An implementation of Deflate in Coq

The widely-used compression format "Deflate" is defined in RFC 1951 and is based on prefix-free codings and backreferences. There are unclear points about the way these codings are specified, and several sources for confusion in the standard. We tried to fix this problem by giving a rigorous mathematical specification, which we formalized in Coq. We produced a verified implementation in Coq which achieves competitive performance on inputs of several megabytes. In this paper we present the several parts of our implementation: a fully verified implementation of canonical prefix-free codings, which can be used in other compression formats as well, and an elegant formalism for specifying sophisticated formats, which we used to implement both a compression and decompression algorithm in Coq which we formally prove inverse to each other -- the first time this has been achieved to our knowledge. The compatibility to other Deflate implementations can be shown empirically. We furthermore discuss some of the difficulties, specifically regarding memory and runtime requirements, and our approaches to overcome them

Sam2bam: High-Performance Framework for NGS Data Preprocessing Tools

This paper introduces a high-throughput software tool framework called {\it sam2bam} that enables users to significantly speedup pre-processing for next-generation sequencing data. The sam2bam is especially efficient on single-node multi-core large-memory systems. It can reduce the runtime of data pre-processing in marking duplicate reads on a single node system by 156-186x compared with de facto standard tools. The sam2bam consists of parallel software components that can fully utilize the multiple processors, available memory, high-bandwidth of storage, and hardware compression accelerators if available. The sam2bam provides file format conversion between well-known genome file formats, from SAM to BAM, as a basic feature. Additional features such as analyzing, filtering, and converting the input data are provided by {\it plug-in} tools, e.g., duplicate marking, which can be attached to sam2bam at runtime. We demonstrated that sam2bam could significantly reduce the runtime of NGS data pre-processing from about two hours to about one minute for a whole-exome data set on a 16-core single-node system using up to 130 GB of memory. The sam2bam could reduce the runtime for whole-genome sequencing data from about 20 hours to about nine minutes on the same system using up to 711 GB of memory

Kolmogorov Complexity in perspective. Part II: Classification, Information Processing and Duality

We survey diverse approaches to the notion of information: from Shannon entropy to Kolmogorov complexity. Two of the main applications of Kolmogorov complexity are presented: randomness and classification. The survey is divided in two parts published in a same volume. Part II is dedicated to the relation between logic and information system, within the scope of Kolmogorov algorithmic information theory. We present a recent application of Kolmogorov complexity: classification using compression, an idea with provocative implementation by authors such as Bennett, Vitanyi and Cilibrasi. This stresses how Kolmogorov complexity, besides being a foundation to randomness, is also related to classification. Another approach to classification is also considered: the so-called "Google classification". It uses another original and attractive idea which is connected to the classification using compression and to Kolmogorov complexity from a conceptual point of view. We present and unify these different approaches to classification in terms of Bottom-Up versus Top-Down operational modes, of which we point the fundamental principles and the underlying duality. We look at the way these two dual modes are used in different approaches to information system, particularly the relational model for database introduced by Codd in the 70's. This allows to point out diverse forms of a fundamental duality. These operational modes are also reinterpreted in the context of the comprehension schema of axiomatic set theory ZF. This leads us to develop how Kolmogorov's complexity is linked to intensionality, abstraction, classification and information system.Comment: 43 page

Big-Data-Driven Materials Science and its FAIR Data Infrastructure

This chapter addresses the forth paradigm of materials research -- big-data driven materials science. Its concepts and state-of-the-art are described, and its challenges and chances are discussed. For furthering the field, Open Data and an all-embracing sharing, an efficient data infrastructure, and the rich ecosystem of computer codes used in the community are of critical importance. For shaping this forth paradigm and contributing to the development or discovery of improved and novel materials, data must be what is now called FAIR -- Findable, Accessible, Interoperable and Re-purposable/Re-usable. This sets the stage for advances of methods from artificial intelligence that operate on large data sets to find trends and patterns that cannot be obtained from individual calculations and not even directly from high-throughput studies. Recent progress is reviewed and demonstrated, and the chapter is concluded by a forward-looking perspective, addressing important not yet solved challenges.Comment: submitted to the Handbook of Materials Modeling (eds. S. Yip and W. Andreoni), Springer 2018/201