Proto-Plasm: parallel language for adaptive and scalable modelling of biosystems

This paper discusses the design goals and the first developments of Proto-Plasm, a novel computational environment to produce libraries of executable, combinable and customizable computer models of natural and synthetic biosystems, aiming to provide a supporting framework for predictive understanding of structure and behaviour through multiscale geometric modelling and multiphysics simulations. Admittedly, the Proto-Plasm platform is still in its infancy. Its computational framework—language, model library, integrated development environment and parallel engine—intends to provide patient-specific computational modelling and simulation of organs and biosystem, exploiting novel functionalities resulting from the symbolic combination of parametrized models of parts at various scales. Proto-Plasm may define the model equations, but it is currently focused on the symbolic description of model geometry and on the parallel support of simulations. Conversely, CellML and SBML could be viewed as defining the behavioural functions (the model equations) to be used within a Proto-Plasm program. Here we exemplify the basic functionalities of Proto-Plasm, by constructing a schematic heart model. We also discuss multiscale issues with reference to the geometric and physical modelling of neuromuscular junctions

Deep Understanding of Technical Documents : Automated Generation of Pseudocode from Digital Diagrams & Analysis/Synthesis of Mathematical Formulas

The technical document is an entity that consists of several essential and interconnected parts, often referred to as modalities. Despite the extensive attention that certain parts have already received, per say the textual information, there are several aspects that severely under researched. Two such modalities are the utility of diagram images and the deep automated understanding of mathematical formulas. Inspired by existing holistic approaches to the deep understanding of technical documents, we develop a novel formal scheme for the modelling of digital diagram images. This extends to a generative framework that allows for the creation of artificial images and their annotation. We contribute on the field with the creation of a novel synthetic dataset and its generation mechanism. We propose the conversion of the pseudocode generation problem to an image captioning task and provide a family of techniques based on adaptive image partitioning. We address the mathematical formulas’ semantic understanding by conducting an evaluating survey on the field, published in May 2021. We then propose a formal synthesis framework that utilized formula graphs as metadata, reaching for novel valuable formulas. The synthesis framework is validated by a deep geometric learning mechanism, that outsources formula data to simulate the missing a priori knowledge. We close with the proof of concept, the description of the overall pipeline and our future aims

Dagstuhl News January - December 2002

"Dagstuhl News" is a publication edited especially for the members of the Foundation "Informatikzentrum Schloss Dagstuhl" to thank them for their support. The News give a summary of the scientific work being done in Dagstuhl. Each Dagstuhl Seminar is presented by a small abstract describing the contents and scientific highlights of the seminar as well as the perspectives or challenges of the research topic

Making Presentation Math Computable

This Open-Access-book addresses the issue of translating mathematical expressions from LaTeX to the syntax of Computer Algebra Systems (CAS). Over the past decades, especially in the domain of Sciences, Technology, Engineering, and Mathematics (STEM), LaTeX has become the de-facto standard to typeset mathematical formulae in publications. Since scientists are generally required to publish their work, LaTeX has become an integral part of today's publishing workflow. On the other hand, modern research increasingly relies on CAS to simplify, manipulate, compute, and visualize mathematics. However, existing LaTeX import functions in CAS are limited to simple arithmetic expressions and are, therefore, insufficient for most use cases. Consequently, the workflow of experimenting and publishing in the Sciences often includes time-consuming and error-prone manual conversions between presentational LaTeX and computational CAS formats. To address the lack of a reliable and comprehensive translation tool between LaTeX and CAS, this thesis makes the following three contributions. First, it provides an approach to semantically enhance LaTeX expressions with sufficient semantic information for translations into CAS syntaxes. Second, it demonstrates the first context-aware LaTeX to CAS translation framework LaCASt. Third, the thesis provides a novel approach to evaluate the performance for LaTeX to CAS translations on large-scaled datasets with an automatic verification of equations in digital mathematical libraries. This is an open access book

Making Presentation Math Computable

This Open-Access-book addresses the issue of translating mathematical expressions from LaTeX to the syntax of Computer Algebra Systems (CAS). Over the past decades, especially in the domain of Sciences, Technology, Engineering, and Mathematics (STEM), LaTeX has become the de-facto standard to typeset mathematical formulae in publications. Since scientists are generally required to publish their work, LaTeX has become an integral part of today's publishing workflow. On the other hand, modern research increasingly relies on CAS to simplify, manipulate, compute, and visualize mathematics. However, existing LaTeX import functions in CAS are limited to simple arithmetic expressions and are, therefore, insufficient for most use cases. Consequently, the workflow of experimenting and publishing in the Sciences often includes time-consuming and error-prone manual conversions between presentational LaTeX and computational CAS formats. To address the lack of a reliable and comprehensive translation tool between LaTeX and CAS, this thesis makes the following three contributions. First, it provides an approach to semantically enhance LaTeX expressions with sufficient semantic information for translations into CAS syntaxes. Second, it demonstrates the first context-aware LaTeX to CAS translation framework LaCASt. Third, the thesis provides a novel approach to evaluate the performance for LaTeX to CAS translations on large-scaled datasets with an automatic verification of equations in digital mathematical libraries. This is an open access book

ROOT - A C++ Framework for Petabyte Data Storage, Statistical Analysis and Visualization

ROOT is an object-oriented C++ framework conceived in the high-energy physics (HEP) community, designed for storing and analyzing petabytes of data in an efficient way. Any instance of a C++ class can be stored into a ROOT file in a machine-independent compressed binary format. In ROOT the TTree object container is optimized for statistical data analysis over very large data sets by using vertical data storage techniques. These containers can span a large number of files on local disks, the web, or a number of different shared file systems. In order to analyze this data, the user can chose out of a wide set of mathematical and statistical functions, including linear algebra classes, numerical algorithms such as integration and minimization, and various methods for performing regression analysis (fitting). In particular, ROOT offers packages for complex data modeling and fitting, as well as multivariate classification based on machine learning techniques. A central piece in these analysis tools are the histogram classes which provide binning of one- and multi-dimensional data. Results can be saved in high-quality graphical formats like Postscript and PDF or in bitmap formats like JPG or GIF. The result can also be stored into ROOT macros that allow a full recreation and rework of the graphics. Users typically create their analysis macros step by step, making use of the interactive C++ interpreter CINT, while running over small data samples. Once the development is finished, they can run these macros at full compiled speed over large data sets, using on-the-fly compilation, or by creating a stand-alone batch program. Finally, if processing farms are available, the user can reduce the execution time of intrinsically parallel tasks - e.g. data mining in HEP - by using PROOF, which will take care of optimally distributing the work over the available resources in a transparent way

Dagstuhl News January - December 2001

"Dagstuhl News" is a publication edited especially for the members of the Foundation "Informatikzentrum Schloss Dagstuhl" to thank them for their support. The News give a summary of the scientific work being done in Dagstuhl. Each Dagstuhl Seminar is presented by a small abstract describing the contents and scientific highlights of the seminar as well as the perspectives or challenges of the research topic

Visual Techniques for Geological Fieldwork Using Mobile Devices

Visual techniques in general and 3D visualisation in particular have seen considerable adoption within the last 30 years in the geosciences and geology. Techniques such as volume visualisation, for analysing subsurface processes, and photo-coloured LiDAR point-based rendering, to digitally explore rock exposures at the earth’s surface, were applied within geology as one of the first adopting branches of science. A large amount of digital, geological surface- and volume data is nowadays available to desktop-based workflows for geological applications such as hydrocarbon reservoir exploration, groundwater modelling, CO2 sequestration and, in the future, geothermal energy planning. On the other hand, the analysis and data collection during fieldwork has yet to embrace this ”digital revolution”: sedimentary logs, geological maps and stratigraphic sketches are still captured in each geologist’s individual fieldbook, and physical rocks samples are still transported to the lab for subsequent analysis. Is this still necessary, or are there extended digital means of data collection and exploration in the field ? Are modern digital interpretation techniques accurate and intuitive enough to relevantly support fieldwork in geology and other geoscience disciplines ? This dissertation aims to address these questions and, by doing so, close the technological gap between geological fieldwork and office workflows in geology. The emergence of mobile devices and their vast array of physical sensors, combined with touch-based user interfaces, high-resolution screens and digital cameras provide a possible digital platform that can be used by field geologists. Their ubiquitous availability increases the chances to adopt digital workflows in the field without additional, expensive equipment. The use of 3D data on mobile devices in the field is furthered by the availability of 3D digital outcrop models and the increasing ease of their acquisition. This dissertation assesses the prospects of adopting 3D visual techniques and mobile devices within field geology. The research of this dissertation uses previously acquired and processed digital outcrop models in the form of textured surfaces from optical remote sensing and photogrammetry. The scientific papers in this thesis present visual techniques and algorithms to map outcrop photographs in the field directly onto the surface models. Automatic mapping allows the projection of photo interpretations of stratigraphy and sedimentary facies on the 3D textured surface while providing the domain expert with simple-touse, intuitive tools for the photo interpretation itself. The developed visual approach, combining insight from all across the computer sciences dealing with visual information, merits into the mobile device Geological Registration and Interpretation Toolset (GRIT) app, which is assessed on an outcrop analogue study of the Saltwick Formation exposed at Whitby, North Yorkshire, UK. Although being applicable to a diversity of study scenarios within petroleum geology and the geosciences, the particular target application of the visual techniques is to easily provide field-based outcrop interpretations for subsequent construction of training images for multiple point statistics reservoir modelling, as envisaged within the VOM2MPS project. Despite the success and applicability of the visual approach, numerous drawbacks and probable future extensions are discussed in the thesis based on the conducted studies. Apart from elaborating on more obvious limitations originating from the use of mobile devices and their limited computing capabilities and sensor accuracies, a major contribution of this thesis is the careful analysis of conceptual drawbacks of established procedures in modelling, representing, constructing and disseminating the available surface geometry. A more mathematically-accurate geometric description of the underlying algebraic surfaces yields improvements and future applications unaddressed within the literature of geology and the computational geosciences to this date. Also, future extensions to the visual techniques proposed in this thesis allow for expanded analysis, 3D exploration and improved geological subsurface modelling in general.publishedVersio