Machine learning algorithms to infer trait‐matching and predict species interactions in ecological networks

Mutualistic networks: moving closer to a predictive theory

(2019) Fernanda S. Valdovinos   ECOLOGY LETTERS

Identifying a common backbone of interactions underlying food webs from different ecosystems

(2018) Bernat Bramon Mora et al.   Nature Communications

A novel heterogeneous network-based method for drug response prediction in cancer cell lines

(2018) Fei Zhang et al.   Scientific Reports

The spatial scaling of species interaction networks

(2018) Nuria Galiana et al.   Nature Ecology & Evolution

A Survey of Methods for Explaining Black Box Models

(2018) Riccardo Guidotti et al.   ACM COMPUTING SURVEYS

The growing ubiquity of algorithms in society: implications, impacts and innovations

(2018) S. C. Olhede et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Towards global data products of Essential Biodiversity Variables on species traits

(2018) W. Daniel Kissling et al.   Nature Ecology & Evolution

A Convolutional Neural Network for Detecting Sea Turtles in Drone Imagery

(2018) Patrick C. Gray et al.   Methods in Ecology and Evolution

Machine learning to classify animal species in camera trap images: Applications in ecology

(2018) Michael A. Tabak et al.   Methods in Ecology and Evolution

Inferring predator–prey interactions in food webs

(2018) Justin P. F. Pomeranz et al.   Methods in Ecology and Evolution

Trait matching and phylogeny as predictors of predator-prey interactions involving ground beetles

(2017) Pierre-Marc Brousseau et al.   FUNCTIONAL ECOLOGY

Functionally specialised birds respond flexibly to seasonal changes in fruit availability

(2017) Irene M. A. Bender et al.   JOURNAL OF ANIMAL ECOLOGY

Deep-Learning-Based Drug–Target Interaction Prediction

(2017) Ming Wen et al.   JOURNAL OF PROTEOME RESEARCH

SimBoost: a read-across approach for predicting drug–target binding affinities using gradient boosting machines

(2017) Tong He et al.   Journal of Cheminformatics

iDTI-ESBoost: Identification of Drug Target Interaction Using Evolutionary and Structural Features with Boosting

(2017) Farshid Rayhan et al.   Scientific Reports

Statistically reinforced machine learning for nonlinear patterns and variable interactions

(2017) Masahiro Ryo et al.   Ecosphere

Ecological interactions and the Netflix problem

(2017) Philippe Desjardins-Proulx et al.   PeerJ

Higher-order interactions capture unexplained complexity in diverse communities

(2017) Margaret M. Mayfield et al.   Nature Ecology & Evolution

GPCR–drug interactions prediction using random forest with drug-association-matrix-based post-processing procedure

(2016) Jun Hu et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

A common framework for identifying linkage rules across different types of interactions

(2016) Ignasi Bartomeus et al.   FUNCTIONAL ECOLOGY

Safeguarding pollinators and their values to human well-being

(2016) Simon G. Potts et al.   NATURE

Morphology predicts species' functional roles and their degree of specialization in plant–frugivore interactions

(2016) D. Matthias Dehling et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

How can an understanding of plant–pollinator interactions contribute to global food security?

(2015) Emily J Bailes et al.   CURRENT OPINION IN PLANT BIOLOGY

Functional structure and specialization in three tropical plant-hummingbird interaction networks across an elevational gradient in Costa Rica

(2015) María A. Maglianesi et al.   ECOGRAPHY

Quantifying hummingbird preference for floral trait combinations: The role of selection on trait interactions in the evolution of pollination syndromes

(2015) Charles B. Fenster et al.   EVOLUTION

EDITOR'S CHOICE: REVIEW: Trait matching of flower visitors and crops predicts fruit set better than trait diversity

(2015) Lucas A. Garibaldi et al.   JOURNAL OF APPLIED ECOLOGY

Deep learning

(2015) Yann LeCun et al.   NATURE

Inferring biotic interactions from proxies

(2015) Ignacio Morales-Castilla et al.   TRENDS IN ECOLOGY & EVOLUTION

Empirical Evaluation of Neutral Interactions in Host-Parasite Networks

(2014) E. F. Canard et al.   AMERICAN NATURALIST

Multispecies interactions across trophic levels at macroscales: retrospective and future directions

(2014) W. Daniel Kissling et al.   ECOGRAPHY

Predicting ecosystem functions from biodiversity and mutualistic networks: an extension of trait-based concepts to plant-animal interactions

(2014) Matthias Schleuning et al.   ECOGRAPHY

Morphological traits determine specialization and resource use in plant–hummingbird networks in the neotropics

(2014) María Alejandra Maglianesi et al.   ECOLOGY

A quantitative review of pollination syndromes: do floral traits predict effective pollinators?

(2014) Víctor Rosas-Guerrero et al.   ECOLOGY LETTERS

Functional relationships beyond species richness patterns: trait matching in plant-bird mutualisms across scales

(2014) D. Matthias Dehling et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Machine learning-based prediction of drug–drug interactions by integrating drug phenotypic, therapeutic, chemical, and genomic properties

(2014) Feixiong Cheng et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Species traits and abundances predict metrics of plant-pollinator network structure, but not pairwise interactions

(2014) Colin Olito et al.   OIKOS

Beyond species: why ecological interaction networks vary through space and time

(2014) Timothée Poisot et al.   OIKOS

Pollination syndromes in a specialised plant-pollinator interaction: does floral morphology predict pollinators inCalceolaria?

(2014) M. Murúa et al.   PLANT BIOLOGY

Processes entangling interactions in communities: forbidden links are more important than abundance in a hummingbird-plant network

(2014) J. Vizentin-Bugoni et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The dimensionality of ecological networks

(2013) Anna Eklöf et al.   ECOLOGY LETTERS

Predicting novel trophic interactions in a non-native world

(2013) Ian S. Pearse et al.   ECOLOGY LETTERS

Predictions of BuChE Inhibitors Using Support Vector Machine and Naive Bayesian Classification Techniques in Drug Discovery

(2013) Jiansong Fang et al.   Journal of Chemical Information and Modeling

Predicting Drug-Target Interactions for New Drug Compounds Using a Weighted Nearest Neighbor Profile

(2013) Twan van Laarhoven et al.   PLoS One

Machine Learning Prediction of Cancer Cell Sensitivity to Drugs Based on Genomic and Chemical Properties

(2013) Michael P. Menden et al.   PLoS One

Inferring food web structure from predator-prey body size relationships

(2013) Dominique Gravel et al.   Methods in Ecology and Evolution

A method for detecting modules in quantitative bipartite networks

(2013) Carsten F. Dormann et al.   Methods in Ecology and Evolution

Functional traits, the phylogeny of function, and ecosystem service vulnerability

(2013) Sandra Díaz et al.   Ecology and Evolution

Hierarchical Bayesian models in ecology: Reconstructing species interaction networks from non-homogeneous species abundance data

(2012) Andrej Aderhold et al.   Ecological Informatics

MissForest--non-parametric missing value imputation for mixed-type data

(2011) D. J. Stekhoven et al.   BIOINFORMATICS

Do pollination syndromes cause modularity and predict interactions in a pollination network in tropical high-altitude grasslands?

(2011) Aline Danieli-Silva et al.   OIKOS

Discovering drug-drug interactions: a text-mining and reasoning approach based on properties of drug metabolism

(2010) L. Tari et al.   BIOINFORMATICS

Modeling Liver-Related Adverse Effects of Drugs UsingkNearest Neighbor Quantitative Structure−Activity Relationship Method

(2010) Amie D. Rodgers et al.   CHEMICAL RESEARCH IN TOXICOLOGY

A global test of the pollination syndrome hypothesis

(2009) Jeff Ollerton et al.   ANNALS OF BOTANY

Centrality measures and the importance of generalist species in pollination networks

(2009) Ana M. Martín González et al.   Ecological Complexity

Effect of flower shape and size on foraging performance and trade-offs in a tropical hummingbird

(2009) Ethan J. Temeles et al.   ECOLOGY

Predictive learning via rule ensembles

(2008) Jerome H. Friedman et al.   Annals of Applied Statistics

Prediction of drug-target interaction networks from the integration of chemical and genomic spaces

(2008) Y. Yamanishi et al.   BIOINFORMATICS

Simple prediction of interaction strengths in complex food webs

(2008) E. L. Berlow et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA