Ann Transl Med. 2024 Oct 20;12(5):89. doi: 10.21037/atm-24-73. Epub 2024 Oct 12.

ABSTRACT

BACKGROUND: The opaqueness of artificial intelligence (AI) algorithms decision processes limit their application in healthcare. Our objective was to explore discrepancies in heatmaps originated from slightly different retinal images from the same eyes of individuals with diabetes, to gain insights into the deep learning (DL) decision process.

METHODS: Pairs of retinal images from the same eyes of individuals with diabetes, composed of images obtained before and after pupil dilation, underwent automatic analysis by a convolutional neural network for the presence of diabetic retinopathy (DR), output being a score ranging from 0 to 1. Gradient-based Class Activation Maps (GradCam) allowed visualization of activated areas. Pairs of images with discordant DL scores or outputs within the pair were objectively compared to the concordant pairs, regarding the sum of activations of Class Activation Mapping (CAM), the number of activated areas, and DL score differences. Heatmaps of discordant pairs were also qualitatively assessed.

RESULTS: Algorithmic performance for the detection of DR attained 89.8% sensitivity, 96.3% specificity and area under the receiver operating characteristic (ROC) curve of 0.95. Out of 210 comparable pairs of images, 20 eyes and 10 eyes were considered discordant according to DL score difference and regarding DL output, respectively. Comparison of concordant versus discordant groups showed statistically significant differences for all objective variables. Qualitative analysis pointed to subtle differences in image quality within discordant pairs.

CONCLUSIONS: The successfully established relationship among objective parameters extracted from heatmaps and DL output discrepancies reinforces the role of heatmaps for DL explainability, fostering acceptance of DL systems for clinical use.

PMID:39507460 | PMC:PMC11534741 | DOI:10.21037/atm-24-73

Eur J Radiol Open. 2024 Oct 24;13:100606. doi: 10.1016/j.ejro.2024.100606. eCollection 2024 Dec.

ABSTRACT

BACKGROUND: Chest radiographs (CXRs) are widely used to screen for infectious diseases like tuberculosis and COVID-19 among migrants. At such high-volume settings, manual CXR reporting is challenging and integrating artificial intelligence (AI) algorithms into the workflow help to rule out normal findings in minutes, allowing radiologists to focus on abnormal cases.

METHODS: In this post-deployment study, all the CXRs acquired during the visa screening process across 33 centers in United Arab Emirates from January 2021 to June 2022 (18 months) were included. The qXR v2.1 chest X-ray interpretation software was used to classify the scans into normal and abnormal, and its agreement against radiologist was evaluated. Additionally, a digital survey was conducted among 20 healthcare professionals with prior AI experience to understand real-world implementation challenges and impact.

RESULTS: The analysis of 1309,443 CXRs from 1309,431 patients (median age: 35 years; IQR [29-42]; 1030,071 males [78.7 %]) in this study revealed a Negative Predictive Value (NPV) of 99.92 % (95 % CI: 99.92, 99.93), Positive Predictive Value (PPV) of 5.06 % (95 % CI: 4.99, 5.13) and overall percent agreement of the AI with radiologists of 72.90 % (95 % CI: 72.82, 72.98). In the survey, majority (88.2 %) of the radiologists agreed to turnaround time reduction after AI integration, while 82 % suggested that the AI improved their diagnostic accuracy.

DISCUSSION: In contrast with the existing studies, this research uses a substantially large data. A high NPV and satisfactory agreement with human readers indicate that AI can reliably identify normal CXRs, making it suitable for routine applications.

PMID:39507100 | PMC:PMC11539241 | DOI:10.1016/j.ejro.2024.100606

Transl Lung Cancer Res. 2024 Oct 31;13(10):2746-2760. doi: 10.21037/tlcr-24-716. Epub 2024 Oct 17.

ABSTRACT

BACKGROUND: Glycolysis proved to have a prognostic value in lung cancer; however, to identify glycolysis-related genomic markers is expensive and challenging. This study aimed at identifying glycolysis-related computed tomography (CT) radiomics features to develop a deep-learning prognostic model for non-small cell lung cancer (NSCLC).

METHODS: The study included 274 NSCLC patients from cohorts of The Second Affiliated Hospital of Soochow University (SZ; n=64), the Cancer Genome Atlas (TCGA)-NSCLC dataset (n=74), and the Gene Expression Omnibus dataset (n=136). Initially, the glycolysis enrichment scores were evaluated using a single-sample gene set enrichment analysis, and the cut-off values were optimized to investigate the prognostic potential of glycolysis genes. Radiomic features were then extracted using LIFEx software. The least absolute reduction and selection operator (LASSO) algorithm was employed to determine the glycolytic CT radiomics features. A deep-learning prognostic model was constructed by integrating CT radiomics and clinical features. The biological functions of the model were analyzed by incorporating RNA sequencing data.

RESULTS: Kaplan-Meier curves indicated that elevated glycolysis levels were associated with poorer survival outcomes. The LASSO algorithm identified 11 radiomic features that were then selected for inclusion in the deep-learning model. They have shown significant discrimination capability in assessing glycolysis status, achieving an area under the curve value of 0.8442. The glycolysis-based radiomics deep-learning model was named the DeepGR model. This model was able to effectively predict the clinical outcomes of NSCLC patients with AUCs of 0.8760 and 0.8259 in the SZ and TCGA cohorts, respectively. High-risk DeepGR scores were strongly associated with poor overall survival, resting memory CD4+ T cells, and a high response to programmed cell death protein 1 immunotherapy.

CONCLUSIONS: The DeepGR model effectively predicted the prognosis of NSCLC patients.

PMID:39507025 | PMC:PMC11535831 | DOI:10.21037/tlcr-24-716

Heliyon. 2024 Oct 9;10(20):e38915. doi: 10.1016/j.heliyon.2024.e38915. eCollection 2024 Oct 30.

ABSTRACT

This study delves into the intricate interplay between gender stereotypes and financial reporting through an aspect-level sentiment analysis approach. Leveraging Big Data comprising 129,251 human face images extracted from 2085 financial reports in Chile, and employing Deep Learning techniques, we uncover the underlying factors influencing the representation of women in financial reports. Our findings reveal that gender stereotypes, combined with external economic factors, significantly shape the portrayal of women in financial reports, overshadowing intentional efforts by companies to influence stakeholder perceptions of financial performance. Notably, economic expansion periods correlate with a decline in women's representation, while economic instability amplifies their portrayal. Furthermore, the financial inclusion of women positively correlates with their presence in financial report images. Our results underscore a bias in image selection within financial reports, diverging from the neutrality principles advocated by the International Accounting Standards Board (IASB). This pioneering study, combining Big Data and Deep Learning, contributes to gender stereotype literature, financial report soft information research, and business impression management research.

PMID:39506953 | PMC:PMC11538733 | DOI:10.1016/j.heliyon.2024.e38915

ACS Appl Mater Interfaces. 2024 Nov 7. doi: 10.1021/acsami.4c13193. Online ahead of print.

ABSTRACT

Classifications of fluids using miniaturized sensors are of substantial importance for various fields of application. Modified with functional nanomaterials, a moisture-enabled electricity generation (MEG) device can execute a dual-purpose operation as both a self-powered framework and a fluid detection platform. In this study, a novel intelligent self-sustained sensing approach was implemented by integrating MEG with deep learning in microfluidics. Following a multilayer design, the MEG device including three individual units for power generation/fluid classification was fabricated in this study by using nonwoven fabrics, hydroxylated carbon nanotubes, poly(vinyl alcohol)-mixed gels, and indium tin bismuth liquid alloy. A composite configuration utilizing hydrophobic microfluidic channels and hydrophilic porous substrates was conducive to self-regulation of the on-chip flow. As a generator, the MEG device was capable of maintaining a continuous and stable power output for at least 6 h. As a sensor, the on-chip units synchronously measured the voltage (V), current (C), and resistance (R) signals as functions of time, whose transitions were completed using relays. These signals can serve as straightforward indicators of a fluid presence, such as the distinctive "fingerprint". After normalization and Fourier transform of raw V/C/R signals, a lightweight deep learning model (wide-kernel deep convolutional neural network, WDCNN) was employed for classifying pure water, kiwifruit, clementine, and lemon juices. In particular, the accuracy of the sample distinction using the WDCNN model was 100% within 15 s. The proposed integration of MEG, microfluidics, and deep learning provides a novel paradigm for the development of sustainable intelligent environmental perception, as well as new prospects for innovations in analytical science and smart instruments.

PMID:39506898 | DOI:10.1021/acsami.4c13193

Anal Chem. 2024 Nov 7. doi: 10.1021/acs.analchem.4c04479. Online ahead of print.

ABSTRACT

In photoacoustic spectroscopy based multicomponent gas analysis, the overlap of the absorption spectra among different gases can affect the measurement accuracy of gas concentrations. We report a multicomponent gas analysis method based on empirical modal decomposition (EMD), convolutional neural networks (CNN), and long short-term memory (LSTM) networks that can extract the exact concentrations of mixed gases from the overlapping wavelength-modulated spectroscopy with second harmonic (WMS-2f) detection. The WMS-2f signals of 25 different concentration combinations of acetylene-ammonia mixtures are detected using a single distributed feedback laser (DFB) at 1531.5 nm. The acetylene concentrations range from 2.5 to 7.5 ppm and the ammonia concentrations from 12.5 to 37.5 ppm. The data set is enhanced by cyclic shifting and adding Gaussian noise. The classification accuracy of the test set reaches 99.89% after tuning. The mean absolute errors of the five additional sets of data measured under different conditions are 0.092 ppm for acetylene and 1.902 ppm for ammonia, within the above concentration ranges.

PMID:39506893 | DOI:10.1021/acs.analchem.4c04479

J Ovarian Res. 2024 Nov 6;17(1):219. doi: 10.1186/s13048-024-01544-8.

ABSTRACT

OBJECTIVES: The study aimed to compare the diagnostic efficacy of the machine learning models with expert subjective assessment (SA) in assessing the malignancy risk of ovarian tumors using transvaginal ultrasound (TVUS).

METHODS: The retrospective single-center diagnostic study included 1555 consecutive patients from January 2019 to May 2021. Using this dataset, Residual Network(ResNet), Densely Connected Convolutional Network(DenseNet), Vision Transformer(ViT), and Swin Transformer models were established and evaluated separately or combined with Cancer antigen 125 (CA 125). The diagnostic performance was then compared with SA.

RESULTS: Of the 1555 patients, 76.9% were benign, while 23.1% were malignant (including borderline). When differentiating the malignant from ovarian tumors, the SA had an AUC of 0.97 (95% CI, 0.93-0.99), sensitivity of 87.2%, and specificity of 98.4%. Except for Vision Transformer, other machine learning models had diagnostic performance comparable to that of the expert. The DenseNet model had an AUC of 0.91 (95% CI, 0.86-0.95), sensitivity of 84.6%, and specificity of 95.1%. The ResNet50 model had an AUC of 0.91 (0.85-0.95). The Swin Transformer model had an AUC of 0.92 (0.87-0.96), sensitivity of 87.2%, and specificity of 94.3%. There was a statistically significant difference between the Vision Transformer and SA, and between the Vision Transformer and Swin Transformer models (AUC: 0.87 vs. 0.97, P = 0.01; AUC: 0.87 vs. 0.92, P = 0.04). Adding CA125 did not improve the diagnostic performance of the models in distinguishing benign and malignant ovarian tumors.

CONCLUSION: The deep learning model of TVUS can be used in ovarian cancer evaluation, and its diagnostic performance is comparable to that of expert assessment.

PMID:39506832 | DOI:10.1186/s13048-024-01544-8

BMC Bioinformatics. 2024 Nov 6;25(1):348. doi: 10.1186/s12859-024-05961-w.

ABSTRACT

BACKGROUND: Antibodies play a crucial role in disease treatment, leveraging their ability to selectively interact with the specific antigen. However, screening antibody gene sequences for target antigens via biological experiments is extremely time-consuming and labor-intensive. Several computational methods have been developed to predict antibody-antigen interaction while suffering from the lack of characterizing the underlying structure of the antibody.

RESULTS: Beneficial from the recent breakthroughs in deep learning for antibody structure prediction, we propose a novel neural network architecture to predict antibody-antigen interaction. We first introduce AbAgIPA: an antibody structure prediction network to obtain the antibody backbone structure, where the structural features of antibodies and antigens are encoded into representation vectors according to the amino acid physicochemical features and Invariant Point Attention (IPA) computation methods. Finally, the antibody-antigen interaction is predicted by global max pooling, feature concatenation, and a fully connected layer. We evaluated our method on antigen diversity and antigen-specific antibody-antigen interaction datasets. Additionally, our model exhibits a commendable level of interpretability, essential for understanding underlying interaction mechanisms.

CONCLUSIONS: Quantitative experimental results demonstrate that the new neural network architecture significantly outperforms the best sequence-based methods as well as the methods based on residue contact maps and graph convolution networks (GCNs). The source code is freely available on GitHub at https://github.com/gmthu66/AbAgIPA .

PMID:39506679 | DOI:10.1186/s12859-024-05961-w

Neuropsychopharmacology. 2024 Nov 6. doi: 10.1038/s41386-024-02021-y. Online ahead of print.

ABSTRACT

Brain alterations associated with illness severity in schizophrenia remain poorly understood. Establishing linkages between imaging biomarkers and symptom expression may enhance mechanistic understanding of acute psychotic illness. Constructing models using MRI and clinical features together to maximize model validity may be particularly useful for these purposes. A multi-task deep learning model for standard case/control recognition incorporated with psychosis symptom severity regression was constructed with anatomic MRI collected from 286 patients with drug-naïve first-episode schizophrenia and 330 healthy controls from two datasets, and validated with an independent dataset including 40 first-episode schizophrenia. To evaluate the contribution of regression to the case/control recognition, a single-task classification model was constructed. Performance of unprocessed anatomical images and of predefined imaging features obtained using voxel-based morphometry (VBM) and surface-based morphometry (SBM), were examined and compared. Brain regions contributing to the symptom severity regression and illness identification were identified. Models developed with unprocessed images achieved greater group separation than either VBM or SBM measurements, differentiating schizophrenia patients from healthy controls with a balanced accuracy of 83.0% with sensitivity = 76.1% and specificity = 89.0%. The multi-task model also showed superior performance to single-task classification model without considering clinical symptoms. These findings showed high replication in the site-split validation and external validation analyses. Measurements in parietal, occipital and medial frontal cortex and bilateral cerebellum had the greatest contribution to the multi-task model. Incorporating illness severity regression in pattern recognition algorithms, our study developed an MRI-based model that was of high diagnostic value in acutely ill schizophrenia patients, highlighting clinical relevance of the model.

PMID:39506100 | DOI:10.1038/s41386-024-02021-y

Nat Comput Sci. 2024 Nov 6. doi: 10.1038/s43588-024-00720-6. Online ahead of print.

ABSTRACT

RNAs represent a class of programmable biomolecules capable of performing diverse biological functions. Recent studies have developed accurate RNA three-dimensional structure prediction methods, which may enable new RNAs to be designed in a structure-guided manner. Here, we develop a structure-to-sequence deep learning platform for the de novo generative design of RNA aptamers. We show that our approach can design RNA aptamers that are predicted to be structurally similar, yet sequence dissimilar, to known light-up aptamers that fluoresce in the presence of small molecules. We experimentally validate several generated RNA aptamers to have fluorescent activity, show that these aptamers can be optimized for activity in silico, and find that they exhibit a mechanism of fluorescence similar to that of known light-up aptamers. Our results demonstrate how structural predictions can guide the targeted and resource-efficient design of new RNA sequences.

PMID:39506080 | DOI:10.1038/s43588-024-00720-6

Sci Rep. 2024 Nov 6;14(1):27000. doi: 10.1038/s41598-024-78557-2.

ABSTRACT

Traditional English corpora mainly collect information from a single modality, but lack information from multimodal information, resulting in low quality of corpus information and certain problems with recognition accuracy. To solve the above problems, this paper proposes to introduce depth information into multimodal corpora, and studies the construction method of English multimodal corpora that integrates electronic images and depth information, as well as the speech recognition method of the corpus. The multimodal fusion strategy adopted integrates speech signals and image information, including key visual information such as the speaker's lip movements and facial expressions, and uses deep learning technology to mine acoustic and visual features. The acoustic model in the Kaldi toolkit is used for experimental research.Through experimental research, the following conclusions were drawn: Under 15-dimensional lip features, the accuracy of corpus A under monophone model was 2.4% higher than that of corpus B under monophone model when the SNR (signal-to-noise ratio) was 10dB, and the accuracy of corpus A under the triphone model at the signal-to-noise ratio of 10dB was 1.7% higher than that of corpus B under the triphone model at the signal-to-noise ratio of 10dB. Under the 32-dimensional lip features, the speech recognition effect of corpus A under the monophone model at the SNR of 10dB was 1.4% higher than that of corpus B under the monophone model at the SNR of 10dB, and the accuracy of corpus A under the triphone model at the SNR of 10dB was 2.6% higher than that of corpus B under the triphone model at the SNR of 10dB. The English multimodal corpus with image and depth information has a high accuracy, and the depth information helps to improve the accuracy of the corpus.

PMID:39506055 | DOI:10.1038/s41598-024-78557-2

Sci Rep. 2024 Nov 6;14(1):26878. doi: 10.1038/s41598-024-78081-3.

ABSTRACT

It aimed to analyze the value of deep learning algorithm combined with magnetic resonance imaging (MRI) in the risk diagnosis and prognosis of endometrial cancer (EC). Based on the deep learning convolutional neural network (CNN) architecture residual network with 101 layers (ResNet-101), spatial attention and channel attention modules were introduced to optimize the model. A retrospective collection of MRI image data from 210 EC patients was used for model segmentation and reconstruction, with 140 cases as the test set and 70 cases as the validation set. The performance was compared with traditional ResNet-101 model, ResNet-101 model based on spatial attention mechanism (SA-ResNet-101), and ResNet-101 model based on channel attention mechanism (CA-ResNet-101), using accuracy (AC), precision (PR), recall (RE), and F1 score as evaluation metrics. Among the 70 cases in the validation set, there were 45 cases of low-risk EC and 25 cases of high-risk EC. Using ROC curve analysis, it was found that the area under the curve (AUC) for the diagnosis of high-risk EC of the proposed model in this article (0.918) was visibly larger as against traditional ResNet-101 (0.613), SA-ResNet-101 (0.760), and CA-ResNet-101 models (0.758). The AC, PR, RE, and F1 values of the proposed model for the diagnosis of EC risk were visibly higher (P < 0.05). In the validation set, postoperative recurrence occurred in 13 cases and did not occur in 57 cases. Using ROC curve analysis, it was found that the AUC for postoperative recurrence prediction of the patients by the proposed model (0.926) was visibly larger as against traditional ResNet-101 (0.620), SA-ResNet-101 (0.729), and CA-ResNet-101 models (0.767). The AC, PR, RE, and F1 values of the proposed model for postoperative recurrence prediction were visibly higher (P < 0.05). The proposed model in this article, assisted by MRI, presented superior performance in diagnosing high-risk EC patients, with higher sensitivity (Sen) and specificity (Spe), and also demonstrated excellent predictive AC in postoperative recurrence prediction.

PMID:39506051 | DOI:10.1038/s41598-024-78081-3

Sci Rep. 2024 Nov 6;14(1):26993. doi: 10.1038/s41598-024-78041-x.

ABSTRACT

Assessing street walkability is a critical agenda in urban planning and multidisciplinary research, as it facilitates public health, community cohesion, and urban sustainability. Existing evaluation systems primarily focus on objective measurements, often neglecting subjective assessments and the diverse walking needs influenced by different urban spatial elements. This study addresses these gaps by constructing a comprehensive evaluation framework that integrates both subjective and objective dimensions, combining three neighbourhood indicators: Macro-Scale Index, Micro-Scale Index, and Street Walking Preferences Index. A normalization weighting method synthesizes these indicators into a comprehensive index. We applied this framework to assess the street environment within Beijing's Fifth Ring Road. The empirical results demonstrate that: (1) The framework reliably reflects the distribution of walkability. (2) The three indicators show both similarities and differences, underscoring the need to consider the distinct roles of community and street-level elements and the interaction between subjective and objective dimensions. (3) In high-density cities with ring-road development patterns, the Macro-Scale Index closely aligns with the Comprehensive Index, demonstrating its accuracy in reflecting walkability. The proposed framework and findings offer new insights for street walkability research and theoretical support for developing more inclusive, sustainable and walkable cities.

PMID:39506013 | DOI:10.1038/s41598-024-78041-x

Sci Rep. 2024 Nov 6;14(1):26903. doi: 10.1038/s41598-024-77585-2.

ABSTRACT

Early detection and treatment of skin cancer are important for patient recovery and survival. Dermoscopy images can help clinicians for timely identification of cancer, but manual diagnosis is time-consuming, costly, and prone to human error. To conduct this, an innovative deep learning-based approach has been proposed for automatic melanoma detection. The proposed method involves preprocessing dermoscopy images to remove artifacts, enhance contrast, and cancel noise, followed by feeding them into an optimized Convolutional Neural Network (CNN). The CNN is trained using an innovative metaheuristic called the Improved Chameleon Swarm Algorithm (CSA) to optimize its performance. The approach has been validated using the SIIM-ISIC Melanoma dataset and the results have been confirmed through rigorous evaluation metrics. Simulation results demonstrate the efficacy of the proposed method in accurately diagnosing melanoma from dermoscopy images by highlighting its potential as a valuable tool for clinicians in early cancer detection.

PMID:39505992 | DOI:10.1038/s41598-024-77585-2

Sci Rep. 2024 Nov 6;14(1):26937. doi: 10.1038/s41598-024-78424-0.

ABSTRACT

Radiotherapy has been demonstrated to be one of the most significant treatments for cervical cancer, during which accurate and efficient delineation of target volumes is critical. To alleviate the data demand of deep learning and promote the establishment and promotion of auto-segmentation models in small and medium-sized oncology departments and single centres, we proposed an auto-segmentation algorithm to determine the cervical cancer target volume in small samples based on multi-decoder and semi-supervised learning (MDSSL), and we evaluated the accuracy via an independent test cohort. In this study, we retrospectively collected computed tomography (CT) datasets from 71 pelvic cervical cancer patients, and a 3:4 ratio was used for the training and testing sets. The clinical target volumes (CTVs) of the primary tumour area (CTV1) and pelvic lymph drainage area (CTV2) were delineated. For definitive radiotherapy (dRT), the primary gross target volume (GTVp) was simultaneously delineated. According to the data characteristics for small samples, the MDSSL network structure based on 3D U-Net was established to train the model by combining clinical anatomical information, which was compared with other segmentation methods, including supervised learning (SL) and transfer learning (TL). The dice similarity coefficient (DSC), 95% Hausdorff distance (HD95) and average surface distance (ASD) were used to evaluate the segmentation performance. The ability of the segmentation algorithm to improve the efficiency of online adaptive radiation therapy (ART) was assessed via geometric indicators and a subjective evaluation of radiation oncologists (ROs) in prospective clinical applications. Compared with the SL model and TL model, the proposed MDSSL model displayed the best DSC, HD95 and ASD overall, especially for the GTVp of dRT. We calculated the above geometric indicators in the range of the ground truth (head-foot direction). In the test set, the DSC, HD95 and ASD of the MDSSL model were 0.80/5.85 mm/0.95 mm for CTV1 of post-operative radiotherapy (pRT), 0.84/ 4.88 mm/0.73 mm for CTV2 of pRT, 0.84/6.58 mm/0.89 mm for GTVp of dRT, 0.85/5.36 mm/1.35 mm for CTV1 of dRT, and 0.84/4.09 mm/0.73 mm for CTV2 of dRT, respectively. In a prospective clinical study of online ART, the target volume modification time (MTime) was 3-5 min for dRT and 2-4 min for pRT, and the main duration of CTV1 modification was approximately 2 min. The introduction of the MDSSL method successfully improved the accuracy of auto-segmentation for the cervical cancer target volume in small samples, showed good consistency with RO delineation and satisfied clinical requirements. In this prospective online ART study, the application of the segmentation model was demonstrated to be useful for reducing the target volume delineation time and improving the efficiency of the online ART workflow, which can contribute to the development and promotion of cervical cancer online ART.

PMID:39505991 | DOI:10.1038/s41598-024-78424-0

Sci Rep. 2024 Nov 6;14(1):26920. doi: 10.1038/s41598-024-76445-3.

ABSTRACT

Our previous research papers have shown the potential of deep-learning models for real-time detection and control of porosity defects in 3D printing, specifically in the laser powder bed fusion (LPBF) process. Extending these models to identify other defects like surface deformation poses a challenge due to the scarcity of available data. This study introduces the use of Transfer Learning (TL) to train models on limited data for high accuracy in detecting surface deformations, marking the first attempt to apply a model trained on one defect type to another. Our approach demonstrates the power of transfer learning in adapting a model known for porosity detection in LPBF to identify surface deformations with high accuracy (94%), matching the performance of the best existing models but with significantly less complexity. This results in faster training and evaluation, ideal for real-time systems with limited computing capabilities. We further employed Gradient-weighted Class Activation Mapping (Grad-CAM) to visualize the model's decision-making, highlighting the areas influencing defect detection. This step is vital for developing a trustworthy model, showcasing the effectiveness of our approach in broadening the model's applicability while ensuring reliability and efficiency.

PMID:39505970 | DOI:10.1038/s41598-024-76445-3

Sci Rep. 2024 Nov 6;14(1):26970. doi: 10.1038/s41598-024-78040-y.

ABSTRACT

The axillary lymph node status remains an important prognostic factor in breast cancer, and nodal staging using sentinel lymph node biopsy (SLNB) is routine. Randomized clinical trials provide evidence supporting de-escalation of axillary surgery and omission of SLNB in patients at low risk. However, identifying sentinel lymph node macrometastases (macro-SLNMs) is crucial for planning treatment tailored to the individual patient. This study is the first to explore the capacity of deep learning (DL) models to identify macro-SLNMs based on preoperative clinicopathological characteristics. We trained and validated five multivariable models using a population-based cohort of 18,185 patients. DL models outperform logistic regression, with Transformer showing the strongest results, under the constraint that the sensitivity is no less than 90%, reflecting the sensitivity of SLNB. This highlights the feasibility of noninvasive macro-SLNM prediction using DL. Feature importance analysis revealed that patients with similar characteristics exhibited different nodal status predictions, indicating the need for additional predictors for further improvement.

PMID:39505964 | DOI:10.1038/s41598-024-78040-y

Sci Rep. 2024 Nov 6;14(1):26919. doi: 10.1038/s41598-024-78028-8.

ABSTRACT

Cardiovascular diseases are a cause of death making it crucial to accurately diagnose them. Electrocardiography plays a role in detecting heart issues such as heart attacks, bundle branch blocks and irregular heart rhythms. Manual analysis of ECGs is prone to mistakes and time consuming, underscoring the importance of automated methods. This study uses AI models like AlexNet and a dual branch model for categorizing ECG signals from the PTB Diagnostic ECG Database. AlexNet achieved a validation accuracy of 98.64% and a test set accuracy of 99% while the dual branch fusion network model achieved a test set accuracy of 99%. Data preprocessing involved standardizing, balancing and reshaping ECG signals. These models exhibited precision, sensitivity and specificity. In comparison to state of the arts' models such as Hybrid AlexNet SVM and DCNN LSTM our proposed models displayed performance. The high accuracy rates of 99% underscore their potential for ECG classification. These results validate the advantages of incorporating learning models into setups for automated ECG analysis providing adaptable solutions for various healthcare settings including rural areas.

PMID:39505940 | DOI:10.1038/s41598-024-78028-8

Brief Bioinform. 2024 Sep 23;25(6):bbae550. doi: 10.1093/bib/bbae550.

ABSTRACT

Increasing studies have revealed the critical roles of human microbiome in a wide variety of disorders. Identification of disease-associated microbes might improve our knowledge and understanding of disease pathogenesis and treatment. Computational prediction of microbe-disease associations would provide helpful guidance for further biomedical screening, which has received lots of research interest in bioinformatics. In this study, a deep learning-based computational approach entitled SGJMDA is presented for predicting microbe-disease associations. Specifically, SGJMDA first fuses multiple similarities of microbes and diseases using a nonlinear strategy, and extracts feature information from homogeneous networks composed of the fused similarities via a graph convolution network. Second, a heterogeneous microbe-disease network is built to further capture the structural information of microbes and diseases by employing multi-neighborhood graph convolution network and jumping knowledge network. Finally, potential microbe-disease associations are inferred through computing the linear correlation coefficients of their embeddings. Results from cross-validation experiments show that SGJMDA outperforms 6 state-of-the-art computational methods. Furthermore, we carry out case studies on three important diseases using SGJMDA, in which 19, 20, and 11 predictions out of their top 20 results are successfully checked by the latest databases, respectively. The excellent performance of SGJMDA suggests that it could be a valuable and promising tool for inferring disease-associated microbes.

PMID:39504483 | DOI:10.1093/bib/bbae550

Brief Bioinform. 2024 Sep 23;25(6):bbae552. doi: 10.1093/bib/bbae552.

ABSTRACT

The accurate prediction of peptide-major histocompatibility complex (MHC) class I binding probabilities is a critical endeavor in immunoinformatics, with broad implications for vaccine development and immunotherapies. While recent deep neural network based approaches have showcased promise in peptide-MHC (pMHC) prediction, they have two shortcomings: (i) they rely on hand-crafted pseudo-sequence extraction, (ii) they do not generalize well to different datasets, which limits the practicality of these approaches. While existing methods rely on a 34 amino acid pseudo-sequence, our findings uncover the involvement of 147 positions in direct interactions between MHC and peptide. We further show that neural architectures can learn the intricacies of pMHC binding using even full sequences. To this end, we present PerceiverpMHC that is able to learn accurate representations on full-sequences by leveraging efficient transformer based architectures. Additionally, we propose IMGT/RobustpMHC that harnesses the potential of unlabeled data in improving the robustness of pMHC binding predictions through a self-supervised learning strategy. We extensively evaluate RobustpMHC on eight different datasets and showcase an overall improvement of over 6% in binding prediction accuracy compared to state-of-the-art approaches. We compile CrystalIMGT, a crystallography-verified dataset presenting a challenge to existing approaches due to significantly different pMHC distributions. Finally, to mitigate this distribution gap, we further develop a transfer learning pipeline.

PMID:39504482 | DOI:10.1093/bib/bbae552