---
_id: '9930'
abstract:
- lang: eng
text: Adaptive divergence and speciation may happen despite opposition by gene flow.
Identifying the genomic basis underlying divergence with gene flow is a major
task in evolutionary genomics. Most approaches (e.g. outlier scans) focus on genomic
regions of high differentiation. However, not all genomic architectures potentially
underlying divergence are expected to show extreme differentiation. Here, we develop
an approach that combines hybrid zone analysis (i.e. focuses on spatial patterns
of allele frequency change) with system-specific simulations to identify loci
inconsistent with neutral evolution. We apply this to a genome-wide SNP set from
an ideally-suited study organism, the intertidal snail Littorina saxatilis, which
shows primary divergence between ecotypes associated with different shore habitats.
We detect many SNPs with clinal patterns, most of which are consistent with neutrality.
Among non-neutral SNPs, most are located within three large putative inversions
differentiating ecotypes. Many non-neutral SNPs show relatively low levels of
differentiation. We discuss potential reasons for this pattern, including loose
linkage to selected variants, polygenic adaptation and a component of balancing
selection within populations (which may be expected for inversions). Our work
is in line with theory predicting a role for inversions in divergence, and emphasises
that genomic regions contributing to divergence may not always be accessible with
methods purely based on allele frequency differences. These conclusions call for
approaches that take spatial patterns of allele frequency change into account
in other systems.
article_processing_charge: No
author:
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Marina
full_name: Rafajlović, Marina
last_name: Rafajlović
- first_name: Pragya
full_name: Chaube, Pragya
last_name: Chaube
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Tomas
full_name: Larsson, Tomas
last_name: Larsson
- first_name: Marina
full_name: Panova, Marina
last_name: Panova
- first_name: Mark
full_name: Ravinet, Mark
last_name: Ravinet
- first_name: Anders
full_name: Blomberg, Anders
last_name: Blomberg
- first_name: Bernhard
full_name: Mehlig, Bernhard
last_name: Mehlig
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger
full_name: Butlin, Roger
last_name: Butlin
citation:
ama: 'Westram AM, Rafajlović M, Chaube P, et al. Data from: Clines on the seashore:
the genomic architecture underlying rapid divergence in the face of gene flow.
2018. doi:10.5061/dryad.bp25b65'
apa: 'Westram, A. M., Rafajlović, M., Chaube, P., Faria, R., Larsson, T., Panova,
M., … Butlin, R. (2018). Data from: Clines on the seashore: the genomic architecture
underlying rapid divergence in the face of gene flow. Dryad. https://doi.org/10.5061/dryad.bp25b65'
chicago: 'Westram, Anja M, Marina Rafajlović, Pragya Chaube, Rui Faria, Tomas Larsson,
Marina Panova, Mark Ravinet, et al. “Data from: Clines on the Seashore: The Genomic
Architecture Underlying Rapid Divergence in the Face of Gene Flow.” Dryad, 2018.
https://doi.org/10.5061/dryad.bp25b65.'
ieee: 'A. M. Westram et al., “Data from: Clines on the seashore: the genomic
architecture underlying rapid divergence in the face of gene flow.” Dryad, 2018.'
ista: 'Westram AM, Rafajlović M, Chaube P, Faria R, Larsson T, Panova M, Ravinet
M, Blomberg A, Mehlig B, Johannesson K, Butlin R. 2018. Data from: Clines on the
seashore: the genomic architecture underlying rapid divergence in the face of
gene flow, Dryad, 10.5061/dryad.bp25b65.'
mla: 'Westram, Anja M., et al. Data from: Clines on the Seashore: The Genomic
Architecture Underlying Rapid Divergence in the Face of Gene Flow. Dryad,
2018, doi:10.5061/dryad.bp25b65.'
short: A.M. Westram, M. Rafajlović, P. Chaube, R. Faria, T. Larsson, M. Panova,
M. Ravinet, A. Blomberg, B. Mehlig, K. Johannesson, R. Butlin, (2018).
date_created: 2021-08-17T08:58:47Z
date_published: 2018-07-23T00:00:00Z
date_updated: 2023-09-19T15:08:24Z
day: '23'
department:
- _id: BeVi
doi: 10.5061/dryad.bp25b65
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.bp25b65
month: '07'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '9917'
relation: used_in_publication
status: public
status: public
title: 'Data from: Clines on the seashore: the genomic architecture underlying rapid
divergence in the face of gene flow'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9929'
abstract:
- lang: eng
text: 'The evolution of assortative mating is a key part of the speciation process.
Stronger assortment, or greater divergence in mating traits, between species pairs
with overlapping ranges is commonly observed, but possible causes of this pattern
of reproductive character displacement are difficult to distinguish. We use a
multidisciplinary approach to provide a rare example where it is possible to distinguish
among hypotheses concerning the evolution of reproductive character displacement.
We build on an earlier comparative analysis that illustrated a strong pattern
of greater divergence in penis form between pairs of sister species with overlapping
ranges than between allopatric sister-species pairs, in a large clade of marine
gastropods (Littorinidae). We investigate both assortative mating and divergence
in male genitalia in one of the sister-species pairs, discriminating among three
contrasting processes each of which can generate a pattern of reproductive character
displacement: reinforcement, reproductive interference and the Templeton effect.
We demonstrate reproductive character displacement in assortative mating, but
not in genital form between this pair of sister species and use demographic models
to distinguish among the different processes. Our results support a model with
no gene flow since secondary contact and thus favour reproductive interference
as the cause of reproductive character displacement for mate choice, rather than
reinforcement. High gene flow within species argues against the Templeton effect.
Secondary contact appears to have had little impact on genital divergence.'
article_processing_charge: No
author:
- first_name: Johan
full_name: Hollander, Johan
last_name: Hollander
- first_name: Mauricio
full_name: Montaño-Rendón, Mauricio
last_name: Montaño-Rendón
- first_name: Giuseppe
full_name: Bianco, Giuseppe
last_name: Bianco
- first_name: Xi
full_name: Yang, Xi
last_name: Yang
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Ludovic
full_name: Duvaux, Ludovic
last_name: Duvaux
- first_name: David G.
full_name: Reid, David G.
last_name: Reid
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: 'Hollander J, Montaño-Rendón M, Bianco G, et al. Data from: Are assortative
mating and genital divergence driven by reinforcement? 2018. doi:10.5061/dryad.51sd2p5'
apa: 'Hollander, J., Montaño-Rendón, M., Bianco, G., Yang, X., Westram, A. M., Duvaux,
L., … Butlin, R. K. (2018). Data from: Are assortative mating and genital divergence
driven by reinforcement? Dryad. https://doi.org/10.5061/dryad.51sd2p5'
chicago: 'Hollander, Johan, Mauricio Montaño-Rendón, Giuseppe Bianco, Xi Yang, Anja
M Westram, Ludovic Duvaux, David G. Reid, and Roger K. Butlin. “Data from: Are
Assortative Mating and Genital Divergence Driven by Reinforcement?” Dryad, 2018.
https://doi.org/10.5061/dryad.51sd2p5.'
ieee: 'J. Hollander et al., “Data from: Are assortative mating and genital
divergence driven by reinforcement?” Dryad, 2018.'
ista: 'Hollander J, Montaño-Rendón M, Bianco G, Yang X, Westram AM, Duvaux L, Reid
DG, Butlin RK. 2018. Data from: Are assortative mating and genital divergence
driven by reinforcement?, Dryad, 10.5061/dryad.51sd2p5.'
mla: 'Hollander, Johan, et al. Data from: Are Assortative Mating and Genital
Divergence Driven by Reinforcement? Dryad, 2018, doi:10.5061/dryad.51sd2p5.'
short: J. Hollander, M. Montaño-Rendón, G. Bianco, X. Yang, A.M. Westram, L. Duvaux,
D.G. Reid, R.K. Butlin, (2018).
date_created: 2021-08-17T08:51:06Z
date_published: 2018-10-17T00:00:00Z
date_updated: 2023-09-19T15:08:53Z
day: '17'
department:
- _id: BeVi
doi: 10.5061/dryad.51sd2p5
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.51sd2p5
month: '10'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '9915'
relation: used_in_publication
status: public
status: public
title: 'Data from: Are assortative mating and genital divergence driven by reinforcement?'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '10882'
abstract:
- lang: eng
text: 'We introduce Intelligent Annotation Dialogs for bounding box annotation.
We train an agent to automatically choose a sequence of actions for a human annotator
to produce a bounding box in a minimal amount of time. Specifically, we consider
two actions: box verification [34], where the annotator verifies a box generated
by an object detector, and manual box drawing. We explore two kinds of agents,
one based on predicting the probability that a box will be positively verified,
and the other based on reinforcement learning. We demonstrate that (1) our agents
are able to learn efficient annotation strategies in several scenarios, automatically
adapting to the image difficulty, the desired quality of the boxes, and the detector
strength; (2) in all scenarios the resulting annotation dialogs speed up annotation
compared to manual box drawing alone and box verification alone, while also outperforming
any fixed combination of verification and drawing in most scenarios; (3) in a
realistic scenario where the detector is iteratively re-trained, our agents evolve
a series of strategies that reflect the shifting trade-off between verification
and drawing as the detector grows stronger.'
article_processing_charge: No
author:
- first_name: Jasper
full_name: Uijlings, Jasper
last_name: Uijlings
- first_name: Ksenia
full_name: Konyushkova, Ksenia
last_name: Konyushkova
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Vittorio
full_name: Ferrari, Vittorio
last_name: Ferrari
citation:
ama: 'Uijlings J, Konyushkova K, Lampert C, Ferrari V. Learning intelligent dialogs
for bounding box annotation. In: 2018 IEEE/CVF Conference on Computer Vision
and Pattern Recognition. IEEE; 2018:9175-9184. doi:10.1109/cvpr.2018.00956'
apa: 'Uijlings, J., Konyushkova, K., Lampert, C., & Ferrari, V. (2018). Learning
intelligent dialogs for bounding box annotation. In 2018 IEEE/CVF Conference
on Computer Vision and Pattern Recognition (pp. 9175–9184). Salt Lake City,
UT, United States: IEEE. https://doi.org/10.1109/cvpr.2018.00956'
chicago: Uijlings, Jasper, Ksenia Konyushkova, Christoph Lampert, and Vittorio Ferrari.
“Learning Intelligent Dialogs for Bounding Box Annotation.” In 2018 IEEE/CVF
Conference on Computer Vision and Pattern Recognition, 9175–84. IEEE, 2018.
https://doi.org/10.1109/cvpr.2018.00956.
ieee: J. Uijlings, K. Konyushkova, C. Lampert, and V. Ferrari, “Learning intelligent
dialogs for bounding box annotation,” in 2018 IEEE/CVF Conference on Computer
Vision and Pattern Recognition, Salt Lake City, UT, United States, 2018, pp.
9175–9184.
ista: 'Uijlings J, Konyushkova K, Lampert C, Ferrari V. 2018. Learning intelligent
dialogs for bounding box annotation. 2018 IEEE/CVF Conference on Computer Vision
and Pattern Recognition. CVF: Conference on Computer Vision and Pattern Recognition,
9175–9184.'
mla: Uijlings, Jasper, et al. “Learning Intelligent Dialogs for Bounding Box Annotation.”
2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE,
2018, pp. 9175–84, doi:10.1109/cvpr.2018.00956.
short: J. Uijlings, K. Konyushkova, C. Lampert, V. Ferrari, in:, 2018 IEEE/CVF Conference
on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 9175–9184.
conference:
end_date: 2018-06-23
location: Salt Lake City, UT, United States
name: 'CVF: Conference on Computer Vision and Pattern Recognition'
start_date: 2018-06-18
date_created: 2022-03-18T12:45:09Z
date_published: 2018-12-17T00:00:00Z
date_updated: 2023-09-19T15:11:49Z
day: '17'
department:
- _id: ChLa
doi: 10.1109/cvpr.2018.00956
external_id:
arxiv:
- '1712.08087'
isi:
- '000457843609036'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.1712.08087'
month: '12'
oa: 1
oa_version: Preprint
page: 9175-9184
publication: 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition
publication_identifier:
eissn:
- 2575-7075
isbn:
- '9781538664209'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Learning intelligent dialogs for bounding box annotation
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '6558'
abstract:
- lang: eng
text: This paper studies the problem of distributed stochastic optimization in an
adversarial setting where, out of m machines which allegedly compute stochastic
gradients every iteration, an α-fraction are Byzantine, and may behave adversarially.
Our main result is a variant of stochastic gradient descent (SGD) which finds
ε-approximate minimizers of convex functions in T=O~(1/ε²m+α²/ε²) iterations.
In contrast, traditional mini-batch SGD needs T=O(1/ε²m) iterations, but cannot
tolerate Byzantine failures. Further, we provide a lower bound showing that, up
to logarithmic factors, our algorithm is information-theoretically optimal both
in terms of sample complexity and time complexity.
article_processing_charge: No
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: Zeyuan
full_name: Allen-Zhu, Zeyuan
last_name: Allen-Zhu
- first_name: Jerry
full_name: Li, Jerry
last_name: Li
citation:
ama: 'Alistarh D-A, Allen-Zhu Z, Li J. Byzantine stochastic gradient descent. In:
Advances in Neural Information Processing Systems. Vol 2018. Neural Information
Processing Systems Foundation; 2018:4613-4623.'
apa: 'Alistarh, D.-A., Allen-Zhu, Z., & Li, J. (2018). Byzantine stochastic
gradient descent. In Advances in Neural Information Processing Systems
(Vol. 2018, pp. 4613–4623). Montreal, Canada: Neural Information Processing Systems
Foundation.'
chicago: Alistarh, Dan-Adrian, Zeyuan Allen-Zhu, and Jerry Li. “Byzantine Stochastic
Gradient Descent.” In Advances in Neural Information Processing Systems,
2018:4613–23. Neural Information Processing Systems Foundation, 2018.
ieee: D.-A. Alistarh, Z. Allen-Zhu, and J. Li, “Byzantine stochastic gradient descent,”
in Advances in Neural Information Processing Systems, Montreal, Canada,
2018, vol. 2018, pp. 4613–4623.
ista: 'Alistarh D-A, Allen-Zhu Z, Li J. 2018. Byzantine stochastic gradient descent.
Advances in Neural Information Processing Systems. NeurIPS: Conference on Neural
Information Processing Systems vol. 2018, 4613–4623.'
mla: Alistarh, Dan-Adrian, et al. “Byzantine Stochastic Gradient Descent.” Advances
in Neural Information Processing Systems, vol. 2018, Neural Information Processing
Systems Foundation, 2018, pp. 4613–23.
short: D.-A. Alistarh, Z. Allen-Zhu, J. Li, in:, Advances in Neural Information
Processing Systems, Neural Information Processing Systems Foundation, 2018, pp.
4613–4623.
conference:
end_date: 2018-12-08
location: Montreal, Canada
name: 'NeurIPS: Conference on Neural Information Processing Systems'
start_date: 2018-12-02
date_created: 2019-06-13T08:22:37Z
date_published: 2018-12-01T00:00:00Z
date_updated: 2023-09-19T15:12:45Z
day: '01'
department:
- _id: DaAl
external_id:
arxiv:
- '1803.08917'
isi:
- '000461823304061'
intvolume: ' 2018'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1803.08917
month: '12'
oa: 1
oa_version: Published Version
page: 4613-4623
publication: Advances in Neural Information Processing Systems
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
scopus_import: '1'
status: public
title: Byzantine stochastic gradient descent
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2018
year: '2018'
...
---
_id: '6032'
abstract:
- lang: eng
text: The main result of this article is a generalization of the classical blossom
algorithm for finding perfect matchings. Our algorithm can efficiently solve Boolean
CSPs where each variable appears in exactly two constraints (we call it edge CSP)
and all constraints are even Δ-matroid relations (represented by lists of tuples).
As a consequence of this, we settle the complexity classification of planar Boolean
CSPs started by Dvorak and Kupec. Using a reduction to even Δ-matroids, we then
extend the tractability result to larger classes of Δ-matroids that we call efficiently
coverable. It properly includes classes that were known to be tractable before,
namely, co-independent, compact, local, linear, and binary, with the following
caveat:We represent Δ-matroids by lists of tuples, while the last two use a representation
by matrices. Since an n ×n matrix can represent exponentially many tuples, our
tractability result is not strictly stronger than the known algorithm for linear
and binary Δ-matroids.
article_number: '22'
article_processing_charge: No
article_type: original
author:
- first_name: Alexandr
full_name: Kazda, Alexandr
id: 3B32BAA8-F248-11E8-B48F-1D18A9856A87
last_name: Kazda
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Michal
full_name: Rolinek, Michal
id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87
last_name: Rolinek
citation:
ama: Kazda A, Kolmogorov V, Rolinek M. Even delta-matroids and the complexity of
planar boolean CSPs. ACM Transactions on Algorithms. 2018;15(2). doi:10.1145/3230649
apa: Kazda, A., Kolmogorov, V., & Rolinek, M. (2018). Even delta-matroids and
the complexity of planar boolean CSPs. ACM Transactions on Algorithms.
ACM. https://doi.org/10.1145/3230649
chicago: Kazda, Alexandr, Vladimir Kolmogorov, and Michal Rolinek. “Even Delta-Matroids
and the Complexity of Planar Boolean CSPs.” ACM Transactions on Algorithms.
ACM, 2018. https://doi.org/10.1145/3230649.
ieee: A. Kazda, V. Kolmogorov, and M. Rolinek, “Even delta-matroids and the complexity
of planar boolean CSPs,” ACM Transactions on Algorithms, vol. 15, no. 2.
ACM, 2018.
ista: Kazda A, Kolmogorov V, Rolinek M. 2018. Even delta-matroids and the complexity
of planar boolean CSPs. ACM Transactions on Algorithms. 15(2), 22.
mla: Kazda, Alexandr, et al. “Even Delta-Matroids and the Complexity of Planar Boolean
CSPs.” ACM Transactions on Algorithms, vol. 15, no. 2, 22, ACM, 2018, doi:10.1145/3230649.
short: A. Kazda, V. Kolmogorov, M. Rolinek, ACM Transactions on Algorithms 15 (2018).
date_created: 2019-02-17T22:59:25Z
date_published: 2018-12-01T00:00:00Z
date_updated: 2023-09-20T11:20:26Z
day: '01'
department:
- _id: VlKo
doi: 10.1145/3230649
ec_funded: 1
external_id:
arxiv:
- '1602.03124'
isi:
- '000468036500007'
intvolume: ' 15'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1602.03124
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: ACM Transactions on Algorithms
publication_status: published
publisher: ACM
quality_controlled: '1'
related_material:
record:
- id: '1192'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Even delta-matroids and the complexity of planar boolean CSPs
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 15
year: '2018'
...