Machine learning improves predicting species interactions based on traits.
problem Variability in empirical trait-matching studies for ecological networks.
method Compared conventional GLMs with ML models (Random Forest, Boosted Regression Trees, etc.) on simulated and real data.
result ML models outperform GLMs in predicting species interactions and identifying trait-matching combinations.
Deep learning system speeds up wildlife species identification from camera trap images.
problem Manual review of camera trap images is slow and resource-intensive.
method Combines machine and human intelligence for active learning.
result Matches state-of-the-art accuracy with minimal manual labels.
Paper investigates if RL can learn from observing others without explicit modeling.
problem Can RL learn from observing others without explicit modeling?
method Simple scenarios with RL agents observing and learning from another agent's actions.
result RL agents can learn from observing others, leveraging environmental effects.
DMSE embeds multiple species and environmental covariates for better species distribution modeling.
problem Single species models ignore species interactions, DMSE addresses this.
method Deep neural network for joint embedding of multiple species and environmental covariates.
result DMSE outperforms single-species and multi-label models in predicting bird species distributions.
Framework uncovers symmetric and asymmetric species associations from data.
problem Retrieving bidirectional species associations from co-occurrence data.
method Machine learning framework modeling latent embeddings and joint generative model.
result Framework successfully recovers known symmetric and asymmetric associations.
Heterogeneous GNN improves species distribution modeling.
problem Predicting species occurrences and habitat suitability using environmental factors.
method Graph Neural Networks (GNN) for presence-only species distribution modeling.
result Heterogeneous GNN model outperforms single-species SDMs and baseline models.
GeoLifeCLEF 2020 dataset pairs species observations with environmental data.
problem Understanding geographic species distribution.
method Presented a dataset of species observations with environmental features.
result Advances in location-based species recommendation.
SDSR reconstructs species trees from genetic markers efficiently.
problem Challenges in reconstructing species trees from genetic data.
method Spectral divide-and-conquer approach based on graph theory.
result SDSR achieves up to 10-fold faster runtime with comparable accuracy.
SLIC-UAV monitors forest recovery using UAVs and machine learning.
problem Challenges in monitoring forest recovery, especially in logged tropical forests.
method Novel pipeline for UAV imagery analysis, combining crown labelling, species classification, and superpixel segmentation.
result SLIC-UAV achieves high accuracy in species mapping, from 79.3% to 90.5%.
Deep semi-supervised learning identifies tree species from natural images.
problem Identifying tree species in natural settings with limited labeled data.
method Two-fold approach using deep semi-supervised learning.
result Achieves 94.04% top-5 accuracy for leaves and 83.04% for bark.
Forest tree species mapped with high accuracy using satellite data.
problem Classifying dominant tree species in Swedish forests.
method Extreme gradient boosting model with Bayesian optimization, combining Sentinel-1/2 satellite data and field observations.
result Overall accuracy of 85%, F1 score of 0.82, Matthews correlation coefficient of 0.81.
Image classification system identifies bumble bee species from images.
problem Manual identification of bumble bee species is time-consuming and requires expert knowledge.
method Transfer learning using Inception, VGG16, VGG19, and ResNet models.
result Inception and VGG classifiers achieved up to 23% accuracy for single species identification.
This paper compares supervised learning methods for identifying phytoplankton species.
problem Identifying phytoplankton species due to their variability and ambiguity.
method Proposed a new features type from raw signals and compared various classifiers.
result Random Forest using the proposed features gave the best classification results with 98.24% accuracy.
StatEcoNet models species distribution using neural networks to correct observation errors.
problem Correcting observation errors in wildlife surveys for accurate species distribution modeling.
method StatEcoNet integrates a graphical generative model with neural networks to address SDM challenges.
result StatEcoNet outperforms traditional methods on simulated and real datasets.
Machine learning identifies species by voice in remote areas.
problem Continuous monitoring of endangered species in remote areas.
method Training machine learning models on audio data to recognize species.
result Machine learning can accurately classify and recognize various species sounds.
Gaussian process framework learns interaction kernels in multi-species particle systems.
problem Learning interaction kernels in multi-species interacting particle systems from trajectory data.
method Nonparametric Bayesian approach with Gaussian processes.
result Established rigorous statistical guarantees for recoverability and optimality of interaction kernels.
Deep learning identifies moss species from amorphous images.
problem Identifying moss species from ambiguous, amorphous images.
method Used a 'chopped picture' method to classify moss species.
result Model achieved over 90% accuracy in moss species classification.
Improved chemical predictions through compressed atomic species representations.
problem Intractable chemical space of molecules and materials.
method Introducing elemental modes for compressed representation of atomic species.
result Elemental modes enable improvements in machine learning tasks for chemical predictions.
Deep learning identifies frog species and detects new ones.
problem Identifying and detecting new species in morphologically similar groups.
method Machine learning, specifically deep neural networks, applied to frog hind limb skin texture.
result Deep neural networks can classify images into known species and new classes.
PHIBP models complex microbiome data with shared parameters.
problem Complex, sparse count data in microbiome analysis.
method Bayesian nonparametric framework with shared species parameters.
result Flexible multivariate count model with tractable inference.
Interpretable neural network for plant traits and species identification.
problem Plant phenotyping and identification.
method Neural network trained on UPWINS spectral library, with visualization of weights for trait-based spectral features.
result 90% accuracy in species identification with interpretable neural network.
AMP0 predicts antimicrobial peptides targeting specific microbes.
problem Low-throughput screening of antimicrobial peptides.
method Zero-shot and few-shot machine learning.
result AMP0 can predict antimicrobial activity against specific microbes.
AI4AI uses machine learning to classify avian influenza host species from DNA sequences.
problem Classifying avian influenza host species from DNA sequences to reduce emergency response time.
method Quantitative methods using machine learning and deep learning.
result Best deep learning models achieve top-1 classification accuracy of 47%, and top-3 classification accuracy of 82%.
Deep model tackles zero-inflated multi-species abundance estimation.
problem Predicting species distribution across landscapes with inflated zero counts.
method Proposes a novel deep learning model combining multivariate probit and log-normal distributions.
result Model outperforms existing methods on bird and fish population datasets.
DeepMaxent uses neural networks to improve species distribution models.
problem Sampling biases and lack of absence data in presence-only observations.
method DeepMaxent employs neural networks to learn shared features among species using the maximum entropy principle.
result DeepMaxent outperforms traditional methods in predicting species distributions, especially in unevenly sampled regions.
We consider the problem of estimating the evolutionary history of a set of species (phylogeny or species tree) from several genes. It is known that the evolutionary history of individual genes (gene trees) might be topologically distinct from each other and from the underlying species tree, possibly confounding phyloge…
Bayesian method improves estimation of unseen species.
problem Estimating unseen species in biological and physical sciences.
method Bayesian nonparametric approach with Pitman-Yor prior and Gaussian credible intervals.
result Improves asymptotic credible intervals for unseen species estimation.
Unified CNN identifies chemical species from Raman spectra.
problem Challenges in identifying chemical species from Raman spectra due to preprocessing requirements.
method A deep convolutional neural network trained to automatically identify substances from Raman spectra.
result Superior classification performance compared to other machine learning methods.
New estimators predict unseen species up to log(n) times larger than observed.
problem Estimating the number of unseen species in a population.
method Derive a class of provable estimators for predicting unseen species for all t proportional to log(n).
result Provably predict unseen species for all t proportional to log(n), improving on previous methods.
The paper uses VGG-19 for plant species classification from leaf images.
problem Manual inspection of plant species by botanists is time-consuming.
method Transfer learning with VGG-19 for feature extraction and classification.
result The model achieves 99.70% accuracy in predicting plant species.
Paper improves gas species identification in complex mixtures using neural networks.
problem Identifying gas species in multi-gas mixtures with high accuracy.
method Multi-label neural networks with optimal thresholding for IR spectroscopy.
result Optimal thresholding improves classification performance over conventional methods.
DeepWeeds dataset aids in robust weed species classification for rangeland robotics.
problem Robust classification of weed species in rangeland environments.
method Development of a large multiclass image dataset and application of deep learning models.
result Inception-v3 and ResNet-50 achieved 95.1% and 95.7% classification accuracy, respectively.
Method for creating synthetic multi-fidelity data sets.
problem Lack of representative synthetic datasets for multifidelity optimisation benchmarks.
method Systematic generation of synthetic fidelities from preexisting datasets.
result Allows systematic investigation of lower fidelity proxies' influence.
Populations of species in ecosystems are often constrained by availability of resources within their environment. In effect this means that a growth of one population, needs to be balanced by comparable reduction in populations of others. In neutral models of biodiversity all populations are assumed to change increment…
Most animals possess the ability to actuate a vast diversity of movements, ostensibly constrained only by morphology and physics. In practice, however, a frequent assumption in behavioral science is that most of an animal's activities can be described in terms of a small set of stereotyped motifs. Here we introduce a m…
Compact models for methane/air combustion reduce complexity without sacrificing accuracy.
problem Creating accurate, computationally efficient models for methane combustion.
method Data-oriented three-step methodology: 1) Remove non-essential species, 2) Numerically optimize to key species profiles, 3) Machine learning to refine parameters.
result Produced 19 and 15 species compact models that outperform current state-of-the-art models in accuracy and range of conditions.
Translating potential disease biomarkers between multi-species 'omics' experiments is a new direction in biomedical research. The existing methods are limited to simple experimental setups such as basic healthy-diseased comparisons. Most of these methods also require an a priori matching of the variables (e.g., genes o…
ConvNet classifies whale vocalizations and ambient noise in acoustic recordings.
problem Automated detection and classification of marine mammal vocalizations in acoustic recordings.
method Convolutional Neural Network with a novel acoustic representation.
result Classifier accurately detects and classifies whale vocalizations and ambient noise.
Deep learning improves tree species classification accuracy in imbalanced contexts.
problem Inaccurate tree species maps for large areas, especially in imbalanced contexts.
method Used deep learning models (including convolutional and attention-based) on Sentinel-2 multispectral satellite time series data.
result Deep learning models achieve higher accuracy and F1-macro scores compared to Random Forest in imbalanced contexts.
New algorithms improve federated learning accuracy and stability with real-world data.
problem Real-world data diversity and imbalance challenge federated learning.
method Developed new algorithms (FedVC, FedIR) to resample and reweight data.
result Significant improvements in accuracy and stability of federated learning.
New model estimates species population trends from citizen science data.
problem Interannual confounding in citizen science data.
method Double Machine Learning framework to estimate population change and propensity scores for confounding adjustment.
result Spatially detailed trend estimates from citizen science data with low error rates.
Biodiversity monitoring using audio recordings is achievable at a truly global scale via large-scale deployment of inexpensive, unattended recording stations or by large-scale crowdsourcing using recording and species recognition on mobile devices. The ability, however, to reliably identify vocalising animal species is…
A Deep Zero-Inflated Model for Detecting North Atlantic Right Whale Presence
problem Balancing marine conservation and blue economy management
method Deep Zero-Inflated Bernoulli model
result Improved model adequacy and predictive performance
SVM and N-best algorithm classify microbial marker clades from genome sequences.
problem Classifying microbial clades from genome sequences, especially new species.
method Support vector machine (SVM) with N-best algorithm, time series feature extraction, random fragment generation, k-mer size selection.
result Recognition accuracy rates above 28% in top-1 candidate, above 91% in top-10 candidate.
Develops geometry for Lotka-Volterra model of species competition.
problem Population dynamics of competing species.
method Least squares variational method, Lagrange-Hamilton geometry.
result Jacobi stability discussed for the Lotka-Volterra system.
FAA identifies rodent disease carriers for human health.
problem Identifying rodent species that carry zoonotic diseases.
method Applied Formal Concept Analysis to rodent trait data.
result Identified concepts linking rodent traits to zoonotic disease carrier status.
CRNN discovers chemical reaction pathways from data.
problem Challenging to infer reaction pathways for complex systems.
method Neural network approach that satisfies fundamental physics laws.
result CRNN autonomously discovers reaction pathways from species concentration data.
EcoCast predicts biodiversity risks using satellite data and citizen science records.
problem Unprecedented shifts in species distributions due to climate change and habitat loss.
method Spatio-temporal model using sequence-based transformers and continual learning.
result Promising improvements in forecasting bird species distributions compared to Random Forest.