98 research outputs found

    Exact Bayesian Inference for Loopy Probabilistic Programs

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    We present an exact Bayesian inference method for inferring posterior distributions encoded by probabilistic programs featuring possibly unbounded looping behaviors. Our method is built on an extended denotational semantics represented by probability generating functions, which resolves semantic intricacies induced by intertwining discrete probabilistic loops with conditioning (for encoding posterior observations). We implement our method in a tool called Prodigy; it augments existing computer algebra systems with the theory of generating functions for the (semi-)automatic inference and quantitative verification of conditioned probabilistic programs. Experimental results show that Prodigy can handle various infinite-state loopy programs and outperforms state-of-the-art exact inference tools over benchmarks of loop-free programs

    Tools and Algorithms for the Construction and Analysis of Systems

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    This open access book constitutes the proceedings of the 28th International Conference on Tools and Algorithms for the Construction and Analysis of Systems, TACAS 2022, which was held during April 2-7, 2022, in Munich, Germany, as part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2022. The 46 full papers and 4 short papers presented in this volume were carefully reviewed and selected from 159 submissions. The proceedings also contain 16 tool papers of the affiliated competition SV-Comp and 1 paper consisting of the competition report. TACAS is a forum for researchers, developers, and users interested in rigorously based tools and algorithms for the construction and analysis of systems. The conference aims to bridge the gaps between different communities with this common interest and to support them in their quest to improve the utility, reliability, exibility, and efficiency of tools and algorithms for building computer-controlled systems

    Tools and Algorithms for the Construction and Analysis of Systems

    Get PDF
    This open access book constitutes the proceedings of the 28th International Conference on Tools and Algorithms for the Construction and Analysis of Systems, TACAS 2022, which was held during April 2-7, 2022, in Munich, Germany, as part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2022. The 46 full papers and 4 short papers presented in this volume were carefully reviewed and selected from 159 submissions. The proceedings also contain 16 tool papers of the affiliated competition SV-Comp and 1 paper consisting of the competition report. TACAS is a forum for researchers, developers, and users interested in rigorously based tools and algorithms for the construction and analysis of systems. The conference aims to bridge the gaps between different communities with this common interest and to support them in their quest to improve the utility, reliability, exibility, and efficiency of tools and algorithms for building computer-controlled systems

    Reports to the President

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    A compilation of annual reports for the 1988-1989 academic year, including a report from the President of the Massachusetts Institute of Technology, as well as reports from the academic and administrative units of the Institute. The reports outline the year's goals, accomplishments, honors and awards, and future plans

    Reports to the President

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    A compilation of annual reports for the 1989-1990 academic year, including a report from the President of the Massachusetts Institute of Technology, as well as reports from the academic and administrative units of the Institute. The reports outline the year's goals, accomplishments, honors and awards, and future plans

    Reports to the President

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    A compilation of annual reports for the 1982-1983 academic year, including a report from the President of the Massachusetts Institute of Technology, as well as reports from the academic and administrative units of the Institute. The reports outline the year's goals, accomplishments, honors and awards, and future plans

    Building the Hyperconnected Society- Internet of Things Research and Innovation Value Chains, Ecosystems and Markets

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    This book aims to provide a broad overview of various topics of Internet of Things (IoT), ranging from research, innovation and development priorities to enabling technologies, nanoelectronics, cyber-physical systems, architecture, interoperability and industrial applications. All this is happening in a global context, building towards intelligent, interconnected decision making as an essential driver for new growth and co-competition across a wider set of markets. It is intended to be a standalone book in a series that covers the Internet of Things activities of the IERC – Internet of Things European Research Cluster from research to technological innovation, validation and deployment.The book builds on the ideas put forward by the European Research Cluster on the Internet of Things Strategic Research and Innovation Agenda, and presents global views and state of the art results on the challenges facing the research, innovation, development and deployment of IoT in future years. The concept of IoT could disrupt consumer and industrial product markets generating new revenues and serving as a growth driver for semiconductor, networking equipment, and service provider end-markets globally. This will create new application and product end-markets, change the value chain of companies that creates the IoT technology and deploy it in various end sectors, while impacting the business models of semiconductor, software, device, communication and service provider stakeholders. The proliferation of intelligent devices at the edge of the network with the introduction of embedded software and app-driven hardware into manufactured devices, and the ability, through embedded software/hardware developments, to monetize those device functions and features by offering novel solutions, could generate completely new types of revenue streams. Intelligent and IoT devices leverage software, software licensing, entitlement management, and Internet connectivity in ways that address many of the societal challenges that we will face in the next decade

    Evolutionary genomics : statistical and computational methods

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    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

    Computational characterization of tandem repeat and non-globular proteins

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    The first protein structure to be determined was hemoglobin, a globe-like, water-soluble protein with enzymatic activity. Since then, protein science has been biased towards this type, termed globular. However, over the last decades accumulating experimental evidences suggested the functional importance of their counterpart, non-globular proteins (NGPs). The definition includes tandem repetitions, intrinsically disordered regions, aggregating domains and transmembrane domains. NGPs recognition and classification is essential to shed a light on the so called “dark proteome”, i.e. the large fraction that we know almost nothing about. I contributed to this goal through the development of new resources dedicated to NGPs. My main focus are tandem repeat proteins (TRPs). TRPs are characterized by a repeated sequence which folds into a modular architecture, where modules are called “units”. The unit represents not only the structural but also the evolutionary module and base TRPs classification. TRPs are widespread in all type of organisms, where they carry out fundamental functions. The sequences of TRP units diverge quickly while maintaining their fold, hampering detection by traditional methods for sequence analysis. Conversely, the challenges of structure-based repeats detection lie in the multidimensional nature of the data. Specialized methods have been developed for TRPs identification, however few of them annotate single repeat units. RepeatsDB is a database of TRP structures annotated with the position of repeat units and insertions. I contributed to the new version of RepeatsDB database, which was populated taking advantage of ReUPred, predictor of tandem repeat units. The quality of RepeatsDB data is guaranteed by manual validation, a time-consuming task which requires community annotation efforts. To facilitate this process I developed RepeatsDB-lite, web server for the prediction and refinement of tandem repeats in protein structure. Analysing RepeatsDB data, I compared the sequence- and structure-based classification of TRPs. Moreover, I provided insights on TRPs role in the human proteome by characterizing them in terms of function, protein-protein interaction networks and impact on diseases. As a case study, I characterized Collagen V, a repeat protein associated to Ehlers-Danlos syndrome, identifying genotype-phenotype correlations in relation to its interaction network model. Another category of NGPs is intrinsically disordered proteins (IDPs), devoid of order in their native state. Intrinsic disorder was shown to be prevalent in the human proteome, to play important signaling and regulatory roles and to be frequently involved in disease. I contributed to MobiDB, database of protein disorder and mobility annotations that describes several aspects of NGPs structure and mechanism of function. MobiDB provides consensus predictions and functional annotations for all known protein sequences. A common feature of TRPs, IDPs and other NGPs is that they are characterized by low-complexity regions, where the distribution of amino acids deviates from the common amino acid usage. The functional importance of low complexity regions is strictly related to their non-globular arrangement. I contributed to the field with a critical review focusing on the definition of sequence features of low complexity regions and their relationship to structural features. Finally, I exploited the knowledge acquired on NGPs in the previous studies to design one of the first sequence-based methods for the prediction of protein solubility, SODA. SODA uses the aggregation propensity, intrinsic disorder, hydrophobicity and secondary structure preferences from a sequence to evaluate solubility changes introduced by a mutation. The main envisaged applications of SODA are in protein engineering and in the study of the impact of protein mutations in disease insurgence

    Fundamental Approaches to Software Engineering

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    This open access book constitutes the proceedings of the 25th International Conference on Fundamental Approaches to Software Engineering, FASE 2022, which was held during April 4-5, 2022, in Munich, Germany, as part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2022. The 17 regular papers presented in this volume were carefully reviewed and selected from 64 submissions. The proceedings also contain 3 contributions from the Test-Comp Competition. The papers deal with the foundations on which software engineering is built, including topics like software engineering as an engineering discipline, requirements engineering, software architectures, software quality, model-driven development, software processes, software evolution, AI-based software engineering, and the specification, design, and implementation of particular classes of systems, such as (self-)adaptive, collaborative, AI, embedded, distributed, mobile, pervasive, cyber-physical, or service-oriented applications
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