The accurate detection of behavioural changes represents a promising method of detecting the early onset of disease in dairy cows. This study assessed the performance of deep learning (DL) in classifying dairy cows' behaviour from accelerometry data acquired by single sensors on the cows' left flanks and compared the results with those obtained through classical machine learning (ML) from the same raw data. Twelve cows with a tri-axial accelerometer were observed for 136 ± 29 min each to detect five main behaviours: standing still, moving, feeding, ruminating and resting. For each 8 s time interval, 15 metrics were calculated, obtaining a dataset of 211,720 observation units and 15 columns. The entire dataset was randomly split into training (80%) and testing (20%) datasets. The DL accuracy, precision and sensitivity/recall were calculated and compared with the performance of classical ML models. The best predictive model was an 8-layer convolutional neural network (CNN) with an overall accuracy and F1 score equal to 0.96. The precision, sensitivity/recall and F1 score of single behaviours had the following ranges: 0.93-0.99. The CNN outperformed all the classical ML algorithms. The CNN used to monitor the cows' conditions showed an overall high performance in successfully predicting multiple behaviours using a single accelerometer.
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http://dx.doi.org/10.3390/ani13111886 | DOI Listing |
Adv Sci (Weinh)
January 2025
Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.
Protein phosphorylation plays a crucial role in regulating a wide range of biological processes, and its dysregulation is strongly linked to various diseases. While many phosphorylation sites have been identified so far, their functionality and regulatory effects are largely unknown. Here, a deep learning model MMFuncPhos, based on a multi-modal deep learning framework, is developed to predict functional phosphorylation sites.
View Article and Find Full Text PDFGigascience
January 2025
School of Computer Science, Hunan University of Technology, Zhuzhou 412007, Hunan, China.
Background: The accurate deciphering of spatial domains, along with the identification of differentially expressed genes and the inference of cellular trajectory based on spatial transcriptomic (ST) data, holds significant potential for enhancing our understanding of tissue organization and biological functions. However, most of spatial clustering methods can neither decipher complex structures in ST data nor entirely employ features embedded in different layers.
Results: This article introduces STMSGAL, a novel framework for analyzing ST data by incorporating graph attention autoencoder and multiscale deep subspace clustering.
J Med Internet Res
January 2025
Knight Foundation of Computing & Information Sciences, Florida International University, Miami, FL, United States.
Background: Digital biomarkers are increasingly used in clinical decision support for various health conditions. Speech features as digital biomarkers can offer insights into underlying physiological processes due to the complexity of speech production. This process involves respiration, phonation, articulation, and resonance, all of which rely on specific motor systems for the preparation and execution of speech.
View Article and Find Full Text PDFBioinformatics
January 2025
Bioinformatics Lab, Advanced Research Institute for Informatics, Computing and Networking, De La Salle University, Manila, 1004, Philippines.
Motivation: Recent computational approaches for predicting phage-host interaction have explored the use of sequence-only protein language models to produce embeddings of phage proteins without manual feature engineering. However, these embeddings do not directly capture protein structure information and structure-informed signals related to host specificity.
Results: We present PHIStruct, a multilayer perceptron that takes in structure-aware embeddings of receptor-binding proteins, generated via the structure-aware protein language model SaProt, and then predicts the host from among the ESKAPEE genera.
Bioinformatics
January 2025
School of Artificial Intelligence, Jilin University, Jilin, China.
Motivation: Predicting RNA-binding proteins (RBPs) is central to understanding post-transcriptional regulatory mechanisms. Here, we introduce EnrichRBP, an automated and interpretable computational platform specifically designed for the comprehensive analysis of RBP interactions with RNA.
Results: EnrichRBP is a web service that enables researchers to develop original deep learning and machine learning architectures to explore the complex dynamics of RNA-binding proteins.
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