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1st International Conference on Mathematical Modelling in Physical sciences (IC-MSQUARE)

作者： Huelsmann, Marco Kopp, Sonja Huber, Markus Reith, Dirk Fraunhofer Inst Algorithms & Sci Comp SCAT D-53754 Schloss Birlinghoven Sankt Augustin Germany

computer simulations of chemical systems can be used to reliably predict physical properties. Accurate molecular models, which are indispensable, are mathematically described by force fields, which have to be parameterized. Recently, an automated gradient-based parametrization procedure was published by the authors based on the minimization of a loss function between simulated and experimental physical properties. The applicability of the utilized algorithms is not trivial at all because of two reasons: First, simulation data is affected by statistical noise and second, the molecular simulations required for the loss function evaluations (involving finite differences approximations of gradients and Hessians) are extremely time-consuming. In this work, a more efficient approach to compute gradients and Hessians is presented. The method developed here is based on directional instead of partial derivatives. It is shown that up to 75% of the simulations can be avoided using this method.

关键词： Physical properties

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The Autoimmune Disease Database:: a dynamically compiled literature-derived database

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BMC BIOINFORMATICS 2006年第1期7卷 1-17页

作者： Karopka, Thomas Fluck, Juliane Mevissen, Heinz-Theodor Glass, Anne Univ Rostock Inst Med Informat & Biometry D-18055 Rostock Germany Fraunhofer Inst Algorithms & Sci Comp SCAI Dept Bioinformat D-53754 St Augustin Germany

Background: Autoimmune diseases are disorders caused by an immune response directed against the body's own organs, tissues and cells. In practice more than 80 clinically distinct diseases, among them systemic lupus erythematosus and rheumatoid arthritis, are classified as autoimmune diseases. Although their etiology is unclear these diseases share certain similarities at the molecular level i.e. susceptibility regions on the chromosomes or the involvement of common genes. To gain an overview of these related diseases it is not feasible to do a literary review but it requires methods of automated analyses of the more than 500,000 Medline documents related to autoimmune disorders. Results: In this paper we present the first version of the Autoimmune Disease Database which to our knowledge is the first comprehensive literature-based database covering all known or suspected autoimmune diseases. This dynamically compiled database allows researchers to link autoimmune diseases to the candidate genes or proteins through the use of named entity recognition which identifies genes/proteins in the corresponding Medline abstracts. The Autoimmune Disease Database covers 103 autoimmune disease concepts. This list was expanded to include synonyms and spelling variants yielding a list of over 1,200 disease names. The current version of the database provides links to 541,690 abstracts and over 5,000 unique genes/proteins. Conclusion: The Autoimmune Disease Database provides the researcher with a tool to navigate potential gene-disease relationships in Medline abstracts in the context of autoimmune diseases.

关键词： Multiple Sclerosis MeSH Term Unify Medical Language System Gene Entry Medline Abstract

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A Partition of Unity construction of the stabilization function in Nitsche's method for variational problems

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compUTER METHODS IN APPLIED MECHANICS AND ENGINEERING 2024年 426卷

作者： Recio, Pablo Jimenez Schweitzer, Marc Alexander Univ Bonn Inst Numer Simulat Friedrich Hirzebruch Allee 7 D-53115 Bonn Germany Fraunhofer Inst Algorithms & Sci Comp D-53757 St Augustin Germany

In this paper we develop a partition -of -unity construction of the stabilization function required in Nitsche's method, which can be seen as a generalization of the element -wise construction that is widely used in finite element methods. This allows for the use of Nitsche's method within the Partition of Unity Method with a stabilization function that is not simply a constant over the whole boundary. In addition to that, we introduce a patch -aggregation approach designed to avoid arbitrarily large values of the stabilization function and the associated ill -conditioned systems and deteriorated convergence rates. We present numerical results to validate the proposed methods, covering Dirichlet boundary conditions, interface constraints and higherorder problems. These results clearly show that our approach leads to optimal convergence rates.

关键词： Meshfree method Partition of unity method Essential boundary conditions Nitsche's method

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Principal component and clustering analysis on molecular dynamics data of the ribosomal L11•23S subdomain

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JOURNAL OF MOLECULAR MODELING 2013年第2期19卷 539-549页

作者： Wolf, Antje Kirschner, Karl N. Fraunhofer Inst Algorithms & Sci Comp SCAI Dept Bioinformat D-53754 Schloss Birlinghoven Sankt Augustin Germany Univ Bonn Dept Life Sci Informat Bonn Aachen Int Ctr IT D-53113 Bonn Germany Fraunhofer Inst Algorithms & Sci Comp SCAI Dept Simulat Engn D-53754 Schloss Birlinghoven Sankt Augustin Germany

With improvements in computer speed and algorithm efficiency, MD simulations are sampling larger amounts of molecular and biomolecular conformations. Being able to qualitatively and quantitatively sift these conformations into meaningful groups is a difficult and important task, especially when considering the structure-activity paradigm. Here we present a study that combines two popular techniques, principal component (PC) analysis and clustering, for revealing major conformational changes that occur in molecular dynamics (MD) simulations. Specifically, we explored how clustering different PC subspaces effects the resulting clusters versus clustering the complete trajectory data. As a case example, we used the trajectory data from an explicitly solvated simulation of a bacteria's L11 center dot 23S ribosomal subdomain, which is a target of thiopeptide antibiotics. Clustering was performed, using K-means and average-linkage algorithms, on data involving the first two to the first five PC subspace dimensions. For the average-linkage algorithm we found that data-point membership, cluster shape, and cluster size depended on the selected PC subspace data. In contrast, K-means provided very consistent results regardless of the selected subspace. Since we present results on a single model system, generalization concerning the clustering of different PC subspaces of other molecular systems is currently premature. However, our hope is that this study illustrates a) the complexities in selecting the appropriate clustering algorithm, b) the complexities in interpreting and validating their results, and c) by combining PC analysis with subsequent clustering valuable dynamic and conformational information can be obtained.

关键词： Clustering Molecular dynamics Principal component analysis Ribosome

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A Glycam-Based Force Field for Simulations of Lipopolysaccharide Membranes: Parametrization and Validation

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JOURNAL OF CHEMICAL THEORY AND compUTATION 2012年第11期8卷 4719-4731页

作者： Kirschner, Karl N. Lins, Roberto D. Maass, Astrid Soares, Thereza A. Fraunhofer Inst Algorithms & Sci Comp SCAI Dept Bioinformat D-53754 Schloss Birlinghoven Sankt Augustin Germany Fraunhofer Inst Algorithms & Sci Comp SCAI Dept Simulat Engn D-53754 Schloss Birlinghoven Sankt Augustin Germany Univ Fed Pernambuco Dept Fundamental Chem BR-50740560 Recife PE Brazil

Lipopolysaccharides (LPS) comprise the outermost layer of the Gram-negative bacteria cell envelope. Packed onto a lipid layer, the outer membrane displays remarkable physical-chemical differences compared to cell membranes. The carbohydrate-rich region confers a membrane asymmetry that underlies many biological processes such as endotoxicity, antibiotic resistance, and cell adhesion. Furthermore, unlike membrane proteins from other sources, integral outer-membrane proteins do not consist of transmembrane alpha helices;instead they consist of antiparallel beta-barrels, which highlights the importance of the LPS membrane as a medium. In this work, we present an extension of the GLYCAM06 farce field that has been specifically developed for LPS membranes using our Wolf(2)Pack program. This new set of parameters for lipopolysaccharide molecules expands the GLYCAM06 repertoire of monosaccharides to include phosphorylated N- and O-acetylglucosamine, 3-deoxy-D-manno-oct-2-ulosonic acid, L-glycero-D-manno-heptose and its O-carbamoylated Variant, and N-alanine-D-galactoamine. A total of 1 mu s of molecular dynamics simulations of the rough LPS membrane of Pseudomonas aeruginosa PA01 is used to showcase the added parameter set The equilibration of the LPS membrane is shown to be significantly slower compared to phospholipid membranes, on the order of 500 ns. It is further shown that Water molecules penetrate the hydrocarbon region up, to the terminal methyl groups, much deeper than commonly observed for. phospholipid bilayers, and in agreement. With neutron diffraction measurements. A comparison, Of simulated structural, dynamical, and electrostatic properties against corresponding experimentally available data shows that the present parameter set reproduces Well the overall structure and the permeability of LPS membranes in the liquid-crystalline phase.

关键词： Vesicles Lipids Molecules Membranes Molecular mechanics

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PathME: pathway based multi-modal sparse autoencoders for clustering of patient-level multi-omics data

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BMC BIOINFORMATICS 2020年第1期21卷 1-20页

作者： Lemsara, Amina Ouadfel, Salima Froehlich, Holger Univ Constantine 2 Comp Sci Dept Constantine 25016 Algeria Univ Bonn Int Ctr IT D-53115 Bonn Germany Fraunhofer Inst for Algorithms & Sci Comp SCAI D-53754 Sankt Augustin Germany

Background Recent years have witnessed an increasing interest in multi-omics data, because these data allow for better understanding complex diseases such as cancer on a molecular system level. In addition, multi-omics data increase the chance to robustly identify molecular patient sub-groups and hence open the door towards a better personalized treatment of diseases. Several methods have been proposed for unsupervised clustering of multi-omics data. However, a number of challenges remain, such as the magnitude of features and the large difference in dimensionality across different omics data sources. Results We propose a multi-modal sparse denoising autoencoder framework coupled with sparse non-negative matrix factorization to robustly cluster patients based on multi-omics data. The proposed model specifically leverages pathway information to effectively reduce the dimensionality of omics data into a pathway and patient specific score profile. In consequence, our method allows us to understand, which pathway is a feature of which particular patient cluster. Moreover, recently proposed machine learning techniques allow us to disentangle the specific impact of each individual omics feature on a pathway score. We applied our method to cluster patients in several cancer datasets using gene expression, miRNA expression, DNA methylation and CNVs, demonstrating the possibility to obtain biologically plausible disease subtypes characterized by specific molecular features. comparison against several competing methods showed a competitive clustering performance. In addition, post-hoc analysis of somatic mutations and clinical data provided supporting evidence and interpretation of the identified clusters. Conclusions Our suggested multi-modal sparse denoising autoencoder approach allows for an effective and interpretable integration of multi-omics data on pathway level while addressing the high dimensional character of omics data. Patient specific pathway score profiles deri

关键词： Deep learning Patient clustering Multi-omics

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The EU project Real4Reg: unlocking real-world data with AI

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HEALTH RESEARCH POLICY AND SYSTEMS 2025年第1期23卷 1-8页

作者： Peltner, Jonas Becker, Cornelia Wicherski, Julia Wortberg, Silja Aborageh, Mohamed Costa, Ines Ehrenstein, Vera Fernandes, Joana Hess, Steffen Horvath-Puho, Erzsebet Korcinska Handest, Monika Roberta Lentzen, Manuel Maguire, Peggy Meedom, Niels Henrik Moore, Rebecca Moore, Vanessa Nagy, David Mcnamara, Hillary Paakinaho, Anne Pfeifer, Kerstin Pylkkanen, Liisa Rajamaki, Blair Reviers, Evy Roethlein, Christoph Russek, Martin Silva, Celia De Valck, Dirk Vo, Thuan Brauner, Elvira Froehlich, Holger Furtado, Claudia Hartikainen, Sirpa Kallio, Aleksi Tolppanen, Anna-Maija Haenisch, Britta German Ctr Neurodegenerat Dis DZNE Bonn Germany Fed Inst Drugs & Med Devices Div Res Kurt Georg Kiesinger Allee 3 D-53175 Bonn Germany Fraunhofer Inst Algorithms & Sci Comp SCAI Dept Bioinformat D-53754 St Augustin Sankt Augustin Germany Natl Author Med & Hlth Prod IP Hlth Technol Assessment Dept DATS INFARMED Lisbon Portugal Aarhus Univ Dept Clin Med Dept Clin Epidemiol Aarhus Denmark Aarhus Univ Ctr Populat Med Aarhus Denmark Natl Author Med & Hlth Prod IP Informat & Strateg Planning Dept DIPE INFARMED P-1749004 Lisbon Portugal Fed Inst Drugs & Med Devices Hlth Data Lab FDZ D-53175 Bonn Germany Data Analyt Ctr Danish Med Agcy Copenhagen Denmark European Inst Womens Hlth EIWH Dublin Ireland Univ Eastern Finland Sch Pharm Kuopio Finland Univ Turku Dept Oncol Turku Finland Univ Louvain Louvain Belgium Univ Bonn Bonn Aachen Int Ctr IT Bonn Germany NOVA Univ Lisbon NOVA Natl Sch Publ Hlth Lisbon Portugal CSC IT Ctr Sci Ltd Espoo Finland Univ Bonn Med Fac Ctr Translat Med Bonn Germany

BackgroundThe use of real-world data is established in post-authorization regulatory processes such as pharmacovigilance of drugs and medical devices, but is still frequently challenged in the pre-authorization phase of medicinal products. In addition, the use of real-world data, even in post-authorization steps, is constrained by the availability and heterogeneity of real-world data and by challenges in analysing data from different settings and sources. Moreover, there are emerging opportunities in the use of artificial intelligence in healthcare research, but also a lack of knowledge on its appropriate application to heterogeneous real-world data sources to increase evidentiary value in the regulatory decision-making and health technology assessment *** Real4Reg project aims to enable the use of real-world data by developing user-friendly solutions for the data analytical needs of health regulatory and health technology assessment bodies across the European Union. These include artificial intelligence algorithms for the effective analysis of real-world data in regulatory decision-making and health technology assessment. The project aims to investigate the value of real-world data from different sources to generate high-quality, accessible, population-based information relevant along the product life cycle. A total of four use cases are used to provide good practice examples for analyses of real-world data for the evaluation and pre-authorization stage, the improvement of methods for external validity in observational data, for post-authorization safety studies and comparative effectiveness using real-world data. This position paper introduces the objectives and structure of the Real4Reg project and discusses its important role in the context of existing European projects focussing on real-world ***4Reg focusses on the identification and description of benefits and risks of new and optimized methods in real-world data analysis includ

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Benchmarking table recognition performance on biomedical literature on neurological disorders

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BIOINFORMATICS 2022年第6期38卷 1624-1630页

作者： Adams, Tim Namysl, Marcin Kodamullil, Alpha Tom Behnke, Sven Jacobs, Marc Fraunhofer Inst Algorithms & Sci Comp D-53757 St Augustin Germany Fraunhofer Inst Intelligent Anal & Informat Syst D-53757 St Augustin Germany Univ Bonn Comp Sci Inst 6 Autonomous Intelligent Syst D-53115 Bonn Germany

Motivation Table recognition systems are widely used to extract and structure quantitative information from the vast amount of documents that are increasingly available from different open sources. While many systems already perform well on tables with a simple layout, tables in the biomedical domain are often much more complex. Benchmark and training data for such tables are however very limited. Results To address this issue, we present a novel, highly curated benchmark dataset based on a hand-curated literature corpus on neurological disorders, which can be used to tune and evaluate table extraction applications for this challenging domain. We evaluate several state-of-the-art table extraction systems based on our proposed benchmark and discuss challenges that emerged during the benchmark creation as well as factors that can impact the performance of recognition methods. For the evaluation procedure, we propose a new metric as well as several improvements that result in a better performance evaluation.

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OSIRISv1.2: A named entity recognition system for sequence variants of genes in biomedical literature

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BMC BIOINFORMATICS 2008年第1期9卷 1-16页

作者： Furlong, Laura I. Dach, Holger Hofmann-Apitius, Martin Sanz, Ferran IMIM UPF PRBB GRIBRes Unit Biomed Informat E-08003 Barcelona Spain Fraunhofer Inst Algorithms & Sci Comp Dept Bioinformat St Augustin Germany

Background: Single Nucleotide Polymorphisms, among other type of sequence variants, constitute key elements in genetic epidemiology and pharmacogenomics. While sequence data about genetic variation is found at databases such as dbSNP, clues about the functional and phenotypic consequences of the variations are generally found in biomedical literature. The identification of the relevant documents and the extraction of the information from them are hampered by the large size of literature databases and the lack of widely accepted standard notation for biomedical entities. Thus, automatic systems for the identification of citations of allelic variants of genes in biomedical texts are required. Results: Our group has previously reported the development of OSIRIS, a system aimed at the retrieval of literature about allelic variants of genes http://***/***. Here we describe the development of a new version of OSIRIS (OSIRISv1.2, http://***/***) which incorporates a new entity recognition module and is built on top of a local mirror of the MEDLINE collection and HgenetInfoDB: a database that collects data on human gene sequence variations. The new entity recognition module is based on a pattern-based search algorithm for the identification of variation terms in the texts and their mapping to dbSNP identifiers. The performance of OSIRISv1.2 was evaluated on a manually annotated corpus, resulting in 99% precision, 82% recall, and an F-score of 0.89. As an example, the application of the system for collecting literature citations for the allelic variants of genes related to the diseases intracranial aneurysm and breast cancer is presented. Conclusion: OSIRISv1.2 can be used to link literature references to dbSNP database entries with high accuracy, and therefore is suitable for collecting current knowledge on gene sequence variations and supporting the functional annotation of variation databases. The application of OSIRISv1.2 in combin

关键词： MeSH Intracranial Aneurysm Name Entity Recognition Entity Recognition Text Passage

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Iterative methods for reluctance based PEEC models

Iterative methods for reluctance based PEEC models

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17th International Zurich Symposium on Electromagnetic compatibility

作者： Zitzmann, Martin L. Clees, Tania Weigel, Robert Univ Erlangen Nurnberg Inst Elect Engn Erlangen Germany Fraunhofer Inst Algorithms & Sci Comp Augustin Germany

ISBN: (纸本)9783952299036

This paper presents the application of iterative solution techniques to large sparse equation systems derived from PEEC modeling. The PEEC method (partial element equivalent circuit) is an approach to transform conducting objects into linear networks with basic electrical elements. Such equivalent circuit models can be simulated by conventional circuit solvers such as SPICE (simulation program for integrated circuit emphasis) based on the MNA (modified nodal analysis) approach. By applying appropriate sparsification techniques sparse system matrices can be obtained, adequate for iterative solvers. By using multilevel approaches linear complexity in time and memory requirements can be achieved in the best case. The suitability of different iterative methods as applied to such systems is compared by means of examples.

关键词： Circuit theory

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