Tree Diet: Reducing the Treewidth to Unlock FPT Algorithms in RNA Bioinformatics

Hard graph problems are ubiquitous in Bioinformatics, inspiring the design of specialized Fixed-Parameter Tractable algorithms, many of which rely on a combination of tree-decomposition and dynamic programming. The time/space complexities of such approaches hinge critically on low values for the treewidth tw of the input graph. In order to extend their scope of applicability, we introduce the Tree-Diet problem, i.e. the removal of a minimal set of edges such that a given tree-decomposition can be slimmed down to a prescribed treewidth tw\u27. Our rationale is that the time gained thanks to a smaller treewidth in a parameterized algorithm compensates the extra post-processing needed to take deleted edges into account. Our core result is an FPT dynamic programming algorithm for Tree-Diet, using 2^{O(tw)}n time and space. We complement this result with parameterized complexity lower-bounds for stronger variants (e.g., NP-hardness when tw\u27 or tw-tw\u27 is constant). We propose a prototype implementation for our approach which we apply on difficult instances of selected RNA-based problems: RNA design, sequence-structure alignment, and search of pseudoknotted RNAs in genomes, revealing very encouraging results. This work paves the way for a wider adoption of tree-decomposition-based algorithms in Bioinformatics

Staged parser combinators for efficient data processing

Parsers are ubiquitous in computing, and many applications depend on their performance for decoding data efficiently. Parser combinators are an intuitive tool for writing parsers: tight integration with the host language enables grammar specifications to be interleaved with processing of parse results. Unfortunately, parser combinators are typically slow due to the high overhead of the host language abstraction mechanisms that enable composition. We present a technique for eliminating such overhead. We use staging, a form of runtime code generation, to dissociate input parsing from parser composition, and eliminate intermediate data structures and computations associated with parser composition at staging time. A key challenge is to maintain support for input dependent grammars, which have no clear stage distinction. Our approach applies to top-down recursive-descent parsers as well as bottom-up nondeterministic parsers with key applications in dynamic programming on sequences, where we auto-generate code for parallel hardware. We achieve performance comparable to specialized, hand-written parsers

Efficient abstractions for visualization and interaction

Abstractions, such as functions and methods, are an essential tool for any programmer. Abstractions encapsulate the details of a computation: the programmer only needs to know what the abstraction achieves, not how it achieves it. However, using abstractions can come at a cost: the resulting program may be inefficient. This can lead to programmers not using some abstractions, instead writing the entire functionality from the ground up. In this thesis, we present several results that make this situation less likely when programming interactive visualizations. We present results that make abstractions more efficient in the areas of graphics, layout and events

Programming and Proving with Distributed Protocols

Distributed systems play a crucial role in modern infrastructure, but are notoriously difficult to implement correctly. This difficulty arises from two main challenges: (a) correctly implementing core system components (e.g., two-phase commit), so all their internal invariants hold, and (b) correctly composing standalone system components into functioning trustworthy applications (e.g., persistent storage built on top of a two-phase commit instance). Recent work has developed several approaches for addressing (a) by means of mechanically verifying implementations of core distributed components, but no methodology exists to address (b) by composing such verified components into larger verified applications. As a result, expensive verification efforts for key system components are not easily reusable, which hinders further verification efforts. In this paper, we present Disel, the first framework for implementation and compositional verification of distributed systems and their clients, all within the mechanized, foundational context of the Coq proof assistant. In Disel, users implement distributed systems using a domain specific language shallowly embedded in Coq and providing both high-level programming constructs as well as low-level communication primitives. Components of composite systems are specified in Disel as protocols, which capture system-specific logic and disentangle system definitions from implementation details. By virtue of Disel’s dependent type system, well-typed implementations always satisfy their protocols’ invariants and never go wrong, allowing users to verify system implementations interactively using Disel’s Hoare-style program logic, which extends state-of-the-art techniques for concurrency verification to the distributed setting. By virtue of the substitution principle and frame rule provided by Disel’s logic, system components can be composed leading to modular, reusable verified distributed systems. We describe Disel, illustrate its use with a series of examples, outline its logic and metatheory, and report on our experience using it as a framework for implementing, specifying, and verifying distributed systems

Theorem Provers as Libraries -- An Approach to Formally Verifying Functional Programs

Property-directed verification of functional programs tends to take one of two paths. First, is the traditional testing approach, where properties are expressed in the original programming language and checked with a collection of test data. Alternatively, for those desiring a more rigorous approach, properties can be written and checked with a formal tool; typically, an external proof system. This dissertation details a hybrid approach that captures the best of both worlds: the formality of a proof system paired with the native integration of an embedded, domain specific language (EDSL) for testing. At the heart of this hybridization is the titular concept -- a theorem prover as a library. The verification capabilities of this prover, HaskHOL, are introduced to a Haskell development environment as a GHC compiler plugin. Operating at the compiler level provides for a comparatively simpler integration and allows verification to co-exist with the numerous other passes that stand between source code and program

Verasco: un analyseur statique pour C formellement vérifié

In order to develop safer software for critical applications, some static analyzers aim at establishing, with mathematical certitude, the absence of some classes of bug in the input program. A possible limit to this approach is the possibility of a soundness bug in the static analyzer itself, which would nullify the guarantees it is supposed to deliver.In this thesis, we propose to establish formal guarantees on the static analyzer itself: we present the design, implementation and proof of soundness using Coq of Verasco, a formally verified static analyzer based on abstract interpretation handling most of the ISO C99 language, including IEEE754 floating-point arithmetic (except recursion and dynamic memory allocation). Verasco aims at establishing the absence of erroneous behavior of the given programs. It enjoys a modular extendable architecture with several abstract domains and well-specified interfaces. We present the abstract iterator of Verasco, its handling of bounded machine arithmetic, its interval abstract domain, its symbolic abstract domain and its abstract domain of octagons. Verasco led to the development of new techniques for implementing data structure with sharing in Coq.Afin de développer des logiciels plus sûrs pour des applications critiques, certains analyseurs statiques tentent d'établir, avec une certitude mathématique, l'absence de certains types de bugs dans un programme donné. Une limite possible à cette approche est l'éventualité d'un bug affectant la correction de l'analyseur lui-même, éliminant ainsi les garanties qu'il est censé apporter.Dans cette thèse, nous proposons d'établir des garanties formelles sur l'analyseur lui-même : nous présentons la conception, l'implantation et la preuve de sûreté en Coq de Verasco, un analyseur statique formellement vérifié utilisant l'interprétation abstraite pour le langage ISO C99 avec l'arithmétique flottante IEEE754 (à l'exception de la récursion et de l'allocation dynamique de mémoire). Verasco a pour but d'établir l'absence d'erreur à l'exécution des programmes donnés. Il est conçu selon une architecture modulaire et extensible contenant plusieurs domaines abstraits et des interfaces bien spécifiées. Nous détaillons le fonctionnement de l'itérateur abstrait de Verasco, son traitement des entiers bornés de la machine, son domaine abstrait d'intervalles, son domaine abstrait symbolique et son domaine abstrait d'octogones. Verasco a donné lieu au développement de nouvelles techniques pour implémenter des structures de données avec partage dans Coq

Programming Languages and Systems

This open access book constitutes the proceedings of the 28th European Symposium on Programming, ESOP 2019, which took place in Prague, Czech Republic, in April 2019, held as Part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2019