middle Ages – Latin Middle Ages – Western Europe 1400–1600 – 17th century – 18th century – 19th century. For each period, a general description of scientific thought is offered, embedded within its social context, together with a number of shorter or longer commented extracts from original works in English translation