---
OA_place: publisher
OA_type: free access
_id: '18443'
abstract:
- lang: eng
  text: "In [KW06] Kapustin and Witten conjectured that there is a mirror symmetry
    relation between\r\nthe hyperkähler structures on certain Higgs bundle moduli
    spaces. As a consequence, they\r\nconjecture an equivalence between categories
    of BBB and BAA-branes. At the classical\r\nlevel, this mirror symmetry is given
    by T-duality between semi-flat hyperkähler structures on\r\nalgebraic integrable
    systems.\r\nIn this thesis, we investigate the T-duality relation between hyperkähler
    structures and the\r\ncorresponding branes on affine torus bundles. We use the
    techniques of generalized geometry\r\nto show that semi-flat hyperkähler structures
    are T-dual on algebraic integrable systems.\r\nWe also describe T-duality for
    generalized branes. Motivated by Fourier-Mukai transform\r\nwe upgrade the T-duality
    between generalized branes to T-duality of submanifolds endowed\r\nwith U(1)-bundles
    and connections. This T-duality in the appropriate context specializes to\r\nT-duality
    between BBB and BAA-branes.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Maria A
  full_name: Sisak, Maria A
  id: 44A03D04-AEA4-11E9-B225-EA2DE6697425
  last_name: Sisak
citation:
  ama: Sisak MA. T-dual branes on hyperkähler manifolds. 2024. doi:<a href="https://doi.org/10.15479/at:ista:18443">10.15479/at:ista:18443</a>
  apa: Sisak, M. A. (2024). <i>T-dual branes on hyperkähler manifolds</i>. Institute
    of Science and Technology Austria. <a href="https://doi.org/10.15479/at:ista:18443">https://doi.org/10.15479/at:ista:18443</a>
  chicago: Sisak, Maria A. “T-Dual Branes on Hyperkähler Manifolds.” Institute of
    Science and Technology Austria, 2024. <a href="https://doi.org/10.15479/at:ista:18443">https://doi.org/10.15479/at:ista:18443</a>.
  ieee: M. A. Sisak, “T-dual branes on hyperkähler manifolds,” Institute of Science
    and Technology Austria, 2024.
  ista: Sisak MA. 2024. T-dual branes on hyperkähler manifolds. Institute of Science
    and Technology Austria.
  mla: Sisak, Maria A. <i>T-Dual Branes on Hyperkähler Manifolds</i>. Institute of
    Science and Technology Austria, 2024, doi:<a href="https://doi.org/10.15479/at:ista:18443">10.15479/at:ista:18443</a>.
  short: M.A. Sisak, T-Dual Branes on Hyperkähler Manifolds, Institute of Science
    and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-10-19T12:00:37Z
date_published: 2024-10-24T00:00:00Z
date_updated: 2026-04-07T12:42:44Z
day: '24'
ddc:
- '516'
degree_awarded: PhD
department:
- _id: GradSch
- _id: TaHa
doi: 10.15479/at:ista:18443
file:
- access_level: open_access
  checksum: 8c4893e726aaa4b3efb82758da9b6851
  content_type: application/pdf
  creator: msisak
  date_created: 2024-10-23T14:42:45Z
  date_updated: 2024-10-23T14:42:45Z
  file_id: '18467'
  file_name: MASisak_dissertation.pdf
  file_size: 1672547
  relation: main_file
  success: 1
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  checksum: 1831b072e861a1e5481024ca9d02b036
  content_type: application/x-zip-compressed
  creator: msisak
  date_created: 2024-10-23T14:43:56Z
  date_updated: 2024-10-24T08:09:13Z
  file_id: '18468'
  file_name: MASisak_source.zip
  file_size: 617913
  relation: source_file
file_date_updated: 2024-10-24T08:09:13Z
has_accepted_license: '1'
keyword:
- hyperkaehler geometry
- branes
- mirror symmetry
- T-duality
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '10'
oa: 1
oa_version: Published Version
page: '178'
project:
- _id: 6286e8c4-2b32-11ec-9570-f5297902f67f
  grant_number: '26069'
  name: Branes on hyperkÃ¤hler manifolds
publication_identifier:
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Tamás
  full_name: Hausel, Tamás
  id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
  last_name: Hausel
  orcid: 0000-0002-9582-2634
title: T-dual branes on hyperkähler manifolds
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'
...
---
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:<a href="https://doi.org/10.15479/at:ista:17485">10.15479/at:ista:17485</a>'
  apa: 'Frantar, E. (2024). <i>Compressing large neural networks : Algorithms, systems
    and scaling laws</i>. Institute of Science and Technology Austria. <a href="https://doi.org/10.15479/at:ista:17485">https://doi.org/10.15479/at:ista:17485</a>'
  chicago: 'Frantar, Elias. “Compressing Large Neural Networks : Algorithms, Systems
    and Scaling Laws.” Institute of Science and Technology Austria, 2024. <a href="https://doi.org/10.15479/at:ista:17485">https://doi.org/10.15479/at:ista:17485</a>.'
  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. <i>Compressing Large Neural Networks : Algorithms, Systems
    and Scaling Laws</i>. Institute of Science and Technology Austria, 2024, doi:<a
    href="https://doi.org/10.15479/at:ista:17485">10.15479/at:ista:17485</a>.'
  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: 2026-04-07T12:43:04Z
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: '18062'
    relation: part_of_dissertation
    status: public
  - id: '18061'
    relation: part_of_dissertation
    status: public
  - id: '17378'
    relation: part_of_dissertation
    status: public
  - id: '17087'
    relation: part_of_dissertation
    status: public
  - id: '14458'
    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: '18061'
abstract:
- lang: eng
  text: 'Mixture-of-Experts (MoE) architectures offer a general solution to the high
    inference costs of large language models (LLMs) via sparse routing, bringing faster
    and more accurate models, at the cost of massive parameter counts. For example,
    the SwitchTransformer-c2048 model has 1.6 trillion parameters, requiring 3.2TB
    of accelerator memory to run efficiently, which makes practical deployment challenging
    and expensive. In this paper, we present a solution to this memory problem, in
    form of a new compression and execution framework called QMoE. Specifically, QMoE
    consists of a scalable algorithm which accurately compresses trillion-parameter
    MoEs to less than 1 bit per parameter, in a custom format co-designed with bespoke
    GPU decoding kernels to facilitate efficient end-to-end compressed inference,
    with minor runtime overheads relative to uncompressed execution. Concretely, QMoE
    can compress the 1.6 trillion parameter SwitchTransformer-c2048 model to less
    than 160GB (20x compression, 0.8 bits per parameter) at only minor accuracy loss,
    in less than a day on a single GPU. This enables, for the first time, the execution
    of a trillion-parameter model on affordable commodity hardware, like a single
    server with 4x NVIDIA A6000 or 8x NVIDIA 3090 GPUs, at less than 5% runtime overhead
    relative to ideal uncompressed inference. The anonymized code is available at:
    github.com/mlsys24-qmoe/qmoe.'
article_processing_charge: No
author:
- first_name: Elias
  full_name: Frantar, Elias
  id: 09a8f98d-ec99-11ea-ae11-c063a7b7fe5f
  last_name: Frantar
- 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: 'Frantar E, Alistarh D-A. QMoE: Sub-1-bit compression of trillion parameter
    models. In: Gibbons P, Pekhimenko G, De Sa C, eds. <i> Proceedings of Machine
    Learning and Systems</i>. Vol 6. ; 2024.'
  apa: 'Frantar, E., &#38; Alistarh, D.-A. (2024). QMoE: Sub-1-bit compression of
    trillion parameter models. In P. Gibbons, G. Pekhimenko, &#38; C. De Sa (Eds.),
    <i> Proceedings of Machine Learning and Systems</i> (Vol. 6). Santa Clara, CA,
    USA.'
  chicago: 'Frantar, Elias, and Dan-Adrian Alistarh. “QMoE: Sub-1-Bit Compression
    of Trillion Parameter Models.” In <i> Proceedings of Machine Learning and Systems</i>,
    edited by P. Gibbons, G. Pekhimenko, and C. De Sa, Vol. 6, 2024.'
  ieee: 'E. Frantar and D.-A. Alistarh, “QMoE: Sub-1-bit compression of trillion parameter
    models,” in <i> Proceedings of Machine Learning and Systems</i>, Santa Clara,
    CA, USA, 2024, vol. 6.'
  ista: 'Frantar E, Alistarh D-A. 2024. QMoE: Sub-1-bit compression of trillion parameter
    models.  Proceedings of Machine Learning and Systems. MLSys: Machine Learning
    and Systems vol. 6.'
  mla: 'Frantar, Elias, and Dan-Adrian Alistarh. “QMoE: Sub-1-Bit Compression of Trillion
    Parameter Models.” <i> Proceedings of Machine Learning and Systems</i>, edited
    by P. Gibbons et al., vol. 6, 2024.'
  short: E. Frantar, D.-A. Alistarh, in:, P. Gibbons, G. Pekhimenko, C. De Sa (Eds.),  Proceedings
    of Machine Learning and Systems, 2024.
conference:
  end_date: 2024-05-16
  location: Santa Clara, CA, USA
  name: 'MLSys: Machine Learning and Systems'
  start_date: 2024-05-13
corr_author: '1'
date_created: 2024-09-13T10:01:38Z
date_published: 2024-05-01T00:00:00Z
date_updated: 2026-04-07T12:43:03Z
day: '01'
department:
- _id: DaAl
editor:
- first_name: P.
  full_name: Gibbons, P.
  last_name: Gibbons
- first_name: G.
  full_name: Pekhimenko, G.
  last_name: Pekhimenko
- first_name: C.
  full_name: De Sa, C.
  last_name: De Sa
intvolume: '         6'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://proceedings.mlsys.org/paper_files/paper/2024/hash/c74b624843218d9b6713fcf299d6d5e4-Abstract-Conference.html
month: '05'
oa: 1
oa_version: Published Version
publication: ' Proceedings of Machine Learning and Systems'
publication_status: published
quality_controlled: '1'
related_material:
  record:
  - id: '17485'
    relation: dissertation_contains
    status: public
status: public
title: 'QMoE: Sub-1-bit compression of trillion parameter models'
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 6
year: '2024'
...
---
_id: '18062'
abstract:
- lang: eng
  text: 'We explore the impact of parameter sparsity on the scaling behavior of Transformers
    trained on massive datasets (i.e., "foundation models"), in both vision and language
    domains. In this setting, we identify the first scaling law describing the relationship
    between weight sparsity, number of non-zero parameters, and amount of training
    data, which we validate empirically across model and data scales; on ViT/JFT-4B
    and T5/C4. These results allow us to characterize the "optimal sparsity", the
    sparsity level which yields the best performance for a given effective model size
    and training budget. For a fixed number of non-zero parameters, we identify that
    the optimal sparsity increases with the amount of data used for training. We also
    extend our study to different sparsity structures (such as the hardware-friendly
    n:m pattern) and strategies (such as starting from a pretrained dense model).
    Our findings shed light on the power and limitations of weight sparsity across
    various parameter and computational settings, offering both theoretical understanding
    and practical implications for leveraging sparsity towards computational efficiency
    improvements. We provide pruning and scaling law fitting code at: github.com/google-research/jaxpruner/tree/main/jaxpruner/projects/bigsparse.'
article_processing_charge: No
arxiv: 1
author:
- first_name: Elias
  full_name: Frantar, Elias
  id: 09a8f98d-ec99-11ea-ae11-c063a7b7fe5f
  last_name: Frantar
- first_name: Carlos Riquelme
  full_name: Ruiz, Carlos Riquelme
  last_name: Ruiz
- first_name: Neil
  full_name: Houlsby, Neil
  last_name: Houlsby
- first_name: Dan-Adrian
  full_name: Alistarh, Dan-Adrian
  id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
  last_name: Alistarh
  orcid: 0000-0003-3650-940X
- first_name: Utku
  full_name: Evci, Utku
  last_name: Evci
citation:
  ama: 'Frantar E, Ruiz CR, Houlsby N, Alistarh D-A, Evci U. Scaling laws for sparsely-connected
    foundation models. In: <i>The Twelfth International Conference on Learning Representations</i>.
    ; 2024.'
  apa: Frantar, E., Ruiz, C. R., Houlsby, N., Alistarh, D.-A., &#38; Evci, U. (2024).
    Scaling laws for sparsely-connected foundation models. In <i>The Twelfth International
    Conference on Learning Representations</i>. Vienna, Austria.
  chicago: Frantar, Elias, Carlos Riquelme Ruiz, Neil Houlsby, Dan-Adrian Alistarh,
    and Utku Evci. “Scaling Laws for Sparsely-Connected Foundation Models.” In <i>The
    Twelfth International Conference on Learning Representations</i>, 2024.
  ieee: E. Frantar, C. R. Ruiz, N. Houlsby, D.-A. Alistarh, and U. Evci, “Scaling
    laws for sparsely-connected foundation models,” in <i>The Twelfth International
    Conference on Learning Representations</i>, Vienna, Austria, 2024.
  ista: 'Frantar E, Ruiz CR, Houlsby N, Alistarh D-A, Evci U. 2024. Scaling laws for
    sparsely-connected foundation models. The Twelfth International Conference on
    Learning Representations. ICLR: International Conference on Learning Representations.'
  mla: Frantar, Elias, et al. “Scaling Laws for Sparsely-Connected Foundation Models.”
    <i>The Twelfth International Conference on Learning Representations</i>, 2024.
  short: E. Frantar, C.R. Ruiz, N. Houlsby, D.-A. Alistarh, U. Evci, in:, The Twelfth
    International Conference on Learning Representations, 2024.
conference:
  end_date: 2024-05-07
  location: Vienna, Austria
  name: 'ICLR: International Conference on Learning Representations'
  start_date: 2024-05-07
corr_author: '1'
date_created: 2024-09-13T10:31:08Z
date_published: 2024-01-16T00:00:00Z
date_updated: 2026-04-07T12:43:03Z
day: '16'
department:
- _id: DaAl
external_id:
  arxiv:
  - '2309.08520'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://openreview.net/forum?id=i9K2ZWkYIP
month: '01'
oa: 1
oa_version: Published Version
publication: The Twelfth International Conference on Learning Representations
publication_status: published
quality_controlled: '1'
related_material:
  record:
  - id: '17485'
    relation: dissertation_contains
    status: public
scopus_import: '1'
status: public
title: Scaling laws for sparsely-connected foundation models
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2024'
...
---
OA_place: publisher
_id: '17208'
abstract:
- lang: eng
  text: "Can current quantum computers provide a speedup over their classical counterparts
    for some kinds of problems? In this thesis, with a focus on ground state search/preparation,
    we address some of the challenges that both quantum annealing and variational
    quantum algorithms suffer from, hindering any possible practical speedup in comparison
    to the best classical counterparts. \r\n\r\nIn the first part of the thesis, we
    study the performance of quantum annealing for solving a particular combinatorial
    optimization problem called 3-XOR satisfability (3-XORSAT). The classical problem
    is mapped into a ground state search of a 3-local classical Hamiltonian $H_C$.
    We consider how modifying the initial problem, by adding more interaction terms
    to the corresponding Hamiltonian, leads to the emergence of a first-order phase
    transition during the annealing process. This phenomenon causes the total annealing
    duration, $T$, required to prepare the ground state of $H_C$ with a high probability
    to increase exponentially with the size of the problem. Our findings indicate
    that with the growing complexity of problem instances, the likelihood of encountering
    first-order phase transitions also increases, making quantum annealing an impractical
    solution for these types of combinatorial optimization problems.\r\n\r\nIn the
    second part, we focus on the problem of barren plateaus in generic variational
    quantum algorithms. Barren plateaus correspond to flat regions in the parameter
    space where the gradient of the cost function is zero in expectation, and with
    the variance decaying exponentially with the system size, thus obstructing an
    efficient parameter optimization.  We propose an algorithm to circumvent Barren
    Plateaus by monitoring the entanglement entropy of k-local reduced density matrices,
    alongside a method for estimating entanglement entropy via classical shadow tomography.
    We illustrate the approach with the paradigmatic example of the variational quantum
    eigensolver, and show that our algorithm effectively avoids barren plateaus in
    the initialization as well as during the optimization stage. \r\n\r\nLastly, in
    the last two Chapters of this thesis, we focus on the quantum approximate optimization
    algorithm (QAOA), originally introduced as an algorithm for solving generic combinatorial
    optimization problems in near-term quantum devices. Specifically, we focus on
    how to develop rigorous initialization strategies with guarantee improvement.
    Our motivation for this study lies in that for random initialization, the optimization
    typically leads to local minima with poor performance. Our main result corresponds
    to the analytical construction of index-1 saddle points or transition states,
    stationary points with a single direction of descent, as a tool for systematically
    exploring the QAOA optimization landscape. This leads us to propose a novel greedy
    parameter initialization strategy that guarantees for the energy to decrease with
    an increasing number of circuit layers. Furthermore, with precise estimates for
    the negative Hessian eigenvalue and its eigenvector, we establish a lower bound
    for energy improvement following a QAOA iteration."
acknowledged_ssus:
- _id: ScienComp
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Raimel A
  full_name: Medina Ramos, Raimel A
  id: CE680B90-D85A-11E9-B684-C920E6697425
  last_name: Medina Ramos
  orcid: 0000-0002-5383-2869
citation:
  ama: Medina Ramos RA. Exploring the optimization landscape of variational quantum
    algorithms. 2024. doi:<a href="https://doi.org/10.15479/at:ista:17208">10.15479/at:ista:17208</a>
  apa: Medina Ramos, R. A. (2024). <i>Exploring the optimization landscape of variational
    quantum algorithms</i>. Institute of Science and Technology Austria. <a href="https://doi.org/10.15479/at:ista:17208">https://doi.org/10.15479/at:ista:17208</a>
  chicago: Medina Ramos, Raimel A. “Exploring the Optimization Landscape of Variational
    Quantum Algorithms.” Institute of Science and Technology Austria, 2024. <a href="https://doi.org/10.15479/at:ista:17208">https://doi.org/10.15479/at:ista:17208</a>.
  ieee: R. A. Medina Ramos, “Exploring the optimization landscape of variational quantum
    algorithms,” Institute of Science and Technology Austria, 2024.
  ista: Medina Ramos RA. 2024. Exploring the optimization landscape of variational
    quantum algorithms. Institute of Science and Technology Austria.
  mla: Medina Ramos, Raimel A. <i>Exploring the Optimization Landscape of Variational
    Quantum Algorithms</i>. Institute of Science and Technology Austria, 2024, doi:<a
    href="https://doi.org/10.15479/at:ista:17208">10.15479/at:ista:17208</a>.
  short: R.A. Medina Ramos, Exploring the Optimization Landscape of Variational Quantum
    Algorithms, Institute of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-07-09T09:14:24Z
date_published: 2024-07-09T00:00:00Z
date_updated: 2026-04-07T12:43:22Z
day: '09'
ddc:
- '539'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MaSe
doi: 10.15479/at:ista:17208
ec_funded: 1
file:
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  date_created: 2024-07-09T09:21:44Z
  date_updated: 2024-07-10T11:34:09Z
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  file_size: 11253627
  relation: main_file
  success: 1
file_date_updated: 2024-07-17T09:23:24Z
has_accepted_license: '1'
keyword:
- Quantum computing
- Variational Quantum Algorithms
- Optimization
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '133'
project:
- _id: 23841C26-32DE-11EA-91FC-C7463DDC885E
  call_identifier: H2020
  grant_number: '850899'
  name: 'Non-Ergodic Quantum Matter: Universality, Dynamics and Control'
publication_identifier:
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
  record:
  - id: '10545'
    relation: part_of_dissertation
    status: public
  - id: '10067'
    relation: part_of_dissertation
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    relation: part_of_dissertation
    status: public
  - id: '13125'
    relation: part_of_dissertation
    status: public
  - id: '11471'
    relation: part_of_dissertation
    status: public
status: public
supervisor:
- first_name: Maksym
  full_name: Serbyn, Maksym
  id: 47809E7E-F248-11E8-B48F-1D18A9856A87
  last_name: Serbyn
  orcid: 0000-0002-2399-5827
title: Exploring the optimization landscape of variational quantum algorithms
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'
...
---
OA_place: repository
_id: '17222'
abstract:
- lang: eng
  text: "The quantum approximate optimization algorithm (QAOA) uses a quantum computer\r\nto
    implement a variational method with $2p$ layers of alternating unitary\r\noperators,
    optimized by a classical computer to minimize a cost function. While\r\nrigorous
    performance guarantees exist for the QAOA at small depths $p$, the\r\nbehavior
    at large depths remains less clear, though simulations suggest\r\nexponentially
    fast convergence for certain problems. In this work, we gain\r\ninsights into
    the deep QAOA using an analytic expansion of the cost function\r\naround transition
    states. Transition states are constructed in a recursive\r\nmanner: from the local
    minima of the QAOA with $p$ layers we obtain transition\r\nstates of the QAOA
    with $p+1$ layers, which are stationary points characterized\r\nby a unique direction
    of negative curvature. We construct an analytic estimate\r\nof the negative curvature
    and the corresponding direction in parameter space at\r\neach transition state.
    The expansion of the QAOA cost function along the\r\nnegative direction to the
    quartic order gives a lower bound of the QAOA cost\r\nfunction improvement. We
    provide physical intuition behind the analytic\r\nexpressions for the local curvature
    and quartic expansion coefficient. Our\r\nnumerical study confirms the accuracy
    of our approximations and reveals that\r\nthe obtained bound and the true value
    of the QAOA cost function gain have a\r\ncharacteristic exponential decrease with
    the number of layers $p$, with the\r\nbound decreasing more rapidly. Our study
    establishes an analytical method for\r\nrecursively studying the QAOA that is
    applicable in the regime of high circuit\r\ndepth."
article_number: '2405.10125'
article_processing_charge: No
arxiv: 1
author:
- first_name: Raimel A
  full_name: Medina Ramos, Raimel A
  id: CE680B90-D85A-11E9-B684-C920E6697425
  last_name: Medina Ramos
  orcid: 0000-0002-5383-2869
- first_name: Maksym
  full_name: Serbyn, Maksym
  id: 47809E7E-F248-11E8-B48F-1D18A9856A87
  last_name: Serbyn
  orcid: 0000-0002-2399-5827
citation:
  ama: Medina Ramos RA, Serbyn M. A recursive lower bound on the energy improvement
    of the quantum approximate optimization algorithm. <i>arXiv</i>. doi:<a href="https://doi.org/10.48550/arXiv.2405.10125">10.48550/arXiv.2405.10125</a>
  apa: Medina Ramos, R. A., &#38; Serbyn, M. (n.d.). A recursive lower bound on the
    energy improvement of the quantum approximate optimization algorithm. <i>arXiv</i>.
    <a href="https://doi.org/10.48550/arXiv.2405.10125">https://doi.org/10.48550/arXiv.2405.10125</a>
  chicago: Medina Ramos, Raimel A, and Maksym Serbyn. “A Recursive Lower Bound on
    the Energy Improvement of the Quantum Approximate Optimization Algorithm.” <i>ArXiv</i>,
    n.d. <a href="https://doi.org/10.48550/arXiv.2405.10125">https://doi.org/10.48550/arXiv.2405.10125</a>.
  ieee: R. A. Medina Ramos and M. Serbyn, “A recursive lower bound on the energy improvement
    of the quantum approximate optimization algorithm,” <i>arXiv</i>. .
  ista: Medina Ramos RA, Serbyn M. A recursive lower bound on the energy improvement
    of the quantum approximate optimization algorithm. arXiv, 2405.10125.
  mla: Medina Ramos, Raimel A., and Maksym Serbyn. “A Recursive Lower Bound on the
    Energy Improvement of the Quantum Approximate Optimization Algorithm.” <i>ArXiv</i>,
    2405.10125, doi:<a href="https://doi.org/10.48550/arXiv.2405.10125">10.48550/arXiv.2405.10125</a>.
  short: R.A. Medina Ramos, M. Serbyn, ArXiv (n.d.).
corr_author: '1'
date_created: 2024-07-10T13:12:09Z
date_published: 2024-05-16T00:00:00Z
date_updated: 2026-04-07T12:43:22Z
day: '16'
department:
- _id: MaSe
doi: 10.48550/arXiv.2405.10125
external_id:
  arxiv:
  - '2405.10125'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.48550/arXiv.2405.10125
month: '05'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: draft
related_material:
  record:
  - id: '17208'
    relation: dissertation_contains
    status: public
status: public
title: A recursive lower bound on the energy improvement of the quantum approximate
  optimization algorithm
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: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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:<a href="https://doi.org/10.15479/at:ista:18132">10.15479/at:ista:18132</a>
  apa: Glas, J. (2024). <i>Counting rational points over function fields</i>. Institute
    of Science and Technology Austria. <a href="https://doi.org/10.15479/at:ista:18132">https://doi.org/10.15479/at:ista:18132</a>
  chicago: Glas, Jakob. “Counting Rational Points over Function Fields.” Institute
    of Science and Technology Austria, 2024. <a href="https://doi.org/10.15479/at:ista:18132">https://doi.org/10.15479/at:ista:18132</a>.
  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. <i>Counting Rational Points over Function Fields</i>. Institute
    of Science and Technology Austria, 2024, doi:<a href="https://doi.org/10.15479/at:ista:18132">10.15479/at:ista:18132</a>.
  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
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  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
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  checksum: 08bb6f14c42b47ff25882a2ce3ea0d8a
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  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'
...
---
_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). <i>Journal of the London Mathematical Society</i>. 2024;110(4). doi:<a
    href="https://doi.org/10.1112/jlms.12991">10.1112/jlms.12991</a>
  apa: Glas, J. (2024). Rational points on complete intersections of cubic and quadric
    hypersurfaces over Fq(t). <i>Journal of the London Mathematical Society</i>. London
    Mathematical Society. <a href="https://doi.org/10.1112/jlms.12991">https://doi.org/10.1112/jlms.12991</a>
  chicago: Glas, Jakob. “Rational Points on Complete Intersections of Cubic and Quadric
    Hypersurfaces over Fq(T).” <i>Journal of the London Mathematical Society</i>.
    London Mathematical Society, 2024. <a href="https://doi.org/10.1112/jlms.12991">https://doi.org/10.1112/jlms.12991</a>.
  ieee: J. Glas, “Rational points on complete intersections of cubic and quadric hypersurfaces
    over Fq(t),” <i>Journal of the London Mathematical Society</i>, 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).” <i>Journal of the London Mathematical Society</i>,
    vol. 110, no. 4, e12991, London Mathematical Society, 2024, doi:<a href="https://doi.org/10.1112/jlms.12991">10.1112/jlms.12991</a>.
  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
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  creator: dernst
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  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'
...
---
OA_place: repository
_id: '18295'
abstract:
- lang: eng
  text: By developing a suitable version of the circle method, we show that the space
    of degree e rational curves on a smooth hypersurface of degree d has only canonical
    singularities provided its dimension is sufficiently large with respect to e and
    d.
article_processing_charge: No
arxiv: 1
author:
- first_name: Jakob
  full_name: Glas, Jakob
  id: d6423cba-dc74-11ea-a0a7-ee61689ff5fb
  last_name: Glas
citation:
  ama: Glas J. Canonical singularities on moduli spaces of rational curves via the 
    circle method. <i>arXiv</i>. doi:<a href="https://doi.org/10.48550/arXiv.2405.16648">10.48550/arXiv.2405.16648</a>
  apa: Glas, J. (n.d.). Canonical singularities on moduli spaces of rational curves
    via the  circle method. <i>arXiv</i>. <a href="https://doi.org/10.48550/arXiv.2405.16648">https://doi.org/10.48550/arXiv.2405.16648</a>
  chicago: Glas, Jakob. “Canonical Singularities on Moduli Spaces of Rational Curves
    via the  Circle Method.” <i>ArXiv</i>, n.d. <a href="https://doi.org/10.48550/arXiv.2405.16648">https://doi.org/10.48550/arXiv.2405.16648</a>.
  ieee: J. Glas, “Canonical singularities on moduli spaces of rational curves via
    the  circle method,” <i>arXiv</i>. .
  ista: Glas J. Canonical singularities on moduli spaces of rational curves via the 
    circle method. arXiv, <a href="https://doi.org/10.48550/arXiv.2405.16648">10.48550/arXiv.2405.16648</a>.
  mla: Glas, Jakob. “Canonical Singularities on Moduli Spaces of Rational Curves via
    the  Circle Method.” <i>ArXiv</i>, doi:<a href="https://doi.org/10.48550/arXiv.2405.16648">10.48550/arXiv.2405.16648</a>.
  short: J. Glas, ArXiv (n.d.).
corr_author: '1'
date_created: 2024-10-10T13:15:43Z
date_published: 2024-05-26T00:00:00Z
date_updated: 2026-04-07T12:53:53Z
day: '26'
department:
- _id: TiBr
doi: 10.48550/arXiv.2405.16648
external_id:
  arxiv:
  - '2405.16648'
language:
- iso: eng
main_file_link:
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month: '05'
oa: 1
oa_version: Preprint
project:
- _id: bd8a4fdc-d553-11ed-ba76-80a0167441a3
  grant_number: P36278
  name: Rational curves via function field analytic number theory
publication: arXiv
publication_status: submitted
related_material:
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    relation: later_version
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status: public
title: Canonical singularities on moduli spaces of rational curves via the  circle
  method
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: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2024'
...
---
OA_place: publisher
_id: '18667'
abstract:
- lang: eng
  text: "Many chemical and physical properties of materials are determined by the
    material’s shape,\r\nfor example the size of its pores and the width of its tunnels.
    This makes materials science\r\na prime application area for geometrical and topological
    methods. Nevertheless many\r\nmethods in topological data analysis have not been
    satisfyingly extended to the needs of\r\nmaterials science. This thesis provides
    new methods and new mathematical theorems\r\ntargeted at those specific needs
    by answering four different research questions. While the\r\nmotivation for each
    of the research questions arises from materials science, the methods\r\nare versatile
    and can be applied in different areas as well. \r\n\r\nThe first research question
    is concerned with image data, for example a three-dimensional\r\ncomputed tomography
    (CT) scan of a material, like sand or stone. There are two commonly\r\nused topologies
    for digital images and depending on the application either of them might be\r\nrequired.
    However, software for computing the topological data analysis method persistence\r\nhomology,
    usually supports only one of the two topologies. We answer the question how to\r\ncompute
    persistent homology of an image with respect to one of the two topologies using\r\nsoftware
    that is intended for the other topology. \r\n\r\nThe second research question
    is concerned with image data as well, and asks how much\r\nof the topological
    information of an image is lost when the resolution is coarsened. As\r\ncomputer
    tomography scanners are more expensive the higher the resolution, it is an\r\nimportant
    question in materials science to know which resolution is enough to get satisfying\r\npersistent
    homology. We give theoretical bounds on the information loss based on different\r\ngeometrical
    properties of the object to be scanned. In addition, we conduct experiments on\r\nsand
    and stone CT image data. \r\n\r\nThe third research question is motivated by comparing
    crystalline materials efficiently. As\r\nthe atoms within a crystal repeat periodically,
    crystalline materials are either modeled by\r\nunmanageable infinite periodic
    point sets, or by one of their fundamental domains, which is\r\nunstable under
    perturbation. Therefore a fingerprint of crystalline materials is needed, with\r\nappropriate
    properties such that comparing the crystals can be eased by comparing the\r\nfingerprints
    instead. We define the density fingerprint and prove the necessary properties.
    \r\n\r\nThe fourth research question is motivated by studying the hole-structure
    or connectedness,\r\ni.e. persistent homology or merge trees, of crystalline materials.
    A common way to deal\r\nwith periodicity is to take a fundamental domain and identify
    opposite boundaries to form a\r\ntorus. However, computing persistent homology
    or merge trees on that torus loses some\r\nof the information materials scientists
    are interested in and is additionally not stable under\r\ncertain noise. We therefore
    decorate the merge tree stemming from the torus with additional\r\ninformation
    describing the density and growth rate of the periodic copies of a component\r\nwithin
    a growing spherical window. We prove all desired properties, like stability and
    efficient\r\ncomputability."
acknowledgement: "I was supported by the European Research Council (ERC) Horizon 2020
  project\r\n“Alpha Shape Theory Extended” No. 788183 and by the Pöttinger Scholarship.
  In addition,\r\nI am very thankful for having been able to attend the second Workshop
  for Women in\r\nComputational Topology in July 2019, funded by the Mathematical
  Sciences Institute at\r\nANU, the US National Science Foundation through the award
  CCF-1841455, the Australian\r\nMathematical Sciences Institute and the Association
  for Women in Mathematics. Two of the\r\nprojects presented in this thesis started
  there. One of them reached completion thanks to\r\nfunding from the MSRI Summer
  Research in Mathematics program awarded to me and my\r\ncollaborators in 2020."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Teresa
  full_name: Heiss, Teresa
  id: 4879BB4E-F248-11E8-B48F-1D18A9856A87
  last_name: Heiss
  orcid: 0000-0002-1780-2689
citation:
  ama: Heiss T. New methods for applying topological data analysis to materials science.
    2024. doi:<a href="https://doi.org/10.15479/at:ista:18667">10.15479/at:ista:18667</a>
  apa: Heiss, T. (2024). <i>New methods for applying topological data analysis to
    materials science</i>. Institute of Science and Technology Austria. <a href="https://doi.org/10.15479/at:ista:18667">https://doi.org/10.15479/at:ista:18667</a>
  chicago: Heiss, Teresa. “New Methods for Applying Topological Data Analysis to Materials
    Science.” Institute of Science and Technology Austria, 2024. <a href="https://doi.org/10.15479/at:ista:18667">https://doi.org/10.15479/at:ista:18667</a>.
  ieee: T. Heiss, “New methods for applying topological data analysis to materials
    science,” Institute of Science and Technology Austria, 2024.
  ista: Heiss T. 2024. New methods for applying topological data analysis to materials
    science. Institute of Science and Technology Austria.
  mla: Heiss, Teresa. <i>New Methods for Applying Topological Data Analysis to Materials
    Science</i>. Institute of Science and Technology Austria, 2024, doi:<a href="https://doi.org/10.15479/at:ista:18667">10.15479/at:ista:18667</a>.
  short: T. Heiss, New Methods for Applying Topological Data Analysis to Materials
    Science, Institute of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-12-17T16:17:55Z
date_published: 2024-12-17T00:00:00Z
date_updated: 2026-04-07T12:54:10Z
day: '17'
ddc:
- '514'
- '516'
- '004'
degree_awarded: PhD
department:
- _id: GradSch
- _id: HeEd
doi: 10.15479/at:ista:18667
ec_funded: 1
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  creator: theiss
  date_created: 2024-12-19T10:24:46Z
  date_updated: 2024-12-19T10:24:46Z
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  relation: source_file
file_date_updated: 2024-12-19T10:24:50Z
has_accepted_license: '1'
keyword:
- persistent homology
- topological data analysis
- periodic
- crystalline materials
- images
- fingerprint
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '111'
project:
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  call_identifier: H2020
  grant_number: '788183'
  name: Alpha Shape Theory Extended
publication_identifier:
  isbn:
  - 978-3-99078-052-7
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
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    relation: part_of_dissertation
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  - id: '9345'
    relation: part_of_dissertation
    status: public
status: public
supervisor:
- first_name: Herbert
  full_name: Edelsbrunner, Herbert
  id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
  last_name: Edelsbrunner
  orcid: 0000-0002-9823-6833
title: New methods for applying topological data analysis to materials science
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  short: CC BY (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...
---
OA_place: repository
_id: '18673'
abstract:
- lang: eng
  text: "Motivated by applications to crystalline materials, we generalize the merge
    tree and the related barcode of a filtered complex to the periodic setting in
    Euclidean space. They are invariant under isometries, changing bases, and indeed
    changing lattices. In addition, we prove stability under perturbations and provide
    an algorithm that under mild geometric conditions typically satisfied by crystalline
    materials takes O((n+m)logn) time, in which n and m are the numbers of vertices
    and edges in the quotient complex, respectively.\r\n"
acknowledgement: "Both authors are partially supported by the European Research Council
  (ERC) Horizon 2020 project\r\n‘Alpha Shape Theory Extended’, grant no. 788183. The
  first author is also partially supported by the DFG\r\nCollaborative Research Center
  TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund\r\n(FWF),
  grant no. I 02979-N35."
article_processing_charge: No
arxiv: 1
author:
- first_name: Herbert
  full_name: Edelsbrunner, Herbert
  id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
  last_name: Edelsbrunner
  orcid: 0000-0002-9823-6833
- first_name: Teresa
  full_name: Heiss, Teresa
  id: 4879BB4E-F248-11E8-B48F-1D18A9856A87
  last_name: Heiss
  orcid: 0000-0002-1780-2689
citation:
  ama: Edelsbrunner H, Heiss T. Merge trees of periodic filtrations. <i>arXiv</i>.
    doi:<a href="https://doi.org/10.48550/arXiv.2408.16575">10.48550/arXiv.2408.16575</a>
  apa: Edelsbrunner, H., &#38; Heiss, T. (n.d.). Merge trees of periodic filtrations.
    <i>arXiv</i>. <a href="https://doi.org/10.48550/arXiv.2408.16575">https://doi.org/10.48550/arXiv.2408.16575</a>
  chicago: Edelsbrunner, Herbert, and Teresa Heiss. “Merge Trees of Periodic Filtrations.”
    <i>ArXiv</i>, n.d. <a href="https://doi.org/10.48550/arXiv.2408.16575">https://doi.org/10.48550/arXiv.2408.16575</a>.
  ieee: H. Edelsbrunner and T. Heiss, “Merge trees of periodic filtrations,” <i>arXiv</i>.
    .
  ista: Edelsbrunner H, Heiss T. Merge trees of periodic filtrations. arXiv, <a href="https://doi.org/10.48550/arXiv.2408.16575">10.48550/arXiv.2408.16575</a>.
  mla: Edelsbrunner, Herbert, and Teresa Heiss. “Merge Trees of Periodic Filtrations.”
    <i>ArXiv</i>, doi:<a href="https://doi.org/10.48550/arXiv.2408.16575">10.48550/arXiv.2408.16575</a>.
  short: H. Edelsbrunner, T. Heiss, ArXiv (n.d.).
corr_author: '1'
date_created: 2024-12-18T14:06:57Z
date_published: 2024-08-29T00:00:00Z
date_updated: 2026-04-07T12:54:09Z
day: '29'
department:
- _id: HeEd
doi: 10.48550/arXiv.2408.16575
ec_funded: 1
external_id:
  arxiv:
  - '2408.16575'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.48550/arXiv.2408.16575
month: '08'
oa: 1
oa_version: Preprint
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '788183'
  name: Alpha Shape Theory Extended
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: I02979-N35
  name: Persistence and stability of geometric complexes
publication: arXiv
publication_status: draft
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title: Merge trees of periodic filtrations
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  short: CC BY (4.0)
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_place: publisher
_id: '14711'
abstract:
- lang: eng
  text: "In nature, different species find their niche in a range of environments,
    each with its unique characteristics. While some thrive in uniform (homogeneous)
    landscapes where environmental conditions stay relatively consistent across space,
    others traverse the complexities of spatially heterogeneous terrains. Comprehending
    how species are distributed and how they interact within these landscapes holds
    the key to gaining insights into their evolutionary dynamics while also informing
    conservation and management strategies.\r\n\r\nFor species inhabiting heterogeneous
    landscapes, when the rate of dispersal is low compared to spatial fluctuations
    in selection pressure, localized adaptations may emerge. Such adaptation in response
    to varying selection strengths plays an important role in the persistence of populations
    in our rapidly changing world. Hence, species in nature are continuously in a
    struggle to adapt to local environmental conditions, to ensure their continued
    survival. Natural populations can often adapt in time scales short enough for
    evolutionary changes to influence ecological dynamics and vice versa, thereby
    creating a feedback between evolution and demography. The analysis of this feedback
    and the relative contributions of gene flow, demography, drift, and natural selection
    to genetic variation and differentiation has remained a recurring theme in evolutionary
    biology. Nevertheless, the effective role of these forces in maintaining variation
    and shaping patterns of diversity is not fully understood. Even in homogeneous
    environments devoid of local adaptations, such understanding remains elusive.
    Understanding this feedback is crucial, for example in determining the conditions
    under which extinction risk can be mitigated in peripheral populations subject
    to deleterious mutation accumulation at the edges of species’ ranges\r\nas well
    as in highly fragmented populations.\r\n\r\nIn this thesis we explore both uniform
    and spatially heterogeneous metapopulations, investigating and providing theoretical
    insights into the dynamics of local adaptation in the latter and examining the
    dynamics of load and extinction as well as the impact of joint ecological and
    evolutionary (eco-evolutionary) dynamics in the former. The thesis is divided
    into 5 chapters.\r\n\r\nChapter 1 provides a general introduction into the subject
    matter, clarifying concepts and ideas used throughout the thesis. In chapter 2,
    we explore how fast a species distributed across a heterogeneous landscape adapts
    to changing conditions marked by alterations in carrying capacity, selection pressure,
    and migration rate.\r\n\r\nIn chapter 3, we investigate how migration selection
    and drift influences adaptation and the maintenance of variation in a metapopulation
    with three habitats, an extension of previous models of adaptation in two habitats.
    We further develop analytical approximations for the critical threshold required
    for polymorphism to persist.\r\n\r\nThe focus of chapter 4 of the thesis is on
    understanding the interplay between ecology and evolution as coupled processes.
    We investigate how eco-evolutionary feedback between migration, selection, drift,
    and demography influences eco-evolutionary outcomes in marginal populations subject
    to deleterious mutation accumulation. Using simulations as well as theoretical
    approximations of the coupled dynamics of population size and allele frequency,
    we analyze how gene flow from a large mainland source influences genetic load
    and population size on an island (i.e., in a marginal population) under genetically
    realistic assumptions. Analyses of this sort are important because small isolated
    populations, are repeatedly affected by complex interactions between ecological
    and evolutionary processes, which can lead to their death. Understanding these
    interactions can therefore provide an insight into the conditions under which
    extinction risk can be mitigated in peripheral populations thus, contributing
    to conservation and restoration efforts.\r\n\r\nChapter 5 extends the analysis
    in chapter 4 to consider the dynamics of load (due to deleterious mutation accumulation)
    and extinction risk in a metapopulation. We explore the role of gene flow, selection,
    and dominance on load and extinction risk and further pinpoint critical thresholds
    required for metapopulation persistence.\r\n\r\nOverall this research contributes
    to our understanding of ecological and evolutionary mechanisms that shape species’
    persistence in fragmented landscapes, a crucial foundation for successful conservation
    efforts and biodiversity management."
acknowledged_ssus:
- _id: SSU
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Oluwafunmilola O
  full_name: Olusanya, Oluwafunmilola O
  id: 41AD96DC-F248-11E8-B48F-1D18A9856A87
  last_name: Olusanya
  orcid: 0000-0003-1971-8314
citation:
  ama: Olusanya OO. Local adaptation, genetic load and extinction in metapopulations.
    2024. doi:<a href="https://doi.org/10.15479/at:ista:14711">10.15479/at:ista:14711</a>
  apa: Olusanya, O. O. (2024). <i>Local adaptation, genetic load and extinction in
    metapopulations</i>. Institute of Science and Technology Austria. <a href="https://doi.org/10.15479/at:ista:14711">https://doi.org/10.15479/at:ista:14711</a>
  chicago: Olusanya, Oluwafunmilola O. “Local Adaptation, Genetic Load and Extinction
    in Metapopulations.” Institute of Science and Technology Austria, 2024. <a href="https://doi.org/10.15479/at:ista:14711">https://doi.org/10.15479/at:ista:14711</a>.
  ieee: O. O. Olusanya, “Local adaptation, genetic load and extinction in metapopulations,”
    Institute of Science and Technology Austria, 2024.
  ista: Olusanya OO. 2024. Local adaptation, genetic load and extinction in metapopulations.
    Institute of Science and Technology Austria.
  mla: Olusanya, Oluwafunmilola O. <i>Local Adaptation, Genetic Load and Extinction
    in Metapopulations</i>. Institute of Science and Technology Austria, 2024, doi:<a
    href="https://doi.org/10.15479/at:ista:14711">10.15479/at:ista:14711</a>.
  short: O.O. Olusanya, Local Adaptation, Genetic Load and Extinction in Metapopulations,
    Institute of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2023-12-26T22:49:53Z
date_published: 2024-01-19T00:00:00Z
date_updated: 2026-04-07T12:54:29Z
day: '19'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: NiBa
- _id: GradSch
doi: 10.15479/at:ista:14711
ec_funded: 1
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month: '01'
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page: '183'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '665385'
  name: International IST Doctoral Program
- _id: c08d3278-5a5b-11eb-8a69-fdb09b55f4b8
  grant_number: P32896
  name: Causes and consequences of population fragmentation
- _id: 34c872fe-11ca-11ed-8bc3-8534b82131e6
  grant_number: '26380'
  name: Polygenic Adaptation in a Metapopulation
publication_identifier:
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
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status: public
supervisor:
- first_name: Nicholas H
  full_name: Barton, Nicholas H
  id: 4880FE40-F248-11E8-B48F-1D18A9856A87
  last_name: Barton
  orcid: 0000-0002-8548-5240
- first_name: Jitka
  full_name: Polechova, Jitka
  last_name: Polechova
- first_name: Himani
  full_name: Sachdeva, Himani
  last_name: Sachdeva
title: Local adaptation, genetic load and extinction in metapopulations
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type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
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...
---
OA_place: publisher
_id: '17156'
abstract:
- lang: eng
  text: "This dissertation is the summary of the author’s work, concerning the relations
    between\r\ncohomology rings of algebraic varieties and rings of functions on zero
    schemes and fixed\r\npoint schemes. For most of the thesis, the focus is on smooth
    complex varieties with\r\nan action of a principally paired group, e.g. a parabolic
    subgroup of a reductive group.\r\nThe fundamental theorem 5.2.11 from co-authored
    article [66] says that if the principal\r\nnilpotent has a unique zero, then the
    zero scheme over the Kostant section is isomorphic\r\nto the spectrum of the equivariant
    cohomology ring, remembering the grading in terms of\r\na C^* action. A similar
    statement is proved also for the G-invariant functions on the total\r\nzero scheme
    over the whole Lie algebra. Additionally, we are able to prove an analogous\r\nresult
    for the GKM spaces, which poses the question on a joint generalisation.\r\nWe
    also tackle the situation of a singular variety. As long as it is embedded in
    a smooth\r\nvariety with regular action, we are able to study its cohomology as
    well by means of\r\nthe zero scheme. In case of e.g. Schubert varieties this determines
    the cohomology ring\r\ncompletely. In largest generality, this allows us to see
    a significant part of the cohomology\r\nring.\r\nWe also show (Theorem 6.2.1)
    that the cohomology ring of spherical varieties appears as\r\nthe ring of functions
    on the zero scheme. The computational aspect is not easy, but one\r\ncan hope
    that this can bring some concrete information about such cohomology rings.\r\nLastly,
    the K-theory conjecture 6.3.1 is studied, with some results attained for GKM\r\nspaces.\r\nThe
    thesis includes also an introduction to group actions on algebraic varieties.
    In\r\nparticular, the vector fields associated to the actions are extensively
    studied. We also\r\nprovide a version of the Kostant section for arbitrary principally
    paired group, which\r\nparametrises the regular orbits in the Lie algebra of an
    algebraic group. Before proving\r\nthe main theorem, we also include a historical
    overview of the field. In particular we bring\r\ntogether the results of Akyildiz,
    Carrell and Lieberman on non-equivariant cohomology\r\nrings."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Kamil P
  full_name: Rychlewicz, Kamil P
  id: 85A07246-A8BF-11E9-B4FA-D9E3E5697425
  last_name: Rychlewicz
citation:
  ama: Rychlewicz KP. Equivariant cohomology and rings of functions. 2024. doi:<a
    href="https://doi.org/10.15479/at:ista:17156">10.15479/at:ista:17156</a>
  apa: Rychlewicz, K. P. (2024). <i>Equivariant cohomology and rings of functions</i>.
    Institute of Science and Technology Austria. <a href="https://doi.org/10.15479/at:ista:17156">https://doi.org/10.15479/at:ista:17156</a>
  chicago: Rychlewicz, Kamil P. “Equivariant Cohomology and Rings of Functions.” Institute
    of Science and Technology Austria, 2024. <a href="https://doi.org/10.15479/at:ista:17156">https://doi.org/10.15479/at:ista:17156</a>.
  ieee: K. P. Rychlewicz, “Equivariant cohomology and rings of functions,” Institute
    of Science and Technology Austria, 2024.
  ista: Rychlewicz KP. 2024. Equivariant cohomology and rings of functions. Institute
    of Science and Technology Austria.
  mla: Rychlewicz, Kamil P. <i>Equivariant Cohomology and Rings of Functions</i>.
    Institute of Science and Technology Austria, 2024, doi:<a href="https://doi.org/10.15479/at:ista:17156">10.15479/at:ista:17156</a>.
  short: K.P. Rychlewicz, Equivariant Cohomology and Rings of Functions, Institute
    of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-06-23T15:07:06Z
date_published: 2024-06-25T00:00:00Z
date_updated: 2026-04-07T12:55:46Z
day: '25'
ddc:
- '516'
degree_awarded: PhD
department:
- _id: TaHa
- _id: GradSch
doi: 10.15479/at:ista:17156
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  file_size: 3695952
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keyword:
- equivariant cohomology
- zero schemes
- algebraic groups
- Lie algebras
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '117'
project:
- _id: 34cd0f74-11ca-11ed-8bc3-bf0492a14a24
  grant_number: '26525'
  name: Topology of open smooth varieties with a torus action
publication_identifier:
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
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    relation: part_of_dissertation
    status: public
status: public
supervisor:
- first_name: Tamás
  full_name: Hausel, Tamás
  id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
  last_name: Hausel
  orcid: 0000-0002-9582-2634
title: Equivariant cohomology and rings of functions
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  short: CC BY-NC-SA (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...
---
OA_place: publisher
OA_type: gold
_id: '18515'
abstract:
- lang: eng
  text: "Understanding the role of evolutionary processes in shaping genetic variation
    has been a\r\nprimary goal in evolutionary genetics. In this regard, a key question
    is how genetically\r\ndistinct populations evolve in the face of gene flow, thereby
    generating genetic and\r\nphenotypic divergence and reproductive isolation (RI).
    This requires quantifying the role\r\nand relative contributions of prezygotic
    and postzygotic isolating mechanisms on the\r\nreduction of gene exchange between
    populations, and identifying regions in the genome\r\nthat mediate RI, which is
    often polygenic. Further, this needs distinguishing neutral and\r\nselected regions
    in the genome, and discerning how selection influences patterns of neutral\r\ndivergence.\r\nPopulation
    structure, defined as any deviation from panmixia, such as geographic distribution,
    movement and mating patterns of individuals, influences how genetic variation
    is\r\nstructured in space and shapes the neutral null model. Availability of large
    scale spatial\r\ngenomic datasets now enables us to detect signatures of population
    structure in genetic\r\ndata and infer population genetic parameters. Such inferences
    are crucial and have wide\r\napplications in biodiversity, conservation genetics,
    population management and medical\r\ngenetics. However, inferences are based on
    assumptions that do not always match the\r\ncomplex reality, thus leading to erroneous
    conclusions. Moreover, the role and interaction\r\nof heterogeneous population
    density and dispersal, which are ubiquitous in nature, has\r\nbeen challenging
    to study owing to their mathematical complexity. In such scenarios,\r\nfeedback
    between theory, data and simulations can prove to be useful.\r\nIn this thesis,
    I examine the effect of population structure on neutral genetic variation\r\nand
    barriers to gene exchange in hybridising populations, thereby bridging together
    the\r\nfields of spatial population genetics and speciation.\r\nDespite being
    a key concept in speciation, reproductive isolation (RI) lacks a quantitative\r\ndefinition
    and has been used and measured differently across different fields. Chapter 2\r\ngives
    a quantitative definition of RI, in terms of the effect of genetic differences
    on gene\r\nflow. We give analytical predictions for RI in a range of scenarios,
    in terms of effective migration rates for discrete populations and barrier strength
    for continuous populations.\r\nIn addition to this, we discuss current measures
    of RI and their limitations, and propose\r\nthe need for new measures that combine
    organismal and genetic perspectives of RI.\r\nIn chapter 3, I examine the combined
    effect of assortative mating, sexual selection\r\nand viability selection on RI.
    For this, we consider a polygenic ‘magic’ trait under a\r\nmainland-island model.
    We obtain novel theoretical predictions for molecular divergence\r\nin terms of
    effective migration rates, which bears a simple relationship to measurable\r\nfitness
    components of migrants and various early generation hybrids. We explore the\r\nconditions
    under which local adaptation can be maintained despite maladaptive gene flow\r\nand
    quantify the relative contributions of viability and sexual selection to genome-wide\r\nbarriers
    to gene flow.\r\nThe next two chapters of the thesis focus on a hybrid zone of
    Antirrhinum majus that\r\nconsist of two subspecies- the magenta flowered A. m.
    pseudomajus and the yellow\r\nflowered A.m. striatum. Previous studies have suggested
    that flower colour is target of\r\npollinator mediated selection and is influenced
    only by few genes. While these regions\r\nshow high genetic differentiation between
    the subspecies, the rest of the genome is seen\r\nto be well mixed. Chapter 4
    examines the effects of heterogeneous population density\r\nand leptokurtic dispersal
    on isolation by distance and the distribution of heterozygosity\r\nby focusing
    on non-flower colour markers.\r\nChapter 5 analyses cline shapes and associations
    among 6 focal flower colour markers to\r\nunderstand how selection and dispersal
    maintain this hybrid zone. We see sharp coincident\r\nstepped clines at all loci
    and positive associations throughout the hybrid zone, contrary to\r\nthe expected
    patterns from diffusive gene flow. With a novel scheme of inferring dispersal\r\ncombined
    with multilocus simulations, we show that stepped clines do not reflect genetic\r\nbarriers
    to gene flow, but are rather a result of long-distance migration. This framework\r\nallows
    us to get realistic estimates gene flow and selection and shows how traditional
    cline\r\nanalysis may lead to inaccurate conclusions when assumptions of the theory
    are not met.\r\nOverall, this thesis investigates how different features of population
    structure leave\r\ndetectable signatures in genetic variation, namely in patterns
    of isolation by distance,\r\nlinkage disequilibrium and genetic divergence. It
    also highlights how effective migration\r\nrates provide useful way of analysing
    polygenic architectures and shed new light into\r\nhybrid zones. In doing so,
    I identify scenarios when simple models become insufficient\r\nand suggest possibe
    directions by combining genetic data with simulations."
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "I also acknowledge the funding agencies Marie Curie COFUND Doctoral
  Fellowship,\r\nAustrian Science Fund FWF (grant P32166) and ERC (grant PR1000ERC02)
  for financially\r\nsupporting my research over the years."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Parvathy
  full_name: Surendranadh, Parvathy
  id: 455235B8-F248-11E8-B48F-1D18A9856A87
  last_name: Surendranadh
  orcid: 0000-0001-6395-386X
citation:
  ama: Surendranadh P. Effect of population structure on neutral genetic variation
    and barriers to gene exchange. 2024. doi:<a href="https://doi.org/10.15479/at:ista:18515">10.15479/at:ista:18515</a>
  apa: Surendranadh, P. (2024). <i>Effect of population structure on neutral genetic
    variation and barriers to gene exchange</i>. Institute of Science and Technology
    Austria. <a href="https://doi.org/10.15479/at:ista:18515">https://doi.org/10.15479/at:ista:18515</a>
  chicago: Surendranadh, Parvathy. “Effect of Population Structure on Neutral Genetic
    Variation and Barriers to Gene Exchange.” Institute of Science and Technology
    Austria, 2024. <a href="https://doi.org/10.15479/at:ista:18515">https://doi.org/10.15479/at:ista:18515</a>.
  ieee: P. Surendranadh, “Effect of population structure on neutral genetic variation
    and barriers to gene exchange,” Institute of Science and Technology Austria, 2024.
  ista: Surendranadh P. 2024. Effect of population structure on neutral genetic variation
    and barriers to gene exchange. Institute of Science and Technology Austria.
  mla: Surendranadh, Parvathy. <i>Effect of Population Structure on Neutral Genetic
    Variation and Barriers to Gene Exchange</i>. Institute of Science and Technology
    Austria, 2024, doi:<a href="https://doi.org/10.15479/at:ista:18515">10.15479/at:ista:18515</a>.
  short: P. Surendranadh, Effect of Population Structure on Neutral Genetic Variation
    and Barriers to Gene Exchange, Institute of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-11-06T21:25:37Z
date_published: 2024-11-07T00:00:00Z
date_updated: 2026-04-07T12:56:52Z
day: '07'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: GradSch
- _id: NiBa
doi: 10.15479/at:ista:18515
file:
- access_level: open_access
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  creator: psurendr
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  date_updated: 2024-11-07T10:59:29Z
  file_id: '18519'
  file_name: PhD_Thesis__Parvathy_071124_PDFA.pdf
  file_size: 37019760
  relation: main_file
  success: 1
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  checksum: 4417e02d54084d89e75734e18caaa96d
  content_type: application/zip
  creator: psurendr
  date_created: 2024-11-07T10:59:42Z
  date_updated: 2024-11-07T10:59:42Z
  file_id: '18520'
  file_name: PhD Thesis- Parvathy_071124.zip
  file_size: 41198857
  relation: source_file
file_date_updated: 2024-11-07T10:59:42Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '219'
project:
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
  grant_number: P32166
  name: Snapdragon Speciation
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
  grant_number: '101055327'
  name: Understanding the evolution of continuous genomes
publication_identifier:
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Nicholas H
  full_name: Barton, Nicholas H
  id: 4880FE40-F248-11E8-B48F-1D18A9856A87
  last_name: Barton
  orcid: 0000-0002-8548-5240
title: Effect of population structure on neutral genetic variation and barriers to
  gene exchange
tmp:
  image: /images/cc_by_nc_sa.png
  legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
    BY-NC-SA 4.0)
  short: CC BY-NC-SA (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2024'
...
---
OA_place: repository
_id: '18689'
abstract:
- lang: eng
  text: Multiplexed fluorescence microscopy imaging is widely used in biomedical applications.
    However, simultaneous imaging of multiple fluorophores can result in spectral
    leaks and overlapping, which greatly degrades image quality and subsequent analysis.
    Existing popular spectral unmixing methods are mainly based on computational intensive
    linear models and the performance is heavily dependent on the reference spectra,
    which may greatly preclude its further applications. In this paper, we propose
    a deep learning-based blindly spectral unmixing method, termed AutoUnmix, to imitate
    the physical spectral mixing process. A tranfer learning framework is further
    devised to allow our AutoUnmix adapting to a variety of imaging systems without
    retraining the network. Our proposed method has demonstrated real-time unmixing
    capabilities, surpassing existing methods by up to 100-fold in terms of unmixing
    speed. We further validate the reconstruction performance on both synthetic datasets
    and biological samples. The unmixing results of AutoUnmix achieve a highest SSIM
    of 0.99 in both three- and four-color imaging, with nearly up to 20% higher than
    other popular unmixing methods. Due to the desirable property of data independency
    and superior blind unmixing performance, we believe AutoUnmix is a powerful tool
    to study the interaction process of different organelles labeled by multiple fluorophores.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: M-Shop
- _id: E-Lib
acknowledgement: "We gratefully acknowledge support by the Scientific Service Units
  at ISTA, including the Imaging and Optics and Lab Support facilities and the mechanical
  workshop and Library. We thank Philipp Velicky for STED microscope alignment.\r\n\r\nThis
  project has received funding from the Austrian Science Fund (FWF): I 3630-B25 (J.G.D)
  and the European Research Council (ERC) under the European Union’s Horizon 2020
  research and innovation programme (grant agreement No 742985, J.F.). It has also
  received funding from the European Union’s Horizon 2020 research and innovation
  programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. S.T. has
  received funding as an ISTplus Fellow from the European Union’s Horizon 2020 Research
  and Innovation Programme under Marie Skłodowska-Curie grant agreement no. 754411
  and from an EMBO Long-Term Fellowship (grant number ALTF 679-2018). It has further
  received funding from the Austrian Science Fund (FWF) grant DK W1232 (M.T, N.A-D.,
  J.G.D). W.J. received funding via a Human Frontier Science Program postdoctoral
  fellowship LT000557/2018.\r\n\r\nThe funders had no role in study design, data collection
  and analysis, decision to publish or preparation of the manuscript."
article_processing_charge: No
author:
- first_name: Michelle C
  full_name: Gallei, Michelle C
  id: 35A03822-F248-11E8-B48F-1D18A9856A87
  last_name: Gallei
  orcid: 0000-0003-1286-7368
- first_name: Sven M
  full_name: Truckenbrodt, Sven M
  id: 45812BD4-F248-11E8-B48F-1D18A9856A87
  last_name: Truckenbrodt
- first_name: Caroline
  full_name: Kreuzinger, Caroline
  id: 382077BA-F248-11E8-B48F-1D18A9856A87
  last_name: Kreuzinger
- first_name: Syamala
  full_name: Inumella, Syamala
  id: F8660870-D756-11E9-98C5-34DFE5697425
  last_name: Inumella
  orcid: 0009-0002-5890-120X
- first_name: Vitali
  full_name: Vistunou, Vitali
  id: 7e146587-8972-11ed-ae7b-d7a32ea86a81
  last_name: Vistunou
- first_name: Christoph M
  full_name: Sommer, Christoph M
  id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
  last_name: Sommer
  orcid: 0000-0003-1216-9105
- first_name: Mojtaba
  full_name: Tavakoli, Mojtaba
  id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
  last_name: Tavakoli
  orcid: 0000-0002-7667-6854
- first_name: Nathalie
  full_name: Agudelo Duenas, Nathalie
  id: 40E7F008-F248-11E8-B48F-1D18A9856A87
  last_name: Agudelo Duenas
- first_name: Jakob
  full_name: Vorlaufer, Jakob
  id: 937696FA-C996-11E9-8C7C-CF13E6697425
  last_name: Vorlaufer
  orcid: 0009-0000-7590-3501
- first_name: Wiebke
  full_name: Jahr, Wiebke
  id: 425C1CE8-F248-11E8-B48F-1D18A9856A87
  last_name: Jahr
  orcid: 0000-0003-0201-2315
- first_name: Marek
  full_name: Randuch, Marek
  id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae
  last_name: Randuch
- first_name: Alexander J
  full_name: Johnson, Alexander J
  id: 46A62C3A-F248-11E8-B48F-1D18A9856A87
  last_name: Johnson
  orcid: 0000-0002-2739-8843
- first_name: Eva
  full_name: Benková, Eva
  id: 38F4F166-F248-11E8-B48F-1D18A9856A87
  last_name: Benková
  orcid: 0000-0002-8510-9739
- first_name: Jiří
  full_name: Friml, Jiří
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
- first_name: Johann G
  full_name: Danzl, Johann G
  id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
  last_name: Danzl
  orcid: 0000-0001-8559-3973
citation:
  ama: Gallei MC, Truckenbrodt SM, Kreuzinger C, et al. Super-resolution expansion
    microscopy in plant roots. <i>bioRxiv</i>. doi:<a href="https://doi.org/10.1101/2024.02.21.581330">10.1101/2024.02.21.581330</a>
  apa: Gallei, M. C., Truckenbrodt, S. M., Kreuzinger, C., Inumella, S., Vistunou,
    V., Sommer, C. M., … Danzl, J. G. (n.d.). Super-resolution expansion microscopy
    in plant roots. <i>bioRxiv</i>. <a href="https://doi.org/10.1101/2024.02.21.581330">https://doi.org/10.1101/2024.02.21.581330</a>
  chicago: Gallei, Michelle C, Sven M Truckenbrodt, Caroline Kreuzinger, Syamala Inumella,
    Vitali Vistunou, Christoph M Sommer, Mojtaba Tavakoli, et al. “Super-Resolution
    Expansion Microscopy in Plant Roots.” <i>BioRxiv</i>, n.d. <a href="https://doi.org/10.1101/2024.02.21.581330">https://doi.org/10.1101/2024.02.21.581330</a>.
  ieee: M. C. Gallei <i>et al.</i>, “Super-resolution expansion microscopy in plant
    roots,” <i>bioRxiv</i>. .
  ista: Gallei MC, Truckenbrodt SM, Kreuzinger C, Inumella S, Vistunou V, Sommer CM,
    Tavakoli M, Agudelo Duenas N, Vorlaufer J, Jahr W, Randuch M, Johnson AJ, Benková
    E, Friml J, Danzl JG. Super-resolution expansion microscopy in plant roots. bioRxiv,
    <a href="https://doi.org/10.1101/2024.02.21.581330">10.1101/2024.02.21.581330</a>.
  mla: Gallei, Michelle C., et al. “Super-Resolution Expansion Microscopy in Plant
    Roots.” <i>BioRxiv</i>, doi:<a href="https://doi.org/10.1101/2024.02.21.581330">10.1101/2024.02.21.581330</a>.
  short: M.C. Gallei, S.M. Truckenbrodt, C. Kreuzinger, S. Inumella, V. Vistunou,
    C.M. Sommer, M. Tavakoli, N. Agudelo Duenas, J. Vorlaufer, W. Jahr, M. Randuch,
    A.J. Johnson, E. Benková, J. Friml, J.G. Danzl, BioRxiv (n.d.).
corr_author: '1'
date_created: 2024-12-19T12:28:00Z
date_published: 2024-02-21T00:00:00Z
date_updated: 2026-04-07T12:56:36Z
day: '21'
department:
- _id: EvBe
- _id: JoDa
- _id: JiFr
doi: 10.1101/2024.02.21.581330
ec_funded: 1
language:
- iso: eng
main_file_link:
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  url: https://doi.org/10.1101/2024.02.21.581330
month: '02'
oa: 1
oa_version: Preprint
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '742985'
  name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '665385'
  name: International IST Doctoral Program
- _id: 260C2330-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '754411'
  name: ISTplus - Postdoctoral Fellowships
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: W1232-B24
  name: Molecular Drug Targets
- _id: 269B5B22-B435-11E9-9278-68D0E5697425
  grant_number: ALTF 679-2018
  name: UltraX - achieving sub-nanometer resolution in light microscopy using iterative
    X10 microscopy in combination with nanobodies and STED
publication: bioRxiv
publication_status: draft
related_material:
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status: public
title: Super-resolution expansion microscopy in plant roots
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: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_embargo: '20'
OA_place: publisher
_id: '18681'
acknowledged_ssus:
- _id: Bio
- _id: PreCl
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Mojtaba
  full_name: Tavakoli, Mojtaba
  id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
  last_name: Tavakoli
  orcid: 0000-0002-7667-6854
citation:
  ama: 'Tavakoli M. Developing molecular and structural tools for studying brain architecture
    with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics
    reconstruction with light microscopy. 2024. doi:<a href="https://doi.org/10.15479/at:ista:18681">10.15479/at:ista:18681</a>'
  apa: 'Tavakoli, M. (2024). <i>Developing molecular and structural tools for studying
    brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed
    connectomics reconstruction with light microscopy</i>. Institute of Science and
    Technology Austria. <a href="https://doi.org/10.15479/at:ista:18681">https://doi.org/10.15479/at:ista:18681</a>'
  chicago: 'Tavakoli, Mojtaba. “Developing Molecular and Structural Tools for Studying
    Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed
    Connectomics Reconstruction with Light Microscopy.” Institute of Science and Technology
    Austria, 2024. <a href="https://doi.org/10.15479/at:ista:18681">https://doi.org/10.15479/at:ista:18681</a>.'
  ieee: 'M. Tavakoli, “Developing molecular and structural tools for studying brain
    architecture with super resolution expansion microscopy. LICONN: Molecularly-informed
    connectomics reconstruction with light microscopy,” Institute of Science and Technology
    Austria, 2024.'
  ista: 'Tavakoli M. 2024. Developing molecular and structural tools for studying
    brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed
    connectomics reconstruction with light microscopy. Institute of Science and Technology
    Austria.'
  mla: 'Tavakoli, Mojtaba. <i>Developing Molecular and Structural Tools for Studying
    Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed
    Connectomics Reconstruction with Light Microscopy</i>. Institute of Science and
    Technology Austria, 2024, doi:<a href="https://doi.org/10.15479/at:ista:18681">10.15479/at:ista:18681</a>.'
  short: 'M. Tavakoli, Developing Molecular and Structural Tools for Studying Brain
    Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed
    Connectomics Reconstruction with Light Microscopy, Institute of Science and Technology
    Austria, 2024.'
corr_author: '1'
date_created: 2024-12-19T02:30:39Z
date_published: 2024-12-20T00:00:00Z
date_updated: 2026-04-07T12:56:37Z
day: '20'
ddc:
- '600'
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: JoDa
doi: 10.15479/at:ista:18681
file:
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  date_created: 2024-12-20T10:23:17Z
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language:
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month: '12'
oa_version: Published Version
page: '230'
project:
- _id: 6285a163-2b32-11ec-9570-8e204ca2dba5
  grant_number: '26137'
  name: Studying Organelle Structure and Function at Nanoscale Resolution with Expansion
    Microscopy
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: W1232-B24
  name: Molecular Drug Targets
publication_identifier:
  isbn:
  - 978-3-99078-048-0
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
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    relation: part_of_dissertation
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  - id: '18688'
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  - id: '18677'
    relation: part_of_dissertation
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  - id: '18689'
    relation: part_of_dissertation
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status: public
supervisor:
- first_name: Johann G
  full_name: Danzl, Johann G
  id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
  last_name: Danzl
  orcid: 0000-0001-8559-3973
title: 'Developing molecular and structural tools for studying brain architecture
  with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics
  reconstruction with light microscopy'
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'
...
---
OA_place: publisher
_id: '15094'
abstract:
- lang: eng
  text: "Point sets, geometric networks, and arrangements of hyperplanes are fundamental
    objects in\r\ndiscrete geometry that have captivated mathematicians for centuries,
    if not millennia. This\r\nthesis seeks to cast new light on these structures by
    illustrating specific instances where a\r\ntopological perspective, specifically
    through discrete Morse theory and persistent homology,\r\nprovides valuable insights.\r\n\r\nAt
    first glance, the topology of these geometric objects might seem uneventful: point
    sets\r\nessentially lack of topology, arrangements of hyperplanes are a decomposition
    of Rd, which\r\nis a contractible space, and the topology of a network primarily
    involves the enumeration\r\nof connected components and cycles within the network.
    However, beneath this apparent\r\nsimplicity, there lies an array of intriguing
    structures, a small subset of which will be uncovered\r\nin this thesis.\r\n\r\nFocused
    on three case studies, each addressing one of the mentioned objects, this work\r\nwill
    showcase connections that intertwine topology with diverse fields such as combinatorial\r\ngeometry,
    algorithms and data structures, and emerging applications like spatial biology.\r\n\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Sebastiano
  full_name: Cultrera di Montesano, Sebastiano
  id: 34D2A09C-F248-11E8-B48F-1D18A9856A87
  last_name: Cultrera di Montesano
  orcid: 0000-0001-6249-0832
citation:
  ama: Cultrera di Montesano S. Persistence and Morse theory for discrete geometric
    structures. 2024. doi:<a href="https://doi.org/10.15479/at:ista:15094">10.15479/at:ista:15094</a>
  apa: Cultrera di Montesano, S. (2024). <i>Persistence and Morse theory for discrete
    geometric structures</i>. Institute of Science and Technology Austria. <a href="https://doi.org/10.15479/at:ista:15094">https://doi.org/10.15479/at:ista:15094</a>
  chicago: Cultrera di Montesano, Sebastiano. “Persistence and Morse Theory for Discrete
    Geometric Structures.” Institute of Science and Technology Austria, 2024. <a href="https://doi.org/10.15479/at:ista:15094">https://doi.org/10.15479/at:ista:15094</a>.
  ieee: S. Cultrera di Montesano, “Persistence and Morse theory for discrete geometric
    structures,” Institute of Science and Technology Austria, 2024.
  ista: Cultrera di Montesano S. 2024. Persistence and Morse theory for discrete geometric
    structures. Institute of Science and Technology Austria.
  mla: Cultrera di Montesano, Sebastiano. <i>Persistence and Morse Theory for Discrete
    Geometric Structures</i>. Institute of Science and Technology Austria, 2024, doi:<a
    href="https://doi.org/10.15479/at:ista:15094">10.15479/at:ista:15094</a>.
  short: S. Cultrera di Montesano, Persistence and Morse Theory for Discrete Geometric
    Structures, Institute of Science and Technology Austria, 2024.
corr_author: '1'
date_created: 2024-03-08T15:28:10Z
date_published: 2024-03-08T00:00:00Z
date_updated: 2026-04-07T12:58:48Z
day: '08'
ddc:
- '514'
- '500'
- '516'
degree_awarded: PhD
department:
- _id: GradSch
- _id: HeEd
doi: 10.15479/at:ista:15094
ec_funded: 1
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month: '03'
oa: 1
oa_version: Published Version
page: '108'
project:
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  call_identifier: H2020
  grant_number: '788183'
  name: Alpha Shape Theory Extended
- _id: 268116B8-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: Z00342
  name: Mathematics, Computer Science
- _id: 0aa4bc98-070f-11eb-9043-e6fff9c6a316
  grant_number: I4887
  name: Persistent Homology, Algorithms and Stochastic Geometry
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: I02979-N35
  name: Persistence and stability of geometric complexes
publication_identifier:
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
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supervisor:
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  full_name: Edelsbrunner, Herbert
  id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
  last_name: Edelsbrunner
  orcid: 0000-0002-9823-6833
title: Persistence and Morse theory for discrete geometric structures
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...
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abstract:
- lang: eng
  text: "We characterize critical points of 1-dimensional maps paired in persistent
    homology\r\ngeometrically and this way get elementary proofs of theorems about
    the symmetry\r\nof persistence diagrams and the variation of such maps. In particular,
    we identify\r\nbranching points and endpoints of networks as the sole source of
    asymmetry and\r\nrelate the cycle basis in persistent homology with a version
    of the stable marriage\r\nproblem. Our analysis provides the foundations of fast
    algorithms for maintaining a\r\ncollection of sorted lists together with its persistence
    diagram."
acknowledgement: Open access funding provided by Austrian Science Fund (FWF). This
  project has received funding from the European Research Council (ERC) under the
  European Union’s Horizon 2020 research and innovation programme, grant no. 788183,
  from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and
  from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry
  and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35. The authors of
  this paper thank anonymous reviewers for their constructive criticism and Monika
  Henzinger for detailed comments on an earlier version of this paper.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Ranita
  full_name: Biswas, Ranita
  id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
  last_name: Biswas
  orcid: 0000-0002-5372-7890
- first_name: Sebastiano
  full_name: Cultrera Di Montesano, Sebastiano
  id: 34D2A09C-F248-11E8-B48F-1D18A9856A87
  last_name: Cultrera Di Montesano
  orcid: 0000-0001-6249-0832
- first_name: Herbert
  full_name: Edelsbrunner, Herbert
  id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
  last_name: Edelsbrunner
  orcid: 0000-0002-9823-6833
- first_name: Morteza
  full_name: Saghafian, Morteza
  id: f86f7148-b140-11ec-9577-95435b8df824
  last_name: Saghafian
citation:
  ama: Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Geometric characterization
    of the persistence of 1D maps. <i>Journal of Applied and Computational Topology</i>.
    2024;8:1101-1119. doi:<a href="https://doi.org/10.1007/s41468-023-00126-9">10.1007/s41468-023-00126-9</a>
  apa: Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., &#38; Saghafian, M.
    (2024). Geometric characterization of the persistence of 1D maps. <i>Journal of
    Applied and Computational Topology</i>. Springer Nature. <a href="https://doi.org/10.1007/s41468-023-00126-9">https://doi.org/10.1007/s41468-023-00126-9</a>
  chicago: Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner,
    and Morteza Saghafian. “Geometric Characterization of the Persistence of 1D Maps.”
    <i>Journal of Applied and Computational Topology</i>. Springer Nature, 2024. <a
    href="https://doi.org/10.1007/s41468-023-00126-9">https://doi.org/10.1007/s41468-023-00126-9</a>.
  ieee: R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “Geometric
    characterization of the persistence of 1D maps,” <i>Journal of Applied and Computational
    Topology</i>, vol. 8. Springer Nature, pp. 1101–1119, 2024.
  ista: Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. 2024. Geometric
    characterization of the persistence of 1D maps. Journal of Applied and Computational
    Topology. 8, 1101–1119.
  mla: Biswas, Ranita, et al. “Geometric Characterization of the Persistence of 1D
    Maps.” <i>Journal of Applied and Computational Topology</i>, vol. 8, Springer
    Nature, 2024, pp. 1101–19, doi:<a href="https://doi.org/10.1007/s41468-023-00126-9">10.1007/s41468-023-00126-9</a>.
  short: R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, Journal
    of Applied and Computational Topology 8 (2024) 1101–1119.
corr_author: '1'
date_created: 2023-07-02T22:00:44Z
date_published: 2024-10-01T00:00:00Z
date_updated: 2026-04-07T12:58:47Z
day: '01'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1007/s41468-023-00126-9
ec_funded: 1
external_id:
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  - '39678706'
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intvolume: '         8'
language:
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month: '10'
oa: 1
oa_version: Published Version
page: 1101-1119
pmid: 1
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '788183'
  name: Alpha Shape Theory Extended
- _id: 0aa4bc98-070f-11eb-9043-e6fff9c6a316
  grant_number: I4887
  name: Persistent Homology, Algorithms and Stochastic Geometry
- _id: 268116B8-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: Z00342
  name: Mathematics, Computer Science
publication: Journal of Applied and Computational Topology
publication_identifier:
  eissn:
  - 2367-1734
  issn:
  - 2367-1726
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
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scopus_import: '1'
status: public
title: Geometric characterization of the persistence of 1D maps
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  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2024'
...
---
_id: '15093'
abstract:
- lang: eng
  text: We present a dynamic data structure for maintaining the persistent homology
    of a time series of real numbers. The data structure supports local operations,
    including the insertion and deletion of an item and the cutting and concatenating
    of lists, each in time O(log n + k), in which n counts the critical items and
    k the changes in the augmented persistence diagram. To achieve this, we design
    a tailor-made tree structure with an unconventional representation, referred to
    as banana tree, which may be useful in its own right.
acknowledgement: The  first  and  second  authors  are  funded  by  the  European  Research  Council  under  the
  European Union’s Horizon 2020 research and innovation programme, ERC grant no. 788183,“Alpha
  Shape Theory Extended (Alpha)”, by the Wittgenstein Prize, FWF grant no. Z 342-N31,
  and by the DFG Collaborative Research Center TRR 109, FWF grant no. I 02979-N35.The
  third author received funding by the European Research Council under the European
  Union’s Horizon 2020research  and  innovation  programme,  ERC  grant  no.  101019564,  “The  Design  of  Modern  Fully  Dynamic  DataStructures
  (MoDynStruct)”, and by the Austrian Science Fund through the Wittgenstein Prize
  with FWF grant no. Z 422-N, and also by FWF grant no. I 5982-N, and by FWF grant
  no. P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.  The
  fourth author is funded by the Vienna Graduate School on Computational Optimization,
  FWF project no. W1260-N35.
article_processing_charge: No
arxiv: 1
author:
- first_name: Sebastiano
  full_name: Cultrera di Montesano, Sebastiano
  id: 34D2A09C-F248-11E8-B48F-1D18A9856A87
  last_name: Cultrera di Montesano
  orcid: 0000-0001-6249-0832
- first_name: Herbert
  full_name: Edelsbrunner, Herbert
  id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
  last_name: Edelsbrunner
  orcid: 0000-0002-9823-6833
- first_name: Monika H
  full_name: Henzinger, Monika H
  id: 540c9bbd-f2de-11ec-812d-d04a5be85630
  last_name: Henzinger
  orcid: 0000-0002-5008-6530
- first_name: Lara
  full_name: Ost, Lara
  last_name: Ost
citation:
  ama: 'Cultrera di Montesano S, Edelsbrunner H, Henzinger M, Ost L. Dynamically maintaining
    the persistent homology of time series. In: Woodruff DP, ed. <i>Proceedings of
    the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA)</i>. Society
    for Industrial and Applied Mathematics; 2024:243-295. doi:<a href="https://doi.org/10.1137/1.9781611977912.11">10.1137/1.9781611977912.11</a>'
  apa: 'Cultrera di Montesano, S., Edelsbrunner, H., Henzinger, M., &#38; Ost, L.
    (2024). Dynamically maintaining the persistent homology of time series. In D.
    P. Woodruff (Ed.), <i>Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete
    Algorithms (SODA)</i> (pp. 243–295). Alexandria, VA, USA: Society for Industrial
    and Applied Mathematics. <a href="https://doi.org/10.1137/1.9781611977912.11">https://doi.org/10.1137/1.9781611977912.11</a>'
  chicago: Cultrera di Montesano, Sebastiano, Herbert Edelsbrunner, Monika Henzinger,
    and Lara Ost. “Dynamically Maintaining the Persistent Homology of Time Series.”
    In <i>Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms
    (SODA)</i>, edited by David P. Woodruff, 243–95. Society for Industrial and Applied
    Mathematics, 2024. <a href="https://doi.org/10.1137/1.9781611977912.11">https://doi.org/10.1137/1.9781611977912.11</a>.
  ieee: S. Cultrera di Montesano, H. Edelsbrunner, M. Henzinger, and L. Ost, “Dynamically
    maintaining the persistent homology of time series,” in <i>Proceedings of the
    2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA)</i>, Alexandria,
    VA, USA, 2024, pp. 243–295.
  ista: 'Cultrera di Montesano S, Edelsbrunner H, Henzinger M, Ost L. 2024. Dynamically
    maintaining the persistent homology of time series. Proceedings of the 2024 Annual
    ACM-SIAM Symposium on Discrete Algorithms (SODA). SODA: Symposium on Discrete
    Algorithms, 243–295.'
  mla: Cultrera di Montesano, Sebastiano, et al. “Dynamically Maintaining the Persistent
    Homology of Time Series.” <i>Proceedings of the 2024 Annual ACM-SIAM Symposium
    on Discrete Algorithms (SODA)</i>, edited by David P. Woodruff, Society for Industrial
    and Applied Mathematics, 2024, pp. 243–95, doi:<a href="https://doi.org/10.1137/1.9781611977912.11">10.1137/1.9781611977912.11</a>.
  short: S. Cultrera di Montesano, H. Edelsbrunner, M. Henzinger, L. Ost, in:, D.P.
    Woodruff (Ed.), Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete
    Algorithms (SODA), Society for Industrial and Applied Mathematics, 2024, pp. 243–295.
conference:
  end_date: 2024-01-10
  location: Alexandria, VA, USA
  name: 'SODA: Symposium on Discrete Algorithms'
  start_date: 2024-01-07
corr_author: '1'
date_created: 2024-03-08T10:27:39Z
date_published: 2024-01-04T00:00:00Z
date_updated: 2026-04-07T12:58:47Z
day: '04'
department:
- _id: HeEd
- _id: MoHe
doi: 10.1137/1.9781611977912.11
ec_funded: 1
editor:
- first_name: David P.
  full_name: Woodruff, David P.
  last_name: Woodruff
external_id:
  arxiv:
  - '2311.01115'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/2311.01115
month: '01'
oa: 1
oa_version: Preprint
page: 243 - 295
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '788183'
  name: Alpha Shape Theory Extended
- _id: 268116B8-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: Z00342
  name: Mathematics, Computer Science
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
  call_identifier: H2020
  grant_number: '101019564'
  name: The design and evaluation of modern fully dynamic data structures
- _id: 34def286-11ca-11ed-8bc3-da5948e1613c
  grant_number: Z00422
  name: Efficient algorithms
- _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe
  grant_number: P33775
  name: Fast Algorithms for a Reactive Network Layer
publication: Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms
  (SODA)
publication_identifier:
  eisbn:
  - '9781611977912'
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
related_material:
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scopus_import: '1'
status: public
title: Dynamically maintaining the persistent homology of time series
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_place: repository
_id: '15091'
abstract:
- lang: eng
  text: "Motivated by applications in the medical sciences, we study finite chromatic\r\nsets
    in Euclidean space from a topological perspective. Based on the persistent\r\nhomology
    for images, kernels and cokernels, we design provably stable\r\nhomological quantifiers
    that describe the geometric micro- and macro-structure\r\nof how the color classes
    mingle. These can be efficiently computed using\r\nchromatic variants of Delaunay
    and alpha complexes, and code that does these\r\ncomputations is provided."
article_number: '2212.03128'
article_processing_charge: No
arxiv: 1
author:
- first_name: Sebastiano
  full_name: Cultrera di Montesano, Sebastiano
  id: 34D2A09C-F248-11E8-B48F-1D18A9856A87
  last_name: Cultrera di Montesano
  orcid: 0000-0001-6249-0832
- first_name: Ondrej
  full_name: Draganov, Ondrej
  id: 2B23F01E-F248-11E8-B48F-1D18A9856A87
  last_name: Draganov
  orcid: 0000-0003-0464-3823
- first_name: Herbert
  full_name: Edelsbrunner, Herbert
  id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
  last_name: Edelsbrunner
  orcid: 0000-0002-9823-6833
- first_name: Morteza
  full_name: Saghafian, Morteza
  id: f86f7148-b140-11ec-9577-95435b8df824
  last_name: Saghafian
citation:
  ama: Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic
    alpha complexes. <i>arXiv</i>. doi:<a href="https://doi.org/10.48550/arXiv.2212.03128">10.48550/arXiv.2212.03128</a>
  apa: Cultrera di Montesano, S., Draganov, O., Edelsbrunner, H., &#38; Saghafian,
    M. (n.d.). Chromatic alpha complexes. <i>arXiv</i>. <a href="https://doi.org/10.48550/arXiv.2212.03128">https://doi.org/10.48550/arXiv.2212.03128</a>
  chicago: Cultrera di Montesano, Sebastiano, Ondrej Draganov, Herbert Edelsbrunner,
    and Morteza Saghafian. “Chromatic Alpha Complexes.” <i>ArXiv</i>, n.d. <a href="https://doi.org/10.48550/arXiv.2212.03128">https://doi.org/10.48550/arXiv.2212.03128</a>.
  ieee: S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, and M. Saghafian,
    “Chromatic alpha complexes,” <i>arXiv</i>. .
  ista: Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic
    alpha complexes. arXiv, 2212.03128.
  mla: Cultrera di Montesano, Sebastiano, et al. “Chromatic Alpha Complexes.” <i>ArXiv</i>,
    2212.03128, doi:<a href="https://doi.org/10.48550/arXiv.2212.03128">10.48550/arXiv.2212.03128</a>.
  short: S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, M. Saghafian, ArXiv
    (n.d.).
corr_author: '1'
date_created: 2024-03-08T10:13:59Z
date_published: 2024-02-07T00:00:00Z
date_updated: 2026-04-07T12:58:47Z
day: '07'
department:
- _id: HeEd
doi: 10.48550/arXiv.2212.03128
external_id:
  arxiv:
  - '2212.03128'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/2212.03128
month: '02'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: draft
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    relation: dissertation_contains
    status: public
status: public
title: Chromatic alpha complexes
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: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2024'
...
