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  1. AU="Krach, Florian"
  2. AU="Modak, Manisha A"
  3. AU="Ottolini, Matteo"
  4. AU="Douglas Hanahan"
  5. AU="Bieniaszewska, Maria"
  6. AU="Alovisi, Camilla"
  7. AU="Lijfering, Willem M."
  8. AU="Rademacher, Jessica"
  9. AU="Dartigues, Jean-François"
  10. AU="Denicola, Anthony J"
  11. AU="Zhang, Xuewei"
  12. AU="Li, Yanjiao"
  13. AU="Botelho Meireles de Souza, Guilherme"
  14. AU="Gong, Yu-Qing"
  15. AU="Eisch, J"
  16. AU=De Vito Eduardo L
  17. AU="Lowsky, Robert"
  18. AU="Lindner, M."
  19. AU="Mugnai, Giacomo"
  20. AU="Chollet-Krugler, Marylène"
  21. AU="Firsanov, Denis"
  22. AU="Jo, Dong-Gyu"
  23. AU="Greenland, John R"
  24. AU="J Natale"
  25. AU="Drost, Carolin Christina"
  26. AU="Silvera, Risset"
  27. AU="Zgubič, M"
  28. AU="Russo, Rosita"
  29. AU="Ruiz-Ortega, Marta"
  30. AU="T Talbot"
  31. AU="Emoto, Kasey C"
  32. AU="Moos, W H" AU="Moos, W H"
  33. AU=Singh Sweta AU=Singh Sweta
  34. AU="Pimentel, Mauricio"
  35. AU="Kim, Ji Hee"
  36. AU=Ross Jeffrey S
  37. AU=Malhotra Atul
  38. AU="Tiesler, Carla M T"
  39. AU="Merighi, Adalberto" AU="Merighi, Adalberto"

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  1. Buch ; Online: Optimal Estimation of Generic Dynamics by Path-Dependent Neural Jump ODEs

    Krach, Florian / Nübel, Marc / Teichmann, Josef

    2022  

    Abstract: This paper studies the problem of forecasting general stochastic processes using a path-dependent extension of the Neural Jump ODE (NJ-ODE) framework \citep{herrera2021neural}. While NJ-ODE was the first framework to establish convergence guarantees for ... ...

    Abstract This paper studies the problem of forecasting general stochastic processes using a path-dependent extension of the Neural Jump ODE (NJ-ODE) framework \citep{herrera2021neural}. While NJ-ODE was the first framework to establish convergence guarantees for the prediction of irregularly observed time series, these results were limited to data stemming from It\^o-diffusions with complete observations, in particular Markov processes, where all coordinates are observed simultaneously. In this work, we generalise these results to generic, possibly non-Markovian or discontinuous, stochastic processes with incomplete observations, by utilising the reconstruction properties of the signature transform. These theoretical results are supported by empirical studies, where it is shown that the path-dependent NJ-ODE outperforms the original NJ-ODE framework in the case of non-Markovian data. Moreover, we show that PD-NJ-ODE can be applied successfully to classical stochastic filtering problems and to limit order book (LOB) data.
    Schlagwörter Statistics - Machine Learning ; Computer Science - Machine Learning ; Mathematics - Numerical Analysis ; Mathematics - Probability
    Thema/Rubrik (Code) 006
    Erscheinungsdatum 2022-06-28
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    Dokumenttyp Buch ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  2. Artikel ; Online: Decoding Parkinson's disease - iPSC-derived models in the OMICs era.

    Krach, Florian / Bogiongko, Marios-Evangelos / Winner, Beate

    Molecular and cellular neurosciences

    2020  Band 106, Seite(n) 103501

    Abstract: Parkinson's disease (PD) is a neurodegenerative disorder characterized by the loss of dopaminergic neurons in the midbrain. In recent years, researchers have started studying PD using induced pluripotent stem cell (iPSC) models of the disease. ... ...

    Abstract Parkinson's disease (PD) is a neurodegenerative disorder characterized by the loss of dopaminergic neurons in the midbrain. In recent years, researchers have started studying PD using induced pluripotent stem cell (iPSC) models of the disease. Surprisingly, few studies have combined iPSC-technology with the so-called powerful 'omics' approaches. Here, we review the current state of omics applications used in combination with iPSC-derived models to study PD. Our focus is on studies investigating transcriptional changes and publications using proteomics applications. Lastly, we discuss current caveats in the field and identify potential future directions to obtain novel insights into PD pathology.
    Mesh-Begriff(e) Animals ; Dopaminergic Neurons/metabolism ; Dopaminergic Neurons/pathology ; Humans ; Induced Pluripotent Stem Cells/metabolism ; Induced Pluripotent Stem Cells/pathology ; Models, Biological ; Parkinson Disease/metabolism ; Parkinson Disease/pathology ; Proteomics
    Sprache Englisch
    Erscheinungsdatum 2020-05-18
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1046640-x
    ISSN 1095-9327 ; 1044-7431
    ISSN (online) 1095-9327
    ISSN 1044-7431
    DOI 10.1016/j.mcn.2020.103501
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Buch ; Online: Optimal Stopping via Randomized Neural Networks

    Herrera, Calypso / Krach, Florian / Ruyssen, Pierre / Teichmann, Josef

    2021  

    Abstract: This paper presents the benefits of using randomized neural networks instead of standard basis functions or deep neural networks to approximate the solutions of optimal stopping problems. The key idea is to use neural networks, where the parameters of ... ...

    Abstract This paper presents the benefits of using randomized neural networks instead of standard basis functions or deep neural networks to approximate the solutions of optimal stopping problems. The key idea is to use neural networks, where the parameters of the hidden layers are generated randomly and only the last layer is trained, in order to approximate the continuation value. Our approaches are applicable to high dimensional problems where the existing approaches become increasingly impractical. In addition, since our approaches can be optimized using simple linear regression, they are easy to implement and theoretical guarantees can be provided. We test our approaches for American option pricing on Black--Scholes, Heston and rough Heston models and for optimally stopping a fractional Brownian motion. In all cases, our algorithms outperform the state-of-the-art and other relevant machine learning approaches in terms of computation time while achieving comparable results. Moreover, we show that they can also be used to efficiently compute Greeks of American options.
    Schlagwörter Statistics - Machine Learning ; Computer Science - Machine Learning ; Mathematics - Numerical Analysis ; Mathematics - Probability ; Quantitative Finance - Computational Finance ; 60G40 (Primary) ; 68T07 (Secondary)
    Thema/Rubrik (Code) 006
    Erscheinungsdatum 2021-04-28
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    Dokumenttyp Buch ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  4. Buch ; Online: Local Lipschitz Bounds of Deep Neural Networks

    Herrera, Calypso / Krach, Florian / Teichmann, Josef

    2020  

    Abstract: The Lipschitz constant is an important quantity that arises in analysing the convergence of gradient-based optimization methods. It is generally unclear how to estimate the Lipschitz constant of a complex model. Thus, this paper studies an important ... ...

    Abstract The Lipschitz constant is an important quantity that arises in analysing the convergence of gradient-based optimization methods. It is generally unclear how to estimate the Lipschitz constant of a complex model. Thus, this paper studies an important problem that may be useful to the broader area of non-convex optimization. The main result provides a local upper bound on the Lipschitz constants of a multi-layer feed-forward neural network and its gradient. Moreover, lower bounds are established as well, which are used to show that it is impossible to derive global upper bounds for the Lipschitz constants. In contrast to previous works, we compute the Lipschitz constants with respect to the network parameters and not with respect to the inputs. These constants are needed for the theoretical description of many step size schedulers of gradient based optimization schemes and their convergence analysis. The idea is both simple and effective. The results are extended to a generalization of neural networks, continuously deep neural networks, which are described by controlled ODEs.
    Schlagwörter Statistics - Machine Learning ; Computer Science - Machine Learning ; Quantitative Finance - Mathematical Finance
    Thema/Rubrik (Code) 510
    Erscheinungsdatum 2020-04-27
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    Dokumenttyp Buch ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  5. Buch ; Online: Neural Jump Ordinary Differential Equations

    Herrera, Calypso / Krach, Florian / Teichmann, Josef

    Consistent Continuous-Time Prediction and Filtering

    2020  

    Abstract: Combinations of neural ODEs with recurrent neural networks (RNN), like GRU-ODE-Bayes or ODE-RNN are well suited to model irregularly observed time series. While those models outperform existing discrete-time approaches, no theoretical guarantees for ... ...

    Abstract Combinations of neural ODEs with recurrent neural networks (RNN), like GRU-ODE-Bayes or ODE-RNN are well suited to model irregularly observed time series. While those models outperform existing discrete-time approaches, no theoretical guarantees for their predictive capabilities are available. Assuming that the irregularly-sampled time series data originates from a continuous stochastic process, the $L^2$-optimal online prediction is the conditional expectation given the currently available information. We introduce the Neural Jump ODE (NJ-ODE) that provides a data-driven approach to learn, continuously in time, the conditional expectation of a stochastic process. Our approach models the conditional expectation between two observations with a neural ODE and jumps whenever a new observation is made. We define a novel training framework, which allows us to prove theoretical guarantees for the first time. In particular, we show that the output of our model converges to the $L^2$-optimal prediction. This can be interpreted as solution to a special filtering problem. We provide experiments showing that the theoretical results also hold empirically. Moreover, we experimentally show that our model outperforms the baselines in more complex learning tasks and give comparisons on real-world datasets.
    Schlagwörter Statistics - Machine Learning ; Computer Science - Machine Learning ; Mathematics - Probability ; Quantitative Finance - Computational Finance ; Quantitative Finance - Statistical Finance
    Thema/Rubrik (Code) 006
    Erscheinungsdatum 2020-06-08
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    Dokumenttyp Buch ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  6. Artikel ; Online: Efficient and Easy Conversion of Human iPSCs into Functional Induced Microglia-like Cells.

    Lanfer, Jonas / Kaindl, Johanna / Krumm, Laura / Gonzalez Acera, Miguel / Neurath, Markus / Regensburger, Martin / Krach, Florian / Winner, Beate

    International journal of molecular sciences

    2022  Band 23, Heft 9

    Abstract: Current protocols converting human induced pluripotent stem cells (iPSCs) into induced microglia-like cells (iMGL) are either dependent on overexpression of transcription factors or require substantial experience in stem-cell technologies. Here, we ... ...

    Abstract Current protocols converting human induced pluripotent stem cells (iPSCs) into induced microglia-like cells (iMGL) are either dependent on overexpression of transcription factors or require substantial experience in stem-cell technologies. Here, we developed an easy-to-use two-step protocol to convert iPSCs into functional iMGL via: (1) highly efficient differentiation of hematopoietic progenitor cells (HPCs) from iPSCs, and (2) optimized maturation of HPCs to iMGL. A sequential harvesting approach led to an increased HPC yield. The protocol implemented a freezing step, thus allowing HPC biobanking and flexible timing of differentiation into iMGL. Our iMGL responded adequately to the inflammatory stimuli LPS, and iMGL RNAseq analysis matched those of other frequently used protocols. Comparing three different coating modalities, we increased the iMGL yield by culturing on uncoated glass surfaces, thereby retaining differentiation efficiency and functional hallmarks of iMGL. In summary, we provide a high-quality, easy-to-use protocol, rendering generation and functional studies on iMGL an accessible lab resource.
    Mesh-Begriff(e) Biological Specimen Banks ; Cell Differentiation ; Hematopoietic Stem Cells ; Humans ; Induced Pluripotent Stem Cells ; Microglia
    Sprache Englisch
    Erscheinungsdatum 2022-04-20
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms23094526
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  7. Artikel ; Online: Zika virus is transmitted in neural progenitor cells via cell-to-cell spread and infection is inhibited by the autophagy inducer trehalose.

    Clark, Alex E / Zhu, Zhe / Krach, Florian / Rich, Jeremy N / Yeo, Gene W / Spector, Deborah H

    Journal of virology

    2020  Band 95, Heft 5

    Abstract: Zika virus (ZIKV) is a mosquito-borne human pathogen that causes congenital Zika syndrome and neurological symptoms in some adults. There are currently no approved treatments or vaccines for ZIKV, and exploration of therapies targeting host processes ... ...

    Abstract Zika virus (ZIKV) is a mosquito-borne human pathogen that causes congenital Zika syndrome and neurological symptoms in some adults. There are currently no approved treatments or vaccines for ZIKV, and exploration of therapies targeting host processes could avoid viral development of drug resistance. The purpose of our study was to determine if the non-toxic and widely used disaccharide trehalose, which showed antiviral activity against Human Cytomegalovirus (HCMV) in our previous work, could restrict ZIKV infection in clinically relevant neural progenitor cells (NPCs). Trehalose is known to induce autophagy, the degradation and recycling of cellular components. Whether autophagy is proviral or antiviral for ZIKV is controversial and depends on cell type and specific conditions used to activate or inhibit autophagy. We show here that trehalose treatment of NPCs infected with recent ZIKV isolates from Panama and Puerto Rico significantly reduces viral replication and spread. In addition, we demonstrate that ZIKV infection in NPCs spreads primarily cell-to-cell as an expanding infectious center, and NPCs are infected via contact with infected cells far more efficiently than by cell-free virus. Importantly, ZIKV was able to spread in NPCs in the presence of neutralizing antibody.
    Sprache Englisch
    Erscheinungsdatum 2020-12-16
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 80174-4
    ISSN 1098-5514 ; 0022-538X
    ISSN (online) 1098-5514
    ISSN 0022-538X
    DOI 10.1128/JVI.02024-20
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  8. Artikel ; Online: The effect of body compartments on lung function in childhood and adolescence.

    Ofenheimer, Alina / Breyer, Marie-Kathrin / Wouters, Emiel F M / Schiffers, Caspar / Hartl, Sylvia / Burghuber, Otto C / Krach, Florian / Maninno, David M / Franssen, Frits M E / Mraz, Tobias / Puchhammer, Patricia / Breyer-Kohansal, Robab

    Clinical nutrition (Edinburgh, Scotland)

    2023  Band 43, Heft 2, Seite(n) 476–481

    Abstract: Background: There is an association between body composition and lung function, assessed by spirometry, but the effects of body compartments on static lung volumes and its changes during lung growth remain to be explored. We aimed to investigate the ... ...

    Abstract Background: There is an association between body composition and lung function, assessed by spirometry, but the effects of body compartments on static lung volumes and its changes during lung growth remain to be explored. We aimed to investigate the association of appendicular lean mass, reflecting skeletal muscle mass, and fat mass on forced and static lung function measures in childhood and adolescence.
    Methods: In total, 1489 children and adolescents (6-18 years) of the observational, longitudinal (first and second visit within 4 years), general population-based LEAD study have been investigated. The association of appendicular lean mass and fat mass indices (ALMI and FMI; assessed by dual-energy X-ray absorptiometry) on lung function by spirometry (FEV
    Findings: The ALMI is positively associated with FEV
    Interpretation: This study demonstrates the different effects of muscle and fat mass on forced expiratory and static lung volumes. Achieving and maintaining muscle mass in childhood and adolescence might become an important preventive strategy for lung health in adulthood.
    Mesh-Begriff(e) Child ; Humans ; Adolescent ; Body Composition/physiology ; Lung ; Respiratory Function Tests ; Spirometry ; Absorptiometry, Photon ; Forced Expiratory Volume
    Sprache Englisch
    Erscheinungsdatum 2023-12-27
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 604812-2
    ISSN 1532-1983 ; 0261-5614
    ISSN (online) 1532-1983
    ISSN 0261-5614
    DOI 10.1016/j.clnu.2023.12.010
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  9. Buch ; Online: Denise

    Herrera, Calypso / Krach, Florian / Kratsios, Anastasis / Ruyssen, Pierre / Teichmann, Josef

    Deep Robust Principal Component Analysis for Positive Semidefinite Matrices

    2020  

    Abstract: The robust PCA of covariance matrices plays an essential role when isolating key explanatory features. The currently available methods for performing such a low-rank plus sparse decomposition are matrix specific, meaning, those algorithms must re-run for ...

    Abstract The robust PCA of covariance matrices plays an essential role when isolating key explanatory features. The currently available methods for performing such a low-rank plus sparse decomposition are matrix specific, meaning, those algorithms must re-run for every new matrix. Since these algorithms are computationally expensive, it is preferable to learn and store a function that nearly instantaneously performs this decomposition when evaluated. Therefore, we introduce Denise, a deep learning-based algorithm for robust PCA of covariance matrices, or more generally, of symmetric positive semidefinite matrices, which learns precisely such a function. Theoretical guarantees for Denise are provided. These include a novel universal approximation theorem adapted to our geometric deep learning problem and convergence to an optimal solution to the learning problem. Our experiments show that Denise matches state-of-the-art performance in terms of decomposition quality, while being approximately $2000\times$ faster than the state-of-the-art, principal component pursuit (PCP), and $200 \times$ faster than the current speed-optimized method, fast PCP.
    Schlagwörter Statistics - Machine Learning ; Computer Science - Machine Learning ; Mathematics - Optimization and Control ; Quantitative Finance - Computational Finance
    Thema/Rubrik (Code) 006
    Erscheinungsdatum 2020-04-28
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    Dokumenttyp Buch ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  10. Artikel: Axon-Specific Mitochondrial Pathology in SPG11 Alpha Motor Neurons.

    Güner, Fabian / Pozner, Tatyana / Krach, Florian / Prots, Iryna / Loskarn, Sandra / Schlötzer-Schrehardt, Ursula / Winkler, Jürgen / Winner, Beate / Regensburger, Martin

    Frontiers in neuroscience

    2021  Band 15, Seite(n) 680572

    Abstract: Pathogenic variants ... ...

    Abstract Pathogenic variants in
    Sprache Englisch
    Erscheinungsdatum 2021-07-07
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article
    ZDB-ID 2411902-7
    ISSN 1662-453X ; 1662-4548
    ISSN (online) 1662-453X
    ISSN 1662-4548
    DOI 10.3389/fnins.2021.680572
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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