Sci Adv. 2024 Jun 14;10(24):eadn9420. doi: 10.1126/sciadv.adn9420. Epub 2024 Jun 12.

ABSTRACT

We introduce an information-hiding camera integrated with an electronic decoder that is jointly optimized through deep learning. This system uses a diffractive optical processor, which transforms and hides input images into ordinary-looking patterns that deceive/mislead observers. This information-hiding transformation is valid for infinitely many combinations of secret messages, transformed into ordinary-looking output images through passive light-matter interactions within the diffractive processor. By processing these output patterns, an electronic decoder network accurately reconstructs the original information hidden within the deceptive output. We demonstrated our approach by designing information-hiding diffractive cameras operating under various lighting conditions and noise levels, showing their robustness. We further extended this framework to multispectral operation, allowing the concealment and decoding of multiple images at different wavelengths, performed simultaneously. The feasibility of our framework was also validated experimentally using terahertz radiation. This optical encoder-electronic decoder-based codesign provides a high speed and energy efficient information-hiding camera, offering a powerful solution for visual information security.

PMID:38865455 | DOI:10.1126/sciadv.adn9420

IEEE Trans Pattern Anal Mach Intell. 2024 Jun 12;PP. doi: 10.1109/TPAMI.2024.3413026. Online ahead of print.

ABSTRACT

Graph Convolutional Networks (GCN) have shown outstanding performance in skeleton-based behavior recognition. However, their opacity hampers further development. Researches on the explainability of deep learning have provided solutions to this issue, with Class Activation Map (CAM) algorithms being a class of explainable methods. However, existing CAM algorithms applies to GCN often independently compute the contribution of individual nodes, overlooking the interactions between nodes in the skeleton. Therefore, we propose a game theory based class activation map for GCN (GT-CAM). Firstly, GT-CAM integrates Shapley values with gradient weights to calculate node importance, producing an activation map that highlights the critical role of nodes in decision-making. It also reveals the cooperative dynamics between nodes or local subgraphs for a more comprehensive explanation. Secondly, to reduce the computational burden of Shapley values, we propose a method for calculating Shapley values of node coalitions. Lastly, to evaluate the rationality of coalition partitioning, we propose a rationality evaluation method based on bipartite game interaction and cooperative game theory. Additionally, we introduce an efficient calculation method for the coalition rationality coefficient based on the Monte Carlo method. Experimental results demonstrate that GT-CAM outperforms other competitive interpretation methods in visualization and quantitative analysis.

PMID:38865236 | DOI:10.1109/TPAMI.2024.3413026

IEEE J Biomed Health Inform. 2024 Jun 12;PP. doi: 10.1109/JBHI.2024.3413628. Online ahead of print.

ABSTRACT

Motion mode (M-mode) echocardiography is essential for measuring cardiac dimension and ejection fraction. However, the current diagnosis is time-consuming and suffers from diagnosis accuracy variance. This work resorts to building an automatic scheme through well-designed and well-trained deep learning to conquer the situation. That is, we proposed RAMEM, an automatic scheme of real-time M-mode echocardiography, which contributes three aspects to address the challenges: 1) provide MEIS, the first dataset of M-mode echocardiograms, to enable consistent results and support developing an automatic scheme; For detecting objects accurately in echocardiograms, it requires big receptive field for covering long-range diastole to systole cycle. However, the limited receptive field in the typical backbone of convolutional neural networks (CNN) and the losing information risk in non-local block (NL) equipped CNN risk the accuracy requirement. Therefore, we 2) propose panel attention embedding with updated UPANets V2, a convolutional backbone network, in a real-time instance segmentation (RIS) scheme for boosting big object detection performance; 3) introduce AMEM, an efficient algorithm of automatic M-mode echocardiography measurement, for automatic diagnosis; The experimental results show that RAMEM surpasses existing RIS schemes (CNNs with NL & Transformers as the backbone) in PASCAL 2012 SBD and human performances in MEIS. The implemented code and dataset are available at https://github.com/hanktseng131415go/RAMEM.

PMID:38865231 | DOI:10.1109/JBHI.2024.3413628

IEEE Trans Med Imaging. 2024 Jun 12;PP. doi: 10.1109/TMI.2024.3413537. Online ahead of print.

ABSTRACT

Minimally invasive surgery (MIS) remains technically demanding due to the difficulty of tracking hidden critical structures within the moving anatomy of the patient. In this study, we propose a soft tissue deformation tracking augmented reality (AR) navigation pipeline for laparoscopic surgery of the kidneys. The proposed navigation pipeline addresses two main sub-problems: the initial registration and deformation tracking. Our method utilizes preoperative MR or CT data and binocular laparoscopes without any additional interventional hardware. The initial registration is resolved through a probabilistic rigid registration algorithm and elastic compensation based on dense point cloud reconstruction. For deformation tracking, the sparse feature point displacement vector field continuously provides temporal boundary conditions for the biomechanical model. To enhance the accuracy of the displacement vector field, a novel feature points selection strategy based on deep learning is proposed. Moreover, an ex-vivo experimental method for internal structures error assessment is presented. The ex-vivo experiments indicate an external surface reprojection error of 4.07 ± 2.17mm and a maximum mean absolutely error for internal structures of 2.98mm. In-vivo experiments indicate mean absolutely error of 3.28 ± 0.40mm and 1.90±0.24mm, respectively. The combined qualitative and quantitative findings indicated the potential of our AR-assisted navigation system in improving the clinical application of laparoscopic kidney surgery.

PMID:38865220 | DOI:10.1109/TMI.2024.3413537

Chaos. 2024 Jun 1;34(6):063128. doi: 10.1063/5.0187511.

ABSTRACT

We study the tipping point collective dynamics of an adaptive susceptible-infected-susceptible (SIS) epidemiological network in a data-driven, machine learning-assisted manner. We identify a parameter-dependent effective stochastic differential equation (eSDE) in terms of physically meaningful coarse mean-field variables through a deep-learning ResNet architecture inspired by numerical stochastic integrators. We construct an approximate effective bifurcation diagram based on the identified drift term of the eSDE and contrast it with the mean-field SIS model bifurcation diagram. We observe a subcritical Hopf bifurcation in the evolving network's effective SIS dynamics that causes the tipping point behavior; this takes the form of large amplitude collective oscillations that spontaneously-yet rarely-arise from the neighborhood of a (noisy) stationary state. We study the statistics of these rare events both through repeated brute force simulations and by using established mathematical/computational tools exploiting the right-hand side of the identified SDE. We demonstrate that such a collective SDE can also be identified (and the rare event computations also performed) in terms of data-driven coarse observables, obtained here via manifold learning techniques, in particular, Diffusion Maps. The workflow of our study is straightforwardly applicable to other complex dynamic problems exhibiting tipping point dynamics.

PMID:38865091 | DOI:10.1063/5.0187511

Int J Comput Assist Radiol Surg. 2024 Jun 12. doi: 10.1007/s11548-024-03204-0. Online ahead of print.

ABSTRACT

PURPOSE: Wearable ultrasound devices can be used to continuously monitor muscle activity. One possible application is to provide real-time feedback during physiotherapy, to show a patient whether an exercise is performed correctly. Algorithms which automatically analyze the data can be of importance to overcome the need for manual assessment and annotations and speed up evaluations especially when considering real-time video sequences. They even could be used to present feedback in an understandable manner to patients in a home-use scenario. The following work investigates three deep learning based segmentation approaches for abdominal muscles in ultrasound videos during a segmental stabilizing exercise. The segmentations are used to automatically classify the contraction state of the muscles.

METHODS: The first approach employs a simple 2D network, while the remaining two integrate the time information from the videos either via additional tracking or directly into the network architecture. The contraction state is determined by comparing measures such as muscle thickness and center of mass between rest and exercise. A retrospective analysis is conducted but also a real-time scenario is simulated, where classification is performed during exercise.

RESULTS: Using the proposed segmentation algorithms, 71% of the muscle states are classified correctly in the retrospective analysis in comparison to 90% accuracy with manual reference segmentation. For the real-time approach the majority of given feedback during exercise is correct when the retrospective analysis had come to the correct result, too.

CONCLUSION: Both retrospective and real-time analysis prove to be feasible. While no substantial differences between the algorithms were observed regarding classification, the networks incorporating the time information showed temporally more consistent segmentations. Limitations of the approaches as well as reasons for failing cases in segmentation, classification and real-time assessment are discussed and requirements regarding image quality and hardware design are derived.

PMID:38865060 | DOI:10.1007/s11548-024-03204-0

Vis Comput Ind Biomed Art. 2024 Jun 12;7(1):14. doi: 10.1186/s42492-024-00165-8.

ABSTRACT

Low-dose computed tomography (LDCT) has gained increasing attention owing to its crucial role in reducing radiation exposure in patients. However, LDCT-reconstructed images often suffer from significant noise and artifacts, negatively impacting the radiologists' ability to accurately diagnose. To address this issue, many studies have focused on denoising LDCT images using deep learning (DL) methods. However, these DL-based denoising methods have been hindered by the highly variable feature distribution of LDCT data from different imaging sources, which adversely affects the performance of current denoising models. In this study, we propose a parallel processing model, the multi-encoder deep feature transformation network (MDFTN), which is designed to enhance the performance of LDCT imaging for multisource data. Unlike traditional network structures, which rely on continual learning to process multitask data, the approach can simultaneously handle LDCT images within a unified framework from various imaging sources. The proposed MDFTN consists of multiple encoders and decoders along with a deep feature transformation module (DFTM). During forward propagation in network training, each encoder extracts diverse features from its respective data source in parallel and the DFTM compresses these features into a shared feature space. Subsequently, each decoder performs an inverse operation for multisource loss estimation. Through collaborative training, the proposed MDFTN leverages the complementary advantages of multisource data distribution to enhance its adaptability and generalization. Numerous experiments were conducted on two public datasets and one local dataset, which demonstrated that the proposed network model can simultaneously process multisource data while effectively suppressing noise and preserving fine structures. The source code is available at https://github.com/123456789ey/MDFTN .

PMID:38865022 | DOI:10.1186/s42492-024-00165-8

J Imaging Inform Med. 2024 Jun 12. doi: 10.1007/s10278-024-01160-4. Online ahead of print.

NO ABSTRACT

PMID:38864948 | DOI:10.1007/s10278-024-01160-4

J Imaging Inform Med. 2024 Jun 12. doi: 10.1007/s10278-024-01164-0. Online ahead of print.

ABSTRACT

Life-threatening acute aortic dissection (AD) demands timely diagnosis for effective intervention. To streamline intrahospital workflows, automated detection of AD in abdominal computed tomography (CT) scans seems useful to assist humans. We aimed at creating a robust convolutional neural network (CNN)-based pipeline capable of real-time screening for signs of abdominal AD in CT. In this retrospective study, abdominal CT data from AD patients presenting with AD and from non-AD patients were collected (n 195, AD cases 94, mean age 65.9 years, female ratio 35.8%). A CNN-based algorithm was developed with the goal of enabling a robust, automated, and highly sensitive detection of abdominal AD. Two sets from internal (n = 32, AD cases 16) and external sources (n = 1189, AD cases 100) were procured for validation. The abdominal region was extracted, followed by the automatic isolation of the aorta region of interest (ROI) and highlighting of the membrane via edge extraction, followed by classification of the aortic ROI as dissected/healthy. A fivefold cross-validation was employed on the internal set, and an ensemble of the 5 trained models was used to predict the internal and external validation set. Evaluation metrics included receiver operating characteristic curve (AUC) and balanced accuracy. The AUC, balanced accuracy, and sensitivity scores of the internal dataset were 0.932 (CI 0.891-0.963), 0.860, and 0.885, respectively. For the internal validation dataset, the AUC, balanced accuracy, and sensitivity scores were 0.887 (CI 0.732-0.988), 0.781, and 0.875, respectively. Furthermore, for the external validation dataset, AUC, balanced accuracy, and sensitivity scores were 0.993 (CI 0.918-0.994), 0.933, and 1.000, respectively. The proposed automated pipeline could assist humans in expediting acute aortic dissection management when integrated into clinical workflows.

PMID:38864947 | DOI:10.1007/s10278-024-01164-0

Radiologie (Heidelb). 2024 Jun 12. doi: 10.1007/s00117-024-01325-w. Online ahead of print.

ABSTRACT

CLINICAL/METHODICAL ISSUE: Magnetic resonance imaging (MRI) is a central component of musculoskeletal imaging. However, long image acquisition times can pose practical barriers in clinical practice.

STANDARD RADIOLOGICAL METHODS: MRI is the established modality of choice in the diagnostic workup of injuries and diseases of the musculoskeletal system due to its high spatial resolution, excellent signal-to-noise ratio (SNR), and unparalleled soft tissue contrast.

METHODOLOGICAL INNOVATIONS: Continuous advances in hardware and software technology over the last few decades have enabled four-fold acceleration of 2D turbo-spin-echo (TSE) without compromising image quality or diagnostic performance. The recent clinical introduction of deep learning (DL)-based image reconstruction algorithms helps to minimize further the interdependency between SNR, spatial resolution and image acquisition time and allows the use of higher acceleration factors.

PERFORMANCE: The combined use of advanced acceleration techniques and DL-based image reconstruction holds enormous potential to maximize efficiency, patient comfort, access, and value of musculoskeletal MRI while maintaining excellent diagnostic accuracy.

ACHIEVEMENTS: Accelerated MRI with DL-based image reconstruction has rapidly found its way into clinical practice and proven to be of added value. Furthermore, recent investigations suggest that the potential of this technology does not yet appear to be fully harvested.

PRACTICAL RECOMMENDATIONS: Deep learning-reconstructed fast musculoskeletal MRI examinations can be reliably used for diagnostic work-up and follow-up of musculoskeletal pathologies in clinical practice.

PMID:38864874 | DOI:10.1007/s00117-024-01325-w

Radiol Artif Intell. 2024 Jul;6(4):e240117. doi: 10.1148/ryai.240117.

NO ABSTRACT

PMID:38864744 | DOI:10.1148/ryai.240117

ACS Appl Mater Interfaces. 2024 Jun 12. doi: 10.1021/acsami.4c06122. Online ahead of print.

ABSTRACT

Enhancing the sensitivity of capacitive pressure sensors through microstructure design may compromise the reliability of the device and rely on intricate manufacturing processes. It is an effective way to solve this issue by balancing the intrinsic properties (elastic modulus and dielectric constant) of the dielectric layer materials. Here, we introduce a liquid metal (LM) hybrid elastomer prepared by a chain-extension-free polyurethane (PU) and LM. The synergistic strategies of extender-free and LM doping effectively reduce the elastic modulus (7.6 ± 0.2-2.1 ± 0.3 MPa) and enhance the dielectric constant (5.12-8.17 @1 kHz) of LM hybrid elastomers. Interestingly, the LM hybrid elastomer combines reprocessability, recyclability, and photothermal conversion. The obtained flexible pressure sensor can be used for detecting hand and throat muscle movements, and high-precision speech recognition of seven words has been using a convolutional neural network (CNN) in deep learning. This work provides an idea for designing and manufacturing wearable, recyclable, and intelligent control pressure sensors.

PMID:38864718 | DOI:10.1021/acsami.4c06122

Protein Sci. 2024 Jul;33(7):e5033. doi: 10.1002/pro.5033.

ABSTRACT

In silico validation of de novo designed proteins with deep learning (DL)-based structure prediction algorithms has become mainstream. However, formal evidence of the relationship between a high-quality predicted model and the chance of experimental success is lacking. We used experimentally characterized de novo water-soluble and transmembrane β-barrel designs to show that AlphaFold2 and ESMFold excel at different tasks. ESMFold can efficiently identify designs generated based on high-quality (designable) backbones. However, only AlphaFold2 can predict which sequences have the best chance of experimentally folding among similar designs. We show that ESMFold can generate high-quality structures from just a few predicted contacts and introduce a new approach based on incremental perturbation of the prediction ("in silico melting"), which can reveal differences in the presence of favorable contacts between designs. This study provides a new insight on DL-based structure prediction models explainability and on how they could be leveraged for the design of increasingly complex proteins; in particular membrane proteins which have historically lacked basic in silico validation tools.

PMID:38864690 | DOI:10.1002/pro.5033

Adv Sci (Weinh). 2024 Jun 12:e2307591. doi: 10.1002/advs.202307591. Online ahead of print.

ABSTRACT

Image-based cytometry faces challenges due to technical variations arising from different experimental batches and conditions, such as differences in instrument configurations or image acquisition protocols, impeding genuine biological interpretation of cell morphology. Existing solutions, often necessitating extensive pre-existing data knowledge or control samples across batches, have proved limited, especially with complex cell image data. To overcome this, "Cyto-Morphology Adversarial Distillation" (CytoMAD), a self-supervised multi-task learning strategy that distills biologically relevant cellular morphological information from batch variations, is introduced to enable integrated analysis across multiple data batches without complex data assumptions or extensive manual annotation. Unique to CytoMAD is its "morphology distillation", symbiotically paired with deep-learning image-contrast translation-offering additional interpretable insights into label-free cell morphology. The versatile efficacy of CytoMAD is demonstrated in augmenting the power of biophysical imaging cytometry. It allows integrated label-free classification of human lung cancer cell types and accurately recapitulates their progressive drug responses, even when trained without the drug concentration information. CytoMAD also allows joint analysis of tumor biophysical cellular heterogeneity, linked to epithelial-mesenchymal plasticity, that standard fluorescence markers overlook. CytoMAD can substantiate the wide adoption of biophysical cytometry for cost-effective diagnosis and screening.

PMID:38864546 | DOI:10.1002/advs.202307591

Health Informatics J. 2024 Apr-Jun;30(2):14604582241259328. doi: 10.1177/14604582241259328.

ABSTRACT

OBJECTIVES: In this article, we provide a database of nonproliferative diabetes retinopathy, which focuses on early diabetes retinopathy with hard exudation, and further explore its clinical application in disease recognition.

METHODS: We collect the photos of nonproliferative diabetes retinopathy taken by Optos Panoramic 200 laser scanning ophthalmoscope, filter out the pictures with poor quality, and label the hard exudative lesions in the images under the guidance of professional medical personnel. To validate the effectiveness of the datasets, five deep learning models are used to perform learning predictions on the datasets. Furthermore, we evaluate the performance of the model using evaluation metrics.

RESULTS: Nonproliferative diabetes retinopathy is smaller than proliferative retinopathy and more difficult to identify. The existing segmentation models have poor lesion segmentation performance, while the intersection over union (IOU) value for deep lesion segmentation of models targeting small lesions can reach 66.12%, which is higher than ordinary lesion segmentation models, but there is still a lot of room for improvement.

CONCLUSION: The segmentation of small hard exudative lesions is more challenging than that of large hard exudative lesions. More targeted datasets are needed for model training. Compared with the previous diabetes retina datasets, the NDRD dataset pays more attention to micro lesions.

PMID:38864242 | DOI:10.1177/14604582241259328

Cureus. 2024 May 12;16(5):e60145. doi: 10.7759/cureus.60145. eCollection 2024 May.

ABSTRACT

Chronic kidney disease (CKD) is a progressive condition characterized by gradual loss of kidney function, necessitating timely monitoring and interventions. This systematic review comprehensively evaluates the application of artificial intelligence (AI) and machine learning (ML) techniques for predicting CKD progression. A rigorous literature search identified 13 relevant studies employing diverse AI/ML algorithms, including logistic regression, support vector machines, random forests, neural networks, and deep learning approaches. These studies primarily aimed to predict CKD progression to end-stage renal disease (ESRD) or the need for renal replacement therapy, with some focusing on diabetic kidney disease progression, proteinuria, or estimated glomerular filtration rate (GFR) decline. The findings highlight the promising predictive performance of AI/ML models, with several achieving high accuracy, sensitivity, specificity, and area under the receiver operating characteristic curve scores. Key factors contributing to enhanced prediction included incorporating longitudinal data, baseline characteristics, and specific biomarkers such as estimated GFR, proteinuria, serum albumin, and hemoglobin levels. Integration of these predictive models with electronic health records and clinical decision support systems offers opportunities for timely risk identification, early interventions, and personalized management strategies. While challenges related to data quality, bias, and ethical considerations exist, the reviewed studies underscore the potential of AI/ML techniques to facilitate early detection, risk stratification, and targeted interventions for CKD patients. Ongoing research, external validation, and careful implementation are crucial to leveraging these advanced analytical approaches in clinical practice, ultimately improving outcomes and reducing the burden of CKD.

PMID:38864072 | PMC:PMC11166249 | DOI:10.7759/cureus.60145

Front Neurosci. 2024 May 27;18:1351387. doi: 10.3389/fnins.2024.1351387. eCollection 2024.

ABSTRACT

INTRODUCTION: Multiple sclerosis (MS) and neuromyelitis optic spectrum disorder (NMOSD) are mimic autoimmune diseases of the central nervous system with a very high disability rate. Their clinical symptoms and imaging findings are similar, making it difficult to diagnose and differentiate. Existing research typically employs the T2-weighted fluid-attenuated inversion recovery (T2-FLAIR) MRI imaging technique to focus on a single task in MS and NMOSD lesion segmentation or disease classification, while ignoring the collaboration between the tasks.

METHODS: To make full use of the correlation between lesion segmentation and disease classification tasks of MS and NMOSD, so as to improve the accuracy and speed of the recognition and diagnosis of MS and NMOSD, a joint model is proposed in this study. The joint model primarily comprises three components: an information-sharing subnetwork, a lesion segmentation subnetwork, and a disease classification subnetwork. Among them, the information-sharing subnetwork adopts a dualbranch structure composed of a convolution module and a Swin Transformer module to extract local and global features, respectively. These features are then input into the lesion segmentation subnetwork and disease classification subnetwork to obtain results for both tasks simultaneously. In addition, to further enhance the mutual guidance between the tasks, this study proposes two information interaction methods: a lesion guidance module and a crosstask loss function. Furthermore, the lesion location maps provide interpretability for the diagnosis process of the deep learning model.

RESULTS: The joint model achieved a Dice similarity coefficient (DSC) of 74.87% on the lesion segmentation task and accuracy (ACC) of 92.36% on the disease classification task, demonstrating its superior performance. By setting up ablation experiments, the effectiveness of information sharing and interaction between tasks is verified.

DISCUSSION: The results show that the joint model can effectively improve the performance of the two tasks.

PMID:38863883 | PMC:PMC11166028 | DOI:10.3389/fnins.2024.1351387

Front Immunol. 2024 May 28;15:1407470. doi: 10.3389/fimmu.2024.1407470. eCollection 2024.

ABSTRACT

INTRODUCTION: Somatic hypermutation (SHM) of immunoglobulin variable (V) regions by activation induced deaminase (AID) is essential for robust, long-term humoral immunity against pathogen and vaccine antigens. AID mutates cytosines preferentially within WRCH motifs (where W=A or T, R=A or G and H=A, C or T). However, it has been consistently observed that the mutability of WRCH motifs varies substantially, with large variations in mutation frequency even between multiple occurrences of the same motif within a single V region. This has led to the notion that the immediate sequence context of WRCH motifs contributes to mutability. Recent studies have highlighted the potential role of local DNA sequence features in promoting mutagenesis of AGCT, a commonly mutated WRCH motif. Intriguingly, AGCT motifs closer to 5' ends of V regions, within the framework 1 (FW1) sub-region1, mutate less frequently, suggesting an SHM-suppressing sequence context.

METHODS: Here, we systematically examined the basis of AGCT positional biases in human SHM datasets with DeepSHM, a machine-learning model designed to predict SHM patterns. This was combined with integrated gradients, an interpretability method, to interrogate the basis of DeepSHM predictions.

RESULTS: DeepSHM predicted the observed positional differences in mutation frequencies at AGCT motifs with high accuracy. For the conserved, lowly mutating AGCT motifs in FW1, integrated gradients predicted a large negative contribution of 5'C and 3'G flanking residues, suggesting that a CAGCTG context in this location was suppressive for SHM. CAGCTG is the recognition motif for E-box transcription factors, including E2A, which has been implicated in SHM. Indeed, we found a strong, inverse relationship between E-box motif fidelity and mutation frequency. Moreover, E2A was found to associate with the V region locale in two human B cell lines. Finally, analysis of human SHM datasets revealed that naturally occurring mutations in the 3'G flanking residues, which effectively ablate the E-box motif, were associated with a significantly increased rate of AGCT mutation.

DISCUSSION: Our results suggest an antagonistic relationship between mutation frequency and the binding of E-box factors like E2A at specific AGCT motif contexts and, therefore, highlight a new, suppressive mechanism regulating local SHM patterns in human V regions.

PMID:38863710 | PMC:PMC11165027 | DOI:10.3389/fimmu.2024.1407470

Front Plant Sci. 2024 May 28;15:1367738. doi: 10.3389/fpls.2024.1367738. eCollection 2024.

ABSTRACT

Currently, foliar diseases of chili have significantly impacted both yield and quality. Despite effective advancements in deep learning techniques for the classification of chili leaf diseases, most existing classification models still face challenges in terms of accuracy and practical application in disease identification. Therefore, in this study, an optimized and enhanced convolutional neural network model named MCCM (MCSAM-ConvNeXt-MSFFM) is proposed by introducing ConvNeXt. The model incorporates a Multi-Scale Feature Fusion Module (MSFFM) aimed at better capturing disease features of various sizes and positions within the images. Moreover, adjustments are made to the positioning, activation functions, and normalization operations of the MSFFM module to further optimize the overall model. Additionally, a proposed Mixed Channel Spatial Attention Mechanism (MCSAM) strengthens the correlation between non-local channels and spatial features, enhancing the model's extraction of fundamental characteristics of chili leaf diseases. During the training process, pre-trained weights are obtained from the Plant Village dataset using transfer learning to accelerate the model's convergence. Regarding model evaluation, the MCCM model is compared with existing CNN models (Vgg16, ResNet34, GoogLeNet, MobileNetV2, ShuffleNet, EfficientNetV2, ConvNeXt), and Swin-Transformer. The results demonstrate that the MCCM model achieves average improvements of 3.38%, 2.62%, 2.48%, and 2.53% in accuracy, precision, recall, and F1 score, respectively. Particularly noteworthy is that compared to the original ConvNeXt model, the MCCM model exhibits significant enhancements across all performance metrics. Furthermore, classification experiments conducted on rice and maize disease datasets showcase the MCCM model's strong generalization performance. Finally, in terms of application, a chili leaf disease classification website is successfully developed using the Flask framework. This website accurately identifies uploaded chili leaf disease images, demonstrating the practical utility of the model.

PMID:38863551 | PMC:PMC11165206 | DOI:10.3389/fpls.2024.1367738

Bioinformatics. 2024 Jun 11:btae355. doi: 10.1093/bioinformatics/btae355. Online ahead of print.

ABSTRACT

MOTIVATION: Protein-protein interactions (PPIs) provide the skeleton for signal transduction in the cell. Current PPI measurement techniques do not provide information on their directionality which is critical for elucidating signaling pathways. To date, there are hundreds of thousands of known PPIs in public databases, yet only a small fraction of them have an assigned direction. This information gap calls for computational approaches for inferring the directionality of PPIs, aka network orientation.

RESULTS: In this work we propose a novel deep learning approach for PPI network orientation. Our method first generates a set of proximity scores between a protein interaction and sets of cause and effect proteins using a network propagation procedure. Each of these score sets is fed, one at a time, to a deep set encoder whose outputs are used as features for predicting the interaction's orientation. On a comprehensive data set of oriented protein-protein interactions taken from five different sources, we achieve an area under the precision-recall curve of 0.89-0.92, outperforming previous methods. We further demonstrate the utility of the oriented network in prioritizing cancer driver genes and disease genes.

AVAILABILITY: D'or is implemented in Python and is publicly available at https://github.com/pirakd/DeepOrienter.

PMID:38862241 | DOI:10.1093/bioinformatics/btae355