Process Mining Handbook

This is an open access book. This book comprises all the single courses given as part of the First Summer School on Process Mining, PMSS 2022, which was held in Aachen, Germany, during July 4-8, 2022. This volume contains 17 chapters organized into the following topical sections: Introduction; process discovery; conformance checking; data preprocessing; process enhancement and monitoring; assorted process mining topics; industrial perspective and applications; and closing

IST Austria Thesis

This dissertation concerns the automatic verification of probabilistic systems and programs with arrays by statistical and logical methods. Although statistical and logical methods are different in nature, we show that they can be successfully combined for system analysis. In the first part of the dissertation we present a new statistical algorithm for the verification of probabilistic systems with respect to unbounded properties, including linear temporal logic. Our algorithm often performs faster than the previous approaches, and at the same time requires less information about the system. In addition, our method can be generalized to unbounded quantitative properties such as mean-payoff bounds. In the second part, we introduce two techniques for comparing probabilistic systems. Probabilistic systems are typically compared using the notion of equivalence, which requires the systems to have the equal probability of all behaviors. However, this notion is often too strict, since probabilities are typically only empirically estimated, and any imprecision may break the relation between processes. On the one hand, we propose to replace the Boolean notion of equivalence by a quantitative distance of similarity. For this purpose, we introduce a statistical framework for estimating distances between Markov chains based on their simulation runs, and we investigate which distances can be approximated in our framework. On the other hand, we propose to compare systems with respect to a new qualitative logic, which expresses that behaviors occur with probability one or a positive probability. This qualitative analysis is robust with respect to modeling errors and applicable to many domains. In the last part, we present a new quantifier-free logic for integer arrays, which allows us to express counting. Counting properties are prevalent in array-manipulating programs, however they cannot be expressed in the quantified fragments of the theory of arrays. We present a decision procedure for our logic, and provide several complexity results

Energy efficient hardware acceleration of multimedia processing tools

The world of mobile devices is experiencing an ongoing trend of feature enhancement and generalpurpose multimedia platform convergence. This trend poses many grand challenges, the most pressing being their limited battery life as a consequence of delivering computationally demanding features. The envisaged mobile application features can be considered to be accelerated by a set of underpinning hardware blocks Based on the survey that this thesis presents on modem video compression standards and their associated enabling technologies, it is concluded that tight energy and throughput constraints can still be effectively tackled at algorithmic level in order to design re-usable optimised hardware acceleration cores. To prove these conclusions, the work m this thesis is focused on two of the basic enabling technologies that support mobile video applications, namely the Shape Adaptive Discrete Cosine Transform (SA-DCT) and its inverse, the SA-IDCT. The hardware architectures presented in this work have been designed with energy efficiency in mind. This goal is achieved by employing high level techniques such as redundant computation elimination, parallelism and low switching computation structures. Both architectures compare favourably against the relevant pnor art in the literature. The SA-DCT/IDCT technologies are instances of a more general computation - namely, both are Constant Matrix Multiplication (CMM) operations. Thus, this thesis also proposes an algorithm for the efficient hardware design of any general CMM-based enabling technology. The proposed algorithm leverages the effective solution search capability of genetic programming. A bonus feature of the proposed modelling approach is that it is further amenable to hardware acceleration. Another bonus feature is an early exit mechanism that achieves large search space reductions .Results show an improvement on state of the art algorithms with future potential for even greater savings

Computational design of orthogonal microRNAs for synthetic biology

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.Upcoming applications of synthetic biology will require access to a wide array of robust genetic components (parts). The logic of a genetic system is encoded with regulatory elements such as pairs of transcription factors:promoters, miRNAs:target sites, or ribozymes:aptamers among others. Due to a relatively simple form and mode of operation of miRNAs, it is possible to design their synthetic variants. Out of all possible miRNA sequences the ones chosen should perform efficiently and should avoid cross-talk with both the host system circuits and within the imported synthetic ones. In this work, a computational method involving a series of heuristics is developed that can be used to design ensembles of such sequences depending on the host transcriptome. As an example, an ensemble of eight such miRNA sequences is produced using this method for use in a human host. Those have then been validated experimentally against the above-mentioned requirements by transfection into HEK 293 cells and flow cytometry measurements of fluorescent markers. The produced sequences are available for use from pENTR vectors of the Gateway cloning system. The required computations were facilitated by a modern cluster computing system—Kaichu—especially developed for this project, but fit for general purpose use and available under an open-source license.EPSR

Weirton Steel Corporation logistics and integrated scheduling. Final report

In order to remain competitive in the changing steel market, US steel producers restructured by taking on foreign and domestic partners, closing facilities and/or trimming work forces, and modernizing their steel making facilities. However, very little was done to develop production management technology to complement these changes. The Logistics and Integrated Scheduling program (LIS) was undertaken to address this issue. LIS is an information management system that delivers better customer service, better quality materials, and a just-in-time delivery system. It involves three major components: (1) material marking and sensing: advanced R&D applied to determining cost effective, feasible solutions to passive inventory; (2) material inventory and tracking: advanced technology applied to managing inventory movement; (3) planning and scheduling: beginning with annual production plans, order management, and operational constraints, the ability to build integrated schedules capable of pull through and push through scheduling for various plant capability levels and location configurations with rapid turnaround capability. LIS provides accurate, automated tracking of material flows throughout the mill, the collection and analysis of production data, and automated schedule optimization

Identification of genetic markers associated with growth and morphology quality in senegalese sole (solea senegalensis) to boost aquaculture production

The Senegalese sole (Solea senegalensis) is one of the most valuable flatfish in aquaculture in Southern Europe and although the production has grown exponentially in the last decade, reproduction success, health status, and the improvement of growth rates and morphology quality still remain as important limitations for industrial exploitation. The development of breeding programs is a fundamental tool to solve these problems but requires estimate genetic components of economically valuable traits such as those growth and morphology related under industrial conditions. By other side, the advances in genomics provide new highly powerful analysis tools to determine more accurately genetic components productive traits. In this thesis, new genomic tools and molecular markers as well as the genetic components of growth and morphology quality traits have been developed in sole. For this purpose, firstly, a highdensity SNP genetic map and a de novo sole genome assembly were generated. Later, genetic and physical maps were anchored and integrated into 21 linkage groups (SseLGs) corresponding to the expected number of chromosomes of this species. Genetic map was bigger in female than male (1.49) observing also a different recombination rate landscape between sexes. The integrated physical map obtained was used for an association study to identify sex-linked markers. Seven families were analyzed using ddRAD and 30 significant sex-associated SNP markers located onto SseLG18 were identified. Searching for candidate genes for sex determination identified the follicle stimulating hormone receptor (fshr) that it was located within a hot recombination region although with an incomplete penetrance. In addition to SNP markers, genome information was used for searching and identifying SSR markers. Hence, 108 new SSR markers distributed throughout the genome were identified. They were structured in 13 PCR Multiplex assays (with up to 10‐plex) and the amplification conditions were optimized and validated with a high‐quality score. A subset of 40 highly polymorphic markers were selected to optimize four supermultiplex PCR Multiplex assays (8-11 SSRs per assay) were designed for use in pedigree analysis. Moreover, a new integrated genetic map with 229 SSRs distributed in 21 SseLGs was created by in silico genomic analysis. Both maps generated in this thesis were used to carry out evolutive genome studies in flatfish to identify lineage-specific Robertsonian fusions and several other rearrangements that explain changes in chromosome number in the karyotype of Pleuronectiformes.To investigate the genetic components of growth and morphology-related traits, estimates for different variables were determine before on-growing (400 days) and at harvest (800 days). Growth-related traits such as body weight (W), standard length (SL), width (W) and body area (A) showed high heritabilities (ranging from 0.568 to 0.609 at 400 d and from 0.424 to 0.500 at 800 d) with very high genetic correlations (>0.94) at both ages. With respect to morphology quality traits, six quality predictors including ellipticity (E), body height at the pectoral fin base (BHP), body maximum height (BMH) and caudal peduncle height (CPH) and two ratios (BMH/BHP and BMH/CPH) were evaluated. Results showed high heritabilities (0.463-0.774) for E, BHP, BMH and CPH which were higher at 400 d than 800 d. In contrast, the BMH/BHP and BMH/CPH ratios showed low-moderate heritabilities (0.144-0.306). High positive correlations (>0.95) were found between growth traits and the three heights, which decreased with age. In contrast, ellipticity showed negative and medium-high genetic correlations with growth traits and heights, indicating that fish selected for larger size will also be less elliptical. Finally, an association study to find genetic markers linked to growth traits was carried out. A low-density DNA chip was designed and validated for 49 SNPs distributed in 17 SseLGs. The analysis of fast and slow-growing families identified two significant markers within the general transcription factor 3C polypeptide 4 and the mitochondrial fission process protein 1. All these results provide powerful tools for genomic analysis as well as genetic highly valuable information to design genetic breeding programs in Senegalese sole to optimize to boost the industrial production in aquaculture

Structure discovery techniques for circuit design and process model visualization

Graphs are one of the most used abstractions in many knowledge fields because of the easy and flexibility by which graphs can represent relationships between objects. The pervasiveness of graphs in many disciplines means that huge amounts of data are available in graph form, allowing many opportunities for the extraction of useful structure from these graphs in order to produce insight into the data. In this thesis we introduce a series of techniques to resolve well-known challenges in the areas of digital circuit design and process mining. The underlying idea that ties all the approaches together is discovering structures in graphs. We show how many problems of practical importance in these areas can be solved utilizing both common and novel structure mining approaches. In the area of digital circuit design, this thesis proposes automatically discovering frequent, repetitive structures in a circuit netlist in order to improve the quality of physical planning. These structures can be used during floorplanning to produce regular designs, which are known to be highly efficient and economical. At the same time, detecting these repeating structures can exponentially reduce the total design time. The second focus of this thesis is in the area of the visualization of process models. Process mining is a recent area of research which centers on studying the behavior of real-life systems and their interactions with the environment. Complicated process models, however, hamper this goal. By discovering the important structures in these models, we propose a series of methods that can derive visualization-friendly process models with minimal loss in accuracy. In addition, and combining the areas of circuit design and process mining, this thesis opens the area of specification mining in asynchronous circuits. Instead of the usual design flow, which involves synthesizing circuits from specifications, our proposal discovers specifications from implemented circuits. This area allows for many opportunities for verification and re-synthesis of asynchronous circuits. The proposed methods have been tested using real-life benchmarks, and the quality of the results compared to the state-of-the-art.Els grafs són una de les representacions abstractes més comuns en molts camps de recerca, gràcies a la facilitat i flexibilitat amb la que poden representar relacions entre objectes. Aquesta popularitat fa que una gran quantitat de dades es puguin trobar en forma de graf, i obre moltes oportunitats per a extreure estructures d'aquest grafs, útils per tal de donar una intuïció millor de les dades subjacents. En aquesta tesi introduïm una sèrie de tècniques per resoldre reptes habitualment trobats en les àrees de disseny de circuits digitals i mineria de processos industrials. La idea comú sota tots els mètodes proposats es descobrir automàticament estructures en grafs. En la tesi es mostra que molts problemes trobats a la pràctica en aquestes àrees poden ser resolts utilitzant nous mètodes de descobriment d'estructures. En l'àrea de disseny de circuits, proposem descobrir, automàticament, estructures freqüents i repetitives en les definicions del circuit per tal de millorar la qualitat de les etapes posteriors de planificació física. Les estructures descobertes poden fer-se servir durant la planificació per produir dissenys regulars, que son molt més econòmics d'implementar. Al mateix temps, la descoberta i ús d'aquestes estructures pot reduir exponencialment el temps total de disseny. El segon punt focal d'aquesta tesi és en l'àrea de la visualització de models de processos industrials. La mineria de processos industrials es un tema jove de recerca que es centra en estudiar el comportament de sistemes reals i les interaccions d'aquests sistemes amb l'entorn. No obstant, quan d'aquest anàlisi s'obtenen models massa complexos visualment, l'estudi n'és problemàtic. Proposem una sèrie de mètodes que, gràcies al descobriment automàtic de les estructures més importants, poden generar models molt més fàcils de visualitzar que encara descriuen el comportament del sistema amb gran precisió. Combinant les àrees de disseny de circuits i mineria de processos, aquesta tesi també obre un nou tema de recerca: la mineria d'especificacions per circuits asíncrons. En l'estil de disseny asíncron habitual, sintetitzadors automàtics generen circuits a partir de les especificacions. En aquesta tesi proposem el pas invers: descobrir automàticament les especificacions de circuits ja implementats. Així, creem noves oportunitats per a la verificació i la re-síntesi de circuits asíncrons. Els mètodes proposats en aquesta tesi s'han validat fent servir dades obtingudes d'aplicacions pràctiques, i en comparem els resultats amb els mètodes existents