A novel computer Scrabble engine based on probability that performs at championship leve

The thesis starts by giving an introduction to the game of Scrabble, then mentions state-of-the-art computer Scrabble programs and presents some characteristics of our developed Scrabble engine Heuri. Some brief notions of Game Theory are given, along with history of some games in Artificial Intelligence; the fundamental algorithms for game playing, as well as state-of-the-art engines and the algorithms used by them, are presented. Basic elements of Scrabble, such as the Scrabble rules and the letter distribution, are given. Some history and state-of-the-art of Computer Scrabble are commented. For instance, the generation methods of valid moves based on the data structure DAWG (Directed Acyclic Word Graph) and also the variant GADDAG are recalled. These methods are used by the state-of-the-art Scrabble engines Quackle and Maven. Then, the contributions of this thesis are presented. A Spanish lexicon for playing Scrabble has been built that is used by Heuri engines. From this construction, a detailed study and classification of Spanish irregular verbs has been provided. A novel Scrabble move generator based on anagrams has been designed and implemented, which has been shown to be faster than the GADDAG-based generator used in Quackle engine. This method is similar to the way Scrabble players look for a move, searching for anagrams and a spot to play on the board. Next, we address the evaluation of moves when playing Scrabble; the quality of your game depends on deciding what move should be played given a certain board and a rack with tiles. This decision was made initially by Heuri trying several heuristics which ended up with the construction of several engines. We give the explanation of the heuristics used in these engines, all of them based on probabilities. All these initial heuristic evaluation functions (up to six) do not use forward looking, they are static evaluators. They have shown, after testing, an increasing playing performance, which allow Heuri to beat (top-level) expert human players in Spanish, without the need of using sampling and simulation techniques. These heuristics mainly consider the possibility of achieving a bingo on the actual board, whereas Quackle used pre-calculated values (superleaves) regardless of the latter. Then, in order to improve the quality of play of Heuri even more, some additional engines are presented in which look ahead is employed. The HeuriSamp engine, which evaluates a 2-ply search, permits to obtain a defense value. The HeuriSim engine uses a 3-ply adversarial search tree; it contemplates the best first moves (according to Heuri sixth engine heuristic) from Player 1, then some replies to these moves (Player 2 moves) and then some replies to these replies (Player 1 moves). Finally, to improve these engines, opponent modeling is used; this technique makes predictions on some of the opponents' tiles based on the last play made by the opponent. We present results obtained by playing thousands of Heuri vs Heuri games, collecting important information: general statistics of Scrabble game, like a 16 point handicap of the second player, and word statistics in Spanish, like a list of the most frequently played bingos (words that use all 7 tiles of a player's rack). In addition, we present results of matches played by Heuri against top-level humans in Spanish and results obtained by massive playing of different Heuri engines against the Quackle engine in Spanish, French and English. All these match results demonstrate the championship level performance of the Heuri engines in the three languages, especially of the last developed engine that includes simulation and opponent modeling techniques. From here, conclusions of the thesis are drawn and work for the future is envisaged.La tesi comença introduint el joc del Scrabble, esmentant els programes d’ordinador de l’estat de l’art que juguen Scrabble, i presentant algunes característiques del motor de joc de Scrabble que s’ha desenvolupat anomenat Heuri. Es donen breus nocions de la Teoria de Jocs, junt amb la història d’alguns jocs en Intel·ligència Artificial; es presenten els algorismes fonamentals per jugar, així com els motors de joc de l’estat de l’art en diferents jocs i els algorismes que usen. Es comenta també la història i estat de l’art del Computer Scrabble. Es recorden els mètodes de generació de moviments vàlids basats en l’estructura de dades DAWG (Directed Acyclic Word Graph) i en la variant GADDAG, que són usats pels motors de joc de Scrabble Quackle i Maven. A continuació es presenten les contribucions de la tesi. S’ha construït un diccionari per jugar Scrabble en espanyol, el qual és usat per les diferentes versions del motor de joc Heuri. S’ha fet un estudi detallat i una classificació dels verbs irregulars en espanyol. S’ha dissenyat i implementat un nou generador de moviments de Scrabble basat en anagrames, que ha demostrat ser més ràpid que el generador basat en GADDAG usat al motor Quackle. Aquest mètode és similar a la manera en la que els jugadors de Scrabble cerquen un moviment, buscant anagrames i un lloc del tauler on col·locar-los. Seguidament, es tracta l’evacuació dels moviments quan es juga Scrabble; la qualitat del joc depèn de decidir quin moviment cal jugar donat un cert tauler i un faristol amb fitxes. En Heuri, inicialment, aquesta decisió es va prendre provant diferents heurístiques que van dur a la construcció de diversos motors. Donem l’explicació de les heurístiques usades en aquests motors, totes elles basades en probabilitats. Totes aquestes funcions d’avaluació heurística inicials (fins a sis) no miren cap endavant, fan avaluacions estàtiques. Han mostrat, després de ser provades, un rendiment creixent de nivell de joc, el que ha permès Heuri derrotar a jugadors humans experts de màxim nivell en espanyol, sense necessitat d’usar tècniques de mostreig i de simulació. Aquestes heurístiques consideren principalment la possibilitat d’aconseguir un bingo en el tauler actual, mentre que Quackle usa uns valors pre-calculats (superleaves) que no tenen en compte l’anterior. Amb l’objectiu de millorar la qualitat de joc de Heuri encara més, es presenten uns motors de joc addicionals que sí miren cap endavant. El motor HeuriSamp, que realitza una cerca 2-ply, permet obtenir un valor de defensa. El motor HeuriSim usa un arbre de cerca 3-ply; contempla els millors primers moviments (d’acord al sisè motor heurístic d’Heuri) del Jugador 1, després algunes respostes a aquests moviments (moviments del Jugador 2) i llavors algunes rèpliques a aquestes respostes (moviments del Jugador 1). Finalment, per a millorar aquests motors, es proposa usar modelatge d’oponents; aquesta tècnica realitza prediccions d’algunes de les fitxes de l’oponent basant-se en l’últim moviment jugat per aquest. Es presenten resultats obtinguts de jugar milers de partides d’Heuri contra Heuri, que recullen important informació: estadístiques generals del joc del Scrabble, com un handicap de 16 punts del segon jugador, i estadístiques de paraules en espanyol, com una llista dels bingos (paraules que usen les 7 fitxes del faristol d’un jugador) que es juguen més freqüentment. A més, es presenten resultats de partides jugades per Heuri contra jugadors humans de màxim nivell en espanyol i resultats obtinguts d'un gran nombre d’enfrontaments entre els diferents motors de joc d’Heuri contra el motor Quackle en espanyol, francès i anglès. Tots aquests resultats de partides jugades demostren el rendiment de nivell de campió dels motors d’Heuri en les tres llengües, especialment el de l’últim motor desenvolupat que inclou tècniques de de simulació i modelatge d'oponents. A partir d'aquí s'extreuen les conclusions de la tesi i es preveu treballar de cara al futur.Postprint (published version

An Algorithm to Compute the Character Access Count Distribution for Pattern Matching Algorithms

We propose a framework for the exact probabilistic analysis of window-based pattern matching algorithms, such as Boyer--Moore, Horspool, Backward DAWG Matching, Backward Oracle Matching, and more. In particular, we develop an algorithm that efficiently computes the distribution of a pattern matching algorithm's running time cost (such as the number of text character accesses) for any given pattern in a random text model. Text models range from simple uniform models to higher-order Markov models or hidden Markov models (HMMs). Furthermore, we provide an algorithm to compute the exact distribution of \emph{differences} in running time cost of two pattern matching algorithms. Methodologically, we use extensions of finite automata which we call \emph{deterministic arithmetic automata} (DAAs) and \emph{probabilistic arithmetic automata} (PAAs)~\cite{Marschall2008}. Given an algorithm, a pattern, and a text model, a PAA is constructed from which the sought distributions can be derived using dynamic programming. To our knowledge, this is the first time that substring- or suffix-based pattern matching algorithms are analyzed exactly by computing the whole distribution of running time cost. Experimentally, we compare Horspool's algorithm, Backward DAWG Matching, and Backward Oracle Matching on prototypical patterns of short length and provide statistics on the size of minimal DAAs for these computations

Melhorando a precisão do reconhecimento de texto usando técnicas baseadas em sintaxe

Orientadores: Guido Costa Souza de Araújo, Marcio Machado PereiraDissertação (mestrado) - Universidade Estadual de Campinas, Instituto de ComputaçãoResumo: Devido à grande quantidade de informações visuais disponíveis atualmente, a detecção e o reconhecimento de texto em imagens de cenas naturais começaram a ganhar importância nos últimos tempos. Seu objetivo é localizar regiões da imagem onde há texto e reconhecê-lo. Essas tarefas geralmente são divididas em duas partes: detecção de texto e reconhecimento de texto. Embora as técnicas para resolver esse problema tenham melhorado nos últimos anos, o uso excessivo de recursos de hardware e seus altos custos computacionais impactaram significativamente a execução de tais tarefas em sistemas integrados altamente restritos (por exemplo, celulares e TVs inteligentes). Embora existam métodos de detecção e reconhecimento de texto executados em tais sistemas, eles não apresentam bom desempenho quando comparados à soluções de ponta em outras plataformas de computação. Embora atualmente existam vários métodos de pós-correção que melhoram os resultados em documentos históricos digitalizados, há poucas explorações sobre o seu uso nos resultados de imagens de cenas naturais. Neste trabalho, exploramos um conjunto de métodos de pós-correção, bem como propusemos novas heuríticas para melhorar os resultados em imagens de cenas naturais, tendo como base de prototipação o software de reconhecimento de textos Tesseract. Realizamos uma análise com os principais métodos disponíveis na literatura para correção dos erros e encontramos a melhor combinação que incluiu os métodos de substituição, eliminação nos últimos caracteres e composição. Somado a isto, os resultados mostraram uma melhora quando introduzimos uma nova heurística baseada na frequência com que os possíveis resultados aparecem em bases de dados de magazines, jornais, textos de ficção, web, etc. Para localizar erros e evitar overcorrection foram consideradas diferentes restrições obtidas através do treinamento da base de dados do Tesseract. Selecionamos como melhor restrição a incerteza do melhor resultado obtido pelo Tesseract. Os experimentos foram realizados com sete banco de dados usados em sites de competição na área, considerando tanto banco de dados para desafio em reconhecimento de texto e aqueles com o desafio de detecção e reconhecimento de texto. Em todos os bancos de dados, tanto nos dados de treinamento como de testes, os resultados do Tesseract com o método proposto de pós-correção melhorou consideravelmente em comparação com os resultados obtidos somente com o TesseractAbstract: Due to a large amount of visual information available today, Text Detection and Recognition in scene images have begun to receive an increasing importance. The goal of this task is to locate regions of the image where there is text and recognize them. Such tasks are typically divided into two parts: Text Detection and Text Recognition. Although the techniques to solve this problem have improved in recent years, the excessive usage of hardware resources and its corresponding high computational costs have considerably impacted the execution of such tasks in highly constrained embedded systems (e.g., cellphones and smart TVs). Although there are Text Detection and Recognition methods that run in such systems they do not have good performance when compared to state-of-the-art solutions in other computing platforms. Although there are currently various post-correction methods to improve the results of scanned documents, there is a little effort in applying them on scene images. In this work, we explored a set of post-correction methods, as well as proposed new heuristics to improve the results in scene images, using the Tesseract text recognition software as a prototyping base. We performed an analysis with the main methods available in the literature to correct errors and found the best combination that included the methods of substitution, elimination in the last characters, and compounder. In addition, results showed an improvement when we introduced a new heuristic based on the frequency with which the possible results appear in the frequency databases for categories such as magazines, newspapers, fiction texts, web, etc. In order to locate errors and avoid overcorrection, different restrictions were considered through Tesseract with the training database. We selected as the best restriction the certainty of the best result obtained by Tesseract. The experiments were carried out with seven databases used in Text Recognition and Text Detection/Recognition competitions. In all databases, for both training and testing, the results of Tesseract with the proposed post-correction method considerably improved when compared to the results obtained only with TesseractMestradoCiência da ComputaçãoMestra em Ciência da Computação4716-1488887.335287/2019-00, 1774549FuncampCAPE

Infobiotics : computer-aided synthetic systems biology

Until very recently Systems Biology has, despite its stated goals, been too reductive in terms of the models being constructed and the methods used have been, on the one hand, unsuited for large scale adoption or integration of knowledge across scales, and on the other hand, too fragmented. The thesis of this dissertation is that better computational languages and seamlessly integrated tools are required by systems and synthetic biologists to enable them to meet the significant challenges involved in understanding life as it is, and by designing, modelling and manufacturing novel organisms, to understand life as it could be. We call this goal, where everything necessary to conduct model-driven investigations of cellular circuitry and emergent effects in populations of cells is available without significant context-switching, “one-pot” in silico synthetic systems biology in analogy to “one-pot” chemistry and “one-pot” biology. Our strategy is to increase the understandability and reusability of models and experiments, thereby avoiding unnecessary duplication of effort, with practical gains in the efficiency of delivering usable prototype models and systems. Key to this endeavour are graphical interfaces that assists novice users by hiding complexity of the underlying tools and limiting choices to only what is appropriate and useful, thus ensuring that the results of in silico experiments are consistent, comparable and reproducible. This dissertation describes the conception, software engineering and use of two novel software platforms for systems and synthetic biology: the Infobiotics Workbench for modelling, in silico experimentation and analysis of multi-cellular biological systems; and DNA Library Designer with the DNALD language for the compact programmatic specification of combinatorial DNA libraries, as the first stage of a DNA synthesis pipeline, enabling methodical exploration biological problem spaces. Infobiotics models are formalised as Lattice Population P systems, a novel framework for the specification of spatially-discrete and multi-compartmental rule-based models, imbued with a stochastic execution semantics. This framework was developed to meet the needs of real systems biology problems: hormone transport and signalling in the root of Arabidopsis thaliana, and quorum sensing in the pathogenic bacterium Pseudomonas aeruginosa. Our tools have also been used to prototype a novel synthetic biological system for pattern formation, that has been successfully implemented in vitro. Taken together these novel software platforms provide a complete toolchain, from design to wet-lab implementation, of synthetic biological circuits, enabling a step change in the scale of biological investigations that is orders of magnitude greater than could previously be performed in one in silico “pot”

Benchmarking RDF Storage Engines

In this deliverable, we present version V1.0 of SRBench, the first benchmark for Streaming RDF engines, designed in the context of Task 1.4 of PlanetData, completely based on real-world datasets. With the increasing problem of too much streaming data but not enough knowledge, researchers have set out for solutions in which Semantic Web technologies are adapted and extended for the publishing, sharing, analysing and understanding of such data. Various approaches are emerging. To help researchers and users to compare streaming RDF engines in a standardised application scenario, we propose SRBench, with which one can assess the abilities of a streaming RDF engine to cope with a broad range of use cases typically encountered in real-world scenarios. We offer a set of queries that cover the major aspects of streaming RDF engines, ranging from simple pattern matching queries to queries with complex reasoning tasks. To give a first baseline and illustrate the state of the art, we show results obtained from implementing SRBench using the SPARQLStream query-processing engine developed by UPM

Infobiotics : computer-aided synthetic systems biology

Until very recently Systems Biology has, despite its stated goals, been too reductive in terms of the models being constructed and the methods used have been, on the one hand, unsuited for large scale adoption or integration of knowledge across scales, and on the other hand, too fragmented. The thesis of this dissertation is that better computational languages and seamlessly integrated tools are required by systems and synthetic biologists to enable them to meet the significant challenges involved in understanding life as it is, and by designing, modelling and manufacturing novel organisms, to understand life as it could be. We call this goal, where everything necessary to conduct model-driven investigations of cellular circuitry and emergent effects in populations of cells is available without significant context-switching, “one-pot” in silico synthetic systems biology in analogy to “one-pot” chemistry and “one-pot” biology. Our strategy is to increase the understandability and reusability of models and experiments, thereby avoiding unnecessary duplication of effort, with practical gains in the efficiency of delivering usable prototype models and systems. Key to this endeavour are graphical interfaces that assists novice users by hiding complexity of the underlying tools and limiting choices to only what is appropriate and useful, thus ensuring that the results of in silico experiments are consistent, comparable and reproducible. This dissertation describes the conception, software engineering and use of two novel software platforms for systems and synthetic biology: the Infobiotics Workbench for modelling, in silico experimentation and analysis of multi-cellular biological systems; and DNA Library Designer with the DNALD language for the compact programmatic specification of combinatorial DNA libraries, as the first stage of a DNA synthesis pipeline, enabling methodical exploration biological problem spaces. Infobiotics models are formalised as Lattice Population P systems, a novel framework for the specification of spatially-discrete and multi-compartmental rule-based models, imbued with a stochastic execution semantics. This framework was developed to meet the needs of real systems biology problems: hormone transport and signalling in the root of Arabidopsis thaliana, and quorum sensing in the pathogenic bacterium Pseudomonas aeruginosa. Our tools have also been used to prototype a novel synthetic biological system for pattern formation, that has been successfully implemented in vitro. Taken together these novel software platforms provide a complete toolchain, from design to wet-lab implementation, of synthetic biological circuits, enabling a step change in the scale of biological investigations that is orders of magnitude greater than could previously be performed in one in silico “pot”

Development of a read mapping analysis software and computational pan genome analysis of 20 Pseudomonas aeruginosa strains

Hilker R. Development of a read mapping analysis software and computational pan genome analysis of 20 Pseudomonas aeruginosa strains. Bielefeld: Bielefeld University; 2015.In times of multi-resistant pathogenic bacteria, their detailed study is of utmost importance. Their comparative analysis can even aid the emerging field of personalized medicine by enabling optimized treatment depending on the presence of virulence factors and antibiotic resistances in the infection concerned. The weaknesses and functionality of these pathogenic bacteria can be investigated using modern computer science and novel sequencing technologies. One of these methods is the bioinformatics evaluation of high-throughput sequencing data. A pathogenic bacterium posing severe health care issues is the ubiquitous Pseudomonas aeruginosa. It is involved in a wide range of infections mainly affecting the pulmonary or urinary tract, open wounds and burns. The prevalence of chronic obstructive pulmonary disease cases with P. aeruginosa in Germany alone is ~600,000 per year. Within the framework of this dissertation, computational comparative genomics experiments were conducted with a panel of 20 of the most abundant Pseudomonas aeruginosa strains. 15 of these strains were isolated from clinical cases, while the remaining 5 were strains without a known infection history isolated from the environment. This division was chosen to enable direct comparison of the pathogenic potential of clinical and environmental strains and identification of their possible characteristic differences. When designing the bioinformatics experiments and searching for an efficient visualization and automatic analysis platform for read alignment (mapping) data, it became evident that no adequate solution was available that included all required functionalities. On these grounds, the decision was made to define two main subjects for this dissertation. Besides the P. aeruginosa pan genome analysis, a novel read mapping visualization and analysis software was developed and published in the journal Bioinformatics. This software - ReadXplorer - is partly based upon a prototype, which was developed during a preceding master's thesis at the Center for Biotechnology of the Bielefeld University under the name VAMP. The software was developed into a comprehensive user-friendly platform augmented with several newly developed and implemented automatic bioinformatics read mapping analyses. Two examples of these are the transcription start site detection and the single nucleotide polymorphism detection. Moreover, new intuitive visualizations were added to the existent ones and existing visualizations were greatly enhanced. ReadXplorer is designed to support not only DNA-seq data as accrued in the P. aeruginosa experiments, but also any kind of standard read mapping data as obtained from RNA-seq or ChIP-seq experiments. The data management was designed to comply with the latest performance and efficiency needs emerging from the large next generation sequencing data sets. Finally, ReadXplorer was empowered to deal with eukaryotic read mapping data as well. Amongst other software, ReadXplorer was then used to analyze different comparative genomics aspects of P. aeruginosa and to draw conclusions regarding the development of their pathogenicity. The list of conducted experiments includes phylogeny and gene set determination, analysis of regions of genomic plasticity and identification of single nucleotide polymorphisms. The achieved results were published in the journal Environmental Biology