Decoding Sequence Classification Models for Acquiring New Biological Insights

Classifying biological sequences is one of the most important tasks in computational biology. In the last decade, support vector machines (SVMs) in combination with sequence kernels have emerged as a de-facto standard. These methods are theoretically well-founded, reliable, and provide high-accuracy solutions at low computational cost. However, obtaining a highly accurate classifier is rarely the end of the story in many practical situations. Instead, one often aims to acquire biological knowledge about the principles underlying a given classification task. SVMs with traditional sequence kernels do not offer a straightforward way of accessing this knowledge.

In this contribution, we propose a new approach to analyzing biological sequences on the basis of support vector machines with sequence kernels. We first extract explicit pattern weights from a given SVM. When classifying a sequence, we then compute a prediction profile by distributing the weight of each pattern to the sequence positions that match the pattern. The final profile not only allows assessing the importance of a position, but also determining for which class it is indicative. Since it is unfeasible to analyze profiles of all sequences in a given data set, we advocate using affinity propagation (AP) clustering to narrow down the analysis to a small set of typical sequences.

The proposed approach is applicable to a wide range of biological sequences and a wide selection of sequence kernels. To illustrate our framework, we present the prediction of oligomerization tendencies of coiled coil proteins as a case study.
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The ENJOY MAP for HEALTH: Exercise interveNtion outdoor proJect in the cOmmunitY for older people—More Active People for HEALTHier communities: a study protocol

Background: Physical activity is important to maintain health in older age, with physical activity in the outdoors providing mental and physical health benefits for all age groups. One way by which older people can engage in physical activity in the outdoors is through using suitable age-friendly outdoor exercise equipment, the Seniors Exercise Park. The ENJOY MAP for HEALTH aims to evaluate the effect of the Seniors Exercise Park installation and associated capacity building activities on park visitation, park-based physical activity by older people and delivery of community physical activity programs. Method: This study is a quasi-experimental (natural experiment) with pre and post study design evaluating the effect of age-friendly outdoor spaces with specialised outdoor exercise equipment on older people’s physical activity and wellbeing in six Victorian municipalities (local governments/councils). Each council will undergo four stages (site construction and development, promotion and marketing, capacity building and training, evaluation and sustainability). Several activities and methods will be employed from stage one through stage four to evaluate the potential impact of the age-friendly outdoor spaces on physical activity and wellbeing and will comprise the following elements: site observation and equipment utilisation, face to face intercept surveys, development of an online access monitor and community building activities. Discussion: The project is expected to result in a significant change in the physical outdoor environment for the participating councils and communities whereby older people and other community members will be able to engage in safe physical and social activity programs, socialise more and hence improve the overall wellbeing of older people. Trial registration: This trial is retrospectively registered with the Australian New Zealand Clinical Trials Registry. Trial registration number ACTRN12621000965808. Date registered 23/07/2021

Computing folding pathways between RNA secondary structures

Given an RNA sequence and two designated secondary structures A, B, we describe a new algorithm that computes a nearly optimal folding pathway from A to B. The algorithm, RNAtabupath, employs a tabu semi-greedy heuristic, known to be an effective search strategy in combinatorial optimization. Folding pathways, sometimes called routes or trajectories, are computed by RNAtabupath in a fraction of the time required by the barriers program of Vienna RNA Package. We benchmark RNAtabupath with other algorithms to compute low energy folding pathways between experimentally known structures of several conformational switches. The RNApathfinder web server, source code for algorithms to compute and analyze pathways and supplementary data are available at http://bioinformatics.bc.edu/clotelab/RNApathfinder

Adaptor Signature Based Atomic Swaps Between Bitcoin and a Mimblewimble Based Cryptocurrency

Arbeit an der Bibliothek noch nicht eingelangt - Daten nicht geprüftAbweichender Titel nach Übersetzung der Verfasserin/des VerfassersSeit der Einführung von Bitcoin im Jahr 2008 haben wir ein kontinuierliches Wachstum im Bitcoin- und Blockchain-Bereich erlebt. Da die Anzahl der Kryptowährungen steigt, wird die Interoperabilität zwischen ihnen zu einem interessanten Thema, zum Beispiel um dezentralen Exchange zwischen den Kryptowährungen zu ermöglichen. Durch die Nutzung von Smart Contracts oder Skriptkonstrukten, die auf den meisten Blockchain-Systemen verfügbar sind, ist die Verbindung zweier Kryptowährungen über sogenannte Atomic Swaps möglich. Für Währungen, die sich auf die Verbesserung der Privatsphäre konzentrieren, gibt es jedoch keine solchen Möglichkeiten. Diese Arbeit erforscht das Mimblewimble-Protokoll, eine Konstruktion einer außergewöhnlich effizienten, die Privatsphäre verbessernden Kryptowährung. Aufbauend auf früheren Arbeiten anderer Autoren formalisieren wir verschiedene Arten von Mimblewimble-Transaktionen, die primitive Smart Contracts ermöglichen, und beweisen ihre Sicherheit und Korrektheit. Wir verbessern das Sicherheitsmodell des Protokolls, indem wir eine Schwäche in früheren Formalisierungen identifizieren und beheben. Unter Verwendung unserer fortschrittlichen Transaktionsprotokolle gelingt es uns, ein Atomic-Swap-Protokoll für Mimblewimble-basierte Systeme zu entwerfen, das ausschließlich aus kryptografischen Primitiven aufgebaut ist. Außerdem formalisieren wir ein Atomic Swap-Protokoll zwischen Bitcoin und Grin, einer Mimblewimble-basierten Kryptowährung. Anschließend implementieren wir einen Proof of Concept in der Programmiersprache Rust, den wir erfolgreich in den Testnets von Bitcoin und Grin einsetzen und evaluieren.Since the inception of Bitcoin in 2008, we have witnessed continuous growth in the Bitcoin and blockchain space. As the number of individual cryptocurrencies rises, interoperability between them becomes a critical topic, for instance, to allow for decentralized coin exchange. By utilizing smart contracts or script constructs available on most blockchain systems, connecting two cryptocurrencies is possible via so-called Atomic Swaps. However, for the currencies focusing on privacy enhancements, no such capabilities exist. This thesis explores the Mimblewimble protocol, a construction of an exceptionally efficient privacy-enhancing cryptocurrency. By building on other authors' previous work, we formalize different kinds of Mimblewimble transactions that allow for shared coin ownership and simple contracts and prove their security and correctness. We improve on the protocol's security model by identifying and resolving a weakness in prior formalizations. Utilizing our advanced transaction protocols, we manage to design an Atomic Swap protocol for Mimblewimble-based systems built solely with cryptographic primitives. We further formalize an Atomic Swap protocol between Bitcoin and Grin, a Mimblewimble-based cryptocurrency. We then implement a proof of concept in the programming language Rust, which we successfully deploy and evaluate on the Bitcoin and Grin testnets.10

Token Economy as an Intervention for a First Grade Student Struggling With Aggression and Following Directions

This school-based project explored an intervention for students who struggle with behaviors in school. Behavior problems in schools can cause a student to struggle in academics and social skills, along with problems in their later school years. A form of token economy was implemented with a first grade student struggling with aggressive behaviors and following directions. The student carried around a binder that had 10 token spots on the front and he got a reward break when he filled them all in. He could choose between several different activities to do on his breaks. He could also ask for calm down breaks during the day and had different options for these breaks. The results of this study showed that the token economy did not change this student’s negative behaviors, although there were several limitations to how the intervention was implemented