9,351 research outputs found

    Towards A Practical High-Assurance Systems Programming Language

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    Writing correct and performant low-level systems code is a notoriously demanding job, even for experienced developers. To make the matter worse, formally reasoning about their correctness properties introduces yet another level of complexity to the task. It requires considerable expertise in both systems programming and formal verification. The development can be extremely costly due to the sheer complexity of the systems and the nuances in them, if not assisted with appropriate tools that provide abstraction and automation. Cogent is designed to alleviate the burden on developers when writing and verifying systems code. It is a high-level functional language with a certifying compiler, which automatically proves the correctness of the compiled code and also provides a purely functional abstraction of the low-level program to the developer. Equational reasoning techniques can then be used to prove functional correctness properties of the program on top of this abstract semantics, which is notably less laborious than directly verifying the C code. To make Cogent a more approachable and effective tool for developing real-world systems, we further strengthen the framework by extending the core language and its ecosystem. Specifically, we enrich the language to allow users to control the memory representation of algebraic data types, while retaining the automatic proof with a data layout refinement calculus. We repurpose existing tools in a novel way and develop an intuitive foreign function interface, which provides users a seamless experience when using Cogent in conjunction with native C. We augment the Cogent ecosystem with a property-based testing framework, which helps developers better understand the impact formal verification has on their programs and enables a progressive approach to producing high-assurance systems. Finally we explore refinement type systems, which we plan to incorporate into Cogent for more expressiveness and better integration of systems programmers with the verification process

    Spooker Trouper : ABBA Voyage, Virtual Humans and the Rise of the Digital Apparition

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    This article analyses the ‘live’ virtual human in ABBA Voyage, the long-awaited concert reunion of the Swedish pop group ABBA, via Vilém Flusser’s concept of the digital apparition. It first argues for these virtual performers (dubbed ‘ABBA-tars’) to be understood as externalized computational codes which shift the grounds of ownership over and consent to the use of one’s likeness. They are also key to disproportionate and as yet unaccountable power held by technology companies. Secondly, ABBA Voyage’s presentation of ABBA as their past selves places time in a capitalism of immateriality profiting from the protean temporality of bodies. This temporal discombobulation thwarts finitude and confounds time in meanings of life, death and growth. The article thus addresses urgent confrontations between actual and virtual humans placed in the same physical environment, and paves the way for thinking about how we are going to deal and live with their virtuality

    Using machine learning to predict pathogenicity of genomic variants throughout the human genome

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    Geschätzt mehr als 6.000 Erkrankungen werden durch Veränderungen im Genom verursacht. Ursachen gibt es viele: Eine genomische Variante kann die Translation eines Proteins stoppen, die Genregulation stören oder das Spleißen der mRNA in eine andere Isoform begünstigen. All diese Prozesse müssen überprüft werden, um die zum beschriebenen Phänotyp passende Variante zu ermitteln. Eine Automatisierung dieses Prozesses sind Varianteneffektmodelle. Mittels maschinellem Lernen und Annotationen aus verschiedenen Quellen bewerten diese Modelle genomische Varianten hinsichtlich ihrer Pathogenität. Die Entwicklung eines Varianteneffektmodells erfordert eine Reihe von Schritten: Annotation der Trainingsdaten, Auswahl von Features, Training verschiedener Modelle und Selektion eines Modells. Hier präsentiere ich ein allgemeines Workflow dieses Prozesses. Dieses ermöglicht es den Prozess zu konfigurieren, Modellmerkmale zu bearbeiten, und verschiedene Annotationen zu testen. Der Workflow umfasst außerdem die Optimierung von Hyperparametern, Validierung und letztlich die Anwendung des Modells durch genomweites Berechnen von Varianten-Scores. Der Workflow wird in der Entwicklung von Combined Annotation Dependent Depletion (CADD), einem Varianteneffektmodell zur genomweiten Bewertung von SNVs und InDels, verwendet. Durch Etablierung des ersten Varianteneffektmodells für das humane Referenzgenome GRCh38 demonstriere ich die gewonnenen Möglichkeiten Annotationen aufzugreifen und neue Modelle zu trainieren. Außerdem zeige ich, wie Deep-Learning-Scores als Feature in einem CADD-Modell die Vorhersage von RNA-Spleißing verbessern. Außerdem werden Varianteneffektmodelle aufgrund eines neuen, auf Allelhäufigkeit basierten, Trainingsdatensatz entwickelt. Diese Ergebnisse zeigen, dass der entwickelte Workflow eine skalierbare und flexible Möglichkeit ist, um Varianteneffektmodelle zu entwickeln. Alle entstandenen Scores sind unter cadd.gs.washington.edu und cadd.bihealth.org frei verfügbar.More than 6,000 diseases are estimated to be caused by genomic variants. This can happen in many possible ways: a variant may stop the translation of a protein, interfere with gene regulation, or alter splicing of the transcribed mRNA into an unwanted isoform. It is necessary to investigate all of these processes in order to evaluate which variant may be causal for the deleterious phenotype. A great help in this regard are variant effect scores. Implemented as machine learning classifiers, they integrate annotations from different resources to rank genomic variants in terms of pathogenicity. Developing a variant effect score requires multiple steps: annotation of the training data, feature selection, model training, benchmarking, and finally deployment for the model's application. Here, I present a generalized workflow of this process. It makes it simple to configure how information is converted into model features, enabling the rapid exploration of different annotations. The workflow further implements hyperparameter optimization, model validation and ultimately deployment of a selected model via genome-wide scoring of genomic variants. The workflow is applied to train Combined Annotation Dependent Depletion (CADD), a variant effect model that is scoring SNVs and InDels genome-wide. I show that the workflow can be quickly adapted to novel annotations by porting CADD to the genome reference GRCh38. Further, I demonstrate the integration of deep-neural network scores as features into a new CADD model, improving the annotation of RNA splicing events. Finally, I apply the workflow to train multiple variant effect models from training data that is based on variants selected by allele frequency. In conclusion, the developed workflow presents a flexible and scalable method to train variant effect scores. All software and developed scores are freely available from cadd.gs.washington.edu and cadd.bihealth.org

    Knowledge Distillation and Continual Learning for Optimized Deep Neural Networks

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    Over the past few years, deep learning (DL) has been achieving state-of-theart performance on various human tasks such as speech generation, language translation, image segmentation, and object detection. While traditional machine learning models require hand-crafted features, deep learning algorithms can automatically extract discriminative features and learn complex knowledge from large datasets. This powerful learning ability makes deep learning models attractive to both academia and big corporations. Despite their popularity, deep learning methods still have two main limitations: large memory consumption and catastrophic knowledge forgetting. First, DL algorithms use very deep neural networks (DNNs) with many billion parameters, which have a big model size and a slow inference speed. This restricts the application of DNNs in resource-constraint devices such as mobile phones and autonomous vehicles. Second, DNNs are known to suffer from catastrophic forgetting. When incrementally learning new tasks, the model performance on old tasks significantly drops. The ability to accommodate new knowledge while retaining previously learned knowledge is called continual learning. Since the realworld environments in which the model operates are always evolving, a robust neural network needs to have this continual learning ability for adapting to new changes

    Meso-scale FDM material layout design strategies under manufacturability constraints and fracture conditions

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    In the manufacturability-driven design (MDD) perspective, manufacturability of the product or system is the most important of the design requirements. In addition to being able to ensure that complex designs (e.g., topology optimization) are manufacturable with a given process or process family, MDD also helps mechanical designers to take advantage of unique process-material effects generated during manufacturing. One of the most recognizable examples of this comes from the scanning-type family of additive manufacturing (AM) processes; the most notable and familiar member of this family is the fused deposition modeling (FDM) or fused filament fabrication (FFF) process. This process works by selectively depositing uniform, approximately isotropic beads or elements of molten thermoplastic material (typically structural engineering plastics) in a series of pre-specified traces to build each layer of the part. There are many interesting 2-D and 3-D mechanical design problems that can be explored by designing the layout of these elements. The resulting structured, hierarchical material (which is both manufacturable and customized layer-by-layer within the limits of the process and material) can be defined as a manufacturing process-driven structured material (MPDSM). This dissertation explores several practical methods for designing these element layouts for 2-D and 3-D meso-scale mechanical problems, focusing ultimately on design-for-fracture. Three different fracture conditions are explored: (1) cases where a crack must be prevented or stopped, (2) cases where the crack must be encouraged or accelerated, and (3) cases where cracks must grow in a simple pre-determined pattern. Several new design tools, including a mapping method for the FDM manufacturability constraints, three major literature reviews, the collection, organization, and analysis of several large (qualitative and quantitative) multi-scale datasets on the fracture behavior of FDM-processed materials, some new experimental equipment, and the refinement of a fast and simple g-code generator based on commercially-available software, were developed and refined to support the design of MPDSMs under fracture conditions. The refined design method and rules were experimentally validated using a series of case studies (involving both design and physical testing of the designs) at the end of the dissertation. Finally, a simple design guide for practicing engineers who are not experts in advanced solid mechanics nor process-tailored materials was developed from the results of this project.U of I OnlyAuthor's request

    Vision on Vision: Defining Similarities Among Early Modern Illustrations on Cosmology

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    ON EXPRESSIVENESS, INFERENCE, AND PARAMETER ESTIMATION OF DISCRETE SEQUENCE MODELS

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    Huge neural autoregressive sequence models have achieved impressive performance across different applications, such as NLP, reinforcement learning, and bioinformatics. However, some lingering problems (e.g., consistency and coherency of generated texts) continue to exist, regardless of the parameter count. In the first part of this thesis, we chart a taxonomy of the expressiveness of various sequence model families (Ch 3). In particular, we put forth complexity-theoretic proofs that string latent-variable sequence models are strictly more expressive than energy-based sequence models, which in turn are more expressive than autoregressive sequence models. Based on these findings, we introduce residual energy-based sequence models, a family of energy-based sequence models (Ch 4) whose sequence weights can be evaluated efficiently, and also perform competitively against autoregressive models. However, we show how unrestricted energy-based sequence models can suffer from uncomputability; and how such a problem is generally unfixable without knowledge of the true sequence distribution (Ch 5). In the second part of the thesis, we study practical sequence model families and algorithms based on theoretical findings in the first part of the thesis. We introduce neural particle smoothing (Ch 6), a family of approximate sampling methods that work with conditional latent variable models. We also introduce neural finite-state transducers (Ch 7), which extend weighted finite state transducers with the introduction of mark strings, allowing scoring transduction paths in a finite state transducer with a neural network. Finally, we propose neural regular expressions (Ch 8), a family of neural sequence models that are easy to engineer, allowing a user to design flexible weighted relations using Marked FSTs, and combine these weighted relations together with various operations

    University of South Dakota 2023 AASHE STARS Assessment Report

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    https://red.library.usd.edu/sustainability-projects/1008/thumbnail.jp
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