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Article: Clone temporal centrality measures for incomplete sequences of graph snapshots

Foraita, Ronja / Hanke, Moritz

BMC bioinformatics, 18: 261

2017

Abstract: BACKGROUND: Different phenomena like the spread of a disease, social interactions or the biological relation between genes can be thought of as dynamic networks. These can be represented as a sequence of static graphs (so called graph snapshots). Based ... ...

Institution	Leibniz-Institut für Präventionsforschung und Epidemiologie
Abstract	BACKGROUND: Different phenomena like the spread of a disease, social interactions or the biological relation between genes can be thought of as dynamic networks. These can be represented as a sequence of static graphs (so called graph snapshots). Based on this graph sequences, classical vertex centrality measures like closeness and betweenness centrality have been extended to quantify the importance of single vertices within a dynamic network. An implicit assumption for the calculation of temporal centrality measures is that the graph sequence contains all information about the network dynamics over time. This assumption is unlikely to be justified in many real world applications due to limited access to fully observed network data. Incompletely observed graph sequences lack important information about duration or existence of edges and may result in biased temporal centrality values. RESULTS: To account for this incompleteness, we introduce the idea of extending original temporal centrality metrics by cloning graphs of an incomplete graph sequence. Focusing on temporal betweenness centrality as an example, we show for different simulated scenarios of incomplete graph sequences that our approach improves the accuracy of detecting important vertices in dynamic networks compared to the original methods. An age-related gene expression data set from the human brain illustrates the new measures. Additional results for the temporal closeness centrality based on cloned snapshots support our findings. We further introduce a new algorithm called REN to calculate temporal centrality measures. Its computational effort is linear in the number of snapshots and benefits from sparse or very dense dynamic networks. CONCLUSIONS: We suggest to use clone temporal centrality measures in incomplete graph sequences settings. Compared to approaches that do not compensate for incompleteness our approach will improve the detection rate of important vertices. The proposed REN algorithm allows to calculate (clone) temporal centrality measures even for long snapshot sequences.
Keywords	Centrality measures ; Closeness ; Betweenness ; Dynamic graphs ; Dynamic networks ; Shortest temporal path ; Time varying networks
Language	English
Document type	Article
Database	Repository for Life Sciences

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Article ; Online: Variable selection in linear regression models: Choosing the best subset is not always the best choice.

Hanke, Moritz / Dijkstra, Louis / Foraita, Ronja / Didelez, Vanessa

Biometrical journal. Biometrische Zeitschrift

2023 Volume 66, Issue 1, Page(s) e2200209

Abstract: We consider the question of variable selection in linear regressions, in the sense of identifying the correct direct predictors (those variables that have nonzero coefficients given all candidate predictors). Best subset selection (BSS) is often ... ...

Abstract	We consider the question of variable selection in linear regressions, in the sense of identifying the correct direct predictors (those variables that have nonzero coefficients given all candidate predictors). Best subset selection (BSS) is often considered the "gold standard," with its use being restricted only by its NP-hard nature. Alternatives such as the least absolute shrinkage and selection operator (Lasso) or the Elastic net (Enet) have become methods of choice in high-dimensional settings. A recent proposal represents BSS as a mixed-integer optimization problem so that large problems have become computationally feasible. We present an extensive neutral comparison assessing the ability to select the correct direct predictors of BSS compared to forward stepwise selection (FSS), Lasso, and Enet. The simulation considers a range of settings that are challenging regarding dimensionality (number of observations and variables), signal-to-noise ratios, and correlations between predictors. As fair measure of performance, we primarily used the best possible F1-score for each method, and results were confirmed by alternative performance measures and practical criteria for choosing the tuning parameters and subset sizes. Surprisingly, it was only in settings where the signal-to-noise ratio was high and the variables were uncorrelated that BSS reliably outperformed the other methods, even in low-dimensional settings. Furthermore, FSS performed almost identically to BSS. Our results shed new light on the usual presumption of BSS being, in principle, the best choice for selecting the correct direct predictors. Especially for correlated variables, alternatives like Enet are faster and appear to perform better in practical settings.
MeSH term(s)	Linear Models ; Computer Simulation
Language	English
Publishing date	2023-08-29
Publishing country	Germany
Document type	Journal Article
ZDB-ID	131640-0
ISSN	1521-4036 ; 0323-3847 ; 0006-3452
ISSN (online)	1521-4036
ISSN	0323-3847 ; 0006-3452
DOI	10.1002/bimj.202200209
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Article ; Online: No robust online effects of transcranial direct current stimulation on corticospinal excitability.

Pillen, Steven / Knodel, Nicole / Hermle, Dominik / Hanke, Moritz / Ziemann, Ulf / Bergmann, Til Ole

Brain stimulation

2022 Volume 15, Issue 5, Page(s) 1254–1268

Abstract: Transcranial direct current stimulation (tDCS) has been used for over twenty years to modulate cortical (particularly motor corticospinal) excitability both during (online) and outlasting (offline) the stimulation, with the former effects associated to ... ...

Abstract	Transcranial direct current stimulation (tDCS) has been used for over twenty years to modulate cortical (particularly motor corticospinal) excitability both during (online) and outlasting (offline) the stimulation, with the former effects associated to the latter. However, tDCS effects are highly variable, partially because stimulation intensity is commonly not adjusted individually (in contrast to transcranial magnetic stimulation, TMS). In Experiment 1, we therefore explored an empirical approach of personalizing tDCS intensity for the primary motor cortex (M1) based on dose-response curves (DRCs), individually relating tDCS Intensity (in steps from 0.3 to 2.0 mA) and Polarity (anodal, cathodal) to the online modulation of concurrent TMS motor evoked potentials (MEP), assessing DRC reliability across two separate days. No robust DRCs could be observed, neither at the individual nor at the group level, with the only robust effect being a (paradoxical) MEP facilitation during cathodal tDCS at 2.0 mA, but no modulation at traditional intensities of or near 1 mA. In Experiment 2, we therefore attempted to replicate the classical bidirectional online MEP modulation during 1 mA tDCS that had been reported by several of the early seminal tDCS papers. We either closely recreated stimulation parameters and temporal protocol of these original studies (Experiment 2A) or slightly modernized them according to current standards (Experiment 2B). In neither experiment did we observed any significant online MEP modulation. We conclude that an empirical titration of individually effective tDCS intensities may not be feasible as online tDCS effects do not appear to be sufficiently robust.
MeSH term(s)	Evoked Potentials, Motor/physiology ; Motor Cortex/physiology ; Reproducibility of Results ; Transcranial Direct Current Stimulation/methods ; Transcranial Magnetic Stimulation/methods
Language	English
Publishing date	2022-09-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	2394410-9
ISSN	1876-4754 ; 1935-861X
ISSN (online)	1876-4754
ISSN	1935-861X
DOI	10.1016/j.brs.2022.08.024
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Article ; Online: Clone temporal centrality measures for incomplete sequences of graph snapshots.

Hanke, Moritz / Foraita, Ronja

BMC bioinformatics

2017 Volume 18, Issue 1, Page(s) 261

Abstract: Background: Different phenomena like the spread of a disease, social interactions or the biological relation between genes can be thought of as dynamic networks. These can be represented as a sequence of static graphs (so called graph snapshots). Based ... ...

Abstract	Background: Different phenomena like the spread of a disease, social interactions or the biological relation between genes can be thought of as dynamic networks. These can be represented as a sequence of static graphs (so called graph snapshots). Based on this graph sequences, classical vertex centrality measures like closeness and betweenness centrality have been extended to quantify the importance of single vertices within a dynamic network. An implicit assumption for the calculation of temporal centrality measures is that the graph sequence contains all information about the network dynamics over time. This assumption is unlikely to be justified in many real world applications due to limited access to fully observed network data. Incompletely observed graph sequences lack important information about duration or existence of edges and may result in biased temporal centrality values. Results: To account for this incompleteness, we introduce the idea of extending original temporal centrality metrics by cloning graphs of an incomplete graph sequence. Focusing on temporal betweenness centrality as an example, we show for different simulated scenarios of incomplete graph sequences that our approach improves the accuracy of detecting important vertices in dynamic networks compared to the original methods. An age-related gene expression data set from the human brain illustrates the new measures. Additional results for the temporal closeness centrality based on cloned snapshots support our findings. We further introduce a new algorithm called REN to calculate temporal centrality measures. Its computational effort is linear in the number of snapshots and benefits from sparse or very dense dynamic networks. Conclusions: We suggest to use clone temporal centrality measures in incomplete graph sequences settings. Compared to approaches that do not compensate for incompleteness our approach will improve the detection rate of important vertices. The proposed REN algorithm allows to calculate (clone) temporal centrality measures even for long snapshot sequences.
MeSH term(s)	Algorithms ; Brain/metabolism ; Humans ; Metabolic Networks and Pathways ; Protein Interaction Maps
Language	English
Publishing date	2017-05-16
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-017-1677-x
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Article ; Online: Non-contrast-enhanced MR-angiography (MRA) of lower extremity peripheral arterial disease at 3 tesla: Examination time and diagnostic performance of 2D quiescent-interval single-shot MRA vs. 3D fast spin-Echo MRA.

Knobloch, Gesine / Lauff, Marie-Teres / Hanke, Moritz / Schwenke, Carsten / Hamm, Bernd / Wagner, Moritz

Magnetic resonance imaging

2020 Volume 76, Page(s) 17–25

Abstract: Purpose: Non-contrast enhanced MRA is a promising diagnostic alternative to contrast-enhanced (CE-) MRA or CT in patients with lower extremity peripheral arterial disease (PAD) but potentially associated with prolonged examination times and inferior ... ...

Abstract	Purpose: Non-contrast enhanced MRA is a promising diagnostic alternative to contrast-enhanced (CE-) MRA or CT in patients with lower extremity peripheral arterial disease (PAD) but potentially associated with prolonged examination times and inferior diagnostic performance. We aimed to compare examination times and diagnostic performance of non-contrast enhanced quiescent-interval slice-selective (QISS)-MRA and fast-spin-echo (FSE)-MRA at 3.0 T. Materials and methods: Forty-five patients with PAD were recruited for this IRB approved prospective study. Subjects underwent lower extremity MRA with 1) QISS-MRA, 2) FSE-MRA, and 3) CE-MRA (continuous table movement MRA and time-resolved MRA of the calf), which served as the standard of reference. Scan times for each examination step and total examination times for each of the three techniques was determined. Image quality and degree of stenosis were rated by two readers on a 5-point Likert scale. Sensitivity, specificity and diagnostic accuracy for relevant (>50%) stenosis were calculated. Results: Median total examination time was 27:02 min for QISS-MRA (IQR, 25:13-31:01 min), 28:37 min for FSE-MRA (IQR, 25:51-33:12 min), and 31:22 min for CE-MRA (IQR, 26:41-33:23 min). Acquisition time for QISS-MRA was significantly longer compared to FSE-MRA and CE-MRA (p ≤ 0.0001), while time for localizers, scouts and planning of the MRA sequence was significantly shorter for QISS-MRA compared to FSE-MRA and CE-MRA (p ≤ 0.0001). QISS-MRA had significantly better image quality compared to FSE-MRA with less segments classified as non-diagnostic (Reader 1: 3% vs. 35%; Reader 2: 3% vs. 50%, p ≤ 0.0001). Overall, QISS-MRA showed significantly better diagnostic performance than FSE-MRA (sensitivity, 85% vs. 54%; specificity, 90% vs. 47%, diagnostic accuracy, 89% vs. 48%; p ≤ 0.0001). Conclusion: Total examination time of QISS-MRA and FSE-MRA was comparable with a conventional CE-MRA protocol. QISS-MRA showed significantly higher diagnostic performance than FSE-MRA.
MeSH term(s)	Adult ; Aged ; Constriction, Pathologic/diagnostic imaging ; Female ; Humans ; Lower Extremity/blood supply ; Lower Extremity/diagnostic imaging ; Magnetic Resonance Angiography ; Male ; Middle Aged ; Peripheral Arterial Disease/diagnostic imaging ; Prospective Studies ; Reproducibility of Results ; Sensitivity and Specificity
Language	English
Publishing date	2020-11-04
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	604885-7
ISSN	1873-5894 ; 0730-725X
ISSN (online)	1873-5894
ISSN	0730-725X
DOI	10.1016/j.mri.2020.10.016
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Book ; Online: ICON-Sapphire

Hohenegger, Cathy / Korn, Peter / Linardakis, Leonidas / Redler, René / Schnur, Reiner / Adamidis, Panagiotis / Bao, Jiawei / Bastin, Swantje / Behravesh, Milad / Bergemann, Martin / Biercamp, Joachim / Bockelmann, Hendryk / Brokopf, Renate / Brüggemann, Nils / Casaroli, Lucas / Chegini, Fatemeh / Datseris, George / Esch, Monika / George, Geet /

Giorgetta, Marco / Gutjahr, Oliver / Haak, Helmuth / Hanke, Moritz / Ilyina, Tatiana / Jahns, Thomas / Jungclaus, Johann / Kern, Marcel / Klocke, Daniel / Kluft, Lukas / Kölling, Tobias / Kornblueh, Luis / Kosukhin, Sergey / Kroll, Clarissa / Lee, Junhong / Mauritsen, Thorsten / Mehlmann, Carolin / Mieslinger, Theresa / Naumann, Ann Kristin / Paccini, Laura / Peinado, Angel / Praturi, Divya Sri / Putrasahan, Dian / Rast, Sebastian / Riddick, Thomas / Roeber, Niklas / Schmidt, Hauke / Schulzweida, Uwe / Schütte, Florian / Segura, Hans / Shevchenko, Radomyra

eISSN: 1991-9603

simulating the components of the Earth system and their interactions at kilometer and subkilometer scales

2023

Abstract: State-of-the-art Earth system models typically employ grid spacings of O(100 km), which is too coarse to explicitly resolve main drivers of the flow of energy and matter across the Earth system. In this paper, we present the new ICON-Sapphire model ... ...

Abstract	State-of-the-art Earth system models typically employ grid spacings of O(100 km), which is too coarse to explicitly resolve main drivers of the flow of energy and matter across the Earth system. In this paper, we present the new ICON-Sapphire model configuration, which targets a representation of the components of the Earth system and their interactions with a grid spacing of 10 km and finer. Through the use of selected simulation examples, we demonstrate that ICON-Sapphire can (i) be run coupled globally on seasonal timescales with a grid spacing of 5 km, on monthly timescales with a grid spacing of 2.5 km, and on daily timescales with a grid spacing of 1.25 km; (ii) resolve large eddies in the atmosphere using hectometer grid spacings on limited-area domains in atmosphere-only simulations; (iii) resolve submesoscale ocean eddies by using a global uniform grid of 1.25 km or a telescoping grid with the finest grid spacing at 530 m, the latter coupled to a uniform atmosphere; and (iv) simulate biogeochemistry in an ocean-only simulation integrated for 4 years at 10 km. Comparison of basic features of the climate system to observations reveals no obvious pitfalls, even though some observed aspects remain difficult to capture. The throughput of the coupled 5 km global simulation is 126 simulated days per day employing 21 % of the latest machine of the German Climate Computing Center. Extrapolating from these results, multi-decadal global simulations including interactive carbon are now possible, and short global simulations resolving large eddies in the atmosphere and submesoscale eddies in the ocean are within reach.
Subject code	551
Language	English
Publishing date	2023-01-31
Publishing country	de
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: ICON-Sapphire

simulating the components of the Earth system and their interactions at kilometer and subkilometer scales

2023

Abstract	State-of-the-art Earth system models typically employ grid spacings of O(100 km), which is too coarse to explicitly resolve main drivers of the flow of energy and matter across the Earth system. In this paper, we present the new ICON-Sapphire model configuration, which targets a representation of the components of the Earth system and their interactions with a grid spacing of 10 km and finer. Through the use of selected simulation examples, we demonstrate that ICON-Sapphire can (i) be run coupled globally on seasonal timescales with a grid spacing of 5 km, on monthly timescales with a grid spacing of 2.5 km, and on daily timescales with a grid spacing of 1.25 km; (ii) resolve large eddies in the atmosphere using hectometer grid spacings on limited-area domains in atmosphere-only simulations; (iii) resolve submesoscale ocean eddies by using a global uniform grid of 1.25 km or a telescoping grid with the finest grid spacing at 530 m, the latter coupled to a uniform atmosphere; and (iv) simulate biogeochemistry in an ocean-only simulation integrated for 4 years at 10 km. Comparison of basic features of the climate system to observations reveals no obvious pitfalls, even though some observed aspects remain difficult to capture. The throughput of the coupled 5 km global simulation is 126 simulated days per day employing 21 % of the latest machine of the German Climate Computing Center. Extrapolating from these results, multi-decadal global simulations including interactive carbon are now possible, and short global simulations resolving large eddies in the atmosphere and submesoscale eddies in the ocean are within reach.
Subject code	551
Language	English
Publishing date	2023-01-31
Publisher	Copernicus Publications (EGU)
Publishing country	de
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: ICON-Sapphire

eISSN: 1991-9603

simulating the components of the Earth System and their interactions at kilometer and subkilometer scales

2022

Abstract: State-of-the-art Earth System models typically employ grid spacings of O(100 km), too coarse to explicitly resolve main drivers of the flow of energy and matter across the Earth System. In this paper, we present the new ICON-Sapphire model configuration, ...

Abstract	State-of-the-art Earth System models typically employ grid spacings of O(100 km), too coarse to explicitly resolve main drivers of the flow of energy and matter across the Earth System. In this paper, we present the new ICON-Sapphire model configuration, which targets a representation of the components of the Earth System and their interactions with a grid spacing of 10 km and finer. Through the use of selected simulation examples, we demonstrate that ICON-Sapphire can already now (i) be run coupled globally on seasonal time scales with a grid spacing of 5 km and on monthly time scales with a grid spacing of 2.5 km, (ii) resolve large eddies in the atmosphere using hectometer grid spacings on limited-area domains in atmosphere-only simulations, (iii) resolve submesoscale ocean eddies by using a global uniform grid of 1.25 km or a telescoping grid with a finest grid spacing of 530 m, the latter coupled to a uniform atmosphere and (iv) simulate biogeochemistry in an ocean-only simulation integrated for 4 years at 10 km. Comparison to observations of these various configurations reveals no obvious pitfall. The throughput of the coupled 5-km global simulation is 126 simulated days per day employing 21 % of the latest machine of the German Climate Computing Center. Extrapolating from these results, multi-decadal global simulations including interactive carbon are now possible and short global simulations resolving large eddies in the atmosphere and submesoscale eddies in the ocean are within reach.
Subject code	551
Language	English
Publishing date	2022-07-21
Publishing country	de
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Full text

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Article: Variable selection in linear regression models: Choosing the best subset is not always the best choice

Hanke, Moritz / Foraita, Ronja / Didelez, Vanessa

http://lobid.org/resources/990108705040206441#!, 66(1):2200209

2023

Institution	Leibniz-Institut für Präventionsforschung und Epidemiologie
Abstract	We consider the question of variable selection in linear regressions, in the sense of identifying the correct direct predictors (those variables that have nonzero coefficients given all candidate predictors). Best subset selection (BSS) is often considered the “gold standard,” with its use being restricted only by its NP-hard nature. Alternatives such as the least absolute shrinkage and selection operator (Lasso) or the Elastic net (Enet) have become methods of choice in high-dimensional settings. A recent proposal represents BSS as a mixed-integer optimization problem so that large problems have become computationally feasible. We present an extensive neutral comparison assessing the ability to select the correct direct predictors of BSS compared to forward stepwise selection (FSS), Lasso, and Enet. The simulation considers a range of settings that are challenging regarding dimensionality (number of observations and variables), signal-to-noise ratios, and correlations between predictors. As fair measure of performance, we primarily used the best possible F1-score for each method, and results were confirmed by alternative performance measures and practical criteria for choosing the tuning parameters and subset sizes. Surprisingly, it was only in settings where the signal-to-noise ratio was high and the variables were uncorrelated that BSS reliably outperformed the other methods, even in low-dimensional settings. Furthermore, FSS performed almost identically to BSS. Our results shed new light on the usual presumption of BSS being, in principle, the best choice for selecting the correct direct predictors. Especially for correlated variables, alternatives like Enet are faster and appear to perform better in practical settings.
Keywords	Lasso ; best subset selection ; linear regression ; mixed-integer optimization ; variable selection
Language	English
Document type	Article
Database	Repository for Life Sciences

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