Most machine learning algorithms are configured by a set of hyperparameters whose values must be carefully chosen and which often considerably impact performance. To avoid a time‐consuming and ...irreproducible manual process of trial‐and‐error to find well‐performing hyperparameter configurations, various automatic hyperparameter optimization (HPO) methods—for example, based on resampling error estimation for supervised machine learning—can be employed. After introducing HPO from a general perspective, this paper reviews important HPO methods, from simple techniques such as grid or random search to more advanced methods like evolution strategies, Bayesian optimization, Hyperband, and racing. This work gives practical recommendations regarding important choices to be made when conducting HPO, including the HPO algorithms themselves, performance evaluation, how to combine HPO with machine learning pipelines, runtime improvements, and parallelization.
This article is categorized under:
Algorithmic Development > Statistics
Technologies > Machine Learning
Technologies > Prediction
After a general introduction of hyperparameter optimization, we review important HPO methods such as grid or random search, evolutionary algorithms, Bayesian optimization, Hyperband and racing. We include many practical recommendations w.r.t. performance evaluation, how to combine HPO with ML pipelines, runtime improvements and parallelization.
Abstract
Motivation
Estimating microbial association networks from high-throughput sequencing data is a common exploratory data analysis approach aiming at understanding the complex interplay of ...microbial communities in their natural habitat. Statistical network estimation workflows comprise several analysis steps, including methods for zero handling, data normalization and computing microbial associations. Since microbial interactions are likely to change between conditions, e.g. between healthy individuals and patients, identifying network differences between groups is often an integral secondary analysis step. Thus far, however, no unifying computational tool is available that facilitates the whole analysis workflow of constructing, analysing and comparing microbial association networks from high-throughput sequencing data.
Results
Here, we introduce NetCoMi (Network Construction and comparison for Microbiome data), an R package that integrates existing methods for each analysis step in a single reproducible computational workflow. The package offers functionality for constructing and analysing single microbial association networks as well as quantifying network differences. This enables insights into whether single taxa, groups of taxa or the overall network structure change between groups. NetCoMi also contains functionality for constructing differential networks, thus allowing to assess whether single pairs of taxa are differentially associated between two groups. Furthermore, NetCoMi facilitates the construction and analysis of dissimilarity networks of microbiome samples, enabling a high-level graphical summary of the heterogeneity of an entire microbiome sample collection. We illustrate NetCoMi’s wide applicability using data sets from the GABRIELA study to compare microbial associations in settled dust from children’s rooms between samples from two study centers (Ulm and Munich).
Availability
R scripts used for producing the examples shown in this manuscript are provided as supplementary data. The NetCoMi package, together with a tutorial, is available at https://github.com/stefpeschel/NetCoMi.
Contact
Tel:+49 89 3187 43258; stefanie.peschel@mail.de
Supplementary information
Supplementary data are available at Briefings in Bioinformatics online.
Asexual lineages often exhibit broad distributions and can thrive in extreme habitats compared to their sexual counterparts. Several hypotheses can be proposed to explain this pattern. Asexual ...lineages could be versatile genotypes with wide environmental tolerance, enabling their dispersal and persistence across large geographic areas. Alternatively, asexual genotypes could be ecological specialists that thrive in specific environments and outcompete relative colonizing distantly related with similar conditions in the process. Several aphid species feature widespread obligate asexual lineages, commonly known as ‘superclones'. Yet it is often unknown whether these clones are widespread ecological generalists or successful specialists. To explore these hypotheses, we examined climatic niche differentiation among six globally distributed obligate asexual lineages of the cosmopolitan aphid pest, Brachycaudus helichrysi. To ensure that we were investigating the aphid genotype niche and not a by‐product of their association with endosymbionts mediating thermal tolerance, we first verified that clones hosted similar endosymbiont communities. Subsequently, we conducted multivariate analyses on clone occurrence data on a worldwide scale. Our results revealed that, despite their global distribution, B. helichrysi superclones occupy different climatic niches. This study represents the first evidence that aphid superclone distribution can be mediated by distinctive ranges of climatic tolerance.
Ideology in Management Studies Seeck, Hannele; Sturdy, Andrew; Boncori, Anne‐Laure ...
International journal of management reviews : IJMR,
January 2020, 2020-01-00, 20200101, Letnik:
22, Številka:
1
Journal Article
Recenzirano
Odprti dostop
Ideology is a core and contested concept in the social sciences, but also long deployed in management research to highlight the political, embedded and/or obscuring nature of ideas. Indeed, many ...would argue that management itself is inherently ideological in legitimating or privileging managerial interests and concealing other groups and ways of organizing. In the first systematic review of how ideology has been conceptualized in management studies, this paper explores its diverse and changing meanings in order to develop and sustain the concept. It is based on a heuristic review of 175 articles and 41 books published between 1956 and 2018. Further developing categories used in the social sciences around its role, we found views of ideology as: (1) domination; (2) legitimation; (3) interpretation; (4) integration; and (5) normative logic. In addition, emerging perspectives were identified where ideology was (6) an object of critique or (7) fantasy structuring social reality. We describe, illustrate and evaluate these often internally diverse and interrelated perspectives, as well as comparing them with sometimes competing notions within the management field, such as discourse, culture and legitimation. We also bring together the different approaches and argue for a pluralist, but not infinitely flexible, approach to the concept. In doing so, we identify research agendas for ideology within management and organization studies.
Our knowledge of the role of cytokines in pathologic conditions has increased considerably with the emergence of molecular and genetic studies, particularly in the case of autoinflammatory monogenic ...diseases. Many rare disorders, considered orphan until recently, are directly related to abnormal gene regulation, and the treatment with biologic agents (biologics) targeting cytokine receptors, intracellular signaling or specific cytokines improve the symptoms of an increasing number of chronic inflammatory diseases. As it is currently impossible to systematically conduct genetic studies for all patients with autoinflammatory and autoimmune diseases, the evaluation of cytokines can be seen as a simple, less time consuming, and less expensive alternative. This approach could be especially useful when the diagnosis of syndromes of diseases of unknown etiology remains problematic. The evaluation of cytokines could also help avoid the current trial-and-error approach, which has the disadvantages of exposing patients to ineffective drugs with possible unnecessary side effects and permanent organ damages. In this review, we discuss the various possibilities, as well as the limitations of evaluating the cytokine profiles of patients suffering from autoinflammatory and autoimmune diseases, with methods such as direct detection of cytokines in the plasma/serum or following ex vivo stimulation of PBMCs leading to the production of their cytokine secretome. The patients' secretome, combined with biomarkers ranging from genetic and epigenetic analyses to immunologic biomarkers, may help not only the diagnosis but also guide the choice of biologics for more efficient and rapid treatments.
A common strategy among microbes living in iron-limited environments is the secretion of siderophores, which can bind poorly soluble iron and make it available to cells via active transport ...mechanisms. Such siderophore–iron complexes can be thought of as public goods that can be exploited by local communities and drive diversification, for example by the evolution of “cheating.” However, it is unclear whether bacterial populations in the environment form stable enough communities such that social interactions significantly impact evolutionary dynamics. Here we show that public good games drive the evolution of iron acquisition strategies in wild populations of marine bacteria. We found that within nonclonal but ecologically cohesive genotypic clusters of closely related Vibrionaceae, only an intermediate percentage of genotypes are able to produce siderophores. Nonproducers within these clusters exhibited selective loss of siderophore biosynthetic pathways, whereas siderophore transport mechanisms were retained, suggesting that these nonproducers can act as cheaters that benefit from siderophore producers in their local environment. In support of this hypothesis, these nonproducers in iron-limited media suffer a significant decrease in growth, which can be alleviated by siderophores, presumably owing to the retention of transport mechanisms. Moreover, using ecological data of resource partitioning, we found that cheating coevolves with the ecological specialization toward association with larger particles in the water column, suggesting that these can harbor stable enough communities for dependencies among organisms to evolve.
The objectives of the present work were to study the evolution of the sensory properties and overall liking of four sourdough breads over their lifespans and to determine their sensory shelf life ...(SSL). We also intended to identify the main sensory characteristics leading to a decrease in overall liking and the end of the consumption of the breads. Seventy‐eight consumers evaluated different 1 kg sourdough breads at home. Two methods were used to describe the evolution of the sensory properties and overall liking: one based on ratings of descriptors’ intensities and the other based on the magnitude of the changes observed since the previous consumption. As expected, the results showed that sensory properties and liking scores evolved over time. While the aroma and taste properties changed little, the texture deteriorated significantly. The overall liking scores decreased steadily over time, while the percentage of subjects who stopped eating bread increased. “Easiness to cut with the teeth,” “easiness to chew,” “crispness,” and “softness” were the main characteristics positively correlated with the overall liking scores and negatively correlated with the percentage of rejection. In contrast, “dryness of the crumb” was negatively correlated with the liking scores and positively correlated with the percentage of rejection. A survival analysis determined that the SSL (50% rejection) of the breads was approximately 2.5 days. Interestingly, we highlighted that the average liking score corresponding to the SSL was just below the middle of the overall liking scale.
Practical Application
The results of this work could be of interest to bread‐making professionals who will be able to use the main conclusions to advise their clients and possibly adapt the bread format to their sensory shelf life. This work was also an opportunity to highlight sourdough bread, which offers more flexibility than French baguette in managing the consumption of the bread purchased. The alternative approach tested to measure the evolution of sensory characteristics and overall liking could interest the professionals of sensory analysis.
As in many other locations in the world, honeybee colony losses and disorders have increased in Belgium. Some of the symptoms observed rest unspecific and their causes remain unknown. The present ...study aims to determine the role of both pesticide exposure and virus load on the appraisal of unexplained honeybee colony disorders in field conditions. From July 2011 to May 2012, 330 colonies were monitored. Honeybees, wax, beebread and honey samples were collected. Morbidity and mortality information provided by beekeepers, colony clinical visits and availability of analytical matrix were used to form 2 groups: healthy colonies and colonies with disorders (n = 29, n = 25, respectively). Disorders included: (1) dead colonies or colonies in which part of the colony appeared dead, or had disappeared; (2) weak colonies; (3) queen loss; (4) problems linked to brood and not related to any known disease. Five common viruses and 99 pesticides (41 fungicides, 39 insecticides and synergist, 14 herbicides, 5 acaricides and metabolites) were quantified in the samples.The main symptoms observed in the group with disorders are linked to brood and queens. The viruses most frequently found are Black Queen Cell Virus, Sac Brood Virus, Deformed Wing Virus. No significant difference in virus load was observed between the two groups. Three acaricides, 5 insecticides and 13 fungicides were detected in the analysed samples. A significant correlation was found between the presence of fungicide residues and honeybee colony disorders. A significant positive link could also be established between the observation of disorder and the abundance of crop surface around the beehive. According to our results, the role of fungicides as a potential stressor for honeybee colonies should be further studied, either by their direct and/or indirect impacts on bees and bee colonies.
Investigating the relative importance of neutral versus selective processes governing the accumulation of genetic variants is a key goal in both evolutionary and conservation biology. This is ...particularly true in the context of small populations, where genetic drift can counteract the effect of selection. Using Brook Charr (Salvelinus fontinalis) from Québec, Canada, as a case study, we investigated the importance of demographic versus selective processes governing the accumulation of both adaptive and maladaptive mutations in closed versus open and connected populations to assess gene flow effect. This was achieved by using 14,779 high‐quality filtered SNPs genotyped among 1,416 fish representing 50 populations from three life history types: lacustrine (closed populations), riverine and anadromous (connected populations). Using the PROVEAN algorithm, we observed a considerable accumulation of putative deleterious mutations across populations. The absence of correlation between the occurrence of putatively beneficial or deleterious mutations and local recombination rate supports the hypothesis that genetic drift might be the main driver of the accumulation of such variants. However, despite a lower genetic diversity observed in lacustrine than in riverine or anadromous populations, lacustrine populations do not exhibit more deleterious mutations than the two other history types, suggesting that the negative effect of genetic drift in lacustrine populations may be mitigated by that of relaxed purifying selection. Moreover, we also identified genomic regions associated with anadromy, as well as an overrepresentation of transposable elements associated with variation in environmental variables, thus supporting the importance of transposable elements in adaptation.
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