---
_id: '1363'
abstract:
- lang: eng
text: When aiming to seamlessly integrate a fluid simulation into a larger scenario
(like an open ocean), careful attention must be paid to boundary conditions. In
particular, one must implement special "non-reflecting" boundary conditions,
which dissipate out-going waves as they exit the simulation. Unfortunately, the
state of the art in non-reflecting boundary conditions (perfectly-matched layers,
or PMLs) only permits trivially simple inflow/outflow conditions, so there is
no reliable way to integrate a fluid simulation into a more complicated environment
like a stormy ocean or a turbulent river. This paper introduces the first method
for combining nonreflecting boundary conditions based on PMLs with inflow/outflow
boundary conditions that vary arbitrarily throughout space and time. Our algorithm
is a generalization of stateof- the-art mean-flow boundary conditions in the computational
fluid dynamics literature, and it allows for seamless integration of a fluid simulation
into much more complicated environments. Our method also opens the door for previously-unseen
postprocess effects like retroactively changing the location of solid obstacles,
and locally increasing the visual detail of a pre-existing simulation.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: 'We thank the IST Austria Visual Computing group for helpful feedback
throughout the project. '
alternative_title:
- ACM Transactions on Graphics
article_number: '96'
author:
- first_name: Morten
full_name: Bojsen-Hansen, Morten
id: 439F0C8C-F248-11E8-B48F-1D18A9856A87
last_name: Bojsen-Hansen
orcid: 0000-0002-4417-3224
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: 'Bojsen-Hansen M, Wojtan C. Generalized non-reflecting boundaries for fluid
re-simulation. In: Vol 35. ACM; 2016. doi:10.1145/2897824.2925963'
apa: 'Bojsen-Hansen, M., & Wojtan, C. (2016). Generalized non-reflecting boundaries
for fluid re-simulation (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim, CA,
USA: ACM. https://doi.org/10.1145/2897824.2925963'
chicago: Bojsen-Hansen, Morten, and Chris Wojtan. “Generalized Non-Reflecting Boundaries
for Fluid Re-Simulation,” Vol. 35. ACM, 2016. https://doi.org/10.1145/2897824.2925963.
ieee: M. Bojsen-Hansen and C. Wojtan, “Generalized non-reflecting boundaries for
fluid re-simulation,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol.
35, no. 4.
ista: Bojsen-Hansen M, Wojtan C. 2016. Generalized non-reflecting boundaries for
fluid re-simulation. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, 96.
mla: Bojsen-Hansen, Morten, and Chris Wojtan. Generalized Non-Reflecting Boundaries
for Fluid Re-Simulation. Vol. 35, no. 4, 96, ACM, 2016, doi:10.1145/2897824.2925963.
short: M. Bojsen-Hansen, C. Wojtan, in:, ACM, 2016.
conference:
end_date: 2016-07-28
location: Anaheim, CA, USA
name: ACM SIGGRAPH
start_date: 2016-07-24
date_created: 2018-12-11T11:51:35Z
date_published: 2016-07-11T00:00:00Z
date_updated: 2023-02-21T10:36:12Z
day: '11'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2897824.2925963
ec_funded: 1
file:
- access_level: open_access
checksum: 140b5532f0a2a006a0149cab7c73c17c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:00Z
date_updated: 2020-07-14T12:44:47Z
file_id: '4981'
file_name: IST-2016-631-v1+2_a96-bojsen-hansen.pdf
file_size: 12422760
relation: main_file
file_date_updated: 2020-07-14T12:44:47Z
has_accepted_license: '1'
intvolume: ' 35'
issue: '4'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 2533E772-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '638176'
name: Efficient Simulation of Natural Phenomena at Extremely Large Scales
publication_status: published
publisher: ACM
publist_id: '5879'
pubrep_id: '631'
quality_controlled: '1'
status: public
title: Generalized non-reflecting boundaries for fluid re-simulation
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2016'
...
---
_id: '2944'
abstract:
- lang: eng
text: 'We propose a two-step procedure for estimating multiple migration rates in
an approximate Bayesian computation (ABC) framework, accounting for global nuisance
parameters. The approach is not limited to migration, but generally of interest
for inference problems with multiple parameters and a modular structure (e.g.
independent sets of demes or loci). We condition on a known, but complex demographic
model of a spatially subdivided population, motivated by the reintroduction of
Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters
ancestral mutation rate and male mating skew have been estimated for the whole
population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step,
we estimate in this study the migration rates independently for clusters of demes
putatively connected by migration. For large clusters (many migration rates),
ABC faces the problem of too many summary statistics. We therefore assess by simulation
if estimation per pair of demes is a valid alternative. We find that the trade-off
between reduced dimensionality for the pairwise estimation on the one hand and
lower accuracy due to the assumption of pairwise independence on the other depends
on the number of migration rates to be inferred: the accuracy of the pairwise
approach increases with the number of parameters, relative to the joint estimation
approach. To distinguish between low and zero migration, we perform ABC-type model
comparison between a model with migration and one without. Applying the approach
to microsatellite data from Alpine ibex, we find no evidence for substantial gene
flow via migration, except for one pair of demes in one direction.'
acknowledged_ssus:
- _id: ScienComp
acknowledgement: This study has made use of the computational resources provided by
IST Austria and the Edinburgh Compute and Data Facility (ECDF; http://www.ecdf.ed.ac.uk).
The ECDF is partially supported by the eDIKT initiative (http://www.edikt.org.uk).
S.A. acknowledges financial support by IST Austria, the Janggen-Pöhn Foundation,
St. Gallen, the Roche Research Foundation, Basel, the University of Edinburgh in
the form of a Torrance Studentship, and the Austrian Science Fund (FWF P21305-N13).
author:
- first_name: Simon
full_name: Aeschbacher, Simon
id: 2D35326E-F248-11E8-B48F-1D18A9856A87
last_name: Aeschbacher
- first_name: Andreas
full_name: Futschik, Andreas
last_name: Futschik
- first_name: Mark
full_name: Beaumont, Mark
last_name: Beaumont
citation:
ama: 'Aeschbacher S, Futschik A, Beaumont M. Approximate Bayesian computation for
modular inference problems with many parameters: the example of migration rates.
. Molecular Ecology. 2013;22(4):987-1002. doi:10.1111/mec.12165'
apa: 'Aeschbacher, S., Futschik, A., & Beaumont, M. (2013). Approximate Bayesian
computation for modular inference problems with many parameters: the example of
migration rates. . Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/mec.12165'
chicago: 'Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Approximate
Bayesian Computation for Modular Inference Problems with Many Parameters: The
Example of Migration Rates. .” Molecular Ecology. Wiley-Blackwell, 2013.
https://doi.org/10.1111/mec.12165.'
ieee: 'S. Aeschbacher, A. Futschik, and M. Beaumont, “Approximate Bayesian computation
for modular inference problems with many parameters: the example of migration
rates. ,” Molecular Ecology, vol. 22, no. 4. Wiley-Blackwell, pp. 987–1002,
2013.'
ista: 'Aeschbacher S, Futschik A, Beaumont M. 2013. Approximate Bayesian computation
for modular inference problems with many parameters: the example of migration
rates. . Molecular Ecology. 22(4), 987–1002.'
mla: 'Aeschbacher, Simon, et al. “Approximate Bayesian Computation for Modular Inference
Problems with Many Parameters: The Example of Migration Rates. .” Molecular
Ecology, vol. 22, no. 4, Wiley-Blackwell, 2013, pp. 987–1002, doi:10.1111/mec.12165.'
short: S. Aeschbacher, A. Futschik, M. Beaumont, Molecular Ecology 22 (2013) 987–1002.
date_created: 2018-12-11T12:00:28Z
date_published: 2013-02-01T00:00:00Z
date_updated: 2023-02-23T14:07:19Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/mec.12165
intvolume: ' 22'
issue: '4'
language:
- iso: eng
month: '02'
oa_version: None
page: 987 - 1002
publication: Molecular Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3788'
quality_controlled: '1'
related_material:
record:
- id: '9758'
relation: research_data
status: public
scopus_import: 1
status: public
title: 'Approximate Bayesian computation for modular inference problems with many
parameters: the example of migration rates. '
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2013'
...
---
_id: '2962'
abstract:
- lang: eng
text: The choice of summary statistics is a crucial step in approximate Bayesian
computation (ABC). Since statistics are often not sufficient, this choice involves
a trade-off between loss of information and reduction of dimensionality. The latter
may increase the efficiency of ABC. Here, we propose an approach for choosing
summary statistics based on boosting, a technique from the machine learning literature.
We consider different types of boosting and compare them to partial least squares
regression as an alternative. To mitigate the lack of sufficiency, we also propose
an approach for choosing summary statistics locally, in the putative neighborhood
of the true parameter value. We study a demographic model motivated by the re-introduction
of Alpine ibex (Capra ibex) into the Swiss Alps. The parameters of interest are
the mean and standard deviation across microsatellites of the scaled ancestral
mutation rate (θanc = 4 Ne u), and the proportion of males obtaining access to
matings per breeding season (ω). By simulation, we assess the properties of the
posterior distribution obtained with the various methods. According to our criteria,
ABC with summary statistics chosen locally via boosting with the L2-loss performs
best. Applying that method to the ibex data, we estimate θanc ≈ 1.288, and find
that most of the variation across loci of the ancestral mutation rate u is between
7.7×10−4 and 3.5×10−3 per locus per generation. The proportion of males with access
to matings is estimated to ω ≈ 0.21, which is in good agreement with recent independent
estimates.
acknowledged_ssus:
- _id: ScienComp
author:
- first_name: Simon
full_name: Aeschbacher, Simon
id: 2D35326E-F248-11E8-B48F-1D18A9856A87
last_name: Aeschbacher
- first_name: Mark
full_name: Beaumont, Mark
last_name: Beaumont
- first_name: Andreas
full_name: Futschik, Andreas
last_name: Futschik
citation:
ama: Aeschbacher S, Beaumont M, Futschik A. A novel approach for choosing summary
statistics in approximate Bayesian computation. Genetics. 2012;192(3):1027-1047.
doi:10.1534/genetics.112.143164
apa: Aeschbacher, S., Beaumont, M., & Futschik, A. (2012). A novel approach
for choosing summary statistics in approximate Bayesian computation. Genetics.
Genetics Society of America. https://doi.org/10.1534/genetics.112.143164
chicago: Aeschbacher, Simon, Mark Beaumont, and Andreas Futschik. “A Novel Approach
for Choosing Summary Statistics in Approximate Bayesian Computation.” Genetics.
Genetics Society of America, 2012. https://doi.org/10.1534/genetics.112.143164.
ieee: S. Aeschbacher, M. Beaumont, and A. Futschik, “A novel approach for choosing
summary statistics in approximate Bayesian computation,” Genetics, vol.
192, no. 3. Genetics Society of America, pp. 1027–1047, 2012.
ista: Aeschbacher S, Beaumont M, Futschik A. 2012. A novel approach for choosing
summary statistics in approximate Bayesian computation. Genetics. 192(3), 1027–1047.
mla: Aeschbacher, Simon, et al. “A Novel Approach for Choosing Summary Statistics
in Approximate Bayesian Computation.” Genetics, vol. 192, no. 3, Genetics
Society of America, 2012, pp. 1027–47, doi:10.1534/genetics.112.143164.
short: S. Aeschbacher, M. Beaumont, A. Futschik, Genetics 192 (2012) 1027–1047.
date_created: 2018-12-11T12:00:34Z
date_published: 2012-11-01T00:00:00Z
date_updated: 2021-01-12T07:40:05Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.112.143164
external_id:
pmid:
- '22960215'
intvolume: ' 192'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3522150/
month: '11'
oa: 1
oa_version: Submitted Version
page: 1027 - 1047
pmid: 1
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '3763'
quality_controlled: '1'
scopus_import: 1
status: public
title: A novel approach for choosing summary statistics in approximate Bayesian computation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 192
year: '2012'
...