---
_id: '3843'
abstract:
- lang: eng
  text: "Within systems biology there is an increasing interest in the stochastic
    behavior of biochemical reaction networks. An appropriate stochastic description
    is provided by the chemical master equation, which represents a continuous- time
    Markov chain (CTMC).\r\nStandard Uniformization (SU) is an efficient method for
    the transient analysis of CTMCs. For systems with very different time scales,
    such as biochemical reaction networks, SU is computationally expensive. In these
    cases, a variant of SU, called adaptive uniformization (AU), is known to reduce
    the large number of iterations needed by SU. The additional difficulty of AU is
    that it requires the solution of a birth process.\r\nIn this paper we present
    an on-the-fly variant of AU, where we improve the original algorithm for AU at
    the cost of a small approximation error. By means of several examples, we show
    that our approach is particularly well-suited for biochemical reaction networks."
acknowledgement: This research has been partially funded by the Swiss National Science
  Foundation under grant 205321-111840 and by the Cluster of Excellence on Multimodal
  Computing and Interaction at Saarland University.
article_processing_charge: No
author:
- first_name: Frédéric
  full_name: Didier, Frédéric
  last_name: Didier
- first_name: Thomas A
  full_name: Henzinger, Thomas A
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000−0002−2985−7724
- first_name: Maria
  full_name: Mateescu, Maria
  id: 3B43276C-F248-11E8-B48F-1D18A9856A87
  last_name: Mateescu
- first_name: Verena
  full_name: Wolf, Verena
  last_name: Wolf
citation:
  ama: 'Didier F, Henzinger TA, Mateescu M, Wolf V. Fast adaptive uniformization of
    the chemical master equation. In: Vol 4. IEEE; 2009:118-127. doi:<a href="https://doi.org/10.1109/HiBi.2009.23">10.1109/HiBi.2009.23</a>'
  apa: 'Didier, F., Henzinger, T. A., Mateescu, M., &#38; Wolf, V. (2009). Fast adaptive
    uniformization of the chemical master equation (Vol. 4, pp. 118–127). Presented
    at the HIBI: High-Performance Computational Systems Biology, Trento, Italy: IEEE.
    <a href="https://doi.org/10.1109/HiBi.2009.23">https://doi.org/10.1109/HiBi.2009.23</a>'
  chicago: Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf.
    “Fast Adaptive Uniformization of the Chemical Master Equation,” 4:118–27. IEEE,
    2009. <a href="https://doi.org/10.1109/HiBi.2009.23">https://doi.org/10.1109/HiBi.2009.23</a>.
  ieee: 'F. Didier, T. A. Henzinger, M. Mateescu, and V. Wolf, “Fast adaptive uniformization
    of the chemical master equation,” presented at the HIBI: High-Performance Computational
    Systems Biology, Trento, Italy, 2009, vol. 4, no. 6, pp. 118–127.'
  ista: 'Didier F, Henzinger TA, Mateescu M, Wolf V. 2009. Fast adaptive uniformization
    of the chemical master equation. HIBI: High-Performance Computational Systems
    Biology vol. 4, 118–127.'
  mla: Didier, Frédéric, et al. <i>Fast Adaptive Uniformization of the Chemical Master
    Equation</i>. Vol. 4, no. 6, IEEE, 2009, pp. 118–27, doi:<a href="https://doi.org/10.1109/HiBi.2009.23">10.1109/HiBi.2009.23</a>.
  short: F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, in:, IEEE, 2009, pp. 118–127.
conference:
  end_date: 2009-10-16
  location: Trento, Italy
  name: 'HIBI: High-Performance Computational Systems Biology'
  start_date: 2009-10-14
date_created: 2018-12-11T12:05:28Z
date_published: 2009-10-30T00:00:00Z
date_updated: 2025-09-30T09:54:51Z
day: '30'
ddc:
- '000'
department:
- _id: ToHe
- _id: CaGu
doi: 10.1109/HiBi.2009.23
external_id:
  isi:
  - '000275038300017'
file:
- access_level: open_access
  checksum: 9a3bde48f43203991a0b3c6a277c2f5b
  content_type: application/pdf
  creator: dernst
  date_created: 2020-05-19T16:33:55Z
  date_updated: 2020-07-14T12:46:17Z
  file_id: '7874'
  file_name: 2009_HIBI_Didier.pdf
  file_size: 222890
  relation: main_file
file_date_updated: 2020-07-14T12:46:17Z
has_accepted_license: '1'
intvolume: '         4'
isi: 1
issue: '6'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 118 - 127
publication_status: published
publisher: IEEE
publist_id: '2348'
quality_controlled: '1'
related_material:
  record:
  - id: '3842'
    relation: later_version
    status: public
scopus_import: '1'
status: public
title: Fast adaptive uniformization of the chemical master equation
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 4
year: '2009'
...