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  • 1.
    Abbaszadeh Shahri, Abbas
    KTH, Skolan för arkitektur och samhällsbyggnad (ABE), Byggvetenskap. Islamic Azad University.
    An Optimized Artificial Neural Network Structure to Predict Clay Sensitivity in a High Landslide Prone Area Using Piezocone Penetration Test (CPTu) Data: A Case Study in Southwest of Sweden2016Inngår i: Geotechnical and Geological Engineering, ISSN 0960-3182, E-ISSN 1573-1529, s. 1-14Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Application of artificial neural networks (ANN) in various aspects of geotechnical engineering problems such as site characterization due to have difficulty to solve or interrupt through conventional approaches has demonstrated some degree of success. In the current paper a developed and optimized five layer feed-forward back-propagation neural network with 4-4-4-3-1 topology, network error of 0.00201 and R2 = 0.941 under the conjugate gradient descent ANN training algorithm was introduce to predict the clay sensitivity parameter in a specified area in southwest of Sweden. The close relation of this parameter to occurred landslides in Sweden was the main reason why this study is focused on. For this purpose, the information of 70 piezocone penetration test (CPTu) points was used to model the variations of clay sensitivity and the influences of direct or indirect related parameters to CPTu has been taken into account and discussed in detail. Applied operation process to find the optimized ANN model using various training algorithms as well as different activation functions was the main advantage of this paper. The performance and feasibility of proposed optimized model has been examined and evaluated using various statistical and analytical criteria as well as regression analyses and then compared to in situ field tests and laboratory investigation results. The sensitivity analysis of this study showed that the depth and pore pressure are the two most and cone tip resistance is the least effective factor on prediction of clay sensitivity.

  • 2. Abrams, M. B.
    et al.
    Bjaalie, J. G.
    Das, S.
    Egan, G. F.
    Ghosh, S. S.
    Goscinski, W. J.
    Grethe, J. S.
    Hellgren Kotaleski, Jeanette
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Datavetenskap, Beräkningsvetenskap och beräkningsteknik (CST).
    Ho, E. T. W.
    Kennedy, D. N.
    Lanyon, L. J.
    Leergaard, T. B.
    Mayberg, H. S.
    Milanesi, L.
    Mouček, R.
    Poline, J. B.
    Roy, P. K.
    Strother, S. C.
    Tang, T. B.
    Tiesinga, P.
    Wachtler, T.
    Wójcik, D. K.
    Martone, M. E.
    A Standards Organization for Open and FAIR Neuroscience: the International Neuroinformatics Coordinating Facility2021Inngår i: Neuroinformatics, ISSN 1539-2791, E-ISSN 1559-0089Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    There is great need for coordination around standards and best practices in neuroscience to support efforts to make neuroscience a data-centric discipline. Major brain initiatives launched around the world are poised to generate huge stores of neuroscience data. At the same time, neuroscience, like many domains in biomedicine, is confronting the issues of transparency, rigor, and reproducibility. Widely used, validated standards and best practices are key to addressing the challenges in both big and small data science, as they are essential for integrating diverse data and for developing a robust, effective, and sustainable infrastructure to support open and reproducible neuroscience. However, developing community standards and gaining their adoption is difficult. The current landscape is characterized both by a lack of robust, validated standards and a plethora of overlapping, underdeveloped, untested and underutilized standards and best practices. The International Neuroinformatics Coordinating Facility (INCF), an independent organization dedicated to promoting data sharing through the coordination of infrastructure and standards, has recently implemented a formal procedure for evaluating and endorsing community standards and best practices in support of the FAIR principles. By formally serving as a standards organization dedicated to open and FAIR neuroscience, INCF helps evaluate, promulgate, and coordinate standards and best practices across neuroscience. Here, we provide an overview of the process and discuss how neuroscience can benefit from having a dedicated standards body.

  • 3. Aidas, Kestutis
    et al.
    Angeli, Celestino
    Bak, Keld L.
    Bakken, Vebjorn
    Bast, Radovan
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Boman, Linus
    Christiansen, Ove
    Cimiraglia, Renzo
    Coriani, Sonia
    Dahle, Pal
    Dalskov, Erik K.
    Ekstrom, Ulf
    Enevoldsen, Thomas
    Eriksen, Janus J.
    Ettenhuber, Patrick
    Fernandez, Berta
    Ferrighi, Lara
    Fliegl, Heike
    Frediani, Luca
    Hald, Kasper
    Halkier, Asger
    Hattig, Christof
    Heiberg, Hanne
    Helgaker, Trygve
    Hennum, Alf Christian
    Hettema, Hinne
    Hjertenaes, Eirik
    Host, Stinne
    Hoyvik, Ida-Marie
    Iozzi, Maria Francesca
    Jansik, Branislav
    Jensen, Hans Jorgen Aa.
    Jonsson, Dan
    Jorgensen, Poul
    Kauczor, Joanna
    Kirpekar, Sheela
    Kjrgaard, Thomas
    Klopper, Wim
    Knecht, Stefan
    Kobayashi, Rika
    Koch, Henrik
    Kongsted, Jacob
    Krapp, Andreas
    Kristensen, Kasper
    Ligabue, Andrea
    Lutnaes, Ola B.
    Melo, Juan I.
    Mikkelsen, Kurt V.
    Myhre, Rolf H.
    Neiss, Christian
    Nielsen, Christian B.
    Norman, Patrick
    Olsen, Jeppe
    Olsen, Jogvan Magnus H.
    Osted, Anders
    Packer, Martin J.
    Pawlowski, Filip
    Pedersen, Thomas B.
    Provasi, Patricio F.
    Reine, Simen
    Rinkevicius, Zilvinas
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Ruden, Torgeir A.
    Ruud, Kenneth
    Rybkin, Vladimir V.
    Salek, Pawel
    Samson, Claire C. M.
    de Meras, Alfredo Sanchez
    Saue, Trond
    Sauer, Stephan P. A.
    Schimmelpfennig, Bernd
    Sneskov, Kristian
    Steindal, Arnfinn H.
    Sylvester-Hvid, Kristian O.
    Taylor, Peter R.
    Teale, Andrew M.
    Tellgren, Erik I.
    Tew, David P.
    Thorvaldsen, Andreas J.
    Thogersen, Lea
    Vahtras, Olav
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Watson, Mark A.
    Wilson, David J. D.
    Ziolkowski, Marcin
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    The Dalton quantum chemistry program system2014Inngår i: Wiley Interdisciplinary Reviews. Computational Molecular Science, ISSN 1759-0876, Vol. 4, nr 3, s. 269-284Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, MOller-Plesset, configuration-interaction, and coupled-cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic-structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge-origin-invariant manner. Frequency-dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one-, two-, and three-photon processes. Environmental effects may be included using various dielectric-medium and quantum-mechanics/molecular-mechanics models. Large molecules may be studied using linear-scaling and massively parallel algorithms. Dalton is distributed at no cost from for a number of UNIX platforms.

  • 4. Alger, Ingela
    et al.
    Weibull, Jörgen W.
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.).
    A generalization of Hamilton's rule-Love others how much?2012Inngår i: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 299, s. 42-54Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    According to Hamilton's (1964a, b) rule, a costly action will be undertaken if its fitness cost to the actor falls short of the discounted benefit to the recipient, where the discount factor is Wright's index of relatedness between the two. We propose a generalization of this rule, and show that if evolution operates at the level of behavior rules, rather than directly at the level of actions, evolution will select behavior rules that induce a degree of cooperation that may differ from that predicted by Hamilton's rule as applied to actions. In social dilemmas there will be less (more) cooperation than under Hamilton's rule if the actions are strategic substitutes (complements). Our approach is based on natural selection, defined in terms of personal (direct) fitness, and applies to a wide range of pairwise interactions.

  • 5.
    Ali, Raja Hashim
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    From genomes to post-processing of Bayesian inference of phylogeny2016Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Life is extremely complex and amazingly diverse; it has taken billions of years of evolution to attain the level of complexity we observe in nature now and ranges from single-celled prokaryotes to multi-cellular human beings. With availability of molecular sequence data, algorithms inferring homology and gene families have emerged and similarity in gene content between two genes has been the major signal utilized for homology inference. Recently there has been a significant rise in number of species with fully sequenced genome, which provides an opportunity to investigate and infer homologs with greater accuracy and in a more informed way. Phylogeny analysis explains the relationship between member genes of a gene family in a simple, graphical and plausible way using a tree representation. Bayesian phylogenetic inference is a probabilistic method used to infer gene phylogenies and posteriors of other evolutionary parameters. Markov chain Monte Carlo (MCMC) algorithm, in particular using Metropolis-Hastings sampling scheme, is the most commonly employed algorithm to determine evolutionary history of genes. There are many softwares available that process results from each MCMC run, and explore the parameter posterior but there is a need for interactive software that can analyse both discrete and real-valued parameters, and which has convergence assessment and burnin estimation diagnostics specifically designed for Bayesian phylogenetic inference.

    In this thesis, a synteny-aware approach for gene homology inference, called GenFamClust (GFC), is proposed that uses gene content and gene order conservation to infer homology. The feature which distinguishes GFC from earlier homology inference methods is that local synteny has been combined with gene similarity to infer homologs, without inferring homologous regions. GFC was validated for accuracy on a simulated dataset. Gene families were computed by applying clustering algorithms on homologs inferred from GFC, and compared for accuracy, dependence and similarity with gene families inferred from other popular gene family inference methods on a eukaryotic dataset. Gene families in fungi obtained from GFC were evaluated against pillars from Yeast Gene Order Browser. Genome-wide gene families for some eukaryotic species are computed using this approach.

    Another topic focused in this thesis is the processing of MCMC traces for Bayesian phylogenetics inference. We introduce a new software VMCMC which simplifies post-processing of MCMC traces. VMCMC can be used both as a GUI-based application and as a convenient command-line tool. VMCMC supports interactive exploration, is suitable for automated pipelines and can handle both real-valued and discrete parameters observed in a MCMC trace. We propose and implement joint burnin estimators that are specifically applicable to Bayesian phylogenetics inference. These methods have been compared for similarity with some other popular convergence diagnostics. We show that Bayesian phylogenetic inference and VMCMC can be applied to infer valuable evolutionary information for a biological case – the evolutionary history of FERM domain.

    Fulltekst (pdf)
    Doctoral Thesis Hashim
  • 6.
    Ali, Raja Hashim
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Bark, Mikael
    KTH, Skolan för informations- och kommunikationsteknik (ICT).
    Miró, Jorge
    KTH, Skolan för informations- och kommunikationsteknik (ICT).
    Muhammad, Sayyed Auwn
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Sjöstrand, J.
    Zubair, Syed M.
    KTH, Skolan för elektro- och systemteknik (EES), Kommunikationsnät. University of Balochistan, Pakistan.
    Abbas, R. M.
    Arvestad, L.
    VMCMC: A graphical and statistical analysis tool for Markov chain Monte Carlo traces2017Inngår i: BMC Bioinformatics, E-ISSN 1471-2105, Vol. 18, nr 1, artikkel-id 97Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: MCMC-based methods are important for Bayesian inference of phylogeny and related parameters. Although being computationally expensive, MCMC yields estimates of posterior distributions that are useful for estimating parameter values and are easy to use in subsequent analysis. There are, however, sometimes practical difficulties with MCMC, relating to convergence assessment and determining burn-in, especially in large-scale analyses. Currently, multiple software are required to perform, e.g., convergence, mixing and interactive exploration of both continuous and tree parameters. Results: We have written a software called VMCMC to simplify post-processing of MCMC traces with, for example, automatic burn-in estimation. VMCMC can also be used both as a GUI-based application, supporting interactive exploration, and as a command-line tool suitable for automated pipelines. Conclusions: VMCMC is a free software available under the New BSD License. Executable jar files, tutorial manual and source code can be downloaded from https://bitbucket.org/rhali/visualmcmc/.

  • 7.
    Ali, Raja Hashim
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Muhammad, Sayyed Auwn
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Khan, Mehmodd Alam
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Arvestad, Lars
    Stockholms universitet.
    Quantitative synteny scoring improves homology inference and partitioning of gene families2013Inngår i: BMC Bioinformatics, E-ISSN 1471-2105, Vol. 14, s. S12-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: Clustering sequences into families has long been an important step in characterization of genes and proteins. There are many algorithms developed for this purpose, most of which are based on either direct similarity between gene pairs or some sort of network structure, where weights on edges of constructed graphs are based on similarity. However, conserved synteny is an important signal that can help distinguish homology and it has not been utilized to its fullest potential. Results: Here, we present GenFamClust, a pipeline that combines the network properties of sequence similarity and synteny to assess homology relationship and merge known homologs into groups of gene families. GenFamClust identifies homologs in a more informed and accurate manner as compared to similarity based approaches. We tested our method against the Neighborhood Correlation method on two diverse datasets consisting of fully sequenced genomes of eukaryotes and synthetic data. Conclusions: The results obtained from both datasets confirm that synteny helps determine homology and GenFamClust improves on Neighborhood Correlation method. The accuracy as well as the definition of synteny scores is the most valuable contribution of GenFamClust.

    Fulltekst (pdf)
    fulltext
  • 8.
    Alneberg, Johannes
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Bioinformatic Methods in Metagenomics2018Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Microbial organisms are a vital part of our global ecosystem. Yet, our knowledge of them is still lacking. Direct sequencing of microbial communities, i.e. metagenomics, have enabled detailed studies of these microscopic organisms by inspection of their DNA sequences without the need to culture them. Furthermore, the development of modern high- throughput sequencing technologies have made this approach more powerful and cost-effective. Taken together, this has shifted the field of microbiology from previously being centered around microscopy and culturing studies, to largely consist of computational analyses of DNA sequences. One such computational analysis which is the main focus of this thesis, aims at reconstruction of the complete DNA sequence of an organism, i.e. its genome, directly from short metagenomic sequences.

    This thesis consists of an introduction to the subject followed by five papers. Paper I describes a large metagenomic data resource spanning the Baltic Sea microbial communities. This dataset is complemented with a web-interface allowing researchers to easily extract and visualize detailed information. Paper II introduces a bioinformatic method which is able to reconstruct genomes from metagenomic data. This method, which is termed CONCOCT, is applied on Baltic Sea metagenomics data in Paper III and Paper V. This enabled the reconstruction of a large number of genomes. Analysis of these genomes in Paper III led to the proposal of, and evidence for, a global brackish microbiome. Paper IV presents a comparison between genomes reconstructed from metagenomes with single-cell sequenced genomes. This further validated the technique presented in Paper II as it was found to produce larger and more complete genomes than single-cell sequencing.

    Fulltekst (pdf)
    fulltext
  • 9.
    Alneberg, Johannes
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Sundh, John
    Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.
    Bennke, Christin
    Leibniz Institute for Baltic Sea Research, Warnemünde, Germany.
    Beier, Sara
    Leibniz Institute for Baltic Sea Research, Warnemünde, Germany.
    Lundin, Daniel
    Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden.
    Hugerth, Luisa
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Skolan för bioteknologi (BIO).
    Pinhassi, Jarone
    Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden.
    Kisand, Veljo
    University of Tartu, Institute of Technology, Tartu, Estonia.
    Riemann, Lasse
    Section for Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark.
    Jürgens, Klaus
    Leibniz Institute for Baltic Sea Research, Warnemünde, Germany.
    Labrenz, Matthias
    Leibniz Institute for Baltic Sea Research, Warnemünde, Germany.
    Andersson, Anders F.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic SeaManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    The Baltic Sea is one of the world’s largest brackish water bodies and is characterised by pronounced physicochemical gradients where microbes are the main biogeochemical catalysts. Meta-omic methods provide rich information on the composition of, and activities within microbial ecosystems, but are computationally heavy to perform. We here present the BAltic Sea Reference Metagenome (BARM), complete with annotated genes to facilitate further studies with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly. This capability is demonstrated by the successful mapping and annotation of 24 external samples. In addition, we present a public web interface, BalticMicrobeDB, for interactive exploratory analysis of the dataset.

    Fulltekst (pdf)
    fulltext
  • 10.
    Andeer, Robin
    et al.
    Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholms, Sweden.
    Magnusson, Måns
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab. Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden; Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden.
    Wedell, Anna
    Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden; Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden.
    Stranneheim, Henrik
    Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden; Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden.
    Chanjo: Clincal grade sequence coverage analysis2020Inngår i: F1000 Research, E-ISSN 2046-1402, Vol. 9, artikkel-id 615Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Coverage analysis is essential when analysing massive parallel sequencing (MPS) data. The analysis indicates existence of false negatives or positives in a region of interest or poorly covered genomic regions. There are several tools that have excellent performance when doing coverage analysis on a few samples with predefined regions. However, there is no current tool for collecting samples over a longer period of time for aggregated coverage analysis of multiple samples or sequencing methods. Furthermore, current coverage analysis tools do not generate customized coverage reports or enable exploratory coverage analysis without extensive bioinformatic skill and access to the original alignment files. We present Chanjo, a user friendly coverage analysis tool for persistent storage of coverage data, that, accompanied with Chanjo Report, produces coverage reports that summarize coverage data for predefined regions in an elegant manner. Chanjo Report can produce both structured coverage reports and dynamic reports tailored to a subset of genomic regions, coverage cut-offs or samples. Chanjo stores data in an SQL database where thousands of samples can be added over time, which allows for aggregate queries to discover problematic regions. Chanjo is well tested, supports whole exome and genome sequencing, and follows common UNIX standards, allowing for easy integration into existing pipelines. Chanjo is easy to install and operate, and provides a solution for persistent coverage analysis and clinical-grade reporting. It makes it easy to set up a local database and automate the addition of multiple samples and report generation. To our knowledge there is no other tool with matching capabilities. Chanjo handles the common file formats in genetics, such as BED and BAM, and makes it easy to produce PDF coverage reports that are highly valuable for individuals with limited bioinformatic expertise. We believe Chanjo to be a vital tool for clinicians and researchers performing MPS analysis.

  • 11.
    Andersson, Samuel A.
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Numerisk Analys och Datalogi, NADA.
    Lagergren, Jens
    KTH, Skolan för datavetenskap och kommunikation (CSC), Numerisk Analys och Datalogi, NADA.
    Motif Yggdrasil: Sampling from a tree mixture model2006Inngår i: Research In Computational Molecular Biology, Proceedings / [ed] Apostolico, A; Guerra, C; Istrail, S; Pevzner, P; Waterman, M, 2006, Vol. 3909, s. 458-472Konferansepaper (Fagfellevurdert)
    Abstract [en]

    In phylogenetic foot-printing, putative regulatory elements are found in upstream regions of orthologous genes by searching for common motifs. Motifs in different upstream sequences are subject to mutations along the edges of the corresponding phylogenetic tree, consequently taking advantage of the tree in the motif search is an appealing idea. We describe the Motif Yggdrasil sampler; the first Gibbs sampler based on a general tree that uses unaligned sequences. Previous tree-based Gibbs samplers have assumed a star-shaped tree or partially aligned upstream regions. We give a probabilistic model describing upstream sequences with regulatory elements and build a Gibbs sampler with respect to this model. We apply the collapsing technique to eliminate the need to sample nuisance parameters, and give a derivation of the predictive update formula. The use of the tree achieves a substantial increase in nucleotide level correlation coefficient both for synthetic data and 37 bacterial lexA genes.

  • 12.
    Andrade, Jorge
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Grid and High-Performance Computing for Applied Bioinformatics2007Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    The beginning of the twenty-first century has been characterized by an explosion of biological information. The avalanche of data grows daily and arises as a consequence of advances in the fields of molecular biology and genomics and proteomics. The challenge for nowadays biologist lies in the de-codification of this huge and complex data, in order to achieve a better understanding of how our genes shape who we are, how our genome evolved, and how we function.

    Without the annotation and data mining, the information provided by for example high throughput genomic sequencing projects is not very useful. Bioinformatics is the application of computer science and technology to the management and analysis of biological data, in an effort to address biological questions. The work presented in this thesis has focused on the use of Grid and High Performance Computing for solving computationally expensive bioinformatics tasks, where, due to the very large amount of available data and the complexity of the tasks, new solutions are required for efficient data analysis and interpretation.

    Three major research topics are addressed; First, the use of grids for distributing the execution of sequence based proteomic analysis, its application in optimal epitope selection and in a proteome-wide effort to map the linear epitopes in the human proteome. Second, the application of grid technology in genetic association studies, which enabled the analysis of thousand of simulated genotypes, and finally the development and application of a economic based model for grid-job scheduling and resource administration.

    The applications of the grid based technology developed in the present investigation, results in successfully tagging and linking chromosomes regions in Alzheimer disease, proteome-wide mapping of the linear epitopes, and the development of a Market-Based Resource Allocation in Grid for Scientific Applications.

    Fulltekst (pdf)
    FULLTEXT01
  • 13.
    Andrade, Jorge
    et al.
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Andersen, Malin
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Berglund, Lisa
    KTH, Skolan för bioteknologi (BIO), Proteomik.
    Odeberg, Jacob
    KTH, Skolan för bioteknologi (BIO), Genteknologi.
    Applications of grid computing in genetics and proteomics2007Inngår i: Applied Parallel Computing: State Of The Art In Scientific Computing / [ed] Kagstrom, B; Elmroth, E; Dongarra, J; Wasniewski, J, 2007, Vol. 4699, s. 791-798Konferansepaper (Fagfellevurdert)
    Abstract [en]

    The potential for Grid technologies in applied bioinformatics is largely unexplored. We have developed a model for solving computationally demanding bioinformatics tasks in distributed Grid environments, designed to ease the usability for scientists unfamiliar with Grid computing. With a script-based implementation that uses a strategy of temporary installations of databases and existing executables on remote nodes at submission, we propose a generic solution that do not rely on predefined Grid runtime environments and that can easily be adapted to other bioinformatics tasks suitable for parallelization. This implementation has been successfully applied to whole proteome sequence similarity analyses and to genome-wide genotype simulations, where computation time was reduced from years to weeks. We conclude that computational Grid technology is a useful resource for solving high compute tasks in genetics and proteomics using existing algorithms.

  • 14. Ansotegui, Carlos
    et al.
    Luisa Bonet, Maria
    Giraldez-Cru, Jesus
    KTH, Skolan för datavetenskap och kommunikation (CSC), Teoretisk datalogi, TCS. Spanish National Research Council, Spain.
    Levy, Jordi
    Structure features for SAT instances classification2017Inngår i: Journal of Applied Logic, ISSN 1570-8683, E-ISSN 1570-8691, Vol. 23, s. 27-39Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The success of portfolio approaches in SAT solving relies on the observation that different SAT solvers may dramatically change their performance depending on the class of SAT instances they are trying to solve. In these approaches, a set of features of the problem is used to build a prediction model, which classifies instances into classes, and computes the fastest algorithm to solve each of them. Therefore, the set of features used to build these classifiers plays a crucial role. Traditionally, portfolio SAT solvers include features about the structure of the problem and its hardness. Recently, there have been some attempts to better characterize the structure of industrial SAT instances. In this paper, we use some structure features of industrial SAT instances to build some classifiers of industrial SAT families of instances. Namely, they are the scale-free structure, the community structure and the self similar structure. First, we measure the effectiveness of these classifiers by comparing them to other sets of SAT features commonly used in portfolio SAT solving approaches. Then, we evaluate the performance of this set of structure features when used in a real portfolio SAT solver. Finally, we analyze the relevance of these features on the analyzed classifiers.

  • 15.
    Arvestad, Lars
    KTH, Tidigare Institutioner (före 2005), Numerisk analys och datalogi, NADA.
    Aligning coding DNA in the presence of frame-shift errors1997Inngår i: Combinatorial Pattern Matching, 1997, s. 180-190Konferansepaper (Annet vitenskapelig)
    Abstract [en]

    The problem of aligning two DNA sequences with respect to the fact that they are coding for proteins is discussed. Criteria for a good alignment of coding DNA, together with an algorithm that satisfies them, are presented. The algorithm is robust against frame-shifts and forgiving towards silent substitutions. The important choice of objective function is examined and several variants are proposed.

    Fulltekst (pdf)
    fulltext
  • 16.
    Arvestad, Lars
    et al.
    Center for Genomics and Bioinformatics, Karolinska Institutet.
    Berglund, Ann-Charlotte
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Lagergren, Jens
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Sennblad, Bengt
    Center for Genomics and Bioinformatics, Karolinska Institutet.
    Bayesian gene/species tree reconciliation and orthology analysis using MCMC2003Inngår i: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 19, s. i7-i15Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Motivation: Comparative genomics in general and orthology analysis in particular are becoming increasingly important parts of gene function prediction. Previously, orthology analysis and reconciliation has been performed only with respect to the parsimony model. This discards many plausible solutions and sometimes precludes finding the correct one. In many other areas in bioinformatics probabilistic models have proven to be both more realistic and powerful than parsimony models. For instance, they allow for assessing solution reliability and consideration of alternative solutions in a uniform way. There is also an added benefit in making model assumptions explicit and therefore making model comparisons possible. For orthology analysis, uncertainty has recently been addressed using parsimonious reconciliation combined with bootstrap techniques. However, until now no probabilistic methods have been available.

    Results: We introduce a probabilistic gene evolution model based on a birth-death process in which a gene tree evolves ‘inside’ a species tree. Based on this model, we develop a tool with the capacity to perform practical orthology analysis, based on Fitch’s original definition, and more generally for reconciling pairs of gene and species trees. Our gene evolution model is biologically sound (Nei et al., 1997) and intuitively attractive. We develop a Bayesian analysis based on MCMC which facilitates approximation of an a posteriori distribution for reconciliations. That is, we can find the most probable reconciliations and estimate the probability of any reconciliation, given the observed gene tree. This also gives a way to estimate the probability that a pair of genes are orthologs. The main algorithmic contribution presented here consists of an algorithm for computing the likelihood of a given reconciliation. To the best of our knowledge, this is the first successful introduction of this type of probabilistic methods, which flourish in phylogeny analysis, into reconciliation and orthology analysis. The MCMC algorithm has been implemented and, although not yet being in its final form, tests show that it performs very well on synthetic as well as biological data. Using standard correspondences, our results carry over to allele trees as well as biogeography.

  • 17.
    Arvestad, Lars
    et al.
    KTH, Tidigare Institutioner (före 2005), Numerisk analys och datalogi, NADA.
    Bruno, William
    Los Alamos National Laboratory.
    Estimation of Reversible Substitution Matrices from Multiple Pairs of Sequences1997Inngår i: Journal of Molecular Evolution, ISSN 0022-2844, E-ISSN 1432-1432, Vol. 45, nr 6, s. 696-703Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We present a method for estimating the most general reversible substitution matrix corresponding to a given collection of pairwise aligned DNA sequences. This matrix can then be used to calculate evolutionary distances between pairs of sequences in the collection. If only two sequences are considered, our method is equivalent to that of Lanave et al. (1984). The main novelty of our approach is in combining data from different sequence pairs. We describe a weighting method for pairs of taxa related by a known tree that results in uniform weights for all branches. Our method for estimating the rate matrix results in fast execution times, even on large data sets, and does not require knowledge of the phylogenetic relationships among sequences. In a test case on a primate pseudogene, the matrix we arrived at resembles one obtained using maximum likelihood, and the resulting distance measure is shown to have better linearity than is obtained in a less general model.

  • 18.
    Auffarth, Benjamin
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Kaplan, Bernhard
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Anders, Lansner
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Map formation in the olfactory bulb by axon guidance of olfactory neurons2011Inngår i: Frontiers in Systems Neuroscience, E-ISSN 1662-5137, Vol. 5, nr 0Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The organization of representations in the brain has been observed to locally reflect subspaces of inputs that are relevant to behavioral or perceptual feature combinations, such as in areas receptive to lower and higher-order features in the visual system. The early olfactory system developed highly plastic mechanisms and convergent evidence indicates that projections from primary neurons converge onto the glomerular level of the olfactory bulb (OB) to form a code composed of continuous spatial zones that are differentially active for particular physico?-chemical feature combinations, some of which are known to trigger behavioral responses. In a model study of the early human olfactory system, we derive a glomerular organization based on a set of real-world,biologically-relevant stimuli, a distribution of receptors that respond each to a set of odorants of similar ranges of molecular properties, and a mechanism of axon guidance based on activity. Apart from demonstrating activity-dependent glomeruli formation and reproducing the relationship of glomerular recruitment with concentration, it is shown that glomerular responses reflect similarities of human odor category perceptions and that further, a spatial code provides a better correlation than a distributed population code. These results are consistent with evidence of functional compartmentalization in the OB and could suggest a function for the bulb in encoding of perceptual dimensions.

    Fulltekst (pdf)
    Auffahrt Kaplan Lansner 2011 Map formation in the olfactory bulb by axon guidance of olfactory neurons.pdf
  • 19.
    Aurell, Erik
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). Aalto University, Finland.
    Innocenti, Nicolas
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). The Hebrew University of Jerusalem, Israel.
    Zhou, Hai-Jun
    State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China.
    The bulk and the tail of minimal absent words in genome sequences2016Inngår i: Physical Biology, ISSN 1478-3967, E-ISSN 1478-3975, Vol. 13, nr 2, artikkel-id 026004Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Minimal absent words (MAW) of a genomic sequence are subsequences that are absent themselves but the subwords of which are all present in the sequence. The characteristic distribution of genomic MAWs as a function of their length has been observed to be qualitatively similar for all living organisms, the bulk being rather short, and only relatively few being long. It has been an open issue whether the reason behind this phenomenon is statistical or reflects a biological mechanism, and what biological information is contained in absent words. % In this work we demonstrate that the bulk can be described by a probabilistic model of sampling words from random sequences, while the tail of long MAWs is of biological origin. We introduce the novel concept of a core of a minimal absent word, which are sequences present in the genome and closest to a given MAW. We show that in bacteria and yeast the cores of the longest MAWs, which exist in two or more copies, are located in highly conserved regions the most prominent example being ribosomal RNAs (rRNAs). We also show that while the distribution of the cores of long MAWs is roughly uniform over these genomes on a coarse-grained level, on a more detailed level it is strongly enhanced in 3' untranslated regions (UTRs) and, to a lesser extent, also in 5' UTRs. This indicates that MAWs and associated MAW cores correspond to fine-tuned evolutionary relationships, and suggest that they can be more widely used as markers for genomic complexity.

  • 20.
    Bahuguna, Jyotika
    et al.
    Aix Marseille Univ, Inst Syst Neurosci, Marseille, France..
    Sahasranamam, Ajith
    Ongil Pvt Ltd, Singapore, Singapore..
    Kumar, Arvind
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Datavetenskap, Beräkningsvetenskap och beräkningsteknik (CST).
    Uncoupling the roles of firing rates and spike bursts in shaping the STN-GPe beta band oscillations2020Inngår i: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 16, nr 3Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The excess of 15-30 Hz (beta-band) oscillations in the basal ganglia is one of the key signatures of Parkinson's disease (PD). The STN-GPe network is integral to generation and modulation of beta band oscillations in basal ganglia. However, the role of changes in the firing rates and spike bursting of STN and GPe neurons in shaping these oscillations has remained unclear. In order to uncouple their effects, we studied the dynamics of STN-GPe network using numerical simulations. In particular, we used a neuron model, in which firing rates and spike bursting can be independently controlled. Using this model, we found that while STN firing rate is predictive of oscillations but GPe firing rate is not. The effect of spike bursting in STN and GPe neurons was state-dependent. That is, only when the network was operating in a state close to the border of oscillatory and non-oscillatory regimes, spike bursting had a qualitative effect on the beta band oscillations. In these network states, an increase in GPe bursting enhanced the oscillations whereas an equivalent proportion of spike bursting in STN suppressed the oscillations. These results provide new insights into the mechanisms underlying the transient beta bursts and how duration and power of beta band oscillations may be controlled by an interplay of GPe and STN firing rates and spike bursts. Author summary The STN-GPe network undergoes a change in firing rates as well as increased bursting during excessive beta band oscillations during Parkinson's disease. In this work we uncouple their effects by using a novel neuron model and show that presence of oscillations is contingent on the increase in STN firing rates, however the effect of spike bursting on oscillations depends on the network state. In a network state on the border of oscillatory and non-oscillatory regime, GPe spike bursting strengthens oscillations. The effect of spike bursting in the STN depends on the proportion of GPe neurons bursting. These results suggest a mechanism underlying a transient beta band oscillation bursts often seen in experimental data.

  • 21. Balbi, P.
    et al.
    Massobrio, P.
    Hellgren Kotaleski, Jeanette
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    A single Markov-type kinetic model accounting for the macroscopic currents of all human voltage-gated sodium channel isoforms2017Inngår i: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 13, nr 9, artikkel-id e1005737Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Modelling ionic channels represents a fundamental step towards developing biologically detailed neuron models. Until recently, the voltage-gated ion channels have been mainly modelled according to the formalism introduced by the seminal works of Hodgkin and Huxley (HH). However, following the continuing achievements in the biophysical and molecular comprehension of these pore-forming transmembrane proteins, the HH formalism turned out to carry limitations and inconsistencies in reproducing the ion-channels electrophysiological behaviour. At the same time, Markov-type kinetic models have been increasingly proven to successfully replicate both the electrophysiological and biophysical features of different ion channels. However, in order to model even the finest non-conducting molecular conformational change, they are often equipped with a considerable number of states and related transitions, which make them computationally heavy and less suitable for implementation in conductance-based neurons and large networks of those. In this purely modelling study we develop a Markov-type kinetic model for all human voltage-gated sodium channels (VGSCs). The model framework is detailed, unifying (i.e., it accounts for all ion-channel isoforms) and computationally efficient (i.e. with a minimal set of states and transitions). The electrophysiological data to be modelled are gathered from previously published studies on whole-cell patch-clamp experiments in mammalian cell lines heterologously expressing the human VGSC subtypes (from NaV1.1 to NaV1.9). By adopting a minimum sequence of states, and using the same state diagram for all the distinct isoforms, the model ensures the lightest computational load when used in neuron models and neural networks of increasing complexity. The transitions between the states are described by original ordinary differential equations, which represent the rate of the state transitions as a function of voltage (i.e., membrane potential). The kinetic model, developed in the NEURON simulation environment, appears to be the simplest and most parsimonious way for a detailed phenomenological description of the human VGSCs electrophysiological behaviour.

  • 22.
    Baldassarre, Federico
    et al.
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Intelligenta system, Robotik, perception och lärande, RPL.
    Menéndez Hurtado, David
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Biofysik. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Elofsson, Arne
    Azizpour, Hossein
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Intelligenta system, Robotik, perception och lärande, RPL.
    GraphQA: Protein Model Quality Assessment using Graph Convolutional Networks2020Inngår i: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 37, nr 3, s. 360-366Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Motivation

    Proteins are ubiquitous molecules whose function in biological processes is determined by their 3D structure. Experimental identification of a protein’s structure can be time-consuming, prohibitively expensive, and not always possible. Alternatively, protein folding can be modeled using computational methods, which however are not guaranteed to always produce optimal results.

    GraphQA is a graph-based method to estimate the quality of protein models, that possesses favorable properties such as representation learning, explicit modeling of both sequential and 3D structure, geometric invariance, and computational efficiency.

    Results

    GraphQA performs similarly to state-of-the-art methods despite using a relatively low number of input features. In addition, the graph network structure provides an improvement over the architecture used in ProQ4 operating on the same input features. Finally, the individual contributions of GraphQA components are carefully evaluated.

    Availability and implementation

    PyTorch implementation, datasets, experiments, and link to an evaluation server are available through this GitHub repository: github.com/baldassarreFe/graphqa

    Supplementary information

    Supplementary material is available at Bioinformatics online.

  • 23.
    Bekkouche, Bo
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). KTH.
    Classification of Neuronal Subtypes in the Striatum and the Effect of Neuronal Heterogeneity on the Activity Dynamics2016Independent thesis Advanced level (degree of Master (Two Years)), 20 poäng / 30 hpOppgave
    Abstract [en]

    Clustering of single-cell RNA sequencing data is often used to show what states and subtypes cells have. Using this technique, striatal cells were clustered into subtypes using different clustering algorithms. Previously known subtypes were confirmed and new subtypes were found. One of them is a third medium spiny neuron subtype. Using the observed heterogeneity, as a second task, this project questions whether or not differences in individual neurons have an impact on the network dynamics. By clustering spiking activity from a neural network model, inconclusive results were found. Both algorithms indicating low heterogeneity, but by altering the quantity of a subtype between a low and high number, and clustering the network activity in each case, results indicate that there is an increase in the heterogeneity. This project shows a list of potential striatal subtypes and gives reasons to keep giving attention to biologically observed heterogeneity.

    Fulltekst (pdf)
    fulltext
  • 24. Bem, T.
    et al.
    Cabelguen, J. M.
    Ekeberg, Örjan
    KTH, Tidigare Institutioner (före 2005), Numerisk analys och datalogi, NADA.
    Grillner, S.
    From swimming to walking: a single basic network for two different behaviors2003Inngår i: Biological Cybernetics, ISSN 0340-1200, E-ISSN 1432-0770, Vol. 88, nr 2, s. 79-90Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In this paper we consider the hypothesis that the spinal locomotor network controlling trunk movements has remained essentially unchanged during the evolutionary transition from aquatic to terrestrial locomotion. The wider repertoire of axial motor patterns expressed by amphibians would then be explained by the influence from separate limb pattern generators, added during this evolution. This study is based on EMG data recorded in vivo from epaxial musculature in the newt Pleurodeles waltl during unrestrained swimming and walking, and on a simplified model of the lamprey spinal pattern generator for swimming. Using computer simulations, we have examined the output generated by the lamprey model network for different input drives. Two distinct inputs were identified which reproduced the main features of the swimming and walking motor patterns in the newt. The swimming pattern is generated when the network receives tonic excitation with local intensity gradients near the neck and girdle regions. To produce the walking pattern, the network must receive (in addition to a tonic excitation at the girdles) a phasic drive which is out of phase in the neck and tail regions in relation to the middle part of the body. To fit the symmetry of the walking pattern, however, the intersegmental connectivity of the network had to be modified by reversing the direction of the crossed inhibitory pathways in the rostral part of the spinal cord. This study suggests that the 'input drive required for the generation of the distinct walking pattern could, at least partly, be attributed to mechanosensory feedback received by the network directly from the intraspinal stretch-receptor system. Indeed, the input drive required resembles the pattern of activity of stretch receptors sensing the lateral bending of the trunk, as expressed during walking in urodeles. Moreover, our results indicate that a nonuniform distribution of these stretch receptors along the trunk can explain the discontinuities exhibited in the swimming pattern of the newt. Thus, original network controlling axial movements not only through a direct coupling at the central level but also via a mechanical coupling between trunk and limbs, which in turn influences the sensory signals sent back to the network. Taken together, our findings support the hypothesis of a phylogenetic conservatism of the spinal locomotor networks generating axial motor patterns from agnathans to amphibians.

  • 25.
    Benjaminsson, Simon
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Fransson, Peter
    Department of Clinical Neuroscience, Karolinska Institute.
    Lansner, Anders
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    A Novel Model-Free Data Analysis Technique Based on Clustering in a Mutual Information Space: Application to Resting-State fMRI2010Inngår i: Frontiers in Systems Neuroscience, E-ISSN 1662-5137, Vol. 4, s. 34:1-34:8Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Non-parametric data-driven analysis techniques can be used to study datasets with few assumptions about the data and underlying experiment. Variations of independent component analysis (ICA) have been the methods mostly used on fMRI data, e.g., in finding resting-state networks thought to reflect the connectivity of the brain. Here we present a novel data analysis technique and demonstrate it on resting-state fMRI data. It is a generic method with few underlying assumptions about the data. The results are built from the statistical relations between all input voxels, resulting in a whole-brain analysis on a voxel level. It has good scalability properties and the parallel implementation is capable of handling large datasets and databases. From the mutual information between the activities of the voxels over time, a distance matrix is created for all voxels in the input space. Multidimensional scaling is used to put the voxels in a lower-dimensional space reflecting the dependency relations based on the distance matrix. By performing clustering in this space we can find the strong statistical regularities in the data, which for the resting-state data turns out to be the resting-state networks. The decomposition is performed in the last step of the algorithm and is computationally simple. This opens up for rapid analysis and visualization of the data on different spatial levels, as well as automatically finding a suitable number of decomposition components.

  • 26.
    Benjaminsson, Simon
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Herman, Pawel
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Lansner, Anders
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Odour discrimination and mixture segmentation in a holistic model of the mammalian olfactory systemManuskript (preprint) (Annet vitenskapelig)
  • 27.
    Benjaminsson, Simon
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC).
    Herman, Pawel
    KTH, Skolan för datavetenskap och kommunikation (CSC).
    Lansner, Anders
    KTH, Skolan för datavetenskap och kommunikation (CSC).
    Performance of a computational model of the mammalian olfactory system2016Inngår i: Neuromorphic Olfaction, CRC Press , 2016, s. 173-211Kapittel i bok, del av antologi (Annet vitenskapelig)
  • 28.
    Benjaminsson, Simon
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Lansner, Anders
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Nexa: A scalable neural simulator with integrated analysis2012Inngår i: Network, ISSN 0954-898X, E-ISSN 1361-6536, Vol. 23, nr 4, s. 254-271Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Large-scale neural simulations encompass challenges in simulator design, data handling and understanding of simulation output. As the computational power of supercomputers and the size of network models increase, these challenges become even more pronounced. Here we introduce the experimental scalable neural simulator Nexa, for parallel simulation of large-scale neural network models at a high level of biological abstraction and for exploration of the simulation methods involved. It includes firing-rate models and capabilities to build networks using machine learning inspired methods for e. g. self-organization of network architecture and for structural plasticity. We show scalability up to the size of the largest machines currently available for a number of model scenarios. We further demonstrate simulator integration with online analysis and real-time visualization as scalable solutions for the data handling challenges.

  • 29.
    Benjaminsson, Simon
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Lundqvist, Mikael
    A model of categorization, learning of invariant representations and sequence prediction utilizing top-down activityManuskript (preprint) (Annet vitenskapelig)
  • 30.
    Bergenstråhle, Ludvig
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Computational Models of Spatial Transcriptomes2024Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Spatial biology is a rapidly growing field that has seen tremendous progress over the last decade. We are now able to measure how the morphology, genome, transcriptome, and proteome of a tissue vary across space. Datasets generated by spatial technologies reflect the complexity of the systems they measure: They are multi-modal, high-dimensional, and layer an intricate web of dependencies between biological compartments at different length scales. To add to this complexity, measurements are often sparse and noisy, obfuscating the underlying biological signal and making the data difficult to interpret. In this thesis, we describe how data from spatial biology experiments can be analyzed with methods from deep learning and generative modeling to accelerate biological discovery. The thesis is divided into two parts. The first part provides an introduction to the fields of deep learning and spatial biology, and how the two can be combined to model spatial biology data. The second part consists of four papers describing methods that we have developed for this purpose. Paper I presents a method for inferring spatial gene expression from hematoxylin and eosin stains. The proposed method offers a data-driven approach to analyzing histopathology images without relying on expert annotations and could be a valuable tool for cancer screening and diagnosis in the clinics. Paper II introduces a method for jointly modeling spatial gene expression with histology images. We show that the method can predict super-resolved gene expression and transcriptionally characterize small-scale anatomical structures. Paper III proposes a method for learning flexible Markov kernels to model continuous and discrete data distributions. We demonstrate the method on various image synthesis tasks, including unconditional image generation and inpainting. Paper IV leverages the techniques introduced in Paper III to integrate data from different spatial biology experiments. The proposed method can be used for data imputation, super resolution, and cross-modality data transfer.

    Download (pdf)
    summary
  • 31.
    Bergenstråhle, Ludvig
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Lundeberg, Joakim
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Multi-Modal Modeling of Spatial Biology DataManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    Spatial biology technologies provide complementary information about tissue anatomy but are often challenging or costly to combine experimentally. Here, we propose a method for multi-modal modeling of spatial biology data that integrates diverse data types and can be used for cross-modality data transfer. We demonstrate the method on histology-guided gene expression imputation and super resolution in sequencing-based spatial transcriptomics, and on feature imputation in high-resolution in situ data.

  • 32.
    Berthet, Pierre
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Hällgren Kotaleski, Jeanette
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Lansner, Anders
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Action selection performance of a reconfigurable Basal Ganglia inspired model with Hebbian-Bayesian Go-NoGo connectivity2012Inngår i: Frontiers in Behavioral Neuroscience, ISSN 1662-5153, E-ISSN 1662-5153, Vol. 6, s. 65-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Several studies have shown a strong involvement of the basal ganglia (BG) in action selection and dopamine dependent learning. The dopaminergic signal to striatum, the input stage of the BG, has been commonly described as coding a reward prediction error (RPE), i.e. the difference between the predicted and actual reward. The RPE has been hypothesized to be critical in the modulation of the synaptic plasticity in cortico-striatal synapses in the direct and indirect pathway. We developed an abstract computational model of the BG, with a dual pathway structure functionally corresponding to the direct and indirect pathways, and compared its behaviour to biological data as well as other reinforcement learning models. The computations in our model are inspired by Bayesian inference, and the synaptic plasticity changes depend on a three factor Hebbian-Bayesian learning rule based on co-activation of pre- and post-synaptic units and on the value of the RPE. The model builds on a modified Actor-Critic architecture and implements the direct (Go) and the indirect (NoGo) pathway, as well as the reward prediction (RP) system, acting in a complementary fashion. We investigated the performance of the model system when different configurations of the Go, NoGo and RP system were utilized, e.g. using only the Go, NoGo, or RP system, or combinations of those. Learning performance was investigated in several types of learning paradigms, such as learning-relearning, successive learning, stochastic learning, reversal learning and a two-choice task. The RPE and the activity of the model during learning were similar to monkey electrophysiological and behavioural data. Our results, however, show that there is not a unique best way to configure this BG model to handle well all the learning paradigms tested. We thus suggest that an agent might dynamically configure its action selection mode, possibly depending on task characteristics and also on how much time is available.

  • 33.
    Berthet, Pierre
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Lansner, Anders
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Optogenetic Stimulation in a Computational Model of the Basal Ganglia Biases Action Selection and Reward Prediction Error2014Inngår i: PLOS ONE, E-ISSN 1932-6203, Vol. 9, nr 3, s. e90578-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Optogenetic stimulation of specific types of medium spiny neurons (MSNs) in the striatum has been shown to bias the selection of mice in a two choices task. This shift is dependent on the localisation and on the intensity of the stimulation but also on the recent reward history. We have implemented a way to simulate this increased activity produced by the optical flash in our computational model of the basal ganglia (BG). This abstract model features the direct and indirect pathways commonly described in biology, and a reward prediction pathway (RP). The framework is similar to Actor-Critic methods and to the ventral/ dorsal distinction in the striatum. We thus investigated the impact on the selection caused by an added stimulation in each of the three pathways. We were able to reproduce in our model the bias in action selection observed in mice. Our results also showed that biasing the reward prediction is sufficient to create a modification in the action selection. However, we had to increase the percentage of trials with stimulation relative to that in experiments in order to impact the selection. We found that increasing only the reward prediction had a different effect if the stimulation in RP was action dependent (only for a specific action) or not. We further looked at the evolution of the change in the weights depending on the stage of learning within a block. A bias in RP impacts the plasticity differently depending on that stage but also on the outcome. It remains to experimentally test how the dopaminergic neurons are affected by specific stimulations of neurons in the striatum and to relate data to predictions of our model.

  • 34. Birin, H.
    et al.
    Gal-Or, Z.
    Elias, Isaac
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Tuller, T.
    Inferring horizontal transfers in the presence of rearrangements by the minimum evolution criterion2008Inngår i: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 24, nr 6, s. 826-832Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Motivation: The evolution of viruses is very rapid and in addition to local point mutations (insertion, deletion, substitution) it also includes frequent recombinations, genome rearrangements and horizontal transfer of genetic materials (HGTS). Evolutionary analysis of viral sequences is therefore a complicated matter for two main reasons: First, due to HGTs and recombinations, the right model of evolution is a network and not a tree. Second, due to genome rearrangements, an alignment of the input sequences is not guaranteed. These facts encourage developing methods for inferring phylogenetic networks that do not require aligned sequences as input. Results: In this work, we present the first computational approach which deals with both genome rearrangements and horizontal gene transfers and does not require a multiple alignment as input. We formalize a new set of computational problems which involve analyzing such complex models of evolution. We investigate their computational complexity, and devise algorithms for solving them. Moreover, we demonstrate the viability of our methods on several synthetic datasets as well as four biological datasets.

  • 35. Birin, Hadas
    et al.
    Gal-Or, Zohar
    Elias, Isaac
    KTH, Skolan för datavetenskap och kommunikation (CSC), Numerisk Analys och Datalogi, NADA.
    Tuller, Tamir
    Inferring models of rearrangements, recombinations, and horizontal transfers by the minimum evolution criterion2007Inngår i: Algorithms in Bioinformatics, Proceedings / [ed] Giancarlo, R; Hannenhalli, S, 2007, Vol. 4645, s. 111-123Konferansepaper (Fagfellevurdert)
    Abstract [en]

    The evolution of viruses is very rapid and in addition to local point mutations (insertion, deletion, substitution) it also includes frequent recombinations, genome rearrangements, and horizontal transfer of genetic material. Evolutionary analysis of viral sequences is therefore a complicated matter for two main reasons: First, due to HGTs and recombinations, the right model of evolution is a network and not a tree. Second, due to genome rearrangements, an alignment of the input sequences is not guaranteed. Since contemporary methods for inferring phylogenetic networks require aligned sequences as input, they cannot deal with viral evolution. In this work we present the first computational approach which deals with both genome rearrangements and horizontal gene transfers and does not require a multiple alignment as input. We formalize a new set of computational problems which involve analyzing such complex models of evolution, investigate their computational complexity, and devise algorithms for solving them. Moreover, we demonstrate the viability of our methods on several synthetic datasets as well as biological datasets.

  • 36. Björkman, Eva
    et al.
    Zagal, Juan Cristobal
    Lindeberg, Tony
    KTH, Tidigare Institutioner (före 2005), Numerisk analys och datalogi, NADA.
    Roland, Per E.
    Evaluation of design options for the scale-space primal sketch analysis of brain activation images2000Inngår i: : HBM'00, published in Neuroimage, volume 11, number 5, 2000, 2000, Vol. 11, s. 656-656Konferansepaper (Fagfellevurdert)
    Abstract [en]

    A key issue in brain imaging concerns how to detect the functionally activated regions from PET and fMRI images. In earlier work, it has been shown that the scale-space primal sketch provides a useful tool for such analysis [1]. The method includes presmoothing with different filter widths and automatic estimation of the spatial extent of the activated regions (blobs).

    The purpose is to present two modifications of the scale-space primal sketch, as well as a quantitative evaluation which shows that these modifications improve the performance, measured as the separation between blob descriptors extracted from PET images and from noise images. This separation is essential for future work of associating a statistical p-value with the scale-space blob descriptors.

    Fulltekst (pdf)
    fulltext
  • 37.
    Blau, Christian
    et al.
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Biofysik.
    Yvonnesdotter, Linnea
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Stockholm, Sweden..
    Lindahl, Erik
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Biofysik. Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Stockholm, Sweden..
    Gentle and fast all-atom model refinement to cryo-EM densities via a maximum likelihood approach2023Inngår i: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 19, nr 7, s. e1011255-, artikkel-id e1011255Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Better detectors and automated data collection have generated a flood of high-resolution cryo-EM maps, which in turn has renewed interest in improving methods for determining structure models corresponding to these maps. However, automatically fitting atoms to densities becomes difficult as their resolution increases and the refinement potential has a vast number of local minima. In practice, the problem becomes even more complex when one also wants to achieve a balance between a good fit of atom positions to the map, while also establishing good stereochemistry or allowing protein secondary structure to change during fitting. Here, we present a solution to this challenge using a maximum likelihood approach by formulating the problem as identifying the structure most likely to have produced the observed density map. This allows us to derive new types of smooth refinement potential-based on relative entropy-in combination with a novel adaptive force scaling algorithm to allow balancing of force-field and density-based potentials. In a low-noise scenario, as expected from modern cryo-EM data, the relative-entropy based refinement potential outperforms alternatives, and the adaptive force scaling appears to aid all existing refinement potentials. The method is available as a component in the GROMACS molecular simulation toolkit. Author summaryCryo-electron microscopy has gone through a revolution and now regularly produces data with 2 & ANGS; resolution. However, this data comes in the shape of density maps, and fitting atomic coordinates into these maps can be a labor-intensive and challenging problem. This is particularly valid when there are multiple conformations, flexible regions, or parts of the structure with lower resolution. In many cases it is also desirable to to understand how a molecule moves between such conformations. This can be addressed with molecular dynamics simulations using densities as target restraints, but the refinement potentials commonly used can distort protein structure or get stuck in local minima when the cryo-EM map has high resolution. This work derives new refinement potentials based on models of the cryo-EM scattering process that provide a gentle way to fit protein structures to densities in simulations, and we also suggest an automated heuristic way to balance the influence of the map and simulation force field.

  • 38.
    Bresin, Roberto
    KTH, Skolan för datavetenskap och kommunikation (CSC), Tal, musik och hörsel, TMH.
    What is the color of that music performance?2005Inngår i: Proceedings of the International Computer Music Conference - ICMC 2005, Barcelona, 2005, s. 367-370Konferansepaper (Fagfellevurdert)
    Abstract [en]

    The representation of expressivity in music is still a fairlyunexplored field. Alternative ways of representing musicalinformation are necessary when providing feedback onemotion expression in music such as in real-time tools formusic education, or in the display of large music databases.One possible solution could be a graphical non-verbal representationof expressivity in music performance using coloras index of emotion. To determine which colors aremost suitable for an emotional expression, a test was run.Subjects rated how well each of 8 colors and their 3 nuancescorresponds to each of 12 music performances expressingdifferent emotions. Performances were playedby professional musicians with 3 instruments, saxophone,guitar, and piano. Results show that subjects associateddifferent hues to different emotions. Also, dark colorswere associated to music in minor tonality and light colorsto music in major tonality. Correspondence betweenspectrum energy and color hue are preliminary discussed.

  • 39.
    Bresin, Roberto
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Tal, musik och hörsel, TMH, Musikakustik.
    Delle Monache, Stefano
    University of Verona.
    Fontana, Federico
    University of Verona.
    Papetti, Stefano
    University of Verona.
    Polotti, Pietro
    University of Verona.
    Visell, Yon
    McGill University.
    Auditory feedback through continuous control of crumpling sound synthesis2008Inngår i: Proceedings of Sonic Interaction Design: Sound, Information and Experience. A CHI 2008 Workshop organized by COST Action IC0601, IUAV University of Venice , 2008, s. 23-28Konferansepaper (Fagfellevurdert)
    Abstract [en]

    A realtime model for the synthesis of crumpling sounds ispresented. By capturing the statistics of short sonic transients which give rise to crackling noise, it allows for a consistent description of a broad spectrum of audible physical processes which emerge in several everyday interaction contexts.The model drives a nonlinear impactor that sonifies every transient, and it can be parameterized depending on the physical attributes of the crumpling material. Three different scenarios are described, respectively simulating the foot interaction with aggregate ground materials, augmenting a dining scenario, and affecting the emotional content of a footstep sequence. Taken altogether, they emphasize the potential generalizability of the model to situations in which a precise control of auditory feedback can significantly increase the enactivity and ecological validity of an interface.

  • 40.
    Carannante, Ilaria
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Datavetenskap, Beräkningsvetenskap och beräkningsteknik (CST). KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Computational Modelling and Topological Analysis of the striatal microcircuitry in health and Parkinson's disease2023Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    The basal ganglia are evolutionary conserved nuclei located at the base of the forebrain. They are a central hub in the control of motion and their dysfunctions lead to a variety of movement related disorders, including Parkinson's disease (PD).

    The largest nucleus and main input stage of the basal ganglia is the striatum. It receives excitatory glutamatergic projections primarily from cortex and thalamus as well as modulatory dopaminergic input from the substantia nigra pars compacta and the ventral tegmental area. Striatal output is mediated by the direct and indirect pathway striatal projection neurons (dSPNs and iSPNs, respectively). In rodents, they account for 95% of the neurons, while the remaining 5% are interneurons, which do not project outside the striatum.

    The aim of this thesis is to develop an in silico striatal microcircuit in health and PD, and to compare these two networks using electrophysiological simulations and topological analysis.

    The neuron types included are the striatal projection neurons (dSPN and iSPN) and three of the main interneuron classes: FS, LTS and ChIN. Their multi-compartmental models are based on detailed morphological reconstructions, ion channels expression and electrophysiological ex vivo rodents experimental data from control and PD brains.

    In Paper A, a comparison between two methods commonly used to model ion channels was presented.

    In Paper B, the healthy striatal microcircuit was created. We presented a modelling framework called Snudda. It enables the creation of large-scale networks by: placing neurons using appropriate density, predicting synaptic connectivity based on touch detection and a set of pruning rules, setting up external input and modulation, and finally running the simulations. It is written in Python and uses the NEURON simulator.

    In Paper C, we conducted a computational study on the reciprocal interaction between ChIN and LTS interneurons. Specifically, we simulate the inhibition of LTS via muscarinic M4 receptors following acetylcholine release from ChIN as well as the prolonged depolarization of ChIN subsequent to the release of nitric oxide from LTS.

    In Paper D, we developed a pipeline to model the NMDA and AMPA postsynaptic currents in striatal neurons following glutamate release from cortex and thalamus. This was done to improve the accuracy of the existing synaptic models.

    In Paper E, the PD striatal microcircuit was created. First, we modelled the morphological changes in both SPNs and FS as well as the electrophysiological alterations in SPNs. Then we predicted and quantified how the intrastriatal connectivity is altered using anatomically constrained synapse placement and topological analysis of the resulting network. Finally we investigated how the effective glutamatergic drive to SPNs is modified.

    Overall, in this thesis we further advanced the development of the simulation framework for the study of the basal ganglia function and initiated systematic model-based large-scale computational analysis of their abnormal PD state.

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    summary
  • 41.
    Carlsson, Leo
    et al.
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap.
    Samuelsson, Peter
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap, Processer.
    A Proposed Methodology to Evaluate Machine Learning Models at Near-Upper-Bound Predictive Performance—Some Practical Cases from the Steel Industry2023Inngår i: Processes, ISSN 2227-9717, Vol. 11, nr 12, artikkel-id 3447Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The present work aims to answer three essential research questions (RQs) that have previously not been explicitly dealt with in the field of applied machine learning (ML) in steel process engineering. RQ1: How many training data points are needed to create a model with near-upper-bound predictive performance on test data? RQ2: What is the near-upper-bound predictive performance on test data? RQ3: For how long can a model be used before its predictive performance starts to decrease? A methodology to answer these RQs is proposed. The methodology uses a developed sampling algorithm that samples numerous unique training and test datasets. Each sample was used to create one ML model. The predictive performance of the resulting ML models was analyzed using common statistical tools. The proposed methodology was applied to four disparate datasets from the steel industry in order to externally validate the experimental results. It was shown that the proposed methodology can be used to answer each of the three RQs. Furthermore, a few findings that contradict established ML knowledge were also found during the application of the proposed methodology.

  • 42. Cervenka, Simon
    et al.
    Varrone, Andrea
    Fransén, Erik
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Halldin, Christer
    Farde, Lars
    PET Studies of D2-Receptor Binding in Striatal and Extrastriatal Brain Regions: Biochemical Support In Vivo for Separate Dopaminergic Systems in Humans2010Inngår i: Synapse, ISSN 0887-4476, E-ISSN 1098-2396, Vol. 64, nr 6, s. 478-485Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Most molecular imaging studies of the dopamine (DA) system performed to date have focused on the striatum, a region receiving dense dopaminergic innervation. In clinical research on the DA D2-receptor, striatal binding has often been regarded as an index of global DA function, based on the underlying assumption of common regulatory mechanisms for receptor expression across brain regions. Recent data has challenged this view, suggesting differences in genetic regulation between striatal and extrastriatal brain regions. The relationship between binding levels in brain regions has, however, not been directly examined in the same sample. In this study, we searched for interregional correlations between DA D2-receptor availability as determined with Positron Emission Tomography in 16 control subjects. The radioligands [C-11]raclopride and [C-11]FLB 457 were used for measurements of D2-receptor binding in striatal and extrastriatal regions, respectively. No correlation was observed between D2-receptor availability in striatum and any of the extrastriatal regions, as assessed using both region of interest- and voxel-based analyses. Instead, the pattern of correlations was consistent with the model of separate dopaminergic systems as has been originally observed in rodents. These preliminary results encourage approaches searching for individual patterns of receptor binding across the whole brain volume in clinical studies on the dopamine system.

  • 43.
    Chatterjee, Saikat
    et al.
    KTH, Skolan för elektro- och systemteknik (EES), Kommunikationsteori.
    Koslicki, David
    Dept of Mathematics, Oregon State University, Corvallis, USA.
    Dong, Siyuan
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Innocenti, Nicolas
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Cheng, Lu
    Dept of Mathematics and Statistics, University of Helsinki, Finland.
    Lan, Yueheng
    Dept of Physics, Tsinghua University, Beijing, China.
    Vehkaperä, Mikko
    KTH, Skolan för elektro- och systemteknik (EES), Kommunikationsteori.
    Skoglund, Mikael
    KTH, Skolan för elektro- och systemteknik (EES), Centra, ACCESS Linnaeus Centre. KTH, Skolan för elektro- och systemteknik (EES), Kommunikationsteori.
    K. Rasmussen, Lars
    KTH, Skolan för elektro- och systemteknik (EES), Kommunikationsteori.
    Aurell, Erik
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Corander, Jukka
    Dept of Signal Processing, Aalto University, Finland.
    SEK: Sparsity exploiting k-mer-based estimation of bacterial community composition2014Inngår i: Bioinformatics, ISSN 1460-2059, Vol. 30, nr 17, s. 2423-2431Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Motivation: Estimation of bacterial community composition from a high-throughput sequenced sample is an important task in metagenomics applications. As the sample sequence data typically harbors reads of variable lengths and different levels of biological and technical noise, accurate statistical analysis of such data is challenging. Currently popular estimation methods are typically time-consuming in a desktop computing environment.

    Results: Using sparsity enforcing methods from the general sparse signal processing field (such as compressed sensing), we derive a solution to the community composition estimation problem by a simultaneous assignment of all sample reads to a pre-processed reference database. A general statistical model based on kernel density estimation techniques is introduced for the assignment task, and the model solution is obtained using convex optimization tools. Further, we design a greedy algorithm solution for a fast solution. Our approach offers a reasonably fast community composition estimation method, which is shown to be more robust to input data variation than a recently introduced related method.

    Availability and implementation: A platform-independent Matlab implementation of the method is freely available at http://www.ee.kth.se/ctsoftware; source code that does not require access to Matlab is currently being tested and will be made available later through the above Web site.

    Fulltekst (pdf)
    SEK paper
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    SEK Code
  • 44. Chaudhry, Q. A.
    et al.
    Hanke, Michael
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA.
    Morgenstern, R.
    Dreij, K.
    Surface reactions on the cytoplasmatic membranes - Mathematical modeling of reaction and diffusion systems in a cell2014Inngår i: Journal of Computational and Applied Mathematics, ISSN 0377-0427, E-ISSN 1879-1778, Vol. 262, s. 244-260Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A human cell consists schematically of an outer cellular membrane, a cytoplasm containing a large number of organelles (mitochondria, endoplasmatic reticulum etc.), a nuclear membrane and finally the cellular nucleus containing DNA. The organelles create a complex and dense system of membranes or sub-domains throughout the cytoplasm. The mathematical description leads to a system of reaction-diffusion equations in a complex geometrical domain, dominated by thin membranous structures with similar physical and chemical properties. In a previous model, we considered only spatially distributed reaction and diffusion processes. However, from experiments it is known that membrane bound proteins play an important role in the metabolism of certain substances. In the present paper we develop a homogenization strategy which includes both volume and surface reactions. The homogenized system is a reaction-diffusion system in the cytoplasm which is coupled to the surrounding cell components by correspondingly modified transfer conditions. The approach is verified by application to a system modeling the cellular uptake and intracellular dynamics of carcinogenic polycyclic aromatic hydrocarbons.

  • 45.
    Chen, Fengnong
    et al.
    KTH.
    Chen, P. -L
    Xie, Y. -P
    Ying, N. -J
    Hamid Muhammed, Hamed
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH).
    Yang, Y.
    Rapid Detection for Toxic Capsules with Chromium Based on Hyperspectral Imaging Technology2017Inngår i: Jiliang Xuebao/Acta Metrologica Sinica, ISSN 1000-1158, Vol. 38, nr 6, s. 765-769Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The rapid detection method of chromium content in medicinal capsules based on hyperspectral imaging was studied. Firstly, analysis of medical empty hard gelatin capsule was used as the control group by traditional atomic absorption spectroscopy. Then, the hyperspectral data of 1048 samples were analyzed by dimensionality reduction and qualitative analysis. Finally, the partial least squares discriminant analysis method was used to process the spectral data. If 4 LV are as input features in the partial lease squares discrimination analysis model, the classification accuracy reached 100%, the correlation coefficient of cross validation and sample prediction are 0.923 and 0.972, respectively. Sensitivity and specificity are both 100%. 

  • 46.
    Chrysanthidis, Nikolaos
    et al.
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Datavetenskap, Beräkningsvetenskap och beräkningsteknik (CST). Aristotle University of Thessaloniki, Faculty of Engineering, School of Electrical and Computer Engineering, 54124, Thessaloniki, Greece.
    Fiebig, Florian
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Datavetenskap, Beräkningsvetenskap och beräkningsteknik (CST). Institute for Adaptive and Neural Computation, Edinburgh University, EH8 9AB Edinburgh, Scotland.
    Lansner, Anders
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Datavetenskap, Beräkningsvetenskap och beräkningsteknik (CST). Department of Numerical Analysis and Computer Science, Stockholm University, 10691 Stockholm, Sweden.
    Introducing double bouquet cells into a modular cortical associative memory modelManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    We present an electrophysiological model of double bouquet cells and integrate them into an established cortical columnar microcircuit model that has previously been used as a spiking attractor model for memory. Learning in that model relies on a Bayesian-Hebbian learning rule to condition recurrent connectivity between pyramidal cells. We here demonstrate that the inclusion of a biophysically plausible double bouquet cell model can solve earlier concerns about learning rules that simultaneously learn excitation and inhibition and might thus violate Dale's Principle. We show that learning ability and resulting effective connectivity between functional columns of previous network models is preserved when pyramidal synapses onto double-bouquet cells are plastic under the same Hebbian-Bayesian learning rule. The proposed architecture draws on experimental evidence on double bouquet cells and effectively solves the problem of duplexed learning of inhibition and excitation by replacing recurrent inhibition between pyramidal cells in functional columns of different stimulus selectivity with a plastic disynaptic pathway. We thus show that the resulting change to the microcircuit architecture improves the model's biological plausibility without otherwise impacting the models spiking activity, basic operation, and learning abilities.

    Fulltekst (pdf)
    fulltext
  • 47.
    Cürüklü, Baran
    et al.
    Department of Computer Science and Engineering, Mälardalen University.
    Lansner, Anders
    KTH, Skolan för datavetenskap och kommunikation (CSC), Numerisk Analys och Datalogi, NADA.
    A model of the summation pools within the layer 4 (area 17)2005Inngår i: Neurocomputing, ISSN 0925-2312, E-ISSN 1872-8286, Vol. 65, s. 167-172Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We propose a developmental model of the summation pools within the layer 4. The model is based on the modular structure of the neocortex and captures some of the known properties of layer 4. Connections between the orientation minicolumns are developed during exposure to visual input. Excitatory local connections are dense and biased towards the iso-orientation domain. Excitatory long-range connections are sparse and target all orientation domains equally. Inhibition is local. The summation pools are elongated along the orientation axis. These summation pools can facilitate weak and poorly tuned LGN input and explain improved visibility as an effect of enlargement of a stimulus.

  • 48.
    Dahl, Sofia
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Tal, musik och hörsel, TMH, Musikakustik.
    Bevilacqua, Frédéric
    Bresin, Roberto
    KTH, Skolan för datavetenskap och kommunikation (CSC), Tal, musik och hörsel, TMH, Musikakustik.
    Clayton, Martin
    Leante, Laura
    Poggi, Isabella
    Rasamimanana, Nicolas
    Gestures in performance2009Inngår i: Musical Gestures: Sound, Movement, and Meaning / [ed] Godøy, Rolf Inge; Leman, Marc, New York: Routledge , 2009, s. 36-68Kapittel i bok, del av antologi (Fagfellevurdert)
    Abstract [en]

    We experience and understand the world, including music, through body movement–when we hear something, we are able to make sense of it by relating it to our body movements, or form an image in our minds of body movements. Musical Gestures is a collection of essays that explore the relationship between sound and movement. It takes an interdisciplinary approach to the fundamental issues of this subject, drawing on ideas, theories and methods from disciplines such as musicology, music perception, human movement science, cognitive psychology, and computer science.

  • 49. De Schutter, E.
    et al.
    Ekeberg, Örjan
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Hellgren Kotaleski, Jeanette
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Achard, P.
    Lansner, Anders
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB.
    Biophysically detailed modelling of microcircuits and beyond2005Inngår i: TINS - Trends in Neurosciences, ISSN 0166-2236, E-ISSN 1878-108X, Vol. 28, nr 10, s. 562-569Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Realistic bottom-up modelling has been seminal to understanding which properties of microcircuits control their dynamic behaviour, such as the locomotor rhythms generated by central pattern generators. In this article of the TINS Microcircuits Special Feature, we review recent modelling work on the leech-heartbeat and lamprey-swimming pattern generators as examples. Top-down mathematical modelling also has an important role in analyzing microcircuit properties but it has not always been easy to reconcile results from the two modelling approaches. Most realistic microcircuit models are relatively simple and need to be made more detailed to represent complex processes more accurately. We review methods to add neuromechanical feedback, biochemical pathways or full dendritic morphologies to microcircuit models. Finally, we consider the advantages and challenges of full-scale simulation of networks of microcircuits.

  • 50.
    Dennler, Nik
    et al.
    Univ Zurich, Inst Neuroinformat, Zurich, Switzerland.;Swiss Fed Inst Technol, Zurich, Switzerland..
    Haessig, Germain
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Datavetenskap. Univ Zurich, Inst Neuroinformat, Zurich, Switzerland.;Swiss Fed Inst Technol, Zurich, Switzerland.
    Cartiglia, Matteo
    Univ Zurich, Inst Neuroinformat, Zurich, Switzerland.;Swiss Fed Inst Technol, Zurich, Switzerland..
    Indiveri, Giacomo
    Univ Zurich, Inst Neuroinformat, Zurich, Switzerland.;Swiss Fed Inst Technol, Zurich, Switzerland..
    Online Detection of Vibration Anomalies Using Balanced Spiking Neural Networks2021Inngår i: 2021 IEEE 3Rd International Conference On Artificial Intelligence Circuits And Systems (Aicas), Institute of Electrical and Electronics Engineers (IEEE) , 2021Konferansepaper (Fagfellevurdert)
    Abstract [en]

    Vibration patterns yield valuable information about the health state of a running machine, which is commonly exploited in predictive maintenance tasks for large industrial systems. However, the overhead, in terms of size, complexity and power budget, required by classical methods to exploit this information is often prohibitive for smaller-scale applications such as autonomous cars, drones or robotics. Here we propose a neuromorphic approach to perform vibration analysis using spiking neural networks that can be applied to a wide range of scenarios. We present a spike-based end-to-end pipeline able to detect system anomalies from vibration data, using building blocks that are compatible with analog-digital neuromorphic circuits. This pipeline operates in an online unsupervised fashion, and relies on a cochlea model, on feedback adaptation and on a balanced spiking neural network. We show that the proposed method achieves state-of-the-art performance or better against two publicly available data sets. Further, we demonstrate a working proof-of-concept implemented on an asynchronous neuromorphic processor device. This work represents a significant step towards the design and implementation of autonomous low-power edge-computing devices for online vibration monitoring.

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