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Biology subjects

Brun, L.

Publications and source records attributed to Brun, L..

2 recordsLinked to original sources

Classifier architecture and data preprocessing jointly shape accelerometer-based behavioural inference

O_LIAlthough the use of accelerometer-based behavioural classification to quantify animal activity budgets is gaining widespread traction, the interactions between key preprocessing decisions and modern classification algorithms remain poorly understood. Moreover, classification pipelines are commonly assessed using global performance metrics, despite increasing evidence that such metrics poorly reflect behaviour-specific patterns and ecological reliability. C_LIO_LIUsing a free-ranging primate (Chlorocebus pygerythrus) as a case study, we benchmarked how temporal segmentation (burst length), collar orientation correction, and model architecture jointly shape behavioural inference. We compared nine supervised algorithms spanning classical machine learning, feature-based deep learning including a tabular foundation model (TabPFN), and state of the art time-series architectures (HydraMultiROCKET). Beyond conventional metrics, performance was further evaluated using ecological validation against independent focal observations to assess model stability and biological plausibility. C_LIO_LIModel architecture exerted the strongest influence on classification outcomes. Modern deep-learning approaches substantially outperformed classical models, doubling recall for rare behaviours (e.g., grooming, self-scratching) without compromising precision. In contrast, burst length and collar orientation correction had little effect on global metrics but produced substantial, behaviour-specific trade-offs. Shorter bursts improved the detection of rare events by increasing training instances, while orientation correction suppressed dataset-specific artifacts at the cost of degrading common behaviours. Crucially, models with similar global and behaviour-level validation metrics produced divergent predictions when applied outside the annotated context. C_LIO_LIOur findings reveal that global metrics are insufficient for optimizing behavioural inference in complex wild systems. We demonstrate that modern deep-learning architectures, such as the ROCKET family, provide a robust, accessible baseline that handles class imbalance more effectively than traditional methods. We propose that reliable inference requires behaviour-aware evaluation frameworks that integrate ecological validation, and advocate for ensemble or hierarchical strategies to leverage the complementary strengths of different preprocessing and modelling configurations. C_LI

animal behavior and cognition↗

Investigating the genetic architecture of biotic stress response in stone fruit tree orchards under natural infections with a multi-environment GWAS approach

The mapping and introduction of sustainable plant immunity to pests and diseases in fruit tree is still a major challenge in modern breeding. This study aims at deciphering the genetic architecture underlying resistance or tolerance across environments for major pests and diseases in peach (P. persica) and apricot (P. armeniaca). We set up a multi-environment trial (MET) approach by studying two core collections of 206 peach and 150 apricot accessions deployed under low phytosanitary conditions in respectively three and two environmentally contrasted locations in South-East of France. To capture the complex dynamics of pest and disease spread in naturally infected orchards, visual scoring of symptoms was repeated within and between 3 years, for five and two pests and diseases respectively for peach and apricot, resulting in the maximum of damage score and the AUDPC. These traits were used as phenotypic inputs in our genome-wide association studies (GWAS) strategy, and leading to the identification of: i) non-additive genotype-phenotype associations, ii) environment-shared QTLs iii) environment-specific QTLs, and iv) interactive QTLs which changes in direction ( antagonist) or intensity ( differential) according to the environment. By conducting GWAS with multiple methods, we successfully identified a total of 60 high confidence QTLs, leading to the identification of 87 candidate genes, the majority belonging to the Leucine-rich repeat containing receptors (LRR-CRs) family gene. Finally, we provided a comparative analysis of our results on peach and apricot, two closely related species. The present results contribute to the development of genomics-assisted breeding to improve biotic resilience in Prunus varieties.

plant biology↗