--- OA_place: publisher _id: '12378' abstract: - lang: eng text: "Environmental cues influence the highly dynamic morphology of microglia. Strategies to \r\ncharacterize these changes usually involve user-selected morphometric features, which \r\npreclude the identification of a spectrum of context-dependent morphological phenotypes. \r\nHere, we develop MorphOMICs, a topological data analysis approach, which enables semi\x02automatic mapping of microglial morphology into an atlas of cue-dependent phenotypes,\r\novercomes feature-selection bias and minimizes biological variability. \r\nFirst, with MorphOMICs we derive the morphological spectrum of microglia across seven \r\nbrain regions during postnatal development and in two distinct Alzheimer’s disease \r\ndegeneration mouse models. We uncover region-specific and sexually dimorphic\r\nmorphological trajectories, with females showing an earlier morphological shift than males in \r\nthe degenerating brain. Overall, we demonstrate that both long primary- and short terminal \r\nprocesses provide distinct insights to morphological phenotypes. Moreover, using machine \r\nlearning to map novel condition on the spectrum, we observe that microglia morphologies \r\nreflect a dose-dependent adaptation upon ketamine anesthesia and do not recover to control \r\nmorphologies.\r\nNext, we took advantage of MorphOMICs to build a high-resolution and layer-specific map of \r\nmicroglial morphological spectrum in the retina, covering postnatal development and rd10 \r\ndegeneration. Here, following photoreceptor death, microglia assume an early development\x02like morphology. Finally, we map microglial morphology following optic nerve crush on the \r\nretinal spectrum and observe a layer- and sex-dependent response. \r\nOverall, MorphOMICs opens a new perspective to analyze microglial morphology across \r\nmultiple conditions, and provides a novel tool to characterize microglial morphology beyond \r\nthe traditionally dichotomized view of microglia." acknowledged_ssus: - _id: PreCl - _id: Bio - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Gloria full_name: Colombo, Gloria id: 3483CF6C-F248-11E8-B48F-1D18A9856A87 last_name: Colombo orcid: 0000-0001-9434-8902 citation: ama: Colombo G. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. 2022. doi:10.15479/at:ista:12378 apa: Colombo, G. (2022). MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12378 chicago: Colombo, Gloria. “MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12378. ieee: G. Colombo, “MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes,” Institute of Science and Technology Austria, 2022. ista: Colombo G. 2022. MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes. Institute of Science and Technology Austria. mla: Colombo, Gloria. MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12378. short: G. Colombo, MorphOMICs, a Tool for Mapping Microglial Morphology, Reveals Brain Region- and Sex-Dependent Phenotypes, Institute of Science and Technology Austria, 2022. corr_author: '1' date_created: 2023-01-25T14:27:43Z date_published: 2022-11-11T00:00:00Z date_updated: 2026-04-07T14:29:41Z day: '11' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: SaSi doi: 10.15479/at:ista:12378 ec_funded: 1 file: - access_level: closed checksum: 8cd3ddfe9b53381dcf086023d8d8893a content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: cchlebak date_created: 2023-01-25T14:31:32Z date_updated: 2023-04-12T22:30:03Z embargo_to: open_access file_id: '12379' file_name: Gloria_Colombo_Thesis.docx file_size: 23890382 relation: source_file - access_level: open_access checksum: 8af4319c18b516e8758e9a6cb02b103b content_type: application/pdf creator: cchlebak date_created: 2023-01-25T14:31:36Z date_updated: 2023-04-12T22:30:03Z embargo: 2023-04-11 file_id: '12380' file_name: Gloria_Colombo_Thesis.pdf file_size: 13802421 relation: main_file file_date_updated: 2023-04-12T22:30:03Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '142' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12244' relation: part_of_dissertation status: public status: public supervisor: - first_name: Sandra full_name: Siegert, Sandra id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 title: MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes 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: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2022' ... --- OA_place: publisher _id: '11388' abstract: - lang: eng text: "In evolve and resequence experiments, a population is sequenced, subjected to selection and\r\nthen sequenced again, so that genetic changes before and after selection can be observed at\r\nthe genetic level. Here, I use these studies to better understand the genetic basis of complex\r\ntraits - traits which depend on more than a few genes.\r\nIn the first chapter, I discuss the first evolve and resequence experiment, in which a population\r\nof mice, the so-called \"Longshanks\" mice, were selected for tibia length while their body mass\r\nwas kept constant. The full pedigree is known. We observed a selection response on all\r\nchromosomes and used the infinitesimal model with linkage, a model which assumes an infinite\r\nnumber of genes with infinitesimally small effect sizes, as a null model. Results implied a very\r\npolygenic basis with a few loci of major effect standing out and changing in parallel. There\r\nwas large variability between the different chromosomes in this study, probably due to LD.\r\nIn chapter two, I go on to discuss the impact of LD, on the variability in an allele-frequency\r\nbased summary statistic, giving an equation based on the initial allele frequencies, average\r\npairwise LD, and the first four moments of the haplotype block copy number distribution. I\r\ndescribe this distribution by referring back to the founder generation. I then demonstrate\r\nhow to infer selection via a maximum likelihood scheme on the example of a single locus and\r\ndiscuss how to extend this to more realistic scenarios.\r\nIn chapter three, I discuss the second evolve and resequence experiment, in which a small\r\npopulation of Drosophila melanogaster was selected for increased pupal case size over 6\r\ngenerations. The experiment was highly replicated with 27 lines selected within family and a\r\nknown pedigree. We observed a phenotypic selection response of over one standard deviation.\r\nI describe the patterns in allele frequency data, including allele frequency changes and patterns\r\nof heterozygosity, and give ideas for future work." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Stefanie full_name: Belohlavy, Stefanie id: 43FE426A-F248-11E8-B48F-1D18A9856A87 last_name: Belohlavy orcid: 0000-0002-9849-498X citation: ama: Belohlavy S. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. 2022. doi:10.15479/at:ista:11388 apa: Belohlavy, S. (2022). The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11388 chicago: Belohlavy, Stefanie. “The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11388. ieee: S. Belohlavy, “The genetic basis of complex traits studied via analysis of evolve and resequence experiments,” Institute of Science and Technology Austria, 2022. ista: Belohlavy S. 2022. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria. mla: Belohlavy, Stefanie. The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11388. short: S. Belohlavy, The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments, Institute of Science and Technology Austria, 2022. corr_author: '1' date_created: 2022-05-16T16:49:18Z date_published: 2022-05-18T00:00:00Z date_updated: 2026-04-07T14:29:57Z day: '18' ddc: - '576' degree_awarded: PhD department: - _id: GradSch - _id: NiBa doi: 10.15479/at:ista:11388 file: - access_level: open_access checksum: 4d75e6a619df7e8a9d6e840aee182380 content_type: application/pdf creator: sbelohla date_created: 2022-05-19T13:03:13Z date_updated: 2023-05-20T22:30:03Z embargo: 2023-05-19 file_id: '11398' file_name: thesis_sb_final_pdfa.pdf file_size: 8247240 relation: main_file - access_level: closed checksum: 7a5d8b6dd0ca00784f860075b0a7d8f0 content_type: application/x-zip-compressed creator: sbelohla date_created: 2022-05-19T13:07:47Z date_updated: 2023-05-20T22:30:03Z embargo_to: open_access file_id: '11399' file_name: thesis_sb_final.zip file_size: 7094 relation: source_file file_date_updated: 2023-05-20T22:30:03Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '98' publication_identifier: isbn: - 978-3-99078-018-3 publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '6713' relation: part_of_dissertation status: public status: public supervisor: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 title: The genetic basis of complex traits studied via analysis of evolve and resequence experiments 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: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2022' ... --- _id: '10703' abstract: - lang: eng text: 'When crawling through the body, leukocytes often traverse tissues that are densely packed with extracellular matrix and other cells, and this raises the question: How do leukocytes overcome compressive mechanical loads? Here, we show that the actin cortex of leukocytes is mechanoresponsive and that this responsiveness requires neither force sensing via the nucleus nor adhesive interactions with a substrate. Upon global compression of the cell body as well as local indentation of the plasma membrane, Wiskott-Aldrich syndrome protein (WASp) assembles into dot-like structures, providing activation platforms for Arp2/3 nucleated actin patches. These patches locally push against the external load, which can be obstructing collagen fibers or other cells, and thereby create space to facilitate forward locomotion. We show in vitro and in vivo that this WASp function is rate limiting for ameboid leukocyte migration in dense but not in loose environments and is required for trafficking through diverse tissues such as skin and lymph nodes.' acknowledged_ssus: - _id: LifeSc - _id: Bio - _id: EM-Fac acknowledgement: We thank N. Darwish-Miranda, F. Leite, F.P. Assen, and A. Eichner for advice and help with experiments. We thank J. Renkawitz, E. Kiermaier, A. Juanes Garcia, and M. Avellaneda for critical reading of the manuscript. We thank M. Driscoll for advice on fluorescent labeling of collagen gels. This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Molecular Biology Services/Lab Support Facility (LSF)/Bioimaging Facility/Electron Microscopy Facility. This work was funded by grants from the European Research Council ( CoG 724373 ) and the Austrian Science Foundation (FWF) to M.S. F.G. received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 747687. article_processing_charge: No article_type: original author: - first_name: Florian full_name: Gaertner, Florian last_name: Gaertner - first_name: Patricia full_name: Dos Reis Rodrigues, Patricia id: 26E95904-5160-11E9-9C0B-C5B0DC97E90F last_name: Dos Reis Rodrigues orcid: 0000-0003-1681-508X - first_name: Ingrid full_name: De Vries, Ingrid id: 4C7D837E-F248-11E8-B48F-1D18A9856A87 last_name: De Vries - first_name: Miroslav full_name: Hons, Miroslav id: 4167FE56-F248-11E8-B48F-1D18A9856A87 last_name: Hons orcid: 0000-0002-6625-3348 - first_name: Juan full_name: Aguilera, Juan last_name: Aguilera - first_name: Michael full_name: Riedl, Michael id: 3BE60946-F248-11E8-B48F-1D18A9856A87 last_name: Riedl orcid: 0000-0003-4844-6311 - first_name: Alexander F full_name: Leithner, Alexander F id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87 last_name: Leithner orcid: 0000-0002-1073-744X - first_name: Saren full_name: Tasciyan, Saren id: 4323B49C-F248-11E8-B48F-1D18A9856A87 last_name: Tasciyan orcid: 0000-0003-1671-393X - first_name: Aglaja full_name: Kopf, Aglaja id: 31DAC7B6-F248-11E8-B48F-1D18A9856A87 last_name: Kopf orcid: 0000-0002-2187-6656 - first_name: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 - first_name: Vanessa full_name: Zheden, Vanessa id: 39C5A68A-F248-11E8-B48F-1D18A9856A87 last_name: Zheden orcid: 0000-0002-9438-4783 - first_name: Walter full_name: Kaufmann, Walter id: 3F99E422-F248-11E8-B48F-1D18A9856A87 last_name: Kaufmann orcid: 0000-0001-9735-5315 - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Gaertner F, Dos Reis Rodrigues P, de Vries I, et al. WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues. Developmental Cell. 2022;57(1):47-62.e9. doi:10.1016/j.devcel.2021.11.024 apa: Gaertner, F., Dos Reis Rodrigues, P., de Vries, I., Hons, M., Aguilera, J., Riedl, M., … Sixt, M. K. (2022). WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2021.11.024 chicago: Gaertner, Florian, Patricia Dos Reis Rodrigues, Ingrid de Vries, Miroslav Hons, Juan Aguilera, Michael Riedl, Alexander F Leithner, et al. “WASp Triggers Mechanosensitive Actin Patches to Facilitate Immune Cell Migration in Dense Tissues.” Developmental Cell. Cell Press, 2022. https://doi.org/10.1016/j.devcel.2021.11.024. ieee: F. Gaertner et al., “WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues,” Developmental Cell, vol. 57, no. 1. Cell Press, p. 47–62.e9, 2022. ista: Gaertner F, Dos Reis Rodrigues P, de Vries I, Hons M, Aguilera J, Riedl M, Leithner AF, Tasciyan S, Kopf A, Merrin J, Zheden V, Kaufmann W, Hauschild R, Sixt MK. 2022. WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues. Developmental Cell. 57(1), 47–62.e9. mla: Gaertner, Florian, et al. “WASp Triggers Mechanosensitive Actin Patches to Facilitate Immune Cell Migration in Dense Tissues.” Developmental Cell, vol. 57, no. 1, Cell Press, 2022, p. 47–62.e9, doi:10.1016/j.devcel.2021.11.024. short: F. Gaertner, P. Dos Reis Rodrigues, I. de Vries, M. Hons, J. Aguilera, M. Riedl, A.F. Leithner, S. Tasciyan, A. Kopf, J. Merrin, V. Zheden, W. Kaufmann, R. Hauschild, M.K. Sixt, Developmental Cell 57 (2022) 47–62.e9. corr_author: '1' date_created: 2022-01-30T23:01:33Z date_published: 2022-01-10T00:00:00Z date_updated: 2026-06-20T22:31:00Z day: '10' ddc: - '570' department: - _id: MiSi - _id: EM-Fac - _id: NanoFab - _id: BjHo doi: 10.1016/j.devcel.2021.11.024 ec_funded: 1 external_id: isi: - '000768933800005' pmid: - '34919802' intvolume: ' 57' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://www.sciencedirect.com/science/article/pii/S1534580721009497 month: '01' oa: 1 oa_version: Published Version page: 47-62.e9 pmid: 1 project: - _id: 260AA4E2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '747687' name: Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells - _id: 25FE9508-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '724373' name: Cellular Navigation Along Spatial Gradients publication: Developmental Cell publication_identifier: eissn: - 1878-1551 issn: - 1534-5807 publication_status: published publisher: Cell Press quality_controlled: '1' related_material: record: - id: '20149' relation: dissertation_contains status: public - id: '12726' relation: dissertation_contains status: public - id: '14530' relation: dissertation_contains status: public - id: '12401' relation: dissertation_contains status: public scopus_import: '1' status: public title: WASp triggers mechanosensitive actin patches to facilitate immune cell migration in dense tissues 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: 57 year: '2022' ... --- OA_place: publisher _id: '12401' abstract: - lang: eng text: "Detachment of the cancer cells from the bulk of the tumor is the first step of metastasis, which\r\nis the primary cause of cancer related deaths. It is unclear, which factors contribute to this step.\r\nRecent studies indicate a crucial role of the tumor microenvironment in malignant\r\ntransformation and metastasis. Studying cancer cell invasion and detachments quantitatively in\r\nthe context of its physiological microenvironment is technically challenging. Especially, precise\r\ncontrol of microenvironmental properties in vivo is currently not possible. Here, I studied the\r\nrole of microenvironment geometry in the invasion and detachment of cancer cells from the\r\nbulk with a simplistic and reductionist approach. In this approach, I engineered microfluidic\r\ndevices to mimic a pseudo 3D extracellular matrix environment, where I was able to\r\nquantitatively tune the geometrical configuration of the microenvironment and follow tumor\r\ncells with fluorescence live imaging. To aid quantitative analysis I developed a widely applicable\r\nsoftware application to automatically analyze and visualize particle tracking data.\r\nQuantitative analysis of tumor cell invasion in isotropic and anisotropic microenvironments\r\nshowed that heterogeneity in the microenvironment promotes faster invasion and more\r\nfrequent detachment of cells. These observations correlated with overall higher speed of cells at\r\nthe edge of the bulk of the cells. In heterogeneous microenvironments cells preferentially\r\npassed through larger pores, thus invading areas of least resistance and generating finger-like\r\ninvasive structures. The detachments occurred mostly at the tips of these structures.\r\nTo investigate the potential mechanism, we established a two dimensional model to simulate\r\nactive Brownian particles representing the cell nuclei dynamics. These simulations backed our in\r\nvitro observations without the need of precise fitting the simulation parameters. Our model\r\nsuggests the importance of the pore heterogeneity in the direction perpendicular to the\r\norientation of bias field (lateral heterogeneity), which causes the interface roughening." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Saren full_name: Tasciyan, Saren id: 4323B49C-F248-11E8-B48F-1D18A9856A87 last_name: Tasciyan orcid: 0000-0003-1671-393X citation: ama: Tasciyan S. Role of microenvironment heterogeneity in cancer cell invasion. 2022. doi:10.15479/at:ista:12401 apa: Tasciyan, S. (2022). Role of microenvironment heterogeneity in cancer cell invasion. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12401 chicago: Tasciyan, Saren. “Role of Microenvironment Heterogeneity in Cancer Cell Invasion.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:12401. ieee: S. Tasciyan, “Role of microenvironment heterogeneity in cancer cell invasion,” Institute of Science and Technology Austria, 2022. ista: Tasciyan S. 2022. Role of microenvironment heterogeneity in cancer cell invasion. Institute of Science and Technology Austria. mla: Tasciyan, Saren. Role of Microenvironment Heterogeneity in Cancer Cell Invasion. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:12401. short: S. Tasciyan, Role of Microenvironment Heterogeneity in Cancer Cell Invasion, Institute of Science and Technology Austria, 2022. corr_author: '1' date_created: 2023-01-26T11:55:16Z date_published: 2022-12-22T00:00:00Z date_updated: 2026-04-14T09:07:14Z day: '22' ddc: - '610' degree_awarded: PhD department: - _id: GradSch - _id: MiSi doi: 10.15479/at:ista:12401 file: - access_level: open_access checksum: cc4a2b4a7e3c4ee8ef7f2dbf909b12bd content_type: application/pdf creator: cchlebak date_created: 2023-01-26T11:58:14Z date_updated: 2023-12-21T23:30:03Z embargo: 2023-12-20 file_id: '12402' file_name: PhD-Thesis_Saren Tasciyan_formatted_aftercrash_fixed_600dpi_95pc_final_PDFA3b.pdf file_size: 42059787 relation: main_file - access_level: closed checksum: f1b4ca98b8ab0cb043b1830971e9bd9c content_type: application/x-zip-compressed creator: cchlebak date_created: 2023-01-26T12:00:10Z date_updated: 2023-12-21T23:30:03Z embargo_to: open_access file_id: '12403' file_name: Source Files - Saren Tasciyan - PhD Thesis.zip file_size: 261256696 relation: source_file file_date_updated: 2023-12-21T23:30:03Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '105' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '7885' relation: part_of_dissertation status: public - id: '10703' relation: part_of_dissertation status: public - id: '679' relation: part_of_dissertation status: public - id: '9429' relation: part_of_dissertation status: public status: public supervisor: - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 title: Role of microenvironment heterogeneity in cancer cell invasion type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2022' ... --- _id: '12248' abstract: - lang: eng text: Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species Artemia sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species Artemia sp. Kazakhstan and several asexual lineages of Artemia parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality. acknowledged_ssus: - _id: ScienComp acknowledgement: "This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 715257) and by the Austrian Science Foundation (FWF SFB F88-10).\r\nWe thank the Vicoso group for comments on the manuscript and the ISTA Scientific computing team and the Vienna Biocenter Sequencing facility for technical support." article_number: iyac123 article_processing_charge: No article_type: original author: - first_name: Marwan N full_name: Elkrewi, Marwan N id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425 last_name: Elkrewi orcid: 0000-0002-5328-7231 - first_name: Uladzislava full_name: Khauratovich, Uladzislava id: 5eba06f4-97d8-11ed-9f8f-d826ebdd9434 last_name: Khauratovich - first_name: Melissa A full_name: Toups, Melissa A id: 4E099E4E-F248-11E8-B48F-1D18A9856A87 last_name: Toups orcid: 0000-0002-9752-7380 - first_name: Vincent K full_name: Bett, Vincent K id: 57854184-AAE0-11E9-8D04-98D6E5697425 last_name: Bett - first_name: Andrea full_name: Mrnjavac, Andrea id: 353FAC84-AE61-11E9-8BFC-00D3E5697425 last_name: Mrnjavac - first_name: Ariana full_name: Macon, Ariana id: 2A0848E2-F248-11E8-B48F-1D18A9856A87 last_name: Macon - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: Luca full_name: Sax, Luca id: 701c5602-97d8-11ed-96b5-b52773c70189 last_name: Sax - first_name: Ann K full_name: Huylmans, Ann K id: 4C0A3874-F248-11E8-B48F-1D18A9856A87 last_name: Huylmans orcid: 0000-0001-8871-4961 - first_name: Francisco full_name: Hontoria, Francisco last_name: Hontoria - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Elkrewi MN, Khauratovich U, Toups MA, et al. ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. Genetics. 2022;222(2). doi:10.1093/genetics/iyac123 apa: Elkrewi, M. N., Khauratovich, U., Toups, M. A., Bett, V. K., Mrnjavac, A., Macon, A., … Vicoso, B. (2022). ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. Genetics. Oxford University Press. https://doi.org/10.1093/genetics/iyac123 chicago: Elkrewi, Marwan N, Uladzislava Khauratovich, Melissa A Toups, Vincent K Bett, Andrea Mrnjavac, Ariana Macon, Christelle Fraisse, et al. “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.” Genetics. Oxford University Press, 2022. https://doi.org/10.1093/genetics/iyac123. ieee: M. N. Elkrewi et al., “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp,” Genetics, vol. 222, no. 2. Oxford University Press, 2022. ista: Elkrewi MN, Khauratovich U, Toups MA, Bett VK, Mrnjavac A, Macon A, Fraisse C, Sax L, Huylmans AK, Hontoria F, Vicoso B. 2022. ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. Genetics. 222(2), iyac123. mla: Elkrewi, Marwan N., et al. “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.” Genetics, vol. 222, no. 2, iyac123, Oxford University Press, 2022, doi:10.1093/genetics/iyac123. short: M.N. Elkrewi, U. Khauratovich, M.A. Toups, V.K. Bett, A. Mrnjavac, A. Macon, C. Fraisse, L. Sax, A.K. Huylmans, F. Hontoria, B. Vicoso, Genetics 222 (2022). corr_author: '1' date_created: 2023-01-16T09:56:10Z date_published: 2022-10-01T00:00:00Z date_updated: 2026-06-20T22:31:10Z day: '01' ddc: - '570' department: - _id: BeVi doi: 10.1093/genetics/iyac123 ec_funded: 1 external_id: isi: - '000850270300001' pmid: - '35977389' file: - access_level: open_access checksum: f79ff5383e882ea3f95f3da47a78029d content_type: application/pdf creator: dernst date_created: 2023-01-30T08:59:58Z date_updated: 2023-01-30T08:59:58Z file_id: '12440' file_name: 2022_Genetics_Elkrewi.pdf file_size: 1347136 relation: main_file success: 1 file_date_updated: 2023-01-30T08:59:58Z has_accepted_license: '1' intvolume: ' 222' isi: 1 issue: '2' keyword: - Genetics language: - iso: eng month: '10' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 250BDE62-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715257' name: Prevalence and Influence of Sexual Antagonism on Genome Evolution - _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396 grant_number: F8810 name: The highjacking of meiosis for asexual reproduction publication: Genetics publication_identifier: issn: - 1943-2631 publication_status: published publisher: Oxford University Press quality_controlled: '1' related_material: record: - id: '11653' relation: research_data status: public - id: '19386' relation: dissertation_contains status: public scopus_import: '1' status: public title: ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 222 year: '2022' ... --- _id: '10767' abstract: - lang: eng text: The t-haplotype of mice is a classical model for autosomal transmission distortion. A largely non-recombining variant of the proximal region of chromosome 17, it is transmitted to more than 90% of the progeny of heterozygous males through the disabling of sperm carrying a standard chromosome. While extensive genetic and functional work has shed light on individual genes involved in drive, much less is known about the evolution and function of the rest of its hundreds of genes. Here, we characterize the sequence and expression of dozens of t-specific transcripts and of their chromosome 17 homologues. Many genes showed reduced expression of the t-allele, but an equal number of genes showed increased expression of their t-copy, consistent with increased activity or a newly evolved function. Genes on the t-haplotype had a significantly higher non-synonymous substitution rate than their homologues on the standard chromosome, with several genes harbouring dN/dS ratios above 1. Finally, the t-haplotype has acquired at least two genes from other chromosomes, which show high and tissue-specific expression. These results provide a first overview of the gene content of this selfish element, and support a more dynamic evolutionary scenario than expected of a large genomic region with almost no recombination. acknowledgement: "This project has received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 715257) and from the Swiss National Science Foundation (grant no. 310030_189145).\r\nWe thank Jari Garbely of the Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland, for conducting the PCR verification. Barbara\r\nKonig, Gabi Stichel and A.K.L. collected mouse tissue samples, from the field study led by R.K.K. " article_processing_charge: No article_type: original author: - first_name: Réka K full_name: Kelemen, Réka K id: 48D3F8DE-F248-11E8-B48F-1D18A9856A87 last_name: Kelemen orcid: 0000-0002-8489-9281 - first_name: Marwan N full_name: Elkrewi, Marwan N id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425 last_name: Elkrewi orcid: 0000-0002-5328-7231 - first_name: Anna K. full_name: Lindholm, Anna K. last_name: Lindholm - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: 'Kelemen RK, Elkrewi MN, Lindholm AK, Vicoso B. Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. Proceedings of the Royal Society B: Biological Sciences. 2022;289(1968):20211985. doi:10.1098/rspb.2021.1985' apa: 'Kelemen, R. K., Elkrewi, M. N., Lindholm, A. K., & Vicoso, B. (2022). Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. Proceedings of the Royal Society B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rspb.2021.1985' chicago: 'Kelemen, Réka K, Marwan N Elkrewi, Anna K. Lindholm, and Beatriz Vicoso. “Novel Patterns of Expression and Recruitment of New Genes on the T-Haplotype, a Mouse Selfish Chromosome.” Proceedings of the Royal Society B: Biological Sciences. The Royal Society, 2022. https://doi.org/10.1098/rspb.2021.1985.' ieee: 'R. K. Kelemen, M. N. Elkrewi, A. K. Lindholm, and B. Vicoso, “Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome,” Proceedings of the Royal Society B: Biological Sciences, vol. 289, no. 1968. The Royal Society, p. 20211985, 2022.' ista: 'Kelemen RK, Elkrewi MN, Lindholm AK, Vicoso B. 2022. Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. Proceedings of the Royal Society B: Biological Sciences. 289(1968), 20211985.' mla: 'Kelemen, Réka K., et al. “Novel Patterns of Expression and Recruitment of New Genes on the T-Haplotype, a Mouse Selfish Chromosome.” Proceedings of the Royal Society B: Biological Sciences, vol. 289, no. 1968, The Royal Society, 2022, p. 20211985, doi:10.1098/rspb.2021.1985.' short: 'R.K. Kelemen, M.N. Elkrewi, A.K. Lindholm, B. Vicoso, Proceedings of the Royal Society B: Biological Sciences 289 (2022) 20211985.' corr_author: '1' date_created: 2022-02-20T23:01:31Z date_published: 2022-02-09T00:00:00Z date_updated: 2026-06-20T22:31:11Z day: '09' ddc: - '570' department: - _id: BeVi doi: 10.1098/rspb.2021.1985 ec_funded: 1 external_id: isi: - '000752812800012' pmid: - '35135349' file: - access_level: open_access checksum: 27042a3706ae52a919fed1ac114bf7bb content_type: application/pdf creator: dernst date_created: 2022-02-21T08:17:38Z date_updated: 2022-02-21T08:17:38Z file_id: '10779' file_name: 2022_ProceedingsRoyalSocB_Kelemen.pdf file_size: 2366976 relation: main_file success: 1 file_date_updated: 2022-02-21T08:17:38Z has_accepted_license: '1' intvolume: ' 289' isi: 1 issue: '1968' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '20211985' pmid: 1 project: - _id: 250BDE62-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715257' name: Prevalence and Influence of Sexual Antagonism on Genome Evolution publication: 'Proceedings of the Royal Society B: Biological Sciences' publication_identifier: eissn: - 1471-2954 publication_status: published publisher: The Royal Society quality_controlled: '1' related_material: record: - id: '17119' relation: dissertation_contains status: public - id: '19386' relation: dissertation_contains status: public scopus_import: '1' status: public title: Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome 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: 289 year: '2022' ... --- _id: '10924' abstract: - lang: eng text: Solid-state microwave systems offer strong interactions for fast quantum logic and sensing but photons at telecom wavelength are the ideal choice for high-density low-loss quantum interconnects. A general-purpose interface that can make use of single photon effects requires < 1 input noise quanta, which has remained elusive due to either low efficiency or pump induced heating. Here we demonstrate coherent electro-optic modulation on nanosecond-timescales with only 0.16+0.02−0.01 microwave input noise photons with a total bidirectional transduction efficiency of 8.7% (or up to 15% with 0.41+0.02−0.02), as required for near-term heralded quantum network protocols. The use of short and high-power optical pump pulses also enables near-unity cooperativity of the electro-optic interaction leading to an internal pure conversion efficiency of up to 99.5%. Together with the low mode occupancy this provides evidence for electro-optic laser cooling and vacuum amplification as predicted a decade ago. acknowledged_ssus: - _id: M-Shop acknowledgement: "The authors thank S. Wald and F. Diorico for their help with optical filtering, O. Hosten\r\nand M. Aspelmeyer for equipment, H.G.L. Schwefel for materials and discussions, L.\r\nDrmic and P. Zielinski for software support, and the MIBA workshop at IST Austria for\r\nmachining the microwave cavity. This work was supported by the European Research\r\nCouncil under grant agreement no. 758053 (ERC StG QUNNECT) and the European\r\nUnion’s Horizon 2020 research and innovation program under grant agreement no.\r\n899354 (FETopen SuperQuLAN). W.H. is the recipient of an ISTplus postdoctoral fellowship\r\nwith funding from the European Union’s Horizon 2020 research and innovation\r\nprogram under the Marie Skłodowska-Curie grant agreement no. 754411. G.A. is the\r\nrecipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F.\r\nacknowledges support from the Austrian Science Fund (FWF) through BeyondC (F7105)\r\nand the European Union’s Horizon 2020 research and innovation programs under grant\r\nagreement no. 862644 (FETopen QUARTET)." article_number: '1276' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Rishabh full_name: Sahu, Rishabh id: 47D26E34-F248-11E8-B48F-1D18A9856A87 last_name: Sahu orcid: 0000-0001-6264-2162 - first_name: William J full_name: Hease, William J id: 29705398-F248-11E8-B48F-1D18A9856A87 last_name: Hease orcid: 0000-0001-9868-2166 - first_name: Alfredo R full_name: Rueda Sanchez, Alfredo R id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87 last_name: Rueda Sanchez orcid: 0000-0001-6249-5860 - first_name: Georg M full_name: Arnold, Georg M id: 3770C838-F248-11E8-B48F-1D18A9856A87 last_name: Arnold orcid: 0000-0003-1397-7876 - first_name: Liu full_name: Qiu, Liu id: 45e99c0d-1eb1-11eb-9b96-ed8ab2983cac last_name: Qiu orcid: 0000-0003-4345-4267 - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: Sahu R, Hease WJ, Rueda Sanchez AR, Arnold GM, Qiu L, Fink JM. Quantum-enabled operation of a microwave-optical interface. Nature Communications. 2022;13. doi:10.1038/s41467-022-28924-2 apa: Sahu, R., Hease, W. J., Rueda Sanchez, A. R., Arnold, G. M., Qiu, L., & Fink, J. M. (2022). Quantum-enabled operation of a microwave-optical interface. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-022-28924-2 chicago: Sahu, Rishabh, William J Hease, Alfredo R Rueda Sanchez, Georg M Arnold, Liu Qiu, and Johannes M Fink. “Quantum-Enabled Operation of a Microwave-Optical Interface.” Nature Communications. Springer Nature, 2022. https://doi.org/10.1038/s41467-022-28924-2. ieee: R. Sahu, W. J. Hease, A. R. Rueda Sanchez, G. M. Arnold, L. Qiu, and J. M. Fink, “Quantum-enabled operation of a microwave-optical interface,” Nature Communications, vol. 13. Springer Nature, 2022. ista: Sahu R, Hease WJ, Rueda Sanchez AR, Arnold GM, Qiu L, Fink JM. 2022. Quantum-enabled operation of a microwave-optical interface. Nature Communications. 13, 1276. mla: Sahu, Rishabh, et al. “Quantum-Enabled Operation of a Microwave-Optical Interface.” Nature Communications, vol. 13, 1276, Springer Nature, 2022, doi:10.1038/s41467-022-28924-2. short: R. Sahu, W.J. Hease, A.R. Rueda Sanchez, G.M. Arnold, L. Qiu, J.M. Fink, Nature Communications 13 (2022). corr_author: '1' date_created: 2022-03-27T22:01:45Z date_published: 2022-03-11T00:00:00Z date_updated: 2026-06-20T22:31:12Z day: '11' ddc: - '530' department: - _id: JoFi doi: 10.1038/s41467-022-28924-2 ec_funded: 1 external_id: arxiv: - '2107.08303' isi: - '000767892300013' pmid: - '35277488' file: - access_level: open_access checksum: 7c5176db7b8e2ed18a4e0c5aca70a72c content_type: application/pdf creator: dernst date_created: 2022-03-28T08:02:12Z date_updated: 2022-03-28T08:02:12Z file_id: '10929' file_name: 2022_NatureCommunications_Sahu.pdf file_size: 1167492 relation: main_file success: 1 file_date_updated: 2022-03-28T08:02:12Z has_accepted_license: '1' intvolume: ' 13' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 26336814-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '758053' name: A Fiber Optic Transceiver for Superconducting Qubits - _id: 9B868D20-BA93-11EA-9121-9846C619BF3A call_identifier: H2020 grant_number: '899354' name: Quantum Local Area Networks with Superconducting Qubits - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 237CBA6C-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '862644' name: Quantum readout techniques and technologies - _id: bdb108fd-d553-11ed-ba76-83dc74a9864f grant_number: F07105 name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '13175' relation: dissertation_contains status: public - id: '12900' relation: dissertation_contains status: public - id: '18871' relation: dissertation_contains status: public scopus_import: '1' status: public title: Quantum-enabled operation of a microwave-optical interface 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: 13 year: '2022' ... --- OA_place: publisher _id: '11196' abstract: - lang: eng text: "One of the fundamental questions in Neuroscience is how the structure of synapses and their physiological properties are related. While synaptic transmission remains a dynamic process, electron microscopy provides images with comparably low temporal resolution (Studer et al., 2014). The current work overcomes this challenge and describes an improved “Flash and Freeze” technique (Watanabe et al., 2013a; Watanabe et al., 2013b) to study synaptic transmission at the hippocampal mossy fiber-CA3 pyramidal neuron synapses, using mouse acute brain slices and organotypic slices culture. The improved method allowed for selective stimulation of presynaptic mossy fiber boutons and the observation of synaptic vesicle pool dynamics at the active zones. Our results uncovered several intriguing morphological features of mossy fiber boutons. First, the docked vesicle pool was largely depleted (more than 70%) after stimulation, implying that the docked synaptic vesicles pool and readily releasable pool are vastly overlapping in mossy fiber boutons. Second, the synaptic vesicles are skewed towards larger diameters, displaying a wide range of sizes. An increase in the mean diameter of synaptic vesicles, after single and repetitive stimulation, suggests that smaller vesicles have a higher release probability. Third, we observed putative endocytotic structures after moderate light stimulation, matching the timing of previously described ultrafast endocytosis (Watanabe et al., 2013a; Delvendahl et al., 2016). \r\n\tIn addition, synaptic transmission depends on a sophisticated system of protein machinery and calcium channels (Südhof, 2013b), which amplifies the challenge in studying synaptic communication as these interactions can be potentially modified during synaptic plasticity. And although recent study elucidated the potential correlation between physiological and morphological properties of synapses during synaptic plasticity (Vandael et al., 2020), the molecular underpinning of it remains unknown. Thus, the presented work tries to overcome this challenge and aims to pinpoint changes in the molecular architecture at hippocampal mossy fiber bouton synapses during short- and long-term potentiation (STP and LTP), we combined chemical potentiation, with the application of a cyclic adenosine monophosphate agonist (i.e. forskolin) and freeze-fracture replica immunolabelling. This method allowed the localization of membrane-bound proteins with nanometer precision within the active zone, in particular, P/Q-type calcium channels and synaptic vesicle priming proteins Munc13-1/2. First, we found that the number of clusters of Munc13-1 in the mossy fiber bouton active zone increased significantly during STP, but decreased to lower than the control value during LTP. Secondly, although the distance between the calcium channels and Munc13-1s did not change after induction of STP, it shortened during the LTP phase. Additionally, forskolin did not affect Munc13-2 distribution during STP and LTP. These results indicate the existence of two distinct mechanisms that govern STP and LTP at mossy fiber bouton synapses: an increase in the readily realizable pool in the case of STP and a potential increase in release probability during LTP. “Flash and freeze” and functional electron microscopy, are versatile methods that can be successfully applied to intact brain circuits to study synaptic transmission even at the molecular level.\r\n" acknowledged_ssus: - _id: EM-Fac - _id: PreCl alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Olena full_name: Kim, Olena id: 3F8ABDDA-F248-11E8-B48F-1D18A9856A87 last_name: Kim orcid: 0000-0003-2344-1039 citation: ama: Kim O. Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses. 2022. doi:10.15479/at:ista:11196 apa: Kim, O. (2022). Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11196 chicago: Kim, Olena. “Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron Synapses.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11196. ieee: O. Kim, “Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses,” Institute of Science and Technology Austria, 2022. ista: Kim O. 2022. Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses. Institute of Science and Technology Austria. mla: Kim, Olena. Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron Synapses. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11196. short: O. Kim, Nanoarchitecture of Hippocampal Mossy Fiber-CA3 Pyramidal Neuron Synapses, Institute of Science and Technology Austria, 2022. corr_author: '1' date_created: 2022-04-20T09:47:12Z date_published: 2022-04-20T00:00:00Z date_updated: 2026-06-18T10:49:27Z day: '20' ddc: - '570' degree_awarded: PhD department: - _id: PeJo - _id: GradSch doi: 10.15479/at:ista:11196 ec_funded: 1 file: - access_level: open_access checksum: 1616a8bf6f13a57c892dac873dcd0936 content_type: application/pdf creator: okim date_created: 2022-04-20T14:21:56Z date_updated: 2023-04-20T22:30:03Z embargo: 2023-04-19 file_id: '11220' file_name: Olena_KIM_thesis_final.pdf file_size: 21273537 relation: main_file - access_level: closed checksum: 1acb433f98dc42abb0b4b0cbb0c4b918 content_type: application/x-zip-compressed creator: okim date_created: 2022-04-20T14:22:56Z date_updated: 2023-04-20T22:30:03Z embargo_to: open_access file_id: '11221' file_name: KIM_thesis_final.zip file_size: 59248569 relation: source_file file_date_updated: 2023-04-20T22:30:03Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '132' project: - _id: 25BAF7B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '708497' name: Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glutamatergic synapse - _id: 25C3DBB6-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W01205 name: Zellkommunikation in Gesundheit und Krankheit - _id: 25C5A090-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00312 name: Synaptic communication in neuronal microcircuits publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '7473' relation: part_of_dissertation status: public - id: '11222' relation: part_of_dissertation status: public status: public supervisor: - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 title: Nanoarchitecture of hippocampal mossy fiber-CA3 pyramidal neuron synapses 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: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2022' ... --- _id: '12272' abstract: - lang: eng text: Reading, interpreting and crawling along gradients of chemotactic cues is one of the most complex questions in cell biology. In this issue, Georgantzoglou et al. (2022. J. Cell. Biol.https://doi.org/10.1083/jcb.202103207) use in vivo models to map the temporal sequence of how neutrophils respond to an acutely arising gradient of chemoattractant. article_number: e202206127 article_processing_charge: No article_type: original author: - first_name: Julian A full_name: Stopp, Julian A id: 489E3F00-F248-11E8-B48F-1D18A9856A87 last_name: Stopp - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: 'Stopp JA, Sixt MK. Plan your trip before you leave: The neutrophils’ search-and-run journey. Journal of Cell Biology. 2022;221(8). doi:10.1083/jcb.202206127' apa: 'Stopp, J. A., & Sixt, M. K. (2022). Plan your trip before you leave: The neutrophils’ search-and-run journey. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202206127' chicago: 'Stopp, Julian A, and Michael K Sixt. “Plan Your Trip before You Leave: The Neutrophils’ Search-and-Run Journey.” Journal of Cell Biology. Rockefeller University Press, 2022. https://doi.org/10.1083/jcb.202206127.' ieee: 'J. A. Stopp and M. K. Sixt, “Plan your trip before you leave: The neutrophils’ search-and-run journey,” Journal of Cell Biology, vol. 221, no. 8. Rockefeller University Press, 2022.' ista: 'Stopp JA, Sixt MK. 2022. Plan your trip before you leave: The neutrophils’ search-and-run journey. Journal of Cell Biology. 221(8), e202206127.' mla: 'Stopp, Julian A., and Michael K. Sixt. “Plan Your Trip before You Leave: The Neutrophils’ Search-and-Run Journey.” Journal of Cell Biology, vol. 221, no. 8, e202206127, Rockefeller University Press, 2022, doi:10.1083/jcb.202206127.' short: J.A. Stopp, M.K. Sixt, Journal of Cell Biology 221 (2022). corr_author: '1' date_created: 2023-01-16T10:01:08Z date_published: 2022-07-20T00:00:00Z date_updated: 2026-06-20T22:31:20Z day: '20' ddc: - '570' department: - _id: MiSi doi: 10.1083/jcb.202206127 external_id: isi: - '000874717200001' pmid: - '35856919' file: - access_level: open_access checksum: 6b1620743669679b48b9389bb40f5a11 content_type: application/pdf creator: dernst date_created: 2023-01-30T10:39:34Z date_updated: 2023-01-30T10:39:34Z file_id: '12451' file_name: 2022_JourCellBiology_Stopp.pdf file_size: 969969 relation: main_file success: 1 file_date_updated: 2023-01-30T10:39:34Z has_accepted_license: '1' intvolume: ' 221' isi: 1 issue: '8' keyword: - Cell Biology language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: Journal of Cell Biology publication_identifier: eissn: - 1540-8140 issn: - 0021-9525 publication_status: published publisher: Rockefeller University Press quality_controlled: '1' related_material: record: - id: '14697' relation: dissertation_contains status: public scopus_import: '1' status: public title: 'Plan your trip before you leave: The neutrophils’ search-and-run journey' tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 221 year: '2022' ... --- _id: '11420' abstract: - lang: eng text: 'Understanding the properties of neural networks trained via stochastic gradient descent (SGD) is at the heart of the theory of deep learning. In this work, we take a mean-field view, and consider a two-layer ReLU network trained via noisy-SGD for a univariate regularized regression problem. Our main result is that SGD with vanishingly small noise injected in the gradients is biased towards a simple solution: at convergence, the ReLU network implements a piecewise linear map of the inputs, and the number of “knot” points -- i.e., points where the tangent of the ReLU network estimator changes -- between two consecutive training inputs is at most three. In particular, as the number of neurons of the network grows, the SGD dynamics is captured by the solution of a gradient flow and, at convergence, the distribution of the weights approaches the unique minimizer of a related free energy, which has a Gibbs form. Our key technical contribution consists in the analysis of the estimator resulting from this minimizer: we show that its second derivative vanishes everywhere, except at some specific locations which represent the “knot” points. We also provide empirical evidence that knots at locations distinct from the data points might occur, as predicted by our theory.' acknowledgement: "We would like to thank Mert Pilanci for several exploratory discussions in the early stage\r\nof the project, Jan Maas for clarifications about Jordan et al. (1998), and Max Zimmer for\r\nsuggestive numerical experiments. A. Shevchenko and M. Mondelli are partially supported\r\nby the 2019 Lopez-Loreta Prize. V. Kungurtsev acknowledges support to the OP VVV\r\nproject CZ.02.1.01/0.0/0.0/16 019/0000765 Research Center for Informatics.\r\n" article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Aleksandr full_name: Shevchenko, Aleksandr id: F2B06EC2-C99E-11E9-89F0-752EE6697425 last_name: Shevchenko - first_name: Vyacheslav full_name: Kungurtsev, Vyacheslav last_name: Kungurtsev - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 citation: ama: Shevchenko A, Kungurtsev V, Mondelli M. Mean-field analysis of piecewise linear solutions for wide ReLU networks. Journal of Machine Learning Research. 2022;23(130):1-55. apa: Shevchenko, A., Kungurtsev, V., & Mondelli, M. (2022). Mean-field analysis of piecewise linear solutions for wide ReLU networks. Journal of Machine Learning Research. Journal of Machine Learning Research. chicago: Shevchenko, Alexander, Vyacheslav Kungurtsev, and Marco Mondelli. “Mean-Field Analysis of Piecewise Linear Solutions for Wide ReLU Networks.” Journal of Machine Learning Research. Journal of Machine Learning Research, 2022. ieee: A. Shevchenko, V. Kungurtsev, and M. Mondelli, “Mean-field analysis of piecewise linear solutions for wide ReLU networks,” Journal of Machine Learning Research, vol. 23, no. 130. Journal of Machine Learning Research, pp. 1–55, 2022. ista: Shevchenko A, Kungurtsev V, Mondelli M. 2022. Mean-field analysis of piecewise linear solutions for wide ReLU networks. Journal of Machine Learning Research. 23(130), 1–55. mla: Shevchenko, Alexander, et al. “Mean-Field Analysis of Piecewise Linear Solutions for Wide ReLU Networks.” Journal of Machine Learning Research, vol. 23, no. 130, Journal of Machine Learning Research, 2022, pp. 1–55. short: A. Shevchenko, V. Kungurtsev, M. Mondelli, Journal of Machine Learning Research 23 (2022) 1–55. corr_author: '1' date_created: 2022-05-29T22:01:54Z date_published: 2022-04-01T00:00:00Z date_updated: 2026-06-20T22:31:21Z day: '01' ddc: - '000' department: - _id: MaMo - _id: DaAl external_id: arxiv: - '2111.02278' file: - access_level: open_access checksum: d4ff5d1affb34848b5c5e4002483fc62 content_type: application/pdf creator: cchlebak date_created: 2022-05-30T08:22:55Z date_updated: 2022-05-30T08:22:55Z file_id: '11422' file_name: 21-1365.pdf file_size: 1521701 relation: main_file success: 1 file_date_updated: 2022-05-30T08:22:55Z has_accepted_license: '1' intvolume: ' 23' issue: '130' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 1-55 project: - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli publication: Journal of Machine Learning Research publication_identifier: eissn: - 1533-7928 issn: - 1532-4435 publication_status: published publisher: Journal of Machine Learning Research quality_controlled: '1' related_material: link: - relation: other url: https://www.jmlr.org/papers/v23/21-1365.html record: - id: '17465' relation: dissertation_contains status: public scopus_import: '1' status: public title: Mean-field analysis of piecewise linear solutions for wide ReLU networks 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: 23 year: '2022' ... --- _id: '12186' abstract: - lang: eng text: Activation of cell-surface and intracellular receptor-mediated immunity results in rapid transcriptional reprogramming that underpins disease resistance. However, the mechanisms by which co-activation of both immune systems lead to transcriptional changes are not clear. Here, we combine RNA-seq and ATAC-seq to define changes in gene expression and chromatin accessibility. Activation of cell-surface or intracellular receptor-mediated immunity, or both, increases chromatin accessibility at induced defence genes. Analysis of ATAC-seq and RNA-seq data combined with publicly available information on transcription factor DNA-binding motifs enabled comparison of individual gene regulatory networks activated by cell-surface or intracellular receptor-mediated immunity, or by both. These results and analyses reveal overlapping and conserved transcriptional regulatory mechanisms between the two immune systems. acknowledgement: "We thank the Gatsby Foundation (UK) for funding to the JDGJ laboratory. PD acknowledges support from the European Union’s Horizon 2020 Research and Innovation Program under Marie Skłodowska Curie Actions (grant agreement: 656243) and a Future Leader Fellowship from the Biotechnology and Biological Sciences Research Council (BBSRC) (grant agreement: BB/R012172/1). TS, RKS, DM, and JDGJ were supported by the Gatsby Foundation funding to the\r\nSainsbury Laboratory. NMP and KV were supported by a BOF grant from Ghent University (grant agreement: BOF24Y2019001901). WG and RZ were supported by the Scottish Government Rural and Environment Science and Analytical Services division (RESAS), and RZ also acknowledges the support from a BBSRC Bioinformatics and Biological Resources Fund (grant agreement: BB/S020160/1).BPMN was supported by the Norwich Research Park (NRP) Biosciences Doctoral Training Partnership (DTP) funded by the BBSRC (grant agreement: BB/M011216/1). SH and XF were supported by a BBSRC Responsive Mode grant (grant agreement: BB/S009620/1) and a European Research Council Starting grant ‘SexMeth’ (grant agreement: 804981). CL was supported by Deutsche Forschungsgemeinschaft (grant agreement: LI 2862/4). " article_processing_charge: No article_type: original author: - first_name: Pingtao full_name: Ding, Pingtao last_name: Ding - first_name: Toshiyuki full_name: Sakai, Toshiyuki last_name: Sakai - first_name: Ram full_name: Krishna Shrestha, Ram last_name: Krishna Shrestha - first_name: Nicolas full_name: Manosalva Perez, Nicolas last_name: Manosalva Perez - first_name: Wenbin full_name: Guo, Wenbin last_name: Guo - first_name: Bruno Pok Man full_name: Ngou, Bruno Pok Man last_name: Ngou - first_name: Shengbo full_name: He, Shengbo last_name: He - first_name: Chang full_name: Liu, Chang last_name: Liu - first_name: Xiaoqi full_name: Feng, Xiaoqi id: e0164712-22ee-11ed-b12a-d80fcdf35958 last_name: Feng orcid: 0000-0002-4008-1234 - first_name: Runxuan full_name: Zhang, Runxuan last_name: Zhang - first_name: Klaas full_name: Vandepoele, Klaas last_name: Vandepoele - first_name: Dan full_name: MacLean, Dan last_name: MacLean - first_name: Jonathan D G full_name: Jones, Jonathan D G last_name: Jones citation: ama: Ding P, Sakai T, Krishna Shrestha R, et al. Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors. Journal of Experimental Botany. 2021;72(22):7927-7941. doi:10.1093/jxb/erab373 apa: Ding, P., Sakai, T., Krishna Shrestha, R., Manosalva Perez, N., Guo, W., Ngou, B. P. M., … Jones, J. D. G. (2021). Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erab373 chicago: Ding, Pingtao, Toshiyuki Sakai, Ram Krishna Shrestha, Nicolas Manosalva Perez, Wenbin Guo, Bruno Pok Man Ngou, Shengbo He, et al. “Chromatin Accessibility Landscapes Activated by Cell-Surface and Intracellular Immune Receptors.” Journal of Experimental Botany. Oxford University Press, 2021. https://doi.org/10.1093/jxb/erab373. ieee: P. Ding et al., “Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors,” Journal of Experimental Botany, vol. 72, no. 22. Oxford University Press, pp. 7927–7941, 2021. ista: Ding P, Sakai T, Krishna Shrestha R, Manosalva Perez N, Guo W, Ngou BPM, He S, Liu C, Feng X, Zhang R, Vandepoele K, MacLean D, Jones JDG. 2021. Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors. Journal of Experimental Botany. 72(22), 7927–7941. mla: Ding, Pingtao, et al. “Chromatin Accessibility Landscapes Activated by Cell-Surface and Intracellular Immune Receptors.” Journal of Experimental Botany, vol. 72, no. 22, Oxford University Press, 2021, pp. 7927–41, doi:10.1093/jxb/erab373. short: P. Ding, T. Sakai, R. Krishna Shrestha, N. Manosalva Perez, W. Guo, B.P.M. Ngou, S. He, C. Liu, X. Feng, R. Zhang, K. Vandepoele, D. MacLean, J.D.G. Jones, Journal of Experimental Botany 72 (2021) 7927–7941. date_created: 2023-01-16T09:14:35Z date_published: 2021-08-13T00:00:00Z date_updated: 2023-05-08T11:01:18Z day: '13' department: - _id: XiFe doi: 10.1093/jxb/erab373 extern: '1' external_id: pmid: - '34387350' intvolume: ' 72' issue: '22' keyword: - Plant Science - Physiology language: - iso: eng month: '08' oa_version: None page: 7927-7941 pmid: 1 publication: Journal of Experimental Botany publication_identifier: issn: - 0022-0957 - 1460-2431 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 72 year: '2021' ... --- _id: '14117' abstract: - lang: eng text: 'The two fields of machine learning and graphical causality arose and are developed separately. However, there is, now, cross-pollination and increasing interest in both fields to benefit from the advances of the other. In this article, we review fundamental concepts of causal inference and relate them to crucial open problems of machine learning, including transfer and generalization, thereby assaying how causality can contribute to modern machine learning research. This also applies in the opposite direction: we note that most work in causality starts from the premise that the causal variables are given. A central problem for AI and causality is, thus, causal representation learning, that is, the discovery of high-level causal variables from low-level observations. Finally, we delineate some implications of causality for machine learning and propose key research areas at the intersection of both communities.' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Bernhard full_name: Scholkopf, Bernhard last_name: Scholkopf - 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: Nan Rosemary full_name: Ke, Nan Rosemary last_name: Ke - first_name: Nal full_name: Kalchbrenner, Nal last_name: Kalchbrenner - first_name: Anirudh full_name: Goyal, Anirudh last_name: Goyal - first_name: Yoshua full_name: Bengio, Yoshua last_name: Bengio citation: ama: Scholkopf B, Locatello F, Bauer S, et al. Toward causal representation learning. Proceedings of the IEEE. 2021;109(5):612-634. doi:10.1109/jproc.2021.3058954 apa: Scholkopf, B., Locatello, F., Bauer, S., Ke, N. R., Kalchbrenner, N., Goyal, A., & Bengio, Y. (2021). Toward causal representation learning. Proceedings of the IEEE. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/jproc.2021.3058954 chicago: Scholkopf, Bernhard, Francesco Locatello, Stefan Bauer, Nan Rosemary Ke, Nal Kalchbrenner, Anirudh Goyal, and Yoshua Bengio. “Toward Causal Representation Learning.” Proceedings of the IEEE. Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/jproc.2021.3058954. ieee: B. Scholkopf et al., “Toward causal representation learning,” Proceedings of the IEEE, vol. 109, no. 5. Institute of Electrical and Electronics Engineers, pp. 612–634, 2021. ista: Scholkopf B, Locatello F, Bauer S, Ke NR, Kalchbrenner N, Goyal A, Bengio Y. 2021. Toward causal representation learning. Proceedings of the IEEE. 109(5), 612–634. mla: Scholkopf, Bernhard, et al. “Toward Causal Representation Learning.” Proceedings of the IEEE, vol. 109, no. 5, Institute of Electrical and Electronics Engineers, 2021, pp. 612–34, doi:10.1109/jproc.2021.3058954. short: B. Scholkopf, F. Locatello, S. Bauer, N.R. Ke, N. Kalchbrenner, A. Goyal, Y. Bengio, Proceedings of the IEEE 109 (2021) 612–634. date_created: 2023-08-21T12:19:30Z date_published: 2021-05-01T00:00:00Z date_updated: 2023-09-11T11:43:35Z day: '01' department: - _id: FrLo doi: 10.1109/jproc.2021.3058954 extern: '1' external_id: arxiv: - '2102.11107' intvolume: ' 109' issue: '5' keyword: - Electrical and Electronic Engineering language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1109/JPROC.2021.3058954 month: '05' oa: 1 oa_version: Published Version page: 612-634 publication: Proceedings of the IEEE publication_identifier: eissn: - 1558-2256 issn: - 0018-9219 publication_status: published publisher: Institute of Electrical and Electronics Engineers quality_controlled: '1' scopus_import: '1' status: public title: Toward causal representation learning type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 109 year: '2021' ... --- _id: '14176' abstract: - lang: eng text: "Intensive care units (ICU) are increasingly looking towards machine learning for methods to provide online monitoring of critically ill patients. In machine learning, online monitoring is often formulated as a supervised learning problem. Recently, contrastive learning approaches have demonstrated promising improvements over competitive supervised benchmarks. These methods rely on well-understood data augmentation techniques developed for image data which do not apply to online monitoring. In this work, we overcome this limitation by\r\nsupplementing time-series data augmentation techniques with a novel contrastive\r\nlearning objective which we call neighborhood contrastive learning (NCL). Our objective explicitly groups together contiguous time segments from each patient while maintaining state-specific information. Our experiments demonstrate a marked improvement over existing work applying contrastive methods to medical time-series." alternative_title: - PMLR article_processing_charge: No arxiv: 1 author: - first_name: Hugo full_name: Yèche, Hugo last_name: Yèche - first_name: Gideon full_name: Dresdner, Gideon last_name: Dresdner - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Matthias full_name: Hüser, Matthias last_name: Hüser - first_name: Gunnar full_name: Rätsch, Gunnar last_name: Rätsch citation: ama: 'Yèche H, Dresdner G, Locatello F, Hüser M, Rätsch G. Neighborhood contrastive learning applied to online patient monitoring. In: Proceedings of 38th International Conference on Machine Learning. Vol 139. ML Research Press; 2021:11964-11974.' apa: 'Yèche, H., Dresdner, G., Locatello, F., Hüser, M., & Rätsch, G. (2021). Neighborhood contrastive learning applied to online patient monitoring. In Proceedings of 38th International Conference on Machine Learning (Vol. 139, pp. 11964–11974). Virtual: ML Research Press.' chicago: Yèche, Hugo, Gideon Dresdner, Francesco Locatello, Matthias Hüser, and Gunnar Rätsch. “Neighborhood Contrastive Learning Applied to Online Patient Monitoring.” In Proceedings of 38th International Conference on Machine Learning, 139:11964–74. ML Research Press, 2021. ieee: H. Yèche, G. Dresdner, F. Locatello, M. Hüser, and G. Rätsch, “Neighborhood contrastive learning applied to online patient monitoring,” in Proceedings of 38th International Conference on Machine Learning, Virtual, 2021, vol. 139, pp. 11964–11974. ista: Yèche H, Dresdner G, Locatello F, Hüser M, Rätsch G. 2021. Neighborhood contrastive learning applied to online patient monitoring. Proceedings of 38th International Conference on Machine Learning. International Conference on Machine Learning, PMLR, vol. 139, 11964–11974. mla: Yèche, Hugo, et al. “Neighborhood Contrastive Learning Applied to Online Patient Monitoring.” Proceedings of 38th International Conference on Machine Learning, vol. 139, ML Research Press, 2021, pp. 11964–74. short: H. Yèche, G. Dresdner, F. Locatello, M. Hüser, G. Rätsch, in:, Proceedings of 38th International Conference on Machine Learning, ML Research Press, 2021, pp. 11964–11974. conference: end_date: 2021-07-24 location: Virtual name: International Conference on Machine Learning start_date: 2021-07-18 date_created: 2023-08-22T14:03:04Z date_published: 2021-08-01T00:00:00Z date_updated: 2023-09-11T10:16:55Z day: '01' department: - _id: FrLo extern: '1' external_id: arxiv: - '2106.05142' intvolume: ' 139' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2106.05142 month: '08' oa: 1 oa_version: Preprint page: 11964-11974 publication: Proceedings of 38th International Conference on Machine Learning publication_status: published publisher: ML Research Press quality_controlled: '1' scopus_import: '1' status: public title: Neighborhood contrastive learning applied to online patient monitoring type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 139 year: '2021' ... --- _id: '14177' abstract: - lang: eng text: "The focus of disentanglement approaches has been on identifying independent factors of variation in data. However, the causal variables underlying real-world observations are often not statistically independent. In this work, we bridge the gap to real-world scenarios by analyzing the behavior of the most prominent disentanglement approaches on correlated data in a large-scale empirical study (including 4260 models). We show and quantify that systematically induced correlations in the dataset are being learned and reflected in the latent representations, which has implications for downstream applications of disentanglement such as fairness. We also demonstrate how to resolve these latent correlations, either using weak supervision during\r\ntraining or by post-hoc correcting a pre-trained model with a small number of labels." alternative_title: - PMLR article_processing_charge: No arxiv: 1 author: - first_name: Frederik full_name: Träuble, Frederik last_name: Träuble - first_name: Elliot full_name: Creager, Elliot last_name: Creager - first_name: Niki full_name: Kilbertus, Niki last_name: Kilbertus - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Andrea full_name: Dittadi, Andrea last_name: Dittadi - first_name: Anirudh full_name: Goyal, Anirudh last_name: Goyal - first_name: Bernhard full_name: Schölkopf, Bernhard last_name: Schölkopf - first_name: Stefan full_name: Bauer, Stefan last_name: Bauer citation: ama: 'Träuble F, Creager E, Kilbertus N, et al. On disentangled representations learned from correlated data. In: Proceedings of the 38th International Conference on Machine Learning. Vol 139. ML Research Press; 2021:10401-10412.' apa: 'Träuble, F., Creager, E., Kilbertus, N., Locatello, F., Dittadi, A., Goyal, A., … Bauer, S. (2021). On disentangled representations learned from correlated data. In Proceedings of the 38th International Conference on Machine Learning (Vol. 139, pp. 10401–10412). Virtual: ML Research Press.' chicago: Träuble, Frederik, Elliot Creager, Niki Kilbertus, Francesco Locatello, Andrea Dittadi, Anirudh Goyal, Bernhard Schölkopf, and Stefan Bauer. “On Disentangled Representations Learned from Correlated Data.” In Proceedings of the 38th International Conference on Machine Learning, 139:10401–12. ML Research Press, 2021. ieee: F. Träuble et al., “On disentangled representations learned from correlated data,” in Proceedings of the 38th International Conference on Machine Learning, Virtual, 2021, vol. 139, pp. 10401–10412. ista: 'Träuble F, Creager E, Kilbertus N, Locatello F, Dittadi A, Goyal A, Schölkopf B, Bauer S. 2021. On disentangled representations learned from correlated data. Proceedings of the 38th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 139, 10401–10412.' mla: Träuble, Frederik, et al. “On Disentangled Representations Learned from Correlated Data.” Proceedings of the 38th International Conference on Machine Learning, vol. 139, ML Research Press, 2021, pp. 10401–12. short: F. Träuble, E. Creager, N. Kilbertus, F. Locatello, A. Dittadi, A. Goyal, B. Schölkopf, S. Bauer, in:, Proceedings of the 38th International Conference on Machine Learning, ML Research Press, 2021, pp. 10401–10412. conference: end_date: 2021-07-24 location: Virtual name: 'ICML: International Conference on Machine Learning' start_date: 2021-07-18 date_created: 2023-08-22T14:03:47Z date_published: 2021-08-01T00:00:00Z date_updated: 2023-09-11T10:18:48Z day: '01' department: - _id: FrLo extern: '1' external_id: arxiv: - '2006.07886' intvolume: ' 139' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2006.07886 month: '08' oa: 1 oa_version: Published Version page: 10401-10412 publication: Proceedings of the 38th International Conference on Machine Learning publication_status: published publisher: ML Research Press quality_controlled: '1' scopus_import: '1' status: public title: On disentangled representations learned from correlated data type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 139 year: '2021' ... --- _id: '14178' abstract: - lang: eng text: Learning meaningful representations that disentangle the underlying structure of the data generating process is considered to be of key importance in machine learning. While disentangled representations were found to be useful for diverse tasks such as abstract reasoning and fair classification, their scalability and real-world impact remain questionable. We introduce a new high-resolution dataset with 1M simulated images and over 1,800 annotated real-world images of the same setup. In contrast to previous work, this new dataset exhibits correlations, a complex underlying structure, and allows to evaluate transfer to unseen simulated and real-world settings where the encoder i) remains in distribution or ii) is out of distribution. We propose new architectures in order to scale disentangled representation learning to realistic high-resolution settings and conduct a large-scale empirical study of disentangled representations on this dataset. We observe that disentanglement is a good predictor for out-of-distribution (OOD) task performance. article_processing_charge: No arxiv: 1 author: - first_name: Andrea full_name: Dittadi, Andrea last_name: Dittadi - first_name: Frederik full_name: Träuble, Frederik last_name: Träuble - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Manuel full_name: Wüthrich, Manuel last_name: Wüthrich - first_name: Vaibhav full_name: Agrawal, Vaibhav last_name: Agrawal - first_name: Ole full_name: Winther, Ole last_name: Winther - first_name: Stefan full_name: Bauer, Stefan last_name: Bauer - first_name: Bernhard full_name: Schölkopf, Bernhard last_name: Schölkopf citation: ama: 'Dittadi A, Träuble F, Locatello F, et al. On the transfer of disentangled representations in realistic settings. In: The Ninth International Conference on Learning Representations. ; 2021.' apa: Dittadi, A., Träuble, F., Locatello, F., Wüthrich, M., Agrawal, V., Winther, O., … Schölkopf, B. (2021). On the transfer of disentangled representations in realistic settings. In The Ninth International Conference on Learning Representations. Virtual. chicago: Dittadi, Andrea, Frederik Träuble, Francesco Locatello, Manuel Wüthrich, Vaibhav Agrawal, Ole Winther, Stefan Bauer, and Bernhard Schölkopf. “On the Transfer of Disentangled Representations in Realistic Settings.” In The Ninth International Conference on Learning Representations, 2021. ieee: A. Dittadi et al., “On the transfer of disentangled representations in realistic settings,” in The Ninth International Conference on Learning Representations, Virtual, 2021. ista: 'Dittadi A, Träuble F, Locatello F, Wüthrich M, Agrawal V, Winther O, Bauer S, Schölkopf B. 2021. On the transfer of disentangled representations in realistic settings. The Ninth International Conference on Learning Representations. ICLR: International Conference on Learning Representations.' mla: Dittadi, Andrea, et al. “On the Transfer of Disentangled Representations in Realistic Settings.” The Ninth International Conference on Learning Representations, 2021. short: A. Dittadi, F. Träuble, F. Locatello, M. Wüthrich, V. Agrawal, O. Winther, S. Bauer, B. Schölkopf, in:, The Ninth International Conference on Learning Representations, 2021. conference: end_date: 2021-05-07 location: Virtual name: 'ICLR: International Conference on Learning Representations' start_date: 2021-05-03 date_created: 2023-08-22T14:04:16Z date_published: 2021-05-04T00:00:00Z date_updated: 2023-09-11T10:55:30Z day: '04' department: - _id: FrLo extern: '1' external_id: arxiv: - '2010.14407' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2010.14407 month: '05' oa: 1 oa_version: Preprint publication: The Ninth International Conference on Learning Representations publication_status: published quality_controlled: '1' status: public title: On the transfer of disentangled representations in realistic settings type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '14179' abstract: - lang: eng text: Self-supervised representation learning has shown remarkable success in a number of domains. A common practice is to perform data augmentation via hand-crafted transformations intended to leave the semantics of the data invariant. We seek to understand the empirical success of this approach from a theoretical perspective. We formulate the augmentation process as a latent variable model by postulating a partition of the latent representation into a content component, which is assumed invariant to augmentation, and a style component, which is allowed to change. Unlike prior work on disentanglement and independent component analysis, we allow for both nontrivial statistical and causal dependencies in the latent space. We study the identifiability of the latent representation based on pairs of views of the observations and prove sufficient conditions that allow us to identify the invariant content partition up to an invertible mapping in both generative and discriminative settings. We find numerical simulations with dependent latent variables are consistent with our theory. Lastly, we introduce Causal3DIdent, a dataset of high-dimensional, visually complex images with rich causal dependencies, which we use to study the effect of data augmentations performed in practice. article_processing_charge: No arxiv: 1 author: - first_name: Julius von full_name: Kügelgen, Julius von last_name: Kügelgen - first_name: Yash full_name: Sharma, Yash last_name: Sharma - first_name: Luigi full_name: Gresele, Luigi last_name: Gresele - first_name: Wieland full_name: Brendel, Wieland last_name: Brendel - first_name: Bernhard full_name: Schölkopf, Bernhard last_name: Schölkopf - first_name: Michel full_name: Besserve, Michel last_name: Besserve - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 citation: ama: 'Kügelgen J von, Sharma Y, Gresele L, et al. Self-supervised learning with data augmentations provably isolates content from style. In: Advances in Neural Information Processing Systems. Vol 34. ; 2021:16451-16467.' apa: Kügelgen, J. von, Sharma, Y., Gresele, L., Brendel, W., Schölkopf, B., Besserve, M., & Locatello, F. (2021). Self-supervised learning with data augmentations provably isolates content from style. In Advances in Neural Information Processing Systems (Vol. 34, pp. 16451–16467). Virtual. chicago: Kügelgen, Julius von, Yash Sharma, Luigi Gresele, Wieland Brendel, Bernhard Schölkopf, Michel Besserve, and Francesco Locatello. “Self-Supervised Learning with Data Augmentations Provably Isolates Content from Style.” In Advances in Neural Information Processing Systems, 34:16451–67, 2021. ieee: J. von Kügelgen et al., “Self-supervised learning with data augmentations provably isolates content from style,” in Advances in Neural Information Processing Systems, Virtual, 2021, vol. 34, pp. 16451–16467. ista: 'Kügelgen J von, Sharma Y, Gresele L, Brendel W, Schölkopf B, Besserve M, Locatello F. 2021. Self-supervised learning with data augmentations provably isolates content from style. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 34, 16451–16467.' mla: Kügelgen, Julius von, et al. “Self-Supervised Learning with Data Augmentations Provably Isolates Content from Style.” Advances in Neural Information Processing Systems, vol. 34, 2021, pp. 16451–67. short: J. von Kügelgen, Y. Sharma, L. Gresele, W. Brendel, B. Schölkopf, M. Besserve, F. Locatello, in:, Advances in Neural Information Processing Systems, 2021, pp. 16451–16467. conference: end_date: 2021-12-10 location: Virtual name: 'NeurIPS: Neural Information Processing Systems' start_date: 2021-12-07 date_created: 2023-08-22T14:04:36Z date_published: 2021-06-08T00:00:00Z date_updated: 2023-09-11T10:33:19Z day: '08' department: - _id: FrLo extern: '1' external_id: arxiv: - '2106.04619' intvolume: ' 34' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2106.04619 month: '06' oa: 1 oa_version: Preprint page: 16451-16467 publication: Advances in Neural Information Processing Systems publication_identifier: isbn: - '9781713845393' publication_status: published quality_controlled: '1' status: public title: Self-supervised learning with data augmentations provably isolates content from style type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2021' ... --- _id: '14180' abstract: - lang: eng text: 'Modern neural network architectures can leverage large amounts of data to generalize well within the training distribution. However, they are less capable of systematic generalization to data drawn from unseen but related distributions, a feat that is hypothesized to require compositional reasoning and reuse of knowledge. In this work, we present Neural Interpreters, an architecture that factorizes inference in a self-attention network as a system of modules, which we call \emph{functions}. Inputs to the model are routed through a sequence of functions in a way that is end-to-end learned. The proposed architecture can flexibly compose computation along width and depth, and lends itself well to capacity extension after training. To demonstrate the versatility of Neural Interpreters, we evaluate it in two distinct settings: image classification and visual abstract reasoning on Raven Progressive Matrices. In the former, we show that Neural Interpreters perform on par with the vision transformer using fewer parameters, while being transferrable to a new task in a sample efficient manner. In the latter, we find that Neural Interpreters are competitive with respect to the state-of-the-art in terms of systematic generalization. ' article_processing_charge: No arxiv: 1 author: - first_name: Nasim full_name: Rahaman, Nasim last_name: Rahaman - first_name: Muhammad Waleed full_name: Gondal, Muhammad Waleed last_name: Gondal - first_name: Shruti full_name: Joshi, Shruti last_name: Joshi - first_name: Peter full_name: Gehler, Peter last_name: Gehler - first_name: Yoshua full_name: Bengio, Yoshua last_name: Bengio - 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: 'Rahaman N, Gondal MW, Joshi S, et al. Dynamic inference with neural interpreters. In: Advances in Neural Information Processing Systems. Vol 34. ; 2021:10985-10998.' apa: Rahaman, N., Gondal, M. W., Joshi, S., Gehler, P., Bengio, Y., Locatello, F., & Schölkopf, B. (2021). Dynamic inference with neural interpreters. In Advances in Neural Information Processing Systems (Vol. 34, pp. 10985–10998). Virtual. chicago: Rahaman, Nasim, Muhammad Waleed Gondal, Shruti Joshi, Peter Gehler, Yoshua Bengio, Francesco Locatello, and Bernhard Schölkopf. “Dynamic Inference with Neural Interpreters.” In Advances in Neural Information Processing Systems, 34:10985–98, 2021. ieee: N. Rahaman et al., “Dynamic inference with neural interpreters,” in Advances in Neural Information Processing Systems, Virtual, 2021, vol. 34, pp. 10985–10998. ista: 'Rahaman N, Gondal MW, Joshi S, Gehler P, Bengio Y, Locatello F, Schölkopf B. 2021. Dynamic inference with neural interpreters. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 34, 10985–10998.' mla: Rahaman, Nasim, et al. “Dynamic Inference with Neural Interpreters.” Advances in Neural Information Processing Systems, vol. 34, 2021, pp. 10985–98. short: N. Rahaman, M.W. Gondal, S. Joshi, P. Gehler, Y. Bengio, F. Locatello, B. Schölkopf, in:, Advances in Neural Information Processing Systems, 2021, pp. 10985–10998. conference: end_date: 2021-12-10 location: Virtual name: 'NeurIPS: Neural Information Processing Systems' start_date: 2021-12-07 date_created: 2023-08-22T14:04:55Z date_published: 2021-10-12T00:00:00Z date_updated: 2024-10-14T12:27:25Z day: '12' department: - _id: FrLo extern: '1' external_id: arxiv: - '2110.06399' intvolume: ' 34' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2110.06399 month: '10' oa: 1 oa_version: Preprint page: 10985-10998 publication: Advances in Neural Information Processing Systems publication_identifier: isbn: - '9781713845393' publication_status: published quality_controlled: '1' status: public title: Dynamic inference with neural interpreters type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2021' ... --- _id: '14181' abstract: - lang: eng text: Variational Inference makes a trade-off between the capacity of the variational family and the tractability of finding an approximate posterior distribution. Instead, Boosting Variational Inference allows practitioners to obtain increasingly good posterior approximations by spending more compute. The main obstacle to widespread adoption of Boosting Variational Inference is the amount of resources necessary to improve over a strong Variational Inference baseline. In our work, we trace this limitation back to the global curvature of the KL-divergence. We characterize how the global curvature impacts time and memory consumption, address the problem with the notion of local curvature, and provide a novel approximate backtracking algorithm for estimating local curvature. We give new theoretical convergence rates for our algorithms and provide experimental validation on synthetic and real-world datasets. article_processing_charge: No arxiv: 1 author: - first_name: Gideon full_name: Dresdner, Gideon last_name: Dresdner - first_name: Saurav full_name: Shekhar, Saurav last_name: Shekhar - first_name: Fabian full_name: Pedregosa, Fabian last_name: Pedregosa - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Gunnar full_name: Rätsch, Gunnar last_name: Rätsch citation: ama: 'Dresdner G, Shekhar S, Pedregosa F, Locatello F, Rätsch G. Boosting variational inference with locally adaptive step-sizes. In: Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence. International Joint Conferences on Artificial Intelligence; 2021:2337-2343. doi:10.24963/ijcai.2021/322' apa: 'Dresdner, G., Shekhar, S., Pedregosa, F., Locatello, F., & Rätsch, G. (2021). Boosting variational inference with locally adaptive step-sizes. In Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence (pp. 2337–2343). Montreal, Canada: International Joint Conferences on Artificial Intelligence. https://doi.org/10.24963/ijcai.2021/322' chicago: Dresdner, Gideon, Saurav Shekhar, Fabian Pedregosa, Francesco Locatello, and Gunnar Rätsch. “Boosting Variational Inference with Locally Adaptive Step-Sizes.” In Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence, 2337–43. International Joint Conferences on Artificial Intelligence, 2021. https://doi.org/10.24963/ijcai.2021/322. ieee: G. Dresdner, S. Shekhar, F. Pedregosa, F. Locatello, and G. Rätsch, “Boosting variational inference with locally adaptive step-sizes,” in Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence, Montreal, Canada, 2021, pp. 2337–2343. ista: 'Dresdner G, Shekhar S, Pedregosa F, Locatello F, Rätsch G. 2021. Boosting variational inference with locally adaptive step-sizes. Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence. IJCAI: International Joint Conference on Artificial Intelligence, 2337–2343.' mla: Dresdner, Gideon, et al. “Boosting Variational Inference with Locally Adaptive Step-Sizes.” Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence, International Joint Conferences on Artificial Intelligence, 2021, pp. 2337–43, doi:10.24963/ijcai.2021/322. short: G. Dresdner, S. Shekhar, F. Pedregosa, F. Locatello, G. Rätsch, in:, Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence, International Joint Conferences on Artificial Intelligence, 2021, pp. 2337–2343. conference: end_date: 2021-08-27 location: Montreal, Canada name: 'IJCAI: International Joint Conference on Artificial Intelligence' start_date: 2021-08-19 date_created: 2023-08-22T14:05:14Z date_published: 2021-05-19T00:00:00Z date_updated: 2023-09-11T11:14:30Z day: '19' department: - _id: FrLo doi: 10.24963/ijcai.2021/322 extern: '1' external_id: arxiv: - '2105.09240' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2105.09240 month: '05' oa: 1 oa_version: Published Version page: 2337-2343 publication: Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence publication_identifier: eisbn: - '9780999241196' publication_status: published publisher: International Joint Conferences on Artificial Intelligence quality_controlled: '1' status: public title: Boosting variational inference with locally adaptive step-sizes type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '14182' abstract: - lang: eng text: "When machine learning systems meet real world applications, accuracy is only\r\none of several requirements. In this paper, we assay a complementary\r\nperspective originating from the increasing availability of pre-trained and\r\nregularly improving state-of-the-art models. While new improved models develop\r\nat a fast pace, downstream tasks vary more slowly or stay constant. Assume that\r\nwe have a large unlabelled data set for which we want to maintain accurate\r\npredictions. Whenever a new and presumably better ML models becomes available,\r\nwe encounter two problems: (i) given a limited budget, which data points should\r\nbe re-evaluated using the new model?; and (ii) if the new predictions differ\r\nfrom the current ones, should we update? Problem (i) is about compute cost,\r\nwhich matters for very large data sets and models. Problem (ii) is about\r\nmaintaining consistency of the predictions, which can be highly relevant for\r\ndownstream applications; our demand is to avoid negative flips, i.e., changing\r\ncorrect to incorrect predictions. In this paper, we formalize the Prediction\r\nUpdate Problem and present an efficient probabilistic approach as answer to the\r\nabove questions. In extensive experiments on standard classification benchmark\r\ndata sets, we show that our method outperforms alternative strategies along key\r\nmetrics for backward-compatible prediction updates." article_processing_charge: No arxiv: 1 author: - first_name: Frederik full_name: Träuble, Frederik last_name: Träuble - first_name: Julius von full_name: Kügelgen, Julius von last_name: Kügelgen - first_name: Matthäus full_name: Kleindessner, Matthäus last_name: Kleindessner - 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 - first_name: Peter full_name: Gehler, Peter last_name: Gehler citation: ama: 'Träuble F, Kügelgen J von, Kleindessner M, Locatello F, Schölkopf B, Gehler P. Backward-compatible prediction updates: A probabilistic approach. In: 35th Conference on Neural Information Processing Systems. Vol 34. ; 2021:116-128.' apa: 'Träuble, F., Kügelgen, J. von, Kleindessner, M., Locatello, F., Schölkopf, B., & Gehler, P. (2021). Backward-compatible prediction updates: A probabilistic approach. In 35th Conference on Neural Information Processing Systems (Vol. 34, pp. 116–128). Virtual.' chicago: 'Träuble, Frederik, Julius von Kügelgen, Matthäus Kleindessner, Francesco Locatello, Bernhard Schölkopf, and Peter Gehler. “Backward-Compatible Prediction Updates: A Probabilistic Approach.” In 35th Conference on Neural Information Processing Systems, 34:116–28, 2021.' ieee: 'F. Träuble, J. von Kügelgen, M. Kleindessner, F. Locatello, B. Schölkopf, and P. Gehler, “Backward-compatible prediction updates: A probabilistic approach,” in 35th Conference on Neural Information Processing Systems, Virtual, 2021, vol. 34, pp. 116–128.' ista: 'Träuble F, Kügelgen J von, Kleindessner M, Locatello F, Schölkopf B, Gehler P. 2021. Backward-compatible prediction updates: A probabilistic approach. 35th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 34, 116–128.' mla: 'Träuble, Frederik, et al. “Backward-Compatible Prediction Updates: A Probabilistic Approach.” 35th Conference on Neural Information Processing Systems, vol. 34, 2021, pp. 116–28.' short: F. Träuble, J. von Kügelgen, M. Kleindessner, F. Locatello, B. Schölkopf, P. Gehler, in:, 35th Conference on Neural Information Processing Systems, 2021, pp. 116–128. conference: end_date: 2021-12-10 location: Virtual name: 'NeurIPS: Neural Information Processing Systems' start_date: 2021-12-07 date_created: 2023-08-22T14:05:41Z date_published: 2021-07-02T00:00:00Z date_updated: 2023-09-11T11:31:59Z day: '02' department: - _id: FrLo extern: '1' external_id: arxiv: - '2107.01057' intvolume: ' 34' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2107.01057 month: '07' oa: 1 oa_version: Preprint page: 116-128 publication: 35th Conference on Neural Information Processing Systems publication_identifier: isbn: - '9781713845393' publication_status: published quality_controlled: '1' status: public title: 'Backward-compatible prediction updates: A probabilistic approach' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2021' ... --- OA_place: repository _id: '14185' abstract: - lang: eng text: A method involves receiving a perceptual representation including a plurality of feature vectors, and initializing a plurality of slot vectors represented by a neural network memory unit. Each respective slot vector is configured to represent a corresponding entity in the perceptual representation. The method also involves determining an attention matrix based on a product of the plurality of feature vectors transformed by a key function and the plurality of slot vectors transformed by a query function. Each respective value of a plurality of values along each respective dimension of the attention matrix is normalized with respect to the plurality of values. The method additionally involves determining an update matrix based on the plurality of feature vectors transformed by a value function and the attention matrix, and updating the plurality of slot vectors based on the update matrix by way of the neural network memory unit. applicant: - Google LLC application_date: 2020-07-13 application_number: '16 / 927,018 ' article_processing_charge: No arxiv: 1 author: - first_name: Dirk full_name: Weissenborn, Dirk last_name: Weissenborn - first_name: Jakob full_name: Uszkoreit, Jakob last_name: Uszkoreit - first_name: Thomas full_name: Unterthiner, Thomas last_name: Unterthiner - first_name: Aravindh full_name: Mahendran, Aravindh last_name: Mahendran - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Thomas full_name: Kipf, Thomas last_name: Kipf - first_name: Georg full_name: Heigold, Georg last_name: Heigold - first_name: Alexey full_name: Dosovitskiy, Alexey last_name: Dosovitskiy citation: ama: Weissenborn D, Uszkoreit J, Unterthiner T, et al. Object-centric learning with slot attention. 2021. apa: Weissenborn, D., Uszkoreit, J., Unterthiner, T., Mahendran, A., Locatello, F., Kipf, T., … Dosovitskiy, A. (2021). Object-centric learning with slot attention. chicago: Weissenborn, Dirk, Jakob Uszkoreit, Thomas Unterthiner, Aravindh Mahendran, Francesco Locatello, Thomas Kipf, Georg Heigold, and Alexey Dosovitskiy. “Object-Centric Learning with Slot Attention,” 2021. ieee: D. Weissenborn et al., “Object-centric learning with slot attention.” 2021. ista: Weissenborn D, Uszkoreit J, Unterthiner T, Mahendran A, Locatello F, Kipf T, Heigold G, Dosovitskiy A. 2021. Object-centric learning with slot attention. mla: Weissenborn, Dirk, et al. Object-Centric Learning with Slot Attention. 2021. short: D. Weissenborn, J. Uszkoreit, T. Unterthiner, A. Mahendran, F. Locatello, T. Kipf, G. Heigold, A. Dosovitskiy, (2021). date_created: 2023-08-22T14:07:06Z date_published: 2021-12-09T00:00:00Z date_updated: 2025-01-31T11:35:46Z day: '09' department: - _id: FrLo extern: '1' external_id: arxiv: - '2006.15055' ipc: G06N 3/063 ; G06N 3/08 ; G06F 17/16 ipn: US20210383199A1 main_file_link: - open_access: '1' url: https://patents.google.com/patent/US20210383199A1/en month: '12' oa: 1 oa_version: Published Version publication_date: 2021-12-09 status: public title: Object-centric learning with slot attention type: patent user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2021' ...