--- OA_place: publisher _id: '19836' abstract: - lang: eng text: "Over the past century, researchers have been fascinated by the quantum nature of the\r\nphysical world, initially striving to understand its fundamental principles and consequences, and\r\neventually progressing toward engineering systems that can control and manipulate quantum\r\nproperties. Today, we stand at the dawn of the quantum technology era. While some quantum\r\ntechnologies follow well-defined roadmaps, others are still in the exciting and uncertain early\r\nstages of development. In the fields of quantum computing and quantum simulation, research\r\nis being conducted across a wide variety of platforms. Each of these demonstrates control over\r\nquantum properties but also faces challenges in scaling up to the level of a mature technology.\r\nThis thesis explores some of the fundamental properties of hole spin qubits in planar germanium.\r\nSemiconductor spin qubits are considered strong candidates for the realization of quantum\r\nprocessors, owing to their long relaxation and coherence times, as well as their compatibility\r\nwith existing semiconductor industry infrastructure. Among these, hole spin qubits in planar\r\ngermanium are particularly promising. Their advantages include a large effective mass, which\r\neases fabrication constraints; inherent protection from hyperfine noise; and strong spin-orbit\r\ninteraction, which enables fast and purely electrical control. However, spin-orbit coupling also\r\nintroduces site-dependent variability across qubits, particularly in the g-tensors and spin-flip\r\ntunneling, which might cause that the quantization axes are not aligned. In this thesis, we\r\ninvestigate the tilt between the quantization axes of two hole spins hosted in a double quantum\r\ndot as a function of both the magnetic field direction and various electrostatic configurations,\r\ndemonstrating that both parameters influence this tilt. We conclude by introducing a machine-learning-assisted routine to automatically tune baseband spin qubits. This approach may prove\r\nto be a powerful tool for characterizing spin-orbit effects and gaining deeper insight into the\r\nphysics governing spin qubit behavior.\r\n" acknowledged_ssus: - _id: NanoFab - _id: M-Shop acknowledgement: "This research was supported by the Scientific Service Units of ISTA through resources provided\r\nby the MIBA Machine Shop and the Nanofabrication facility. We acknowledge the support from\r\nthe European Commission with the project Integrated Germanium Quantum Technology (with\r\nDOI:10.3030/101069515), the NOMIS Foundation, the HORIZON-RIA 101069515 project and\r\nthe FWF Projects Center for Correlated Quantum Materials and Solid State Quantum Systems:\r\nConventional and unconventional topological superconductors (with DOI:10.55776/F86) and\r\nHigh impedance circuit quantum electrodynamics with hole spins (with DOI:10.55776/I5060).\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Jaime full_name: Saez Mollejo, Jaime id: e0390f72-f6e0-11ea-865d-862393336714 last_name: Saez Mollejo citation: ama: 'Saez Mollejo J. Singlet-triplet qubits in planar Germanium : From exchange anisotropies to autonomous tuning . 2025. doi:10.15479/AT-ISTA-19836' apa: 'Saez Mollejo, J. (2025). Singlet-triplet qubits in planar Germanium : From exchange anisotropies to autonomous tuning . Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19836' chicago: 'Saez Mollejo, Jaime. “Singlet-Triplet Qubits in Planar Germanium : From Exchange Anisotropies to Autonomous Tuning .” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19836.' ieee: 'J. Saez Mollejo, “Singlet-triplet qubits in planar Germanium : From exchange anisotropies to autonomous tuning ,” Institute of Science and Technology Austria, 2025.' ista: 'Saez Mollejo J. 2025. Singlet-triplet qubits in planar Germanium : From exchange anisotropies to autonomous tuning . Institute of Science and Technology Austria.' mla: 'Saez Mollejo, Jaime. Singlet-Triplet Qubits in Planar Germanium : From Exchange Anisotropies to Autonomous Tuning . Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19836.' short: 'J. Saez Mollejo, Singlet-Triplet Qubits in Planar Germanium : From Exchange Anisotropies to Autonomous Tuning , Institute of Science and Technology Austria, 2025.' corr_author: '1' date_created: 2025-06-13T09:01:50Z date_published: 2025-06-13T00:00:00Z date_updated: 2026-05-20T06:42:16Z day: '13' ddc: - '530' - '539' degree_awarded: PhD department: - _id: GradSch - _id: GeKa doi: 10.15479/AT-ISTA-19836 file: - access_level: closed checksum: 643bfddead59857536cce4d57c775b32 content_type: application/x-zip-compressed creator: jsaezmol date_created: 2025-06-16T09:38:49Z date_updated: 2026-04-01T22:30:07Z embargo_to: open_access file_id: '19849' file_name: istaustriathesis-master - Copy.zip file_size: 59892829 relation: source_file - access_level: open_access checksum: e3dcb767fcc2b1787a455fdda991cefb content_type: application/pdf creator: jsaezmol date_created: 2025-06-18T08:50:16Z date_updated: 2026-04-01T22:30:07Z embargo: 2026-04-01 file_id: '19851' file_name: SaezMollejo_PhDFinal_pdfa-1b.pdf file_size: 22382376 relation: main_file file_date_updated: 2026-04-01T22:30:07Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '06' oa: 1 oa_version: Published Version page: '175' project: - _id: 34c0acea-11ca-11ed-8bc3-8775e10fd452 grant_number: '101069515' name: Integrated Germanium Quantum Technology - _id: 34a66131-11ca-11ed-8bc3-a31681c6b03e grant_number: F8606 name: 'Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional and unconventional topological superconductors' - _id: c0977eea-5a5b-11eb-8a69-a862db0cf4d1 grant_number: I05060 name: High impedance circuit quantum electrodynamics with hole spins publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '19424' relation: part_of_dissertation status: public status: public supervisor: - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X title: 'Singlet-triplet qubits in planar Germanium : From exchange anisotropies to autonomous tuning ' 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: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher _id: '20470' abstract: - lang: eng text: "Systems design has classically relied on composable systems, in which individual subsystems\r\nhave defined inputs, outputs, and interactions with each other; however, attempts at\r\ndesigning complex systems in synthetic biology has often run in to issues of crosstalk and\r\ninterference, given that these systems must function within the context of the host. In nature,\r\nmobile genetic elements are systems that have evolved to travel between hosts, and thus\r\nappear to be a good candidate with which to evaluate composability. Selecting temperate\r\nphages as a model system, I used mathematical modelling to identify sources of information\r\nthat temperate phages should respond to. I found that essential proteins of temperate phages\r\ncan interfere with potential hosts, indicating limitations to composability. I also designed a\r\nlysogeny reporter construct and characterize its behavior across various laboratory and\r\nenvironmental strains, finding differences in phage lambda lysogens, and potential\r\ninterference from prophages that already exist within the environmental strains. Although\r\nthe information gathered is not conclusive, it suggests that composability is not a key property\r\nof temperate phages, implying that biological systems may not be composable, and that other\r\nsystem design principles should be considered when designing synthetic systems." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Bryan full_name: Wu, Bryan id: 3C521EBA-F248-11E8-B48F-1D18A9856A87 last_name: Wu citation: ama: Wu B. An examination on phages as a naturally composable system. 2025. doi:10.15479/AT-ISTA-20470 apa: Wu, B. (2025). An examination on phages as a naturally composable system. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20470 chicago: Wu, Bryan. “An Examination on Phages as a Naturally Composable System.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20470. ieee: B. Wu, “An examination on phages as a naturally composable system,” Institute of Science and Technology Austria, 2025. ista: Wu B. 2025. An examination on phages as a naturally composable system. Institute of Science and Technology Austria. mla: Wu, Bryan. An Examination on Phages as a Naturally Composable System. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20470. short: B. Wu, An Examination on Phages as a Naturally Composable System, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-10-15T13:30:21Z date_published: 2025-10-30T00:00:00Z date_updated: 2026-05-06T08:01:28Z day: '30' ddc: - '579' degree_awarded: PhD department: - _id: GradSch - _id: CaGu doi: 10.15479/AT-ISTA-20470 file: - access_level: closed checksum: d32ea83f259f6b0506325cd57b1d44c3 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: brwu date_created: 2025-10-21T17:33:27Z date_updated: 2026-04-30T22:30:02Z embargo_to: open_access file_id: '20516' file_name: 2025_Wu_Bryan_Thesis.docx file_size: 10603235 relation: source_file - access_level: open_access checksum: 53590046fd3244c5550b4022282449d2 content_type: application/pdf creator: brwu date_created: 2025-10-21T17:33:26Z date_updated: 2026-04-30T22:30:02Z embargo: 2026-04-30 file_id: '20517' file_name: 2025_Wu_Bryan_Thesis.pdf file_size: 6251936 relation: main_file file_date_updated: 2026-04-30T22:30:02Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '102' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 title: An examination on phages as a naturally composable system type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_place: publisher _id: '19533' abstract: - lang: eng text: "This thesis explores advancements in quantum remote sensing and non-equilibrium phase\r\ntransitions in the microwave regime, with a focus on dissipative phase transitions and quantumenhanced sensing.\r\nIn the first project, I experimentally studied photon blockade breakdown as a dissipative phase\r\ntransition in a zero-dimensional cavity-qubit system. By defining an appropriate thermodynamic\r\nlimit, we demonstrated that the observed bistability is a genuine signature of a first-order\r\nphase transition in this system. This work provides insight into non-equilibrium quantum\r\ndynamics and phase transitions in driven-dissipative open quantum systems.\r\nThe second project focuses on the experimental realization of a phase-conjugate receiver for\r\nquantum illumination (QI), a quantum sensing protocol that enhances target detection in noisy\r\nenvironments using entangled light. While an ideal spontaneous parametric down-conversion\r\n(SPDC) source and receiver could, in theory, provide up to a 6 dB advantage over classical\r\nillumination, no such ideal receiver exists. Instead, we explore an experimental realization of a\r\nphase-conjugate receiver for QI in the microwave regime at millikelvin temperatures using a\r\nJosephson parametric converter (JPC) as a source of continuous-variable Gaussian entangled\r\nsignal-idler pairs, where a maximum 3 dB advantage is theoretically achievable. We investigate\r\nkey experimental limitations that constrain practical QI performance, contributing to the\r\ndevelopment of quantum-enhanced sensing.\r\nAdditionally, this thesis presents efficient digital signal processing (DSP) techniques implemented in C++ and Python in collaboration with Przemysław Zieliński and Luka Drmić. These\r\nmethods, optimized using the Intel Integrated Performance Primitives (IPP) library, have been\r\nessential in data acquisition, noise filtering, and correlation analysis across multiple research\r\nprojects. Although not real-time, these DSP techniques significantly enhance the accuracy of\r\nquantum measurements.\r\nOverall, this thesis advances quantum-enhanced sensing by establishing the thermodynamic\r\nlimit in a single transmon-cavity system and experimentally exploring a phase-conjugate receiver\r\nfor QI. These findings contribute to quantum metrology, particularly for weak signal detection\r\nand remote sensing in noisy environments.\r\n" acknowledged_ssus: - _id: ScienComp - _id: M-Shop - _id: NanoFab - _id: LifeSc - _id: SSU acknowledgement: "I acknowledge the generous financial support of the Austrian Science Fund (FWF) via BeyondC\r\n(F7105) and the European Union’s Horizon 2020 research and innovation program (FETopen\r\nQUARTET, Grant Agreement No. 862644), which made this research possible. I also extend\r\nmy sincere appreciation to the MIBA workshop and the Institute of Science and Technology\r\nAustria nanofabrication facility for their technical assistance, which was instrumental in realizing\r\nthis work." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Riya full_name: Sett, Riya id: 2E6D040E-F248-11E8-B48F-1D18A9856A87 last_name: Sett orcid: 0000-0001-7641-8348 citation: ama: Sett R. Quantum remote sensing and non-equilibrium phase transitions in the microwave regime. 2025. doi:10.15479/AT-ISTA-19533 apa: Sett, R. (2025). Quantum remote sensing and non-equilibrium phase transitions in the microwave regime. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19533 chicago: Sett, Riya. “ Quantum Remote Sensing and Non-Equilibrium Phase Transitions in the Microwave Regime.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19533. ieee: R. Sett, “ Quantum remote sensing and non-equilibrium phase transitions in the microwave regime,” Institute of Science and Technology Austria, 2025. ista: Sett R. 2025. Quantum remote sensing and non-equilibrium phase transitions in the microwave regime. Institute of Science and Technology Austria. mla: Sett, Riya. Quantum Remote Sensing and Non-Equilibrium Phase Transitions in the Microwave Regime. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19533. short: R. Sett, Quantum Remote Sensing and Non-Equilibrium Phase Transitions in the Microwave Regime, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-04-09T16:44:26Z date_published: 2025-04-01T00:00:00Z date_updated: 2026-06-03T07:16:05Z day: '1' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: JoFi doi: 10.15479/AT-ISTA-19533 ec_funded: 1 file: - access_level: open_access checksum: ba6cd2289d0141a160a14fc97df1632f content_type: application/pdf creator: rsett date_created: 2025-04-10T11:33:22Z date_updated: 2025-10-11T22:30:02Z embargo: 2025-10-11 file_id: '19538' file_name: PhD_Thesis_Riya_Sett_pdfa.pdf file_size: 4129208 relation: main_file - access_level: closed checksum: ee63a94cb8f7adf5e766903028b81ed6 content_type: application/x-zip-compressed creator: rsett date_created: 2025-04-10T11:34:08Z date_updated: 2025-10-11T22:30:02Z embargo_to: open_access file_id: '19539' file_name: PhD Thesis Riya Sett.zip file_size: 6646110 relation: source_file file_date_updated: 2025-10-11T22:30:02Z has_accepted_license: '1' keyword: - phase transition - open quantum system - phase diagram - cavity quantum electrodynamics - superconducting qubits - semiclassical physics - quantum optics - josephson junction - parametric converter - phase conjugation - quantum radar - quantum entanglement - correlation - quantum sensing language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '109' project: - _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_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '18978' relation: research_data status: public - id: '19280' relation: part_of_dissertation status: public - id: '17183' relation: part_of_dissertation status: public - id: '13117' relation: part_of_dissertation status: public status: public supervisor: - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X title: ' Quantum remote sensing and non-equilibrium phase transitions in the microwave regime' 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2025' ... --- OA_place: publisher _id: '20449' abstract: - lang: eng text: "Males and females of many species differ in morphology, physiology, and behavior. In taxa\r\nwith genetic sex determination, sexual differentiation arises largely from sex-biased gene\r\nexpression, which varies across tissues, developmental stages, and lineages. Increasing\r\nevidence highlights chromatin configuration, which can exist in open or closed states, and can\r\nbe shaped by sex-determination path ways, as a key regulatory layer of this dimorphism.\r\nDegeneration of the Y or W chromosome further contributes to sex -specific differences by\r\naltering gene copy numbers relative to autosomes in heterogametic sex. To mitigate these\r\nimbalances, many eukaryotes have independently evolved dosage compensation mechanisms,\r\noften mediated through chromatin -level regulation. In this thesis, we investigate the\r\nevolutionary dynamics of sex chromosome differentiation in two species, Artemia franciscana\r\nand Cameraria ohridella , with a particular focus on the extent of dosage compensation\r\nfollowing gene loss in the heterogametic sex and the potential chromatin-based mechanisms\r\nunderlying this process. We further characterize sex -biased gene expression and its regulation\r\nthrough histone modifications. Our analyses also reveal that the A. franciscana genome is\r\nhighly repetitive, with many genes containing intronic transposable elements. We find that\r\nenrichment of histonemo difications associated with constitutive heterochromatin, positively\r\ncorrelates with variation in gene expression levels. Collectively, these findings underscore role\r\nof chromatin regulation in shaping the evolution of sex chromosomes and sexual\r\ndifferentiation. " acknowledged_ssus: - _id: ScienComp acknowledgement: "This work was supported by the Austrian Science Fund (FWF) through grants PAT8748323\r\nand SFB F88-10 awarded to Professor Beatriz Vicoso." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Vincent K full_name: Bett, Vincent K id: 57854184-AAE0-11E9-8D04-98D6E5697425 last_name: Bett citation: ama: Bett VK. Evolution and regulation of the Z chromosome. 2025. doi:10.15479/AT-ISTA-20449 apa: Bett, V. K. (2025). Evolution and regulation of the Z chromosome. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20449 chicago: Bett, Vincent K. “Evolution and Regulation of the Z Chromosome.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20449. ieee: V. K. Bett, “Evolution and regulation of the Z chromosome,” Institute of Science and Technology Austria, 2025. ista: Bett VK. 2025. Evolution and regulation of the Z chromosome. Institute of Science and Technology Austria. mla: Bett, Vincent K. Evolution and Regulation of the Z Chromosome. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20449. short: V.K. Bett, Evolution and Regulation of the Z Chromosome, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-10-11T08:18:51Z date_published: 2025-10-10T00:00:00Z date_updated: 2026-06-12T08:32:16Z day: '10' ddc: - '576' degree_awarded: PhD department: - _id: GradSch - _id: BeVi doi: 10.15479/AT-ISTA-20449 file: - access_level: open_access checksum: 26905c22bca417198a733d792d8ce422 content_type: application/pdf creator: vbett date_created: 2025-10-20T13:32:29Z date_updated: 2026-06-01T22:30:04Z embargo: 2026-06-01 file_id: '20507' file_name: 2025_Bett_Vincent_Thesis.pdf file_size: 18507283 relation: main_file - access_level: closed checksum: 6a09a8d126d3628bfd8a35202735f267 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: vbett date_created: 2025-10-20T13:35:34Z date_updated: 2026-06-01T22:30:04Z embargo_to: open_access file_id: '20508' file_name: 2025_Bett_Vincent_Thesis.docx file_size: 17163921 relation: source_file file_date_updated: 2026-06-01T22:30:04Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '114' project: - _id: 8ed82125-16d5-11f0-9cad-fbcae312235b grant_number: PAT 8748323 name: Sex chromosomes in evolution and development - _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396 grant_number: F8810 name: The highjacking of meiosis for asexual reproduction publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '19735' relation: part_of_dissertation status: public - id: '15009' relation: part_of_dissertation status: public status: public supervisor: - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 title: Evolution and regulation of the Z 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: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- OA_embargo: '12' OA_place: publisher _id: '19722' abstract: - lang: eng text: "As root epidermal cells progress from a phase of elongation to differentiation, their\r\ncortical microtubule (MT) arrays exhibit a transversal-to-longitudinal reorientation. The\r\nhormone cytokinin, a key regulator of root development, facilitates these cytoskeletal\r\nchanges. However, the molecular mechanisms underlying hormone-mediated MT\r\nreorientation during root development are still unknown. Here, we find that MT reorientation\r\nin root cells differs from the existing model in hypocotyl cells, as it does not rely on MT plusend rescue. We show that cytokinin facilitates MT array reorganization during cell\r\ndifferentiation by promoting katanin’s (KTN1) severing activity, and by modulating KTN1’s\r\nassociation with microtubules. Cytokinin regulates SPIRAL2 (SPR2) in a phosphorylationdependent manner, directing its localization to, and stabilization of, the new MT minus-end\r\ncreated by katanin-mediated severing at crossovers. Notably, our findings suggest that\r\ndynamic and reversible phosphorylation at S579 of SPR2 is crucial for the proper functioning\r\nof the MT severing machinery. Finally, we identify MAP65-1 and CLASP as additional targets\r\nof cytokinin-dependent phosphoregulation. Cytokinin treatment decreases MT-MAP65-1\r\nassociation in elongating cells, likely to expose MTs to KTN1-mediated severing, whereas it\r\nincreases MT-CLASP association to stabilize the growing plus-end. In this way, cytokinin drives\r\nMT reorganization during cell development by simultaneously modulating several\r\nmicrotubule-associated proteins. These results reveal key molecular players in hormonemediated cytoskeletal regulation, and highlight protein phosphorylation as a powerful tool\r\nduring this process." acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: Special thanks to the Plant Facility. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Syamala full_name: Inumella, Syamala id: F8660870-D756-11E9-98C5-34DFE5697425 last_name: Inumella orcid: 0009-0002-5890-120X citation: ama: Inumella S. Molecular mechanisms of microtubule reorganization in elongating root epidermal cells. 2025. doi:10.15479/AT-ISTA-19722 apa: Inumella, S. (2025). Molecular mechanisms of microtubule reorganization in elongating root epidermal cells. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-19722 chicago: Inumella, Syamala. “Molecular Mechanisms of Microtubule Reorganization in Elongating Root Epidermal Cells.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-19722. ieee: S. Inumella, “Molecular mechanisms of microtubule reorganization in elongating root epidermal cells,” Institute of Science and Technology Austria, 2025. ista: Inumella S. 2025. Molecular mechanisms of microtubule reorganization in elongating root epidermal cells. Institute of Science and Technology Austria. mla: Inumella, Syamala. Molecular Mechanisms of Microtubule Reorganization in Elongating Root Epidermal Cells. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-19722. short: S. Inumella, Molecular Mechanisms of Microtubule Reorganization in Elongating Root Epidermal Cells, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-05-23T15:21:29Z date_published: 2025-05-23T00:00:00Z date_updated: 2026-06-12T08:34:29Z day: '23' ddc: - '580' degree_awarded: PhD department: - _id: GradSch - _id: EvBe doi: 10.15479/AT-ISTA-19722 file: - access_level: open_access checksum: 847ec70b2e40f50e0ddc7b8da201d52c content_type: application/pdf creator: sinumell date_created: 2025-05-28T11:59:11Z date_updated: 2026-05-23T22:30:02Z embargo: 2026-05-23 file_id: '19757' file_name: Final Thesis_Syamala Inumella.pdf file_size: 8292363 relation: main_file - access_level: closed checksum: 17cdffdae13a5f65bdad9c84e9e0e3bd content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: sinumell date_created: 2025-05-28T11:59:11Z date_updated: 2026-05-23T22:30:02Z embargo_to: open_access file_id: '19758' file_name: Final Thesis_Syamala Inumella.docx file_size: 7145703 relation: source_file file_date_updated: 2026-05-23T22:30:02Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '113' publication_identifier: isbn: - 978-3-99078-059-6 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 title: Molecular mechanisms of microtubule reorganization in elongating root epidermal cells type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2025' ... --- _id: '14543' abstract: - lang: eng text: The acyl-CoA-binding domain-containing protein 6 (ACBD6) is ubiquitously expressed, plays a role in the acylation of lipids and proteins, and regulates the N-myristoylation of proteins via N-myristoyltransferase enzymes (NMTs). However, its precise function in cells is still unclear, as is the consequence of ACBD6 defects on human pathophysiology. Utilizing exome sequencing and extensive international data sharing efforts, we identified 45 affected individuals from 28 unrelated families (consanguinity 93%) with bi-allelic pathogenic, predominantly loss-of-function (18/20) variants in ACBD6. We generated zebrafish and Xenopus tropicalis acbd6 knockouts by CRISPR/Cas9 and characterized the role of ACBD6 on protein N-myristoylation with YnMyr chemical proteomics in the model organisms and human cells, with the latter also being subjected further to ACBD6 peroxisomal localization studies. The affected individuals (23 males and 22 females), with ages ranging from 1 to 50 years old, typically present with a complex and progressive disease involving moderate-to-severe global developmental delay/intellectual disability (100%) with significant expressive language impairment (98%), movement disorders (97%), facial dysmorphism (95%), and mild cerebellar ataxia (85%) associated with gait impairment (94%), limb spasticity/hypertonia (76%), oculomotor (71%) and behavioural abnormalities (65%), overweight (59%), microcephaly (39%) and epilepsy (33%). The most conspicuous and common movement disorder was dystonia (94%), frequently leading to early-onset progressive postural deformities (97%), limb dystonia (55%), and cervical dystonia (31%). A jerky tremor in the upper limbs (63%), a mild head tremor (59%), parkinsonism/hypokinesia developing with advancing age (32%), and simple motor and vocal tics were among other frequent movement disorders. Midline brain malformations including corpus callosum abnormalities (70%), hypoplasia/agenesis of the anterior commissure (66%), short midbrain and small inferior cerebellar vermis (38% each), as well as hypertrophy of the clava (24%) were common neuroimaging findings. acbd6-deficient zebrafish and Xenopus models effectively recapitulated many clinical phenotypes reported in patients including movement disorders, progressive neuromotor impairment, seizures, microcephaly, craniofacial dysmorphism, and midbrain defects accompanied by developmental delay with increased mortality over time. Unlike ACBD5, ACBD6 did not show a peroxisomal localisation and ACBD6-deficiency was not associated with altered peroxisomal parameters in patient fibroblasts. Significant differences in YnMyr-labelling were observed for 68 co- and 18 post-translationally N-myristoylated proteins in patient-derived fibroblasts. N-Myristoylation was similarly affected in acbd6-deficient zebrafish and Xenopus tropicalis models, including Fus, Marcks, and Chchd-related proteins implicated in neurological diseases. The present study provides evidence that bi-allelic pathogenic variants in ACBD6 lead to a distinct neurodevelopmental syndrome accompanied by complex and progressive cognitive and movement disorders. article_processing_charge: No article_type: original author: - first_name: Rauan full_name: Kaiyrzhanov, Rauan last_name: Kaiyrzhanov - first_name: Aboulfazl full_name: Rad, Aboulfazl last_name: Rad - first_name: Sheng-Jia full_name: Lin, Sheng-Jia last_name: Lin - first_name: Aida full_name: Bertoli-Avella, Aida last_name: Bertoli-Avella - first_name: Wouter W full_name: Kallemeijn, Wouter W last_name: Kallemeijn - first_name: Annie full_name: Godwin, Annie last_name: Godwin - first_name: Maha S full_name: Zaki, Maha S last_name: Zaki - first_name: Kevin full_name: Huang, Kevin id: 3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3 last_name: Huang orcid: 0000-0002-2512-7812 - first_name: Tracy full_name: Lau, Tracy last_name: Lau - first_name: Cassidy full_name: Petree, Cassidy last_name: Petree - first_name: Stephanie full_name: Efthymiou, Stephanie last_name: Efthymiou - first_name: Ehsan full_name: Ghayoor Karimiani, Ehsan last_name: Ghayoor Karimiani - first_name: Maja full_name: Hempel, Maja last_name: Hempel - first_name: Elizabeth A full_name: Normand, Elizabeth A last_name: Normand - first_name: Sabine full_name: Rudnik-Schöneborn, Sabine last_name: Rudnik-Schöneborn - first_name: Ulrich A full_name: Schatz, Ulrich A last_name: Schatz - first_name: Marc P full_name: Baggelaar, Marc P last_name: Baggelaar - first_name: Muhammad full_name: Ilyas, Muhammad last_name: Ilyas - first_name: Tipu full_name: Sultan, Tipu last_name: Sultan - first_name: Javeria Raza full_name: Alvi, Javeria Raza last_name: Alvi - first_name: Manizha full_name: Ganieva, Manizha last_name: Ganieva - first_name: Ben full_name: Fowler, Ben last_name: Fowler - first_name: Ruxandra full_name: Aanicai, Ruxandra last_name: Aanicai - first_name: Gulsen full_name: Akay Tayfun, Gulsen last_name: Akay Tayfun - first_name: Abdulaziz full_name: Al Saman, Abdulaziz last_name: Al Saman - first_name: Abdulrahman full_name: Alswaid, Abdulrahman last_name: Alswaid - first_name: Nafise full_name: Amiri, Nafise last_name: Amiri - first_name: Nilufar full_name: Asilova, Nilufar last_name: Asilova - first_name: Vorasuk full_name: Shotelersuk, Vorasuk last_name: Shotelersuk - first_name: Patra full_name: Yeetong, Patra last_name: Yeetong - first_name: Matloob full_name: Azam, Matloob last_name: Azam - first_name: Meisam full_name: Babaei, Meisam last_name: Babaei - first_name: Gholamreza full_name: Bahrami Monajemi, Gholamreza last_name: Bahrami Monajemi - first_name: Pouria full_name: Mohammadi, Pouria last_name: Mohammadi - first_name: Saeed full_name: Samie, Saeed last_name: Samie - first_name: Selina Husna full_name: Banu, Selina Husna last_name: Banu - first_name: Jorge Pinto full_name: Basto, Jorge Pinto last_name: Basto - first_name: Fanny full_name: Kortüm, Fanny last_name: Kortüm - first_name: Mislen full_name: Bauer, Mislen last_name: Bauer - first_name: Peter full_name: Bauer, Peter last_name: Bauer - first_name: Christian full_name: Beetz, Christian last_name: Beetz - first_name: Masoud full_name: Garshasbi, Masoud last_name: Garshasbi - first_name: Awatif full_name: Hameed Issa, Awatif last_name: Hameed Issa - first_name: Wafaa full_name: Eyaid, Wafaa last_name: Eyaid - first_name: Hind full_name: Ahmed, Hind last_name: Ahmed - first_name: Narges full_name: Hashemi, Narges last_name: Hashemi - first_name: Kazem full_name: Hassanpour, Kazem last_name: Hassanpour - first_name: Isabella full_name: Herman, Isabella last_name: Herman - first_name: Sherozjon full_name: Ibrohimov, Sherozjon last_name: Ibrohimov - first_name: Ban A full_name: Abdul-Majeed, Ban A last_name: Abdul-Majeed - first_name: Maria full_name: Imdad, Maria last_name: Imdad - first_name: Maksudjon full_name: Isrofilov, Maksudjon last_name: Isrofilov - first_name: Qassem full_name: Kaiyal, Qassem last_name: Kaiyal - first_name: Suliman full_name: Khan, Suliman last_name: Khan - first_name: Brian full_name: Kirmse, Brian last_name: Kirmse - first_name: Janet full_name: Koster, Janet last_name: Koster - first_name: Charles Marques full_name: Lourenço, Charles Marques last_name: Lourenço - first_name: Tadahiro full_name: Mitani, Tadahiro last_name: Mitani - first_name: Oana full_name: Moldovan, Oana last_name: Moldovan - first_name: David full_name: Murphy, David last_name: Murphy - first_name: Maryam full_name: Najafi, Maryam last_name: Najafi - first_name: Davut full_name: Pehlivan, Davut last_name: Pehlivan - first_name: Maria Eugenia full_name: Rocha, Maria Eugenia last_name: Rocha - first_name: Vincenzo full_name: Salpietro, Vincenzo last_name: Salpietro - first_name: Miriam full_name: Schmidts, Miriam last_name: Schmidts - first_name: Adel full_name: Shalata, Adel last_name: Shalata - first_name: Mohammad full_name: Mahroum, Mohammad last_name: Mahroum - first_name: Jawabreh Kassem full_name: Talbeya, Jawabreh Kassem last_name: Talbeya - first_name: Robert W full_name: Taylor, Robert W last_name: Taylor - first_name: Dayana full_name: Vazquez, Dayana last_name: Vazquez - first_name: Annalisa full_name: Vetro, Annalisa last_name: Vetro - first_name: Hans R full_name: Waterham, Hans R last_name: Waterham - first_name: Mashaya full_name: Zaman, Mashaya last_name: Zaman - first_name: Tina A full_name: Schrader, Tina A last_name: Schrader - first_name: Wendy K full_name: Chung, Wendy K last_name: Chung - first_name: Renzo full_name: Guerrini, Renzo last_name: Guerrini - first_name: James R full_name: Lupski, James R last_name: Lupski - first_name: Joseph full_name: Gleeson, Joseph last_name: Gleeson - first_name: Mohnish full_name: Suri, Mohnish last_name: Suri - first_name: Yalda full_name: Jamshidi, Yalda last_name: Jamshidi - first_name: Kailash P full_name: Bhatia, Kailash P last_name: Bhatia - first_name: Barbara full_name: Vona, Barbara last_name: Vona - first_name: Michael full_name: Schrader, Michael last_name: Schrader - first_name: Mariasavina full_name: Severino, Mariasavina last_name: Severino - first_name: Matthew full_name: Guille, Matthew last_name: Guille - first_name: Edward W full_name: Tate, Edward W last_name: Tate - first_name: Gaurav K full_name: Varshney, Gaurav K last_name: Varshney - first_name: Henry full_name: Houlden, Henry last_name: Houlden - first_name: Reza full_name: Maroofian, Reza last_name: Maroofian citation: ama: Kaiyrzhanov R, Rad A, Lin S-J, et al. Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain. 2024;147(4):1436-1456. doi:10.1093/brain/awad380 apa: Kaiyrzhanov, R., Rad, A., Lin, S.-J., Bertoli-Avella, A., Kallemeijn, W. W., Godwin, A., … Maroofian, R. (2024). Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain. Oxford University Press. https://doi.org/10.1093/brain/awad380 chicago: Kaiyrzhanov, Rauan, Aboulfazl Rad, Sheng-Jia Lin, Aida Bertoli-Avella, Wouter W Kallemeijn, Annie Godwin, Maha S Zaki, et al. “Bi-Allelic ACBD6 Variants Lead to a Neurodevelopmental Syndrome with Progressive and Complex Movement Disorders.” Brain. Oxford University Press, 2024. https://doi.org/10.1093/brain/awad380. ieee: R. Kaiyrzhanov et al., “Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders,” Brain, vol. 147, no. 4. Oxford University Press, pp. 1436–1456, 2024. ista: Kaiyrzhanov R, Rad A, Lin S-J, Bertoli-Avella A, Kallemeijn WW, Godwin A, Zaki MS, Huang K, Lau T, Petree C, Efthymiou S, Ghayoor Karimiani E, Hempel M, Normand EA, Rudnik-Schöneborn S, Schatz UA, Baggelaar MP, Ilyas M, Sultan T, Alvi JR, Ganieva M, Fowler B, Aanicai R, Akay Tayfun G, Al Saman A, Alswaid A, Amiri N, Asilova N, Shotelersuk V, Yeetong P, Azam M, Babaei M, Bahrami Monajemi G, Mohammadi P, Samie S, Banu SH, Basto JP, Kortüm F, Bauer M, Bauer P, Beetz C, Garshasbi M, Hameed Issa A, Eyaid W, Ahmed H, Hashemi N, Hassanpour K, Herman I, Ibrohimov S, Abdul-Majeed BA, Imdad M, Isrofilov M, Kaiyal Q, Khan S, Kirmse B, Koster J, Lourenço CM, Mitani T, Moldovan O, Murphy D, Najafi M, Pehlivan D, Rocha ME, Salpietro V, Schmidts M, Shalata A, Mahroum M, Talbeya JK, Taylor RW, Vazquez D, Vetro A, Waterham HR, Zaman M, Schrader TA, Chung WK, Guerrini R, Lupski JR, Gleeson J, Suri M, Jamshidi Y, Bhatia KP, Vona B, Schrader M, Severino M, Guille M, Tate EW, Varshney GK, Houlden H, Maroofian R. 2024. Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain. 147(4), 1436–1456. mla: Kaiyrzhanov, Rauan, et al. “Bi-Allelic ACBD6 Variants Lead to a Neurodevelopmental Syndrome with Progressive and Complex Movement Disorders.” Brain, vol. 147, no. 4, Oxford University Press, 2024, pp. 1436–56, doi:10.1093/brain/awad380. short: R. Kaiyrzhanov, A. Rad, S.-J. Lin, A. Bertoli-Avella, W.W. Kallemeijn, A. Godwin, M.S. Zaki, K. Huang, T. Lau, C. Petree, S. Efthymiou, E. Ghayoor Karimiani, M. Hempel, E.A. Normand, S. Rudnik-Schöneborn, U.A. Schatz, M.P. Baggelaar, M. Ilyas, T. Sultan, J.R. Alvi, M. Ganieva, B. Fowler, R. Aanicai, G. Akay Tayfun, A. Al Saman, A. Alswaid, N. Amiri, N. Asilova, V. Shotelersuk, P. Yeetong, M. Azam, M. Babaei, G. Bahrami Monajemi, P. Mohammadi, S. Samie, S.H. Banu, J.P. Basto, F. Kortüm, M. Bauer, P. Bauer, C. Beetz, M. Garshasbi, A. Hameed Issa, W. Eyaid, H. Ahmed, N. Hashemi, K. Hassanpour, I. Herman, S. Ibrohimov, B.A. Abdul-Majeed, M. Imdad, M. Isrofilov, Q. Kaiyal, S. Khan, B. Kirmse, J. Koster, C.M. Lourenço, T. Mitani, O. Moldovan, D. Murphy, M. Najafi, D. Pehlivan, M.E. Rocha, V. Salpietro, M. Schmidts, A. Shalata, M. Mahroum, J.K. Talbeya, R.W. Taylor, D. Vazquez, A. Vetro, H.R. Waterham, M. Zaman, T.A. Schrader, W.K. Chung, R. Guerrini, J.R. Lupski, J. Gleeson, M. Suri, Y. Jamshidi, K.P. Bhatia, B. Vona, M. Schrader, M. Severino, M. Guille, E.W. Tate, G.K. Varshney, H. Houlden, R. Maroofian, Brain 147 (2024) 1436–1456. date_created: 2023-11-16T12:36:51Z date_published: 2024-04-01T00:00:00Z date_updated: 2024-07-16T08:23:24Z day: '01' ddc: - '570' department: - _id: GradSch doi: 10.1093/brain/awad380 extern: '1' external_id: pmid: - '37951597' file: - access_level: open_access checksum: 0ee7a8ab9300225d60968f7a3e3cfa0d content_type: application/pdf creator: dernst date_created: 2024-07-16T08:22:13Z date_updated: 2024-07-16T08:22:13Z file_id: '17254' file_name: 2024_Brain_Kaiyrzhanov.pdf file_size: 2641456 relation: main_file success: 1 file_date_updated: 2024-07-16T08:22:13Z has_accepted_license: '1' intvolume: ' 147' issue: '4' keyword: - Neurology (clinical) language: - iso: eng month: '04' oa: 1 oa_version: Submitted Version page: 1436-1456 pmid: 1 publication: Brain publication_identifier: eissn: - 1460-2156 issn: - 0006-8950 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders 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: 147 year: '2024' ... --- _id: '14653' abstract: - lang: eng text: 'Mass spectrometry imaging (MSI) is a powerful analytical technique for the two-dimensional (2D) localization of chemicals on surfaces. Conventional MSI experiments require to predefine the surface of interest based on photographic or microscopic images. Typically, these boundaries can no longer be changed or adjusted once the experiment has been started. In terms of a more interactive approach we recently developed a pen-like ionization interface which is directly connected to the mass spectrometer. The device allows the user to ionize chemicals by desorption electrospray ionization (DESI) and to freely move the interface over a surface of interest. A mini camera, which is mounted on the tip of the pen, magnifies the desorption area and enables a simple positioning of the pen. The combination of optical data from the camera module and chemical data obtained by mass analysis facilitates a novel type of imaging experiment: interactive mass spectrometry imaging (IMSI). For this application, we present a novel approach for a robust, optical flow-based motion detection. While the live video stream from the camera is used to track the pen''s motion across the surface a post-acquisition algorithm correlates the coordinates of the pen trajectory with respective mass spectra obtained from a simultaneous mass spectrometric data acquisition. This algorithm is no longer dependent on a single, manually applied optical marker on the sample surface, which has to be visible on all video frames throughout the analysis. The advanced DESI-IMSI method was successfully tested on inkjet-printed letters as well as mouse brain tissue samples. Validation of the results was done by comparing DESI-IMSI with standard DESI-MSI data.' acknowledgement: We would like to thank Marco Sealey Cardona, PhD for help with the mouse brain samples and acknowledge the financial support by 1669 Förderkreis of the University of Innsbruck, Austria Wirtschaftsservice (AWS), D. Swarovski KG and Tyrolean Science Fund (TWF). article_number: '117168' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Florian full_name: Kluibenschedl, Florian id: 7499e70e-eb2c-11ec-b98b-f925648bc9d9 last_name: Kluibenschedl - first_name: Anna full_name: Ploner, Anna last_name: Ploner - first_name: Christina full_name: Meisenbichler, Christina last_name: Meisenbichler - first_name: Robert full_name: Konrat, Robert last_name: Konrat - first_name: Thomas full_name: Müller, Thomas last_name: Müller citation: ama: Kluibenschedl F, Ploner A, Meisenbichler C, Konrat R, Müller T. Advanced motion tracking for interactive mass spectrometry imaging (IMSI). International Journal of Mass Spectrometry. 2024;495. doi:10.1016/j.ijms.2023.117168 apa: Kluibenschedl, F., Ploner, A., Meisenbichler, C., Konrat, R., & Müller, T. (2024). Advanced motion tracking for interactive mass spectrometry imaging (IMSI). International Journal of Mass Spectrometry. Elsevier. https://doi.org/10.1016/j.ijms.2023.117168 chicago: Kluibenschedl, Florian, Anna Ploner, Christina Meisenbichler, Robert Konrat, and Thomas Müller. “Advanced Motion Tracking for Interactive Mass Spectrometry Imaging (IMSI).” International Journal of Mass Spectrometry. Elsevier, 2024. https://doi.org/10.1016/j.ijms.2023.117168. ieee: F. Kluibenschedl, A. Ploner, C. Meisenbichler, R. Konrat, and T. Müller, “Advanced motion tracking for interactive mass spectrometry imaging (IMSI),” International Journal of Mass Spectrometry, vol. 495. Elsevier, 2024. ista: Kluibenschedl F, Ploner A, Meisenbichler C, Konrat R, Müller T. 2024. Advanced motion tracking for interactive mass spectrometry imaging (IMSI). International Journal of Mass Spectrometry. 495, 117168. mla: Kluibenschedl, Florian, et al. “Advanced Motion Tracking for Interactive Mass Spectrometry Imaging (IMSI).” International Journal of Mass Spectrometry, vol. 495, 117168, Elsevier, 2024, doi:10.1016/j.ijms.2023.117168. short: F. Kluibenschedl, A. Ploner, C. Meisenbichler, R. Konrat, T. Müller, International Journal of Mass Spectrometry 495 (2024). date_created: 2023-12-10T23:00:57Z date_published: 2024-01-01T00:00:00Z date_updated: 2025-09-04T11:30:59Z day: '01' ddc: - '540' department: - _id: GradSch doi: 10.1016/j.ijms.2023.117168 external_id: isi: - '001125054400001' file: - access_level: open_access checksum: 6c5eb6dc07af70a59251d2c6fed38894 content_type: application/pdf creator: dernst date_created: 2024-07-16T08:27:34Z date_updated: 2024-07-16T08:27:34Z file_id: '17256' file_name: 2024_IJMS_Kluibenschedl.pdf file_size: 3003139 relation: main_file success: 1 file_date_updated: 2024-07-16T08:27:34Z has_accepted_license: '1' intvolume: ' 495' isi: 1 language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: International Journal of Mass Spectrometry publication_identifier: issn: - 1387-3806 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Advanced motion tracking for interactive mass spectrometry imaging (IMSI) 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 495 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '14703' abstract: - lang: eng text: We present a discretization of the dynamic optimal transport problem for which we can obtain the convergence rate for the value of the transport cost to its continuous value when the temporal and spatial stepsize vanish. This convergence result does not require any regularity assumption on the measures, though experiments suggest that the rate is not sharp. Via an analysis of the duality gap we also obtain the convergence rates for the gradient of the optimal potentials and the velocity field under mild regularity assumptions. To obtain such rates we discretize the dual formulation of the dynamic optimal transport problem and use the mature literature related to the error due to discretizing the Hamilton-Jacobi equation. acknowledgement: 'The authors would like to thank Chris Wojtan for his continuous support and several interesting discussions. Part of this research was performed during two visits: one of SI to the BIDSA research center at Bocconi University, and one of HL to the Institute of Science and Technology Austria. Both host institutions are warmly acknowledged for the hospitality. HL is partially supported by the MUR-Prin 2022-202244A7YL “Gradient Flows and Non-Smooth Geometric Structures with Applications to Optimization and Machine Learning”, funded by the European Union - Next Generation EU. SI is supported in part by ERC Consolidator Grant 101045083 “CoDiNA” funded by the European Research Council.' article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Sadashige full_name: Ishida, Sadashige id: 6F7C4B96-A8E9-11E9-A7CA-09ECE5697425 last_name: Ishida - first_name: Hugo full_name: Lavenant, Hugo last_name: Lavenant citation: ama: Ishida S, Lavenant H. Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. Foundations of Computational Mathematics. 2024. doi:10.1007/s10208-024-09686-3 apa: Ishida, S., & Lavenant, H. (2024). Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. Foundations of Computational Mathematics. Springer Nature. https://doi.org/10.1007/s10208-024-09686-3 chicago: Ishida, Sadashige, and Hugo Lavenant. “Quantitative Convergence of a Discretization of Dynamic Optimal Transport Using the Dual Formulation.” Foundations of Computational Mathematics. Springer Nature, 2024. https://doi.org/10.1007/s10208-024-09686-3. ieee: S. Ishida and H. Lavenant, “Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation,” Foundations of Computational Mathematics. Springer Nature, 2024. ista: Ishida S, Lavenant H. 2024. Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. Foundations of Computational Mathematics. mla: Ishida, Sadashige, and Hugo Lavenant. “Quantitative Convergence of a Discretization of Dynamic Optimal Transport Using the Dual Formulation.” Foundations of Computational Mathematics, Springer Nature, 2024, doi:10.1007/s10208-024-09686-3. short: S. Ishida, H. Lavenant, Foundations of Computational Mathematics (2024). corr_author: '1' date_created: 2023-12-21T10:14:37Z date_published: 2024-11-11T00:00:00Z date_updated: 2025-09-04T11:35:55Z day: '11' department: - _id: GradSch - _id: ChWo doi: 10.1007/s10208-024-09686-3 external_id: arxiv: - '2312.12213' isi: - '001352503300001' isi: 1 keyword: - Optimal transport - Hamilton-Jacobi equation - convex optimization language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/s10208-024-09686-3 month: '11' oa: 1 oa_version: Published Version project: - _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088 grant_number: '101045083' name: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena publication: Foundations of Computational Mathematics publication_identifier: eissn: - 1615-3383 issn: - 1615-3375 publication_status: epub_ahead publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- _id: '14705' abstract: - lang: eng text: Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, are still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of Artemia franciscana (Kellogg 1906), from the Great Salt Lake, USA. The genome is 1GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species. article_processing_charge: No author: - first_name: Marwan N full_name: Elkrewi, Marwan N id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425 last_name: Elkrewi orcid: 0000-0002-5328-7231 citation: ama: Elkrewi MN. Data from “Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.” 2024. doi:10.15479/AT:ISTA:14705 apa: Elkrewi, M. N. (2024). Data from “Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14705 chicago: Elkrewi, Marwan N. “Data from ‘Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex-Chromosome Differentiation.’” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:14705. ieee: M. N. Elkrewi, “Data from ‘Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.’” Institute of Science and Technology Austria, 2024. ista: Elkrewi MN. 2024. Data from ‘Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14705. mla: Elkrewi, Marwan N. Data from “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex-Chromosome Differentiation.” Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:14705. short: M.N. Elkrewi, (2024). contributor: - contributor_type: researcher first_name: Vincent K id: 57854184-AAE0-11E9-8D04-98D6E5697425 last_name: Bett - contributor_type: project_member first_name: Ariana id: 2A0848E2-F248-11E8-B48F-1D18A9856A87 last_name: Macon - contributor_type: supervisor first_name: Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 - contributor_type: researcher first_name: Marwan N id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425 last_name: Elkrewi orcid: 0000-0002-5328-7231 corr_author: '1' date_created: 2023-12-22T13:40:48Z date_published: 2024-01-02T00:00:00Z date_updated: 2025-09-04T12:05:42Z day: '02' ddc: - '576' department: - _id: GradSch - _id: BeVi doi: 10.15479/AT:ISTA:14705 file: - access_level: open_access checksum: bdaf1392867786634ec5466d528c36ca content_type: text/plain creator: melkrewi date_created: 2023-12-22T13:54:21Z date_updated: 2023-12-22T13:54:21Z file_id: '14707' file_name: readme.txt.txt file_size: 847 relation: main_file success: 1 - access_level: open_access checksum: 973e1cbdab923a71709782177980829f content_type: application/x-zip-compressed creator: melkrewi date_created: 2023-12-22T14:14:06Z date_updated: 2023-12-22T14:14:06Z file_id: '14708' file_name: data_artemia_franciscana_genome.zip file_size: 343632753 relation: main_file success: 1 file_date_updated: 2023-12-22T14:14:06Z has_accepted_license: '1' keyword: - sex chromosome evolution - genome assembly - dosage compensation month: '01' oa: 1 oa_version: Published Version project: - _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396 grant_number: F8810 name: The highjacking of meiosis for asexual reproduction publisher: Institute of Science and Technology Austria related_material: record: - id: '15009' relation: used_in_publication status: public status: public title: Data from "Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation" 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: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: publisher OA_type: gold _id: '18068' abstract: - lang: eng text: "We study the following refinement relation between nondeterministic state-transition models: model ℬ strategically dominates model \U0001D49C iff every deterministic refinement of \U0001D49C is language contained in some deterministic refinement of ℬ. While language containment is trace inclusion, and the (fair) simulation preorder coincides with tree inclusion, strategic dominance falls strictly between the two and can be characterized as \"strategy inclusion\" between \U0001D49C and ℬ: every strategy that resolves the nondeterminism of \U0001D49C is dominated by a strategy that resolves the nondeterminism of ℬ. Strategic dominance can be checked in 2-ExpTime by a decidable first-order Presburger logic with quantification over words and strategies, called resolver logic. We give several other applications of resolver logic, including checking the co-safety, co-liveness, and history-determinism of boolean and quantitative automata, and checking the inclusion between hyperproperties that are specified by nondeterministic boolean and quantitative automata." acknowledgement: This work was supported in part by the ERC-2020-AdG 101020093. N. Mazzocchi was affiliated with ISTA when this work was submitted for publication. alternative_title: - LIPIcs article_number: '29' article_processing_charge: Yes arxiv: 1 author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 - first_name: Nicolas Adrien full_name: Mazzocchi, Nicolas Adrien id: b26baa86-3308-11ec-87b0-8990f34baa85 last_name: Mazzocchi - first_name: Naci E full_name: Sarac, Naci E id: 8C6B42F8-C8E6-11E9-A03A-F2DCE5697425 last_name: Sarac citation: ama: 'Henzinger TA, Mazzocchi NA, Sarac NE. Strategic dominance: A new preorder for nondeterministic processes. In: 35th International Conference on Concurrency Theory. Vol 311. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.CONCUR.2024.29' apa: 'Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2024). Strategic dominance: A new preorder for nondeterministic processes. In 35th International Conference on Concurrency Theory (Vol. 311). Calgary, Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2024.29' chicago: 'Henzinger, Thomas A, Nicolas Adrien Mazzocchi, and Naci E Sarac. “Strategic Dominance: A New Preorder for Nondeterministic Processes.” In 35th International Conference on Concurrency Theory, Vol. 311. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.CONCUR.2024.29.' ieee: 'T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “Strategic dominance: A new preorder for nondeterministic processes,” in 35th International Conference on Concurrency Theory, Calgary, Canada, 2024, vol. 311.' ista: 'Henzinger TA, Mazzocchi NA, Sarac NE. 2024. Strategic dominance: A new preorder for nondeterministic processes. 35th International Conference on Concurrency Theory. CONCUR: Conference on Concurrency Theory, LIPIcs, vol. 311, 29.' mla: 'Henzinger, Thomas A., et al. “Strategic Dominance: A New Preorder for Nondeterministic Processes.” 35th International Conference on Concurrency Theory, vol. 311, 29, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.CONCUR.2024.29.' short: T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 35th International Conference on Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. conference: end_date: 2024-09-13 location: Calgary, Canada name: 'CONCUR: Conference on Concurrency Theory' start_date: 2024-09-09 corr_author: '1' date_created: 2024-09-15T22:01:40Z date_published: 2024-09-01T00:00:00Z date_updated: 2025-12-02T13:45:38Z day: '01' ddc: - '000' department: - _id: ToHe - _id: GradSch doi: 10.4230/LIPIcs.CONCUR.2024.29 ec_funded: 1 external_id: arxiv: - '2407.10473' isi: - '001556847400029' file: - access_level: open_access checksum: 555bd343e1fb38adeab8fc465ff4fad8 content_type: application/pdf creator: dernst date_created: 2024-09-17T07:48:56Z date_updated: 2024-09-17T07:48:56Z file_id: '18081' file_name: 2024_LIPICS_Henzinger.pdf file_size: 964124 relation: main_file success: 1 file_date_updated: 2024-09-17T07:48:56Z has_accepted_license: '1' intvolume: ' 311' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publication: 35th International Conference on Concurrency Theory publication_identifier: isbn: - '9783959773393' issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: '1' status: public title: 'Strategic dominance: A new preorder for nondeterministic processes' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 311 year: '2024' ... --- _id: '18113' abstract: - lang: eng text: 'The emergence of accurate open large language models (LLMs) has led to a race towards performant quantization techniques which can enable their execution on end-user devices. In this paper, we revisit the problem of “extreme” LLM compression—defined as targeting extremely low bit counts, such as 2 to 3 bits per parameter—from the point of view of classic methods in Multi-Codebook Quantization (MCQ). Our algorithm, called AQLM, generalizes the classic Additive Quantization (AQ) approach for information retrieval to advance the state-of-the-art in LLM compression, via two innovations: 1) learned additive quantization of weight matrices in input-adaptive fashion, and 2) joint optimization of codebook parameters across each transformer blocks. Broadly, AQLM is the first scheme that is Pareto optimal in terms of accuracy-vs-model-size when compressing to less than 3 bits per parameter, and significantly improves upon all known schemes in the extreme compression (2bit) regime. In addition, AQLM is practical: we provide fast GPU and CPU implementations of AQLM for token generation, which enable us to match or outperform optimized FP16 implementations for speed, while executing in a much smaller memory footprint.' acknowledgement: "Authors would like to thank Ruslan Svirschevski for his help in solving technical issues with AQLM and baselines. We also thank Tim Dettmers for helpful discussions on the structure of weights in modern LLMs and size-accuracy trade-offs. The authors would also like to thank Daniil Pavlov for his assistance with CPU benchmarking. Finally, authors would like to thank the communities of ML enthusiasts known as LocalLLaMA5 and Petals community on discord6\r\nfor the crowd wisdom about running LLMs on consumer devices. Egiazarian Vage and Denis Kuznedelev and Andrei Panferov were supported by the grant for research centers in the field of AI provided by the Analytical Center for the Government of the Russian Federation (ACRF) in\r\naccordance with the agreement on the provision of subsidies (identifier of the agreement 000000D730321P5Q0002) and the agreement with HSE University No. 70-2021-00139." alternative_title: - PMLR article_processing_charge: No arxiv: 1 author: - first_name: Vage full_name: Egiazarian, Vage last_name: Egiazarian - first_name: Andrei full_name: Panferov, Andrei id: 2c18daae-4dbe-11ef-8491-98ce2d960f09 last_name: Panferov - first_name: Denis full_name: Kuznedelev, Denis last_name: Kuznedelev - first_name: Elias full_name: Frantar, Elias id: 09a8f98d-ec99-11ea-ae11-c063a7b7fe5f last_name: Frantar - first_name: Artem full_name: Babenko, Artem last_name: Babenko - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X citation: ama: 'Egiazarian V, Panferov A, Kuznedelev D, Frantar E, Babenko A, Alistarh D-A. Extreme compression of large language models via additive quantization. In: Proceedings of the 41st International Conference on Machine Learning. Vol 235. ML Research Press; 2024:12284-12303.' apa: 'Egiazarian, V., Panferov, A., Kuznedelev, D., Frantar, E., Babenko, A., & Alistarh, D.-A. (2024). Extreme compression of large language models via additive quantization. In Proceedings of the 41st International Conference on Machine Learning (Vol. 235, pp. 12284–12303). Vienna, Austria: ML Research Press.' chicago: Egiazarian, Vage, Andrei Panferov, Denis Kuznedelev, Elias Frantar, Artem Babenko, and Dan-Adrian Alistarh. “Extreme Compression of Large Language Models via Additive Quantization.” In Proceedings of the 41st International Conference on Machine Learning, 235:12284–303. ML Research Press, 2024. ieee: V. Egiazarian, A. Panferov, D. Kuznedelev, E. Frantar, A. Babenko, and D.-A. Alistarh, “Extreme compression of large language models via additive quantization,” in Proceedings of the 41st International Conference on Machine Learning, Vienna, Austria, 2024, vol. 235, pp. 12284–12303. ista: 'Egiazarian V, Panferov A, Kuznedelev D, Frantar E, Babenko A, Alistarh D-A. 2024. Extreme compression of large language models via additive quantization. Proceedings of the 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 235, 12284–12303.' mla: Egiazarian, Vage, et al. “Extreme Compression of Large Language Models via Additive Quantization.” Proceedings of the 41st International Conference on Machine Learning, vol. 235, ML Research Press, 2024, pp. 12284–303. short: V. Egiazarian, A. Panferov, D. Kuznedelev, E. Frantar, A. Babenko, D.-A. Alistarh, in:, Proceedings of the 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 12284–12303. conference: end_date: 2024-07-27 location: Vienna, Austria name: 'ICML: International Conference on Machine Learning' start_date: 2024-07-21 corr_author: '1' date_created: 2024-09-22T22:01:43Z date_published: 2024-09-01T00:00:00Z date_updated: 2024-10-01T08:13:05Z day: '01' department: - _id: DaAl - _id: GradSch external_id: arxiv: - '2401.06118' intvolume: ' 235' language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.2401.06118' month: '09' oa: 1 oa_version: Preprint page: 12284-12303 publication: Proceedings of the 41st International Conference on Machine Learning publication_identifier: eissn: - 2640-3498 publication_status: published publisher: ML Research Press quality_controlled: '1' scopus_import: '1' status: public title: Extreme compression of large language models via additive quantization type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 235 year: '2024' ... --- _id: '18117' abstract: - lang: eng text: "We investigate parameter-efficient fine-tuning (PEFT) methods that can provide good accuracy under limited computational and memory budgets in the context of large language models (LLMs). We present a new PEFT method called Robust Adaptation (RoSA) inspired by robust principal component analysis that jointly trains low-rank\r\n and highly-sparse components on top of a set of fixed pretrained weights to efficiently approximate the performance of a full-fine-tuning (FFT) solution. Across a series of challenging generative tasks such as grade-school math and SQL query generation, which require fine-tuning for good performance, we show that RoSA outperforms LoRA, pure sparse fine-tuning, and alternative hybrid methods at the same parameter budget, and can even recover the performance of FFT on some tasks. We provide system support for RoSA to complement the training algorithm, specifically in the form of sparse GPU kernels which enable memory- and computationally-efficient training, and show that it is also compatible with low-precision base weights, resulting in the first joint representation combining quantization, low-rank and sparse approximations. Our code is available at https://github.com/IST-DASLab/RoSA." acknowledgement: The authors would like to thank Eldar Kurtic for experimental support and useful suggestions throughout the project article_processing_charge: No arxiv: 1 author: - first_name: Mahdi full_name: Nikdan, Mahdi id: 66374281-f394-11eb-9cf6-869147deecc0 last_name: Nikdan - first_name: Soroush full_name: Tabesh, Soroush id: 06000900-6068-11ef-8d61-c2472ef2e752 last_name: Tabesh orcid: 0009-0003-4119-6281 - first_name: Elvir full_name: Crncevic, Elvir id: 41888001-440d-11ef-8299-d0e838b8185e last_name: Crncevic - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X citation: ama: 'Nikdan M, Tabesh S, Crncevic E, Alistarh D-A. RoSA: Accurate parameter-efficient fine-tuning via robust adaptation. In: Proceedings of the 41st International Conference on Machine Learning. Vol 235. ML Research Press; 2024:38187-38206.' apa: 'Nikdan, M., Tabesh, S., Crncevic, E., & Alistarh, D.-A. (2024). RoSA: Accurate parameter-efficient fine-tuning via robust adaptation. In Proceedings of the 41st International Conference on Machine Learning (Vol. 235, pp. 38187–38206). Vienna, Austria: ML Research Press.' chicago: 'Nikdan, Mahdi, Soroush Tabesh, Elvir Crncevic, and Dan-Adrian Alistarh. “RoSA: Accurate Parameter-Efficient Fine-Tuning via Robust Adaptation.” In Proceedings of the 41st International Conference on Machine Learning, 235:38187–206. ML Research Press, 2024.' ieee: 'M. Nikdan, S. Tabesh, E. Crncevic, and D.-A. Alistarh, “RoSA: Accurate parameter-efficient fine-tuning via robust adaptation,” in Proceedings of the 41st International Conference on Machine Learning, Vienna, Austria, 2024, vol. 235, pp. 38187–38206.' ista: 'Nikdan M, Tabesh S, Crncevic E, Alistarh D-A. 2024. RoSA: Accurate parameter-efficient fine-tuning via robust adaptation. Proceedings of the 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 235, 38187–38206.' mla: 'Nikdan, Mahdi, et al. “RoSA: Accurate Parameter-Efficient Fine-Tuning via Robust Adaptation.” Proceedings of the 41st International Conference on Machine Learning, vol. 235, ML Research Press, 2024, pp. 38187–206.' short: M. Nikdan, S. Tabesh, E. Crncevic, D.-A. Alistarh, in:, Proceedings of the 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 38187–38206. conference: end_date: 2024-07-27 location: Vienna, Austria name: 'ICML: International Conference on Machine Learning' start_date: 2024-07-21 corr_author: '1' date_created: 2024-09-22T22:01:44Z date_published: 2024-09-01T00:00:00Z date_updated: 2024-10-01T08:22:01Z day: '01' department: - _id: DaAl - _id: GradSch external_id: arxiv: - '2401.04679' intvolume: ' 235' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2401.04679 month: '09' oa: 1 oa_version: Preprint page: 38187-38206 publication: Proceedings of the 41st International Conference on Machine Learning publication_identifier: eissn: - 2640-3498 publication_status: published publisher: ML Research Press quality_controlled: '1' related_material: link: - relation: software url: https://github.com/IST-DASLab/RoSA scopus_import: '1' status: public title: 'RoSA: Accurate parameter-efficient fine-tuning via robust adaptation' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 235 year: '2024' ... --- _id: '18174' abstract: - lang: eng text: We investigate the phase ordering (pattern formation) of systems of two-dimensional core–shell particles using Monte Carlo (MC) computer simulations and classical density functional theory (DFT). The particles interact via a pair potential having a hard core and a repulsive square shoulder. Our simulations show that on cooling, the liquid state structure becomes increasingly characterized by long wavelength density modulations and on further cooling forms a variety of other phases, including clustered, striped, and other patterned phases. In DFT, the hard core part of the potential is treated using either fundamental measure theory or a simple local density approximation, whereas the soft shoulder is treated using the random phase approximation. The different DFTs are benchmarked using large-scale grand-canonical-MC and Gibbs-ensemble-MC simulations, demonstrating their predictive capabilities and shortcomings. We find that having the liquid state static structure factor S(k) for wavenumber k is sufficient to identify the Fourier modes governing both the liquid and solid phases. This allows us to identify from easier-to-obtain liquid state data the wavenumbers relevant to the periodic phases and to predict roughly where in the phase diagram these patterned phases arise. acknowledgement: The computational results presented here were enabled via a generous share of CPU time, offered by the Vienna Scientific Cluster (VSC) under Project No. 71263. The authors thank Ms. Katrin Muck for her guidance related to the use of HPC. A.J.A. gratefully acknowledges support from the EPSRC under Grant No. EP/P015689/1. article_number: '124503 ' article_processing_charge: Yes (in subscription journal) article_type: original arxiv: 1 author: - first_name: Michael full_name: Wassermair, Michael id: 23d132c4-4e98-11ef-b275-9e8d4cd8c917 last_name: Wassermair - first_name: Gerhard full_name: Kahl, Gerhard last_name: Kahl - first_name: Roland full_name: Roth, Roland last_name: Roth - first_name: Andrew J. full_name: Archer, Andrew J. last_name: Archer citation: ama: Wassermair M, Kahl G, Roth R, Archer AJ. Fingerprints of ordered self-assembled structures in the liquid phase of a hard-core, square-shoulder system. The Journal of chemical physics. 2024;161(12). doi:10.1063/5.0226954 apa: Wassermair, M., Kahl, G., Roth, R., & Archer, A. J. (2024). Fingerprints of ordered self-assembled structures in the liquid phase of a hard-core, square-shoulder system. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0226954 chicago: Wassermair, Michael, Gerhard Kahl, Roland Roth, and Andrew J. Archer. “Fingerprints of Ordered Self-Assembled Structures in the Liquid Phase of a Hard-Core, Square-Shoulder System.” The Journal of Chemical Physics. AIP Publishing, 2024. https://doi.org/10.1063/5.0226954. ieee: M. Wassermair, G. Kahl, R. Roth, and A. J. Archer, “Fingerprints of ordered self-assembled structures in the liquid phase of a hard-core, square-shoulder system,” The Journal of chemical physics, vol. 161, no. 12. AIP Publishing, 2024. ista: Wassermair M, Kahl G, Roth R, Archer AJ. 2024. Fingerprints of ordered self-assembled structures in the liquid phase of a hard-core, square-shoulder system. The Journal of chemical physics. 161(12), 124503. mla: Wassermair, Michael, et al. “Fingerprints of Ordered Self-Assembled Structures in the Liquid Phase of a Hard-Core, Square-Shoulder System.” The Journal of Chemical Physics, vol. 161, no. 12, 124503, AIP Publishing, 2024, doi:10.1063/5.0226954. short: M. Wassermair, G. Kahl, R. Roth, A.J. Archer, The Journal of Chemical Physics 161 (2024). corr_author: '1' date_created: 2024-10-06T22:01:12Z date_published: 2024-09-28T00:00:00Z date_updated: 2025-09-08T09:55:52Z day: '28' ddc: - '530' department: - _id: GradSch doi: 10.1063/5.0226954 external_id: arxiv: - '2409.06447' isi: - '001325268300004' pmid: - '39344889' file: - access_level: open_access checksum: f3874e64ef94e94b2376f00a1fee24c3 content_type: application/pdf creator: dernst date_created: 2024-10-07T11:25:00Z date_updated: 2024-10-07T11:25:00Z file_id: '18185' file_name: 2024_JourChemicalPhysics_Wassermair.pdf file_size: 15009000 relation: main_file success: 1 file_date_updated: 2024-10-07T11:25:00Z has_accepted_license: '1' intvolume: ' 161' isi: 1 issue: '12' language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 publication: The Journal of chemical physics publication_identifier: eissn: - 1089-7690 publication_status: published publisher: AIP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Fingerprints of ordered self-assembled structures in the liquid phase of a hard-core, square-shoulder system 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 161 year: '2024' ... --- OA_type: closed access _id: '18450' abstract: - lang: eng text: In this work we present the engineering of a portable platform for sensing SERS signals in droplets microfluidics. This system comprised not only the read-out platform but also a design for the microfluidic devices optimized to enhanced the obtained SERS signals. acknowledgement: The authors acknowledge the financial support of the project HfPT – Health from Portugal, with the reference n.° C644937233-00000047, co-funded by Component C5 – Capitalisation and Business Innovation under the Portuguese Resilience and Recovery Plan, through the NextGenerationEU Fund. article_processing_charge: No author: - first_name: Sergio full_name: Quintero, Sergio last_name: Quintero - first_name: Maria full_name: Relvas, Maria last_name: Relvas - first_name: Marta full_name: Aranda, Marta last_name: Aranda - first_name: Fernando full_name: Nodal, Fernando id: 8ad43d5a-1ffe-11ee-8b67-8176f59de781 last_name: Nodal orcid: 0009-0006-4119-4376 - first_name: Lorena full_name: Dieguez, Lorena last_name: Dieguez - first_name: Sara full_name: Abalde-Cela, Sara last_name: Abalde-Cela citation: ama: 'Quintero S, Relvas M, Aranda M, Nodal F, Dieguez L, Abalde-Cela S. Portable Raman platform for SERS droplets microfludics. In: 2024 International Conference on Optical MEMS and Nanophotonics. Institute of Electrical and Electronics Engineers; 2024. doi:10.1109/OMN61224.2024.10685279' apa: 'Quintero, S., Relvas, M., Aranda, M., Nodal, F., Dieguez, L., & Abalde-Cela, S. (2024). Portable Raman platform for SERS droplets microfludics. In 2024 International Conference on Optical MEMS and Nanophotonics. San Sebastian, Spain: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/OMN61224.2024.10685279' chicago: Quintero, Sergio, Maria Relvas, Marta Aranda, Fernando Nodal, Lorena Dieguez, and Sara Abalde-Cela. “Portable Raman Platform for SERS Droplets Microfludics.” In 2024 International Conference on Optical MEMS and Nanophotonics. Institute of Electrical and Electronics Engineers, 2024. https://doi.org/10.1109/OMN61224.2024.10685279. ieee: S. Quintero, M. Relvas, M. Aranda, F. Nodal, L. Dieguez, and S. Abalde-Cela, “Portable Raman platform for SERS droplets microfludics,” in 2024 International Conference on Optical MEMS and Nanophotonics, San Sebastian, Spain, 2024. ista: 'Quintero S, Relvas M, Aranda M, Nodal F, Dieguez L, Abalde-Cela S. 2024. Portable Raman platform for SERS droplets microfludics. 2024 International Conference on Optical MEMS and Nanophotonics. OMN: Conference on Optical MEMS and Nanophotonics.' mla: Quintero, Sergio, et al. “Portable Raman Platform for SERS Droplets Microfludics.” 2024 International Conference on Optical MEMS and Nanophotonics, Institute of Electrical and Electronics Engineers, 2024, doi:10.1109/OMN61224.2024.10685279. short: S. Quintero, M. Relvas, M. Aranda, F. Nodal, L. Dieguez, S. Abalde-Cela, in:, 2024 International Conference on Optical MEMS and Nanophotonics, Institute of Electrical and Electronics Engineers, 2024. conference: end_date: 2024-08-01 location: San Sebastian, Spain name: 'OMN: Conference on Optical MEMS and Nanophotonics' start_date: 2024-07-28 date_created: 2024-10-20T22:02:07Z date_published: 2024-09-27T00:00:00Z date_updated: 2025-09-08T14:19:49Z day: '27' department: - _id: GradSch doi: 10.1109/OMN61224.2024.10685279 external_id: isi: - '001327768000060' isi: 1 language: - iso: eng month: '09' oa_version: None publication: 2024 International Conference on Optical MEMS and Nanophotonics publication_identifier: eissn: - 2160-5041 isbn: - '9798350384925' issn: - 2160-5033 publication_status: published publisher: Institute of Electrical and Electronics Engineers quality_controlled: '1' scopus_import: '1' status: public title: Portable Raman platform for SERS droplets microfludics type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- OA_type: closed access _id: '18482' abstract: - lang: eng text: "This paper is dedicated to an optimization problem. Let A, B ⊂ Rn be compact convex sets. Consider the minimal number t0 > 0 such that t0B covers A after a shift to a vector x0 ∈ \r\nRn. The goal is to find t0 and x0. In the special case of B being a unit ball centered at zero, x0 and t0 are known as the Chebyshev center and the Chebyshev radius of A. This paper focuses on the case in which A and B are defined with their black-box support functions. An algorithm for solving such problems efficiently is suggested. The algorithm has a superlinear convergence rate, and it can solve hundred-dimensional test problems in a reasonable time, but some additional conditions on A and B are required to guarantee the presence of convergence. Additionally, the behavior of the algorithm for a simple special case is investigated, which leads to a number of theoretical results. Perturbations of this special case are also studied." acknowledgement: The author is grateful to Maxim Balashov for setting the problem, providing useful literature, important discussions and text review. Also, I thank Dmitry Tsarev and Kseniia Petukhova for meaningful talks and support. article_processing_charge: No article_type: original author: - first_name: Pavel full_name: Arkhipov, Pavel id: b25f2ab2-1fed-11ee-8599-fe02d211784f last_name: Arkhipov citation: ama: Arkhipov P. An algorithm for finding the generalized Chebyshev center of sets defined via their support functions. Automation and Remote Control. 2024;85(6):522-532. doi:10.1134/S0005117924060031 apa: Arkhipov, P. (2024). An algorithm for finding the generalized Chebyshev center of sets defined via their support functions. Automation and Remote Control. Springer Nature. https://doi.org/10.1134/S0005117924060031 chicago: Arkhipov, Pavel. “An Algorithm for Finding the Generalized Chebyshev Center of Sets Defined via Their Support Functions.” Automation and Remote Control. Springer Nature, 2024. https://doi.org/10.1134/S0005117924060031. ieee: P. Arkhipov, “An algorithm for finding the generalized Chebyshev center of sets defined via their support functions,” Automation and Remote Control, vol. 85, no. 6. Springer Nature, pp. 522–532, 2024. ista: Arkhipov P. 2024. An algorithm for finding the generalized Chebyshev center of sets defined via their support functions. Automation and Remote Control. 85(6), 522–532. mla: Arkhipov, Pavel. “An Algorithm for Finding the Generalized Chebyshev Center of Sets Defined via Their Support Functions.” Automation and Remote Control, vol. 85, no. 6, Springer Nature, 2024, pp. 522–32, doi:10.1134/S0005117924060031. short: P. Arkhipov, Automation and Remote Control 85 (2024) 522–532. corr_author: '1' date_created: 2024-10-27T23:01:45Z date_published: 2024-06-01T00:00:00Z date_updated: 2025-09-08T14:27:08Z day: '01' department: - _id: GradSch doi: 10.1134/S0005117924060031 external_id: isi: - '001338721700007' intvolume: ' 85' isi: 1 issue: '6' language: - iso: eng month: '06' oa_version: None page: 522-532 publication: Automation and Remote Control publication_identifier: eissn: - 1608-3032 issn: - 0005-1179 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: An algorithm for finding the generalized Chebyshev center of sets defined via their support functions type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 85 year: '2024' ... --- OA_place: publisher OA_type: gold _id: '18847' abstract: - lang: eng text: "Machine Learning and AI have the potential to transform data-driven\r\nscientific discovery, enabling accurate predictions for several scientific\r\nphenomena. As many scientific questions are inherently causal, this paper looks\r\nat the causal inference task of treatment effect estimation, where the outcome\r\nof interest is recorded in high-dimensional observations in a Randomized\r\nControlled Trial (RCT). Despite being the simplest possible causal setting and\r\na perfect fit for deep learning, we theoretically find that many common choices\r\nin the literature may lead to biased estimates. To test the practical impact of\r\nthese considerations, we recorded ISTAnt, the first real-world benchmark for\r\ncausal inference downstream tasks on high-dimensional observations as an RCT\r\nstudying how garden ants (Lasius neglectus) respond to microparticles applied\r\nonto their colony members by hygienic grooming. Comparing 6 480 models\r\nfine-tuned from state-of-the-art visual backbones, we find that the sampling\r\nand modeling choices significantly affect the accuracy of the causal estimate,\r\nand that classification accuracy is not a proxy thereof. We further validated\r\nthe analysis, repeating it on a synthetically generated visual data set\r\ncontrolling the causal model. Our results suggest that future benchmarks should\r\ncarefully consider real downstream scientific questions, especially causal\r\nones. Further, we highlight guidelines for representation learning methods to\r\nhelp answer causal questions in the sciences." acknowledgement: We thank Piersilvio De Bartolomeis, and the full Causal Learning and Artificial Intelligence (CLAI) group at ISTA for the extremely helpful discussions. Riccardo Cadei was supported by a Google Research Scholar Award and a Google Initiated Gift to Francesco Locatello. We thank the Social Immunity team at ISTA particularly Michaela Hönigsberger and Wilfrid Jean Louis, for supporting the ecological experiment and Farnaz Beikzadeh Abbasi, Luisa Fiebig and Martin Estermann for annotating ant behavior in ISTAnt. article_processing_charge: No arxiv: 1 author: - first_name: Riccardo full_name: Cadei, Riccardo id: 0fa8b76f-72f0-11ef-b75a-a5da96e5ad6b last_name: Cadei - first_name: Lukas full_name: Lindorfer, Lukas id: 85f0e6d3-06b3-11ec-8982-8c5049fa4455 last_name: Lindorfer - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Cordelia full_name: Schmid, Cordelia last_name: Schmid - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 citation: ama: 'Cadei R, Lindorfer L, Cremer S, Schmid C, Locatello F. Smoke and mirrors in causal downstream tasks. In: ICML 2024 Workshop AI4Science. Vol 38. Curran Associates; 2024.' apa: Cadei, R., Lindorfer, L., Cremer, S., Schmid, C., & Locatello, F. (2024). Smoke and mirrors in causal downstream tasks. In ICML 2024 Workshop AI4Science (Vol. 38). Curran Associates. chicago: Cadei, Riccardo, Lukas Lindorfer, Sylvia Cremer, Cordelia Schmid, and Francesco Locatello. “Smoke and Mirrors in Causal Downstream Tasks.” In ICML 2024 Workshop AI4Science, Vol. 38. Curran Associates, 2024. ieee: R. Cadei, L. Lindorfer, S. Cremer, C. Schmid, and F. Locatello, “Smoke and mirrors in causal downstream tasks,” in ICML 2024 Workshop AI4Science, 2024, vol. 38. ista: 'Cadei R, Lindorfer L, Cremer S, Schmid C, Locatello F. 2024. Smoke and mirrors in causal downstream tasks. ICML 2024 Workshop AI4Science. ICML: International Conference on Machine Learning vol. 38.' mla: Cadei, Riccardo, et al. “Smoke and Mirrors in Causal Downstream Tasks.” ICML 2024 Workshop AI4Science, vol. 38, Curran Associates, 2024. short: R. Cadei, L. Lindorfer, S. Cremer, C. Schmid, F. Locatello, in:, ICML 2024 Workshop AI4Science, Curran Associates, 2024. conference: end_date: 2024-07-26 name: 'ICML: International Conference on Machine Learning' start_date: 2024-07-26 corr_author: '1' date_created: 2025-01-14T07:27:26Z date_published: 2024-09-25T00:00:00Z date_updated: 2025-07-10T11:51:50Z day: '25' ddc: - '000' - '570' department: - _id: SyCr - _id: FrLo - _id: GradSch external_id: arxiv: - '2405.17151' file: - access_level: open_access checksum: beedf05388bbdb7ddda81ec3d5ec7026 content_type: application/pdf creator: dernst date_created: 2025-01-27T11:42:24Z date_updated: 2025-01-27T11:42:24Z file_id: '18896' file_name: 2024_ICML_Cadei.pdf file_size: 4453014 relation: main_file success: 1 file_date_updated: 2025-01-27T11:42:24Z has_accepted_license: '1' intvolume: ' 38' language: - iso: eng month: '09' oa: 1 oa_version: Published Version publication: ICML 2024 Workshop AI4Science publication_status: published publisher: Curran Associates quality_controlled: '1' related_material: link: - relation: software url: https://github.com/CausalLearningAI/ISTAnt record: - id: '18895' relation: research_data status: public - id: '19509' relation: is_continued_by status: for_moderation scopus_import: '1' status: public title: Smoke and mirrors in causal downstream tasks tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 38 year: '2024' ... --- OA_place: publisher OA_type: gold _id: '18875' abstract: - lang: eng text: Current state-of-the-art methods for differentially private model training are based on matrix factorization techniques. However, these methods suffer from high computational overhead because they require numerically solving a demanding optimization problem to determine an approximately optimal factorization prior to the actual model training. In this work, we present a new matrix factorization approach, BSR, which overcomes this computational bottleneck. By exploiting properties of the standard matrix square root, BSR allows to efficiently handle also large-scale problems. For the key scenario of stochastic gradient descent with momentum and weight decay, we even derive analytical expressions for BSR that render the computational overhead negligible. We prove bounds on the approximation quality that hold both in the centralized and in the federated learning setting. Our numerical experiments demonstrate that models trained using BSR perform on par with the best existing methods, while completely avoiding their computational overhead. alternative_title: - Advances in Neural Information Processing Systems article_processing_charge: No arxiv: 1 author: - first_name: Nikita full_name: Kalinin, Nikita id: 4b14526e-14d2-11ed-ba64-c14c9553d137 last_name: Kalinin - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Kalinin N, Lampert C. Banded square root matrix factorization for differentially private model training. In: 38th Annual Conference on Neural Information Processing Systems. Vol 37. Neural Information Processing Systems Foundation; 2024.' apa: 'Kalinin, N., & Lampert, C. (2024). Banded square root matrix factorization for differentially private model training. In 38th Annual Conference on Neural Information Processing Systems (Vol. 37). Vancouver, Canada: Neural Information Processing Systems Foundation.' chicago: Kalinin, Nikita, and Christoph Lampert. “Banded Square Root Matrix Factorization for Differentially Private Model Training.” In 38th Annual Conference on Neural Information Processing Systems, Vol. 37. Neural Information Processing Systems Foundation, 2024. ieee: N. Kalinin and C. Lampert, “Banded square root matrix factorization for differentially private model training,” in 38th Annual Conference on Neural Information Processing Systems, Vancouver, Canada, 2024, vol. 37. ista: 'Kalinin N, Lampert C. 2024. Banded square root matrix factorization for differentially private model training. 38th Annual Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 37.' mla: Kalinin, Nikita, and Christoph Lampert. “Banded Square Root Matrix Factorization for Differentially Private Model Training.” 38th Annual Conference on Neural Information Processing Systems, vol. 37, Neural Information Processing Systems Foundation, 2024. short: N. Kalinin, C. Lampert, in:, 38th Annual Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2024. conference: end_date: 2024-12-16 location: Vancouver, Canada name: 'NeurIPS: Neural Information Processing Systems' start_date: 2024-12-16 corr_author: '1' date_created: 2025-01-24T17:58:16Z date_published: 2024-12-01T00:00:00Z date_updated: 2025-05-14T11:34:20Z day: '01' ddc: - '000' department: - _id: GradSch - _id: ChLa external_id: arxiv: - '2405.13763' file: - access_level: open_access checksum: a216cab8eddc1fe7840aede0e2c0d41e content_type: application/pdf creator: dernst date_created: 2025-01-27T09:52:15Z date_updated: 2025-01-27T09:52:15Z file_id: '18888' file_name: 2024_NeurIPS_Nikita.pdf file_size: 1144656 relation: main_file success: 1 file_date_updated: 2025-01-27T09:52:15Z has_accepted_license: '1' intvolume: ' 37' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: 38th Annual Conference on Neural Information Processing Systems publication_identifier: eissn: - 1049-5258 publication_status: published publisher: Neural Information Processing Systems Foundation quality_controlled: '1' scopus_import: '1' status: public title: Banded square root matrix factorization for differentially private model training tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 37 year: '2024' ... --- OA_place: repository OA_type: green _id: '18890' abstract: - lang: eng text: Deep Neural Collapse (DNC) refers to the surprisingly rigid structure of the data representations in the final layers of Deep Neural Networks (DNNs). Though the phenomenon has been measured in a variety of settings, its emergence is typically explained via data-agnostic approaches, such as the unconstrained features model. In this work, we introduce a data-dependent setting where DNC forms due to feature learning through the average gradient outer product (AGOP). The AGOP is defined with respect to a learned predictor and is equal to the uncentered covariance matrix of its input-output gradients averaged over the training dataset. The Deep Recursive Feature Machine (Deep RFM) is a method that constructs a neural network by iteratively mapping the data with the AGOP and applying an untrained random feature map. We demonstrate empirically that DNC occurs in Deep RFM across standard settings as a consequence of the projection with the AGOP matrix computed at each layer. Further, we theoretically explain DNC in Deep RFM in an asymptotic setting and as a result of kernel learning. We then provide evidence that this mechanism holds for neural networks more generally. In particular, we show that the right singular vectors and values of the weights can be responsible for the majority of within-class variability collapse for DNNs trained in the feature learning regime. As observed in recent work, this singular structure is highly correlated with that of the AGOP. acknowledgement: 'We acknowledge support from the National Science Foundation (NSF) and the Simons Foundation for the Collaboration on the Theoretical Foundations of Deep Learning through awards DMS-2031883 and #814639 as well as the TILOS institute (NSF CCF-2112665). This work used the programs (1) XSEDE (Extreme science and engineering discovery environment) which is supported by NSF grant numbers ACI-1548562, and (2) ACCESS (Advanced cyberinfrastructure coordination ecosystem: services & support) which is supported by NSF grants numbers #2138259, #2138286, #2138307, #2137603, and #2138296. Specifically, we used the resources from SDSC Expanse GPU compute nodes, and NCSA Delta system, via allocations TG-CIS220009. Marco Mondelli is supported by the 2019 Lopez-Loreta prize. We also acknowledge useful feedback from anonymous reviewers. ' alternative_title: - Advances in Neural Information Processing Systems article_processing_charge: No arxiv: 1 author: - first_name: Daniel full_name: Beaglehole, Daniel last_name: Beaglehole - first_name: Peter full_name: Súkeník, Peter id: d64d6a8d-eb8e-11eb-b029-96fd216dec3c last_name: Súkeník - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Mikhail full_name: Belkin, Mikhail last_name: Belkin citation: ama: 'Beaglehole D, Súkeník P, Mondelli M, Belkin M. Average gradient outer product as a mechanism for deep neural collapse. In: 38th Annual Conference on Neural Information Processing Systems. Vol 37. Neural Information Processing Systems Foundation; 2024.' apa: 'Beaglehole, D., Súkeník, P., Mondelli, M., & Belkin, M. (2024). Average gradient outer product as a mechanism for deep neural collapse. In 38th Annual Conference on Neural Information Processing Systems (Vol. 37). Vancouver, Canada: Neural Information Processing Systems Foundation.' chicago: Beaglehole, Daniel, Peter Súkeník, Marco Mondelli, and Mikhail Belkin. “Average Gradient Outer Product as a Mechanism for Deep Neural Collapse.” In 38th Annual Conference on Neural Information Processing Systems, Vol. 37. Neural Information Processing Systems Foundation, 2024. ieee: D. Beaglehole, P. Súkeník, M. Mondelli, and M. Belkin, “Average gradient outer product as a mechanism for deep neural collapse,” in 38th Annual Conference on Neural Information Processing Systems, Vancouver, Canada, 2024, vol. 37. ista: 'Beaglehole D, Súkeník P, Mondelli M, Belkin M. 2024. Average gradient outer product as a mechanism for deep neural collapse. 38th Annual Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 37.' mla: Beaglehole, Daniel, et al. “Average Gradient Outer Product as a Mechanism for Deep Neural Collapse.” 38th Annual Conference on Neural Information Processing Systems, vol. 37, Neural Information Processing Systems Foundation, 2024. short: D. Beaglehole, P. Súkeník, M. Mondelli, M. Belkin, in:, 38th Annual Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2024. conference: end_date: 2024-12-16 location: Vancouver, Canada name: 'NeurIPS: Neural Information Processing Systems' start_date: 2024-12-16 corr_author: '1' date_created: 2025-01-27T11:11:40Z date_published: 2024-12-01T00:00:00Z date_updated: 2025-05-14T11:29:45Z day: '01' department: - _id: GradSch - _id: MaMo external_id: arxiv: - '2402.13728' intvolume: ' 37' language: - iso: eng main_file_link: - open_access: '1' url: https://openreview.net/forum?id=lJ1jdl2K9k month: '12' oa: 1 oa_version: Preprint project: - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli publication: 38th Annual Conference on Neural Information Processing Systems publication_identifier: eissn: - 1049-5258 publication_status: published publisher: Neural Information Processing Systems Foundation quality_controlled: '1' scopus_import: '1' status: public title: Average gradient outer product as a mechanism for deep neural collapse type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 37 year: '2024' ... --- OA_place: publisher OA_type: gold _id: '18891' abstract: - lang: eng text: "Deep neural networks (DNNs) exhibit a surprising structure in their final layer\r\nknown as neural collapse (NC), and a growing body of works has currently investigated the propagation of neural collapse to earlier layers of DNNs – a phenomenon\r\ncalled deep neural collapse (DNC). However, existing theoretical results are restricted to special cases: linear models, only two layers or binary classification.\r\nIn contrast, we focus on non-linear models of arbitrary depth in multi-class classification and reveal a surprising qualitative shift. As soon as we go beyond two\r\nlayers or two classes, DNC stops being optimal for the deep unconstrained features\r\nmodel (DUFM) – the standard theoretical framework for the analysis of collapse.\r\nThe main culprit is a low-rank bias of multi-layer regularization schemes: this bias\r\nleads to optimal solutions of even lower rank than the neural collapse. We support\r\nour theoretical findings with experiments on both DUFM and real data, which show\r\nthe emergence of the low-rank structure in the solution found by gradient descent." acknowledged_ssus: - _id: ScienComp acknowledgement: Marco Mondelli is partially supported by the 2019 Lopez-Loreta prize. This research was supported by the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp). alternative_title: - Advances in Neural Information Processing Systems article_processing_charge: No arxiv: 1 author: - first_name: Peter full_name: Súkeník, Peter id: d64d6a8d-eb8e-11eb-b029-96fd216dec3c last_name: Súkeník - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 citation: ama: 'Súkeník P, Lampert C, Mondelli M. Neural collapse versus low-rank bias: Is deep neural collapse really optimal? In: 38th Annual Conference on Neural Information Processing Systems. Vol 37. Neural Information Processing Systems Foundation; 2024.' apa: 'Súkeník, P., Lampert, C., & Mondelli, M. (2024). Neural collapse versus low-rank bias: Is deep neural collapse really optimal? In 38th Annual Conference on Neural Information Processing Systems (Vol. 37). Vancouver, Canada: Neural Information Processing Systems Foundation.' chicago: 'Súkeník, Peter, Christoph Lampert, and Marco Mondelli. “Neural Collapse versus Low-Rank Bias: Is Deep Neural Collapse Really Optimal?” In 38th Annual Conference on Neural Information Processing Systems, Vol. 37. Neural Information Processing Systems Foundation, 2024.' ieee: 'P. Súkeník, C. Lampert, and M. Mondelli, “Neural collapse versus low-rank bias: Is deep neural collapse really optimal?,” in 38th Annual Conference on Neural Information Processing Systems, Vancouver, Canada, 2024, vol. 37.' ista: 'Súkeník P, Lampert C, Mondelli M. 2024. Neural collapse versus low-rank bias: Is deep neural collapse really optimal? 38th Annual Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 37.' mla: 'Súkeník, Peter, et al. “Neural Collapse versus Low-Rank Bias: Is Deep Neural Collapse Really Optimal?” 38th Annual Conference on Neural Information Processing Systems, vol. 37, Neural Information Processing Systems Foundation, 2024.' short: P. Súkeník, C. Lampert, M. Mondelli, in:, 38th Annual Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2024. conference: end_date: 2024-12-16 location: Vancouver, Canada name: 'NeurIPS: Neural Information Processing Systems' start_date: 2024-12-16 corr_author: '1' date_created: 2025-01-27T11:15:18Z date_published: 2024-12-01T00:00:00Z date_updated: 2025-06-04T07:19:21Z day: '01' ddc: - '000' department: - _id: GradSch - _id: MaMo - _id: ChLa external_id: arxiv: - '2405.14468' file: - access_level: open_access checksum: b7b79f1ea3ac1e9e11b3d91faaeb0780 content_type: application/pdf creator: dernst date_created: 2025-02-04T08:11:25Z date_updated: 2025-02-04T08:11:25Z file_id: '18989' file_name: 2024_NeurIPS_Sukenik.pdf file_size: 1784118 relation: main_file success: 1 file_date_updated: 2025-02-04T08:11:25Z has_accepted_license: '1' intvolume: ' 37' language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli publication: 38th Annual Conference on Neural Information Processing Systems publication_status: published publisher: Neural Information Processing Systems Foundation quality_controlled: '1' status: public title: 'Neural collapse versus low-rank bias: Is deep neural collapse really optimal?' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 37 year: '2024' ... --- OA_place: repository OA_type: gold _id: '18895' abstract: - lang: eng text: 'ISTAnt is a new ecological dataset for social immunity and represents the first real-world benchmark for causal inference downstream tasks on high-dimensional observations. It analyzes grooming behavior in the ant Lasius neglectus in groups of three worker ants. The workers for the experiment were obtained from their laboratory stock colony, which had been collected from the field in 2022 in the Botanical Garden Jena, Germany. Ant collection and all experimental work were performed in compliance with international, national and institutional regulations and ethical guidelines. For the experiment, the body surface of one of the three ants was treated with a suspension of either of two microparticle types (diameter ~5 µm) to induce grooming by the two nestmates, which were individually color-coded by application of a dot of blue or orange paint, respectively. The three ants were housed in small plastic containers (diameter 28mm, height 30mm) with moistened, plastered ground and the interior walls covered with PTFE (polytetrafluoroethane) to hamper climbing by the ants. Filming occurred in a temperature- and humidity-controlled room at 23°C within a custom-made filming box with controlled lighting and ventilation conditions. We set up nine ant groups at a time (always containing both treatments) and placed them randomly on positions 1-9 marked on the floor in a 3x3 grid, about 3mm from each other. The experiment was performed on two consecutive days. Videos were acquired using a USB camera (FLIR blackfly S BFS-U3-120S4C, Teledyne FLIR) with a high-performance lens (HP Series 25mm Focal Length, Edmund optics 86-572) in OBS studio 29.0.0 \citep{bailey2017obs} at a framerate of 30 FPS and a resolution of 2500x2500 pixels. From each original video (105x105 mm), we generated nine individual videos .mkv (each ~32x32 mm, 770x770 pixels) by determining exact coordinates per container from one frame in GIMP 2.10.36 and cropping of the videos with FFmpeg 6.1.1. Annotation was performed over two consecutive days by three observers who had not been involved in the experimental setup or recording and were unaware of the treatment assignments to ensure bias-free behavioral annotation. They annotated the behavior of the ants during video observations, using custom-made software that saves the start and end frames of behaviors marked in a .csv file (see ''annotations'' folder). In one of the videos, one of the nestmates'' legs got inadvertently stuck to its body surface during the color-coding, interfering with its behavior, so the video was discarded. This left 44 videos from 5 independent setups (n=24 of treatment 1 and n=20 of treatment 2) of 10 minutes each for a total of 792 000 annotated frames (see ''video'' folder). For each video, we provide the following information: the number of the set to which it belongs (1-5); the number of the position within the set reflecting the position of the ant group under the camera (1-9), for which we also provide ‘coordinates’ in the 3x3 grid (taking values -1/0/1 for both X and Y axis); treatment (1 or 2); the hour of the day when the recording was started (in 24h CEST); experimental day (A or B); the top left coordinate of the cropping square from the original video (CropX/CropY); the person annotating the video (given as A, B, C); the date of annotation (1: first day, 2: second day) and in which order the videos were annotated by each person, both reflecting a possible training effect of the person (see ''experiments_settings.csv'' file).' article_processing_charge: No author: - first_name: Riccardo full_name: Cadei, Riccardo id: 0fa8b76f-72f0-11ef-b75a-a5da96e5ad6b last_name: Cadei - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Sylvia M full_name: Cremer, Sylvia M id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Lukas full_name: Lindorfer, Lukas id: 85f0e6d3-06b3-11ec-8982-8c5049fa4455 last_name: Lindorfer - first_name: Cordelia full_name: Schmid, Cordelia last_name: Schmid citation: ama: Cadei R, Locatello F, Cremer S, Lindorfer L, Schmid C. ISTAnt. 2024. doi:10.6084/M9.FIGSHARE.26484934.V2 apa: Cadei, R., Locatello, F., Cremer, S., Lindorfer, L., & Schmid, C. (2024). ISTAnt. Institute of Science and Technology Austria. https://doi.org/10.6084/M9.FIGSHARE.26484934.V2 chicago: Cadei, Riccardo, Francesco Locatello, Sylvia Cremer, Lukas Lindorfer, and Cordelia Schmid. “ISTAnt.” Institute of Science and Technology Austria, 2024. https://doi.org/10.6084/M9.FIGSHARE.26484934.V2. ieee: R. Cadei, F. Locatello, S. Cremer, L. Lindorfer, and C. Schmid, “ISTAnt.” Institute of Science and Technology Austria, 2024. ista: Cadei R, Locatello F, Cremer S, Lindorfer L, Schmid C. 2024. ISTAnt, Institute of Science and Technology Austria, 10.6084/M9.FIGSHARE.26484934.V2. mla: Cadei, Riccardo, et al. ISTAnt. Institute of Science and Technology Austria, 2024, doi:10.6084/M9.FIGSHARE.26484934.V2. short: R. Cadei, F. Locatello, S. Cremer, L. Lindorfer, C. Schmid, (2024). corr_author: '1' date_created: 2025-01-27T11:45:43Z date_published: 2024-10-23T00:00:00Z date_updated: 2025-01-27T11:58:38Z day: '23' ddc: - '570' department: - _id: SyCr - _id: FrLo - _id: GradSch doi: 10.6084/M9.FIGSHARE.26484934.V2 main_file_link: - open_access: '1' url: https://10.6084/M9.FIGSHARE.26484934.V2 month: '10' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '18847' relation: used_in_publication status: public status: public title: ISTAnt type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ...