--- _id: '17476' abstract: - lang: eng text: "Lead halide perovskites have recently been reported to demonstrate an exceptionally high nonlinear (Kerr) refractive index n2 of up to 10−8cm2/W in CH3⁢NH3⁢PbBr3. Other researchers, however, observe different, substantially more conservative numbers. In order to resolve this disagreement, the nonlinear Kerr index of a bulk sample of lead halide perovskite was measured directly by means of an interferometer. This approach has many advantages as compared to the more standard z-scan technique. In particular, this method allows studying the induced changes to the refractive index in a time-resolved manner, thus enabling to separate the different contributions to \U0001D45B2. The extracted \U0001D45B2 values for CsPbBr3 and MAPbBr3 at \U0001D706≈1µ⁢m are \U0001D45B2=+2.1×10−14cm2/W and \U0001D45B2=+6×10−15cm2/W, respectively. Hence, these values are substantially lower than what has been indicated in most of the previous reports, implying the latter one should be regarded with great care." acknowledgement: "We gratefully acknowledge the assistance of Prof. John\r\nDudley." article_number: '085403' article_processing_charge: No article_type: original author: - first_name: Dusan full_name: Lorenc, Dusan id: 40D8A3E6-F248-11E8-B48F-1D18A9856A87 last_name: Lorenc - first_name: Ayan full_name: Zhumekenov, Ayan last_name: Zhumekenov - first_name: Osman M. full_name: Bakr, Osman M. last_name: Bakr - first_name: Zhanybek full_name: Alpichshev, Zhanybek id: 45E67A2A-F248-11E8-B48F-1D18A9856A87 last_name: Alpichshev orcid: 0000-0002-7183-5203 citation: ama: 'Lorenc D, Zhumekenov A, Bakr OM, Alpichshev Z. No extraordinary χ(3) in lead-halide perovskites: Placing an upper bound on Kerr nonlinearity by means of time-resolved interferometry. Physical Review Materials. 2024;8(8). doi:10.1103/PhysRevMaterials.8.085403' apa: 'Lorenc, D., Zhumekenov, A., Bakr, O. M., & Alpichshev, Z. (2024). No extraordinary χ(3) in lead-halide perovskites: Placing an upper bound on Kerr nonlinearity by means of time-resolved interferometry. Physical Review Materials. American Physical Society. https://doi.org/10.1103/PhysRevMaterials.8.085403' chicago: 'Lorenc, Dusan, Ayan Zhumekenov, Osman M. Bakr, and Zhanybek Alpichshev. “No Extraordinary χ(3) in Lead-Halide Perovskites: Placing an Upper Bound on Kerr Nonlinearity by Means of Time-Resolved Interferometry.” Physical Review Materials. American Physical Society, 2024. https://doi.org/10.1103/PhysRevMaterials.8.085403.' ieee: 'D. Lorenc, A. Zhumekenov, O. M. Bakr, and Z. Alpichshev, “No extraordinary χ(3) in lead-halide perovskites: Placing an upper bound on Kerr nonlinearity by means of time-resolved interferometry,” Physical Review Materials, vol. 8, no. 8. American Physical Society, 2024.' ista: 'Lorenc D, Zhumekenov A, Bakr OM, Alpichshev Z. 2024. No extraordinary χ(3) in lead-halide perovskites: Placing an upper bound on Kerr nonlinearity by means of time-resolved interferometry. Physical Review Materials. 8(8), 085403.' mla: 'Lorenc, Dusan, et al. “No Extraordinary χ(3) in Lead-Halide Perovskites: Placing an Upper Bound on Kerr Nonlinearity by Means of Time-Resolved Interferometry.” Physical Review Materials, vol. 8, no. 8, 085403, American Physical Society, 2024, doi:10.1103/PhysRevMaterials.8.085403.' short: D. Lorenc, A. Zhumekenov, O.M. Bakr, Z. Alpichshev, Physical Review Materials 8 (2024). corr_author: '1' date_created: 2024-09-01T22:01:08Z date_published: 2024-08-23T00:00:00Z date_updated: 2025-09-08T09:06:34Z day: '23' department: - _id: ZhAl doi: 10.1103/PhysRevMaterials.8.085403 external_id: isi: - '001299497800001' intvolume: ' 8' isi: 1 issue: '8' language: - iso: eng month: '08' oa_version: None publication: Physical Review Materials publication_identifier: eissn: - 2475-9953 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: 'No extraordinary χ(3) in lead-halide perovskites: Placing an upper bound on Kerr nonlinearity by means of time-resolved interferometry' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 8 year: '2024' ... --- _id: '17481' abstract: - lang: eng text: "Phase-field models such as the Allen–Cahn equation may give rise to the formation and evolution of geometric shapes, a phenomenon that may be analyzed rigorously in suitable scaling regimes. In its sharp-interface limit, the vectorial Allen–Cahn equation with a potential with N≥3 distinct minima has been conjectured to describe the evolution of branched interfaces by multiphase mean curvature flow. In the present work, we give a rigorous proof for this statement in two and three ambient dimensions and for a suitable class of potentials: as long as a strong solution to multiphase mean curvature flow exists, solutions to the vectorial Allen–Cahn equation with well-prepared initial data converge towards multiphase mean curvature flow in the limit of vanishing interface width parameter ε↘0. We even establish the rate of convergence O(ε \r\n1/2\r\n ). Our approach is based on the gradient-flow structure of the Allen–Cahn equation and its limiting motion: building on the recent concept of “gradient-flow calibrations” for multiphase mean curvature flow, we introduce a notion of relative entropy for the vectorial Allen–Cahn equation with multi-well potential. This enables us to overcome the limitations of other approaches, e.g. avoiding the need for a stability analysis of the Allen–Cahn operator or additional convergence hypotheses for the energy at positive times." acknowledgement: "The authors thank Sebastian Hensel for useful and helpful commentson the first draft of this work.\r\nThis project has received funding from the European Research Council (ERC)\r\nunder the European Union’s Horizon 2020 research and innovation programme (grant\r\nagreement no. 948819." article_processing_charge: Yes article_type: original author: - first_name: Julian L full_name: Fischer, Julian L id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X - first_name: Alice full_name: Marveggio, Alice id: 25647992-AA84-11E9-9D75-8427E6697425 last_name: Marveggio citation: ama: Fischer JL, Marveggio A. Quantitative convergence of the vectorial Allen–Cahn equation towards multiphase mean curvature flow. Annales de l’Institut Henri Poincare C. 2024;41(5):1117-1178. doi:10.4171/AIHPC/109 apa: Fischer, J. L., & Marveggio, A. (2024). Quantitative convergence of the vectorial Allen–Cahn equation towards multiphase mean curvature flow. Annales de l’Institut Henri Poincare C. EMS Press. https://doi.org/10.4171/AIHPC/109 chicago: Fischer, Julian L, and Alice Marveggio. “Quantitative Convergence of the Vectorial Allen–Cahn Equation towards Multiphase Mean Curvature Flow.” Annales de l’Institut Henri Poincare C. EMS Press, 2024. https://doi.org/10.4171/AIHPC/109. ieee: J. L. Fischer and A. Marveggio, “Quantitative convergence of the vectorial Allen–Cahn equation towards multiphase mean curvature flow,” Annales de l’Institut Henri Poincare C, vol. 41, no. 5. EMS Press, pp. 1117–1178, 2024. ista: Fischer JL, Marveggio A. 2024. Quantitative convergence of the vectorial Allen–Cahn equation towards multiphase mean curvature flow. Annales de l’Institut Henri Poincare C. 41(5), 1117–1178. mla: Fischer, Julian L., and Alice Marveggio. “Quantitative Convergence of the Vectorial Allen–Cahn Equation towards Multiphase Mean Curvature Flow.” Annales de l’Institut Henri Poincare C, vol. 41, no. 5, EMS Press, 2024, pp. 1117–78, doi:10.4171/AIHPC/109. short: J.L. Fischer, A. Marveggio, Annales de l’Institut Henri Poincare C 41 (2024) 1117–1178. corr_author: '1' date_created: 2024-09-01T22:01:09Z date_published: 2024-01-24T00:00:00Z date_updated: 2025-09-08T09:11:01Z day: '24' ddc: - '510' department: - _id: JuFi doi: 10.4171/AIHPC/109 ec_funded: 1 external_id: isi: - '001293853900003' file: - access_level: open_access checksum: b5ad02d9abd5b4701269cd1ad0a1cc8f content_type: application/pdf creator: dernst date_created: 2024-09-09T07:46:42Z date_updated: 2024-09-09T07:46:42Z file_id: '17923' file_name: 2024_AnnInstHPoincare_Fischer.pdf file_size: 1348896 relation: main_file success: 1 file_date_updated: 2024-09-09T07:46:42Z has_accepted_license: '1' intvolume: ' 41' isi: 1 issue: '5' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 1117-1178 project: - _id: 0aa76401-070f-11eb-9043-b5bb049fa26d call_identifier: H2020 grant_number: '948819' name: Bridging Scales in Random Materials publication: Annales de l'Institut Henri Poincare C publication_identifier: eissn: - 1873-1430 issn: - 0294-1449 publication_status: published publisher: EMS Press quality_controlled: '1' related_material: record: - id: '14597' relation: earlier_version status: public scopus_import: '1' status: public title: Quantitative convergence of the vectorial Allen–Cahn equation towards multiphase mean curvature flow 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: 41 year: '2024' ... --- OA_place: publisher _id: '17485' abstract: - lang: eng text: "Large language models (LLMs) have made tremendous progress in the past few years, from being able to generate coherent text to matching or surpassing humans in a wide variety of creative, knowledge or reasoning tasks. Much of this can be attributed to massively increased scale, both in the size of the model as well as the amount of training data, from 100s of millions to 100s of billions, or even trillions. This trend is expected to continue, which, although exciting, also raises major practical concerns. Already today's 100+ billion parameter LLMs require top-of-the-line hardware just to run. Hence, it is clear that sustaining these developments will require significant efficiency advances.\r\n\r\nHistorically, one of the most practical ways of improving model efficiency has been compression, especially in the form of sparsity or quantization. While this has been studied extensively in the past, existing accurate methods are all designed for models around 100 million parameters; scaling them up to ones literally 1000x larger is highly challenging. In this thesis, we introduce a new unified sparsification and quantization approach OBC, which through additional algorithmic enhancements leads to GPTQ and SparseGPT, the first techniques fast and accurate enough to compress 100+ billion parameter models to 4- or even 3-bit precision and 50% weight-sparsity, respectively. Additionally, we show how weight-only quantizion does not just bring space savings but also up to 4.5x faster generation speed, via custom GPU kernels.\r\n\r\nIn fact, we show for the first time that it is possible to develop an FP16 times INT4 mixed-precision matrix multiplication kernel, called Marlin, which comes close to simultaneously maximizing both memory and compute utilization, making weight-only quantization highly practical even for multi-user serving. Further, we demonstrate that GPTQ can be scaled to widely overparametrized trillion-parameter models, where extreme sub-1-bit compression rates can be achieved without any inference slow-down, by co-designing a bespoke entropy coding scheme together with an efficient kernel.\r\n\r\nFinally, we also study compression from the perspective of someone with access to massive amounts of compute resources for training large models completely from scratch. Here the key questions evolve around the joint scaling behavior between compression, model size, and amount of training data used. Based on extensive experimental results for both vision and text models, we introduce the first scaling law which accurately captures the relationship between weight-sparsity, number of non-zero weights and data. This further allows us to characterize the optimal sparsity, which we find to increase the longer a fixed cost model is being trained.\r\n\r\nOverall, this thesis presents contributions to three different angles of large model efficiency: affordable but accurate algorithms, highly efficient systems implementations, and fundamental scaling laws for compressed training." acknowledged_ssus: - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Elias full_name: Frantar, Elias id: 09a8f98d-ec99-11ea-ae11-c063a7b7fe5f last_name: Frantar citation: ama: 'Frantar E. Compressing large neural networks : Algorithms, systems and scaling laws. 2024. doi:10.15479/at:ista:17485' apa: 'Frantar, E. (2024). Compressing large neural networks : Algorithms, systems and scaling laws. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17485' chicago: 'Frantar, Elias. “Compressing Large Neural Networks : Algorithms, Systems and Scaling Laws.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17485.' ieee: 'E. Frantar, “Compressing large neural networks : Algorithms, systems and scaling laws,” Institute of Science and Technology Austria, 2024.' ista: 'Frantar E. 2024. Compressing large neural networks : Algorithms, systems and scaling laws. Institute of Science and Technology Austria.' mla: 'Frantar, Elias. Compressing Large Neural Networks : Algorithms, Systems and Scaling Laws. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17485.' short: 'E. Frantar, Compressing Large Neural Networks : Algorithms, Systems and Scaling Laws, Institute of Science and Technology Austria, 2024.' corr_author: '1' date_created: 2024-09-02T11:01:48Z date_published: 2024-09-05T00:00:00Z date_updated: 2026-06-18T17:58:39Z day: '05' ddc: - '000' degree_awarded: PhD department: - _id: GradSch - _id: DaAl doi: 10.15479/at:ista:17485 ec_funded: 1 file: - access_level: closed checksum: 5d785645805a78c5b4ce7cc3df557b09 content_type: application/zip creator: efrantar date_created: 2024-09-05T12:04:11Z date_updated: 2024-09-05T12:04:11Z file_id: '17570' file_name: thesis-final.zip file_size: 1615167 relation: source_file - access_level: open_access checksum: a9dd1c2d23734986924eb44ebb55fd8f content_type: application/pdf creator: efrantar date_created: 2024-09-06T16:24:59Z date_updated: 2024-09-06T16:24:59Z file_id: '17880' file_name: frantar_thesis_final.pdf file_size: 2376611 relation: main_file success: 1 file_date_updated: 2024-09-06T16:24:59Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '129' project: - _id: 268A44D6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '805223' name: Elastic Coordination for Scalable Machine Learning publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '17378' relation: part_of_dissertation status: public - id: '17087' relation: part_of_dissertation status: public - id: '14458' relation: part_of_dissertation status: public - id: '18061' relation: part_of_dissertation status: public - id: '18062' relation: part_of_dissertation status: public status: public supervisor: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X title: 'Compressing large neural networks : Algorithms, systems and scaling laws' type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- _id: '17535' abstract: - lang: eng text: Supermassive black holes (SMBHs) with masses of ∼109 M⊙ within the first billion year of the universe challenge our conventional understanding of black hole formation and growth. One pathway to these SMBHs proposes that supermassive stars born in pristine atomic cooling haloes yield massive seed BHs evolving to these early SMBHs. This scenario leads to an overly massive BH galaxy (OMBG), in which the BH to stellar mass ratio is initially Mbh/M* ≥ 1, well in excess of the typical values of ∼10−3 at low redshifts. Previously, we have investigated two massive seed BH candidates from the Renaissance simulation and found that they remain outliers on the Mbh–M* relation until the OMBG merges with a much more massive halo at z = 8. In this work, we use Monte-Carlo merger trees to investigate the evolution of the Mbh–M* relation for 50 000 protogalaxies hosting massive BH seeds, across 10 000 trees that merge into a 1012 M⊙ halo at z = 6. We find that up to 60 per cent (depending on growth parameters) of these OMBGs remain strong outliers for several 100 Myr, down to redshifts detectable with JWST and with sensitive X-ray telescopes. This represents a way to diagnose the massive-seed formation pathway for early SMBHs. We expect to find ∼0.1–1 of these objects per JWST Near Infrared Camera (NIRCam) field per unit redshift at z ≳ 6. Recently detected SMBHs with masses of ∼107 M⊙ and low-inferred stellar-mass hosts may be examples of this population. article_processing_charge: No article_type: original author: - first_name: Matthew T full_name: Scoggins, Matthew T last_name: Scoggins - first_name: Zoltán full_name: Haiman, Zoltán id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36 last_name: Haiman citation: ama: 'Scoggins MT, Haiman Z. Diagnosing the massive-seed pathway to high-redshift black holes: statistics of the evolving black hole to host galaxy mass ratio. Monthly Notices of the Royal Astronomical Society. 2024;531(4):4584-4597. doi:10.1093/mnras/stae1449' apa: 'Scoggins, M. T., & Haiman, Z. (2024). Diagnosing the massive-seed pathway to high-redshift black holes: statistics of the evolving black hole to host galaxy mass ratio. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stae1449' chicago: 'Scoggins, Matthew T, and Zoltán Haiman. “Diagnosing the Massive-Seed Pathway to High-Redshift Black Holes: Statistics of the Evolving Black Hole to Host Galaxy Mass Ratio.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2024. https://doi.org/10.1093/mnras/stae1449.' ieee: 'M. T. Scoggins and Z. Haiman, “Diagnosing the massive-seed pathway to high-redshift black holes: statistics of the evolving black hole to host galaxy mass ratio,” Monthly Notices of the Royal Astronomical Society, vol. 531, no. 4. Oxford University Press, pp. 4584–4597, 2024.' ista: 'Scoggins MT, Haiman Z. 2024. Diagnosing the massive-seed pathway to high-redshift black holes: statistics of the evolving black hole to host galaxy mass ratio. Monthly Notices of the Royal Astronomical Society. 531(4), 4584–4597.' mla: 'Scoggins, Matthew T., and Zoltán Haiman. “Diagnosing the Massive-Seed Pathway to High-Redshift Black Holes: Statistics of the Evolving Black Hole to Host Galaxy Mass Ratio.” Monthly Notices of the Royal Astronomical Society, vol. 531, no. 4, Oxford University Press, 2024, pp. 4584–97, doi:10.1093/mnras/stae1449.' short: M.T. Scoggins, Z. Haiman, Monthly Notices of the Royal Astronomical Society 531 (2024) 4584–4597. date_created: 2024-09-05T09:43:52Z date_published: 2024-06-13T00:00:00Z date_updated: 2024-09-12T09:08:08Z day: '13' doi: 10.1093/mnras/stae1449 extern: '1' intvolume: ' 531' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/https://doi.org/10.1093/mnras/stae1449 month: '06' oa: 1 oa_version: Published Version page: 4584-4597 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: issn: - 0035-8711 - 1365-2966 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'Diagnosing the massive-seed pathway to high-redshift black holes: statistics of the evolving black hole to host galaxy mass ratio' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 531 year: '2024' ... --- APC_amount: 2748 EUR OA_place: publisher OA_type: hybrid _id: '17634' abstract: - lang: eng text: System behaviors are traditionally evaluated through binary classifications of correctness, which do not suffice for properties involving quantitative aspects of systems and executions. Quantitative automata offer a more nuanced approach, mapping each execution to a real number by incorporating weighted transitions and value functions generalizing acceptance conditions. In this paper, we introduce QuAK, the first tool designed to automate the analysis of quantitative automata. QuAK currently supports a variety of quantitative automaton types, including Inf, Sup, LimInf, LimSup, LimInfAvg, and LimSupAvg automata, and implements decision procedures for problems such as emptiness, universality, inclusion, equivalence, as well as for checking whether an automaton is safe, live, or constant. Additionally, QuAK is able to compute extremal values when possible, construct safety-liveness decompositions, and monitor system behaviors. We demonstrate the effectiveness of QuAK through experiments focusing on the inclusion, constant-function check, and monitoring problems. acknowledgement: This work was supported in part by the ERC-2020-AdG 101020093. N. Mazzocchi was affiliated with ISTA when his collaboration started. alternative_title: - LNCS article_processing_charge: Yes (in subscription journal) arxiv: 1 author: - first_name: Marek full_name: Chalupa, Marek id: 87e34708-d6c6-11ec-9f5b-9391e7be2463 last_name: Chalupa - 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: 'Chalupa M, Henzinger TA, Mazzocchi NA, Sarac NE. QuAK: Quantitative Automata Kit. In: 12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation. Vol 15222. Springer Nature; 2024:3-20. doi:10.1007/978-3-031-75387-9_1' apa: 'Chalupa, M., Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2024). QuAK: Quantitative Automata Kit. In 12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation (Vol. 15222, pp. 3–20). Crete, Greece: Springer Nature. https://doi.org/10.1007/978-3-031-75387-9_1' chicago: 'Chalupa, Marek, Thomas A Henzinger, Nicolas Adrien Mazzocchi, and Naci E Sarac. “QuAK: Quantitative Automata Kit.” In 12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation, 15222:3–20. Springer Nature, 2024. https://doi.org/10.1007/978-3-031-75387-9_1.' ieee: 'M. Chalupa, T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “QuAK: Quantitative Automata Kit,” in 12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation, Crete, Greece, 2024, vol. 15222, pp. 3–20.' ista: 'Chalupa M, Henzinger TA, Mazzocchi NA, Sarac NE. 2024. QuAK: Quantitative Automata Kit. 12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation. ISoLA: International Symposium on Leveraging Applications, LNCS, vol. 15222, 3–20.' mla: 'Chalupa, Marek, et al. “QuAK: Quantitative Automata Kit.” 12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation, vol. 15222, Springer Nature, 2024, pp. 3–20, doi:10.1007/978-3-031-75387-9_1.' short: M. Chalupa, T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation, Springer Nature, 2024, pp. 3–20. conference: end_date: 2024-10-31 location: Crete, Greece name: 'ISoLA: International Symposium on Leveraging Applications' start_date: 2024-10-27 corr_author: '1' date_created: 2024-09-05T14:27:08Z date_published: 2024-10-26T00:00:00Z date_updated: 2026-04-07T12:02:57Z day: '26' ddc: - '000' department: - _id: GradSch - _id: ToHe doi: 10.1007/978-3-031-75387-9_1 ec_funded: 1 external_id: arxiv: - '2409.03569' isi: - '001419008700001' file: - access_level: open_access checksum: 43e432f82be376434b358f3dd7a94b71 content_type: application/pdf creator: esarac date_created: 2024-09-05T14:26:02Z date_updated: 2024-09-05T14:26:02Z file_id: '17635' file_name: isola24.pdf file_size: 847422 relation: main_file success: 1 - access_level: open_access checksum: 6bc04f07bb5612c0e7ea00ac121a69b6 content_type: application/pdf creator: dernst date_created: 2025-01-21T14:39:49Z date_updated: 2025-01-21T14:39:49Z file_id: '18865' file_name: 2024_LNCS_Chalupa.pdf file_size: 1358706 relation: main_file success: 1 file_date_updated: 2025-01-21T14:39:49Z has_accepted_license: '1' intvolume: ' 15222' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 3-20 project: - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publication: 12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation publication_identifier: eissn: - 1611-3349 isbn: - '9783031753862' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '20147' relation: dissertation_contains status: public scopus_import: '1' status: public title: 'QuAK: Quantitative Automata Kit' 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 15222 year: '2024' ... --- OA_place: publisher _id: '17850' abstract: - lang: eng text: "Understanding the relationship between a given phenotype and its underlying genotype or genotypes is one of the most pressing challenges of biology, as it lies at the heart of not only basic understanding of evolutionary theory, but also of practical applications in medicine and bioengineering. Understanding this relationship is complicated by the ubiquitous phenomenon of epistasis, wherein mutation effects are dependent on their genetic context. Fitness landscapes — representations of phenotype as a function of genotype — are being increasingly used as a tool to study the effects and interactions of thousands of mutations, but are experimentally limited to exploring a small fraction of a protein’s theoretical sequence space. Furthermore, not all regions of said sequence space are necessarily equally informative. Thus, gene selection for landscape surveys should be carefully considered in order to maximize the usable output of necessarily limited data.\r\n\r\nIn this work, we analyzed the fitness landscapes of orthologous green fluorescent proteins from four different species, by systematically measuring the phenotype, fluorescence, of tens of thousands of mutant genotypes from each protein. These landscapes were highly heterogeneous, with some genes being mutationally robust and displaying epistasis only rarely, and others being highly epistatic and mutationally fragile. We used this data to train machine learning models to predict fluorescence from genotype. Although the training data contained almost exclusively genotypes with less than 3% sequence divergence from the original wild-type sequences, we were able to create novel, functional genotypes with up to 20% sequence divergence. Counterintuitively however, genes with high mutational robustness and rare epistasis were more difficult to introduce large numbers of mutations into, not less. This represents the first study of large-scale fitness landscapes of a protein family, and provides insights into how to approach future landscape surveys and their applications in novel protein design." acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Louisa full_name: Gonzalez Somermeyer, Louisa id: 4720D23C-F248-11E8-B48F-1D18A9856A87 last_name: Gonzalez Somermeyer orcid: 0000-0001-9139-5383 citation: ama: Gonzalez Somermeyer L. Fitness landscapes of orthologous green fluorescent proteins. 2024. doi:10.15479/at:ista:17850 apa: Gonzalez Somermeyer, L. (2024). Fitness landscapes of orthologous green fluorescent proteins. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17850 chicago: Gonzalez Somermeyer, Louisa. “Fitness Landscapes of Orthologous Green Fluorescent Proteins.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17850. ieee: L. Gonzalez Somermeyer, “Fitness landscapes of orthologous green fluorescent proteins,” Institute of Science and Technology Austria, 2024. ista: Gonzalez Somermeyer L. 2024. Fitness landscapes of orthologous green fluorescent proteins. Institute of Science and Technology Austria. mla: Gonzalez Somermeyer, Louisa. Fitness Landscapes of Orthologous Green Fluorescent Proteins. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17850. short: L. Gonzalez Somermeyer, Fitness Landscapes of Orthologous Green Fluorescent Proteins, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-09-06T12:57:44Z date_published: 2024-09-06T00:00:00Z date_updated: 2026-04-07T13:25:01Z day: '06' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: FyKo doi: 10.15479/at:ista:17850 ec_funded: 1 file: - access_level: open_access checksum: d3303724e8d3c91321d71bbad4062048 content_type: application/pdf creator: lgonzale date_created: 2024-09-27T10:32:33Z date_updated: 2024-09-27T10:32:33Z file_id: '18151' file_name: louisa_thesis_draft__240904b.pdf file_size: 11219837 relation: main_file - access_level: closed checksum: 22e63f7f9014dffde2af7a47e7d1d014 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: lgonzale date_created: 2024-09-27T10:34:34Z date_updated: 2024-09-27T10:34:34Z file_id: '18152' file_name: louisa_thesis_draft__240904b.docx file_size: 43338677 relation: source_file file_date_updated: 2024-09-27T10:34:34Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '89' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 26580278-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '771209' name: Characterizing the fitness landscape on population and global scales publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: link: - relation: software url: https://github.com/aequorea238/Orthologous_GFP_Fitness_Peaks record: - id: '11448' relation: part_of_dissertation status: public status: public supervisor: - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 title: Fitness landscapes of orthologous green fluorescent proteins tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '17852' abstract: - lang: eng text: Metal-metal contacts, though not yet widely realized, may provide exciting opportunities to serve as tunable and functional interfaces in single-molecule devices. One of the simplest components which might facilitate such binding interactions is the ferrocene group. Notably, direct bonds between the ferrocene iron center and metals such as Pd or Co have been demonstrated in molecular complexes comprising coordinating ligands attached to the cyclopentadienyl rings. Here, we demonstrate that ferrocene-based single-molecule devices with Fe-Au interfacial contact geometries form at room temperature in the absence of supporting coordinating ligands. Applying a photoredox reaction, we propose that ferrocene only functions effectively as a contact group when oxidized, binding to gold through a formal Fe3+ center. This observation is further supported by a series of control measurements and density functional theory calculations. Our findings extend the scope of junction contact chemistries beyond those involving main group elements, lay the foundation for light switchable ferrocene-based single-molecule devices, and highlight new potential mechanistic function(s) of unsubstituted ferrocenium groups in synthetic processes. article_number: '1439' article_processing_charge: Yes article_type: original author: - first_name: Woojung full_name: Lee, Woojung last_name: Lee - first_name: Liang full_name: Li, Liang last_name: Li - first_name: María full_name: Camarasa-Gómez, María last_name: Camarasa-Gómez - first_name: Daniel full_name: Hernangómez-Pérez, Daniel last_name: Hernangómez-Pérez - first_name: Xavier full_name: Roy, Xavier last_name: Roy - first_name: Ferdinand full_name: Evers, Ferdinand last_name: Evers - first_name: Michael S. full_name: Inkpen, Michael S. last_name: Inkpen - first_name: Latha full_name: Venkataraman, Latha id: 9ebb78a5-cc0d-11ee-8322-fae086a32caf last_name: Venkataraman orcid: 0000-0002-6957-6089 citation: ama: Lee W, Li L, Camarasa-Gómez M, et al. Photooxidation driven formation of Fe-Au linked ferrocene-based single-molecule junctions. Nature Communications. 2024;15. doi:10.1038/s41467-024-45707-z apa: Lee, W., Li, L., Camarasa-Gómez, M., Hernangómez-Pérez, D., Roy, X., Evers, F., … Venkataraman, L. (2024). Photooxidation driven formation of Fe-Au linked ferrocene-based single-molecule junctions. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-45707-z chicago: Lee, Woojung, Liang Li, María Camarasa-Gómez, Daniel Hernangómez-Pérez, Xavier Roy, Ferdinand Evers, Michael S. Inkpen, and Latha Venkataraman. “Photooxidation Driven Formation of Fe-Au Linked Ferrocene-Based Single-Molecule Junctions.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-45707-z. ieee: W. Lee et al., “Photooxidation driven formation of Fe-Au linked ferrocene-based single-molecule junctions,” Nature Communications, vol. 15. Springer Nature, 2024. ista: Lee W, Li L, Camarasa-Gómez M, Hernangómez-Pérez D, Roy X, Evers F, Inkpen MS, Venkataraman L. 2024. Photooxidation driven formation of Fe-Au linked ferrocene-based single-molecule junctions. Nature Communications. 15, 1439. mla: Lee, Woojung, et al. “Photooxidation Driven Formation of Fe-Au Linked Ferrocene-Based Single-Molecule Junctions.” Nature Communications, vol. 15, 1439, Springer Nature, 2024, doi:10.1038/s41467-024-45707-z. short: W. Lee, L. Li, M. Camarasa-Gómez, D. Hernangómez-Pérez, X. Roy, F. Evers, M.S. Inkpen, L. Venkataraman, Nature Communications 15 (2024). date_created: 2024-09-06T12:38:44Z date_published: 2024-02-16T00:00:00Z date_updated: 2024-11-18T10:47:10Z day: '16' doi: 10.1038/s41467-024-45707-z extern: '1' external_id: pmid: - '38365892' intvolume: ' 15' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41467-024-45707-z month: '02' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Photooxidation driven formation of Fe-Au linked ferrocene-based single-molecule junctions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '17885' abstract: - lang: eng text: 'The formation of new ribosomes is tightly coordinated with cell growth and proliferation. In eukaryotes, the correct assembly of all ribosomal proteins and RNAs follows an intricate scheme of maturation and rearrangement steps across three cellular compartments: the nucleolus, nucleoplasm, and cytoplasm. We demonstrate that usnic acid, a lichen secondary metabolite, inhibits the maturation of the large ribosomal subunit in yeast. We combine biochemical characterization of pre-ribosomal particles with a quantitative single-particle cryo-EM approach to monitor changes in nucleolar particle populations upon drug treatment. Usnic acid rapidly blocks the transition from nucleolar state B to C of Nsa1-associated pre-ribosomes, depleting key maturation factors such as Dbp10 and hindering pre-rRNA processing. This primary nucleolar block rapidly rebounds on earlier stages of the pathway which highlights the regulatory linkages between different steps. In summary, we provide an in-depth characterization of the effect of usnic acid on ribosome biogenesis, which may have implications for its reported anti-cancer activities.' acknowledged_ssus: - _id: EM-Fac acknowledgement: We thank Michael A. McAlear, Micheline Fromont-Racin, Philipp Milkereit, Arlen W. Johnson, Sabine Rospert, Ed Hurt, C. Yam, Günter Daum, Wolfgang Zachariae, Katrin Karbstein, Juan P. G. Ballesta, Mercedes Dosil, Miguel Remacha und Jesus de la Cruz for sharing strains or providing antibodies. We thank the members of the Bergler lab and the Haselbach lab for their helpful discussion. We thank Ellen Zhong for helpful discussions about the quantitative cryoDRGN analysis. This research was supported by the Scientific Service Units of IST Austria through resources provided by the Electron Microscopy Facility. This research was funded in whole, or in part, by the Austrian Science Foundation grants [https://doi.org/10.55776/P32977], [https://doi.org/10.55776/P29451] and [https://doi.org/10.55776/P32536] (to H.B.). Research at the IMP is generously supported by Boehringer Ingelheim and the Austrian Research Promotion Agency (Headquarter grant FFG-852936). For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. article_number: '7511' article_processing_charge: Yes article_type: original author: - first_name: Lisa full_name: Kofler, Lisa last_name: Kofler - first_name: Lorenz full_name: Grundmann, Lorenz last_name: Grundmann - first_name: Magdalena full_name: Gerhalter, Magdalena last_name: Gerhalter - first_name: Michael full_name: Prattes, Michael last_name: Prattes - first_name: Juliane full_name: Merl-Pham, Juliane last_name: Merl-Pham - first_name: Gertrude full_name: Zisser, Gertrude last_name: Zisser - first_name: Irina full_name: Grishkovskaya, Irina last_name: Grishkovskaya - first_name: Victor-Valentin full_name: Hodirnau, Victor-Valentin id: 3661B498-F248-11E8-B48F-1D18A9856A87 last_name: Hodirnau orcid: 0000-0003-3904-947X - first_name: Martin full_name: Vareka, Martin last_name: Vareka - first_name: Rolf full_name: Breinbauer, Rolf last_name: Breinbauer - first_name: Stefanie M. full_name: Hauck, Stefanie M. last_name: Hauck - first_name: David full_name: Haselbach, David last_name: Haselbach - first_name: Helmut full_name: Bergler, Helmut last_name: Bergler citation: ama: Kofler L, Grundmann L, Gerhalter M, et al. The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation. Nature Communications. 2024;15. doi:10.1038/s41467-024-51754-3 apa: Kofler, L., Grundmann, L., Gerhalter, M., Prattes, M., Merl-Pham, J., Zisser, G., … Bergler, H. (2024). The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-51754-3 chicago: Kofler, Lisa, Lorenz Grundmann, Magdalena Gerhalter, Michael Prattes, Juliane Merl-Pham, Gertrude Zisser, Irina Grishkovskaya, et al. “The Novel Ribosome Biogenesis Inhibitor Usnic Acid Blocks Nucleolar Pre-60S Maturation.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-51754-3. ieee: L. Kofler et al., “The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation,” Nature Communications, vol. 15. Springer Nature, 2024. ista: Kofler L, Grundmann L, Gerhalter M, Prattes M, Merl-Pham J, Zisser G, Grishkovskaya I, Hodirnau V-V, Vareka M, Breinbauer R, Hauck SM, Haselbach D, Bergler H. 2024. The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation. Nature Communications. 15, 7511. mla: Kofler, Lisa, et al. “The Novel Ribosome Biogenesis Inhibitor Usnic Acid Blocks Nucleolar Pre-60S Maturation.” Nature Communications, vol. 15, 7511, Springer Nature, 2024, doi:10.1038/s41467-024-51754-3. short: L. Kofler, L. Grundmann, M. Gerhalter, M. Prattes, J. Merl-Pham, G. Zisser, I. Grishkovskaya, V.-V. Hodirnau, M. Vareka, R. Breinbauer, S.M. Hauck, D. Haselbach, H. Bergler, Nature Communications 15 (2024). date_created: 2024-09-08T22:01:10Z date_published: 2024-08-29T00:00:00Z date_updated: 2025-09-08T09:13:01Z day: '29' ddc: - '570' department: - _id: EM-Fac doi: 10.1038/s41467-024-51754-3 external_id: isi: - '001457895200001' pmid: - '39209816' file: - access_level: open_access checksum: 7c044538a47182c826d1b526c52958a2 content_type: application/pdf creator: dernst date_created: 2024-09-09T08:56:12Z date_updated: 2024-09-09T08:56:12Z file_id: '17946' file_name: 2024_NatureComm_Kofler.pdf file_size: 3735024 relation: main_file success: 1 file_date_updated: 2024-09-09T08:56:12Z has_accepted_license: '1' intvolume: ' 15' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation 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: 15 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '17886' abstract: - lang: eng text: 'Thin pancake-like neuronal networks cultured on top of a planar microelectrode array have been extensively tried out in neuroengineering, as a substrate for the mobile robot’s control unit, i.e., as a cyborg’s brain. Most of these attempts failed due to intricate self-organizing dynamics in the neuronal systems. In particular, the networks may exhibit an emergent spatial map of steady nucleation sites (“n-sites”) of spontaneous population spikes. Being unpredictable and independent of the surface electrode locations, the n-sites drastically change local ability of the network to generate spikes. Here, using a spiking neuronal network model with generative spatially-embedded connectome, we systematically show in simulations that the number, location, and relative activity of spontaneously formed n-sites (“the vitals”) crucially depend on the samplings of three distributions: (1) the network distribution of neuronal excitability, (2) the distribution of connections between neurons of the network, and (3) the distribution of maximal amplitudes of a single synaptic current pulse. Moreover, blocking the dynamics of a small fraction (about 4%) of non-pacemaker neurons having the highest excitability was enough to completely suppress the occurrence of population spikes and their n-sites. This key result is explained theoretically. Remarkably, the n-sites occur taking into account only short-term synaptic plasticity, i.e., without a Hebbian-type plasticity. As the spiking network model used in this study is strictly deterministic, all simulation results can be accurately reproduced. The model, which has already demonstrated a very high richness-to-complexity ratio, can also be directly extended into the three-dimensional case, e.g., for targeting peculiarities of spiking dynamics in cerebral (or brain) organoids. We recommend the model as an excellent illustrative tool for teaching network-level computational neuroscience, complementing a few benchmark models.' acknowledgement: A.P. is grateful to Chaitanya Chintaluri, Douglas Feitosa Tomé, and Tim P. Vogels for useful discussions. This work was supported by a European Research Council Consolidator Grant (SYNAPSEEK, 819603, to Tim P. Vogels). article_number: '106589' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Dmitrii full_name: Zendrikov, Dmitrii last_name: Zendrikov - first_name: Alexander full_name: Paraskevov, Alexander id: d05e3c56-9262-11ed-9231-be692464e5ac last_name: Paraskevov citation: ama: Zendrikov D, Paraskevov A. The vitals for steady nucleation maps of spontaneous spiking coherence in autonomous two-dimensional neuronal networks. Neural Networks. 2024;180. doi:10.1016/j.neunet.2024.106589 apa: Zendrikov, D., & Paraskevov, A. (2024). The vitals for steady nucleation maps of spontaneous spiking coherence in autonomous two-dimensional neuronal networks. Neural Networks. Elsevier. https://doi.org/10.1016/j.neunet.2024.106589 chicago: Zendrikov, Dmitrii, and Alexander Paraskevov. “The Vitals for Steady Nucleation Maps of Spontaneous Spiking Coherence in Autonomous Two-Dimensional Neuronal Networks.” Neural Networks. Elsevier, 2024. https://doi.org/10.1016/j.neunet.2024.106589. ieee: D. Zendrikov and A. Paraskevov, “The vitals for steady nucleation maps of spontaneous spiking coherence in autonomous two-dimensional neuronal networks,” Neural Networks, vol. 180. Elsevier, 2024. ista: Zendrikov D, Paraskevov A. 2024. The vitals for steady nucleation maps of spontaneous spiking coherence in autonomous two-dimensional neuronal networks. Neural Networks. 180, 106589. mla: Zendrikov, Dmitrii, and Alexander Paraskevov. “The Vitals for Steady Nucleation Maps of Spontaneous Spiking Coherence in Autonomous Two-Dimensional Neuronal Networks.” Neural Networks, vol. 180, 106589, Elsevier, 2024, doi:10.1016/j.neunet.2024.106589. short: D. Zendrikov, A. Paraskevov, Neural Networks 180 (2024). corr_author: '1' date_created: 2024-09-08T22:01:10Z date_published: 2024-12-01T00:00:00Z date_updated: 2025-09-08T09:12:20Z day: '01' ddc: - '570' department: - _id: TiVo doi: 10.1016/j.neunet.2024.106589 ec_funded: 1 external_id: isi: - '001316474600001' pmid: - '39217864' file: - access_level: open_access checksum: 6a194323234e01d4ae725f674529cdb1 content_type: application/pdf creator: dernst date_created: 2025-01-13T08:26:08Z date_updated: 2025-01-13T08:26:08Z file_id: '18825' file_name: 2024_NeuralNetworks_Zendrikov.pdf file_size: 6162281 relation: main_file success: 1 file_date_updated: 2025-01-13T08:26:08Z has_accepted_license: '1' intvolume: ' 180' isi: 1 language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 0aacfa84-070f-11eb-9043-d7eb2c709234 call_identifier: H2020 grant_number: '819603' name: Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning. publication: Neural Networks publication_identifier: eissn: - 1879-2782 issn: - 0893-6080 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: The vitals for steady nucleation maps of spontaneous spiking coherence in autonomous two-dimensional neuronal networks tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 180 year: '2024' ... --- _id: '17888' abstract: - lang: eng text: "Context: Biotic resource exploitation is a critical determinant of species’ distributions. However, quantifying resource exploitation patterns through space and time can be difficult, complicating their incorporation in spatial ecology studies. Therefore, understanding the local drivers of spatial patterns of resource exploitation may contribute to better large-scale species distribution models.\r\nObjectives: We investigated (1) how the resource exploitation patterns of two trophic interactions (plant–insect) are explained by insect behaviour, resource aggregation, and potential insect-insect interactions. We also analyzed how (2) resource patch size and (3) resource accessibility in a heterogeneous landscape affected host exploitation patterns.\r\nMethods: We quantified nectar robbing by insects in the genus Bombus (bumblebees) and seed predation by Brachypterolus vestitus larvae (Antirrhinum beetle) on Antirrhinum majus L. (wild snapdragons) in the Pyrenees Mountains, Catalonia, Spain. We tested hypotheses about resource exploitation by integrating spatial analyses at multiple scales.\r\nResults: Both trophic interactions were aggregated, explained by the aggregation of their resource. At some scales, nectar robbing is more aggregated than the resource. Trophic interaction abundance is proportional to resource patch size, following the ideal free distribution model. Landscape features do not explain the locations exploited. Nectar robbing and seed predation occur together more often than expected.\r\nConclusions: Our findings suggest that multiple biotic and ecological spatial factors may simultaneously affect resource exploitation at a local scale. These findings should be considered when developing agricultural projects, management plans and conservation policies." acknowledgement: "For the beetle barcoding, we are very thankful to Brent Emerson’s laboratory at the Consejo Superior de Investigaciones Científicas (CSIC) at the Instituto de Productos Naturales y Agrobiología (IPNA) in La Laguna, Tenerife. Many thanks to numerous field assistants, especially Sandra Cuevas Gallego, Beatriz Pablo Carmona, Luís Santos Cid and Alex Fuster, for their assistance in data collection. Finally, we thank Jesús Muñoz, Virgilio Gómez-Rubio, and two anonymous reviewers for comments that greatly improved the quality of the manuscript.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria). CB received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. NB was funded by the FWF grant “Löwenmaul speciation” P 32166-B32." article_number: '172' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Guillem full_name: Pocull Belles, Guillem id: 54359172-700c-11ef-a103-c1d91ceac6d6 last_name: Pocull Belles - first_name: Carina full_name: Baskett, Carina id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87 last_name: Baskett orcid: 0000-0002-7354-8574 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Pocull Belles G, Baskett C, Barton NH. Multiscale spatial analysis of two plant–insect interactions: Effects of landscape, resource distribution, and other insects. Landscape Ecology. 2024;39(9). doi:10.1007/s10980-024-01899-9' apa: 'Pocull Belles, G., Baskett, C., & Barton, N. H. (2024). Multiscale spatial analysis of two plant–insect interactions: Effects of landscape, resource distribution, and other insects. Landscape Ecology. Springer Nature. https://doi.org/10.1007/s10980-024-01899-9' chicago: 'Pocull Belles, Guillem, Carina Baskett, and Nicholas H Barton. “Multiscale Spatial Analysis of Two Plant–Insect Interactions: Effects of Landscape, Resource Distribution, and Other Insects.” Landscape Ecology. Springer Nature, 2024. https://doi.org/10.1007/s10980-024-01899-9.' ieee: 'G. Pocull Belles, C. Baskett, and N. H. Barton, “Multiscale spatial analysis of two plant–insect interactions: Effects of landscape, resource distribution, and other insects,” Landscape Ecology, vol. 39, no. 9. Springer Nature, 2024.' ista: 'Pocull Belles G, Baskett C, Barton NH. 2024. Multiscale spatial analysis of two plant–insect interactions: Effects of landscape, resource distribution, and other insects. Landscape Ecology. 39(9), 172.' mla: 'Pocull Belles, Guillem, et al. “Multiscale Spatial Analysis of Two Plant–Insect Interactions: Effects of Landscape, Resource Distribution, and Other Insects.” Landscape Ecology, vol. 39, no. 9, 172, Springer Nature, 2024, doi:10.1007/s10980-024-01899-9.' short: G. Pocull Belles, C. Baskett, N.H. Barton, Landscape Ecology 39 (2024). corr_author: '1' date_created: 2024-09-08T22:01:11Z date_published: 2024-09-01T00:00:00Z date_updated: 2025-09-08T09:20:11Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1007/s10980-024-01899-9 ec_funded: 1 external_id: isi: - '001304011900001' file: - access_level: open_access checksum: 2e1cbc320ec1b4447a5a8562a90bcbc3 content_type: application/pdf creator: dernst date_created: 2024-09-11T07:14:03Z date_updated: 2024-09-11T07:14:03Z file_id: '18054' file_name: 2024_LandscapeEcology_Pocull.pdf file_size: 1494987 relation: main_file success: 1 file_date_updated: 2024-09-11T07:14:03Z has_accepted_license: '1' intvolume: ' 39' isi: 1 issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 05959E1C-7A3F-11EA-A408-12923DDC885E grant_number: P32166 name: Snapdragon Speciation publication: Landscape Ecology publication_identifier: eissn: - 1572-9761 issn: - 0921-2973 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'Multiscale spatial analysis of two plant–insect interactions: Effects of landscape, resource distribution, and other insects' 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: 39 year: '2024' ... --- _id: '17892' abstract: - lang: eng text: "Enzyme-substrate kinetics form the basis of many biomolecular processes. The interplay between substrate binding and substrate geometry can give rise to long-range interactions between enzyme binding events. Here we study a general model of enzyme-substrate kinetics with restricted long-range interactions described by an exponent −\U0001D6FE. We employ a coherent-state path integral and renormalization group approach to calculate the first moment and two-point correlation function of the enzyme-binding profile. We show that starting from an empty substrate the average occupancy follows a power law with an exponent 1/(1−\U0001D6FE) over time. The correlation function decays algebraically with two distinct spatial regimes characterized by exponents −\U0001D6FE on short distances and −(2/3)⁢(2−\U0001D6FE) on long distances. The crossover between both regimes scales inversely with the average substrate occupancy. Our work allows associating experimental measurements of bound enzyme locations with their binding kinetics and the spatial conformation of the substrate." acknowledgement: We thank F. Piazza, M. Henkel, and F. Jülicher for helpful feedback and the entire Rulands group for fruitful discussions. We thank W. Reik, S. Clark, T. Lohoff, and I. Kafetzopoulos for fruitful discussions about the biological aspects of this work. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Grant No. 950349). This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant No. 101034413. article_number: '024404' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Fabrizio full_name: Olmeda, Fabrizio id: 69dbf5fb-8a76-11ed-866b-fb486d8b5689 last_name: Olmeda - first_name: Steffen full_name: Rulands, Steffen last_name: Rulands citation: ama: Olmeda F, Rulands S. Field theory of enzyme-substrate systems with restricted long-range interactions. Physical Review E. 2024;110(2). doi:10.1103/PhysRevE.110.024404 apa: Olmeda, F., & Rulands, S. (2024). Field theory of enzyme-substrate systems with restricted long-range interactions. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.110.024404 chicago: Olmeda, Fabrizio, and Steffen Rulands. “Field Theory of Enzyme-Substrate Systems with Restricted Long-Range Interactions.” Physical Review E. American Physical Society, 2024. https://doi.org/10.1103/PhysRevE.110.024404. ieee: F. Olmeda and S. Rulands, “Field theory of enzyme-substrate systems with restricted long-range interactions,” Physical Review E, vol. 110, no. 2. American Physical Society, 2024. ista: Olmeda F, Rulands S. 2024. Field theory of enzyme-substrate systems with restricted long-range interactions. Physical Review E. 110(2), 024404. mla: Olmeda, Fabrizio, and Steffen Rulands. “Field Theory of Enzyme-Substrate Systems with Restricted Long-Range Interactions.” Physical Review E, vol. 110, no. 2, 024404, American Physical Society, 2024, doi:10.1103/PhysRevE.110.024404. short: F. Olmeda, S. Rulands, Physical Review E 110 (2024). corr_author: '1' date_created: 2024-09-08T22:01:12Z date_published: 2024-08-01T00:00:00Z date_updated: 2025-09-08T09:17:18Z day: '01' ddc: - '530' department: - _id: EdHa doi: 10.1103/PhysRevE.110.024404 ec_funded: 1 external_id: isi: - '001299670100004' pmid: - '39294986' file: - access_level: open_access checksum: 67fc2cc8eee3155e5c3b7380307d8284 content_type: application/pdf creator: dernst date_created: 2024-09-11T05:59:36Z date_updated: 2024-09-11T05:59:36Z file_id: '18053' file_name: 2024_PhysReviewE_Olmeda.pdf file_size: 445696 relation: main_file success: 1 file_date_updated: 2024-09-11T05:59:36Z has_accepted_license: '1' intvolume: ' 110' isi: 1 issue: '2' language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Physical Review E publication_identifier: eissn: - 2470-0053 issn: - 2470-0045 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Field theory of enzyme-substrate systems with restricted long-range interactions 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: 110 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '18065' abstract: - lang: eng text: We establish a close connection between acceleration and dynamical degree for one-frequency quasi-periodic compact cocycles, by showing that two vectors derived separately from each coincide. Based on this, we provide a dynamical classification of one-frequency quasi-periodic SO(3, R)-cocycles. acknowledgement: "X. Hou is partially supported by National Natural Science Foundation of China (Grant \r\n12071083) and Funds for Distinguished Youths of Hubei Province of China (\r\n2019CFA680). Y. Pan is supported by ERC Advanced Grant (#885707). Q. Zhou is partially supported by National Key R&D Program of China (2020YFA0713300), NSFC grant (\r\n12071232) and Nankai Zhide Foundation." article_number: '109943' article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Xuanji full_name: Hou, Xuanji last_name: Hou - first_name: Yi full_name: Pan, Yi id: 1e21c7f7-9070-11eb-847d-8b04c7169523 last_name: Pan - first_name: Qi full_name: Zhou, Qi last_name: Zhou citation: ama: Hou X, Pan Y, Zhou Q. Dynamical classification of analytic one-frequency quasi-periodic SO(3,R)-cocycles. Advances in Mathematics. 2024;457. doi:10.1016/j.aim.2024.109943 apa: Hou, X., Pan, Y., & Zhou, Q. (2024). Dynamical classification of analytic one-frequency quasi-periodic SO(3,R)-cocycles. Advances in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2024.109943 chicago: Hou, Xuanji, Yi Pan, and Qi Zhou. “Dynamical Classification of Analytic One-Frequency Quasi-Periodic SO(3,R)-Cocycles.” Advances in Mathematics. Elsevier, 2024. https://doi.org/10.1016/j.aim.2024.109943. ieee: X. Hou, Y. Pan, and Q. Zhou, “Dynamical classification of analytic one-frequency quasi-periodic SO(3,R)-cocycles,” Advances in Mathematics, vol. 457. Elsevier, 2024. ista: Hou X, Pan Y, Zhou Q. 2024. Dynamical classification of analytic one-frequency quasi-periodic SO(3,R)-cocycles. Advances in Mathematics. 457, 109943. mla: Hou, Xuanji, et al. “Dynamical Classification of Analytic One-Frequency Quasi-Periodic SO(3,R)-Cocycles.” Advances in Mathematics, vol. 457, 109943, Elsevier, 2024, doi:10.1016/j.aim.2024.109943. short: X. Hou, Y. Pan, Q. Zhou, Advances in Mathematics 457 (2024). corr_author: '1' date_created: 2024-09-15T22:01:39Z date_published: 2024-11-01T00:00:00Z date_updated: 2025-09-08T09:44:19Z day: '01' ddc: - '510' department: - _id: VaKa doi: 10.1016/j.aim.2024.109943 ec_funded: 1 external_id: arxiv: - '2311.17537' isi: - '001315306500001' file: - access_level: open_access checksum: 1c80b844a91d93cf4799f4a65873b18d content_type: application/pdf creator: dernst date_created: 2025-01-13T08:29:27Z date_updated: 2025-01-13T08:29:27Z file_id: '18826' file_name: 2024_AdvancesMath_Hou.pdf file_size: 713659 relation: main_file success: 1 file_date_updated: 2025-01-13T08:29:27Z has_accepted_license: '1' intvolume: ' 457' isi: 1 language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 9B8B92DE-BA93-11EA-9121-9846C619BF3A call_identifier: H2020 grant_number: '885707' name: Spectral rigidity and integrability for billiards and geodesic flows publication: Advances in Mathematics publication_identifier: eissn: - 1090-2082 issn: - 0001-8708 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Dynamical classification of analytic one-frequency quasi-periodic SO(3,R)-cocycles 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: 457 year: '2024' ... --- _id: '18086' abstract: - lang: eng text: "Abstract. Continuous group key agreement (CGKA) allows a group of\r\nusers to maintain a continuously updated shared key in an asynchronous\r\nsetting where parties only come online sporadically and their messages\r\nare relayed by an untrusted server. CGKA captures the basic primitive\r\nunderlying group messaging schemes.\r\nCurrent solutions including TreeKEM (“Messaging Layer Security”\r\n(MLS) IETF RFC 9420) cannot handle concurrent requests while retaining low communication complexity. The exception being CoCoA, which\r\nis concurrent while having extremely low communication complexity (in\r\ngroups of size n and for m concurrent updates the communication per\r\nuser is log(n), i.e., independent of m). The main downside of CoCoA\r\nis that in groups of size n, users might have to do up to log(n) update\r\nrequests to the server to ensure their (potentially corrupted) key material has been refreshed.\r\nIn this work we present a “fast healing” concurrent CGKA protocol,\r\nnamed DeCAF, where users will heal after at most log(t) requests, with\r\nt being the number of corrupted users. While also suitable for the standard central-server setting, our protocol is particularly interesting for\r\nrealizing decentralized group messaging, where protocol messages (add,\r\nremove, update) are being posted on some append-only data structure\r\nrather than sent to a server. In this setting, concurrency is crucial once\r\nthe rate of requests exceeds, say, the rate at which new blocks are added\r\nto a blockchain.\r\nIn the central-server setting, CoCoA (the only alternative with concurrency, sub-linear communication and basic post-compromise security)\r\nenjoys much lower download communication. However, in the decentralized setting – where there is no server which can craft specific messages\r\nfor different users to reduce their download communication – our protocol\r\nsignificantly outperforms CoCoA. DeCAF heals in fewer epochs (log(t)\r\nvs. log(n)) while incurring a similar per epoch per user communication\r\ncost." alternative_title: - LNCS article_processing_charge: No author: - first_name: Joel F full_name: Alwen, Joel F id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87 last_name: Alwen - first_name: Benedikt full_name: Auerbach, Benedikt id: D33D2B18-E445-11E9-ABB7-15F4E5697425 last_name: Auerbach orcid: 0000-0002-7553-6606 - first_name: Miguel full_name: Cueto Noval, Miguel id: ffc563a3-f6e0-11ea-865d-e3cce03d17cc last_name: Cueto Noval orcid: 0000-0002-2505-4246 - first_name: Karen full_name: Klein, Karen id: 3E83A2F8-F248-11E8-B48F-1D18A9856A87 last_name: Klein - first_name: Guillermo full_name: Pascual Perez, Guillermo id: 2D7ABD02-F248-11E8-B48F-1D18A9856A87 last_name: Pascual Perez orcid: 0000-0001-8630-415X - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Alwen JF, Auerbach B, Cueto Noval M, Klein K, Pascual Perez G, Pietrzak KZ. DeCAF: Decentralizable CGKA with fast healing. In: Galdi C, Phan DH, eds. Security and Cryptography for Networks: 14th International Conference. Vol 14974. Cham: Springer Nature; 2024:294–313. doi:10.1007/978-3-031-71073-5_14' apa: 'Alwen, J. F., Auerbach, B., Cueto Noval, M., Klein, K., Pascual Perez, G., & Pietrzak, K. Z. (2024). DeCAF: Decentralizable CGKA with fast healing. In C. Galdi & D. H. Phan (Eds.), Security and Cryptography for Networks: 14th International Conference (Vol. 14974, pp. 294–313). Cham: Springer Nature. https://doi.org/10.1007/978-3-031-71073-5_14' chicago: 'Alwen, Joel F, Benedikt Auerbach, Miguel Cueto Noval, Karen Klein, Guillermo Pascual Perez, and Krzysztof Z Pietrzak. “DeCAF: Decentralizable CGKA with Fast Healing.” In Security and Cryptography for Networks: 14th International Conference, edited by Clemente Galdi and Duong Hieu Phan, 14974:294–313. Cham: Springer Nature, 2024. https://doi.org/10.1007/978-3-031-71073-5_14.' ieee: 'J. F. Alwen, B. Auerbach, M. Cueto Noval, K. Klein, G. Pascual Perez, and K. Z. Pietrzak, “DeCAF: Decentralizable CGKA with fast healing,” in Security and Cryptography for Networks: 14th International Conference, Amalfi, Italy, 2024, vol. 14974, pp. 294–313.' ista: 'Alwen JF, Auerbach B, Cueto Noval M, Klein K, Pascual Perez G, Pietrzak KZ. 2024. DeCAF: Decentralizable CGKA with fast healing. Security and Cryptography for Networks: 14th International Conference. SCN: Security and Cryptography for Networks, LNCS, vol. 14974, 294–313.' mla: 'Alwen, Joel F., et al. “DeCAF: Decentralizable CGKA with Fast Healing.” Security and Cryptography for Networks: 14th International Conference, edited by Clemente Galdi and Duong Hieu Phan, vol. 14974, Springer Nature, 2024, pp. 294–313, doi:10.1007/978-3-031-71073-5_14.' short: 'J.F. Alwen, B. Auerbach, M. Cueto Noval, K. Klein, G. Pascual Perez, K.Z. Pietrzak, in:, C. Galdi, D.H. Phan (Eds.), Security and Cryptography for Networks: 14th International Conference, Springer Nature, Cham, 2024, pp. 294–313.' conference: end_date: 2024-09-13 location: Amalfi, Italy name: 'SCN: Security and Cryptography for Networks' start_date: 2024-09-11 corr_author: '1' date_created: 2024-09-18T11:35:14Z date_published: 2024-09-10T00:00:00Z date_updated: 2026-04-07T13:01:26Z day: '10' department: - _id: GradSch - _id: KrPi doi: 10.1007/978-3-031-71073-5_14 editor: - first_name: Clemente full_name: Galdi, Clemente last_name: Galdi - first_name: Duong Hieu full_name: Phan, Duong Hieu last_name: Phan external_id: isi: - '001330408000014' intvolume: ' 14974' isi: 1 language: - iso: eng month: '09' oa_version: None page: 294–313 place: Cham publication: 'Security and Cryptography for Networks: 14th International Conference' publication_identifier: eisbn: - '9783031710735' eissn: - 1611-3349 isbn: - '9783031710728' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '18088' relation: dissertation_contains status: public status: public title: 'DeCAF: Decentralizable CGKA with fast healing' type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 14974 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' ... --- OA_place: publisher _id: '18132' abstract: - lang: eng text: "In this thesis, we are dealing with both arithmetic and geometric problems coming from the\r\nstudy of rational points with a particular focus on function fields over finite fields:\r\n(1) Using the circle method we produce upper bounds for the number of rational points of\r\nbounded height on diagonal cubic surfaces and fourfolds over Fq(t). This is based on\r\njoint work with Leonhard Hochfilzer.\r\n(2) We study rational points on smooth complete intersections X defined by cubic and\r\nquadratic hypersurfaces over Fq(t). We refine the Farey dissection of the “unit square”\r\ndeveloped by Vishe [202] and use the circle method with a Kloosterman refinement to\r\nestablish an asymptotic formula for the number of rational points of bounded height on\r\nX when dim(X) ≥ 23. Under the same hypotheses, we also verify weak approximation.\r\n(3) In joint work with Hochfilzer, we obtain upper bounds for the number of rational points of\r\nbounded height on del Pezzo surfaces of low degree over any global field. Our approach\r\nis to take hyperplane sections, which reduces the problem to uniform estimates for the\r\nnumber of rational points on curves.\r\n(4) We develop a version of the circle method capable of counting Fq-points on jet schemes\r\nof moduli spaces of rational curves on hypersurfaces. Combining this with a spreading\r\nout argument and a result of Mustaţă [150], this allows us to show that these moduli\r\nspaces only have canonical singularities under suitable assumptions on the degree and the\r\ndimension.\r\nIn addition, we give an overview of guiding questions and conjectures in the field of rational\r\npoints and explain the basic mechanism underlying the circle method.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Jakob full_name: Glas, Jakob id: d6423cba-dc74-11ea-a0a7-ee61689ff5fb last_name: Glas citation: ama: Glas J. Counting rational points over function fields. 2024. doi:10.15479/at:ista:18132 apa: Glas, J. (2024). Counting rational points over function fields. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18132 chicago: Glas, Jakob. “Counting Rational Points over Function Fields.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18132. ieee: J. Glas, “Counting rational points over function fields,” Institute of Science and Technology Austria, 2024. ista: Glas J. 2024. Counting rational points over function fields. Institute of Science and Technology Austria. mla: Glas, Jakob. Counting Rational Points over Function Fields. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18132. short: J. Glas, Counting Rational Points over Function Fields, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-09-23T18:58:08Z date_published: 2024-09-23T00:00:00Z date_updated: 2026-04-07T12:53:54Z day: '23' ddc: - '512' degree_awarded: PhD department: - _id: GradSch - _id: TiBr doi: 10.15479/at:ista:18132 file: - access_level: closed checksum: 2f8cf5cefdab108b1979caa8146cae9a content_type: application/x-zip-compressed creator: jglas date_created: 2024-09-23T18:49:22Z date_updated: 2024-09-23T18:49:22Z file_id: '18133' file_name: PhDthesis (3).zip file_size: 5382106 relation: source_file - access_level: open_access checksum: 08bb6f14c42b47ff25882a2ce3ea0d8a content_type: application/pdf creator: jglas date_created: 2024-09-25T14:08:57Z date_updated: 2024-09-25T14:08:57Z file_id: '18140' file_name: example-phd.pdf file_size: 2380127 relation: main_file success: 1 file_date_updated: 2024-09-25T14:08:57Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '09' oa: 1 oa_version: Published Version page: '195' project: - _id: bd8a4fdc-d553-11ed-ba76-80a0167441a3 grant_number: P36278 name: Rational curves via function field analytic number theory publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '18293' relation: part_of_dissertation status: public - id: '18294' relation: part_of_dissertation status: public - id: '18295' relation: part_of_dissertation status: public - id: '18173' relation: part_of_dissertation status: public status: public supervisor: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 title: Counting rational points over function fields tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: publisher _id: '18135' abstract: - lang: eng text: "This thesis consists of two separate parts. In the first part we consider a dilute Fermi gas interacting through a repulsive interaction in dimensions $d=1,2,3$. Our focus is mostly on the physically most relevant dimension $d=3$ \r\nand the setting of a spin-polarized (equivalently spinless) gas, where the Pauli exclusion principle plays a key role. We show that, at zero temperature, the ground state energy density of the interacting spin-polarized gas differs (to leading order) from that of the free (i.e. non-interacting) gas by a term of order $a_p^d\\rho^{2+2/d}$ \ with $a_p$ the $p$-wave scattering length of the repulsive interaction and $\\rho$ the density. Further, we extend this to positive temperature and show that the pressure of an interacting spin-polarized gas differs from that of the free gas by a now temperature dependent term, again of order $a_p^d\\rho^{2+2/d}$. Lastly, we consider the setting of a spin-$\\frac{1}{2}$ Fermi gas in $d=3$ dimensions and show that here, as an upper bound, the ground state energy density differs from that of the free system by a term of order $a_s \\rho^2$ with an error smaller than $a_s \\rho^2 (a_s\\rho^{1/3})^{1-\\eps}$ for any $\\eps > 0$, where $a_s$ is the $s$-wave scattering length of the repulsive interaction. \r\n\r\nThese asymptotic formulas complement the similar formulas in the literature for the dilute Bose and spin-$\\frac{1}{2}$ Fermi gas, where the ground state energies or pressures differ from that of the corresponding free systems by a term of order $a_s \\rho^2$ in dimension $d=3$. In the spin-polarized setting, the corrections, of order $a_p^3\\rho^{8/3}$ in dimension $d=3$, are thus much smaller and requires a more delicate analysis.\r\n\r\nIn the second part of the thesis we consider the Bardeen--Cooper--Schrieffer (BCS) theory of superconductivity and in particular its associated critical temperature and energy gap. We prove that the ratio of the zero-temperature energy gap and critical temperature $\\Xi(T=0)/T_c$ approaches a universal constant $\\pi e^{-\\gamma}\\approx 1.76$ in both the limit of high density in dimension $d=3$ and in the limit of weak coupling in dimensions $d=1,2$. This complements the proofs in the literature of this universal behaviour in the limit of weak coupling or low density in dimension $d=3$. Secondly, we prove that the ratio of the energy gap at positive temperature and critical temperature $\\Xi(T)/T_c$ approaches a universal function of the relative temperature $T/T_c$ in the limit of weak coupling in dimensions $d=1,2,3$." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Asbjørn Bækgaard full_name: Lauritsen, Asbjørn Bækgaard id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1 last_name: Lauritsen orcid: 0000-0003-4476-2288 citation: ama: Lauritsen AB. Energies of dilute Fermi gases and universalities in BCS theory. 2024. doi:10.15479/at:ista:18135 apa: Lauritsen, A. B. (2024). Energies of dilute Fermi gases and universalities in BCS theory. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18135 chicago: Lauritsen, Asbjørn Bækgaard. “Energies of Dilute Fermi Gases and Universalities in BCS Theory.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18135. ieee: A. B. Lauritsen, “Energies of dilute Fermi gases and universalities in BCS theory,” Institute of Science and Technology Austria, 2024. ista: Lauritsen AB. 2024. Energies of dilute Fermi gases and universalities in BCS theory. Institute of Science and Technology Austria. mla: Lauritsen, Asbjørn Bækgaard. Energies of Dilute Fermi Gases and Universalities in BCS Theory. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18135. short: A.B. Lauritsen, Energies of Dilute Fermi Gases and Universalities in BCS Theory, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-09-24T10:56:25Z date_published: 2024-09-23T00:00:00Z date_updated: 2026-04-16T08:17:55Z day: '23' ddc: - '515' - '539' degree_awarded: PhD department: - _id: GradSch - _id: RoSe doi: 10.15479/at:ista:18135 ec_funded: 1 file: - access_level: open_access checksum: c7bc3b31e430d57c65393051ca439575 content_type: application/pdf creator: alaurits date_created: 2024-09-26T13:11:24Z date_updated: 2024-09-26T13:11:24Z file_id: '18147' file_name: Lauritsen-thesis-final.pdf file_size: 3648831 relation: main_file success: 1 - access_level: closed checksum: 39f6b1b7f83e25a3bf9f933f1ea0bc06 content_type: application/x-zip-compressed creator: alaurits date_created: 2024-09-26T13:12:55Z date_updated: 2024-09-26T13:12:55Z file_id: '18148' file_name: Lauritsen-thesis-source.zip file_size: 1625888 relation: source_file file_date_updated: 2024-09-26T13:12:55Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '353' project: - _id: bda63fe5-d553-11ed-ba76-a16e3d2f256b grant_number: I06427 name: Mathematical Challenges in BCS Theory of Superconductivity - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems publication_identifier: isbn: - 978-3-99078-042-8 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11732' relation: part_of_dissertation status: public - id: '14542' relation: part_of_dissertation status: public - id: '18107' relation: part_of_dissertation status: public - id: '17240' relation: part_of_dissertation status: public - id: '14931' relation: part_of_dissertation status: public status: public supervisor: - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 title: Energies of dilute Fermi gases and universalities in BCS theory tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- _id: '18155' abstract: - lang: eng text: We study the classical problem of verifying programs with respect to formal specifications given in the linear temporal logic (LTL). We first present novel sound and complete witnesses for LTL verification over imperative programs. Our witnesses are applicable to both verification (proving) and refutation (finding bugs) settings. We then consider LTL formulas in which atomic propositions can be polynomial constraints and turn our focus to polynomial arithmetic programs, i.e. programs in which every assignment and guard consists only of polynomial expressions. For this setting, we provide an efficient algorithm to automatically synthesize such LTL witnesses. Our synthesis procedure is both sound and semi-complete. Finally, we present experimental results demonstrating the effectiveness of our approach and that it can handle programs which were beyond the reach of previous state-of-the-art tools. acknowledgement: This work was supported in part by the ERC-2020-CoG 863818 (FoRM-SMArt) and the Hong Kong Research Grants Council ECS Project Number 26208122. alternative_title: - LNCS article_processing_charge: Yes (in subscription journal) arxiv: 1 author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Amir Kafshdar full_name: Goharshady, Amir Kafshdar id: 391365CE-F248-11E8-B48F-1D18A9856A87 last_name: Goharshady orcid: 0000-0003-1702-6584 - first_name: Ehsan full_name: Goharshady, Ehsan last_name: Goharshady - first_name: Mehrdad full_name: Karrabi, Mehrdad id: 67638922-f394-11eb-9cf6-f20423e08757 last_name: Karrabi - first_name: Dorde full_name: Zikelic, Dorde id: 294AA7A6-F248-11E8-B48F-1D18A9856A87 last_name: Zikelic orcid: 0000-0002-4681-1699 citation: ama: 'Chatterjee K, Goharshady AK, Goharshady E, Karrabi M, Zikelic D. Sound and complete witnesses for template-based verification of LTL properties on polynomial programs. In: Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol 14933. Springer Nature; 2024:600-619. doi:10.1007/978-3-031-71162-6_31' apa: 'Chatterjee, K., Goharshady, A. K., Goharshady, E., Karrabi, M., & Zikelic, D. (2024). Sound and complete witnesses for template-based verification of LTL properties on polynomial programs. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 14933, pp. 600–619). Milan, Italy: Springer Nature. https://doi.org/10.1007/978-3-031-71162-6_31' chicago: Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Ehsan Goharshady, Mehrdad Karrabi, and Dorde Zikelic. “Sound and Complete Witnesses for Template-Based Verification of LTL Properties on Polynomial Programs.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 14933:600–619. Springer Nature, 2024. https://doi.org/10.1007/978-3-031-71162-6_31. ieee: K. Chatterjee, A. K. Goharshady, E. Goharshady, M. Karrabi, and D. Zikelic, “Sound and complete witnesses for template-based verification of LTL properties on polynomial programs,” in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Milan, Italy, 2024, vol. 14933, pp. 600–619. ista: 'Chatterjee K, Goharshady AK, Goharshady E, Karrabi M, Zikelic D. 2024. Sound and complete witnesses for template-based verification of LTL properties on polynomial programs. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). FM: Formal Methods, LNCS, vol. 14933, 600–619.' mla: Chatterjee, Krishnendu, et al. “Sound and Complete Witnesses for Template-Based Verification of LTL Properties on Polynomial Programs.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 14933, Springer Nature, 2024, pp. 600–19, doi:10.1007/978-3-031-71162-6_31. short: K. Chatterjee, A.K. Goharshady, E. Goharshady, M. Karrabi, D. Zikelic, in:, Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer Nature, 2024, pp. 600–619. conference: end_date: 2024-09-13 location: Milan, Italy name: 'FM: Formal Methods' start_date: 2024-09-09 corr_author: '1' date_created: 2024-09-29T22:01:37Z date_published: 2024-09-11T00:00:00Z date_updated: 2025-09-08T09:51:34Z day: '11' ddc: - '000' department: - _id: KrCh doi: 10.1007/978-3-031-71162-6_31 ec_funded: 1 external_id: arxiv: - '2403.05386' isi: - '001336893300031' file: - access_level: open_access checksum: 223845be9e754681ee218866827c95e7 content_type: application/pdf creator: dernst date_created: 2024-10-01T09:56:54Z date_updated: 2024-10-01T09:56:54Z file_id: '18165' file_name: 2024_LNCS_Chatterjee.pdf file_size: 650495 relation: main_file success: 1 file_date_updated: 2024-10-01T09:56:54Z has_accepted_license: '1' intvolume: ' 14933' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 600-619 project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' publication: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) publication_identifier: eissn: - 1611-3349 isbn: - '9783031711619' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Sound and complete witnesses for template-based verification of LTL properties on polynomial programs 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 14933 year: '2024' ... --- _id: '18173' abstract: - lang: eng text: Using a two-dimensional version of the delta method, we establish an asymptotic formula for the number of rational points of bounded height on non-singular complete intersections of cubic and quadric hypersurfaces of dimension at least 23 over Fq(t), provided char (Fq)>3. Under the same hypotheses, we also verify weak approximation. acknowledgement: The author would like to thank his supervisor Tim Browning for suggesting this project and many helpful conversations and Pankaj Vishe for useful comments. Moreover, he is grateful to Dante Bonolis and Julian Lyczak for sharing their expertise in exponential sums and geometry. While working on this paper, the author was supported by FWF grant (DOI 10.55776/P36278). article_number: e12991 article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Jakob full_name: Glas, Jakob id: d6423cba-dc74-11ea-a0a7-ee61689ff5fb last_name: Glas citation: ama: Glas J. Rational points on complete intersections of cubic and quadric hypersurfaces over Fq(t). Journal of the London Mathematical Society. 2024;110(4). doi:10.1112/jlms.12991 apa: Glas, J. (2024). Rational points on complete intersections of cubic and quadric hypersurfaces over Fq(t). Journal of the London Mathematical Society. London Mathematical Society. https://doi.org/10.1112/jlms.12991 chicago: Glas, Jakob. “Rational Points on Complete Intersections of Cubic and Quadric Hypersurfaces over Fq(T).” Journal of the London Mathematical Society. London Mathematical Society, 2024. https://doi.org/10.1112/jlms.12991. ieee: J. Glas, “Rational points on complete intersections of cubic and quadric hypersurfaces over Fq(t),” Journal of the London Mathematical Society, vol. 110, no. 4. London Mathematical Society, 2024. ista: Glas J. 2024. Rational points on complete intersections of cubic and quadric hypersurfaces over Fq(t). Journal of the London Mathematical Society. 110(4), e12991. mla: Glas, Jakob. “Rational Points on Complete Intersections of Cubic and Quadric Hypersurfaces over Fq(T).” Journal of the London Mathematical Society, vol. 110, no. 4, e12991, London Mathematical Society, 2024, doi:10.1112/jlms.12991. short: J. Glas, Journal of the London Mathematical Society 110 (2024). corr_author: '1' date_created: 2024-10-06T22:01:11Z date_published: 2024-10-01T00:00:00Z date_updated: 2026-04-07T12:53:53Z day: '01' ddc: - '510' department: - _id: TiBr doi: 10.1112/jlms.12991 external_id: arxiv: - '2306.02718' file: - access_level: open_access checksum: 11ebf690363151026ce81f91f2220855 content_type: application/pdf creator: dernst date_created: 2024-10-07T08:51:01Z date_updated: 2024-10-07T08:51:01Z file_id: '18181' file_name: 2024_JLondonMathSoc_Glas.pdf file_size: 579601 relation: main_file success: 1 file_date_updated: 2024-10-07T08:51:01Z has_accepted_license: '1' intvolume: ' 110' issue: '4' language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: bd8a4fdc-d553-11ed-ba76-80a0167441a3 grant_number: P36278 name: Rational curves via function field analytic number theory publication: Journal of the London Mathematical Society publication_identifier: eissn: - 1469-7750 issn: - 0024-6107 publication_status: published publisher: London Mathematical Society quality_controlled: '1' related_material: record: - id: '18132' relation: dissertation_contains status: public scopus_import: '1' status: public title: Rational points on complete intersections of cubic and quadric hypersurfaces over Fq(t) 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: 110 year: '2024' ... --- _id: '18177' abstract: - lang: eng text: Partially Specified Boolean Networks (PSBNs) represent a family of Boolean models resulting from possible interpretations of unknown update logics. Hybrid extension of CTL (HCTL) has the power to express complex dynamical phenomena, such as oscillations or stability. We present BNClassifier to classify Boolean Networks corresponding to a given PSBN according to criteria specified in HCTL. The implementation of the tool is fully symbolic (based on BDDs). The results are visualised using the machine-learning-based technology of decision trees. acknowledgement: The work has been supported by the Czech Science Foundation grant No. GA22-10845S. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 101034413. alternative_title: - LNBI article_processing_charge: No author: - first_name: Nikola full_name: Beneš, Nikola last_name: Beneš - first_name: Luboš full_name: Brim, Luboš last_name: Brim - first_name: Ondřej full_name: Huvar, Ondřej last_name: Huvar - first_name: Samuel full_name: Pastva, Samuel id: 07c5ea74-f61c-11ec-a664-aa7c5d957b2b last_name: Pastva orcid: 0000-0003-1993-0331 - first_name: David full_name: Šafránek, David last_name: Šafránek citation: ama: 'Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. BNClassifier: Classifying boolean models by dynamic properties. In: Computational Methods in Systems Biology. Vol 14971. Springer Nature; 2024:19-26. doi:10.1007/978-3-031-71671-3_2' apa: 'Beneš, N., Brim, L., Huvar, O., Pastva, S., & Šafránek, D. (2024). BNClassifier: Classifying boolean models by dynamic properties. In Computational Methods in Systems Biology (Vol. 14971, pp. 19–26). Springer Nature. https://doi.org/10.1007/978-3-031-71671-3_2' chicago: 'Beneš, Nikola, Luboš Brim, Ondřej Huvar, Samuel Pastva, and David Šafránek. “BNClassifier: Classifying Boolean Models by Dynamic Properties.” In Computational Methods in Systems Biology, 14971:19–26. Springer Nature, 2024. https://doi.org/10.1007/978-3-031-71671-3_2.' ieee: 'N. Beneš, L. Brim, O. Huvar, S. Pastva, and D. Šafránek, “BNClassifier: Classifying boolean models by dynamic properties,” in Computational Methods in Systems Biology, 2024, vol. 14971, pp. 19–26.' ista: 'Beneš N, Brim L, Huvar O, Pastva S, Šafránek D. 2024. BNClassifier: Classifying boolean models by dynamic properties. Computational Methods in Systems Biology. , LNBI, vol. 14971, 19–26.' mla: 'Beneš, Nikola, et al. “BNClassifier: Classifying Boolean Models by Dynamic Properties.” Computational Methods in Systems Biology, vol. 14971, Springer Nature, 2024, pp. 19–26, doi:10.1007/978-3-031-71671-3_2.' short: N. Beneš, L. Brim, O. Huvar, S. Pastva, D. Šafránek, in:, Computational Methods in Systems Biology, Springer Nature, 2024, pp. 19–26. date_created: 2024-10-06T22:01:12Z date_published: 2024-09-19T00:00:00Z date_updated: 2025-09-08T09:54:27Z day: '19' department: - _id: ToHe doi: 10.1007/978-3-031-71671-3_2 ec_funded: 1 external_id: isi: - '001333144400002' intvolume: ' 14971' isi: 1 language: - iso: eng month: '09' oa_version: None page: 19-26 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Computational Methods in Systems Biology publication_identifier: eissn: - 1611-3349 isbn: - '9783031716706' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'BNClassifier: Classifying boolean models by dynamic properties' type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 14971 year: '2024' ... --- _id: '18206' abstract: - lang: eng text: In the context of in vitro fertilization (IVF), selecting embryos for transfer is critical in determining pregnancy outcomes, with implantation as the essential first milestone for a successful pregnancy. This study introduces the Bonna algorithm, an advanced deep-learning framework engineered to predict embryo implantation probabilities. The algorithm employs a sophisticated integration of machine-learning techniques, utilizing MobileNetV2 for pixel and context embedding, a custom Pix2Pix model for precise segmentation, and a Vision Transformer for additional depth in embedding. MobileNetV2 was chosen for its robust feature extraction capabilities, focusing on textures and edges. The custom Pix2Pix model is adapted for precise segmentation of significant biological features such as the zona pellucida and blastocyst cavity. The Vision Transformer adds a global perspective, capturing complex patterns not apparent in local image segments. Tested on a dataset of images of human blastocysts collected from Ukraine, Israel, and Spain, the Bonna algorithm was rigorously validated through 10-fold cross-validation to ensure its robustness and reliability. It demonstrates superior performance with a mean area under the receiver operating characteristic curve (AUC) of 0.754, significantly outperforming existing models. The study not only advances predictive accuracy in embryo selection but also highlights the algorithm’s clinical applicability due to reliable confidence reporting. alternative_title: - LNCS article_processing_charge: No author: - first_name: Gilad full_name: Rave, Gilad last_name: Rave - first_name: Daniel E. full_name: Fordham, Daniel E. last_name: Fordham - first_name: Alexander full_name: Bronstein, Alexander id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6 last_name: Bronstein orcid: 0000-0001-9699-8730 - first_name: David H. full_name: Silver, David H. last_name: Silver citation: ama: 'Rave G, Fordham DE, Bronstein AM, Silver DH. Enhancing predictive accuracy in embryo implantation: The Bonna algorithm and its clinical implications. In: First International Conference on Artificial Intelligence in Healthcare. Vol 14976. Springer Nature; 2024:160-171. doi:10.1007/978-3-031-67285-9_12' apa: 'Rave, G., Fordham, D. E., Bronstein, A. M., & Silver, D. H. (2024). Enhancing predictive accuracy in embryo implantation: The Bonna algorithm and its clinical implications. In First International Conference on Artificial Intelligence in Healthcare (Vol. 14976, pp. 160–171). Swansea, United Kingdom: Springer Nature. https://doi.org/10.1007/978-3-031-67285-9_12' chicago: 'Rave, Gilad, Daniel E. Fordham, Alex M. Bronstein, and David H. Silver. “Enhancing Predictive Accuracy in Embryo Implantation: The Bonna Algorithm and Its Clinical Implications.” In First International Conference on Artificial Intelligence in Healthcare, 14976:160–71. Springer Nature, 2024. https://doi.org/10.1007/978-3-031-67285-9_12.' ieee: 'G. Rave, D. E. Fordham, A. M. Bronstein, and D. H. Silver, “Enhancing predictive accuracy in embryo implantation: The Bonna algorithm and its clinical implications,” in First International Conference on Artificial Intelligence in Healthcare, Swansea, United Kingdom, 2024, vol. 14976, pp. 160–171.' ista: 'Rave G, Fordham DE, Bronstein AM, Silver DH. 2024. Enhancing predictive accuracy in embryo implantation: The Bonna algorithm and its clinical implications. First International Conference on Artificial Intelligence in Healthcare. AIiH: Artificial Intelligence in Healthcare, LNCS, vol. 14976, 160–171.' mla: 'Rave, Gilad, et al. “Enhancing Predictive Accuracy in Embryo Implantation: The Bonna Algorithm and Its Clinical Implications.” First International Conference on Artificial Intelligence in Healthcare, vol. 14976, Springer Nature, 2024, pp. 160–71, doi:10.1007/978-3-031-67285-9_12.' short: G. Rave, D.E. Fordham, A.M. Bronstein, D.H. Silver, in:, First International Conference on Artificial Intelligence in Healthcare, Springer Nature, 2024, pp. 160–171. conference: end_date: 2024-09-06 location: Swansea, United Kingdom name: 'AIiH: Artificial Intelligence in Healthcare' start_date: 2024-09-04 date_created: 2024-10-08T12:46:23Z date_published: 2024-08-15T00:00:00Z date_updated: 2024-10-09T10:33:39Z day: '15' doi: 10.1007/978-3-031-67285-9_12 extern: '1' intvolume: ' 14976' language: - iso: eng month: '08' oa_version: None page: 160-171 publication: First International Conference on Artificial Intelligence in Healthcare publication_identifier: eisbn: - '9783031672859' eissn: - 1611-3349 isbn: - '9783031672842' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'Enhancing predictive accuracy in embryo implantation: The Bonna algorithm and its clinical implications' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14976 year: '2024' ...