Environ Monit Assess. 2024 Feb 17;196(3):279. doi: 10.1007/s10661-024-12410-x.

ABSTRACT

Efficient waste management is essential for human well-being and environmental health, as neglecting proper disposal practices can lead to financial losses and the depletion of natural resources. Given the rapid urbanization and population growth, developing an automated, innovative waste classification model becomes imperative. To address this need, our paper introduces a novel and robust solution - a smart waste classification model that leverages a hybrid deep learning model (Optimized DenseNet-121 + SVM) to categorize waste items using the TrashNet datasets. Our proposed approach uses the advanced deep learning model DenseNet-121, optimized for superior performance, to extract meaningful features from an expanded TrashNet dataset. These features are subsequently fed into a support vector machine (SVM) for precise classification. Employing data augmentation techniques further enhances classification accuracy while mitigating the risk of overfitting, especially when working with limited TrashNet data. The results of our experimental evaluation of this hybrid deep learning model are highly promising, with an impressive accuracy rate of 99.84%. This accuracy surpasses similar existing models, affirming the efficacy and potential of our approach to revolutionizing waste classification for a sustainable and cleaner future.

PMID:38367185 | DOI:10.1007/s10661-024-12410-x

Eur Spine J. 2024 Feb 17. doi: 10.1007/s00586-023-08024-5. Online ahead of print.

ABSTRACT

PURPOSE: The Cobb angle is a standard measurement to qualify and track the progression of scoliosis. However, the Cobb angle has high inter- and intra-observer variability. Consequently, its measurement varies with vertebrae and may even differ when the same vertebra is measured. Therefore, it is not constant and differs with measurements. This study aimed to develop a deep learning model that automatically measures the Cobb angle. The deep learning model for identifying vertebrae on spine radiographs was developed.

METHODS: The dataset consisted of 297 images that were divided into two subsets for training and validation. Two hundred and twenty-seven images (76.4%) were used to train the model, while 70 images (23.6%) were used as the validation dataset. Absolut error between the measurements by the observer and developed deep learning model and intraclass correlation coefficient (ICC).

RESULTS: The average absolute error between the measurements was 1.97° with a standard deviation of 1.57°. In addition, 95.9% of the angles had an absolute error of less than 5°. The ICC was calculated to assess the model's reliability further. The ICC was 0.981, indicating excellent reliability.

CONCLUSIONS: The authors believe the model will be useful in clinical practice by relieving clinicians of the burden of having to manually compute the Cobb angle. Further studies are needed to enhance the accuracy and versatility of this deep learning model.

PMID:38367024 | DOI:10.1007/s00586-023-08024-5

J Chem Inf Model. 2024 Feb 17. doi: 10.1021/acs.jcim.3c00771. Online ahead of print.

ABSTRACT

Predicting the binding affinity of protein-ligand complexes is crucial for computer-aided drug discovery (CADD) and the identification of potential drug candidates. The deep learning-based scoring functions have emerged as promising predictors of binding constants. Building on recent advancements in graph neural networks, we present graphLambda for protein-ligand binding affinity prediction, which utilizes graph convolutional, attention, and isomorphism blocks to enhance the predictive capabilities. The graphLambda model exhibits superior performance across CASF16 and CSAR HiQ NRC benchmarks and demonstrates robustness with respect to different types of train-validation set partitions. The development of graphLambda underscores the potential of graph neural networks in advancing binding affinity prediction models, contributing to more effective CADD methodologies.

PMID:38366974 | DOI:10.1021/acs.jcim.3c00771

Bioinformatics. 2024 Feb 16:btae092. doi: 10.1093/bioinformatics/btae092. Online ahead of print.

ABSTRACT

SUMMARY: Deep neural networks (DNNs) have been widely applied to predict the molecular functions of the non-coding genome. DNNs are data hungry and thus require many training examples to fit data well. However, functional genomics experiments typically generate limited amounts of data, constrained by the activity levels of the molecular function under study inside the cell. Recently, EvoAug was introduced to train a genomic DNN with evolution-inspired augmentations. EvoAug-trained DNNs have demonstrated improved generalization and interpretability with attribution analysis. However, EvoAug only supports PyTorch-based models, which limits its applications to a broad class of genomic DNNs based in TensorFlow. Here, we extend EvoAug's functionality to TensorFlow in a new package we call EvoAug-TF. Through a systematic benchmark, we find that EvoAug-TF yields comparable performance with the original EvoAug package.

AVAILABILITY: EvoAug-TF is freely available for users and is distributed under an open-source MIT license. Researchers can access the open-source code on GitHub (https://github.com/p-koo/evoaug-tf). The pre-compiled package is provided via PyPI (https://pypi.org/project/evoaug-tf) with in-depth documentation on ReadTheDocs (https://evoaug-tf.readthedocs.io). The scripts for reproducing the results are available at (https://github.com/p-koo/evoaug-tf_analysis).

PMID:38366935 | DOI:10.1093/bioinformatics/btae092

Brief Funct Genomics. 2024 Feb 16:elae003. doi: 10.1093/bfgp/elae003. Online ahead of print.

ABSTRACT

Genome sequencing data have become increasingly important in the field of personalized medicine and diagnosis. However, accurately detecting genomic variations remains a challenging task. Traditional variation detection methods rely on manual inspection or predefined rules, which can be time-consuming and prone to errors. Consequently, deep learning-based approaches for variation detection have gained attention due to their ability to automatically learn genomic features that distinguish between variants. In our review, we discuss the recent advancements in deep learning-based algorithms for detecting small variations and structural variations in genomic data, as well as their advantages and limitations.

PMID:38366908 | DOI:10.1093/bfgp/elae003

J Magn Reson Imaging. 2024 Feb 17. doi: 10.1002/jmri.29311. Online ahead of print.

NO ABSTRACT

PMID:38366814 | DOI:10.1002/jmri.29311

Br J Radiol. 2024 Feb 15:tqae026. doi: 10.1093/bjr/tqae026. Online ahead of print.

ABSTRACT

OBJECTIVE: To demonstrate that a T2 periodically rotated overlapping parallel lines with enhanced reconstruction (PROPELLER) technique using deep learning reconstruction (DLR) will provide better image quality and decrease image noise.

METHODS: From December 2020 to March 2021, 35 patients examined cervical spine MRI were included in this study. Four sets of images including FSE, original PROPELLER, PROPELLER DLR50%, and DLR75% were quantitatively and qualitatively reviewed. We calculated the signal-to-noise ratio (SNR) of the spinal cord and sternocleidomastoid (SCM) muscle and the contrast-to-noise ratio (CNR) of the spinal cord by applying region-of-interest at the spinal cord, SCM muscle, and background air. We evaluated image noise with regard to the spinal cord, SCM, and back muscles at each level from C2-3 to C6-7 in the four sets.

RESULTS: At all disc levels, the mean SNR values for the spinal cord and SCM muscles were significantly higher in PROPELLER DLR50% and DLR75% compared to FSE and original PROPELLER images (p < 0.0083). The mean CNR values of the spinal cord were significantly higher in PROPELLER DLR50% and DLR75% compared to FSE at the C3-4 and 4-5 levels and PROPELLER DLR75% compared to FSE at the C6-7 level (p < 0.0083). Qualitative analysis of image noise on the spinal cord, SCM, and back muscles showed that PROPELLER DLR50% and PROPELLER DLR75% images showed a significant denoising effect compared to the FSE and original PROPELLER images.

CONCLUSION: The combination of PROPELLER and DLR improved image quality with a high SNR and CNR and reduced noise.

PMID:38366622 | DOI:10.1093/bjr/tqae026

Bioinformatics. 2024 Feb 15:btae083. doi: 10.1093/bioinformatics/btae083. Online ahead of print.

ABSTRACT

MOTIVATION: Nanopore sequencing is a new macromolecular recognition and perception technology that enables high-throughput sequencing of DNA, RNA, even protein molecules. The sequences generated by nanopore sequencing span a large time frame, and the labor and time costs incurred by traditional analysis methods are substantial. Recently, research on nanopore data analysis using machine learning algorithms has gained unceasing momentum, but there is often a significant gap between traditional and deep learning methods in terms of classification results. To analyze nanopore data using deep learning technologies, measures such as sequence completion and sequence transformation can be employed. However, these technologies do not preserve the local features of the sequences. To address this issue, we propose a sequence-to-image (S2I) module that transforms sequences of unequal length into images. Additionally, we propose the Transformer-based T-S2Inet model to capture the important information and improve the classification accuracy.

RESULTS: Quantitative and qualitative analysis shows that the experimental results have an improvement of around 2% in accuracy compared to previous methods. The proposed method is adaptable to other nanopore platforms, such as the Oxford nanopore. It is worth noting that the proposed method not only aims to achieve the most advanced performance, but also provides a general idea for the analysis of nanopore sequences of unequal length.

AVAILABILITY: The main program is available at https://github.com/guanxiaoyu11/S2Inet.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:38366607 | DOI:10.1093/bioinformatics/btae083

Phys Rev E. 2024 Jan;109(1-1):014212. doi: 10.1103/PhysRevE.109.014212.

ABSTRACT

In order to effectively manage infectious diseases, it is crucial to understand the interplay between disease dynamics and human conduct. Various factors can impact the control of an epidemic, including social interventions, adherence to health protocols, mask-wearing, and vaccination. This article presents the development of an innovative hybrid model, known as the Combined Dynamic-Learning Model, that integrates classical recurrent dynamic models with four different learning methods. The model is composed of two approaches: The first approach introduces a traditional dynamic model that focuses on analyzing the impact of vaccination on the occurrence of an epidemic, and the second approach employs various learning methods to forecast the potential outcomes of an epidemic. Furthermore, our numerical results offer an interesting comparison between the traditional approach and modern learning techniques. Our classic dynamic model is a compartmental model that aims to analyze and forecast the diffusion of epidemics. The model we propose has a recurrent structure with piecewise constant parameters and includes compartments for susceptible, exposed, vaccinated, infected, and recovered individuals. This model can accurately mirror the dynamics of infectious diseases, which enables us to evaluate the impact of restrictive measures on the spread of diseases. We conduct a comprehensive dynamic analysis of our model. Additionally, we suggest an optimal numerical design to determine the parameters of the system. Also, we use regression tree learning, bidirectional long short-term memory, gated recurrent unit, and a combined deep learning method for training and evaluation of an epidemic. In the final section of our paper, we apply these methods to recently published data on COVID-19 in Austria, Brazil, and China from 26 February 2021 to 4 August 2021, which is when vaccination efforts began. To evaluate the numerical results, we utilized various metrics such as RMSE and R-squared. Our findings suggest that the dynamic model is ideal for long-term analysis, data fitting, and identifying parameters that impact epidemics. However, it is not as effective as the supervised learning method for making long-term forecasts. On the other hand, supervised learning techniques, compared to dynamic models, are more effective for predicting the spread of diseases, but not for analyzing the behavior of epidemics.

PMID:38366403 | DOI:10.1103/PhysRevE.109.014212

Nicotine Tob Res. 2024 Feb 15;26(Supplement_1):S43-S48. doi: 10.1093/ntr/ntad189.

ABSTRACT

INTRODUCTION: Instagram is a popular social networking platform for sharing photos with a large proportion of youth and young adult users. We aim to identify key features in anti-vaping Instagram image posts associated with high social media user engagement by artificial intelligence.

AIMS AND METHODS: We collected 8972 anti-vaping Instagram image posts and hand-coded 2200 Instagram images to identify nine image features such as warning signs and person-shown vaping. We utilized a deep-learning model, the OpenAI: contrastive language-image pre-training with ViT-B/32 as the backbone and a 5-fold cross-validation model evaluation, to extract similar features from the Instagram image and further trained logistic regression models for multilabel classification. Latent Dirichlet Allocation model and Valence Aware Dictionary and sEntiment Reasoner were used to extract the topics and sentiment from the captions. Negative binomial regression models were applied to identify features associated with the likes and comments count of posts.

RESULTS: Several features identified in anti-vaping Instagram image posts were significantly associated with high social media user engagement (likes or comments), such as educational warnings and warning signs. Instagram posts with captions about health risks associated with vaping received significantly more likes or comments than those about help quitting smoking or vaping. Compared to the model based on 2200 hand-coded Instagram image posts, more significant features have been identified from 8972 AI-labeled Instagram image posts.

CONCLUSION: Features identified from anti-vaping Instagram image posts will provide a potentially effective way to communicate with the public about the health effects of e-cigarette use.

IMPLICATIONS: Considering the increasing popularity of social media and the current vaping epidemic, especially among youth and young adults, it becomes necessary to understand e-cigarette-related content on social media. Although pro-vaping messages dominate social media, anti-vaping messages are limited and often have low user engagement. Using advanced deep-learning and statistical models, we identified several features in anti-vaping Instagram image posts significantly associated with high user engagement. Our findings provide a potential approach to effectively communicate with the public about the health risks of vaping to protect public health.

PMID:38366336 | DOI:10.1093/ntr/ntad189

J Imaging Inform Med. 2024 Feb 16. doi: 10.1007/s10278-024-01038-5. Online ahead of print.

ABSTRACT

Computed tomography (CT) is the most commonly used diagnostic modality for blunt abdominal trauma (BAT), significantly influencing management approaches. Deep learning models (DLMs) have shown great promise in enhancing various aspects of clinical practice. There is limited literature available on the use of DLMs specifically for trauma image evaluation. In this study, we developed a DLM aimed at detecting solid organ injuries to assist medical professionals in rapidly identifying life-threatening injuries. The study enrolled patients from a single trauma center who received abdominal CT scans between 2008 and 2017. Patients with spleen, liver, or kidney injury were categorized as the solid organ injury group, while others were considered negative cases. Only images acquired from the trauma center were enrolled. A subset of images acquired in the last year was designated as the test set, and the remaining images were utilized to train and validate the detection models. The performance of each model was assessed using metrics such as the area under the receiver operating characteristic curve (AUC), accuracy, sensitivity, specificity, positive predictive value, and negative predictive value based on the best Youden index operating point. The study developed the models using 1302 (87%) scans for training and tested them on 194 (13%) scans. The spleen injury model demonstrated an accuracy of 0.938 and a specificity of 0.952. The accuracy and specificity of the liver injury model were reported as 0.820 and 0.847, respectively. The kidney injury model showed an accuracy of 0.959 and a specificity of 0.989. We developed a DLM that can automate the detection of solid organ injuries by abdominal CT scans with acceptable diagnostic accuracy. It cannot replace the role of clinicians, but we can expect it to be a potential tool to accelerate the process of therapeutic decisions for trauma care.

PMID:38366294 | DOI:10.1007/s10278-024-01038-5

Nat Methods. 2024 Feb 16. doi: 10.1038/s41592-024-02191-z. Online ahead of print.

ABSTRACT

Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of conservation and diversification of cell types. However, interspecies genomic differences limit the joint analysis of cross-species datasets to homologous genes. Here we present SATURN, a deep learning method for learning universal cell embeddings that encodes genes' biological properties using protein language models. By coupling protein embeddings from language models with RNA expression, SATURN integrates datasets profiled from different species regardless of their genomic similarity. SATURN can detect functionally related genes coexpressed across species, redefining differential expression for cross-species analysis. Applying SATURN to three species whole-organism atlases and frog and zebrafish embryogenesis datasets, we show that SATURN can effectively transfer annotations across species, even when they are evolutionarily remote. We also demonstrate that SATURN can be used to find potentially divergent gene functions between glaucoma-associated genes in humans and four other species.

PMID:38366243 | DOI:10.1038/s41592-024-02191-z

Nat Methods. 2024 Feb 16. doi: 10.1038/s41592-024-02171-3. Online ahead of print.

ABSTRACT

Spatial omics technologies can reveal the molecular intricacy of the brain. While mass spectrometry imaging (MSI) provides spatial localization of compounds, comprehensive biochemical profiling at a brain-wide scale in three dimensions by MSI with single-cell resolution has not been achieved. We demonstrate complementary brain-wide and single-cell biochemical mapping using MEISTER, an integrative experimental and computational mass spectrometry (MS) framework. Our framework integrates a deep-learning-based reconstruction that accelerates high-mass-resolving MS by 15-fold, multimodal registration creating three-dimensional (3D) molecular distributions and a data integration method fitting cell-specific mass spectra to 3D datasets. We imaged detailed lipid profiles in tissues with millions of pixels and in large single-cell populations acquired from the rat brain. We identified region-specific lipid contents and cell-specific localizations of lipids depending on both cell subpopulations and anatomical origins of the cells. Our workflow establishes a blueprint for future development of multiscale technologies for biochemical characterization of the brain.

PMID:38366241 | DOI:10.1038/s41592-024-02171-3

Virchows Arch. 2024 Feb 16. doi: 10.1007/s00428-024-03761-4. Online ahead of print.

ABSTRACT

Differentiating BRAF V600E- and RAS-altered encapsulated follicular-patterned thyroid tumors based on morphology remains challenging. This study aimed to validate an 8-score scale nuclear scoring system and investigate the importance of nuclear pseudoinclusions (NPIs) in aiding this differentiation. A cohort of 44 encapsulated follicular-patterned tumors with varying degrees of nuclear atypia and confirmed BRAF V600E or RAS alterations was studied. Nuclear parameters (area, diameter, and optical density) were analyzed using a deep learning model. Twelve pathologists from eight Asian countries visually assessed 22 cases after excluding the cases with any papillae. Eight nuclear features were applied, yielding a semi-quantitative score from 0 to 24. A threshold score of 14 was used to distinguish between RAS- and BRAF V600E-altered tumors. BRAF V600E-altered tumors typically demonstrated higher nuclear scores and notable morphometric alterations. Specifically, the nuclear area and diameter were significantly larger, and nuclear optical density was much lower compared to RAS-altered tumors. Observer accuracy varied, with two pathologists correctly identifying genotype of all cases. Observers were categorized into proficiency groups, with the highest group maintaining consistent accuracy across both evaluation methods. The lower group showed a significant improvement in accuracy upon utilizing the 8-score scale nuclear scoring system, with notably increased sensitivity and negative predictive value in BRAF V600E tumor detection. BRAF V600E-altered tumors had higher median total nuclear scores. Detailed reevaluation revealed NPIs in all BRAF V600E-altered cases, but in only 2 of 14 RAS-altered cases. These results could significantly assist pathologists, particularly those not specializing in thyroid pathology, in making a more accurate diagnosis.

PMID:38366204 | DOI:10.1007/s00428-024-03761-4

Medicine (Baltimore). 2024 Feb 16;103(7):e37150. doi: 10.1097/MD.0000000000037150.

ABSTRACT

BACKGROUND: Deep learning techniques explain the enormous potential of medical image analysis, particularly in digital pathology. Concurrently, molecular markers have gained increasing significance over the past decade in the context of glioma patients, providing novel insights into diagnosis and more personalized treatment options. Deep learning combined with imaging and molecular analysis enables more accurate prognostication of patients, more accurate treatment plan proposals, and accurate biomarker (IDH) prediction for gliomas. This systematic study examines the development of deep learning techniques for IDH prediction using histopathology images, spanning the period from 2019 to 2023.

METHOD: The study adhered to the PRISMA reporting requirements, and databases including PubMed, Google Scholar, Google Search, and preprint repositories (such as arXiv) were systematically queried for pertinent literature spanning the period from 2019 to the 30th of 2023. Search phrases related to deep learning, digital pathology, glioma, and IDH were collaboratively utilized.

RESULTS: Fifteen papers meeting the inclusion criteria were included in the analysis. These criteria specifically encompassed studies utilizing deep learning for the analysis of hematoxylin and eosin images to determine the IDH status in patients with gliomas.

CONCLUSIONS: When predicting the status of IDH, the classifier built on digital pathological images demonstrates exceptional performance. The study's predictive effectiveness is enhanced with the utilization of the appropriate deep learning model. However, external verification is necessary to showcase their resilience and universality. Larger sample sizes and multicenter samples are necessary for more comprehensive research to evaluate performance and confirm clinical advantages.

PMID:38363910 | DOI:10.1097/MD.0000000000037150

PLoS Comput Biol. 2024 Feb 16;20(2):e1011902. doi: 10.1371/journal.pcbi.1011902. Online ahead of print.

ABSTRACT

The pathogenic, tropical Leishmania flagellates belong to an early-branching eukaryotic lineage (Kinetoplastida) with several unique features. Unfortunately, they are poorly understood from a molecular biology perspective, making development of mechanistically novel and selective drugs difficult. Here, we explore three functionally critical targeting short linear motif systems as well as their receptors in depth, using a combination of structural modeling, evolutionary sequence divergence and deep learning. Secretory signal peptides, endoplasmic reticulum (ER) retention motifs (KDEL motifs), and autophagy signals (motifs interacting with ATG8 family members) are ancient and essential components of cellular life. Although expected to be conserved amongst the kinetoplastids, we observe that all three systems show a varying degree of divergence from their better studied equivalents in animals, plants, or fungi. We not only describe their behaviour, but also build models that allow the prediction of localization and potential functions for several uncharacterized Leishmania proteins. The unusually Ala/Val-rich secretory signal peptides, endoplasmic reticulum resident proteins ending in Asp-Leu-COOH and atypical ATG8-like proteins are all unique molecular features of kinetoplastid parasites. Several of their critical protein-protein interactions could serve as targets of selective antimicrobial agents against Leishmaniasis due to their systematic divergence from the host.

PMID:38363808 | DOI:10.1371/journal.pcbi.1011902

Neural Comput. 2024 Feb 16;36(3):475-498. doi: 10.1162/neco_a_01647.

ABSTRACT

Recently, deep learning surrogates and neural operators have shown promise in solving partial differential equations (PDEs). However, they often require a large amount of training data and are limited to bounded domains. In this work, we present a novel physics-informed neural operator method to solve parameterized boundary value problems without labeled data. By reformulating the PDEs into boundary integral equations (BIEs), we can train the operator network solely on the boundary of the domain. This approach reduces the number of required sample points from O(Nd) to O(Nd-1), where d is the domain's dimension, leading to a significant acceleration of the training process. Additionally, our method can handle unbounded problems, which are unattainable for existing physics-informed neural networks (PINNs) and neural operators. Our numerical experiments show the effectiveness of parameterized complex geometries and unbounded problems.

PMID:38363659 | DOI:10.1162/neco_a_01647

Am J Physiol Heart Circ Physiol. 2024 Feb 16. doi: 10.1152/ajpheart.00787.2023. Online ahead of print.

ABSTRACT

CONTEXT: Imaging tools are crucial for studying the vascular network and its barrier function in various physiopathological conditions. Shortwave infrared window (SWIR) optical imaging allows non-invasive, in-depth exploration. We applied SWIR imaging, combined with vessel segmentation and deep learning analyses, to study real-time dextran probe extravasation in mice experiencing intermittent hypoxia-a characteristic of obstructive sleep apnea associated with potential cardiovascular alterations due to early vascular permeability. Evidence for permeability in this context is limited, making our investigation significant.

METHODS: C57Bl/6 mice were exposed to normoxia or intermittent hypoxia for 14 days. Then SWIR imaging between 1250 and 1700 nm was performed on the saphenous artery and vein and on the surrounding tissue after intravenous injection of labeled dextrans of two different sizes (10 or 70 kDa). Post-processing and segmentation of the SWIR images were conducted using deep learning treatment.

RESULTS: We monitored high-resolution signals, distinguishing arteries, veins, and surrounding tissues. In the saphenous artery and vein, post 70kD-dextran injection, tissue/vessel ratio was higher after intermittent hypoxia (IH) than normoxia (N) over 500 seconds (p < 0.05). However, the ratio was similar in N and IH post 10kD-dextran injection.

CONCLUSION: The SWIR imaging technique allows non-invasive real-time monitoring of dextran extravasation in vivo. Dextran-70 extravasation is increased after exposure to IH, suggesting an increased vessel permeability in this mice model of obstructive sleep apnea.

PMID:38363213 | DOI:10.1152/ajpheart.00787.2023

J Magn Reson Imaging. 2024 Feb 16. doi: 10.1002/jmri.29310. Online ahead of print.

NO ABSTRACT

PMID:38363190 | DOI:10.1002/jmri.29310

Front Vet Sci. 2024 Feb 1;11:1357109. doi: 10.3389/fvets.2024.1357109. eCollection 2024.

ABSTRACT

There is a critical need to develop and validate non-invasive animal-based indicators of affective states in livestock species, in order to integrate them into on-farm assessment protocols, potentially via the use of precision livestock farming (PLF) tools. One such promising approach is the use of vocal indicators. The acoustic structure of vocalizations and their functions were extensively studied in important livestock species, such as pigs, horses, poultry, and goats, yet cattle remain understudied in this context to date. Cows were shown to produce two types of vocalizations: low-frequency calls (LF), produced with the mouth closed, or partially closed, for close distance contacts, and open mouth emitted high-frequency calls (HF), produced for long-distance communication, with the latter considered to be largely associated with negative affective states. Moreover, cattle vocalizations were shown to contain information on individuality across a wide range of contexts, both negative and positive. Nowadays, dairy cows are facing a series of negative challenges and stressors in a typical production cycle, making vocalizations during negative affective states of special interest for research. One contribution of this study is providing the largest to date pre-processed (clean from noises) dataset of lactating adult multiparous dairy cows during negative affective states induced by visual isolation challenges. Here, we present two computational frameworks-deep learning based and explainable machine learning based, to classify high and low-frequency cattle calls and individual cow voice recognition. Our models in these two frameworks reached 87.2 and 89.4% accuracy for LF and HF classification, with 68.9 and 72.5% accuracy rates for the cow individual identification, respectively.

PMID:38362300 | PMC:PMC10867142 | DOI:10.3389/fvets.2024.1357109