Efficient, Dependable Storage of Human Genome Sequencing Data

A compreensão do genoma humano impacta várias áreas da vida. Os dados oriundos do genoma humano são enormes pois existem milhões de amostras a espera de serem sequenciadas e cada genoma humano sequenciado pode ocupar centenas de gigabytes de espaço de armazenamento. Os genomas humanos são críticos porque são extremamente valiosos para a investigação e porque podem fornecer informações delicadas sobre o estado de saúde dos indivíduos, identificar os seus dadores ou até mesmo revelar informações sobre os parentes destes. O tamanho e a criticidade destes genomas, para além da quantidade de dados produzidos por instituições médicas e de ciências da vida, exigem que os sistemas informáticos sejam escaláveis, ao mesmo tempo que sejam seguros, confiáveis, auditáveis e com custos acessíveis. As infraestruturas de armazenamento existentes são tão caras que não nos permitem ignorar a eficiência de custos no armazenamento de genomas humanos, assim como em geral estas não possuem o conhecimento e os mecanismos adequados para proteger a privacidade dos dadores de amostras biológicas. Esta tese propõe um sistema de armazenamento de genomas humanos eficiente, seguro e auditável para instituições médicas e de ciências da vida. Ele aprimora os ecossistemas de armazenamento tradicionais com técnicas de privacidade, redução do tamanho dos dados e auditabilidade a fim de permitir o uso eficiente e confiável de infraestruturas públicas de computação em nuvem para armazenar genomas humanos. As contribuições desta tese incluem (1) um estudo sobre a sensibilidade à privacidade dos genomas humanos; (2) um método para detetar sistematicamente as porções dos genomas que são sensíveis à privacidade; (3) algoritmos de redução do tamanho de dados, especializados para dados de genomas sequenciados; (4) um esquema de auditoria independente para armazenamento disperso e seguro de dados; e (5) um fluxo de armazenamento completo que obtém garantias razoáveis de proteção, segurança e confiabilidade a custos modestos (por exemplo, menos de $1/Genoma/Ano), integrando os mecanismos propostos a configurações de armazenamento apropriadasThe understanding of human genome impacts several areas of human life. Data from human genomes is massive because there are millions of samples to be sequenced, and each sequenced human genome may size hundreds of gigabytes. Human genomes are critical because they are extremely valuable to research and may provide hints on individuals’ health status, identify their donors, or reveal information about donors’ relatives. Their size and criticality, plus the amount of data being produced by medical and life-sciences institutions, require systems to scale while being secure, dependable, auditable, and affordable. Current storage infrastructures are too expensive to ignore cost efficiency in storing human genomes, and they lack the proper knowledge and mechanisms to protect the privacy of sample donors. This thesis proposes an efficient storage system for human genomes that medical and lifesciences institutions may trust and afford. It enhances traditional storage ecosystems with privacy-aware, data-reduction, and auditability techniques to enable the efficient, dependable use of multi-tenant infrastructures to store human genomes. Contributions from this thesis include (1) a study on the privacy-sensitivity of human genomes; (2) to detect genomes’ privacy-sensitive portions systematically; (3) specialised data reduction algorithms for sequencing data; (4) an independent auditability scheme for secure dispersed storage; and (5) a complete storage pipeline that obtains reasonable privacy protection, security, and dependability guarantees at modest costs (e.g., less than$1/Genome/Year) by integrating the proposed mechanisms with appropriate storage configurations

Cyber Security of Critical Infrastructures

Critical infrastructures are vital assets for public safety, economic welfare, and the national security of countries. The vulnerabilities of critical infrastructures have increased with the widespread use of information technologies. As Critical National Infrastructures are becoming more vulnerable to cyber-attacks, their protection becomes a significant issue for organizations as well as nations. The risks to continued operations, from failing to upgrade aging infrastructure or not meeting mandated regulatory regimes, are considered highly significant, given the demonstrable impact of such circumstances. Due to the rapid increase of sophisticated cyber threats targeting critical infrastructures with significant destructive effects, the cybersecurity of critical infrastructures has become an agenda item for academics, practitioners, and policy makers. A holistic view which covers technical, policy, human, and behavioural aspects is essential to handle cyber security of critical infrastructures effectively. Moreover, the ability to attribute crimes to criminals is a vital element of avoiding impunity in cyberspace. In this book, both research and practical aspects of cyber security considerations in critical infrastructures are presented. Aligned with the interdisciplinary nature of cyber security, authors from academia, government, and industry have contributed 13 chapters. The issues that are discussed and analysed include cybersecurity training, maturity assessment frameworks, malware analysis techniques, ransomware attacks, security solutions for industrial control systems, and privacy preservation methods

Spoken Corpora Good Practice Guide 2006

International audienceThere is currently a vast amount of fundamental or applied research, which is based on the exploitation of oral corpora (organized recorded collections of oral and multimodal language productions). Created as a result of linguists becoming aware of the importance to ensure the durability of sources and a diversified access to the oral documents they produce, this Guide to good practice mainly deals with “oral corpora”, created for and used by linguists. But the questions raised by the creation and documentary exploitation of these corpora can be found in numerous disciplines: ethnology, anthropology, sociology, psychology, demography, oral history notably use oral surveys, testimonies, interviews, life stories. Based on a linguistic approach, this Guide also touches on the preoccupations of other researchers who use oral corpora (for example in the field of speech synthesis and recognition), even if their specific needs aren’t consistently dealt with in the present document

An annotated checklist of the elasmobranches of the South China Sea, with some global statistics on elasmobranch biodiversity, and an offer to taxonomists

An annotated checklist of the sharks and rays of the South China Sea is described, together with some global statistics on the status and use of elasmobranchs. For each of the 156 recorded species, the checklist contains scientific names, synonyms, common names, global distribution, distribution in the area, status of threat, human uses, key references on taxonomy, identification, reproduction, population dynamics, and a list of people who have contributed information. The checklist is a direct printout from FishBase, a global database on finfish, developed at ICLARM in collaboration with FAO, the California Academy of Sciences, and many other partners, and supported by the European Commission (see www.fishbase.org). The goal of FishBase is to further the conservation and sustainable use of fish by bringing together the knowledge of taxonomists, fisheries experts, and conservationists, providing tools for analysing and updating this knowledge, and making it available to concerned people. How a closer link between FishBase, taxonomists and country experts can benefit the specialists, as well as elasmobranch conservation, is discusse

2015-2016 Course Catalog

An annual catalog of courses and course descriptions offered at the University of Montana.https://scholarworks.umt.edu/coursecatalogs_asc/1046/thumbnail.jp

Enhancing explainability and scrutability of recommender systems

Our increasing reliance on complex algorithms for recommendations calls for models and methods for explainable, scrutable, and trustworthy AI. While explainability is required for understanding the relationships between model inputs and outputs, a scrutable system allows us to modify its behavior as desired. These properties help bridge the gap between our expectations and the algorithm’s behavior and accordingly boost our trust in AI. Aiming to cope with information overload, recommender systems play a crucial role in filtering content (such as products, news, songs, and movies) and shaping a personalized experience for their users. Consequently, there has been a growing demand from the information consumers to receive proper explanations for their personalized recommendations. These explanations aim at helping users understand why certain items are recommended to them and how their previous inputs to the system relate to the generation of such recommendations. Besides, in the event of receiving undesirable content, explanations could possibly contain valuable information as to how the system’s behavior can be modified accordingly. In this thesis, we present our contributions towards explainability and scrutability of recommender systems: • We introduce a user-centric framework, FAIRY, for discovering and ranking post-hoc explanations for the social feeds generated by black-box platforms. These explanations reveal relationships between users’ profiles and their feed items and are extracted from the local interaction graphs of users. FAIRY employs a learning-to-rank (LTR) method to score candidate explanations based on their relevance and surprisal. • We propose a method, PRINCE, to facilitate provider-side explainability in graph-based recommender systems that use personalized PageRank at their core. PRINCE explanations are comprehensible for users, because they present subsets of the user’s prior actions responsible for the received recommendations. PRINCE operates in a counterfactual setup and builds on a polynomial-time algorithm for finding the smallest counterfactual explanations. • We propose a human-in-the-loop framework, ELIXIR, for enhancing scrutability and subsequently the recommendation models by leveraging user feedback on explanations. ELIXIR enables recommender systems to collect user feedback on pairs of recommendations and explanations. The feedback is incorporated into the model by imposing a soft constraint for learning user-specific item representations. We evaluate all proposed models and methods with real user studies and demonstrate their benefits at achieving explainability and scrutability in recommender systems.Unsere zunehmende Abhängigkeit von komplexen Algorithmen für maschinelle Empfehlungen erfordert Modelle und Methoden für erklärbare, nachvollziehbare und vertrauenswürdige KI. Zum Verstehen der Beziehungen zwischen Modellein- und ausgaben muss KI erklärbar sein. Möchten wir das Verhalten des Systems hingegen nach unseren Vorstellungen ändern, muss dessen Entscheidungsprozess nachvollziehbar sein. Erklärbarkeit und Nachvollziehbarkeit von KI helfen uns dabei, die Lücke zwischen dem von uns erwarteten und dem tatsächlichen Verhalten der Algorithmen zu schließen und unser Vertrauen in KI-Systeme entsprechend zu stärken. Um ein Übermaß an Informationen zu verhindern, spielen Empfehlungsdienste eine entscheidende Rolle um Inhalte (z.B. Produkten, Nachrichten, Musik und Filmen) zu filtern und deren Benutzern eine personalisierte Erfahrung zu bieten. Infolgedessen erheben immer mehr In- formationskonsumenten Anspruch auf angemessene Erklärungen für deren personalisierte Empfehlungen. Diese Erklärungen sollen den Benutzern helfen zu verstehen, warum ihnen bestimmte Dinge empfohlen wurden und wie sich ihre früheren Eingaben in das System auf die Generierung solcher Empfehlungen auswirken. Außerdem können Erklärungen für den Fall, dass unerwünschte Inhalte empfohlen werden, wertvolle Informationen darüber enthalten, wie das Verhalten des Systems entsprechend geändert werden kann. In dieser Dissertation stellen wir unsere Beiträge zu Erklärbarkeit und Nachvollziehbarkeit von Empfehlungsdiensten vor. • Mit FAIRY stellen wir ein benutzerzentriertes Framework vor, mit dem post-hoc Erklärungen für die von Black-Box-Plattformen generierten sozialen Feeds entdeckt und bewertet werden können. Diese Erklärungen zeigen Beziehungen zwischen Benutzerprofilen und deren Feeds auf und werden aus den lokalen Interaktionsgraphen der Benutzer extrahiert. FAIRY verwendet eine LTR-Methode (Learning-to-Rank), um die Erklärungen anhand ihrer Relevanz und ihres Grads unerwarteter Empfehlungen zu bewerten. • Mit der PRINCE-Methode erleichtern wir das anbieterseitige Generieren von Erklärungen für PageRank-basierte Empfehlungsdienste. PRINCE-Erklärungen sind für Benutzer verständlich, da sie Teilmengen früherer Nutzerinteraktionen darstellen, die für die erhaltenen Empfehlungen verantwortlich sind. PRINCE-Erklärungen sind somit kausaler Natur und werden von einem Algorithmus mit polynomieller Laufzeit erzeugt , um präzise Erklärungen zu finden. • Wir präsentieren ein Human-in-the-Loop-Framework, ELIXIR, um die Nachvollziehbarkeit der Empfehlungsmodelle und die Qualität der Empfehlungen zu verbessern. Mit ELIXIR können Empfehlungsdienste Benutzerfeedback zu Empfehlungen und Erklärungen sammeln. Das Feedback wird in das Modell einbezogen, indem benutzerspezifischer Einbettungen von Objekten gelernt werden. Wir evaluieren alle Modelle und Methoden in Benutzerstudien und demonstrieren ihren Nutzen hinsichtlich Erklärbarkeit und Nachvollziehbarkeit von Empfehlungsdiensten

2014-2015 Course Catalog

An annual catalog of courses and course descriptions offered at the University of Montana.https://scholarworks.umt.edu/coursecatalogs_asc/1045/thumbnail.jp