--- _id: '14184' abstract: - lang: eng text: "Learning disentangled representations is considered a cornerstone problem in\r\nrepresentation learning. Recently, Locatello et al. (2019) demonstrated that\r\nunsupervised disentanglement learning without inductive biases is theoretically\r\nimpossible and that existing inductive biases and unsupervised methods do not\r\nallow to consistently learn disentangled representations. However, in many\r\npractical settings, one might have access to a limited amount of supervision,\r\nfor example through manual labeling of (some) factors of variation in a few\r\ntraining examples. In this paper, we investigate the impact of such supervision\r\non state-of-the-art disentanglement methods and perform a large scale study,\r\ntraining over 52000 models under well-defined and reproducible experimental\r\nconditions. We observe that a small number of labeled examples (0.01--0.5\\% of\r\nthe data set), with potentially imprecise and incomplete labels, is sufficient\r\nto perform model selection on state-of-the-art unsupervised models. Further, we\r\ninvestigate the benefit of incorporating supervision into the training process.\r\nOverall, we empirically validate that with little and imprecise supervision it\r\nis possible to reliably learn disentangled representations." article_processing_charge: No arxiv: 1 author: - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Michael full_name: Tschannen, Michael last_name: Tschannen - first_name: Stefan full_name: Bauer, Stefan last_name: Bauer - first_name: Gunnar full_name: Rätsch, Gunnar last_name: Rätsch - first_name: Bernhard full_name: Schölkopf, Bernhard last_name: Schölkopf - first_name: Olivier full_name: Bachem, Olivier last_name: Bachem citation: ama: 'Locatello F, Tschannen M, Bauer S, Rätsch G, Schölkopf B, Bachem O. Disentangling factors of variation using few labels. In: 8th International Conference on Learning Representations. ; 2019.' apa: Locatello, F., Tschannen, M., Bauer, S., Rätsch, G., Schölkopf, B., & Bachem, O. (2019). Disentangling factors of variation using few labels. In 8th International Conference on Learning Representations. Virtual. chicago: Locatello, Francesco, Michael Tschannen, Stefan Bauer, Gunnar Rätsch, Bernhard Schölkopf, and Olivier Bachem. “Disentangling Factors of Variation Using Few Labels.” In 8th International Conference on Learning Representations, 2019. ieee: F. Locatello, M. Tschannen, S. Bauer, G. Rätsch, B. Schölkopf, and O. Bachem, “Disentangling factors of variation using few labels,” in 8th International Conference on Learning Representations, Virtual, 2019. ista: 'Locatello F, Tschannen M, Bauer S, Rätsch G, Schölkopf B, Bachem O. 2019. Disentangling factors of variation using few labels. 8th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.' mla: Locatello, Francesco, et al. “Disentangling Factors of Variation Using Few Labels.” 8th International Conference on Learning Representations, 2019. short: F. Locatello, M. Tschannen, S. Bauer, G. Rätsch, B. Schölkopf, O. Bachem, in:, 8th International Conference on Learning Representations, 2019. conference: end_date: 2020-05-01 location: Virtual name: 'ICLR: International Conference on Learning Representations' start_date: 2020-04-26 date_created: 2023-08-22T14:06:37Z date_published: 2019-12-20T00:00:00Z date_updated: 2023-09-12T07:01:34Z day: '20' department: - _id: FrLo extern: '1' external_id: arxiv: - '1905.01258' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1905.01258 month: '12' oa: 1 oa_version: Preprint publication: 8th International Conference on Learning Representations publication_status: published quality_controlled: '1' scopus_import: '1' status: public title: Disentangling factors of variation using few labels type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '14189' abstract: - lang: eng text: "We consider the problem of recovering a common latent source with independent\r\ncomponents from multiple views. This applies to settings in which a variable is\r\nmeasured with multiple experimental modalities, and where the goal is to\r\nsynthesize the disparate measurements into a single unified representation. We\r\nconsider the case that the observed views are a nonlinear mixing of\r\ncomponent-wise corruptions of the sources. When the views are considered\r\nseparately, this reduces to nonlinear Independent Component Analysis (ICA) for\r\nwhich it is provably impossible to undo the mixing. We present novel\r\nidentifiability proofs that this is possible when the multiple views are\r\nconsidered jointly, showing that the mixing can theoretically be undone using\r\nfunction approximators such as deep neural networks. In contrast to known\r\nidentifiability results for nonlinear ICA, we prove that independent latent\r\nsources with arbitrary mixing can be recovered as long as multiple,\r\nsufficiently different noisy views are available." alternative_title: - PMLR article_processing_charge: No arxiv: 1 author: - first_name: Luigi full_name: Gresele, Luigi last_name: Gresele - first_name: Paul K. full_name: Rubenstein, Paul K. last_name: Rubenstein - first_name: Arash full_name: Mehrjou, Arash last_name: Mehrjou - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Bernhard full_name: Schölkopf, Bernhard last_name: Schölkopf citation: ama: 'Gresele L, Rubenstein PK, Mehrjou A, Locatello F, Schölkopf B. The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA. In: Proceedings of the 35th Conference on Uncertainty in Artificial  Intelligence. Vol 115. ML Research Press; 2019:217-227.' apa: 'Gresele, L., Rubenstein, P. K., Mehrjou, A., Locatello, F., & Schölkopf, B. (2019). The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA. In Proceedings of the 35th Conference on Uncertainty in Artificial  Intelligence (Vol. 115, pp. 217–227). Tel Aviv, Israel: ML Research Press.' chicago: 'Gresele, Luigi, Paul K. Rubenstein, Arash Mehrjou, Francesco Locatello, and Bernhard Schölkopf. “The Incomplete Rosetta Stone Problem: Identifiability Results for Multi-View Nonlinear ICA.” In Proceedings of the 35th Conference on Uncertainty in Artificial  Intelligence, 115:217–27. ML Research Press, 2019.' ieee: 'L. Gresele, P. K. Rubenstein, A. Mehrjou, F. Locatello, and B. Schölkopf, “The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA,” in Proceedings of the 35th Conference on Uncertainty in Artificial  Intelligence, Tel Aviv, Israel, 2019, vol. 115, pp. 217–227.' ista: 'Gresele L, Rubenstein PK, Mehrjou A, Locatello F, Schölkopf B. 2019. The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA. Proceedings of the 35th Conference on Uncertainty in Artificial  Intelligence. UAI: Uncertainty in Artificial Intelligence, PMLR, vol. 115, 217–227.' mla: 'Gresele, Luigi, et al. “The Incomplete Rosetta Stone Problem: Identifiability Results for Multi-View Nonlinear ICA.” Proceedings of the 35th Conference on Uncertainty in Artificial  Intelligence, vol. 115, ML Research Press, 2019, pp. 217–27.' short: L. Gresele, P.K. Rubenstein, A. Mehrjou, F. Locatello, B. Schölkopf, in:, Proceedings of the 35th Conference on Uncertainty in Artificial  Intelligence, ML Research Press, 2019, pp. 217–227. conference: end_date: 2019-07-25 location: Tel Aviv, Israel name: 'UAI: Uncertainty in Artificial Intelligence' start_date: 2019-07-22 date_created: 2023-08-22T14:08:35Z date_published: 2019-05-16T00:00:00Z date_updated: 2023-09-12T08:07:38Z day: '16' department: - _id: FrLo extern: '1' external_id: arxiv: - '1905.06642' intvolume: ' 115' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1905.06642 month: '05' oa: 1 oa_version: Preprint page: 217-227 publication: Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence publication_status: published publisher: ML Research Press quality_controlled: '1' scopus_import: '1' status: public title: 'The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 115 year: '2019' ... --- _id: '14190' abstract: - lang: eng text: "Learning meaningful and compact representations with disentangled semantic\r\naspects is considered to be of key importance in representation learning. Since\r\nreal-world data is notoriously costly to collect, many recent state-of-the-art\r\ndisentanglement models have heavily relied on synthetic toy data-sets. In this\r\npaper, we propose a novel data-set which consists of over one million images of\r\nphysical 3D objects with seven factors of variation, such as object color,\r\nshape, size and position. In order to be able to control all the factors of\r\nvariation precisely, we built an experimental platform where the objects are\r\nbeing moved by a robotic arm. In addition, we provide two more datasets which\r\nconsist of simulations of the experimental setup. These datasets provide for\r\nthe first time the possibility to systematically investigate how well different\r\ndisentanglement methods perform on real data in comparison to simulation, and\r\nhow simulated data can be leveraged to build better representations of the real\r\nworld. We provide a first experimental study of these questions and our results\r\nindicate that learned models transfer poorly, but that model and hyperparameter\r\nselection is an effective means of transferring information to the real world." article_processing_charge: No arxiv: 1 author: - first_name: Muhammad Waleed full_name: Gondal, Muhammad Waleed last_name: Gondal - first_name: Manuel full_name: Wüthrich, Manuel last_name: Wüthrich - first_name: Đorđe full_name: Miladinović, Đorđe last_name: Miladinović - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Martin full_name: Breidt, Martin last_name: Breidt - first_name: Valentin full_name: Volchkov, Valentin last_name: Volchkov - first_name: Joel full_name: Akpo, Joel last_name: Akpo - first_name: Olivier full_name: Bachem, Olivier last_name: Bachem - first_name: Bernhard full_name: Schölkopf, Bernhard last_name: Schölkopf - first_name: Stefan full_name: Bauer, Stefan last_name: Bauer citation: ama: 'Gondal MW, Wüthrich M, Miladinović Đ, et al. On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset. In: Advances in Neural Information Processing Systems. Vol 32. ; 2019.' apa: 'Gondal, M. W., Wüthrich, M., Miladinović, Đ., Locatello, F., Breidt, M., Volchkov, V., … Bauer, S. (2019). On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset. In Advances in Neural Information Processing Systems (Vol. 32). Vancouver, Canada.' chicago: 'Gondal, Muhammad Waleed, Manuel Wüthrich, Đorđe Miladinović, Francesco Locatello, Martin Breidt, Valentin Volchkov, Joel Akpo, Olivier Bachem, Bernhard Schölkopf, and Stefan Bauer. “On the Transfer of Inductive Bias from Simulation to the Real World: A New Disentanglement Dataset.” In Advances in Neural Information Processing Systems, Vol. 32, 2019.' ieee: 'M. W. Gondal et al., “On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32.' ista: 'Gondal MW, Wüthrich M, Miladinović Đ, Locatello F, Breidt M, Volchkov V, Akpo J, Bachem O, Schölkopf B, Bauer S. 2019. On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 32.' mla: 'Gondal, Muhammad Waleed, et al. “On the Transfer of Inductive Bias from Simulation to the Real World: A New Disentanglement Dataset.” Advances in Neural Information Processing Systems, vol. 32, 2019.' short: M.W. Gondal, M. Wüthrich, Đ. Miladinović, F. Locatello, M. Breidt, V. Volchkov, J. Akpo, O. Bachem, B. Schölkopf, S. Bauer, in:, Advances in Neural Information Processing Systems, 2019. conference: end_date: 2019-12-14 location: Vancouver, Canada name: 'NeurIPS: Neural Information Processing Systems' start_date: 2019-12-08 date_created: 2023-08-22T14:09:13Z date_published: 2019-06-07T00:00:00Z date_updated: 2023-09-13T09:46:38Z day: '07' department: - _id: FrLo extern: '1' external_id: arxiv: - '1906.03292' intvolume: ' 32' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1906.03292 month: '06' oa: 1 oa_version: Preprint publication: Advances in Neural Information Processing Systems publication_identifier: isbn: - '9781713807933' publication_status: published quality_controlled: '1' status: public title: 'On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset' type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 32 year: '2019' ... --- _id: '14191' abstract: - lang: eng text: A broad class of convex optimization problems can be formulated as a semidefinite program (SDP), minimization of a convex function over the positive-semidefinite cone subject to some affine constraints. The majority of classical SDP solvers are designed for the deterministic setting where problem data is readily available. In this setting, generalized conditional gradient methods (aka Frank-Wolfe-type methods) provide scalable solutions by leveraging the so-called linear minimization oracle instead of the projection onto the semidefinite cone. Most problems in machine learning and modern engineering applications, however, contain some degree of stochasticity. In this work, we propose the first conditional-gradient-type method for solving stochastic optimization problems under affine constraints. Our method guarantees O(k−1/3) convergence rate in expectation on the objective residual and O(k−5/12) on the feasibility gap. article_processing_charge: No arxiv: 1 author: - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Alp full_name: Yurtsever, Alp last_name: Yurtsever - first_name: Olivier full_name: Fercoq, Olivier last_name: Fercoq - first_name: Volkan full_name: Cevher, Volkan last_name: Cevher citation: ama: 'Locatello F, Yurtsever A, Fercoq O, Cevher V. Stochastic Frank-Wolfe for composite convex minimization. In: Advances in Neural Information Processing Systems. Vol 32. ; 2019:14291–14301.' apa: Locatello, F., Yurtsever, A., Fercoq, O., & Cevher, V. (2019). Stochastic Frank-Wolfe for composite convex minimization. In Advances in Neural Information Processing Systems (Vol. 32, pp. 14291–14301). Vancouver, Canada. chicago: Locatello, Francesco, Alp Yurtsever, Olivier Fercoq, and Volkan Cevher. “Stochastic Frank-Wolfe for Composite Convex Minimization.” In Advances in Neural Information Processing Systems, 32:14291–14301, 2019. ieee: F. Locatello, A. Yurtsever, O. Fercoq, and V. Cevher, “Stochastic Frank-Wolfe for composite convex minimization,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32, pp. 14291–14301. ista: 'Locatello F, Yurtsever A, Fercoq O, Cevher V. 2019. Stochastic Frank-Wolfe for composite convex minimization. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 32, 14291–14301.' mla: Locatello, Francesco, et al. “Stochastic Frank-Wolfe for Composite Convex Minimization.” Advances in Neural Information Processing Systems, vol. 32, 2019, pp. 14291–14301. short: F. Locatello, A. Yurtsever, O. Fercoq, V. Cevher, in:, Advances in Neural Information Processing Systems, 2019, pp. 14291–14301. conference: end_date: 2019-12-14 location: Vancouver, Canada name: 'NeurIPS: Neural Information Processing Systems' start_date: 2019-12-08 date_created: 2023-08-22T14:09:35Z date_published: 2019-12-29T00:00:00Z date_updated: 2023-09-12T08:48:45Z day: '29' department: - _id: FrLo extern: '1' external_id: arxiv: - '1901.10348' intvolume: ' 32' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1901.10348 month: '12' oa: 1 oa_version: Preprint page: 14291–14301 publication: Advances in Neural Information Processing Systems publication_identifier: isbn: - '9781713807933' publication_status: published quality_controlled: '1' scopus_import: '1' status: public title: Stochastic Frank-Wolfe for composite convex minimization type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2019' ... --- _id: '14193' abstract: - lang: eng text: "A disentangled representation encodes information about the salient factors\r\nof variation in the data independently. Although it is often argued that this\r\nrepresentational format is useful in learning to solve many real-world\r\ndown-stream tasks, there is little empirical evidence that supports this claim.\r\nIn this paper, we conduct a large-scale study that investigates whether\r\ndisentangled representations are more suitable for abstract reasoning tasks.\r\nUsing two new tasks similar to Raven's Progressive Matrices, we evaluate the\r\nusefulness of the representations learned by 360 state-of-the-art unsupervised\r\ndisentanglement models. Based on these representations, we train 3600 abstract\r\nreasoning models and observe that disentangled representations do in fact lead\r\nto better down-stream performance. In particular, they enable quicker learning\r\nusing fewer samples." article_processing_charge: No arxiv: 1 author: - first_name: Sjoerd van full_name: Steenkiste, Sjoerd van last_name: Steenkiste - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Jürgen full_name: Schmidhuber, Jürgen last_name: Schmidhuber - first_name: Olivier full_name: Bachem, Olivier last_name: Bachem citation: ama: 'Steenkiste S van, Locatello F, Schmidhuber J, Bachem O. Are disentangled representations helpful for abstract visual reasoning? In: Advances in Neural Information Processing Systems. Vol 32. ; 2019.' apa: Steenkiste, S. van, Locatello, F., Schmidhuber, J., & Bachem, O. (2019). Are disentangled representations helpful for abstract visual reasoning? In Advances in Neural Information Processing Systems (Vol. 32). Vancouver, Canada. chicago: Steenkiste, Sjoerd van, Francesco Locatello, Jürgen Schmidhuber, and Olivier Bachem. “Are Disentangled Representations Helpful for Abstract Visual Reasoning?” In Advances in Neural Information Processing Systems, Vol. 32, 2019. ieee: S. van Steenkiste, F. Locatello, J. Schmidhuber, and O. Bachem, “Are disentangled representations helpful for abstract visual reasoning?,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32. ista: 'Steenkiste S van, Locatello F, Schmidhuber J, Bachem O. 2019. Are disentangled representations helpful for abstract visual reasoning? Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 32.' mla: Steenkiste, Sjoerd van, et al. “Are Disentangled Representations Helpful for Abstract Visual Reasoning?” Advances in Neural Information Processing Systems, vol. 32, 2019. short: S. van Steenkiste, F. Locatello, J. Schmidhuber, O. Bachem, in:, Advances in Neural Information Processing Systems, 2019. conference: end_date: 2019-12-14 location: Vancouver, Canada name: 'NeurIPS: Neural Information Processing Systems' start_date: 2019-12-08 date_created: 2023-08-22T14:09:53Z date_published: 2019-05-29T00:00:00Z date_updated: 2023-09-12T09:02:43Z day: '29' department: - _id: FrLo extern: '1' external_id: arxiv: - '1905.12506' intvolume: ' 32' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.1905.12506 month: '05' oa: 1 oa_version: Preprint publication: Advances in Neural Information Processing Systems publication_identifier: isbn: - '9781713807933' publication_status: published quality_controlled: '1' status: public title: Are disentangled representations helpful for abstract visual reasoning? type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2019' ... --- _id: '14197' abstract: - lang: eng text: "Recently there has been a significant interest in learning disentangled\r\nrepresentations, as they promise increased interpretability, generalization to\r\nunseen scenarios and faster learning on downstream tasks. In this paper, we\r\ninvestigate the usefulness of different notions of disentanglement for\r\nimproving the fairness of downstream prediction tasks based on representations.\r\nWe consider the setting where the goal is to predict a target variable based on\r\nthe learned representation of high-dimensional observations (such as images)\r\nthat depend on both the target variable and an \\emph{unobserved} sensitive\r\nvariable. We show that in this setting both the optimal and empirical\r\npredictions can be unfair, even if the target variable and the sensitive\r\nvariable are independent. Analyzing the representations of more than\r\n\\num{12600} trained state-of-the-art disentangled models, we observe that\r\nseveral disentanglement scores are consistently correlated with increased\r\nfairness, suggesting that disentanglement may be a useful property to encourage\r\nfairness when sensitive variables are not observed." article_processing_charge: No arxiv: 1 author: - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Gabriele full_name: Abbati, Gabriele last_name: Abbati - first_name: Tom full_name: Rainforth, Tom last_name: Rainforth - first_name: Stefan full_name: Bauer, Stefan last_name: Bauer - first_name: Bernhard full_name: Schölkopf, Bernhard last_name: Schölkopf - first_name: Olivier full_name: Bachem, Olivier last_name: Bachem citation: ama: 'Locatello F, Abbati G, Rainforth T, Bauer S, Schölkopf B, Bachem O. On the fairness of disentangled representations. In: Advances in Neural Information Processing Systems. Vol 32. ; 2019:14611–14624.' apa: Locatello, F., Abbati, G., Rainforth, T., Bauer, S., Schölkopf, B., & Bachem, O. (2019). On the fairness of disentangled representations. In Advances in Neural Information Processing Systems (Vol. 32, pp. 14611–14624). Vancouver, Canada. chicago: Locatello, Francesco, Gabriele Abbati, Tom Rainforth, Stefan Bauer, Bernhard Schölkopf, and Olivier Bachem. “On the Fairness of Disentangled Representations.” In Advances in Neural Information Processing Systems, 32:14611–14624, 2019. ieee: F. Locatello, G. Abbati, T. Rainforth, S. Bauer, B. Schölkopf, and O. Bachem, “On the fairness of disentangled representations,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32, pp. 14611–14624. ista: 'Locatello F, Abbati G, Rainforth T, Bauer S, Schölkopf B, Bachem O. 2019. On the fairness of disentangled representations. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 32, 14611–14624.' mla: Locatello, Francesco, et al. “On the Fairness of Disentangled Representations.” Advances in Neural Information Processing Systems, vol. 32, 2019, pp. 14611–14624. short: F. Locatello, G. Abbati, T. Rainforth, S. Bauer, B. Schölkopf, O. Bachem, in:, Advances in Neural Information Processing Systems, 2019, pp. 14611–14624. conference: end_date: 2019-12-14 location: Vancouver, Canada name: 'NeurIPS: Neural Information Processing Systems' start_date: 2019-12-08 date_created: 2023-08-22T14:12:28Z date_published: 2019-12-08T00:00:00Z date_updated: 2023-09-12T09:37:22Z day: '08' department: - _id: FrLo extern: '1' external_id: arxiv: - '1905.13662' intvolume: ' 32' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1905.13662 month: '12' oa: 1 oa_version: Preprint page: 14611–14624 publication: Advances in Neural Information Processing Systems publication_identifier: isbn: - '9781713807933' publication_status: published quality_controlled: '1' scopus_import: '1' status: public title: On the fairness of disentangled representations type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2019' ... --- _id: '14200' abstract: - lang: eng text: "The key idea behind the unsupervised learning of disentangled representations\r\nis that real-world data is generated by a few explanatory factors of variation\r\nwhich can be recovered by unsupervised learning algorithms. In this paper, we\r\nprovide a sober look at recent progress in the field and challenge some common\r\nassumptions. We first theoretically show that the unsupervised learning of\r\ndisentangled representations is fundamentally impossible without inductive\r\nbiases on both the models and the data. Then, we train more than 12000 models\r\ncovering most prominent methods and evaluation metrics in a reproducible\r\nlarge-scale experimental study on seven different data sets. We observe that\r\nwhile the different methods successfully enforce properties ``encouraged'' by\r\nthe corresponding losses, well-disentangled models seemingly cannot be\r\nidentified without supervision. Furthermore, increased disentanglement does not\r\nseem to lead to a decreased sample complexity of learning for downstream tasks.\r\nOur results suggest that future work on disentanglement learning should be\r\nexplicit about the role of inductive biases and (implicit) supervision,\r\ninvestigate concrete benefits of enforcing disentanglement of the learned\r\nrepresentations, and consider a reproducible experimental setup covering\r\nseveral data sets." article_processing_charge: No arxiv: 1 author: - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Stefan full_name: Bauer, Stefan last_name: Bauer - first_name: Mario full_name: Lucic, Mario last_name: Lucic - first_name: Gunnar full_name: Rätsch, Gunnar last_name: Rätsch - first_name: Sylvain full_name: Gelly, Sylvain last_name: Gelly - first_name: Bernhard full_name: Schölkopf, Bernhard last_name: Schölkopf - first_name: Olivier full_name: Bachem, Olivier last_name: Bachem citation: ama: 'Locatello F, Bauer S, Lucic M, et al. Challenging common assumptions in the unsupervised learning of disentangled representations. In: Proceedings of the 36th International Conference on Machine Learning. Vol 97. ML Research Press; 2019:4114-4124.' apa: 'Locatello, F., Bauer, S., Lucic, M., Rätsch, G., Gelly, S., Schölkopf, B., & Bachem, O. (2019). Challenging common assumptions in the unsupervised learning of disentangled representations. In Proceedings of the 36th International Conference on Machine Learning (Vol. 97, pp. 4114–4124). Long Beach, CA, United States: ML Research Press.' chicago: Locatello, Francesco, Stefan Bauer, Mario Lucic, Gunnar Rätsch, Sylvain Gelly, Bernhard Schölkopf, and Olivier Bachem. “Challenging Common Assumptions in the Unsupervised Learning of Disentangled Representations.” In Proceedings of the 36th International Conference on Machine Learning, 97:4114–24. ML Research Press, 2019. ieee: F. Locatello et al., “Challenging common assumptions in the unsupervised learning of disentangled representations,” in Proceedings of the 36th International Conference on Machine Learning, Long Beach, CA, United States, 2019, vol. 97, pp. 4114–4124. ista: Locatello F, Bauer S, Lucic M, Rätsch G, Gelly S, Schölkopf B, Bachem O. 2019. Challenging common assumptions in the unsupervised learning of disentangled representations. Proceedings of the 36th International Conference on Machine Learning. International Conference on Machine Learning vol. 97, 4114–4124. mla: Locatello, Francesco, et al. “Challenging Common Assumptions in the Unsupervised Learning of Disentangled Representations.” Proceedings of the 36th International Conference on Machine Learning, vol. 97, ML Research Press, 2019, pp. 4114–24. short: F. Locatello, S. Bauer, M. Lucic, G. Rätsch, S. Gelly, B. Schölkopf, O. Bachem, in:, Proceedings of the 36th International Conference on Machine Learning, ML Research Press, 2019, pp. 4114–4124. conference: end_date: 2019-06-15 location: Long Beach, CA, United States name: International Conference on Machine Learning start_date: 2019-06-10 date_created: 2023-08-22T14:13:08Z date_published: 2019-06-09T00:00:00Z date_updated: 2023-09-13T07:45:30Z day: '09' department: - _id: FrLo extern: '1' external_id: arxiv: - '1811.12359' intvolume: ' 97' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1811.12359 month: '06' oa: 1 oa_version: Preprint page: 4114-4124 publication: Proceedings of the 36th International Conference on Machine Learning publication_status: published publisher: ML Research Press quality_controlled: '1' scopus_import: '1' status: public title: Challenging common assumptions in the unsupervised learning of disentangled representations type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 97 year: '2019' ... --- _id: '9261' abstract: - lang: eng text: 'Bending-active structures are able to efficiently produce complex curved shapes starting from flat panels. The desired deformation of the panels derives from the proper selection of their elastic properties. Optimized panels, called FlexMaps, are designed such that, once they are bent and assembled, the resulting static equilibrium configuration matches a desired input 3D shape. The FlexMaps elastic properties are controlled by locally varying spiraling geometric mesostructures, which are optimized in size and shape to match the global curvature (i.e., bending requests) of the target shape. The design pipeline starts from a quad mesh representing the input 3D shape, which defines the edge size and the total amount of spirals: every quad will embed one spiral. Then, an optimization algorithm tunes the geometry of the spirals by using a simplified pre-computed rod model. This rod model is derived from a non-linear regression algorithm which approximates the non-linear behavior of solid FEM spiral models subject to hundreds of load combinations. This innovative pipeline has been applied to the project of a lightweight plywood pavilion named FlexMaps Pavilion, which is a single-layer piecewise twisted arc that fits a bounding box of 3.90x3.96x3.25 meters.' article_processing_charge: No author: - first_name: Francesco full_name: Laccone, Francesco last_name: Laccone - first_name: Luigi full_name: Malomo, Luigi last_name: Malomo - first_name: Jesus full_name: Perez Rodriguez, Jesus id: 2DC83906-F248-11E8-B48F-1D18A9856A87 last_name: Perez Rodriguez - first_name: Nico full_name: Pietroni, Nico last_name: Pietroni - first_name: Federico full_name: Ponchio, Federico last_name: Ponchio - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Paolo full_name: Cignoni, Paolo last_name: Cignoni citation: ama: 'Laccone F, Malomo L, Perez Rodriguez J, et al. FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels. In: IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE. International Center for Numerical Methods in Engineering; 2019:509-515.' apa: 'Laccone, F., Malomo, L., Perez Rodriguez, J., Pietroni, N., Ponchio, F., Bickel, B., & Cignoni, P. (2019). FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels. In IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE (pp. 509–515). Barcelona, Spain: International Center for Numerical Methods in Engineering.' chicago: 'Laccone, Francesco, Luigi Malomo, Jesus Perez Rodriguez, Nico Pietroni, Federico Ponchio, Bernd Bickel, and Paolo Cignoni. “FlexMaps Pavilion: A Twisted Arc Made of Mesostructured Flat Flexible Panels.” In IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE, 509–15. International Center for Numerical Methods in Engineering, 2019.' ieee: 'F. Laccone et al., “FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels,” in IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE, Barcelona, Spain, 2019, pp. 509–515.' ista: 'Laccone F, Malomo L, Perez Rodriguez J, Pietroni N, Ponchio F, Bickel B, Cignoni P. 2019. FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels. IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE. IASS: International Association for Shell and Spatial Structures, 509–515.' mla: 'Laccone, Francesco, et al. “FlexMaps Pavilion: A Twisted Arc Made of Mesostructured Flat Flexible Panels.” IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE, International Center for Numerical Methods in Engineering, 2019, pp. 509–15.' short: F. Laccone, L. Malomo, J. Perez Rodriguez, N. Pietroni, F. Ponchio, B. Bickel, P. Cignoni, in:, IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE, International Center for Numerical Methods in Engineering, 2019, pp. 509–515. conference: end_date: 2019-10-10 location: Barcelona, Spain name: 'IASS: International Association for Shell and Spatial Structures' start_date: 2019-10-07 date_created: 2021-03-21T23:01:21Z date_published: 2019-10-10T00:00:00Z date_updated: 2023-09-08T11:21:54Z day: '10' department: - _id: BeBi external_id: isi: - '000563497600059' isi: 1 language: - iso: eng month: '10' oa_version: None page: 509-515 publication: IASS Symposium 2019 - 60th Anniversary Symposium of the International Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International Conference on Textile Composites and Inflatable Structures, FORM and FORCE publication_identifier: isbn: - '9788412110104' issn: - 2518-6582 publication_status: published publisher: International Center for Numerical Methods in Engineering quality_controlled: '1' scopus_import: '1' status: public title: 'FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels' type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2019' ... --- _id: '9460' abstract: - lang: eng text: Epigenetic reprogramming is required for proper regulation of gene expression in eukaryotic organisms. In Arabidopsis, active DNA demethylation is crucial for seed viability, pollen function, and successful reproduction. The DEMETER (DME) DNA glycosylase initiates localized DNA demethylation in vegetative and central cells, so-called companion cells that are adjacent to sperm and egg gametes, respectively. In rice, the central cell genome displays local DNA hypomethylation, suggesting that active DNA demethylation also occurs in rice; however, the enzyme responsible for this process is unknown. One candidate is the rice REPRESSOR OF SILENCING 1a (ROS1a) gene, which is related to DME and is essential for rice seed viability and pollen function. Here, we report genome-wide analyses of DNA methylation in wild-type and ros1a mutant sperm and vegetative cells. We find that the rice vegetative cell genome is locally hypomethylated compared with sperm by a process that requires ROS1a activity. We show that many ROS1a target sequences in the vegetative cell are hypomethylated in the rice central cell, suggesting that ROS1a also demethylates the central cell genome. Similar to Arabidopsis, we show that sperm non-CG methylation is indirectly promoted by DNA demethylation in the vegetative cell. These results reveal that DNA glycosylase-mediated DNA demethylation processes are conserved in Arabidopsis and rice, plant species that diverged 150 million years ago. Finally, although global non-CG methylation levels of sperm and egg differ, the maternal and paternal embryo genomes show similar non-CG methylation levels, suggesting that rice gamete genomes undergo dynamic DNA methylation reprogramming after cell fusion. article_processing_charge: No article_type: original author: - first_name: M. Yvonne full_name: Kim, M. Yvonne last_name: Kim - first_name: Akemi full_name: Ono, Akemi last_name: Ono - first_name: Stefan full_name: Scholten, Stefan last_name: Scholten - first_name: Tetsu full_name: Kinoshita, Tetsu last_name: Kinoshita - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 - first_name: Takashi full_name: Okamoto, Takashi last_name: Okamoto - first_name: Robert L. full_name: Fischer, Robert L. last_name: Fischer citation: ama: Kim MY, Ono A, Scholten S, et al. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. 2019;116(19):9652-9657. doi:10.1073/pnas.1821435116 apa: Kim, M. Y., Ono, A., Scholten, S., Kinoshita, T., Zilberman, D., Okamoto, T., & Fischer, R. L. (2019). DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1821435116 chicago: Kim, M. Yvonne, Akemi Ono, Stefan Scholten, Tetsu Kinoshita, Daniel Zilberman, Takashi Okamoto, and Robert L. Fischer. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1821435116. ieee: M. Y. Kim et al., “DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm,” Proceedings of the National Academy of Sciences, vol. 116, no. 19. National Academy of Sciences, pp. 9652–9657, 2019. ista: Kim MY, Ono A, Scholten S, Kinoshita T, Zilberman D, Okamoto T, Fischer RL. 2019. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. 116(19), 9652–9657. mla: Kim, M. Yvonne, et al. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” Proceedings of the National Academy of Sciences, vol. 116, no. 19, National Academy of Sciences, 2019, pp. 9652–57, doi:10.1073/pnas.1821435116. short: M.Y. Kim, A. Ono, S. Scholten, T. Kinoshita, D. Zilberman, T. Okamoto, R.L. Fischer, Proceedings of the National Academy of Sciences 116 (2019) 9652–9657. date_created: 2021-06-04T12:38:20Z date_published: 2019-05-07T00:00:00Z date_updated: 2021-12-14T07:52:30Z day: '07' ddc: - '580' department: - _id: DaZi doi: 10.1073/pnas.1821435116 extern: '1' external_id: pmid: - '31000601' file: - access_level: open_access checksum: 5b0ae3779b8b21b5223bd2d3cceede3a content_type: application/pdf creator: asandaue date_created: 2021-06-04T12:50:47Z date_updated: 2021-06-04T12:50:47Z file_id: '9461' file_name: 2019_PNAS_Kim.pdf file_size: 1142540 relation: main_file success: 1 file_date_updated: 2021-06-04T12:50:47Z has_accepted_license: '1' intvolume: ' 116' issue: '19' keyword: - Multidisciplinary language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '05' oa: 1 oa_version: Published Version page: 9652-9657 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 116 year: '2019' ... --- _id: '9530' abstract: - lang: eng text: "Background\r\nDNA methylation of active genes, also known as gene body methylation, is found in many animal and plant genomes. Despite this, the transcriptional and developmental role of such methylation remains poorly understood. Here, we explore the dynamic range of DNA methylation in honey bee, a model organism for gene body methylation.\r\n\r\nResults\r\nOur data show that CG methylation in gene bodies globally fluctuates during honey bee development. However, these changes cause no gene expression alterations. Intriguingly, despite the global alterations, tissue-specific CG methylation patterns of complete genes or exons are rare, implying robust maintenance of genic methylation during development. Additionally, we show that CG methylation maintenance fluctuates in somatic cells, while reaching maximum fidelity in sperm cells. Finally, unlike universally present CG methylation, we discovered non-CG methylation specifically in bee heads that resembles such methylation in mammalian brain tissue.\r\n\r\nConclusions\r\nBased on these results, we propose that gene body CG methylation can oscillate during development if it is kept to a level adequate to preserve function. Additionally, our data suggest that heightened non-CG methylation is a conserved regulator of animal nervous systems." article_number: '62' article_processing_charge: No article_type: original author: - first_name: Keith D. full_name: Harris, Keith D. last_name: Harris - first_name: James P. B. full_name: Lloyd, James P. B. last_name: Lloyd - first_name: Katherine full_name: Domb, Katherine last_name: Domb - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 - first_name: Assaf full_name: Zemach, Assaf last_name: Zemach citation: ama: Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. 2019;12. doi:10.1186/s13072-019-0307-4 apa: Harris, K. D., Lloyd, J. P. B., Domb, K., Zilberman, D., & Zemach, A. (2019). DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. Springer Nature. https://doi.org/10.1186/s13072-019-0307-4 chicago: Harris, Keith D., James P. B. Lloyd, Katherine Domb, Daniel Zilberman, and Assaf Zemach. “DNA Methylation Is Maintained with High Fidelity in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.” Epigenetics and Chromatin. Springer Nature, 2019. https://doi.org/10.1186/s13072-019-0307-4. ieee: K. D. Harris, J. P. B. Lloyd, K. Domb, D. Zilberman, and A. Zemach, “DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development,” Epigenetics and Chromatin, vol. 12. Springer Nature, 2019. ista: Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. 2019. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. 12, 62. mla: Harris, Keith D., et al. “DNA Methylation Is Maintained with High Fidelity in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.” Epigenetics and Chromatin, vol. 12, 62, Springer Nature, 2019, doi:10.1186/s13072-019-0307-4. short: K.D. Harris, J.P.B. Lloyd, K. Domb, D. Zilberman, A. Zemach, Epigenetics and Chromatin 12 (2019). date_created: 2021-06-08T09:21:51Z date_published: 2019-10-10T00:00:00Z date_updated: 2021-12-14T07:53:00Z day: '10' ddc: - '570' department: - _id: DaZi doi: 10.1186/s13072-019-0307-4 extern: '1' external_id: pmid: - '31601251' file: - access_level: open_access checksum: 86ff50a7517891511af2733c76c81b67 content_type: application/pdf creator: asandaue date_created: 2021-06-08T09:29:19Z date_updated: 2021-06-08T09:29:19Z file_id: '9531' file_name: 2019_EpigeneticsAndChromatin_Harris.pdf file_size: 3221067 relation: main_file success: 1 file_date_updated: 2021-06-08T09:29:19Z has_accepted_license: '1' intvolume: ' 12' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '10' oa: 1 oa_version: Published Version pmid: 1 publication: Epigenetics and Chromatin publication_identifier: eissn: - 1756-8935 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 12 year: '2019' ... --- _id: '10065' abstract: - lang: eng text: We study double quantum dots in a Ge/SiGe heterostructure and test their maturity towards singlet-triplet ($S-T_0$) qubits. We demonstrate a large range of tunability, from two single quantum dots to a double quantum dot. We measure Pauli spin blockade and study the anisotropy of the $g$-factor. We use an adjacent quantum dot for sensing charge transitions in the double quantum dot at interest. In conclusion, Ge/SiGe possesses all ingredients necessary for building a singlet-triplet qubit. acknowledged_ssus: - _id: M-Shop - _id: NanoFab acknowledgement: "We thank Matthias Brauns for helpful discussions and careful proofreading of the manuscript. This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 844511 and from the FWF project P30207. The research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA machine shop and the nanofabrication\r\nfacility." article_number: '1910.05841' article_processing_charge: No arxiv: 1 author: - first_name: Andrea C full_name: Hofmann, Andrea C id: 340F461A-F248-11E8-B48F-1D18A9856A87 last_name: Hofmann - first_name: Daniel full_name: Jirovec, Daniel id: 4C473F58-F248-11E8-B48F-1D18A9856A87 last_name: Jirovec orcid: 0000-0002-7197-4801 - first_name: Maxim full_name: Borovkov, Maxim last_name: Borovkov - first_name: Ivan full_name: Prieto Gonzalez, Ivan id: 2A307FE2-F248-11E8-B48F-1D18A9856A87 last_name: Prieto Gonzalez orcid: 0000-0002-7370-5357 - first_name: Andrea full_name: Ballabio, Andrea last_name: Ballabio - first_name: Jacopo full_name: Frigerio, Jacopo last_name: Frigerio - first_name: Daniel full_name: Chrastina, Daniel last_name: Chrastina - first_name: Giovanni full_name: Isella, Giovanni last_name: Isella - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X citation: ama: Hofmann AC, Jirovec D, Borovkov M, et al. Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits. arXiv. doi:10.48550/arXiv.1910.05841 apa: Hofmann, A. C., Jirovec, D., Borovkov, M., Prieto Gonzalez, I., Ballabio, A., Frigerio, J., … Katsaros, G. (n.d.). Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits. arXiv. https://doi.org/10.48550/arXiv.1910.05841 chicago: Hofmann, Andrea C, Daniel Jirovec, Maxim Borovkov, Ivan Prieto Gonzalez, Andrea Ballabio, Jacopo Frigerio, Daniel Chrastina, Giovanni Isella, and Georgios Katsaros. “Assessing the Potential of Ge/SiGe Quantum Dots as Hosts for Singlet-Triplet Qubits.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1910.05841. ieee: A. C. Hofmann et al., “Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits,” arXiv. . ista: Hofmann AC, Jirovec D, Borovkov M, Prieto Gonzalez I, Ballabio A, Frigerio J, Chrastina D, Isella G, Katsaros G. Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits. arXiv, 1910.05841. mla: Hofmann, Andrea C., et al. “Assessing the Potential of Ge/SiGe Quantum Dots as Hosts for Singlet-Triplet Qubits.” ArXiv, 1910.05841, doi:10.48550/arXiv.1910.05841. short: A.C. Hofmann, D. Jirovec, M. Borovkov, I. Prieto Gonzalez, A. Ballabio, J. Frigerio, D. Chrastina, G. Isella, G. Katsaros, ArXiv (n.d.). date_created: 2021-10-01T12:14:51Z date_published: 2019-10-13T00:00:00Z date_updated: 2024-03-25T23:30:14Z day: '13' department: - _id: GeKa doi: 10.48550/arXiv.1910.05841 ec_funded: 1 external_id: arxiv: - '1910.05841' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1910.05841 month: '10' oa: 1 oa_version: Preprint project: - _id: 26A151DA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '844511' name: Majorana bound states in Ge/SiGe heterostructures - _id: 2641CE5E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P30207 name: Hole spin orbit qubits in Ge quantum wells publication: arXiv publication_status: submitted related_material: record: - id: '10058' relation: dissertation_contains status: public status: public title: Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '10190' abstract: - lang: eng text: 'The verification of concurrent programs remains an open challenge, as thread interaction has to be accounted for, which leads to state-space explosion. Stateless model checking battles this problem by exploring traces rather than states of the program. As there are exponentially many traces, dynamic partial-order reduction (DPOR) techniques are used to partition the trace space into equivalence classes, and explore a few representatives from each class. The standard equivalence that underlies most DPOR techniques is the happens-before equivalence, however recent works have spawned a vivid interest towards coarser equivalences. The efficiency of such approaches is a product of two parameters: (i) the size of the partitioning induced by the equivalence, and (ii) the time spent by the exploration algorithm in each class of the partitioning. In this work, we present a new equivalence, called value-happens-before and show that it has two appealing features. First, value-happens-before is always at least as coarse as the happens-before equivalence, and can be even exponentially coarser. Second, the value-happens-before partitioning is efficiently explorable when the number of threads is bounded. We present an algorithm called value-centric DPOR (VCDPOR), which explores the underlying partitioning using polynomial time per class. Finally, we perform an experimental evaluation of VCDPOR on various benchmarks, and compare it against other state-of-the-art approaches. Our results show that value-happens-before typically induces a significant reduction in the size of the underlying partitioning, which leads to a considerable reduction in the running time for exploring the whole partitioning.' acknowledgement: "The authors would also like to thank anonymous referees for their valuable comments and helpful suggestions. This work is supported by the Austrian Science Fund (FWF) NFN grants S11407-N23 (RiSE/SHiNE) and S11402-N23 (RiSE/SHiNE), by the Vienna Science and Technology Fund (WWTF) Project ICT15-003, and by the Austrian Science Fund (FWF) Schrodinger grant J-4220.\r\n" article_number: '124' article_processing_charge: No arxiv: 1 author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 - first_name: Viktor full_name: Toman, Viktor id: 3AF3DA7C-F248-11E8-B48F-1D18A9856A87 last_name: Toman orcid: 0000-0001-9036-063X citation: ama: 'Chatterjee K, Pavlogiannis A, Toman V. Value-centric dynamic partial order reduction. In: Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications. Vol 3. ACM; 2019. doi:10.1145/3360550' apa: 'Chatterjee, K., Pavlogiannis, A., & Toman, V. (2019). Value-centric dynamic partial order reduction. In Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications (Vol. 3). Athens, Greece: ACM. https://doi.org/10.1145/3360550' chicago: Chatterjee, Krishnendu, Andreas Pavlogiannis, and Viktor Toman. “Value-Centric Dynamic Partial Order Reduction.” In Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications, Vol. 3. ACM, 2019. https://doi.org/10.1145/3360550. ieee: K. Chatterjee, A. Pavlogiannis, and V. Toman, “Value-centric dynamic partial order reduction,” in Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications, Athens, Greece, 2019, vol. 3. ista: 'Chatterjee K, Pavlogiannis A, Toman V. 2019. Value-centric dynamic partial order reduction. Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications. OOPSLA: Object-oriented Programming, Systems, Languages and Applications vol. 3, 124.' mla: Chatterjee, Krishnendu, et al. “Value-Centric Dynamic Partial Order Reduction.” Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications, vol. 3, 124, ACM, 2019, doi:10.1145/3360550. short: K. Chatterjee, A. Pavlogiannis, V. Toman, in:, Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications, ACM, 2019. conference: end_date: 2019-10-25 location: Athens, Greece name: 'OOPSLA: Object-oriented Programming, Systems, Languages and Applications' start_date: 2019-10-23 date_created: 2021-10-27T14:57:06Z date_published: 2019-10-10T00:00:00Z date_updated: 2025-07-14T09:10:15Z day: '10' ddc: - '000' department: - _id: GradSch - _id: KrCh doi: 10.1145/3360550 external_id: arxiv: - '1909.00989' file: - access_level: open_access checksum: 2149979c46964c4d117af06ccb6c0834 content_type: application/pdf creator: cchlebak date_created: 2021-11-12T11:41:56Z date_updated: 2021-11-12T11:41:56Z file_id: '10278' file_name: 2019_ACM_Chatterjee.pdf file_size: 570829 relation: main_file success: 1 file_date_updated: 2021-11-12T11:41:56Z has_accepted_license: '1' intvolume: ' 3' keyword: - safety - risk - reliability and quality - software language: - iso: eng main_file_link: - open_access: '1' url: https://dl.acm.org/doi/10.1145/3360550 month: '10' oa: 1 oa_version: Published Version project: - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms publication: Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications publication_identifier: eissn: - 2475-1421 publication_status: published publisher: ACM quality_controlled: '1' related_material: record: - id: '10199' relation: dissertation_contains status: public status: public title: Value-centric dynamic partial order reduction tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 3 year: '2019' ... --- _id: '105' abstract: - lang: eng text: 'Clinical Utility Gene Card. 1. Name of Disease (Synonyms): Pontocerebellar hypoplasia type 9 (PCH9) and spastic paraplegia-63 (SPG63). 2. OMIM# of the Disease: 615809 and 615686. 3. Name of the Analysed Genes or DNA/Chromosome Segments: AMPD2 at 1p13.3. 4. OMIM# of the Gene(s): 102771.' acknowledgement: 'This work was supported by EuroGentest2 (Unit 2: “Genetic testing as part of health care”), a Coordination Action under FP7 (Grant Agreement Number 261469) and the European Society of Human Genetics. We acknowledge the participation of the patients and their families in these studies, as well as the generous financial support of the Lefroy and Handbury families. APLM was supported by an Australian Postgraduate Award. PJL is supported by an NHMRC Career Development Fellowship (GNT1032364). RJL is supported by a Melbourne Children’s Clinician Scientist Fellowship.' article_processing_charge: No article_type: original author: - first_name: Ashley full_name: Marsh, Ashley last_name: Marsh - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Paul full_name: Lockhart, Paul last_name: Lockhart - first_name: Richard full_name: Leventer, Richard last_name: Leventer citation: ama: Marsh A, Novarino G, Lockhart P, Leventer R. CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics. 2019;27:161-166. doi:10.1038/s41431-018-0231-2 apa: Marsh, A., Novarino, G., Lockhart, P., & Leventer, R. (2019). CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics. Springer Nature. https://doi.org/10.1038/s41431-018-0231-2 chicago: Marsh, Ashley, Gaia Novarino, Paul Lockhart, and Richard Leventer. “CUGC for Pontocerebellar Hypoplasia Type 9 and Spastic Paraplegia-63.” European Journal of Human Genetics. Springer Nature, 2019. https://doi.org/10.1038/s41431-018-0231-2. ieee: A. Marsh, G. Novarino, P. Lockhart, and R. Leventer, “CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63,” European Journal of Human Genetics, vol. 27. Springer Nature, pp. 161–166, 2019. ista: Marsh A, Novarino G, Lockhart P, Leventer R. 2019. CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63. European Journal of Human Genetics. 27, 161–166. mla: Marsh, Ashley, et al. “CUGC for Pontocerebellar Hypoplasia Type 9 and Spastic Paraplegia-63.” European Journal of Human Genetics, vol. 27, Springer Nature, 2019, pp. 161–66, doi:10.1038/s41431-018-0231-2. short: A. Marsh, G. Novarino, P. Lockhart, R. Leventer, European Journal of Human Genetics 27 (2019) 161–166. date_created: 2018-12-11T11:44:39Z date_published: 2019-01-01T00:00:00Z date_updated: 2023-08-24T14:28:24Z day: '01' department: - _id: GaNo doi: 10.1038/s41431-018-0231-2 external_id: isi: - '000454111500019' pmid: - '30089829' intvolume: ' 27' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41431-018-0231-2 month: '01' oa: 1 oa_version: Published Version page: 161-166 pmid: 1 publication: European Journal of Human Genetics publication_status: published publisher: Springer Nature publist_id: '7949' quality_controlled: '1' scopus_import: '1' status: public title: CUGC for pontocerebellar hypoplasia type 9 and spastic paraplegia-63 type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 27 year: '2019' ... --- _id: '12190' abstract: - lang: eng text: Meiotic crossover frequency varies within genomes, which influences genetic diversity and adaptation. In turn, genetic variation within populations can act to modify crossover frequency in cis and trans. To identify genetic variation that controls meiotic crossover frequency, we screened Arabidopsis accessions using fluorescent recombination reporters. We mapped a genetic modifier of crossover frequency in Col × Bur populations of Arabidopsis to a premature stop codon within TBP-ASSOCIATED FACTOR 4b (TAF4b), which encodes a subunit of the RNA polymerase II general transcription factor TFIID. The Arabidopsis taf4b mutation is a rare variant found in the British Isles, originating in South-West Ireland. Using genetics, genomics, and immunocytology, we demonstrate a genome-wide decrease in taf4b crossovers, with strongest reduction in the sub-telomeric regions. Using RNA sequencing (RNA-seq) from purified meiocytes, we show that TAF4b expression is meiocyte enriched, whereas its paralog TAF4 is broadly expressed. Consistent with the role of TFIID in promoting gene expression, RNA-seq of wild-type and taf4b meiocytes identified widespread transcriptional changes, including in genes that regulate the meiotic cell cycle and recombination. Therefore, TAF4b duplication is associated with acquisition of meiocyte-specific expression and promotion of germline transcription, which act directly or indirectly to elevate crossovers. This identifies a novel mode of meiotic recombination control via a general transcription factor. acknowledgement: "We thank Gregory Copenhaver (University of North Carolina), Avraham Levy (The Weizmann Institute), and Scott Poethig (University of Pennsylvania) for FTLs; Piotr Ziolkowski for Col-420/Bur seed; Sureshkumar Balasubramanian\r\n(Monash University) for providing British and Irish Arabidopsis accessions; Mathilde Grelon (INRA, Versailles) for providing the MLH1 antibody; and the Gurdon Institute for access to microscopes. This work was supported by a BBSRC DTP studentship (E.J.L.), European Research Area Network for Coordinating Action in Plant Sciences/BBSRC ‘‘DeCOP’’ (BB/M004937/1; C.L.), a BBSRC David Phillips Fellowship (BB/L025043/1; H.G. and X.F.), the European Research Council (CoG ‘‘SynthHotspot,’’ A.J.T., C.L., and I.R.H.; StG ‘‘SexMeth,’’ X.F.), and a Sainsbury Charitable Foundation Studentship (A.R.B.)." article_processing_charge: No article_type: original author: - first_name: Emma J. full_name: Lawrence, Emma J. last_name: Lawrence - first_name: Hongbo full_name: Gao, Hongbo last_name: Gao - first_name: Andrew J. full_name: Tock, Andrew J. last_name: Tock - first_name: Christophe full_name: Lambing, Christophe last_name: Lambing - first_name: Alexander R. full_name: Blackwell, Alexander R. last_name: Blackwell - first_name: Xiaoqi full_name: Feng, Xiaoqi id: e0164712-22ee-11ed-b12a-d80fcdf35958 last_name: Feng orcid: 0000-0002-4008-1234 - first_name: Ian R. full_name: Henderson, Ian R. last_name: Henderson citation: ama: Lawrence EJ, Gao H, Tock AJ, et al. Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. 2019;29(16):2676-2686.e3. doi:10.1016/j.cub.2019.06.084 apa: Lawrence, E. J., Gao, H., Tock, A. J., Lambing, C., Blackwell, A. R., Feng, X., & Henderson, I. R. (2019). Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. Elsevier BV. https://doi.org/10.1016/j.cub.2019.06.084 chicago: Lawrence, Emma J., Hongbo Gao, Andrew J. Tock, Christophe Lambing, Alexander R. Blackwell, Xiaoqi Feng, and Ian R. Henderson. “Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis.” Current Biology. Elsevier BV, 2019. https://doi.org/10.1016/j.cub.2019.06.084. ieee: E. J. Lawrence et al., “Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis,” Current Biology, vol. 29, no. 16. Elsevier BV, p. 2676–2686.e3, 2019. ista: Lawrence EJ, Gao H, Tock AJ, Lambing C, Blackwell AR, Feng X, Henderson IR. 2019. Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. 29(16), 2676–2686.e3. mla: Lawrence, Emma J., et al. “Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis.” Current Biology, vol. 29, no. 16, Elsevier BV, 2019, p. 2676–2686.e3, doi:10.1016/j.cub.2019.06.084. short: E.J. Lawrence, H. Gao, A.J. Tock, C. Lambing, A.R. Blackwell, X. Feng, I.R. Henderson, Current Biology 29 (2019) 2676–2686.e3. date_created: 2023-01-16T09:16:33Z date_published: 2019-08-19T00:00:00Z date_updated: 2023-05-08T10:54:54Z day: '19' department: - _id: XiFe doi: 10.1016/j.cub.2019.06.084 extern: '1' external_id: pmid: - '31378616' intvolume: ' 29' issue: '16' keyword: - General Agricultural and Biological Sciences - General Biochemistry - Genetics and Molecular Biology language: - iso: eng month: '08' oa_version: None page: 2676-2686.e3 pmid: 1 publication: Current Biology publication_identifier: issn: - 0960-9822 publication_status: published publisher: Elsevier BV quality_controlled: '1' scopus_import: '1' status: public title: Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 29 year: '2019' ... --- _id: '12192' abstract: - lang: eng text: Transposable elements (TEs), the movement of which can damage the genome, are epigenetically silenced in eukaryotes. Intriguingly, TEs are activated in the sperm companion cell – vegetative cell (VC) – of the flowering plant Arabidopsis thaliana. However, the extent and mechanism of this activation are unknown. Here we show that about 100 heterochromatic TEs are activated in VCs, mostly by DEMETER-catalyzed DNA demethylation. We further demonstrate that DEMETER access to some of these TEs is permitted by the natural depletion of linker histone H1 in VCs. Ectopically expressed H1 suppresses TEs in VCs by reducing DNA demethylation and via a methylation-independent mechanism. We demonstrate that H1 is required for heterochromatin condensation in plant cells and show that H1 overexpression creates heterochromatic foci in the VC progenitor cell. Taken together, our results demonstrate that the natural depletion of H1 during male gametogenesis facilitates DEMETER-directed DNA demethylation, heterochromatin relaxation, and TE activation. acknowledgement: We thank David Twell for the pDONR-P4-P1R-pLAT52 and pDONR-P2R-P3-mRFP vectors, the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant Calder) for their assistance with microscopy, and the Norwich BioScience Institute Partnership Computing infrastructure for Science Group for High Performance Computing resources. This work was funded by a Biotechnology and Biological Sciences Research Council (BBSRC) David Phillips Fellowship (BB/L025043/1; SH, JZ and XF), a European Research Council Starting Grant ('SexMeth' 804981; XF) and a Grant to Exceptional Researchers by the Gatsby Charitable Foundation (SH and XF). article_number: '42530' article_processing_charge: No article_type: original author: - first_name: Shengbo full_name: He, Shengbo last_name: He - first_name: Martin full_name: Vickers, Martin last_name: Vickers - first_name: Jingyi full_name: Zhang, Jingyi last_name: Zhang - first_name: Xiaoqi full_name: Feng, Xiaoqi id: e0164712-22ee-11ed-b12a-d80fcdf35958 last_name: Feng orcid: 0000-0002-4008-1234 citation: ama: He S, Vickers M, Zhang J, Feng X. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. eLife. 2019;8. doi:10.7554/elife.42530 apa: He, S., Vickers, M., Zhang, J., & Feng, X. (2019). Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. ELife. eLife Sciences Publications, Ltd. https://doi.org/10.7554/elife.42530 chicago: He, Shengbo, Martin Vickers, Jingyi Zhang, and Xiaoqi Feng. “Natural Depletion of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation and Transposon Activation.” ELife. eLife Sciences Publications, Ltd, 2019. https://doi.org/10.7554/elife.42530. ieee: S. He, M. Vickers, J. Zhang, and X. Feng, “Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation,” eLife, vol. 8. eLife Sciences Publications, Ltd, 2019. ista: He S, Vickers M, Zhang J, Feng X. 2019. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. eLife. 8, 42530. mla: He, Shengbo, et al. “Natural Depletion of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation and Transposon Activation.” ELife, vol. 8, 42530, eLife Sciences Publications, Ltd, 2019, doi:10.7554/elife.42530. short: S. He, M. Vickers, J. Zhang, X. Feng, ELife 8 (2019). date_created: 2023-01-16T09:17:21Z date_published: 2019-05-28T00:00:00Z date_updated: 2023-05-08T10:54:12Z day: '28' ddc: - '580' department: - _id: XiFe doi: 10.7554/elife.42530 extern: '1' external_id: unknown: - '31135340' file: - access_level: open_access checksum: ea6b89c20d59e5eb3646916fe5d568ad content_type: application/pdf creator: alisjak date_created: 2023-02-07T09:42:46Z date_updated: 2023-02-07T09:42:46Z file_id: '12525' file_name: 2019_elife_He.pdf file_size: 2493837 relation: main_file success: 1 file_date_updated: 2023-02-07T09:42:46Z has_accepted_license: '1' intvolume: ' 8' keyword: - General Immunology and Microbiology - General Biochemistry - Genetics and Molecular Biology - General Medicine - General Neuroscience language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6594752/ month: '05' oa: 1 oa_version: Published Version publication: eLife publication_identifier: issn: - 2050-084X publication_status: published publisher: eLife Sciences Publications, Ltd quality_controlled: '1' scopus_import: '1' status: public title: Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2019' ... --- _id: '12901' article_processing_charge: No author: - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: Janos full_name: Kiss, Janos id: 3D3A06F8-F248-11E8-B48F-1D18A9856A87 last_name: Kiss - first_name: Stefano full_name: Elefante, Stefano id: 490F40CE-F248-11E8-B48F-1D18A9856A87 last_name: Elefante citation: ama: 'Schlögl A, Kiss J, Elefante S. Is Debian suitable for running an HPC Cluster? In: AHPC19 - Austrian HPC Meeting 2019 . Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz; 2019:25.' apa: 'Schlögl, A., Kiss, J., & Elefante, S. (2019). Is Debian suitable for running an HPC Cluster? In AHPC19 - Austrian HPC Meeting 2019 (p. 25). Grundlsee, Austria: Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz.' chicago: Schlögl, Alois, Janos Kiss, and Stefano Elefante. “Is Debian Suitable for Running an HPC Cluster?” In AHPC19 - Austrian HPC Meeting 2019 , 25. Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019. ieee: A. Schlögl, J. Kiss, and S. Elefante, “Is Debian suitable for running an HPC Cluster?,” in AHPC19 - Austrian HPC Meeting 2019 , Grundlsee, Austria, 2019, p. 25. ista: 'Schlögl A, Kiss J, Elefante S. 2019. Is Debian suitable for running an HPC Cluster? AHPC19 - Austrian HPC Meeting 2019 . AHPC: Austrian HPC Meeting, 25.' mla: Schlögl, Alois, et al. “Is Debian Suitable for Running an HPC Cluster?” AHPC19 - Austrian HPC Meeting 2019 , Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019, p. 25. short: A. Schlögl, J. Kiss, S. Elefante, in:, AHPC19 - Austrian HPC Meeting 2019 , Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019, p. 25. conference: end_date: 2019-02-27 location: Grundlsee, Austria name: 'AHPC: Austrian HPC Meeting' start_date: 2019-02-25 date_created: 2023-05-05T12:48:48Z date_published: 2019-02-27T00:00:00Z date_updated: 2023-05-16T07:29:32Z day: '27' ddc: - '000' department: - _id: ScienComp file: - access_level: open_access checksum: acc8272027faaf30709c51ac5c58ffa4 content_type: application/pdf creator: dernst date_created: 2023-05-16T07:27:09Z date_updated: 2023-05-16T07:27:09Z file_id: '12970' file_name: 2019_AHPC_Schloegl.pdf file_size: 1097603 relation: main_file success: 1 file_date_updated: 2023-05-16T07:27:09Z has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc19/BOOKLET_AHPC19.pdf month: '02' oa: 1 oa_version: Published Version page: '25' publication: 'AHPC19 - Austrian HPC Meeting 2019 ' publication_status: published publisher: Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz status: public title: Is Debian suitable for running an HPC Cluster? type: conference_abstract user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '9726' abstract: - lang: eng text: A detailed description of the two stochastic models, table of parameters, supplementary data for Figures 4 and 5, parameter dependence of the results, and an analysis on motors with different force–velocity functions (PDF) article_processing_charge: No author: - first_name: Mehmet C full_name: Ucar, Mehmet C id: 50B2A802-6007-11E9-A42B-EB23E6697425 last_name: Ucar orcid: 0000-0003-0506-4217 - first_name: Reinhard full_name: Lipowsky, Reinhard last_name: Lipowsky citation: ama: Ucar MC, Lipowsky R. Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding. 2019. doi:10.1021/acs.nanolett.9b04445.s001 apa: Ucar, M. C., & Lipowsky, R. (2019). Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding. American Chemical Society . https://doi.org/10.1021/acs.nanolett.9b04445.s001 chicago: Ucar, Mehmet C, and Reinhard Lipowsky. “Supplementary Information - Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding.” American Chemical Society , 2019. https://doi.org/10.1021/acs.nanolett.9b04445.s001. ieee: M. C. Ucar and R. Lipowsky, “Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding.” American Chemical Society , 2019. ista: Ucar MC, Lipowsky R. 2019. Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding, American Chemical Society , 10.1021/acs.nanolett.9b04445.s001. mla: Ucar, Mehmet C., and Reinhard Lipowsky. Supplementary Information - Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding. American Chemical Society , 2019, doi:10.1021/acs.nanolett.9b04445.s001. short: M.C. Ucar, R. Lipowsky, (2019). date_created: 2021-07-27T09:51:46Z date_published: 2019-12-19T00:00:00Z date_updated: 2023-08-17T14:07:52Z day: '19' department: - _id: EdHa doi: 10.1021/acs.nanolett.9b04445.s001 month: '12' oa_version: Published Version publisher: 'American Chemical Society ' related_material: record: - id: '7166' relation: used_in_publication status: public status: public title: Supplementary information - Collective force generation by molecular motors is determined by strain-induced unbinding type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '9731' abstract: - lang: eng text: OGs with putative pseudogenes by the number of affected genomes in different chlamydial species. Frameshift and nonsense mutations located less than 60 bp upstreamof the gene end or present in a single genome from the corresponding OG were excluded. (CSV 31 kb) article_processing_charge: No author: - first_name: Olga full_name: Sigalova, Olga last_name: Sigalova - first_name: Andrei full_name: Chaplin, Andrei last_name: Chaplin - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Pavel full_name: Shelyakin, Pavel last_name: Shelyakin - first_name: Vsevolod full_name: Filaretov, Vsevolod last_name: Filaretov - first_name: Evgeny full_name: Akkuratov, Evgeny last_name: Akkuratov - first_name: Valentina full_name: Burskaia, Valentina last_name: Burskaia - first_name: Mikhail S. full_name: Gelfand, Mikhail S. last_name: Gelfand citation: ama: Sigalova O, Chaplin A, Bochkareva O, et al. Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808772.v1 apa: Sigalova, O., Chaplin, A., Bochkareva, O., Shelyakin, P., Filaretov, V., Akkuratov, E., … Gelfand, M. S. (2019). Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808772.v1 chicago: Sigalova, Olga, Andrei Chaplin, Olga Bochkareva, Pavel Shelyakin, Vsevolod Filaretov, Evgeny Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 11 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808772.v1. ieee: O. Sigalova et al., “Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019. ista: Sigalova O, Chaplin A, Bochkareva O, Shelyakin P, Filaretov V, Akkuratov E, Burskaia V, Gelfand MS. 2019. Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808772.v1. mla: Sigalova, Olga, et al. Additional File 11 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808772.v1. short: O. Sigalova, A. Chaplin, O. Bochkareva, P. Shelyakin, V. Filaretov, E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019). date_created: 2021-07-27T14:09:11Z date_published: 2019-09-12T00:00:00Z date_updated: 2023-08-30T06:20:21Z day: '12' department: - _id: FyKo doi: 10.6084/m9.figshare.9808772.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.9808772.v1 month: '09' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '6898' relation: used_in_publication status: public status: public title: Additional file 11 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '9783' abstract: - lang: eng text: Predicted frameshift and nonsense mutations in Chlamydial pan-genome. For the analysis of putative pseudogenes, events located less than 60 bp. away from gene end or present in a single genome from the corresponding OG were excluded. (CSV 600 kb) article_processing_charge: No author: - first_name: Olga M. full_name: Sigalova, Olga M. last_name: Sigalova - first_name: Andrei V. full_name: Chaplin, Andrei V. last_name: Chaplin - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Pavel V. full_name: Shelyakin, Pavel V. last_name: Shelyakin - first_name: Vsevolod A. full_name: Filaretov, Vsevolod A. last_name: Filaretov - first_name: Evgeny E. full_name: Akkuratov, Evgeny E. last_name: Akkuratov - first_name: Valentina full_name: Burskaia, Valentina last_name: Burskaia - first_name: Mikhail S. full_name: Gelfand, Mikhail S. last_name: Gelfand citation: ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808760.v1 apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808760.v1 chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 10 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808760.v1. ieee: O. M. Sigalova et al., “Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019. ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808760.v1. mla: Sigalova, Olga M., et al. Additional File 10 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808760.v1. short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019). date_created: 2021-08-06T07:59:56Z date_published: 2019-09-12T00:00:00Z date_updated: 2023-08-30T06:20:21Z day: '12' department: - _id: FyKo doi: 10.6084/m9.figshare.9808760.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.9808760.v1 month: '09' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '6898' relation: used_in_publication status: public status: public title: Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '9784' abstract: - lang: eng text: 'Additional file 1: Table S1. Kinetics of MDA-MB-231 cell growth in either the presence or absence of 100Â mg/L glyphosate. Cell counts are given at day-1 of seeding flasks and following 6-days of continuous culture. Note: no differences in cell numbers were observed between negative control and glyphosate treated cultures.' article_processing_charge: No author: - first_name: Michael N. full_name: Antoniou, Michael N. last_name: Antoniou - first_name: Armel full_name: Nicolas, Armel id: 2A103192-F248-11E8-B48F-1D18A9856A87 last_name: Nicolas - first_name: Robin full_name: Mesnage, Robin last_name: Mesnage - first_name: Martina full_name: Biserni, Martina last_name: Biserni - first_name: Francesco V. full_name: Rao, Francesco V. last_name: Rao - first_name: Cristina Vazquez full_name: Martin, Cristina Vazquez last_name: Martin citation: ama: Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. 2019. doi:10.6084/m9.figshare.9411761.v1 apa: Antoniou, M. N., Nicolas, A., Mesnage, R., Biserni, M., Rao, F. V., & Martin, C. V. (2019). MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. Springer Nature. https://doi.org/10.6084/m9.figshare.9411761.v1 chicago: Antoniou, Michael N., Armel Nicolas, Robin Mesnage, Martina Biserni, Francesco V. Rao, and Cristina Vazquez Martin. “MOESM1 of Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9411761.v1. ieee: M. N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F. V. Rao, and C. V. Martin, “MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells.” Springer Nature, 2019. ista: Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. 2019. MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells, Springer Nature, 10.6084/m9.figshare.9411761.v1. mla: Antoniou, Michael N., et al. MOESM1 of Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells. Springer Nature, 2019, doi:10.6084/m9.figshare.9411761.v1. short: M.N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F.V. Rao, C.V. Martin, (2019). date_created: 2021-08-06T08:14:05Z date_published: 2019-08-09T00:00:00Z date_updated: 2023-02-23T12:52:29Z day: '09' department: - _id: LifeSc doi: 10.6084/m9.figshare.9411761.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.9411761.v1 month: '08' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '6819' relation: used_in_publication status: public status: public title: MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ...