Branching on multi-aggregated variables

open5siopenGamrath, Gerald; Melchiori, Anna; Berthold, Timo; Gleixner, Ambros M.; Salvagnin, DomenicoGamrath, Gerald; Melchiori, Anna; Berthold, Timo; Gleixner, Ambros M.; Salvagnin, Domenic

Array Designer: automated optimized array design for functional near-infrared spectroscopy

The position of each source and detector "optode" on the scalp, and their relative separations, determines the sensitivity of each functional near-infrared spectroscopy (fNIRS) channel to the underlying cortex. As a result, selecting appropriate scalp locations for the available sources and detectors is critical to every fNIRS experiment. At present, it is standard practice for the user to undertake this task manually; to select what they believe are the best locations on the scalp to place their optodes so as to sample a given cortical region-of-interest (ROI). This process is difficult, time-consuming, and highly subjective. Here, we propose a tool, Array Designer, that is able to automatically design optimized fNIRS arrays given a user-defined ROI and certain features of the available fNIRS device. Critically, the Array Designer methodology is generalizable and will be applicable to almost any subject population or fNIRS device. We describe and validate the algorithmic methodology that underpins Array Designer by running multiple simulations of array design problems in a realistic anatomical model. We believe that Array Designer has the potential to end the need for manual array design, and in doing so save researchers time, improve fNIRS data quality, and promote standardization across the field

A DNA-free editing approach for viticulture sustainability: dual editing of DMR6-1 and DMR6-2 enhances resistance to downy mildew

The sustainability of viticulture hinges on maintaining quality and yield while reducing pesticide use. Promising strides in this direction involve the development of clones with enhanced disease tolerance, particularly through the knockout of plant susceptibility genes. Knocking out of Downy Mildew Resistant 6 (DMR6) led to increased levels of endogenous salicylic acid (SA), a regulator of immunity, resulting in enhanced tolerance to Downy Mildew (DM) and other diseases in various crops. Mutations in both DMR6-1 and DMR6-2 genes were introduced into two grapevine cultivars using CRISPR-Cas9 using two methods. In the first case, transgene delivery mediated by A. tumefaciens was employed, while in the second case, we developed a 'single-cell technology' for gene editing, creating non-transgenic grapevine mutants through the regeneration of protoplasts previously edited with the CRISPR/Cas9 ribonucleoprotein. We tested the susceptibility of single and double mutants to DM through artificial inoculation assays on detached leaves and whole plants. Our findings indicate that a simultaneous mutation in both DMR6-1 and DMR6-2 is needed to significantly enhance resistance to DM, with the double mutant (dmr6-1-dmr6-2) outperforming either single mutant in both cultivars. Elevated levels of endogenous SA were only observed in the double mutant, while single mutation in DMR6-1 or DMR6-2 proved ineffective. Collectively, our data highlight the need for a double knockout to achieve appreciable results against DM-susceptibility. Currenlty, we are adapting the 'single-cell technology' to generate edited vines from various agronomically relevant cultivars. In parallel, we are assessing the performance of plants edited in different susceptibility genes

Gene functional studies and gene editing at work to improve the sustainability of viticulture

Being one of the most cultivated tree crops in mid-temperate regions, grapevine (Vitis vinifera L.) is dangerously affected by the recent and progressive extremization of climatic conditions. This leads to an increase in favorable environments for both existing and emerging fungal pathogens. As a result, pathogen pressure on vineyards is exacerbated, which must be countered with a growing use of fungicides. Today we have the tools to enhance the resilience of this tree species and ensure sustainable production. Indeed, it is now an established practice in some laboratories to regenerate grapevine plants from gene-edited protoplasts, transfected with CRISPR/Cas9 ribonucleoprotein (RNP) complexes. The production of NGT-1 plants by DNA-free approach not only mitigates regulatory and public acceptance issues associated with genetically modified organisms (GMOs), but also ensures that the edited plants retain their original genetic background, thereby preserving varietal identity and quality. We are applying a DNA-free gene editing protocol to produce edited plants of different grapevine cultivars, while studying the function of genes whose mutations are important for the resistance to pathogens and resilience in this crop. As examples, members of the Downy Mildew Resistance 6 gene family were edited in two table grape cultivars, ‘Crimson seedless’ and ‘Sugraone’, to dissect their role in downy mildew (DM) resistance. Our results indicated that reduced susceptibility to DM and increased salicylic acid are obtained by knocking out both VviDMR6-1 and VviDMR6-2. More recently, we obtained similar mutations in the wine cultivar ‘Chardonnay’: these prototypes are now being grafted and will be tested in the field. The editing of genes involved in the cell-wall disassembly, precisely of a member of Pectin Methylesterase gene family in ‘Sugraone’, proved the role of the cell wall disassembly in the response to Botrytis cinerea (Bc). Increased susceptibility to Bc was shown upon artificial inoculation of leaves of knocked-out (KO) edited lines as compared to control plants. These results suggest that the pectin modification mediated by VviPME10 plays an important role in the grapevine response to Bc. Testing the effect of VviPME10 editing on berries and in field conditions are essential steps to determine the effectiveness of this mutation in Bc defense. Other traits currently under examination include transcription factors potentially regulating epidermal cell fate and cuticular wax composition in grapevine leaves and berries. These investigations pave the way for molecular breeding aimed at enhancing plant resilience, improving berry quality, and extending shelf life. Overall, testing all the plants obtained from this pipeline in field conditions is important to evaluate their performance in the light of a more sustainable viticulture

Orbital Shrinking: A New Tool for Hybrid MIP/CP Methods

Abstract. Orbital shrinking is a newly developed technique in the MIP community to deal with symmetry issues, which is based on aggregation rather than on symmetry breaking. In a recent work, a hybrid MIP/CP scheme based on orbital shrinking was developed for the multi-activity shift scheduling problem, showing significant improvements over previ-ous pure MIP approaches. In the present paper we show that the scheme above can be extended to a general framework for solving arbitrary sym-metric MIP instances. This framework naturally provides a new way for devising hybrid MIP/CP decompositions. Finally, we specialize the above framework to the multiple knapsack problem. Computational re-sults show that the resulting method can be orders of magnitude faster than pure MIP approaches on hard symmetric instances.

An exploratory computational analysis of dual degeneracy in mixed-integer programming

Dual degeneracy, i.e., the presence of multiple optimal bases to a linear programming (LP) problem, heavily affects the solution process of mixed integer programming (MIP) solvers. Different optimal bases lead to different cuts being generated, different branching decisions being taken and different solutions being found by primal heuristics. Nevertheless, only a few methods have been published that either avoid or exploit dual degeneracy. The aim of the present paper is to conduct a thorough computational study on the presence of dual degeneracy for the instances of well-known public MIP instance collections. How many instances are affected by dual degeneracy? How degenerate are the affected models? How does branching affect degeneracy: Does it increase or decrease by fixing variables? Can we identify different types of degenerate MIPs? As a tool to answer these questions, we introduce a new measure for dual degeneracy: the variable\u2013constraint ratio of the optimal face. It provides an estimate for the likelihood that a basic variable can be pivoted out of the basis. Furthermore, we study how the so-called cloud intervals\u2014the projections of the optimal face of the LP relaxations onto the individual variables\u2014evolve during tree search and the implications for reducing the set of branching candidates

Implementing Automatic Benders Decomposition in a Modern MIP Solver

We describe the automatic Benders decomposition implemented in the commercial solver IBM CPLEX. We propose several improvements to the state-of-the-art along two lines: making a numerically robust method able to deal with the general case and improving the efficiency of the method on models amenable to decomposition. For the former, we deal with: unboundedness, failures in generating cuts and scaling of the artificial variable representing the objective. For the latter, we propose a new technique to handle so-called generalized bound constraints and we use different types of normalization conditions in the Cut Generating LPs. We present computational experiments aimed at assessing the importance of the various enhancements. In particular, on our test bed of models amenable to a decomposition, our implementation is approximately 5 times faster than CPLEX default branch-and-cut. A remarkable result is that, on the same test bed, default branch-and-cut is faster than a Benders decomposition that doesn’t implement our improvements