A decomposition method for lasso problems with zero-sum constraint

Cristofari, Andrea

doi:10.1016/j.ejor.2022.09.030

Cited by 4 publications

(2 citation statements)

References 41 publications

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“…We focused on methylation patterns at CpG sites for our study, since this is the major methylation context in vertebrates (Klughammer et al 2023). To improve coverage and minimise pseudo-replication, we further de-stranded adjacent cytosines per CpG site using the ‘merge_CpG.py’ script (Cristofari, 2023), as methylation occurs symmetrically at CpG sites in vertebrates (Klughammer et al 2023). On average, this resulted in 24,947,580 ± 825,959 (SD) CpG sites per sample, with a de-stranded coverage of 8.56 ± 0.93 (SD) X ( Table S1 ).…”

Section: Methodsmentioning

confidence: 99%

DNA methylation carries signatures of sublethal effects under thermal stress in loggerhead sea turtles

Yen,

Gilbert,

Balard

et al. 2023

Preprint

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Rising global temperatures are a major threat to biodiversity. Whilst research generally focuses on thermal tolerance and mortality, sublethal effects may alter population dynamics and subsequently the adaptive potential of species. However, detecting such effects in the wild can be challenging, particularly for endangered and long-lived species with cryptic life histories. This necessitates the development of molecular tools to identify their signatures. In a split-clutch design experiment, we relocated clutches of wild, nesting loggerhead sea turtles (Caretta caretta) to a protected,in-situhatchery. Eggs were then split into two sub-clutches incubated under shallow (35cm) or deep (55cm) conditions, with those in the shallow treatment experiencing significantly higher temperatures. Whilst no difference in hatching success was observed between treatments, hatchlings that emerged from the shallow, warmer treatment had altered length-mass relationships, and were weaker at fitness tests of locomotion capacity than their siblings incubated in the deep, cooler treatment. To characterise the molecular signatures of these thermal effects, we performed whole genome bisulfite sequencing on blood samples collected upon emergence. This identified 714 differentially methylated sites between treatments, including on genes with neuronal development, cytoskeleton, and sex determination functions. Taken together, our results show that higher incubation temperatures can induce sublethal effects in hatchlings, which are reflected in their DNA methylation status at identified sites. Such sites could be used as biomarkers of thermal stress, especially if they are retained across life stages. Overall, this study suggests that global warming may have population-level consequences for loggerhead sea turtles, by reducing hatchling quality, dispersal capacity and the adaptive potential of this species. Conservation efforts for climate-threatened taxa like endangered sea turtles will therefore benefit from strategies that monitor and mitigate exposure to incubation temperatures that lead to sublethal effects.

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Section: Methodsmentioning

confidence: 99%

DNA methylation carries signatures of sublethal effects under thermal stress in loggerhead sea turtles

Yen,

Gilbert,

Balard

et al. 2023

Preprint

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“…In the unconstrained case we can choose as working set, for instance, the block corresponding to the largest component of the gradient in absolute value. Also for this rule, exact or inexact minimizations can be carried out to update the variables [14,17,25,37] and extensions to constrained settings were considered in the literature [3,35,44,55,56]. Generally speaking, a greedy rule might make more progress in the objective function, since it uses first (or higher) order information to choose the working set, but might be, in principle, more expensive than cyclic or random selection.…”

Section: Block Coordinate Descent Approachesmentioning

confidence: 99%

Laplacian-based Semi-Supervised Learning in Multilayer Hypergraphs by Coordinate Descent

Venturini¹,

Cristofari²,

Rinaldi³

et al. 2023

Preprint

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Graph Semi-Supervised learning is an important data analysis tool, where given a graph and a set of labeled nodes, the aim is to infer the labels to the remaining unlabeled nodes. In this paper, we start by considering an optimization-based formulation of the problem for an undirected graph, and then we extend this formulation to multilayer hypergraphs. We solve the problem using different coordinate descent approaches and compare the results with the ones obtained by the classic gradient descent method. Experiments on synthetic and real-world datasets show the potential of using coordinate descent methods with suitable selection rules.

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Laplacian-based semi-Supervised learning in multilayer hypergraphs by coordinate descent

Venturini,

Cristofari,

Rinaldi

et al. 2023

EURO Journal on Computational Optimization

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A decomposition method for lasso problems with zero-sum constraint

Cited by 4 publications

References 41 publications

DNA methylation carries signatures of sublethal effects under thermal stress in loggerhead sea turtles

DNA methylation carries signatures of sublethal effects under thermal stress in loggerhead sea turtles

Laplacian-based Semi-Supervised Learning in Multilayer Hypergraphs by Coordinate Descent

Laplacian-based semi-Supervised learning in multilayer hypergraphs by coordinate descent

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