Abstract:
:Species interactions are a key component of ecosystems but we generally have an incomplete picture of who-eats-who in a given community. Different techniques have been devised to predict species interactions using theoretical models or abundances. Here, we explore the K nearest neighbour approach, with a special emphasis on recommendation, along with a supervised machine learning technique. Recommenders are algorithms developed for companies like Netflix to predict whether a customer will like a product given the preferences of similar customers. These machine learning techniques are well-suited to study binary ecological interactions since they focus on positive-only data. By removing a prey from a predator, we find that recommenders can guess the missing prey around 50% of the times on the first try, with up to 881 possibilities. Traits do not improve significantly the results for the K nearest neighbour, although a simple test with a supervised learning approach (random forests) show we can predict interactions with high accuracy using only three traits per species. This result shows that binary interactions can be predicted without regard to the ecological community given only three variables: body mass and two variables for the species' phylogeny. These techniques are complementary, as recommenders can predict interactions in the absence of traits, using only information about other species' interactions, while supervised learning algorithms such as random forests base their predictions on traits only but do not exploit other species' interactions. Further work should focus on developing custom similarity measures specialized for ecology to improve the KNN algorithms and using richer data to capture indirect relationships between species.
journal_name
PeerJjournal_title
PeerJauthors
Desjardins-Proulx P,Laigle I,Poisot T,Gravel Ddoi
10.7717/peerj.3644subject
Has Abstractpub_date
2017-08-10 00:00:00pages
e3644issn
2167-8359pii
3644journal_volume
5pub_type
杂志文章相关文献
PeerJ文献大全abstract:Background:Yunnanolepidoids constitute either the most basal consecutive segments or the most primitive clade of antiarchs, a highly diversified jawed vertebrate group from the Silurian and Early Devonian periods. Although the general morphology of yunnanolepidoids is well established, their endocranial features remain...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.4808
更新日期:2018-05-28 00:00:00
abstract::Secondary cavity nesting (SCN) birds breed in holes that they do not excavate themselves. This is possible where there are large trees whose size and age permit the digging of holes by primary excavators and only rarely happens in forest plantations, where we expected a deficit of both breeding holes and SCN species. ...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.1806
更新日期:2016-03-15 00:00:00
abstract::Flies use specialized photoreceptors R7 and R8 in the dorsal rim area (DRA) to detect skylight polarization. R7 and R8 form a tiered waveguide (central rhabdomere pair, CRP) with R7 on top, filtering light delivered to R8. We examine how the division of a given resource, CRP length, between R7 and R8 affects their abi...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.2772
更新日期:2017-01-12 00:00:00
abstract::Neem (Azadirachta indica A. Juss) is one of the most versatile tropical evergreen tree species known in India since the Vedic period (1500 BC-600 BC). Neem tree is a rich source of limonoids, having a wide spectrum of activity against insect pests and microbial pathogens. Complex tetranortriterpenoids such as azadirac...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.1066
更新日期:2015-08-06 00:00:00
abstract::Excluding grazers is one of most efficient ways to restore degraded grasslands in desert-steppe communities, but may negatively affect the recovery of plant species diversity. However, diversity differences between grazed and fenced grasslands in desert-steppe are poorly known. In a Stipa breviflora desert steppe comm...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.4359
更新日期:2018-02-13 00:00:00
abstract::Spatial genetic variation of river-dwelling freshwater fishes is typically affected by the historical and contemporary river landscape as well as life-history traits. Tropical river and stream landscapes have endured extended geological change, shaping the existing pattern of genetic diversity, but were not directly a...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.4487
更新日期:2018-03-07 00:00:00
abstract:Background:Several field studies have used fuel-cell breathalysers (FCB) to investigate the prevalence of alcohol intoxication. However, there is a lack of evidence evaluating the psychometric properties of these breathalysers outside of the forensic disciplines. Methods:The current research describes four studies des...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.4418
更新日期:2018-03-14 00:00:00
abstract:BACKGROUND:Constant reviews of the caring behavior of nurses and patient satisfaction help to improve the quality of nursing. The aim of our research was to explore relationships between the level of nursing education, the perception of nurses and nursing assistants of Watson's carative factors, and patient satisfactio...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.2940
更新日期:2017-02-07 00:00:00
abstract:Background:Plums are a kind of stone fruit, a category that includes peaches, cherries, apricots, and almonds. In Korea, Japanese plum trees are usually cultivated as they best suit the climate. To date, there have been few studies in Korea on viruses infecting plum trees compared to those infecting peach trees. Metho...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.9588
更新日期:2020-07-29 00:00:00
abstract:BACKGROUND:This study examines the biophysical and preclinical pulmonary activity of synthetic lung surfactants containing novel phospholipase-resistant phosphonolipids or synthetic glycerophospholipids combined with Super Mini-B (S-MB) DATK and/or SP-Css ion-lock 1 peptides that replicate the functional biophysics of ...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.2635
更新日期:2016-10-27 00:00:00
abstract::Nitrogen-fixing microorganisms play important roles in N cycling. However, knowledge related to the changes in the diazotrophic community in response to cropping systems is still rudimentary. In this study, the nifH gene was used to reveal the abundance and community compositions of diazotrophs in the cropping systems...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.9550
更新日期:2020-07-15 00:00:00
abstract::The mammalian pelvis is thought to exhibit adaptations to the functional demands of locomotor behaviors. Previous work in primates has identified form-function relationships between pelvic shape and locomotor behavior; few studies have documented such relationships in carnivorans, instead focusing on long bones. Most ...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.8574
更新日期:2020-02-20 00:00:00
abstract::Populations of passively dispersed organisms in continental aquatic habitats typically show high levels of neutral genetic differentiation despite their high dispersal capabilities. Several evolutionary factors, including founder events, local adaptation, and life cycle features such as high population growth rates an...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.6094
更新日期:2018-12-11 00:00:00
abstract::The Natural Mortality coefficient (M) is a key parameter for stock assessments. The need to establish age-specific natural mortality coefficients is widely recognized because M decreases rapidly over the early stages of the life cycle until it reaches a stable M value around the age-at-maturity. The aim of this study ...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.5235
更新日期:2018-07-18 00:00:00
abstract::Helminths include both parasitic nematodes (roundworms) and platyhelminths (trematode and cestode flatworms) that are abundant, and are of clinical importance. The genetic characterization of parasitic flatworms using advanced molecular tools is central to the diagnosis and control of infections. Although the nuclear ...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.207
更新日期:2013-11-12 00:00:00
abstract::Sea cucumbers possess the remarkable capacity to regenerate their body parts or organs. Regeneration of host organs and/or body parts involves reconstruction of the host associated microbiota, however, the dynamics and contribution of microbiota to the regeneration process are largely unknown due to a lack of experime...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.10260
更新日期:2020-12-01 00:00:00
abstract:BACKGROUND:The human microbiota plays a key role in health and disease, and bacteriocins, which are small, bacterially produced, antimicrobial peptides, are likely to have an important function in the stability and dynamics of this community. Here we examined the density and distribution of the subclass I lantibiotic m...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.3254
更新日期:2017-04-27 00:00:00
abstract::Bovine odorant-binding protein (bOBP) differs from other lipocalins by lacking the conserved disulfide bond and for being able to form the domain-swapped dimers. To identify structural features responsible for the formation of the bOBP unique dimeric structure and to understand the role of the domain swapping on maint...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.1933
更新日期:2016-04-18 00:00:00
abstract:Aims:Periodontitis and psoriatic disease, including psoriasis (PS) and psoriatic arthritis (PsA), share the common risk factors and co-morbidities. However, the risk of periodontitis in patients with psoriatic disease still needs further investigation. This study was a nationwide population-based retrospective cohort s...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.4064
更新日期:2017-11-16 00:00:00
abstract:Background/Aims:Medical and behavioral needs are relevant in organizing and providing support strategies that improve the quality of life for children, along with their families. The present study aims to examine the impact of medical and behavioral needs on the need for support of children with disabilities. Methods:...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.9557
更新日期:2020-09-15 00:00:00
abstract:Background:Immunoglobulin superfamily member 10 (IGSF10) is a member of the immunoglobulin superfamily that is expressed at high levels in both the gallbladder and ovary. Currently, the role and possible mechanism of IGSF10 in breast cancer remain unclear. Method:By applying real-time quantitative polymerase chain rea...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.10128
更新日期:2020-10-21 00:00:00
abstract:Background:Experiencing an adequate amount of cold temperatures over winter is necessary for many temperate tree species to break dormancy and flower in spring. Thus, changes in winter and spring temperatures associated with climate change may influence when trees break dormancy and flower in the future. There have bee...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.5221
更新日期:2018-09-25 00:00:00
abstract::Species identification-of importance for most biological disciplines-is not always straightforward as cryptic species hamper traditional identification. Fibre-optic near-infrared spectroscopy (NIRS) is a rapid and inexpensive method of use in various applications, including the identification of species. Despite its e...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.991
更新日期:2015-09-15 00:00:00
abstract::Background. The age at which most young people are in tertiary education is also the age of peak onset for mental illness. Because mental health problems can have adverse effects on students' academic performance and welfare, institutions require guidance how they can best provide support. However, the scientific evid...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.43
更新日期:2013-02-26 00:00:00
abstract::Crop landraces are fundamental resources to increase the eroded genepool of modern crops in order to adapt agriculture to future challenges; plus, they are of immeasurable heritage and cultural value. Between the 1940s and the 1960s open-pollinated varieties (OPVs) of flint and semi-flint maize in Europe were almost c...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.5123
更新日期:2018-07-04 00:00:00
abstract::The use of small unoccupied aircraft systems (UAS) for ecological studies and wildlife population assessments is increasing. These methods can provide significant benefits in terms of costs and reductions in human risk, but little is known if UAS-based approaches cause disturbance of animals during operations. To addr...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.4467
更新日期:2018-03-19 00:00:00
abstract::Following a radiation incident, preliminary dose estimates made by γ-H2AX foci analysis can supplement the early triage of casualties based on clinical symptoms. Sample processing time is important when many individuals need to be rapidly assessed. A protocol was therefore developed for high sample throughput that req...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.282
更新日期:2014-03-06 00:00:00
abstract:Background:Lysyl oxidases (LOX) have been extensively studied in mammals, whereas properties and functions of recently found homologues in prokaryotic genomes remain enigmatic. Methods:LOX open reading frame was cloned from Haloterrigena turkmenica in an E. coli expression vector. Recombinant Haloterrigena turkmenica ...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.6691
更新日期:2019-04-05 00:00:00
abstract:Background:Quantifying lower-limb load and asymmetry during team sport match-play may be important for injury prevention and understanding performance. However, current analysis methods of lower-limb symmetry during match-play employ wearable microtechnology that may not be best suited to the task. A popular microtechn...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.9366
更新日期:2020-06-23 00:00:00
abstract::Herein, we identified the tomato SlMYB102 gene as a MYB family transcription factor of the R2R3-MYB subfamily. We additionally determined that the SlMYB102 promoter region contains photoresponsive, abiotic stress-responsive, and hormone-responsive regulatory elements, and we detected higher SlMYB102 expression in the ...
journal_title:PeerJ
pub_type: 杂志文章
doi:10.7717/peerj.10059
更新日期:2020-10-07 00:00:00