Dynamic Control of Explore/Exploit Trade-Off In Bayesian Optimization

Bayesian optimization offers the possibility of optimizing black-box operations not accessible through traditional techniques. The success of Bayesian optimization methods such as Expected Improvement (EI) are significantly affected by the degree of trade-off between exploration and exploitation. Too much exploration can lead to inefficient optimization protocols, whilst too much exploitation leaves the protocol open to strong initial biases, and a high chance of getting stuck in a local minimum. Typically, a constant margin is used to control this trade-off, which results in yet another hyper-parameter to be optimized. We propose contextual improvement as a simple, yet effective heuristic to counter this - achieving a one-shot optimization strategy. Our proposed heuristic can be swiftly calculated and improves both the speed and robustness of discovery of optimal solutions. We demonstrate its effectiveness on both synthetic and real world problems and explore the unaccounted for uncertainty in the pre-determination of search hyperparameters controlling explore-exploit trade-off.Comment: Accepted for publication in the proceedings of 2018 Computing Conferenc

Carmen: Software Component Model Checker

International audienceThe challenge of model checking of isolated software components becomes more and more relevant with the boom of component-oriented technologies [20]. An important issue here is how to verify an open model representing an isolated software component (also referred as the missing environment problem in [17]). In this paper, we propose on-the-fly simulation of the component environment to address the issue. We employ behavior protocols [18] and a system coordinating two model checkers: Java PathFinder [4] and BPChecker [15]. This approach allows us to enclose the model represent- ing the behavior of a given component and consequently to exhaustively verify the model. Our solution was implemented as the Carmen tool [1]. We demonstrate scalability of our approach on real-life examples and show that, in comparison with the COMBAT model checker [17], we bring better performance, and also exhaustive and correct verification

Expressiveness modulo Bisimilarity of Regular Expressions with Parallel Composition (Extended Abstract)

The languages accepted by finite automata are precisely the languages denoted by regular expressions. In contrast, finite automata may exhibit behaviours that cannot be described by regular expressions up to bisimilarity. In this paper, we consider extensions of the theory of regular expressions with various forms of parallel composition and study the effect on expressiveness. First we prove that adding pure interleaving to the theory of regular expressions strictly increases its expressiveness up to bisimilarity. Then, we prove that replacing the operation for pure interleaving by ACP-style parallel composition gives a further increase in expressiveness. Finally, we prove that the theory of regular expressions with ACP-style parallel composition and encapsulation is expressive enough to express all finite automata up to bisimilarity. Our results extend the expressiveness results obtained by Bergstra, Bethke and Ponse for process algebras with (the binary variant of) Kleene's star operation.Comment: In Proceedings EXPRESS'10, arXiv:1011.601

Cyclone resilient landscape : the case of Vatomandry, Madagascar

Abstract: Madagascar, one of the poorest countries in the world, has to deal with cyclones every year. The impact of a cyclone can be devastating, leaving areas with houses damaged, floods and damaged crops. The aftermath has an even greater impact.The floods increase the number of people affected by water-borne and related diseases. The NGO CARE, the audience for this thesis, is working with their Disaster Risk Reduction (DRR) program in Madagascar to diminish these effects and to return inhabitants to their original standard of living. In this thesis we note that, within the DRR program of CARE, the landscape-based design approach,a method commonly used in the field of landscape architecture, has not yet been integrated into this program. An integral approach could, however, improve resiliency and the standard of living. The research question relating to this statement is: What measures related to the landscape-based design approach are needed to establish resiliency in a disaster-prone developing region? The measures should relate to CARE’s methods and to physical activities implementable by the inhabitants of Vatomandry, which is the case study for this thesis.To answer this question, different methods have been used and executed, partly in the Netherlands and partly in Madagascar. Landscape analysis was performed and participatory workshops were organised. By means of the landscape analysis, a full understanding of the landscape processes of the study area was generated. The participatory workshops were important as they provided this research with local knowledge; even more relevant was establishing ownership of the project on the part of the inhabitants. The participatory workshops entailed the proven Green Towns workshop of Duchhart and a photomontage workshop.The Green Towns workshop proved insufficient on its own to proceed towards taking active steps for improvement of the environment; therefore, a photomontage workshop was also organised. This then led to an Action Day, in which one of the measures was carried out. Achieving this first measure will hopefully have a positive effect in terms of carrying out the other measures and interventions suggested in this thesis. The data gathered in Madagascar were analysed and ordered in the Netherlands; they were then used as input for the design aimed at enhancing resiliency. The results from the participative workshops were translated from short-term solutions for the benefit of individuals to a long-term landscape plan for the benefit of the community. The design is not a blueprint design. The landscape plan provides recommendations for environmental improvements in Vatomandry, along with design prinxvi ciples generally applicable for similar cities along the east coast. The interventions include a drainage system against floods, shelterbelts, sand fences, and  urifying wetlands and vegetation for shelter, health and income. The final result and answer to the research question can be found in several measures – methodological and physical – aimed at improving the resiliency of the landscape against tropical cyclones. The overall methodology is intended to be replicable for similar cities that also suffer from natural disasters.Résumé: Chaque année, Madagascar, un des pays les plus pauvres du monde, doit faire face à des cyclones. L’impact d’un cyclone peut être dévastateur, laissant des régions avec des maisons détruites, des inondations et les cultures endommagés.La suite a un effet encore plus important. Les inondations augmentent le nombre des personnes qui sont touchées par des maladies portées par les eaux et des maladies connexes. L’ONG CARE, assistance de cette thèse, travaille à Madagascar pour réduire ces effets avec leur programme de Réduction des Risques de Catastrophes (DRR) et à redonner aux habitants leur niveau de vie original. Dans cette thèse nous énonçons que, dans ce programme DRR de CARE, l’approche reposant sur l’aménagement paysager (landscape-based design approach), une méthode souvent utilisée dans l’architecture paysagiste, qui n’a pas encore été intégré ici. Cette approche intégrée pourrait améliorer la résilience et le niveau de vie. La question de recherche au coeur de ce rapport cest: Quelles actions liées à l’approche reposant sur l’aménagement paysager sont nécessaires pour établir de la résilience dans une région en voie de développement enclins aux catastrophes? Les actions devraient se rapporter aux méthodes de CARE et aux actions physiques exécutable par les habitants de Vatomandry, le cas d’étude de cette thèse. Pour répondre à cette question, des méthodes différentes sont employées et exécutées, en partie aux Pays-Bas et en partie au Madagascar. L’analyse de paysage a été exécutée et des ateliers participatifs ont été organisés. Au moyen de l’analyse de paysage, une compréhension complète des processus de paysage du secteur d’étude a été produite. Les ateliers participatifs étaient importants car ils ont fourni à cette étude la connaissance locale nécessaire. Et ils ont permis aux locaux de s’approprier les mesures. Les ateliers participatifs comportent l’atelier nommé Green Towns (les villes vertes) de Duchhart, et un atelier de montage de photos. L’atelier Green Towns lui-même ne suffisait pas pour procéder à l’action pour améliorer l’environnement, donc un atelier de montage de photos a été organisé. Ceci a conduit à une Journée d’Action, où une des actions a été exécutée. L’accomplissement devrait avoir un effet positif afin d’exécuter d’autres actions et les interventions suggérées dans cette thèse. Les données recueillies en Madagascar ont été analysées et organisées aux Pays-Bas et ont été utilisées comme données pour concevoir l’augmentation de la résilience. Les résultats des ateliers participatifs ont été transformés à partir de solutions à court terme pour des avantages individuels en un plan paysagiste à long terme pour des avantages pour toute la communauté. La conception des mesures mises en place n’est pas une conception de modèle universel. Le plan d’aménagement paysager fournit des recommandations pour des améliorations environnementales de Vatomandry et des principes applicables pour des villes similaires le long de la côte est. Les interventions impliquent une canalisation contre les inondations, des brise-vent, des barrières de sable, des lagunes d’épuration et l’utilisation de la végétation comme abri, la santé et des revenus. La réponse finale à la question de recherche ce sont plusieurs actions – méthodologiques et physiques – pour atteindre la résilience améliorée du paysage contre les cyclones tropicaux. La méthodologie générale devrait être reproductible pour les villes semblables qui souffrent également des catastrophes naturelles.ASC – Publicaties niet-programma gebonde

The age of data-driven proteomics : how machine learning enables novel workflows

A lot of energy in the field of proteomics is dedicated to the application of challenging experimental workflows, which include metaproteomics, proteogenomics, data independent acquisition (DIA), non-specific proteolysis, immunopeptidomics, and open modification searches. These workflows are all challenging because of ambiguity in the identification stage; they either expand the search space and thus increase the ambiguity of identifications, or, in the case of DIA, they generate data that is inherently more ambiguous. In this context, machine learning-based predictive models are now generating considerable excitement in the field of proteomics because these predictive models hold great potential to drastically reduce the ambiguity in the identification process of the above-mentioned workflows. Indeed, the field has already produced classical machine learning and deep learning models to predict almost every aspect of a liquid chromatography-mass spectrometry (LC-MS) experiment. Yet despite all the excitement, thorough integration of predictive models in these challenging LC-MS workflows is still limited, and further improvements to the modeling and validation procedures can still be made. In this viewpoint we therefore point out highly promising recent machine learning developments in proteomics, alongside some of the remaining challenges

On CSP and the Algebraic Theory of Effects

We consider CSP from the point of view of the algebraic theory of effects, which classifies operations as effect constructors or effect deconstructors; it also provides a link with functional programming, being a refinement of Moggi's seminal monadic point of view. There is a natural algebraic theory of the constructors whose free algebra functor is Moggi's monad; we illustrate this by characterising free and initial algebras in terms of two versions of the stable failures model of CSP, one more general than the other. Deconstructors are dealt with as homomorphisms to (possibly non-free) algebras. One can view CSP's action and choice operators as constructors and the rest, such as concealment and concurrency, as deconstructors. Carrying this programme out results in taking deterministic external choice as constructor rather than general external choice. However, binary deconstructors, such as the CSP concurrency operator, provide unresolved difficulties. We conclude by presenting a combination of CSP with Moggi's computational {\lambda}-calculus, in which the operators, including concurrency, are polymorphic. While the paper mainly concerns CSP, it ought to be possible to carry over similar ideas to other process calculi

Op weg naar Park Essenburg : advies aan Bewonersgroep ProGroen Rotterdam

Bewonersgroep ProGroen in Rotterdam is voor het behoud van een miskende groenstrook van circa twaalf hectare tussen de spoordijk en Essenburgsingel. Ze wil dat het gebied in de deelgemeente Delfshaven het groene en duurzame karakter behoudt en dat het in de toekomst goed bruikbaar is en blijft voor alle mensen uit de buurt en de stad. De Wetenschapswinkel ziet voor ProGroen de opgave weggelegd om aan te tonen dat de strook een waardevol groenelement is in de stad. Het park draagt bij aan de sociale cohesie: het vergroot het aantal ontmoetingsplekken in de wijk, biedt laagdrempelige aanleidingen om contact te leggen en motiveert bewoners te investeren in relaties in de buurt. Daarnaast biedt het park de wijkbewoners nieuwe mogelijkheden om in contact te komen met groen, met natuur. De eerste concrete invulling van het park is PlukTuin Essenburg RFC. Deze PlukTuin, een buurttuin, wordt aangelegd op een voormalige parkeerplaats. Opzet is dat bewoners de PlukTuin zelf aanleggen en onderhoude

A Branching Time Model of CSP

I present a branching time model of CSP that is finer than all other models of CSP proposed thus far. It is obtained by taking a semantic equivalence from the linear time - branching time spectrum, namely divergence-preserving coupled similarity, and showing that it is a congruence for the operators of CSP. This equivalence belongs to the bisimulation family of semantic equivalences, in the sense that on transition systems without internal actions it coincides with strong bisimilarity. Nevertheless, enough of the equational laws of CSP remain to obtain a complete axiomatisation for closed, recursion-free terms.Comment: Dedicated to Bill Roscoe, on the occasion of his 60th birthda

Hyperparameter Importance Across Datasets

With the advent of automated machine learning, automated hyperparameter optimization methods are by now routinely used in data mining. However, this progress is not yet matched by equal progress on automatic analyses that yield information beyond performance-optimizing hyperparameter settings. In this work, we aim to answer the following two questions: Given an algorithm, what are generally its most important hyperparameters, and what are typically good values for these? We present methodology and a framework to answer these questions based on meta-learning across many datasets. We apply this methodology using the experimental meta-data available on OpenML to determine the most important hyperparameters of support vector machines, random forests and Adaboost, and to infer priors for all their hyperparameters. The results, obtained fully automatically, provide a quantitative basis to focus efforts in both manual algorithm design and in automated hyperparameter optimization. The conducted experiments confirm that the hyperparameters selected by the proposed method are indeed the most important ones and that the obtained priors also lead to statistically significant improvements in hyperparameter optimization.Comment: \c{opyright} 2018. Copyright is held by the owner/author(s). Publication rights licensed to ACM. This is the author's version of the work. It is posted here for your personal use, not for redistribution. The definitive Version of Record was published in Proceedings of the 24th ACM SIGKDD International Conference on Knowledge Discovery & Data Minin

Soundness of Unravelings for Conditional Term Rewriting Systems via Ultra-Properties Related to Linearity

Unravelings are transformations from a conditional term rewriting system (CTRS, for short) over an original signature into an unconditional term rewriting systems (TRS, for short) over an extended signature. They are not sound w.r.t. reduction for every CTRS, while they are complete w.r.t. reduction. Here, soundness w.r.t. reduction means that every reduction sequence of the corresponding unraveled TRS, of which the initial and end terms are over the original signature, can be simulated by the reduction of the original CTRS. In this paper, we show that an optimized variant of Ohlebusch's unraveling for a deterministic CTRS is sound w.r.t. reduction if the corresponding unraveled TRS is left-linear or both right-linear and non-erasing. We also show that soundness of the variant implies that of Ohlebusch's unraveling. Finally, we show that soundness of Ohlebusch's unraveling is the weakest in soundness of the other unravelings and a transformation, proposed by Serbanuta and Rosu, for (normal) deterministic CTRSs, i.e., soundness of them respectively implies that of Ohlebusch's unraveling.Comment: 49 pages, 1 table, publication in Special Issue: Selected papers of the "22nd International Conference on Rewriting Techniques and Applications (RTA'11)