---
_id: '18118'
abstract:
- lang: eng
  text: We introduce a new framework for studying meta-learning methods using PAC-Bayesian
    theory. Its main advantage over previous work is that it allows for more flexibility
    in how the transfer of knowledge between tasks is realized. For previous approaches,
    this could only happen indirectly, by means of learning prior distributions over
    models. In contrast, the new generalization bounds that we prove express the process
    of meta-learning much more directly as learning the learning algorithm that should
    be used for future tasks. The flexibility of our framework makes it suitable to
    analyze a wide range of meta-learning mechanisms and even design new mechanisms.
    Other than our theoretical contributions we also show empirically that our framework
    improves the prediction quality in practical meta-learning mechanisms.
alternative_title:
- PMLR
article_processing_charge: No
arxiv: 1
author:
- first_name: Hossein
  full_name: Zakerinia, Hossein
  id: 653bd8b6-f394-11eb-9cf6-c0bbf6cd78d4
  last_name: Zakerinia
  orcid: 0009-0007-3977-6462
- first_name: Amin
  full_name: Behjati, Amin
  last_name: Behjati
- first_name: Christoph
  full_name: Lampert, Christoph
  id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
  last_name: Lampert
  orcid: 0000-0001-8622-7887
citation:
  ama: 'Zakerinia H, Behjati A, Lampert C. More flexible PAC-Bayesian meta-learning
    by learning learning algorithms. In: <i>Proceedings of the 41st International
    Conference on Machine Learning</i>. Vol 235. ML Research Press; 2024:58122-58139.'
  apa: 'Zakerinia, H., Behjati, A., &#38; Lampert, C. (2024). More flexible PAC-Bayesian
    meta-learning by learning learning algorithms. In <i>Proceedings of the 41st International
    Conference on Machine Learning</i> (Vol. 235, pp. 58122–58139). Vienna, Austria:
    ML Research Press.'
  chicago: Zakerinia, Hossein, Amin Behjati, and Christoph Lampert. “More Flexible
    PAC-Bayesian Meta-Learning by Learning Learning Algorithms.” In <i>Proceedings
    of the 41st International Conference on Machine Learning</i>, 235:58122–39. ML
    Research Press, 2024.
  ieee: H. Zakerinia, A. Behjati, and C. Lampert, “More flexible PAC-Bayesian meta-learning
    by learning learning algorithms,” in <i>Proceedings of the 41st International
    Conference on Machine Learning</i>, Vienna, Austria, 2024, vol. 235, pp. 58122–58139.
  ista: 'Zakerinia H, Behjati A, Lampert C. 2024. More flexible PAC-Bayesian meta-learning
    by learning learning algorithms. Proceedings of the 41st International Conference
    on Machine Learning. ICML: International Conference on Machine Learning, PMLR,
    vol. 235, 58122–58139.'
  mla: Zakerinia, Hossein, et al. “More Flexible PAC-Bayesian Meta-Learning by Learning
    Learning Algorithms.” <i>Proceedings of the 41st International Conference on Machine
    Learning</i>, vol. 235, ML Research Press, 2024, pp. 58122–39.
  short: H. Zakerinia, A. Behjati, C. Lampert, in:, Proceedings of the 41st International
    Conference on Machine Learning, ML Research Press, 2024, pp. 58122–58139.
conference:
  end_date: 2024-07-27
  location: Vienna, Austria
  name: 'ICML: International Conference on Machine Learning'
  start_date: 2024-07-21
corr_author: '1'
das_tickbox: '0'
date_created: 2024-09-22T22:01:45Z
date_published: 2024-09-01T00:00:00Z
date_updated: 2026-10-01T09:28:21Z
day: '01'
ddc:
- '000'
department:
- _id: ChLa
external_id:
  arxiv:
  - '2402.04054'
intvolume: '       235'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: ' https://doi.org/10.48550/arXiv.2402.04054'
month: '09'
oa: 1
oa_version: Published Version
page: 58122-58139
publication: Proceedings of the 41st International Conference on Machine Learning
publication_identifier:
  eissn:
  - 2640-3498
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: More flexible PAC-Bayesian meta-learning by learning learning algorithms
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 235
year: '2024'
...
---
_id: '17332'
abstract:
- lang: eng
  text: 'Tree data structures, such as red-black trees, quad trees, treaps, or tries,
    are fundamental tools in computer science. A classical problem in concurrency
    is to obtain expressive, efficient, and scalable versions of practical tree data
    structures. We are interested in concurrent trees supporting range queries, i.e.,
    queries that involve multiple consecutive data items. Existing implementations
    with this capability can list keys in a specific range, but do not support aggregate
    range queries: for instance, if we want to calculate the number of keys in a range,
    the only choice is to retrieve a whole list and return its size. This is suboptimal:
    in the sequential setting, one can augment a balanced search tree with counters
    and, consequently, perform these aggregate requests in logarithmic rather than
    linear time.In this paper, we propose a generic approach to implement a broad
    class of range queries on concurrent trees in a way that is wait-free, asymptotically
    efficient, and practically scalable. The key idea is a new mechanism for maintaining
    metadata concurrently at tree nodes, which can be seen as a wait-free variant
    of hand-over-hand locking (which we call hand-over-hand helping). We did a preliminary
    implementation of the wait-free binary search tree and preliminary experiments
    have indicated the soundness of our approach.'
acknowledgement: We thank Trevor Brown and Yuanhao Wei for the discussion and anonymous
  reviewers for helping us to improve the paper. Also, we thank JetBrains and Huawei
  for their support.
article_processing_charge: No
arxiv: 1
author:
- first_name: Ilya
  full_name: Kokorin, Ilya
  last_name: Kokorin
- first_name: Victor
  full_name: Yudov, Victor
  last_name: Yudov
- first_name: Vitaly
  full_name: Aksenov, Vitaly
  last_name: Aksenov
- 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: 'Kokorin I, Yudov V, Aksenov V, Alistarh D-A. Wait-free trees with asymptotically-efficient
    range queries. In: <i>2024 IEEE International Parallel and Distributed Processing
    Symposium</i>. IEEE; 2024:169-179. doi:<a href="https://doi.org/10.1109/IPDPS57955.2024.00023">10.1109/IPDPS57955.2024.00023</a>'
  apa: 'Kokorin, I., Yudov, V., Aksenov, V., &#38; Alistarh, D.-A. (2024). Wait-free
    trees with asymptotically-efficient range queries. In <i>2024 IEEE International
    Parallel and Distributed Processing Symposium</i> (pp. 169–179). San Francisco,
    CA, United States: IEEE. <a href="https://doi.org/10.1109/IPDPS57955.2024.00023">https://doi.org/10.1109/IPDPS57955.2024.00023</a>'
  chicago: Kokorin, Ilya, Victor Yudov, Vitaly Aksenov, and Dan-Adrian Alistarh. “Wait-Free
    Trees with Asymptotically-Efficient Range Queries.” In <i>2024 IEEE International
    Parallel and Distributed Processing Symposium</i>, 169–79. IEEE, 2024. <a href="https://doi.org/10.1109/IPDPS57955.2024.00023">https://doi.org/10.1109/IPDPS57955.2024.00023</a>.
  ieee: I. Kokorin, V. Yudov, V. Aksenov, and D.-A. Alistarh, “Wait-free trees with
    asymptotically-efficient range queries,” in <i>2024 IEEE International Parallel
    and Distributed Processing Symposium</i>, San Francisco, CA, United States, 2024,
    pp. 169–179.
  ista: 'Kokorin I, Yudov V, Aksenov V, Alistarh D-A. 2024. Wait-free trees with asymptotically-efficient
    range queries. 2024 IEEE International Parallel and Distributed Processing Symposium.
    IPDPS: International Parallel and Distributed Processing Symposium, 169–179.'
  mla: Kokorin, Ilya, et al. “Wait-Free Trees with Asymptotically-Efficient Range
    Queries.” <i>2024 IEEE International Parallel and Distributed Processing Symposium</i>,
    IEEE, 2024, pp. 169–79, doi:<a href="https://doi.org/10.1109/IPDPS57955.2024.00023">10.1109/IPDPS57955.2024.00023</a>.
  short: I. Kokorin, V. Yudov, V. Aksenov, D.-A. Alistarh, in:, 2024 IEEE International
    Parallel and Distributed Processing Symposium, IEEE, 2024, pp. 169–179.
conference:
  end_date: 2024-05-31
  location: San Francisco, CA, United States
  name: 'IPDPS: International Parallel and Distributed Processing Symposium'
  start_date: 2024-05-27
corr_author: '1'
das_tickbox: '0'
date_created: 2024-07-28T22:01:11Z
date_published: 2024-07-08T00:00:00Z
date_updated: 2026-10-01T09:30:18Z
day: '08'
department:
- _id: DaAl
doi: 10.1109/IPDPS57955.2024.00023
external_id:
  arxiv:
  - '2310.05293'
  isi:
  - '001270389600078'
fulldoi: https://doi.org/10.1109/IPDPS57955.2024.00023
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.48550/arXiv.2310.05293
month: '07'
oa: 1
oa_version: Preprint
page: 169-179
publication: 2024 IEEE International Parallel and Distributed Processing Symposium
publication_identifier:
  eissn:
  - 1530-2075
  isbn:
  - '9798350337662'
publication_status: published
publisher: IEEE
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Wait-free trees with asymptotically-efficient range queries
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
_id: '15011'
abstract:
- lang: eng
  text: Pruning large language models (LLMs) from the BERT family has emerged as a
    standard compression benchmark, and several pruning methods have been proposed
    for this task. The recent “Sparsity May Cry” (SMC) benchmark put into question
    the validity of all existing methods, exhibiting a more complex setup where many
    known pruning methods appear to fail. We revisit the question of accurate BERT-pruning
    during fine-tuning on downstream datasets, and propose a set of general guidelines
    for successful pruning, even on the challenging SMC benchmark. First, we perform
    a cost-vs-benefits analysis of pruning model components, such as the embeddings
    and the classification head; second, we provide a simple-yet-general way of scaling
    training, sparsification and learning rate schedules relative to the desired target
    sparsity; finally, we investigate the importance of proper parametrization for
    Knowledge Distillation in the context of LLMs. Our simple insights lead to state-of-the-art
    results, both on classic BERT-pruning benchmarks, as well as on the SMC benchmark,
    showing that even classic gradual magnitude pruning (GMP) can yield competitive
    results, with the right approach.
alternative_title:
- PMLR
article_processing_charge: No
arxiv: 1
author:
- first_name: Eldar
  full_name: Kurtic, Eldar
  id: 47beb3a5-07b5-11eb-9b87-b108ec578218
  last_name: Kurtic
- first_name: Torsten
  full_name: Hoefler, Torsten
  last_name: Hoefler
- 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: 'Kurtic E, Hoefler T, Alistarh D-A. How to prune your language model: Recovering
    accuracy on the “Sparsity May Cry” benchmark. In: <i>Proceedings of Machine Learning
    Research</i>. Vol 234. ML Research Press; 2024:542-553.'
  apa: 'Kurtic, E., Hoefler, T., &#38; Alistarh, D.-A. (2024). How to prune your language
    model: Recovering accuracy on the “Sparsity May Cry” benchmark. In <i>Proceedings
    of Machine Learning Research</i> (Vol. 234, pp. 542–553). Hongkong, China: ML
    Research Press.'
  chicago: 'Kurtic, Eldar, Torsten Hoefler, and Dan-Adrian Alistarh. “How to Prune
    Your Language Model: Recovering Accuracy on the ‘Sparsity May Cry’ Benchmark.”
    In <i>Proceedings of Machine Learning Research</i>, 234:542–53. ML Research Press,
    2024.'
  ieee: 'E. Kurtic, T. Hoefler, and D.-A. Alistarh, “How to prune your language model:
    Recovering accuracy on the ‘Sparsity May Cry’ benchmark,” in <i>Proceedings of
    Machine Learning Research</i>, Hongkong, China, 2024, vol. 234, pp. 542–553.'
  ista: 'Kurtic E, Hoefler T, Alistarh D-A. 2024. How to prune your language model:
    Recovering accuracy on the ‘Sparsity May Cry’ benchmark. Proceedings of Machine
    Learning Research. CPAL: Conference on Parsimony and Learning, PMLR, vol. 234,
    542–553.'
  mla: 'Kurtic, Eldar, et al. “How to Prune Your Language Model: Recovering Accuracy
    on the ‘Sparsity May Cry’ Benchmark.” <i>Proceedings of Machine Learning Research</i>,
    vol. 234, ML Research Press, 2024, pp. 542–53.'
  short: E. Kurtic, T. Hoefler, D.-A. Alistarh, in:, Proceedings of Machine Learning
    Research, ML Research Press, 2024, pp. 542–553.
conference:
  end_date: 2024-01-06
  location: Hongkong, China
  name: 'CPAL: Conference on Parsimony and Learning'
  start_date: 2024-01-03
corr_author: '1'
das_tickbox: '0'
date_created: 2024-02-18T23:01:03Z
date_published: 2024-01-08T00:00:00Z
date_updated: 2026-10-01T09:31:02Z
day: '08'
department:
- _id: DaAl
external_id:
  arxiv:
  - '2312.13547'
intvolume: '       234'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://proceedings.mlr.press/v234/kurtic24a
month: '01'
oa: 1
oa_version: Preprint
page: 542-553
publication: Proceedings of Machine Learning Research
publication_identifier:
  eissn:
  - 2640-3498
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: 'How to prune your language model: Recovering accuracy on the "Sparsity May
  Cry" benchmark'
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 234
year: '2024'
...
---
_id: '18070'
abstract:
- lang: eng
  text: Parallel SGD in a shared-memory setting is oft-represented by the popular
    Hogwild! algorithm, in which lock-free updates are asynchronously performed by
    multiple computing processes. Unfortunately, scaling Hogwild! to distributed workers
    is largely unexplored. Specifically, it is unknown if any adaptation of Hogwild!
    to the popular decentralized multi-GPU setting offers any competitive speedup,
    either empirically or theoretically. In this work, we investigate the potential
    of decentralizing Hogwild! by incorporating simultaneously (a) asynchronous local
    gradient updates on the shared memory of GPUs, and (b) non-blocking asynchronous
    decentralized federated averaging. A naive direct implementation shows degradation
    in performance, arising from scheduling overheads and concurrent write conflicts
    on GPUs. To mitigate these drawbacks, we investigate and propose a new method,
    based on careful block selection rules, which update only portions of the parameter
    vectors. Our experiments show that the resulting decentralized training method
    exhibits improved throughput and competitive accuracy for standard image classification
    benchmarks on the CIFAR-10, CIFAR-100, and Imagenet datasets. On the theoretical
    side, we prove that our method guarantees sublinear ergodic convergence rates
    for non-convex objectives.
article_processing_charge: No
author:
- first_name: Bapi
  full_name: Chatterjee, Bapi
  id: 3C41A08A-F248-11E8-B48F-1D18A9856A87
  last_name: Chatterjee
  orcid: 0000-0002-2742-4028
- first_name: Vyacheslav
  full_name: Kungurtsev, Vyacheslav
  last_name: Kungurtsev
- 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: 'Chatterjee B, Kungurtsev V, Alistarh D-A. Federated SGD with local asynchrony.
    In: <i>Proceedings of the 44th International Conference on Distributed Computing
    Systems</i>. IEEE; 2024:857-868. doi:<a href="https://doi.org/10.1109/ICDCS60910.2024.00084">10.1109/ICDCS60910.2024.00084</a>'
  apa: 'Chatterjee, B., Kungurtsev, V., &#38; Alistarh, D.-A. (2024). Federated SGD
    with local asynchrony. In <i>Proceedings of the 44th International Conference
    on Distributed Computing Systems</i> (pp. 857–868). Jersey City, NJ, United States:
    IEEE. <a href="https://doi.org/10.1109/ICDCS60910.2024.00084">https://doi.org/10.1109/ICDCS60910.2024.00084</a>'
  chicago: Chatterjee, Bapi, Vyacheslav Kungurtsev, and Dan-Adrian Alistarh. “Federated
    SGD with Local Asynchrony.” In <i>Proceedings of the 44th International Conference
    on Distributed Computing Systems</i>, 857–68. IEEE, 2024. <a href="https://doi.org/10.1109/ICDCS60910.2024.00084">https://doi.org/10.1109/ICDCS60910.2024.00084</a>.
  ieee: B. Chatterjee, V. Kungurtsev, and D.-A. Alistarh, “Federated SGD with local
    asynchrony,” in <i>Proceedings of the 44th International Conference on Distributed
    Computing Systems</i>, Jersey City, NJ, United States, 2024, pp. 857–868.
  ista: 'Chatterjee B, Kungurtsev V, Alistarh D-A. 2024. Federated SGD with local
    asynchrony. Proceedings of the 44th International Conference on Distributed Computing
    Systems. ICDCS: International Conference on Distributed Computing Systems, 857–868.'
  mla: Chatterjee, Bapi, et al. “Federated SGD with Local Asynchrony.” <i>Proceedings
    of the 44th International Conference on Distributed Computing Systems</i>, IEEE,
    2024, pp. 857–68, doi:<a href="https://doi.org/10.1109/ICDCS60910.2024.00084">10.1109/ICDCS60910.2024.00084</a>.
  short: B. Chatterjee, V. Kungurtsev, D.-A. Alistarh, in:, Proceedings of the 44th
    International Conference on Distributed Computing Systems, IEEE, 2024, pp. 857–868.
conference:
  end_date: 2024-07-26
  location: Jersey City, NJ, United States
  name: 'ICDCS: International Conference on Distributed Computing Systems'
  start_date: 2024-07-23
corr_author: '1'
das_tickbox: '0'
date_created: 2024-09-15T22:01:41Z
date_published: 2024-07-26T00:00:00Z
date_updated: 2026-10-01T09:32:24Z
day: '26'
department:
- _id: DaAl
doi: 10.1109/ICDCS60910.2024.00084
external_id:
  isi:
  - '001304430200075'
fulldoi: https://doi.org/10.1109/ICDCS60910.2024.00084
isi: 1
language:
- iso: eng
month: '07'
oa_version: None
page: 857-868
publication: Proceedings of the 44th International Conference on Distributed Computing
  Systems
publication_identifier:
  eissn:
  - 2575-8411
  isbn:
  - '9798350386059'
  issn:
  - 1063-6927
publication_status: published
publisher: IEEE
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: no
title: Federated SGD with local asynchrony
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
_id: '17329'
abstract:
- lang: eng
  text: 'We initiate the study of game dynamics in the population protocol model:
    n agents each maintain a current local strategy and interact in pairs uniformly
    at random. Upon each interaction, the agents play a two-person game and receive
    a payoff from an underlying utility function, and they can subsequently update
    their strategies according to a fixed local algorithm. In this setting, we ask
    how the distribution over agent strategies evolves over a sequence of interactions,
    and we introduce a new distributional equilibrium concept to quantify the quality
    of such distributions. As an initial example, we study a class of repeated prisoner''s
    dilemma games, and we consider a family of simple local update algorithms that
    yield non-trivial dynamics over the distribution of agent strategies. We show
    that these dynamics are related to a new class of high-dimensional Ehrenfest random
    walks, and we derive exact characterizations of their stationary distributions,
    bounds on their mixing times, and prove their convergence to approximate distributional
    equilibria. Our results highlight trade-offs between the local state space of
    each agent, and the convergence rate and approximation factor of the underlying
    dynamics. Our approach opens the door towards the further characterization of
    equilibrium computation for other classes of games and dynamics in the population
    setting.'
acknowledgement: This work was supported in part by the ERC-2020-CoG 863818 (FoRM-SMArt)
  grant. We thank James Aspnes and Thomas Sauerwald for several helpful discussions
  on Ehrenfest random walks.
article_processing_charge: Yes (via OA deal)
author:
- 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: Krishnendu
  full_name: Chatterjee, Krishnendu
  id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
  last_name: Chatterjee
  orcid: 0000-0002-4561-241X
- first_name: Mehrdad
  full_name: Karrabi, Mehrdad
  id: 67638922-f394-11eb-9cf6-f20423e08757
  last_name: Karrabi
  orcid: 0009-0007-5253-9170
- first_name: John M
  full_name: Lazarsfeld, John M
  id: 17ce3656-183e-11ef-84c3-8932383e1b23
  last_name: Lazarsfeld
citation:
  ama: 'Alistarh D-A, Chatterjee K, Karrabi M, Lazarsfeld JM. Game dynamics and equilibrium
    computation in the population protocol model. In: <i>Proceedings of the 43rd Annual
    ACM Symposium on Principles of Distributed Computing</i>. Association for Computing
    Machinery; 2024:40-49. doi:<a href="https://doi.org/10.1145/3662158.3662768">10.1145/3662158.3662768</a>'
  apa: 'Alistarh, D.-A., Chatterjee, K., Karrabi, M., &#38; Lazarsfeld, J. M. (2024).
    Game dynamics and equilibrium computation in the population protocol model. In
    <i>Proceedings of the 43rd Annual ACM Symposium on Principles of Distributed Computing</i>
    (pp. 40–49). Nantes, France: Association for Computing Machinery. <a href="https://doi.org/10.1145/3662158.3662768">https://doi.org/10.1145/3662158.3662768</a>'
  chicago: Alistarh, Dan-Adrian, Krishnendu Chatterjee, Mehrdad Karrabi, and John
    M Lazarsfeld. “Game Dynamics and Equilibrium Computation in the Population Protocol
    Model.” In <i>Proceedings of the 43rd Annual ACM Symposium on Principles of Distributed
    Computing</i>, 40–49. Association for Computing Machinery, 2024. <a href="https://doi.org/10.1145/3662158.3662768">https://doi.org/10.1145/3662158.3662768</a>.
  ieee: D.-A. Alistarh, K. Chatterjee, M. Karrabi, and J. M. Lazarsfeld, “Game dynamics
    and equilibrium computation in the population protocol model,” in <i>Proceedings
    of the 43rd Annual ACM Symposium on Principles of Distributed Computing</i>, Nantes,
    France, 2024, pp. 40–49.
  ista: 'Alistarh D-A, Chatterjee K, Karrabi M, Lazarsfeld JM. 2024. Game dynamics
    and equilibrium computation in the population protocol model. Proceedings of the
    43rd Annual ACM Symposium on Principles of Distributed Computing. PODC: Symposium
    on Principles of Distributed Computing, 40–49.'
  mla: Alistarh, Dan-Adrian, et al. “Game Dynamics and Equilibrium Computation in
    the Population Protocol Model.” <i>Proceedings of the 43rd Annual ACM Symposium
    on Principles of Distributed Computing</i>, Association for Computing Machinery,
    2024, pp. 40–49, doi:<a href="https://doi.org/10.1145/3662158.3662768">10.1145/3662158.3662768</a>.
  short: D.-A. Alistarh, K. Chatterjee, M. Karrabi, J.M. Lazarsfeld, in:, Proceedings
    of the 43rd Annual ACM Symposium on Principles of Distributed Computing, Association
    for Computing Machinery, 2024, pp. 40–49.
conference:
  end_date: 2024-06-21
  location: Nantes, France
  name: 'PODC: Symposium on Principles of Distributed Computing'
  start_date: 2024-06-17
corr_author: '1'
das_tickbox: '0'
date_created: 2024-07-28T22:01:10Z
date_published: 2024-06-17T00:00:00Z
date_updated: 2026-10-01T09:34:57Z
day: '17'
ddc:
- '000'
department:
- _id: DaAl
- _id: KrCh
doi: 10.1145/3662158.3662768
ec_funded: 1
file:
- access_level: open_access
  checksum: 65a40437f83373fa79dd999d5287509e
  content_type: application/pdf
  creator: dernst
  date_created: 2024-07-29T07:37:31Z
  date_updated: 2024-07-29T07:37:31Z
  file_id: '17335'
  file_name: 2024_ACMPODC_Alistarh.pdf
  file_size: 750908
  relation: main_file
  success: 1
file_date_updated: 2024-07-29T07:37:31Z
fulldoi: https://doi.org/10.1145/3662158.3662768
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '06'
oa: 1
oa_version: Published Version
page: 40-49
project:
- _id: 0599E47C-7A3F-11EA-A408-12923DDC885E
  call_identifier: H2020
  grant_number: '863818'
  name: 'Formal Methods for Stochastic Models: Algorithms and Applications'
publication: Proceedings of the 43rd Annual ACM Symposium on Principles of Distributed
  Computing
publication_identifier:
  isbn:
  - '9798400706684'
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Game dynamics and equilibrium computation in the population protocol model
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
_id: '18121'
abstract:
- lang: eng
  text: It is known that sparsity can improve interpretability for deep neural networks.
    However, existing methods in the area either require networks that are pre-trained
    with sparsity constraints, or impose sparsity after the fact, altering the network’s
    general behavior. In this paper, we demonstrate, for the first time, that sparsity
    can instead be incorporated into the interpretation process itself, as a sample-specific
    preprocessing step. Unlike previous work, this approach, which we call SPADE,
    does not place constraints on the trained model and does not affect its behavior
    during inference on the sample. Given a trained model and a target sample, SPADE
    uses sample-targeted pruning to provide a "trace" of the network’s execution on
    the sample, reducing the network to the most important connections prior to computing
    an interpretation. We demonstrate that preprocessing with SPADE significantly
    increases the accuracy of image saliency maps across several interpretability
    methods. Additionally, SPADE improves the usefulness of neuron visualizations,
    aiding humans in reasoning about network behavior. Our code is available at https://github.com/IST-DASLab/SPADE.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: The authors would like to thank Stephen Casper and Tony Wang for
  their feedback on this work, and Eldar Kurtic for his advice on aspects of the project.
  This research was supported by the Scientific Service Units (SSU) of IST Austria
  through resources provided by Scientific Computing (SciComp). EI was supported in
  part by the FWF DK VGSCO, grant agreement number W1260-N35.
alternative_title:
- PMLR
article_processing_charge: No
arxiv: 1
author:
- first_name: Arshia Soltani
  full_name: Moakhar, Arshia Soltani
  last_name: Moakhar
- first_name: Eugenia B
  full_name: Iofinova, Eugenia B
  id: f9a17499-f6e0-11ea-865d-fdf9a3f77117
  last_name: Iofinova
  orcid: 0000-0002-7778-3221
- 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: 'Moakhar AS, Iofinova EB, Frantar E, Alistarh D-A. SPADE: Sparsity-guided debugging
    for deep neural networks. In: <i>Proceedings of the 41st International Conference
    on Machine Learning</i>. Vol 235. ML Research Press; 2024:45955-45987.'
  apa: 'Moakhar, A. S., Iofinova, E. B., Frantar, E., &#38; Alistarh, D.-A. (2024).
    SPADE: Sparsity-guided debugging for deep neural networks. In <i>Proceedings of
    the 41st International Conference on Machine Learning</i> (Vol. 235, pp. 45955–45987).
    Vienna, Austria: ML Research Press.'
  chicago: 'Moakhar, Arshia Soltani, Eugenia B Iofinova, Elias Frantar, and Dan-Adrian
    Alistarh. “SPADE: Sparsity-Guided Debugging for Deep Neural Networks.” In <i>Proceedings
    of the 41st International Conference on Machine Learning</i>, 235:45955–87. ML
    Research Press, 2024.'
  ieee: 'A. S. Moakhar, E. B. Iofinova, E. Frantar, and D.-A. Alistarh, “SPADE: Sparsity-guided
    debugging for deep neural networks,” in <i>Proceedings of the 41st International
    Conference on Machine Learning</i>, Vienna, Austria, 2024, vol. 235, pp. 45955–45987.'
  ista: 'Moakhar AS, Iofinova EB, Frantar E, Alistarh D-A. 2024. SPADE: Sparsity-guided
    debugging for deep neural networks. Proceedings of the 41st International Conference
    on Machine Learning. ICML: International Conference on Machine Learning, PMLR,
    vol. 235, 45955–45987.'
  mla: 'Moakhar, Arshia Soltani, et al. “SPADE: Sparsity-Guided Debugging for Deep
    Neural Networks.” <i>Proceedings of the 41st International Conference on Machine
    Learning</i>, vol. 235, ML Research Press, 2024, pp. 45955–87.'
  short: A.S. Moakhar, E.B. Iofinova, E. Frantar, D.-A. Alistarh, in:, Proceedings
    of the 41st International Conference on Machine Learning, ML Research Press, 2024,
    pp. 45955–45987.
conference:
  end_date: 2024-07-27
  location: Vienna, Austria
  name: 'ICML: International Conference on Machine Learning'
  start_date: 2024-07-21
corr_author: '1'
das_tickbox: '0'
date_created: 2024-09-22T22:01:46Z
date_published: 2024-09-01T00:00:00Z
date_updated: 2026-10-01T09:32:47Z
day: '01'
department:
- _id: DaAl
external_id:
  arxiv:
  - '2310.04519'
intvolume: '       235'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.48550/arXiv.2310.04519
month: '09'
oa: 1
oa_version: Preprint
page: 45955-45987
project:
- _id: 9B9290DE-BA93-11EA-9121-9846C619BF3A
  grant_number: W1260-N35
  name: Vienna Graduate School on Computational Optimization
publication: Proceedings of the 41st International Conference on Machine Learning
publication_identifier:
  eissn:
  - 2640-3498
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
related_material:
  link:
  - relation: software
    url: https://github.com/IST-DASLab/SPADE
  record:
  - id: '21854'
    relation: dissertation_contains
    status: public
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: no
title: 'SPADE: Sparsity-guided debugging for deep neural networks'
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 235
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '18976'
abstract:
- lang: eng
  text: We analyze asynchronous-type algorithms for distributed SGD in the heterogeneous
    setting, where each worker has its own computation and communication speeds, as
    well as data distribution. In these algorithms, workers compute possibly stale
    and stochastic gradients associated with their local data at some iteration back
    in history and then return those gradients to the server without synchronizing
    with other workers. We present a unified convergence theory for non-convex smooth
    functions in the heterogeneous regime. The proposed analysis provides convergence
    for pure asynchronous SGD and its various modifications. Moreover, our theory
    explains what affects the convergence rate and what can be done to improve the
    performance of asynchronous algorithms. In particular, we introduce a novel asynchronous
    method based on worker shuffling. As a by-product of our analysis, we also demonstrate
    convergence guarantees for gradient-type algorithms such as SGD with random reshuffling
    and shuffle-once mini-batch SGD. The derived rates match the best-known results
    for those algorithms, highlighting the tightness of our approach. Finally, our
    numerical evaluations support theoretical findings and show the good practical
    performance of our method.
acknowledgement: "The authors thank all anonymous reviewers for their valuable comments
  and suggestions on how to improve the manuscript. This work was done when Rustem
  Islamov was a Master’s student at Institut Polytechnique de Paris (IP Paris) and
  an intern at Institute of Science and Technology Austria (ISTA). The research of
  Rustem Islamov was supported by ISTA internship\r\nprogram. Mher Safaryan has received
  funding from the European Union’s Horizon 2020 research and innovation program under
  the Marie Skłodowska-Curie grant agreement No 101034413."
alternative_title:
- PMLR
article_processing_charge: No
arxiv: 1
author:
- first_name: Rustem
  full_name: Islamov, Rustem
  last_name: Islamov
- first_name: Mher
  full_name: Safaryan, Mher
  id: dd546b39-0804-11ed-9c55-ef075c39778d
  last_name: Safaryan
- 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: 'Islamov R, Safaryan M, Alistarh D-A. AsGrad: A sharp unified analysis of asynchronous-SGD
    algorithms. In: <i>Proceedings of The 27th International Conference on Artificial
    Intelligence and Statistics</i>. Vol 238. ML Research Press; 2024:649-657.'
  apa: 'Islamov, R., Safaryan, M., &#38; Alistarh, D.-A. (2024). AsGrad: A sharp unified
    analysis of asynchronous-SGD algorithms. In <i>Proceedings of The 27th International
    Conference on Artificial Intelligence and Statistics</i> (Vol. 238, pp. 649–657).
    Valencia, Spain: ML Research Press.'
  chicago: 'Islamov, Rustem, Mher Safaryan, and Dan-Adrian Alistarh. “AsGrad: A Sharp
    Unified Analysis of Asynchronous-SGD Algorithms.” In <i>Proceedings of The 27th
    International Conference on Artificial Intelligence and Statistics</i>, 238:649–57.
    ML Research Press, 2024.'
  ieee: 'R. Islamov, M. Safaryan, and D.-A. Alistarh, “AsGrad: A sharp unified analysis
    of asynchronous-SGD algorithms,” in <i>Proceedings of The 27th International Conference
    on Artificial Intelligence and Statistics</i>, Valencia, Spain, 2024, vol. 238,
    pp. 649–657.'
  ista: 'Islamov R, Safaryan M, Alistarh D-A. 2024. AsGrad: A sharp unified analysis
    of asynchronous-SGD algorithms. Proceedings of The 27th International Conference
    on Artificial Intelligence and Statistics. AISTATS: Conference on Artificial Intelligence
    and Statistics, PMLR, vol. 238, 649–657.'
  mla: 'Islamov, Rustem, et al. “AsGrad: A Sharp Unified Analysis of Asynchronous-SGD
    Algorithms.” <i>Proceedings of The 27th International Conference on Artificial
    Intelligence and Statistics</i>, vol. 238, ML Research Press, 2024, pp. 649–57.'
  short: R. Islamov, M. Safaryan, D.-A. Alistarh, in:, Proceedings of The 27th International
    Conference on Artificial Intelligence and Statistics, ML Research Press, 2024,
    pp. 649–657.
conference:
  end_date: 2024-05-04
  location: Valencia, Spain
  name: 'AISTATS: Conference on Artificial Intelligence and Statistics'
  start_date: 2024-05-02
corr_author: '1'
das_tickbox: '0'
date_created: 2025-01-30T08:15:49Z
date_published: 2024-05-15T00:00:00Z
date_updated: 2026-10-01T09:33:24Z
day: '15'
department:
- _id: DaAl
ec_funded: 1
external_id:
  arxiv:
  - '2310.20452'
intvolume: '       238'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.48550/arXiv.2310.20452
month: '05'
oa: 1
oa_version: Preprint
page: 649-657
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
  call_identifier: H2020
  grant_number: '101034413'
  name: 'IST-BRIDGE: International postdoctoral program'
publication: Proceedings of The 27th International Conference on Artificial Intelligence
  and Statistics
publication_identifier:
  eissn:
  - 2640-3498
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: 'AsGrad: A sharp unified analysis of asynchronous-SGD algorithms'
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 238
year: '2024'
...
---
_id: '18113'
abstract:
- lang: eng
  text: 'The emergence of accurate open large language models (LLMs) has led to a
    race towards performant quantization techniques which can enable their execution
    on end-user devices. In this paper, we revisit the problem of “extreme” LLM compression—defined
    as targeting extremely low bit counts, such as 2 to 3 bits per parameter—from
    the point of view of classic methods in Multi-Codebook Quantization (MCQ). Our
    algorithm, called AQLM, generalizes the classic Additive Quantization (AQ) approach
    for information retrieval to advance the state-of-the-art in LLM compression,
    via two innovations: 1) learned additive quantization of weight matrices in input-adaptive
    fashion, and 2) joint optimization of codebook parameters across each transformer
    blocks. Broadly, AQLM is the first scheme that is Pareto optimal in terms of accuracy-vs-model-size
    when compressing to less than 3 bits per parameter, and significantly improves
    upon all known schemes in the extreme compression (2bit) regime. In addition,
    AQLM is practical: we provide fast GPU and CPU implementations of AQLM for token
    generation, which enable us to match or outperform optimized FP16 implementations
    for speed, while executing in a much smaller memory footprint.'
acknowledgement: "Authors would like to thank Ruslan Svirschevski for his help in
  solving technical issues with AQLM and baselines. We also thank Tim Dettmers for
  helpful discussions on the structure of weights in modern LLMs and size-accuracy
  trade-offs. The authors would also like to thank Daniil Pavlov for his assistance
  with CPU benchmarking. Finally, authors would like to thank the communities of ML
  enthusiasts known as LocalLLaMA5 and Petals community on discord6\r\nfor the crowd
  wisdom about running LLMs on consumer devices. Egiazarian Vage and Denis Kuznedelev
  and Andrei Panferov were supported by the grant for research centers in the field
  of AI provided by the Analytical Center for the Government of the Russian Federation
  (ACRF) in\r\naccordance with the agreement on the provision of subsidies (identifier
  of the agreement 000000D730321P5Q0002) and the agreement with HSE University No.
  70-2021-00139."
alternative_title:
- PMLR
article_processing_charge: No
arxiv: 1
author:
- first_name: Vage
  full_name: Egiazarian, Vage
  last_name: Egiazarian
- first_name: Andrei
  full_name: Panferov, Andrei
  id: 2c18daae-4dbe-11ef-8491-98ce2d960f09
  last_name: Panferov
- first_name: Denis
  full_name: Kuznedelev, Denis
  last_name: Kuznedelev
- first_name: Elias
  full_name: Frantar, Elias
  id: 09a8f98d-ec99-11ea-ae11-c063a7b7fe5f
  last_name: Frantar
- first_name: Artem
  full_name: Babenko, Artem
  last_name: Babenko
- first_name: Dan-Adrian
  full_name: Alistarh, Dan-Adrian
  id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
  last_name: Alistarh
  orcid: 0000-0003-3650-940X
citation:
  ama: 'Egiazarian V, Panferov A, Kuznedelev D, Frantar E, Babenko A, Alistarh D-A.
    Extreme compression of large language models via additive quantization. In: <i>Proceedings
    of the 41st International Conference on Machine Learning</i>. Vol 235. ML Research
    Press; 2024:12284-12303.'
  apa: 'Egiazarian, V., Panferov, A., Kuznedelev, D., Frantar, E., Babenko, A., &#38;
    Alistarh, D.-A. (2024). Extreme compression of large language models via additive
    quantization. In <i>Proceedings of the 41st International Conference on Machine
    Learning</i> (Vol. 235, pp. 12284–12303). Vienna, Austria: ML Research Press.'
  chicago: Egiazarian, Vage, Andrei Panferov, Denis Kuznedelev, Elias Frantar, Artem
    Babenko, and Dan-Adrian Alistarh. “Extreme Compression of Large Language Models
    via Additive Quantization.” In <i>Proceedings of the 41st International Conference
    on Machine Learning</i>, 235:12284–303. ML Research Press, 2024.
  ieee: V. Egiazarian, A. Panferov, D. Kuznedelev, E. Frantar, A. Babenko, and D.-A.
    Alistarh, “Extreme compression of large language models via additive quantization,”
    in <i>Proceedings of the 41st International Conference on Machine Learning</i>,
    Vienna, Austria, 2024, vol. 235, pp. 12284–12303.
  ista: 'Egiazarian V, Panferov A, Kuznedelev D, Frantar E, Babenko A, Alistarh D-A.
    2024. Extreme compression of large language models via additive quantization.
    Proceedings of the 41st International Conference on Machine Learning. ICML: International
    Conference on Machine Learning, PMLR, vol. 235, 12284–12303.'
  mla: Egiazarian, Vage, et al. “Extreme Compression of Large Language Models via
    Additive Quantization.” <i>Proceedings of the 41st International Conference on
    Machine Learning</i>, vol. 235, ML Research Press, 2024, pp. 12284–303.
  short: V. Egiazarian, A. Panferov, D. Kuznedelev, E. Frantar, A. Babenko, D.-A.
    Alistarh, in:, Proceedings of the 41st International Conference on Machine Learning,
    ML Research Press, 2024, pp. 12284–12303.
conference:
  end_date: 2024-07-27
  location: Vienna, Austria
  name: 'ICML: International Conference on Machine Learning'
  start_date: 2024-07-21
corr_author: '1'
das_tickbox: '0'
date_created: 2024-09-22T22:01:43Z
date_published: 2024-09-01T00:00:00Z
date_updated: 2026-10-01T09:34:19Z
day: '01'
department:
- _id: DaAl
- _id: GradSch
external_id:
  arxiv:
  - '2401.06118'
intvolume: '       235'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: ' https://doi.org/10.48550/arXiv.2401.06118'
month: '09'
oa: 1
oa_version: Preprint
page: 12284-12303
publication: Proceedings of the 41st International Conference on Machine Learning
publication_identifier:
  eissn:
  - 2640-3498
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Extreme compression of large language models via additive quantization
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 235
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '18975'
abstract:
- lang: eng
  text: Leveraging second-order information about the loss at the scale of deep networks
    is one of the main lines of approach for improving the performance of current
    optimizers for deep learning. Yet, existing approaches for accurate full-matrix
    preconditioning, such as Full-Matrix Adagrad (GGT) or Matrix-Free Approximate
    Curvature (M-FAC) suffer from massive storage costs when applied even to small-scale
    models, as they must store a sliding window of gradients, whose memory requirements
    are multiplicative in the model dimension. In this paper, we address this issue
    via a novel and efficient error-feedback technique that can be applied to compress
    preconditioners by up to two orders of magnitude in practice, without loss of
    convergence. Specifically, our approach compresses the gradient information via
    sparsification or low-rank compression before it is fed into the preconditioner,
    feeding the compression error back into future iterations. Extensive experiments
    on deep neural networks show that this approach can compress full-matrix preconditioners
    to up to 99% sparsity without accuracy loss, effectively removing the memory overhead
    of fullmatrix preconditioners such as GGT and M-FAC.
acknowledged_ssus:
- _id: CampIT
acknowledgement: The authors thank Adrian Vladu, Razvan Pascanu, Alexandra Peste,
  Mher Safaryan for their valuable feedback, the IT department from Institute of Science
  and Technology Austria for the hardware support and Weights and Biases for the infrastructure
  to track all our experiments.
alternative_title:
- PMLR
article_processing_charge: No
arxiv: 1
author:
- first_name: Ionut-Vlad
  full_name: Modoranu, Ionut-Vlad
  id: 449f7a18-f128-11eb-9611-9b430c0c6333
  last_name: Modoranu
- first_name: Aleksei
  full_name: Kalinov, Aleksei
  id: 44b7120e-eb97-11eb-a6c2-e1557aa81d02
  last_name: Kalinov
  orcid: 0000-0003-2189-3904
- first_name: Eldar
  full_name: Kurtic, Eldar
  id: 47beb3a5-07b5-11eb-9b87-b108ec578218
  last_name: Kurtic
- 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: 'Modoranu I-V, Kalinov A, Kurtic E, Frantar E, Alistarh D-A. Error feedback
    can accurately compress preconditioners. In: <i>41st International Conference
    on Machine Learning</i>. Vol 235. ML Research Press; 2024:35910-35933.'
  apa: 'Modoranu, I.-V., Kalinov, A., Kurtic, E., Frantar, E., &#38; Alistarh, D.-A.
    (2024). Error feedback can accurately compress preconditioners. In <i>41st International
    Conference on Machine Learning</i> (Vol. 235, pp. 35910–35933). Vienna, Austria:
    ML Research Press.'
  chicago: Modoranu, Ionut-Vlad, Aleksei Kalinov, Eldar Kurtic, Elias Frantar, and
    Dan-Adrian Alistarh. “Error Feedback Can Accurately Compress Preconditioners.”
    In <i>41st International Conference on Machine Learning</i>, 235:35910–33. ML
    Research Press, 2024.
  ieee: I.-V. Modoranu, A. Kalinov, E. Kurtic, E. Frantar, and D.-A. Alistarh, “Error
    feedback can accurately compress preconditioners,” in <i>41st International Conference
    on Machine Learning</i>, Vienna, Austria, 2024, vol. 235, pp. 35910–35933.
  ista: 'Modoranu I-V, Kalinov A, Kurtic E, Frantar E, Alistarh D-A. 2024. Error feedback
    can accurately compress preconditioners. 41st International Conference on Machine
    Learning. ICML: International Conference on Machine Learning, PMLR, vol. 235,
    35910–35933.'
  mla: Modoranu, Ionut-Vlad, et al. “Error Feedback Can Accurately Compress Preconditioners.”
    <i>41st International Conference on Machine Learning</i>, vol. 235, ML Research
    Press, 2024, pp. 35910–33.
  short: I.-V. Modoranu, A. Kalinov, E. Kurtic, E. Frantar, D.-A. Alistarh, in:, 41st
    International Conference on Machine Learning, ML Research Press, 2024, pp. 35910–35933.
conference:
  end_date: 2024-07-27
  location: Vienna, Austria
  name: 'ICML: International Conference on Machine Learning'
  start_date: 2024-07-21
corr_author: '1'
das_tickbox: '0'
date_created: 2025-01-30T07:53:22Z
date_published: 2024-07-30T00:00:00Z
date_updated: 2026-10-01T09:33:07Z
day: '30'
department:
- _id: DaAl
external_id:
  arxiv:
  - '2306.06098'
intvolume: '       235'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.48550/arXiv.2306.06098
month: '07'
oa: 1
oa_version: Preprint
page: 35910-35933
publication: 41st International Conference on Machine Learning
publication_identifier:
  eissn:
  - 2640-3498
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: no
title: Error feedback can accurately compress preconditioners
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 235
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '18977'
abstract:
- lang: eng
  text: "Recent advances in large language model (LLM) pretraining have led to high-quality
    LLMs with impressive abilities. By compressing such LLMs via quantization to 3-4
    bits per parameter, they can fit into memory-limited devices such as laptops and
    mobile phones, enabling personalized use. Quantizing models to 3-4 bits per parameter
    can lead to moderate to high accuracy losses, especially for smaller models (1-10B
    parameters), which are suitable for edge deployment. To address this accuracy
    issue, we introduce the Sparse-Quantized Representation (SpQR), a new compressed
    format and quantization technique that enables for the first time \\emph{near-lossless}
    compression of LLMs across model scales while reaching similar compression levels
    to previous methods. SpQR works by identifying and isolating \\emph{outlier weights},
    which cause particularly large quantization errors, and storing them in higher
    precision while compressing all other weights to 3-4 bits, and achieves relative
    accuracy losses of less than \r\n in perplexity for highly-accurate LLaMA and
    Falcon LLMs. This makes it possible to run a 33B parameter LLM on a single 24
    GB consumer GPU without performance degradation at 15% speedup, thus making powerful
    LLMs available to consumers without any downsides. SpQR comes with efficient algorithms
    for both encoding weights into its format, as well as decoding them efficiently
    at runtime. Specifically, we provide an efficient GPU inference algorithm for
    SpQR, which yields faster inference than 16-bit baselines at similar accuracy
    while enabling memory compression gains of more than 4x."
acknowledgement: "Denis Kuznedelev acknowledges the support from the Russian Ministry
  of Science and Higher\r\nEducation, grant No. 075-10-2021-068. Ruslan Svirschevski
  and Vage Egiazarian and Denis\r\nKuznedelev were supported by the grant for research
  centers in the field of AI provided by the\r\nAnalytical Center for the Government
  of the Russian Federation (ACRF) in accordance with the\r\nagreement on the provision
  of subsidies (identifier of the agreement 000000D730321P5Q0002) and the agreement
  with HSE University No. 70-2021-00139."
article_processing_charge: No
arxiv: 1
author:
- first_name: Tim
  full_name: Dettmers, Tim
  last_name: Dettmers
- first_name: Ruslan A.
  full_name: Svirschevski, Ruslan A.
  last_name: Svirschevski
- first_name: Vage
  full_name: Egiazarian, Vage
  last_name: Egiazarian
- first_name: Denis
  full_name: Kuznedelev, Denis
  last_name: Kuznedelev
- first_name: Elias
  full_name: Frantar, Elias
  id: 09a8f98d-ec99-11ea-ae11-c063a7b7fe5f
  last_name: Frantar
- first_name: Saleh
  full_name: Ashkboos, Saleh
  last_name: Ashkboos
- first_name: Alexander
  full_name: Borzunov, Alexander
  last_name: Borzunov
- first_name: Torsten
  full_name: Hoefler, Torsten
  last_name: Hoefler
- 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: 'Dettmers T, Svirschevski RA, Egiazarian V, et al. SpQR: A sparse-quantized
    representation for near-lossless LLM weight compression. In: <i>12th International
    Conference on Learning Representations</i>. OpenReview; 2024.'
  apa: 'Dettmers, T., Svirschevski, R. A., Egiazarian, V., Kuznedelev, D., Frantar,
    E., Ashkboos, S., … Alistarh, D.-A. (2024). SpQR: A sparse-quantized representation
    for near-lossless LLM weight compression. In <i>12th International Conference
    on Learning Representations</i>. Vienna, Austria: OpenReview.'
  chicago: 'Dettmers, Tim, Ruslan A. Svirschevski, Vage Egiazarian, Denis Kuznedelev,
    Elias Frantar, Saleh Ashkboos, Alexander Borzunov, Torsten Hoefler, and Dan-Adrian
    Alistarh. “SpQR: A Sparse-Quantized Representation for near-Lossless LLM Weight
    Compression.” In <i>12th International Conference on Learning Representations</i>.
    OpenReview, 2024.'
  ieee: 'T. Dettmers <i>et al.</i>, “SpQR: A sparse-quantized representation for near-lossless
    LLM weight compression,” in <i>12th International Conference on Learning Representations</i>,
    Vienna, Austria, 2024.'
  ista: 'Dettmers T, Svirschevski RA, Egiazarian V, Kuznedelev D, Frantar E, Ashkboos
    S, Borzunov A, Hoefler T, Alistarh D-A. 2024. SpQR: A sparse-quantized representation
    for near-lossless LLM weight compression. 12th International Conference on Learning
    Representations. ICLR: International Conference on Learning Representations.'
  mla: 'Dettmers, Tim, et al. “SpQR: A Sparse-Quantized Representation for near-Lossless
    LLM Weight Compression.” <i>12th International Conference on Learning Representations</i>,
    OpenReview, 2024.'
  short: T. Dettmers, R.A. Svirschevski, V. Egiazarian, D. Kuznedelev, E. Frantar,
    S. Ashkboos, A. Borzunov, T. Hoefler, D.-A. Alistarh, in:, 12th International
    Conference on Learning Representations, OpenReview, 2024.
conference:
  end_date: 2024-05-11
  location: Vienna, Austria
  name: 'ICLR: International Conference on Learning Representations'
  start_date: 2024-05-07
das_tickbox: '0'
date_created: 2025-01-30T08:26:59Z
date_published: 2024-05-15T00:00:00Z
date_updated: 2026-10-01T09:33:44Z
day: '15'
department:
- _id: DaAl
external_id:
  arxiv:
  - '2306.03078'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.48550/arXiv.2306.03078
month: '05'
oa: 1
oa_version: Preprint
publication: 12th International Conference on Learning Representations
publication_status: published
publisher: OpenReview
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: 'SpQR: A sparse-quantized representation for near-lossless LLM weight compression'
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
_id: '17093'
abstract:
- lang: eng
  text: 'Federated Learning (FL) enables large-scale distributed training of machine
    learning models, while still allowing individual nodes to maintain data locally.
    However, executing FL at scale comes with inherent practical challenges: 1) heterogeneity
    of the local node data distributions, 2) heterogeneity of node computational speeds
    (asynchrony), but also 3) constraints in the amount of communication between the
    clients and the server. In this work, we present the first variant of the classic
    federated averaging (FedAvg) algorithm which, at the same time, supports data
    heterogeneity, partial client asynchrony, and communication compression. Our algorithm
    comes with a novel, rigorous analysis showing that, in spite of these system relaxations,
    it can provide similar convergence to FedAvg in interesting parameter regimes.
    Experimental results in the rigorous LEAF benchmark on setups of up to 300 nodes
    show that our algorithm ensures fast convergence for standard federated tasks,
    improving upon prior quantized and asynchronous approaches.'
alternative_title:
- PMLR
article_processing_charge: No
arxiv: 1
author:
- first_name: Hossein
  full_name: Zakerinia, Hossein
  id: 653bd8b6-f394-11eb-9cf6-c0bbf6cd78d4
  last_name: Zakerinia
  orcid: 0009-0007-3977-6462
- first_name: Shayan
  full_name: Talaei, Shayan
  last_name: Talaei
- first_name: Giorgi
  full_name: Nadiradze, Giorgi
  id: 3279A00C-F248-11E8-B48F-1D18A9856A87
  last_name: Nadiradze
  orcid: 0000-0001-5634-0731
- 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: 'Zakerinia H, Talaei S, Nadiradze G, Alistarh D-A. Communication-efficient
    federated learning with data and client heterogeneity. In: <i>Proceedings of the
    27th International Conference on Artificial Intelligence and Statistics</i>. Vol
    238. ML Research Press; 2024:3448-3456.'
  apa: 'Zakerinia, H., Talaei, S., Nadiradze, G., &#38; Alistarh, D.-A. (2024). Communication-efficient
    federated learning with data and client heterogeneity. In <i>Proceedings of the
    27th International Conference on Artificial Intelligence and Statistics</i> (Vol.
    238, pp. 3448–3456). Valencia, Spain: ML Research Press.'
  chicago: Zakerinia, Hossein, Shayan Talaei, Giorgi Nadiradze, and Dan-Adrian Alistarh.
    “Communication-Efficient Federated Learning with Data and Client Heterogeneity.”
    In <i>Proceedings of the 27th International Conference on Artificial Intelligence
    and Statistics</i>, 238:3448–56. ML Research Press, 2024.
  ieee: H. Zakerinia, S. Talaei, G. Nadiradze, and D.-A. Alistarh, “Communication-efficient
    federated learning with data and client heterogeneity,” in <i>Proceedings of the
    27th International Conference on Artificial Intelligence and Statistics</i>, Valencia,
    Spain, 2024, vol. 238, pp. 3448–3456.
  ista: 'Zakerinia H, Talaei S, Nadiradze G, Alistarh D-A. 2024. Communication-efficient
    federated learning with data and client heterogeneity. Proceedings of the 27th
    International Conference on Artificial Intelligence and Statistics. AISTATS: Conference
    on Artificial Intelligence and Statistics, PMLR, vol. 238, 3448–3456.'
  mla: Zakerinia, Hossein, et al. “Communication-Efficient Federated Learning with
    Data and Client Heterogeneity.” <i>Proceedings of the 27th International Conference
    on Artificial Intelligence and Statistics</i>, vol. 238, ML Research Press, 2024,
    pp. 3448–56.
  short: H. Zakerinia, S. Talaei, G. Nadiradze, D.-A. Alistarh, in:, Proceedings of
    the 27th International Conference on Artificial Intelligence and Statistics, ML
    Research Press, 2024, pp. 3448–3456.
conference:
  end_date: 2024-05-04
  location: Valencia, Spain
  name: 'AISTATS: Conference on Artificial Intelligence and Statistics'
  start_date: 2024-05-02
corr_author: '1'
das_tickbox: '0'
date_created: 2024-06-02T22:00:57Z
date_published: 2024-05-01T00:00:00Z
date_updated: 2026-10-01T09:34:02Z
day: '01'
department:
- _id: DaAl
- _id: ChLa
external_id:
  arxiv:
  - '2206.10032'
intvolume: '       238'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.48550/arXiv.2206.10032
month: '05'
oa: 1
oa_version: Preprint
page: 3448-3456
publication: Proceedings of the 27th International Conference on Artificial Intelligence
  and Statistics
publication_identifier:
  eissn:
  - 2640-3498
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Communication-efficient federated learning with data and client heterogeneity
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 238
year: '2024'
...
---
_id: '18117'
abstract:
- lang: eng
  text: "We investigate parameter-efficient fine-tuning (PEFT) methods that can provide
    good accuracy under limited computational and memory budgets in the context of
    large language models (LLMs). We present a new PEFT method called Robust Adaptation
    (RoSA) inspired by robust principal component analysis that jointly trains low-rank\r\n
    and highly-sparse components on top of a set of fixed pretrained weights to efficiently
    approximate the performance of a full-fine-tuning (FFT) solution. Across a series
    of challenging generative tasks such as grade-school math and SQL query generation,
    which require fine-tuning for good performance, we show that RoSA outperforms
    LoRA, pure sparse fine-tuning, and alternative hybrid methods at the same parameter
    budget, and can even recover the performance of FFT on some tasks. We provide
    system support for RoSA to complement the training algorithm, specifically in
    the form of sparse GPU kernels which enable memory- and computationally-efficient
    training, and show that it is also compatible with low-precision base weights,
    resulting in the first joint representation combining quantization, low-rank and
    sparse approximations. Our code is available at https://github.com/IST-DASLab/RoSA."
acknowledgement: The authors would like to thank Eldar Kurtic for experimental support
  and useful suggestions throughout the project
article_processing_charge: No
arxiv: 1
author:
- first_name: Mahdi
  full_name: Nikdan, Mahdi
  id: 66374281-f394-11eb-9cf6-869147deecc0
  last_name: Nikdan
- first_name: Soroush
  full_name: Tabesh, Soroush
  id: 06000900-6068-11ef-8d61-c2472ef2e752
  last_name: Tabesh
  orcid: 0009-0003-4119-6281
- first_name: Elvir
  full_name: Crncevic, Elvir
  id: 41888001-440d-11ef-8299-d0e838b8185e
  last_name: Crncevic
- first_name: Dan-Adrian
  full_name: Alistarh, Dan-Adrian
  id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
  last_name: Alistarh
  orcid: 0000-0003-3650-940X
citation:
  ama: 'Nikdan M, Tabesh S, Crncevic E, Alistarh D-A. RoSA: Accurate parameter-efficient
    fine-tuning via robust adaptation. In: <i>Proceedings of the 41st International
    Conference on Machine Learning</i>. Vol 235. ML Research Press; 2024:38187-38206.'
  apa: 'Nikdan, M., Tabesh, S., Crncevic, E., &#38; Alistarh, D.-A. (2024). RoSA:
    Accurate parameter-efficient fine-tuning via robust adaptation. In <i>Proceedings
    of the 41st International Conference on Machine Learning</i> (Vol. 235, pp. 38187–38206).
    Vienna, Austria: ML Research Press.'
  chicago: 'Nikdan, Mahdi, Soroush Tabesh, Elvir Crncevic, and Dan-Adrian Alistarh.
    “RoSA: Accurate Parameter-Efficient Fine-Tuning via Robust Adaptation.” In <i>Proceedings
    of the 41st International Conference on Machine Learning</i>, 235:38187–206. ML
    Research Press, 2024.'
  ieee: 'M. Nikdan, S. Tabesh, E. Crncevic, and D.-A. Alistarh, “RoSA: Accurate parameter-efficient
    fine-tuning via robust adaptation,” in <i>Proceedings of the 41st International
    Conference on Machine Learning</i>, Vienna, Austria, 2024, vol. 235, pp. 38187–38206.'
  ista: 'Nikdan M, Tabesh S, Crncevic E, Alistarh D-A. 2024. RoSA: Accurate parameter-efficient
    fine-tuning via robust adaptation. Proceedings of the 41st International Conference
    on Machine Learning. ICML: International Conference on Machine Learning vol. 235,
    38187–38206.'
  mla: 'Nikdan, Mahdi, et al. “RoSA: Accurate Parameter-Efficient Fine-Tuning via
    Robust Adaptation.” <i>Proceedings of the 41st International Conference on Machine
    Learning</i>, vol. 235, ML Research Press, 2024, pp. 38187–206.'
  short: M. Nikdan, S. Tabesh, E. Crncevic, D.-A. Alistarh, in:, Proceedings of the
    41st International Conference on Machine Learning, ML Research Press, 2024, pp.
    38187–38206.
conference:
  end_date: 2024-07-27
  location: Vienna, Austria
  name: 'ICML: International Conference on Machine Learning'
  start_date: 2024-07-21
corr_author: '1'
das_tickbox: '0'
date_created: 2024-09-22T22:01:44Z
date_published: 2024-09-01T00:00:00Z
date_updated: 2026-10-01T09:34:36Z
day: '01'
department:
- _id: DaAl
- _id: GradSch
external_id:
  arxiv:
  - '2401.04679'
intvolume: '       235'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.48550/arXiv.2401.04679
month: '09'
oa: 1
oa_version: Preprint
page: 38187-38206
publication: Proceedings of the 41st International Conference on Machine Learning
publication_identifier:
  eissn:
  - 2640-3498
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
related_material:
  link:
  - relation: software
    url: https://github.com/IST-DASLab/RoSA
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: no
title: 'RoSA: Accurate parameter-efficient fine-tuning via robust adaptation'
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 235
year: '2024'
...
---
_id: '15315'
abstract:
- lang: eng
  text: Single and collective cell migration are fundamental processes critical for
    physiological phenomena ranging from embryonic development and immune response
    to wound healing and cancer metastasis. To understand cell migration from a physical
    perspective, a broad variety of models for the underlying physical mechanisms
    that govern cell motility have been developed. A key challenge in the development
    of such models is how to connect them to experimental observations, which often
    exhibit complex stochastic behaviours. In this review, we discuss recent advances
    in data-driven theoretical approaches that directly connect with experimental
    data to infer dynamical models of stochastic cell migration. Leveraging advances
    in nanofabrication, image analysis, and tracking technology, experimental studies
    now provide unprecedented large datasets on cellular dynamics. In parallel, theoretical
    efforts have been directed towards integrating such datasets into physical models
    from the single cell to the tissue scale with the aim of conceptualising the emergent
    behaviour of cells. We first review how this inference problem has been addressed
    in both freely migrating and confined cells. Next, we discuss why these dynamics
    typically take the form of underdamped stochastic equations of motion, and how
    such equations can be inferred from data. We then review applications of data-driven
    inference and machine learning approaches to heterogeneity in cell behaviour,
    subcellular degrees of freedom, and to the collective dynamics of multicellular
    systems. Across these applications, we emphasise how data-driven methods can be
    integrated with physical active matter models of migrating cells, and help reveal
    how underlying molecular mechanisms control cell behaviour. Together, these data-driven
    approaches are a promising avenue for building physical models of cell migration
    directly from experimental data, and for providing conceptual links between different
    length-scales of description.
acknowledgement: This work was supported by the Deutsche Forschungsgemeinschaft (German
  Research Foundation)—Project-ID 201269156—SFB 1032 (Project B12). D B B was supported
  by an NOMIS Fellowship and an EMBO Fellowship (ALTF 343-2022). We thank Joachim
  Rädler, Alexandra Fink, Erwin Frey, Pierre Ronceray, Ricard Alert, Edouard Hannezo,
  Henrik Flyvbjerg, Ulrich Schwarz, Joshua Shaevitz, Greg Stephens, Andrea Cavagna,
  Grzegorz Gradziuk, Fridtjof Brauns, Nikolas Claussen, Tom Brandstätter, Johannes
  Flommersfeld, Christoph Schreiber, Nicolas Arlt, Matthew Schmitt, Joris Messelink,
  Federico Gnesotto, Federica Mura, Bram Hoogland, Manon Wigbers, Isabella Graf, Jessica
  Lober, and many others for inspiring discussions. We also thank Claudia Flandoli
  for the artwork in figures 1, 5, 8 and 9.
article_number: '056601'
article_processing_charge: Yes (in subscription journal)
article_type: review
arxiv: 1
author:
- first_name: David
  full_name: Brückner, David
  id: e1e86031-6537-11eb-953a-f7ab92be508d
  last_name: Brückner
  orcid: 0000-0001-7205-2975
- first_name: Chase P.
  full_name: Broedersz, Chase P.
  last_name: Broedersz
citation:
  ama: 'Brückner D, Broedersz CP. Learning dynamical models of single and collective
    cell migration: a review. <i>Reports on Progress in Physics</i>. 2024;87(5). doi:<a
    href="https://doi.org/10.1088/1361-6633/ad36d2">10.1088/1361-6633/ad36d2</a>'
  apa: 'Brückner, D., &#38; Broedersz, C. P. (2024). Learning dynamical models of
    single and collective cell migration: a review. <i>Reports on Progress in Physics</i>.
    IOP Publishing. <a href="https://doi.org/10.1088/1361-6633/ad36d2">https://doi.org/10.1088/1361-6633/ad36d2</a>'
  chicago: 'Brückner, David, and Chase P. Broedersz. “Learning Dynamical Models of
    Single and Collective Cell Migration: A Review.” <i>Reports on Progress in Physics</i>.
    IOP Publishing, 2024. <a href="https://doi.org/10.1088/1361-6633/ad36d2">https://doi.org/10.1088/1361-6633/ad36d2</a>.'
  ieee: 'D. Brückner and C. P. Broedersz, “Learning dynamical models of single and
    collective cell migration: a review,” <i>Reports on Progress in Physics</i>, vol.
    87, no. 5. IOP Publishing, 2024.'
  ista: 'Brückner D, Broedersz CP. 2024. Learning dynamical models of single and collective
    cell migration: a review. Reports on Progress in Physics. 87(5), 056601.'
  mla: 'Brückner, David, and Chase P. Broedersz. “Learning Dynamical Models of Single
    and Collective Cell Migration: A Review.” <i>Reports on Progress in Physics</i>,
    vol. 87, no. 5, 056601, IOP Publishing, 2024, doi:<a href="https://doi.org/10.1088/1361-6633/ad36d2">10.1088/1361-6633/ad36d2</a>.'
  short: D. Brückner, C.P. Broedersz, Reports on Progress in Physics 87 (2024).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: No new data were created or analysed in this study.
date_created: 2024-04-14T22:01:01Z
date_published: 2024-04-04T00:00:00Z
date_updated: 2026-10-01T10:09:41Z
day: '04'
ddc:
- '530'
department:
- _id: EdHa
doi: 10.1088/1361-6633/ad36d2
external_id:
  arxiv:
  - '2309.00545'
  isi:
  - '001196692400001'
  pmid:
  - '38518358'
file:
- access_level: open_access
  checksum: c5910078230ade20f4dd83592e862a72
  content_type: application/pdf
  creator: dernst
  date_created: 2024-08-20T11:00:03Z
  date_updated: 2024-08-20T11:00:03Z
  file_id: '17451'
  file_name: 2024_ReportPhysics_Brueckner.pdf
  file_size: 4376898
  relation: main_file
  success: 1
file_date_updated: 2024-08-20T11:00:03Z
fulldoi: https://doi.org/10.1088/1361-6633/ad36d2
has_accepted_license: '1'
intvolume: '        87'
isi: 1
issue: '5'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b
  grant_number: ALTF 343-2022
  name: A mechano-chemical theory for stem cell fate decisions in organoid development
publication: Reports on Progress in Physics
publication_identifier:
  eissn:
  - 1361-6633
  issn:
  - 0034-4885
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
researchdata_availability: not applicable
scopus_import: '1'
status: public
supplementarymaterial: no
title: 'Learning dynamical models of single and collective cell migration: a review'
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
  name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
  short: CC BY (3.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 87
year: '2024'
...
---
_id: '15250'
abstract:
- lang: eng
  text: Orphan solute carrier (SLC) represents a group of membrane transporters whose
    exact functions and substrate specificities are not known. Elucidating the function
    and regulation of orphan SLC transporters is not only crucial for advancing our
    knowledge of cellular and molecular biology but can potentially lead to the development
    of new therapeutic strategies. Here, we provide evidence for the biological function
    of a ubiquitous orphan lysosomal SLC, the Major Facilitator Superfamily Domain-containing
    Protein 1 (MFSD1), which has remained phylogenetically unassigned. Targeted metabolomics
    revealed that dipeptides containing either lysine or arginine residues accumulate
    in lysosomes of cells lacking MFSD1. Whole-cell patch-clamp electrophysiological
    recordings of HEK293-cells expressing MFSD1 on the cell surface displayed transport
    affinities for positively charged dipeptides in the lower mM range, while dipeptides
    that carry a negative net charge were not transported. This was also true for
    single amino acids and tripeptides, which MFSD1 failed to transport. Our results
    identify MFSD1 as a highly selective lysosomal lysine/arginine/histidine-containing
    dipeptide exporter, which functions as a uniporter.
acknowledged_ssus:
- _id: Bio
acknowledgement: We thank the Metabolomics Facility at Vienna BioCenter Core Facilities,
  which is a member of the Vienna BioCenter and funded by the City of Vienna through
  the Vienna Business Agency (shared research facility), for the LC–MS/MS analysis;
  and the BioImaging Facility at IST Austria for technical support and assistance.
  The authors want to thank N. Kastner for help with the live  cell  imaging  and  A.  Korošec  for  help  with  flow  cytometry.  This  work  was  supported
  by the Austrian Science Fund (FWF), grant P 36621- B (to M.R.), grant P 36667 (to
  W.S.), and core funding from IST Austria (to D.S.).
article_number: e2319686121
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Danila
  full_name: Boytsov, Danila
  last_name: Boytsov
- first_name: Gregor M.
  full_name: Madej, Gregor M.
  last_name: Madej
- first_name: Georg
  full_name: Horn, Georg
  last_name: Horn
- first_name: Nadine
  full_name: Blaha, Nadine
  last_name: Blaha
- first_name: Thomas
  full_name: Köcher, Thomas
  last_name: Köcher
- first_name: Harald H.
  full_name: Sitte, Harald H.
  last_name: Sitte
- first_name: Daria E
  full_name: Siekhaus, Daria E
  id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
  last_name: Siekhaus
  orcid: 0000-0001-8323-8353
- first_name: Christine
  full_name: Ziegler, Christine
  last_name: Ziegler
- first_name: Walter
  full_name: Sandtner, Walter
  last_name: Sandtner
- first_name: Marko
  full_name: Roblek, Marko
  id: 3047D808-F248-11E8-B48F-1D18A9856A87
  last_name: Roblek
  orcid: 0000-0001-9588-1389
citation:
  ama: Boytsov D, Madej GM, Horn G, et al. Orphan lysosomal solute carrier MFSD1 facilitates
    highly selective dipeptide transport. <i>Proceedings of the National Academy of
    Sciences of the United States of America</i>. 2024;121(13). doi:<a href="https://doi.org/10.1073/pnas.2319686121">10.1073/pnas.2319686121</a>
  apa: Boytsov, D., Madej, G. M., Horn, G., Blaha, N., Köcher, T., Sitte, H. H., …
    Roblek, M. (2024). Orphan lysosomal solute carrier MFSD1 facilitates highly selective
    dipeptide transport. <i>Proceedings of the National Academy of Sciences of the
    United States of America</i>. National Academy of Sciences. <a href="https://doi.org/10.1073/pnas.2319686121">https://doi.org/10.1073/pnas.2319686121</a>
  chicago: Boytsov, Danila, Gregor M. Madej, Georg Horn, Nadine Blaha, Thomas Köcher,
    Harald H. Sitte, Daria E Siekhaus, Christine Ziegler, Walter Sandtner, and Marko
    Roblek. “Orphan Lysosomal Solute Carrier MFSD1 Facilitates Highly Selective Dipeptide
    Transport.” <i>Proceedings of the National Academy of Sciences of the United States
    of America</i>. National Academy of Sciences, 2024. <a href="https://doi.org/10.1073/pnas.2319686121">https://doi.org/10.1073/pnas.2319686121</a>.
  ieee: D. Boytsov <i>et al.</i>, “Orphan lysosomal solute carrier MFSD1 facilitates
    highly selective dipeptide transport,” <i>Proceedings of the National Academy
    of Sciences of the United States of America</i>, vol. 121, no. 13. National Academy
    of Sciences, 2024.
  ista: Boytsov D, Madej GM, Horn G, Blaha N, Köcher T, Sitte HH, Siekhaus DE, Ziegler
    C, Sandtner W, Roblek M. 2024. Orphan lysosomal solute carrier MFSD1 facilitates
    highly selective dipeptide transport. Proceedings of the National Academy of Sciences
    of the United States of America. 121(13), e2319686121.
  mla: Boytsov, Danila, et al. “Orphan Lysosomal Solute Carrier MFSD1 Facilitates
    Highly Selective Dipeptide Transport.” <i>Proceedings of the National Academy
    of Sciences of the United States of America</i>, vol. 121, no. 13, e2319686121,
    National Academy of Sciences, 2024, doi:<a href="https://doi.org/10.1073/pnas.2319686121">10.1073/pnas.2319686121</a>.
  short: D. Boytsov, G.M. Madej, G. Horn, N. Blaha, T. Köcher, H.H. Sitte, D.E. Siekhaus,
    C. Ziegler, W. Sandtner, M. Roblek, Proceedings of the National Academy of Sciences
    of the United States of America 121 (2024).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: All study data are included in the article and/or SI Appendix.
date_created: 2024-03-31T22:01:12Z
date_published: 2024-03-26T00:00:00Z
date_updated: 2026-10-01T09:36:29Z
day: '26'
ddc:
- '570'
department:
- _id: DaSi
doi: 10.1073/pnas.2319686121
external_id:
  isi:
  - '001206419000003'
  pmid:
  - '38507452'
file:
- access_level: open_access
  checksum: 06f9e60b1146a685d58bf33999422fa8
  content_type: application/pdf
  creator: dernst
  date_created: 2024-04-02T08:54:28Z
  date_updated: 2024-04-02T08:54:28Z
  file_id: '15256'
  file_name: 2024_PNAS_Boytsov.pdf
  file_size: 2483787
  relation: main_file
  success: 1
file_date_updated: 2024-04-02T08:54:28Z
fulldoi: https://doi.org/10.1073/pnas.2319686121
has_accepted_license: '1'
intvolume: '       121'
isi: 1
issue: '13'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: Proceedings of the National Academy of Sciences of the United States
  of America
publication_identifier:
  eissn:
  - 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
researchdata_availability: yes (supplementary data)
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Orphan lysosomal solute carrier MFSD1 facilitates highly selective dipeptide
  transport
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 121
year: '2024'
...
---
_id: '15024'
abstract:
- lang: eng
  text: Electrostatic correlations between ions dissolved in water are known to impact
    their transport properties in numerous ways, from conductivity to ion selectivity.
    The effects of these correlations on the solvent itself remain, however, much
    less clear. In particular, the addition of salt has been consistently reported
    to affect the solution’s viscosity, but most modeling attempts fail to reproduce
    experimental data even at moderate salt concentrations. Here, we use an approach
    based on stochastic density functional theory, which accurately captures charge
    fluctuations and correlations. We derive a simple analytical expression for the
    viscosity correction in concentrated electrolytes, by directly linking it to the
    liquid’s structure factor. Our prediction compares quantitatively to experimental
    data at all temperatures and all salt concentrations up to the saturation limit.
    This universal link between the microscopic structure and viscosity allows us
    to shed light on the nanoscale dynamics of water and ions under highly concentrated
    and correlated conditions.
acknowledgement: The author thanks Lydéric Bocquet, Baptiste Coquinot, and Mathieu
  Lizée for fruitful discussions. This project received funding from the European
  Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie
  Grant Agreement No. 101034413.
article_number: '064503'
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Paul
  full_name: Robin, Paul
  id: 48c58128-57b0-11ee-9095-dc28fd97fc1d
  last_name: Robin
  orcid: 0000-0002-5728-9189
citation:
  ama: Robin P. Correlation-induced viscous dissipation in concentrated electrolytes.
    <i>Journal of Chemical Physics</i>. 2024;160(6). doi:<a href="https://doi.org/10.1063/5.0188215">10.1063/5.0188215</a>
  apa: Robin, P. (2024). Correlation-induced viscous dissipation in concentrated electrolytes.
    <i>Journal of Chemical Physics</i>. AIP Publishing. <a href="https://doi.org/10.1063/5.0188215">https://doi.org/10.1063/5.0188215</a>
  chicago: Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.”
    <i>Journal of Chemical Physics</i>. AIP Publishing, 2024. <a href="https://doi.org/10.1063/5.0188215">https://doi.org/10.1063/5.0188215</a>.
  ieee: P. Robin, “Correlation-induced viscous dissipation in concentrated electrolytes,”
    <i>Journal of Chemical Physics</i>, vol. 160, no. 6. AIP Publishing, 2024.
  ista: Robin P. 2024. Correlation-induced viscous dissipation in concentrated electrolytes.
    Journal of Chemical Physics. 160(6), 064503.
  mla: Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.”
    <i>Journal of Chemical Physics</i>, vol. 160, no. 6, 064503, AIP Publishing, 2024,
    doi:<a href="https://doi.org/10.1063/5.0188215">10.1063/5.0188215</a>.
  short: P. Robin, Journal of Chemical Physics 160 (2024).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: Data sharing is not applicable to this article as no new
  data were created. Data supporting the findings of this study are accessible in
  the literature, as indicated throughout the article.
date_created: 2024-02-25T23:00:55Z
date_published: 2024-02-14T00:00:00Z
date_updated: 2026-10-01T10:08:50Z
day: '14'
ddc:
- '540'
department:
- _id: EdHa
doi: 10.1063/5.0188215
ec_funded: 1
external_id:
  arxiv:
  - '2311.11784'
  isi:
  - '001161104900003'
  pmid:
  - '38349632'
file:
- access_level: open_access
  checksum: 0a5e0ae70849bce674466fc054390ec0
  content_type: application/pdf
  creator: dernst
  date_created: 2024-02-27T08:12:52Z
  date_updated: 2024-02-27T08:12:52Z
  file_id: '15034'
  file_name: 2024_JourChemicalPhysics_Robin.pdf
  file_size: 5452738
  relation: main_file
  success: 1
file_date_updated: 2024-02-27T08:12:52Z
fulldoi: https://doi.org/10.1063/5.0188215
has_accepted_license: '1'
intvolume: '       160'
isi: 1
issue: '6'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
  call_identifier: H2020
  grant_number: '101034413'
  name: 'IST-BRIDGE: International postdoctoral program'
publication: Journal of Chemical Physics
publication_identifier:
  eissn:
  - 1089-7690
  issn:
  - 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
researchdata_availability: not applicable
scopus_import: '1'
status: public
supplementarymaterial: no
title: Correlation-induced viscous dissipation in concentrated electrolytes
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 160
year: '2024'
...
---
_id: '17892'
abstract:
- lang: eng
  text: "Enzyme-substrate kinetics form the basis of many biomolecular processes.
    The interplay between substrate binding and substrate geometry can give rise to
    long-range interactions between enzyme binding events. Here we study a general
    model of enzyme-substrate kinetics with restricted long-range interactions described
    by an exponent −\U0001D6FE. We employ a coherent-state path integral and renormalization
    group approach to calculate the first moment and two-point correlation function
    of the enzyme-binding profile. We show that starting from an empty substrate the
    average occupancy follows a power law with an exponent 1/(1−\U0001D6FE) over time.
    The correlation function decays algebraically with two distinct spatial regimes
    characterized by exponents −\U0001D6FE on short distances and −(2/3)⁢(2−\U0001D6FE)
    on long distances. The crossover between both regimes scales inversely with the
    average substrate occupancy. Our work allows associating experimental measurements
    of bound enzyme locations with their binding kinetics and the spatial conformation
    of the substrate."
acknowledgement: We thank F. Piazza, M. Henkel, and F. Jülicher for helpful feedback
  and the entire Rulands group for fruitful discussions. We thank W. Reik, S. Clark,
  T. Lohoff, and I. Kafetzopoulos for fruitful discussions about the biological aspects
  of this work. This project has received funding from the European Research Council
  (ERC) under the European Union's Horizon 2020 research and innovation program (Grant
  No. 950349). This project has received funding from the European Union's Horizon
  2020 research and innovation programme under the Marie Skłodowska-Curie Grant No.
  101034413.
article_number: '024404'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Fabrizio
  full_name: Olmeda, Fabrizio
  id: 69dbf5fb-8a76-11ed-866b-fb486d8b5689
  last_name: Olmeda
- first_name: Steffen
  full_name: Rulands, Steffen
  last_name: Rulands
citation:
  ama: Olmeda F, Rulands S. Field theory of enzyme-substrate systems with restricted
    long-range interactions. <i>Physical Review E</i>. 2024;110(2). doi:<a href="https://doi.org/10.1103/PhysRevE.110.024404">10.1103/PhysRevE.110.024404</a>
  apa: Olmeda, F., &#38; Rulands, S. (2024). Field theory of enzyme-substrate systems
    with restricted long-range interactions. <i>Physical Review E</i>. American Physical
    Society. <a href="https://doi.org/10.1103/PhysRevE.110.024404">https://doi.org/10.1103/PhysRevE.110.024404</a>
  chicago: Olmeda, Fabrizio, and Steffen Rulands. “Field Theory of Enzyme-Substrate
    Systems with Restricted Long-Range Interactions.” <i>Physical Review E</i>. American
    Physical Society, 2024. <a href="https://doi.org/10.1103/PhysRevE.110.024404">https://doi.org/10.1103/PhysRevE.110.024404</a>.
  ieee: F. Olmeda and S. Rulands, “Field theory of enzyme-substrate systems with restricted
    long-range interactions,” <i>Physical Review E</i>, vol. 110, no. 2. American
    Physical Society, 2024.
  ista: Olmeda F, Rulands S. 2024. Field theory of enzyme-substrate systems with restricted
    long-range interactions. Physical Review E. 110(2), 024404.
  mla: Olmeda, Fabrizio, and Steffen Rulands. “Field Theory of Enzyme-Substrate Systems
    with Restricted Long-Range Interactions.” <i>Physical Review E</i>, vol. 110,
    no. 2, 024404, American Physical Society, 2024, doi:<a href="https://doi.org/10.1103/PhysRevE.110.024404">10.1103/PhysRevE.110.024404</a>.
  short: F. Olmeda, S. Rulands, Physical Review E 110 (2024).
corr_author: '1'
das_tickbox: '0'
date_created: 2024-09-08T22:01:12Z
date_published: 2024-08-01T00:00:00Z
date_updated: 2026-10-01T10:06:45Z
day: '01'
ddc:
- '530'
department:
- _id: EdHa
doi: 10.1103/PhysRevE.110.024404
ec_funded: 1
external_id:
  isi:
  - '001299670100004'
  pmid:
  - '39294986'
file:
- access_level: open_access
  checksum: 67fc2cc8eee3155e5c3b7380307d8284
  content_type: application/pdf
  creator: dernst
  date_created: 2024-09-11T05:59:36Z
  date_updated: 2024-09-11T05:59:36Z
  file_id: '18053'
  file_name: 2024_PhysReviewE_Olmeda.pdf
  file_size: 445696
  relation: main_file
  success: 1
file_date_updated: 2024-09-11T05:59:36Z
fulldoi: https://doi.org/10.1103/PhysRevE.110.024404
has_accepted_license: '1'
intvolume: '       110'
isi: 1
issue: '2'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
  call_identifier: H2020
  grant_number: '101034413'
  name: 'IST-BRIDGE: International postdoctoral program'
publication: Physical Review E
publication_identifier:
  eissn:
  - 2470-0053
  issn:
  - 2470-0045
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Field theory of enzyme-substrate systems with restricted long-range interactions
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 110
year: '2024'
...
---
_id: '17104'
abstract:
- lang: eng
  text: 'The homeostasis of epithelial tissue relies on a balance between the self-renewal
    of stem cell populations, cellular differentiation, and loss. Although this balance
    needs to be tightly regulated to avoid pathologies, such as tumor growth, the
    regulatory mechanisms, both cell-intrinsic and collective, which ensure tissue
    steady-state are still poorly understood. Here, we develop a computational model
    that incorporates basic assumptions of stem cell renewal into distinct populations
    and mechanical interactions between cells. We find that the model generates unexpected
    dynamic features: stem cells repel each other in the bulk tissue and are thus
    found rather isolated, as in a number of in vivo contexts. By mapping the system
    onto a gas of passive Brownian particles with effective repulsive interactions,
    that arise from the generated flows of differentiated cells, we show that we can
    quantitatively describe such stem cell distribution in tissues. The interaction
    potential between a pair of stem cells decays exponentially with a characteristic
    length that spans several cell sizes, corresponding to the volume of cells generated
    per stem cell division. Our findings may help understanding the dynamics of normal
    and cancerous epithelial tissues.'
acknowledgement: JE and JK gratefully acknowledge financial support from the Initiative
  and Networking Fund (IVF) via the grant number ERC-RA-004. Simulations were performed
  with computing resources granted by RWTH Aachen University under project ‘rwth0475’.
article_number: '097'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Johannes C.
  full_name: Krämer, Johannes C.
  last_name: Krämer
- first_name: Edouard B
  full_name: Hannezo, Edouard B
  id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
  last_name: Hannezo
  orcid: 0000-0001-6005-1561
- first_name: Gerhard
  full_name: Gompper, Gerhard
  last_name: Gompper
- first_name: Jens
  full_name: Elgeti, Jens
  last_name: Elgeti
citation:
  ama: Krämer JC, Hannezo EB, Gompper G, Elgeti J. Mechanically-driven stem cell separation
    in tissues caused by proliferating daughter cells. <i>SciPost Physics</i>. 2024;16(4).
    doi:<a href="https://doi.org/10.21468/scipostphys.16.4.097">10.21468/scipostphys.16.4.097</a>
  apa: Krämer, J. C., Hannezo, E. B., Gompper, G., &#38; Elgeti, J. (2024). Mechanically-driven
    stem cell separation in tissues caused by proliferating daughter cells. <i>SciPost
    Physics</i>. SciPost Foundation. <a href="https://doi.org/10.21468/scipostphys.16.4.097">https://doi.org/10.21468/scipostphys.16.4.097</a>
  chicago: Krämer, Johannes C., Edouard B Hannezo, Gerhard Gompper, and Jens Elgeti.
    “Mechanically-Driven Stem Cell Separation in Tissues Caused by Proliferating Daughter
    Cells.” <i>SciPost Physics</i>. SciPost Foundation, 2024. <a href="https://doi.org/10.21468/scipostphys.16.4.097">https://doi.org/10.21468/scipostphys.16.4.097</a>.
  ieee: J. C. Krämer, E. B. Hannezo, G. Gompper, and J. Elgeti, “Mechanically-driven
    stem cell separation in tissues caused by proliferating daughter cells,” <i>SciPost
    Physics</i>, vol. 16, no. 4. SciPost Foundation, 2024.
  ista: Krämer JC, Hannezo EB, Gompper G, Elgeti J. 2024. Mechanically-driven stem
    cell separation in tissues caused by proliferating daughter cells. SciPost Physics.
    16(4), 097.
  mla: Krämer, Johannes C., et al. “Mechanically-Driven Stem Cell Separation in Tissues
    Caused by Proliferating Daughter Cells.” <i>SciPost Physics</i>, vol. 16, no.
    4, 097, SciPost Foundation, 2024, doi:<a href="https://doi.org/10.21468/scipostphys.16.4.097">10.21468/scipostphys.16.4.097</a>.
  short: J.C. Krämer, E.B. Hannezo, G. Gompper, J. Elgeti, SciPost Physics 16 (2024).
das_tickbox: '1'
dataavailabilitystatement: Source code, simulation data, and analysis scripts will
  be made publicly available on zenodo.org (10.5281/zenodo.8410957) after acceptance
  of the manuscript.
date_created: 2024-06-03T08:58:44Z
date_published: 2024-04-08T00:00:00Z
date_updated: 2026-10-01T09:44:06Z
day: '08'
ddc:
- '530'
department:
- _id: EdHa
doi: 10.21468/scipostphys.16.4.097
external_id:
  arxiv:
  - '2310.04272'
  isi:
  - '001202370200001'
file:
- access_level: open_access
  checksum: 6fdeecd21c166db8dedb927ecc2e6025
  content_type: application/pdf
  creator: dernst
  date_created: 2024-06-03T11:18:51Z
  date_updated: 2024-06-03T11:18:51Z
  file_id: '17109'
  file_name: 2024_SciPostPhys_Kraemer.pdf
  file_size: 4973291
  relation: main_file
  success: 1
file_date_updated: 2024-06-03T11:18:51Z
fulldoi: https://doi.org/10.21468/scipostphys.16.4.097
has_accepted_license: '1'
intvolume: '        16'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
publication: SciPost Physics
publication_identifier:
  issn:
  - 2542-4653
publication_status: published
publisher: SciPost Foundation
quality_controlled: '1'
related_material:
  record:
  - id: '23022'
    relation: research_data
    status: public
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Mechanically-driven stem cell separation in tissues caused by proliferating
  daughter cells
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 16
year: '2024'
...
---
OA_type: closed access
_id: '18919'
abstract:
- lang: eng
  text: The integration of theory and experiment makes possible tracking the slow
    evolution of a photodoped Mott insulator to a distinct non-equilibrium metallic
    phase under the influence of electron-lattice coupling.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Denitsa Rangelova
  full_name: Baykusheva, Denitsa Rangelova
  id: 71b4d059-2a03-11ee-914d-dfa3beed6530
  last_name: Baykusheva
  orcid: 0000-0002-7438-1139
citation:
  ama: Baykusheva DR. Through the slopes of a light-induced phase transition. <i>Nature
    Physics</i>. 2024;20(5):684-685. doi:<a href="https://doi.org/10.1038/s41567-024-02401-7">10.1038/s41567-024-02401-7</a>
  apa: Baykusheva, D. R. (2024). Through the slopes of a light-induced phase transition.
    <i>Nature Physics</i>. Springer Nature. <a href="https://doi.org/10.1038/s41567-024-02401-7">https://doi.org/10.1038/s41567-024-02401-7</a>
  chicago: Baykusheva, Denitsa Rangelova. “Through the Slopes of a Light-Induced Phase
    Transition.” <i>Nature Physics</i>. Springer Nature, 2024. <a href="https://doi.org/10.1038/s41567-024-02401-7">https://doi.org/10.1038/s41567-024-02401-7</a>.
  ieee: D. R. Baykusheva, “Through the slopes of a light-induced phase transition,”
    <i>Nature Physics</i>, vol. 20, no. 5. Springer Nature, pp. 684–685, 2024.
  ista: Baykusheva DR. 2024. Through the slopes of a light-induced phase transition.
    Nature Physics. 20(5), 684–685.
  mla: Baykusheva, Denitsa Rangelova. “Through the Slopes of a Light-Induced Phase
    Transition.” <i>Nature Physics</i>, vol. 20, no. 5, Springer Nature, 2024, pp.
    684–85, doi:<a href="https://doi.org/10.1038/s41567-024-02401-7">10.1038/s41567-024-02401-7</a>.
  short: D.R. Baykusheva, Nature Physics 20 (2024) 684–685.
corr_author: '1'
das_tickbox: '0'
date_created: 2025-01-27T14:29:20Z
date_published: 2024-05-01T00:00:00Z
date_updated: 2026-10-01T09:37:00Z
day: '01'
department:
- _id: DeBa
doi: 10.1038/s41567-024-02401-7
external_id:
  isi:
  - '001162208200002'
fulldoi: https://doi.org/10.1038/s41567-024-02401-7
intvolume: '        20'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: 684-685
publication: Nature Physics
publication_identifier:
  eissn:
  - 1745-2481
  issn:
  - 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Through the slopes of a light-induced phase transition
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 20
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '23022'
abstract:
- lang: eng
  text: "Contains animations, data, and source code used for the paper \"Mechanically-driven
    Stem Cell Separation in Tissues caused by Proliferating Daughter Cells\" by the
    same authors. \r\n\r\n\r\nThis repository contains all the data and analysis scripts
    to support the manuscript\r\nThe file structure is as follows:\r\n- \"analysis\"
    contains all the analysis scripts\r\n- \"gfx\" and \"animations\" the figures
    and supporting animations\r\n- \"1-SCpair\", \"2-SCtissue\", \"3-BDsimulation\",
    \"4-tissue-stochdiv\", \"6-inertia-effects\" all the source code and data for
    the respective models."
article_processing_charge: No
author:
- first_name: Jens
  full_name: Elgeti, Jens
  last_name: Elgeti
- first_name: Johannes
  full_name: Krämer, Johannes
  last_name: Krämer
citation:
  ama: Elgeti J, Krämer J. Data for Mechanically-driven Stem Cell Separation in Tissues
    caused by Proliferating Daughter Cells. 2024. doi:<a href="https://doi.org/10.5281/zenodo.8410956">10.5281/zenodo.8410956</a>
  apa: Elgeti, J., &#38; Krämer, J. (2024). Data for Mechanically-driven Stem Cell
    Separation in Tissues caused by Proliferating Daughter Cells. Zenodo. <a href="https://doi.org/10.5281/zenodo.8410956">https://doi.org/10.5281/zenodo.8410956</a>
  chicago: Elgeti, Jens, and Johannes Krämer. “Data for Mechanically-Driven Stem Cell
    Separation in Tissues Caused by Proliferating Daughter Cells.” Zenodo, 2024. <a
    href="https://doi.org/10.5281/zenodo.8410956">https://doi.org/10.5281/zenodo.8410956</a>.
  ieee: J. Elgeti and J. Krämer, “Data for Mechanically-driven Stem Cell Separation
    in Tissues caused by Proliferating Daughter Cells.” Zenodo, 2024.
  ista: Elgeti J, Krämer J. 2024. Data for Mechanically-driven Stem Cell Separation
    in Tissues caused by Proliferating Daughter Cells, Zenodo, <a href="https://doi.org/10.5281/zenodo.8410956">10.5281/zenodo.8410956</a>.
  mla: Elgeti, Jens, and Johannes Krämer. <i>Data for Mechanically-Driven Stem Cell
    Separation in Tissues Caused by Proliferating Daughter Cells</i>. Zenodo, 2024,
    doi:<a href="https://doi.org/10.5281/zenodo.8410956">10.5281/zenodo.8410956</a>.
  short: J. Elgeti, J. Krämer, (2024).
date_created: 2026-10-01T09:44:01Z
date_published: 2024-03-25T00:00:00Z
date_updated: 2026-10-01T09:44:07Z
day: '25'
ddc:
- '530'
department:
- _id: EdHa
doi: 10.5281/zenodo.8410956
fulldoi: https://doi.org/10.5281/zenodo.8410956
main_file_link:
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  url: https://doi.org/10.5281/zenodo.8410956
month: '03'
oa: 1
oa_version: None
publisher: Zenodo
related_material:
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status: public
title: Data for Mechanically-driven Stem Cell Separation in Tissues caused by Proliferating
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type: research_data_reference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2024'
...
---
APC_amount: 2570,79 EUR
OA_place: publisher
OA_type: hybrid
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abstract:
- lang: eng
  text: A key feature of many developmental systems is their ability to self-organize
    spatial patterns of functionally distinct cell fates. To ensure proper biological
    function, such patterns must be established reproducibly, by controlling and even
    harnessing intrinsic and extrinsic fluctuations. While the relevant molecular
    processes are increasingly well understood, we lack a principled framework to
    quantify the performance of such stochastic self-organizing systems. To that end,
    we introduce an information-theoretic measure for self-organized fate specification
    during embryonic development. We show that the proposed measure assesses the total
    information content of fate patterns and decomposes it into interpretable contributions
    corresponding to the positional and correlational information. By optimizing the
    proposed measure, our framework provides a normative theory for developmental
    circuits, which we demonstrate on lateral inhibition, cell type proportioning,
    and reaction–diffusion models of self-organization. This paves a way toward a
    classification of developmental systems based on a common information-theoretic
    language, thereby organizing the zoo of implicated chemical and mechanical signaling
    processes.
acknowledgement: We thank Wiktor Młynarski, Juraj Majek, Michal Hledík, Fridtjof Brauns,
  Nikolas Claussen, Benjamin Zoller, Erwin Frey, Thomas Gregor, and Edouard Hannezo
  for inspiring discussions. D.B.B. was supported by the NOMIS foundation as a NOMIS
  Fellow and by an European Molecular Biology Organization (EMBO) Postdoctoral Fellowship
  (ALTF 343-2022). This research was performed in part at the Aspen Center for Physics,
  which is supported by NSF Grant No. PHY-1607611, and Kavli Institute for Theoretical
  Physics (KITP) Santa Barbara, supported by NSF Grant No. PHY-1748958 and the Gordon
  and Betty Moore Foundation Grant No. 2919.02.
article_number: e2322326121
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: David
  full_name: Brückner, David
  id: e1e86031-6537-11eb-953a-f7ab92be508d
  last_name: Brückner
  orcid: 0000-0001-7205-2975
- first_name: Gašper
  full_name: Tkačik, Gašper
  id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
  last_name: Tkačik
  orcid: 0000-0002-6699-1455
citation:
  ama: Brückner D, Tkačik G. Information content and optimization of self-organized
    developmental systems. <i>Proceedings of the National Academy of Sciences of the
    United States of America</i>. 2024;121(23). doi:<a href="https://doi.org/10.1073/pnas.2322326121">10.1073/pnas.2322326121</a>
  apa: Brückner, D., &#38; Tkačik, G. (2024). Information content and optimization
    of self-organized developmental systems. <i>Proceedings of the National Academy
    of Sciences of the United States of America</i>. National Academy of Sciences.
    <a href="https://doi.org/10.1073/pnas.2322326121">https://doi.org/10.1073/pnas.2322326121</a>
  chicago: Brückner, David, and Gašper Tkačik. “Information Content and Optimization
    of Self-Organized Developmental Systems.” <i>Proceedings of the National Academy
    of Sciences of the United States of America</i>. National Academy of Sciences,
    2024. <a href="https://doi.org/10.1073/pnas.2322326121">https://doi.org/10.1073/pnas.2322326121</a>.
  ieee: D. Brückner and G. Tkačik, “Information content and optimization of self-organized
    developmental systems,” <i>Proceedings of the National Academy of Sciences of
    the United States of America</i>, vol. 121, no. 23. National Academy of Sciences,
    2024.
  ista: Brückner D, Tkačik G. 2024. Information content and optimization of self-organized
    developmental systems. Proceedings of the National Academy of Sciences of the
    United States of America. 121(23), e2322326121.
  mla: Brückner, David, and Gašper Tkačik. “Information Content and Optimization of
    Self-Organized Developmental Systems.” <i>Proceedings of the National Academy
    of Sciences of the United States of America</i>, vol. 121, no. 23, e2322326121,
    National Academy of Sciences, 2024, doi:<a href="https://doi.org/10.1073/pnas.2322326121">10.1073/pnas.2322326121</a>.
  short: D. Brückner, G. Tkačik, Proceedings of the National Academy of Sciences of
    the United States of America 121 (2024).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: There were no data generated as part of this study. Code
  to perform simulations, evaluate entropy and information quantities, and optimize
  parameters is available at https://github.com/dbrueckner/SelforgInformation (90).
date_created: 2024-06-09T22:01:02Z
date_published: 2024-06-04T00:00:00Z
date_updated: 2026-10-01T11:03:59Z
day: '04'
ddc:
- '570'
department:
- _id: EdHa
- _id: GaTk
doi: 10.1073/pnas.2322326121
external_id:
  isi:
  - '001244835000006'
  pmid:
  - '38819997'
file:
- access_level: open_access
  checksum: 59797a75db7beb3721ed7a4d14c241f9
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  creator: dernst
  date_created: 2024-06-10T10:27:37Z
  date_updated: 2024-06-10T10:27:37Z
  file_id: '17130'
  file_name: 2024_PNAS_Brueckner.pdf
  file_size: 12329234
  relation: main_file
  success: 1
file_date_updated: 2024-06-10T10:27:37Z
fulldoi: https://doi.org/10.1073/pnas.2322326121
has_accepted_license: '1'
intvolume: '       121'
isi: 1
issue: '23'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b
  grant_number: ALTF 343-2022
  name: A mechano-chemical theory for stem cell fate decisions in organoid development
publication: Proceedings of the National Academy of Sciences of the United States
  of America
publication_identifier:
  eissn:
  - 1091-6490
  issn:
  - 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
  link:
  - relation: software
    url: https://github.com/dbrueckner/SelforgInformation
  - description: News on the ISTA website
    relation: press_release
    url: https://ista.ac.at/en/news/the-embryo-assembles-itself/
researchdata_availability: not applicable
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Information content and optimization of self-organized developmental systems
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volume: 121
year: '2024'
...
