Toward an Energy Efficient Language and Compiler for (Partially) Reversible Algorithms

We introduce a new programming language for expressing reversibility, Energy-Efficient Language (Eel), geared toward algorithm design and implementation. Eel is the first language to take advantage of a partially reversible computation model, where programs can be composed of both reversible and irreversible operations. In this model, irreversible operations cost energy for every bit of information created or destroyed. To handle programs of varying degrees of reversibility, Eel supports a log stack to automatically trade energy costs for space costs, and introduces many powerful control logic operators including protected conditional, general conditional, protected loops, and general loops. In this paper, we present the design and compiler for the three language levels of Eel along with an interpreter to simulate and annotate incurred energy costs of a program.Comment: 17 pages, 0 additional figures, pre-print to be published in The 8th Conference on Reversible Computing (RC2016

Reversible Computation in Term Rewriting

Essentially, in a reversible programming language, for each forward computation from state $S$ to state $S'$, there exists a constructive method to go backwards from state $S'$ to state $S$. Besides its theoretical interest, reversible computation is a fundamental concept which is relevant in many different areas like cellular automata, bidirectional program transformation, or quantum computing, to name a few. In this work, we focus on term rewriting, a computation model that underlies most rule-based programming languages. In general, term rewriting is not reversible, even for injective functions; namely, given a rewrite step $t_1 \rightarrow t_2$, we do not always have a decidable method to get $t_1$ from $t_2$. Here, we introduce a conservative extension of term rewriting that becomes reversible. Furthermore, we also define two transformations, injectivization and inversion, to make a rewrite system reversible using standard term rewriting. We illustrate the usefulness of our transformations in the context of bidirectional program transformation.Comment: To appear in the Journal of Logical and Algebraic Methods in Programmin

Reversible Term Rewriting

Essentially, in a reversible programming language, for each forward computation step from state S to state S', there exists a constructive and deterministic method to go backwards from state S' to state S. Besides its theoretical interest, reversible computation is a fundamental concept which is relevant in many different areas like cellular automata, bidirectional program transformation, or quantum computing, to name a few. In this paper, we focus on term rewriting, a computation model that underlies most rule-based programming languages. In general, term rewriting is not reversible, even for injective functions; namely, given a rewrite step t1 -> t2, we do not always have a decidable and deterministic method to get t1 from t2. Here, we introduce a conservative extension of term rewriting that becomes reversible. Furthermore, we also define a transformation to make a rewrite system reversible using standard term rewriting.This work has been partially supported by the EU (FEDER) and the Spanish Ministerio de Economía y Competitividad (MINECO) under grant TIN2013-44742-C4-1-R, by the Generalitat Valenciana under grant PROMETEO-II/2015/013 (SmartLogic) and by the COST Action IC 1405 on Reversible Computation. A. Palacios was partially supported by the the EU (FEDER) and the Spanish Ayudas para contratos predoctorales para la formación de doctores de la Sec. Estado de Investigación, Desarrollo e Innovación del MINECO under FPI grant BES-2014-069749. Part of this research was done while the second and third authors were visiting Nagoya University; they gratefully acknowledge their hospitality.Nishida, N.; Palacios Corella, A.; Vidal Oriola, GF.; Nishida (2016). Reversible Term Rewriting. Schloss Dagstuhl-Leibniz-Zentrum für Informatik GmbH, Dagstuhl Publishing. https://doi.org/10.4230/LIPIcs.FSCD.2016.28

Scheduling of guarded command based models

Formal methods provide a means of reasoning about computer programs in order to prove correctness criteria. One subtype of formal methods is based on the weakest precondition predicate transformer semantics and uses guarded commands as the basic modelling construct. Examples of such formalisms are Action Systems and Event-B. Guarded commands can intuitively be understood as actions that may be triggered when an associated guard condition holds. Guarded commands whose guards hold are nondeterministically chosen for execution, but no further control flow is present by default. Such a modelling approach is convenient for proving correctness, and the Refinement Calculus allows for a stepwise development method. It also has a parallel interpretation facilitating development of concurrent software, and it is suitable for describing event-driven scenarios. However, for many application areas, the execution paradigm traditionally used comprises more explicit control flow, which constitutes an obstacle for using the above mentioned formal methods. In this thesis, we study how guarded command based modelling approaches can be conveniently and efficiently scheduled in different scenarios. We first focus on the modelling of trust for transactions in a social networking setting. Due to the event-based nature of the scenario, the use of guarded commands turns out to be relatively straightforward. We continue by studying modelling of concurrent software, with particular focus on compute-intensive scenarios. We go from theoretical considerations to the feasibility of implementation by evaluating the performance and scalability of executing a case study model in parallel using automatic scheduling performed by a dedicated scheduler. Finally, we propose a more explicit and non-centralised approach in which the flow of each task is controlled by a schedule of its own. The schedules are expressed in a dedicated scheduling language, and patterns assist the developer in proving correctness of the scheduled model with respect to the original one

On Distributed Storage Codes

Distributed storage systems are studied. The interest in such system has become relatively wide due to the increasing amount of information needed to be stored in data centers or different kinds of cloud systems. There are many kinds of solutions for storing the information into distributed devices regarding the needs of the system designer. This thesis studies the questions of designing such storage systems and also fundamental limits of such systems. Namely, the subjects of interest of this thesis include heterogeneous distributed storage systems, distributed storage systems with the exact repair property, and locally repairable codes. For distributed storage systems with either functional or exact repair, capacity results are proved. In the case of locally repairable codes, the minimum distance is studied. Constructions for exact-repairing codes between minimum bandwidth regeneration (MBR) and minimum storage regeneration (MSR) points are given. These codes exceed the time-sharing line of the extremal points in many cases. Other properties of exact-regenerating codes are also studied. For the heterogeneous setup, the main result is that the capacity of such systems is always smaller than or equal to the capacity of a homogeneous system with symmetric repair with average node size and average repair bandwidth. A randomized construction for a locally repairable code with good minimum distance is given. It is shown that a random linear code of certain natural type has a good minimum distance with high probability. Other properties of locally repairable codes are also studied.Siirretty Doriast

Computational methods and tools for protein phosphorylation analysis

Signaling pathways represent a central regulatory mechanism of biological systems where a key event in their correct functioning is the reversible phosphorylation of proteins. Protein phosphorylation affects at least one-third of all proteins and is the most widely studied posttranslational modification. Phosphorylation analysis is still perceived, in general, as difficult or cumbersome and not readily attempted by many, despite the high value of such information. Specifically, determining the exact location of a phosphorylation site is currently considered a major hurdle, thus reliable approaches are necessary for the detection and localization of protein phosphorylation. The goal of this PhD thesis was to develop computation methods and tools for mass spectrometry-based protein phosphorylation analysis, particularly validation of phosphorylation sites. In the first two studies, we developed methods for improved identification of phosphorylation sites in MALDI-MS. In the first study it was achieved through the automatic combination of spectra from multiple matrices, while in the second study, an optimized protocol for sample loading and washing conditions was suggested. In the third study, we proposed and evaluated the hypothesis that in ESI-MS, tandem CID and HCD spectra of phosphopeptides can be accurately predicted and used in spectral library searching. This novel strategy for phosphosite validation and identification offered accuracy that outperformed the other currently existing popular methods and proved applicable to complex biological samples. And finally, we significantly improved the performance of our command-line prototype tool, added graphical user interface, and options for customizable simulation parameters and filtering of selected spectra, peptides or proteins. The new software, SimPhospho, is open-source and can be easily integrated in a phosphoproteomics data analysis workflow. Together, these bioinformatics methods and tools enable confident phosphosite assignment and improve reliable phosphoproteome identification and reportin

NASA space station automation: AI-based technology review

Research and Development projects in automation for the Space Station are discussed. Artificial Intelligence (AI) based automation technologies are planned to enhance crew safety through reduced need for EVA, increase crew productivity through the reduction of routine operations, increase space station autonomy, and augment space station capability through the use of teleoperation and robotics. AI technology will also be developed for the servicing of satellites at the Space Station, system monitoring and diagnosis, space manufacturing, and the assembly of large space structures