IEEE Int Conf Telecommun Photonics. 2023 Dec;2023. doi: 10.1109/ictp60248.2023.10490723. Epub 2024 Apr 11.

ABSTRACT

Machine learning applications are widespread due to straightforward supervised learning of known data labels. Many data samples in real-world scenarios, including medicine, are unlabeled because data annotation can be time-consuming and error-prone. The application and evaluation of unsupervised clustering methods are not trivial and are limited to traditional methods (e.g., k-means) when clinicians demand deeper insights into patient data beyond classification accuracy. The contribution of this paper is three-fold: 1) to introduce a patient stratification strategy based on a clinical variable instead of a diagnostic label, 2) to evaluate clustering performance using within-cluster homogeneity and between-cluster statistical difference, and 3) to compare widely used traditional clustering algorithms (e.g., k-means) with a state-of-the-art deep learning solution for clustering tabular data. The deep clustering method achieves superior within-cluster homogeneity and between-cluster separation compared to k-means and identifies three statistically distinct and clinically interpretable high blood pressure patient clusters. The proposed clustering strategy and evaluation metrics will facilitate the stratification of large patient cohorts in health science research without requiring explicit diagnostic labels.

PMID:39027675 | PMC:PMC11255553 | DOI:10.1109/ictp60248.2023.10490723

Comput Struct Biotechnol J. 2024 Jun 20;23:2648-2660. doi: 10.1016/j.csbj.2024.06.016. eCollection 2024 Dec.

ABSTRACT

Therapeutic antibodies are an important class of biopharmaceuticals. With the rapid development of deep learning methods and the increasing amount of antibody data, antibody generative models have made great progress recently. They aim to solve the antibody space searching problems and are widely incorporated into the antibody development process. Therefore, a comprehensive introduction to the development methods in this field is imperative. Here, we collected 34 representative antibody generative models published recently and all generative models can be divided into three categories: sequence-generating models, structure-generating models, and hybrid models, based on their principles and algorithms. We further studied their performance and contributions to antibody sequence prediction, structure optimization, and affinity enhancement. Our manuscript will provide a comprehensive overview of the status of antibody generative models and also offer guidance for selecting different approaches.

PMID:39027650 | PMC:PMC11254834 | DOI:10.1016/j.csbj.2024.06.016

Bioinform Adv. 2024 Apr 24;4(1):vbae060. doi: 10.1093/bioadv/vbae060. eCollection 2024.

ABSTRACT

MOTIVATION: Many diseases are complex heterogeneous conditions that affect multiple organs in the body and depend on the interplay between several factors that include molecular and environmental factors, requiring a holistic approach to better understand disease pathobiology. Most existing methods for integrating data from multiple sources and classifying individuals into one of multiple classes or disease groups have mainly focused on linear relationships despite the complexity of these relationships. On the other hand, methods for nonlinear association and classification studies are limited in their ability to identify variables to aid in our understanding of the complexity of the disease or can be applied to only two data types.

RESULTS: We propose Deep Integrative Discriminant Analysis (IDA), a deep learning method to learn complex nonlinear transformations of two or more views such that resulting projections have maximum association and maximum separation. Further, we propose a feature ranking approach based on ensemble learning for interpretable results. We test Deep IDA on both simulated data and two large real-world datasets, including RNA sequencing, metabolomics, and proteomics data pertaining to COVID-19 severity. We identified signatures that better discriminated COVID-19 patient groups, and related to neurological conditions, cancer, and metabolic diseases, corroborating current research findings and heightening the need to study the post sequelae effects of COVID-19 to devise effective treatments and to improve patient care.

AVAILABILITY AND IMPLEMENTATION: Our algorithms are implemented in PyTorch and available at: https://github.com/JiuzhouW/DeepIDA.

PMID:39027641 | PMC:PMC11256945 | DOI:10.1093/bioadv/vbae060

Bioinform Adv. 2024 May 8;4(1):vbae066. doi: 10.1093/bioadv/vbae066. eCollection 2024.

ABSTRACT

SUMMARY: The increasing number of publicly available bacterial gene expression data sets provides an unprecedented resource for the study of gene regulation in diverse conditions, but emphasizes the need for self-supervised methods for the automated generation of new hypotheses. One approach for inferring coordinated regulation from bacterial expression data is through neural networks known as denoising autoencoders (DAEs) which encode large datasets in a reduced bottleneck layer. We have generalized this application of DAEs to include deep networks and explore the effects of network architecture on gene set inference using deep learning. We developed a DAE-based pipeline to extract gene sets from transcriptomic data in Escherichia coli, validate our method by comparing inferred gene sets with known pathways, and have used this pipeline to explore how the choice of network architecture impacts gene set recovery. We find that increasing network depth leads the DAEs to explain gene expression in terms of fewer, more concisely defined gene sets, and that adjusting the width results in a tradeoff between generalizability and biological inference. Finally, leveraging our understanding of the impact of DAE architecture, we apply our pipeline to an independent uropathogenic E.coli dataset to identify genes uniquely induced during human colonization.

AVAILABILITY AND IMPLEMENTATION: https://github.com/BarquistLab/DAE_architecture_exploration.

PMID:39027639 | PMC:PMC11256956 | DOI:10.1093/bioadv/vbae066

Heliyon. 2024 Jun 19;10(13):e33108. doi: 10.1016/j.heliyon.2024.e33108. eCollection 2024 Jul 15.

ABSTRACT

PURPOSE: Fundus fluorescein angiography (FFA) is the gold standard for retinal vein occlusion (RVO) diagnosis. This study aims to develop a deep learning-based system to diagnose and classify RVO using FFA images, addressing the challenges of time-consuming and variable interpretations by ophthalmologists.

METHODS: 4028 FFA images of 467 eyes from 463 patients were collected and annotated. Three convolutional neural networks (CNN) models (ResNet50, VGG19, InceptionV3) were trained to generate the label of image quality, eye, location, phase, lesions, diagnosis, and macular involvement. The performance of the models was evaluated by accuracy, precision, recall, F-1 score, the area under the curve, confusion matrix, human-machine comparison, and Clinical validation on three external data sets.

RESULTS: The InceptionV3 model outperformed ResNet50 and VGG19 in labeling and interpreting FFA images for RVO diagnosis, achieving 77.63%-96.45% accuracy for basic information labels and 81.72%-96.45% for RVO-relevant labels. The comparison between the best CNN and ophthalmologists showed up to 19% accuracy improvement with the inceptionV3.

CONCLUSION: This study developed a deep learning model capable of automatically multi-label and multi-classification of FFA images for RVO diagnosis. The proposed system is anticipated to serve as a new tool for diagnosing RVO in places short of medical resources.

PMID:39027617 | PMC:PMC11255597 | DOI:10.1016/j.heliyon.2024.e33108

Heliyon. 2024 Jun 15;10(12):e32670. doi: 10.1016/j.heliyon.2024.e32670. eCollection 2024 Jun 30.

ABSTRACT

To prevent convulsions and falls of patients in the absence of medical staff, it is crucial to monitor their physical condition in hospital wards. However, several unresolved challenges in human joint recognition remain, such as object occlusion, human self-occlusion and complex backgrounds, resulting in difficulties in its practical application. In this paper, a multi-LiDAR system is proposed to obtain a multi-view human body point cloud. An improved V2V-Posenet model was introduced to detect the actual position of the human joint. In this system, each point cloud was spliced into a full point cloud and voxelized into the model. We also used a random voxel zero setting for data enhancement, constraining the relative length between human joints into a loss function and three-dimensional Gaussian filtering in a heat map for model learning. The improved model exhibited excellent performance in detecting human joints in hospital wards. The experimental results showed that the improved model achieved 91.6 % mean average precision, compared to 80.1 % for the original model and 77.4 % for the comparison algorithm A2J-Posenet. The speed of the improved model meets the requirements for real-time target detection.

PMID:39027453 | PMC:PMC11254515 | DOI:10.1016/j.heliyon.2024.e32670

Heliyon. 2024 Jun 22;10(12):e33377. doi: 10.1016/j.heliyon.2024.e33377. eCollection 2024 Jun 30.

ABSTRACT

Detecting crop diseases before they spread poses a significant challenge for farmers. While both deep learning (DL) and computer vision are valuable for image classification, DL necessitates larger datasets and more extensive training periods. To overcome the limitations of working with constrained datasets, this paper proposes an ensemble model to enhance overall performance. The proposed ensemble model combines the convolution neural network (CNN)-based models as feature extractors with random forest (RF) as the output classifier. Our method is built on popular CNN-based models such as VGG16, InceptionV3, Xception, and ResNet50. Traditionally, these CNN-based architectures are referred to as one-way models, but in our approach, they are connected in parallel to form a two-way configuration, enabling the extraction of more diverse features and reducing the risk of underfitting, particularly with limited datasets. To demonstrate the effectiveness of our ensemble approach, we train models using the grape leaf dataset, which is divided into two subsets: original and modified. In the original set, background removal is applied to the images, while the modified set includes preprocessing techniques such as intensity averaging and bilateral filtering for noise reduction and image smoothing. Our findings reveal that ensemble models trained on modified images outperform those trained on the original dataset. We observe improvements of up to 5.6 % in accuracy, precision, and sensitivity, thus validating the effectiveness of our approach in enhancing disease pattern recognition within limited datasets.

PMID:39027444 | PMC:PMC11254602 | DOI:10.1016/j.heliyon.2024.e33377

iScience. 2024 Jun 6;27(7):110192. doi: 10.1016/j.isci.2024.110192. eCollection 2024 Jul 19.

ABSTRACT

Sustainable urban transformation requires comprehensive knowledge about the built environment, including people's perceptions, use of sites, and wishes. Qualitative interviews are conducted to understand better people's opinions about a specific topic or location. This study explores the automatization of the interview coding process by investigating how state-of-the-art natural language processing techniques classify sentiment and semantic orientation from interviews transcribed in Swedish. For the sentiment analysis, the Swedish bidirectional encoder representations from transformers (BERT) model KB-BERT was used to perform a multi-class classification task on a text sentence level into three different classes: positive, negative, and neutral. Named entity recognition (NER) and string search were used for the semantic analysis to perform multi-label classification to match domain-related topics to the sentence. The models were trained and evaluated on partially annotated datasets. The results demonstrate that the implemented deep learning techniques are a possible and promising solution to achieve the stated goal.

PMID:39027375 | PMC:PMC11255841 | DOI:10.1016/j.isci.2024.110192

Neurooncol Adv. 2024 Jun 28;6(1):vdae108. doi: 10.1093/noajnl/vdae108. eCollection 2024 Jan-Dec.

ABSTRACT

BACKGROUND: Diffuse midline gliomas (DMG) are aggressive pediatric brain tumors that are diagnosed and monitored through MRI. We developed an automatic pipeline to segment subregions of DMG and select radiomic features that predict patient overall survival (OS).

METHODS: We acquired diagnostic and post-radiation therapy (RT) multisequence MRI (T1, T1ce, T2, and T2 FLAIR) and manual segmentations from 2 centers: 53 from 1 center formed the internal cohort and 16 from the other center formed the external cohort. We pretrained a deep learning model on a public adult brain tumor data set (BraTS 2021), and finetuned it to automatically segment tumor core (TC) and whole tumor (WT) volumes. PyRadiomics and sequential feature selection were used for feature extraction and selection based on the segmented volumes. Two machine learning models were trained on our internal cohort to predict patient 12-month survival from diagnosis. One model used only data obtained at diagnosis prior to any therapy (baseline study) and the other used data at both diagnosis and post-RT (post-RT study).

RESULTS: Overall survival prediction accuracy was 77% and 81% for the baseline study, and 85% and 78% for the post-RT study, for internal and external cohorts, respectively. Homogeneous WT intensity in baseline T2 FLAIR and larger post-RT TC/WT volume ratio indicate shorter OS.

CONCLUSIONS: Machine learning analysis of MRI radiomics has potential to accurately and noninvasively predict which pediatric patients with DMG will survive less than 12 months from the time of diagnosis to provide patient stratification and guide therapy.

PMID:39027132 | PMC:PMC11255990 | DOI:10.1093/noajnl/vdae108

AJNR Am J Neuroradiol. 2024 Jul 18. doi: 10.3174/ajnr.A8301. Online ahead of print.

ABSTRACT

BACKGROUND AND PURPOSE: Delayed cerebral ischemia is hard to diagnose early due to gradual, symptomless development. This study aimed to develop an automated model for predicting delayed cerebral ischemia following aneurysmal SAH on NCCT.

MATERIALS AND METHODS: This retrospective study included 400 patients with aneurysmal SAH (156 with delayed cerebral ischemia) who underwent NCCT. The study used ATT-Deeplabv3+ for automatically segmenting hemorrhagic regions using semisupervised learning. Principal component analysis was used for reducing the dimensionality of deep learning features extracted from the average pooling layer of ATT-DeepLabv3+. The classification model integrated clinical data, radiomics, and deep learning features to predict delayed cerebral ischemia. Feature selection involved Pearson correlation coefficients, least absolute shrinkage, and selection operator regression. We developed models based on clinical features, clinical-radiomics, and a combination of clinical, radiomics, and deep learning. The study selected logistic regression, Naive Bayes, Adaptive Boosting (AdaBoost), and multilayer perceptron as classifiers. The performance of segmentation and classification models was evaluated on their testing sets using the Dice similarity coefficient for segmentation, and the area under the receiver operating characteristic curve (AUC) and calibration curves for classification.

RESULTS: The segmentation process achieved a Dice similarity coefficient of 0.91 and the average time of 0.037 s/image. Seventeen features were selected to calculate the radiomics score. The clinical-radiomics-deep learning model with multilayer perceptron achieved the highest AUC of 0.84 (95% CI, 0.72-0.97), which outperformed the clinical-radiomics model (P = .002) and the clinical features model (P = .001) with multilayer perceptron. The performance of clinical-radiomics-deep learning model using AdaBoost was significantly superior to its clinical-radiomics model (P = .027). The performance of the clinical-radiomics-deep learning model and the clinical-radiomics model with logistic regression notably exceeded that of the model based solely on clinical features (P = .028; P = .046). The AUC of the clinical-radiomics-deep learning model with multilayer perceptron (P < .001) and the clinical-radiomics model with logistic regression (P = .046) were significantly higher than the clinical model with logistic regression. Of all models, the clinical-radiomics-deep learning model with multilayer perceptron showed best calibration.

CONCLUSIONS: The proposed 2-stage end-to-end model not only achieves rapid and accurate segmentation but also demonstrates superior diagnostic performance with high AUC values and good calibration in the clinical-radiomics-deep learning model, suggesting its potential to enhance delayed cerebral ischemia detection and treatment strategies.

PMID:39025637 | DOI:10.3174/ajnr.A8301

Mod Pathol. 2024 Jul 16:100563. doi: 10.1016/j.modpat.2024.100563. Online ahead of print.

ABSTRACT

The biopsy Gleason score is an important prognostic marker for prostate cancer patients. It is, however, subject to substantial variability among pathologists. Artificial intelligence (AI)-based algorithms employing deep learning have shown their ability to match pathologists' performance in assigning Gleason scores, with the potential to enhance pathologists' grading accuracy. The performance of Gleason AI algorithms in research is mostly reported on common benchmark datasets or within public challenges. In contrast, many commercial algorithms are evaluated in clinical studies, for which data is not publicly released. As commercial AI vendors typically do not publish performance on public benchmarks, comparison between research and commercial AI is difficult. The aim of this study is to evaluate and compare the performance of top-ranked public and commercial algorithms using real-world data. We curated a diverse dataset of whole-slide prostate biopsy images through crowdsourcing, containing images with a range of Gleason scores and from diverse sources. Predictions were obtained from five top-ranked public algorithms from the PANDA challenge and from two commercial Gleason grading algorithms. Additionally, ten pathologists evaluated the data set in a reader study. Overall, the pairwise quadratic weighted kappa among pathologists ranged from 0.777 to 0.916. Both public and commercial algorithms showed high agreement with pathologists, with quadratic kappa ranging from 0.617 to 0.900. Commercial algorithms performed on par or outperformed top public algorithms.

PMID:39025402 | DOI:10.1016/j.modpat.2024.100563

Surv Ophthalmol. 2024 Jul 16:S0039-6257(24)00081-X. doi: 10.1016/j.survophthal.2024.07.005. Online ahead of print.

ABSTRACT

Meibomian gland dysfunction (MGD) is increasingly recognized as a critical contributor to evaporative dry eye, significantly impacting visual quality. With a global prevalence estimated at 35.8%, it presents substantial challenges for clinicians. Conventional manual evaluation techniques for MGD face limitations characterized by inefficiencies, high subjectivity, limited big data processing capabilities, and a dearth of quantitative analytical tools. With rapidly advancing artificial intelligence (AI) technique revolutionizing ophthalmology, studies are now leveraging sophisticated AI methodologies, including computer vision, unsupervised learning, and supervised learning, to facilitate comprehensive analyses of meibomian gland (MG) evaluations. These evaluations employ various techniques, including slit lamp examination, infrared imaging, confocal microscopy, optical coherence tomography. This paradigm shift promises enhanced accuracy and consistency in disease evaluation and severity classification. While AI has achieved preliminary strides in meibomian gland evaluation, ongoing advancements in system development and clinical validation are imperative. We review the evolution of MG evaluation, juxtaposes AI-driven methods with traditional approaches, elucidates the specific roles of diverse AI technologies, and explores their practical applications using various evaluation techniques. Moreover, we delve into critical considerations for the clinical deployment of AI technologies and envisages future prospects, providing novel insights into MG evaluation and fostering technological and clinical progress in this arena.

PMID:39025239 | DOI:10.1016/j.survophthal.2024.07.005

Phys Med Biol. 2024 Jul 18. doi: 10.1088/1361-6560/ad6526. Online ahead of print.

ABSTRACT

&#xD;Online adaptive radiation therapy requires fast and automated contouring of daily scans for treatment plan re-optimization. However, automated contouring is imperfect and introduces contour uncertainties. This work aims at developing and comparing robust optimization strategies accounting for such uncertainties.&#xD;&#xD;Approach: &#xD;A deep-learning method was used to predict the uncertainty of deformable image registration, and to generate a finite set of daily contour samples. Ten optimization strategies were compared: two baseline methods, five methods that convert contour samples into voxel-wise probabilities, and three methods accounting explicitly for contour samples as scenarios in robust optimization. Target coverage and organ-at-risk (OAR) sparing were evaluated robustly for simplified proton therapy plans for five head-and-neck cancer patients.&#xD;&#xD;Results: &#xD;We found that explicitly including target contour uncertainty in robust optimization provides robust target coverage with better OAR sparing than the baseline methods, without increasing the optimization time. Although OAR doses first increased when increasing target robustness, this effect could be prevented by additionally including robustness to OAR contour uncertainty. Compared to the probability-based methods, the scenario-based methods spared the OARs more, but increased integral dose and required more computation time.&#xD;&#xD;Significance: &#xD;This work proposed efficient and beneficial strategies to mitigate contour uncertainty in treatment plan optimization. This facilitates the adoption of automatic contouring in online adaptive radiation therapy and, more generally, enables mitigation also of other sources of contour uncertainty in treatment planning.

PMID:39025113 | DOI:10.1088/1361-6560/ad6526

Med Image Anal. 2024 Jul 11;97:103269. doi: 10.1016/j.media.2024.103269. Online ahead of print.

ABSTRACT

Lesion volume is an important predictor for prognosis in breast cancer. However, it is currently impossible to compute lesion volumes accurately from digital mammography data, which is the most popular and readily available imaging modality for breast cancer. We make a step towards a more accurate lesion volume measurement on digital mammograms by developing a model that allows to estimate lesion volumes on processed mammogram. Processed mammograms are the images routinely used by radiologists in clinical practice as well as in breast cancer screening and are available in medical centers. Processed mammograms are obtained from raw mammograms, which are the X-ray data coming directly from the scanner, by applying certain vendor-specific non-linear transformations. At the core of our volume estimation method is a physics-based algorithm for measuring lesion volumes on raw mammograms. We subsequently extend this algorithm to processed mammograms via a deep learning image-to-image translation model that produces synthetic raw mammograms from processed mammograms in a multi-vendor setting. We assess the reliability and validity of our method using a dataset of 1778 mammograms with an annotated mass. Firstly, we investigate the correlations between lesion volumes computed from mediolateral oblique and craniocaudal views, with a resulting Pearson correlation of 0.93 [95% confidence interval (CI) 0.92 - 0.93]. Secondly, we compare the resulting lesion volumes from true and synthetic raw data, with a resulting Pearson correlation of 0.998 [95%CI 0.998 - 0.998] . Finally, for a subset of 100 mammograms with a malignant mass and concurrent MRI examination available, we analyze the agreement between lesion volume on mammography and MRI, resulting in an intraclass correlation coefficient of 0.81 [95%CI 0.73 - 0.87] for consistency and 0.78 [95%CI 0.66 - 0.86] for absolute agreement. In conclusion, we developed an algorithm to measure mammographic lesion volume that reached excellent reliability and good validity, when using MRI as ground truth. The algorithm may play a role in lesion characterization and breast cancer prognostication on mammograms.

PMID:39024973 | DOI:10.1016/j.media.2024.103269

Med Image Anal. 2024 Jul 10;97:103272. doi: 10.1016/j.media.2024.103272. Online ahead of print.

ABSTRACT

Landmark detection is a crucial task in medical image analysis, with applications across various fields. However, current methods struggle to accurately locate landmarks in medical images with blurred tissue boundaries due to low image quality. In particular, in echocardiography, sparse annotations make it challenging to predict landmarks with position stability and temporal consistency. In this paper, we propose a spatio-temporal graph convolutional network tailored for echocardiography landmark detection. We specifically sample landmark labels from the left ventricular endocardium and pre-calculate their correlations to establish structural priors. Our approach involves a graph convolutional neural network that learns the interrelationships among landmarks, significantly enhancing landmark accuracy within ambiguous tissue contexts. Additionally, we integrate gate recurrent units to grasp the temporal consistency of landmarks across consecutive images, augmenting the model's resilience against unlabeled data. Through validation across three echocardiography datasets, our method demonstrates superior accuracy when contrasted with alternative landmark detection models.

PMID:39024972 | DOI:10.1016/j.media.2024.103272

Comput Biol Med. 2024 Jul 17;179:108870. doi: 10.1016/j.compbiomed.2024.108870. Online ahead of print.

ABSTRACT

Accurate segmentation of the liver and tumors from CT volumes is crucial for hepatocellular carcinoma diagnosis and pre-operative resection planning. Despite advances in deep learning-based methods for abdominal CT images, fully-automated segmentation remains challenging due to class imbalance and structural variations, often requiring cascaded approaches that incur significant computational costs. In this paper, we present the Dual-Encoder Double Concatenation Network (DEDC-Net) for simultaneous segmentation of the liver and its tumors. DEDC-Net leverages both residual and skip connections to enhance feature reuse and optimize performance in liver and tumor segmentation tasks. Extensive qualitative and quantitative experiments on the LiTS dataset demonstrate that DEDC-Net outperforms existing state-of-the-art liver segmentation methods. An ablation study was conducted to evaluate different encoder backbones - specifically VGG19 and ResNet - and the impact of incorporating an attention mechanism. Our results indicate that DEDC-Net, without any additional attention gates, achieves a superior mean Dice Score (DS) of 0.898 for liver segmentation. Moreover, integrating residual connections into one encoder yielded the highest DS for tumor segmentation tasks. The robustness of our proposed network was further validated on two additional, unseen CT datasets: IDCARDb-01 and COMET. Our model demonstrated superior lesion segmentation capabilities, particularly on IRCADb-01, achieving a DS of 0.629. The code implementation is publicly available at this website.

PMID:39024904 | DOI:10.1016/j.compbiomed.2024.108870

BMC Med Inform Decis Mak. 2024 Jul 18;24(1):196. doi: 10.1186/s12911-024-02601-4.

ABSTRACT

BACKGROUND: Generalized Joint Hyper-mobility (GJH) can aid in the diagnosis of Ehlers-Danlos Syndrome (EDS), a complex genetic connective tissue disorder with clinical features that can mimic other disease processes. Our study focuses on developing a unique image-based goniometry system, the HybridPoseNet, which utilizes a hybrid deep learning model.

OBJECTIVE: The proposed model is designed to provide the most accurate joint angle measurements in EDS appraisals. Using a hybrid of CNNs and HyperLSTMs in the pose estimation module of HybridPoseNet offers superior generalization and time consistency properties, setting it apart from existing complex libraries.

METHODOLOGY: HybridPoseNet integrates the spatial pattern recognition prowess of MobileNet-V2 with the sequential data processing capability of HyperLSTM units. The system captures the dynamic nature of joint motion by creating a model that learns from individual frames and the sequence of movements. The CNN module of HybridPoseNet was trained on a large and diverse data set before the fine-tuning of video data involving 50 individuals visiting the EDS clinic, focusing on joints that can hyperextend. HyperLSTMs have been incorporated in video frames to avoid any time breakage in joint angle estimation in consecutive frames. The model performance was evaluated using Spearman's coefficient correlation versus manual goniometry measurements, as well as by the human labeling of joint position, the second validation step.

OUTCOME: Preliminary findings demonstrate HybridPoseNet achieving a remarkable correlation with manual Goniometric measurements: thumb (rho = 0.847), elbows (rho = 0.822), knees (rho = 0.839), and fifth fingers (rho = 0.896), indicating that the newest model is considerably better. The model manifested a consistent performance in all joint assessments, hence not requiring selecting a variety of pose-measuring libraries for every joint. The presentation of HybridPoseNet contributes to achieving a combined and normalized approach to reviewing the mobility of joints, which has an overall enhancement of approximately 20% in accuracy compared to the regular pose estimation libraries. This innovation is very valuable to the field of medical diagnostics of connective tissue diseases and a vast improvement to its understanding.

PMID:39026270 | DOI:10.1186/s12911-024-02601-4

BMC Cancer. 2024 Jul 18;24(1):852. doi: 10.1186/s12885-024-12575-1.

ABSTRACT

BACKGROUND: Providing appropriate specialized treatment to the right patient at the right time is considered necessary in cancer management. Targeted therapy tailored to the genetic changes of each breast cancer patient is a desirable feature of precision oncology, which can not only reduce disease progression but also potentially increase patient survival. The use of artificial intelligence alongside precision oncology can help physicians by identifying and selecting more effective treatment factors for patients.

METHOD: A systematic review was conducted using the PubMed, Embase, Scopus, and Web of Science databases in September 2023. We performed the search strategy with keywords, namely: Breast Cancer, Artificial intelligence, and precision Oncology along with their synonyms in the article titles. Descriptive, qualitative, review, and non-English studies were excluded. The quality assessment of the articles and evaluation of bias were determined based on the SJR journal and JBI indices, as well as the PRISMA2020 guideline.

RESULTS: Forty-six studies were selected that focused on personalized breast cancer management using artificial intelligence models. Seventeen studies using various deep learning methods achieved a satisfactory outcome in predicting treatment response and prognosis, contributing to personalized breast cancer management. Two studies utilizing neural networks and clustering provided acceptable indicators for predicting patient survival and categorizing breast tumors. One study employed transfer learning to predict treatment response. Twenty-six studies utilizing machine-learning methods demonstrated that these techniques can improve breast cancer classification, screening, diagnosis, and prognosis. The most frequent modeling techniques used were NB, SVM, RF, XGBoost, and Reinforcement Learning. The average area under the curve (AUC) for the models was 0.91. Moreover, the average values for accuracy, sensitivity, specificity, and precision were reported to be in the range of 90-96% for the models.

CONCLUSION: Artificial intelligence has proven to be effective in assisting physicians and researchers in managing breast cancer treatment by uncovering hidden patterns in complex omics and genetic data. Intelligent processing of omics data through protein and gene pattern classification and the utilization of deep neural patterns has the potential to significantly transform the field of complex disease management.

PMID:39026174 | DOI:10.1186/s12885-024-12575-1

Eur Radiol. 2024 Jul 18. doi: 10.1007/s00330-024-10967-2. Online ahead of print.

ABSTRACT

OBJECTIVES: The aim of this study is to develop a deep-learning model to create synthetic temporal bone computed tomography (CT) images from ultrashort echo-time magnetic resonance imaging (MRI) scans, thereby addressing the intrinsic limitations of MRI in localizing anatomic landmarks in temporal bone CT.

MATERIALS AND METHODS: This retrospective study included patients who underwent temporal MRI and temporal bone CT within one month between April 2020 and March 2023. These patients were randomly divided into training and validation datasets. A CycleGAN model for generating synthetic temporal bone CT images was developed using temporal bone CT and pointwise encoding-time reduction with radial acquisition (PETRA). To assess the model's performance, the pixel count in mastoid air cells was measured. Two neuroradiologists evaluated the successful generation rates of 11 anatomical landmarks.

RESULTS: A total of 102 patients were included in this study (training dataset, n = 54, mean age 58 ± 14, 34 females (63%); validation dataset, n = 48, mean age 61 ± 13, 29 females (60%)). In the pixel count of mastoid air cells, no difference was observed between synthetic and real images (679 ± 342 vs 738 ± 342, p = 0.13). For the six major anatomical sites, the positive generation rates were 97-100%, whereas those of the five major anatomical structures ranged from 24% to 83%.

CONCLUSION: We developed a model to generate synthetic temporal bone CT images using PETRA MRI. This model can provide information regarding the major anatomic sites of the temporal bone using MRI.

CLINICAL RELEVANCE STATEMENT: The proposed algorithm addresses the primary limitations of MRI in localizing anatomic sites within the temporal bone.

KEY POINTS: CT is preferred for imaging the temporal bone, but has limitations in differentiating pathology there. The model achieved a high success rate in generating synthetic images of six anatomic sites. This can overcome the limitations of MRI in visualizing key anatomic sites in the temporal skull.

PMID:39026063 | DOI:10.1007/s00330-024-10967-2

Med Phys. 2024 Jul 18. doi: 10.1002/mp.17308. Online ahead of print.

ABSTRACT

BACKGROUND: The current level of automation in the production of radiotherapy plans for lung cancer patients is relatively low. With the development of artificial intelligence, it has become a reality to use neural networks to predict dose distributions and provide assistance for radiation therapy planning. However, due to the significant individual variability in the distribution of non-small cell lung cancer (NSCLC) planning target volume (PTV) and the complex spatial relationships between the PTV and organs at risk (OARs), there is still a lack of a high-precision dose prediction network tailored to the characteristics of NSCLC.

PURPOSE: To assist in the development of volumetric modulated arc therapy (VMAT) plans for non-small cell lung cancer patients, a deep neural network is proposed to predict high-precision dose distribution.

METHODS: This study has developed a network called MHA-ResUNet, which combines a large-kernel dilated convolution module and multi-head attention (MHA) modules. The network was trained based on 80 VMAT plans of NSCLC patients. CT images, PTV, and OARs were fed into the independent input channel. The dose distribution was taken as the output to train the model. The performance of this network was compared with that of several commonly used networks, and the networks' performance was evaluated based on the voxel-level mean absolute error (MAE) within the PTV and OARs, as well as the error in clinical dose-volume metrics.

RESULTS: The MAE between the predicted dose distribution and the manually planned dose distribution within the PTV is 1.43 Gy, and the D95 error is less than 1 Gy. Compared with the other three commonly used networks, the dose error of the MHA-ResUNet is the smallest in PTV and OARs.

CONCLUSIONS: The proposed MHA-ResUNet network improves the receptive field and filters the shallow features to learn the relative spatial relation between the PTV and the OARs, enabling accurate prediction of dose distributions in NSCLC patients undergoing VMAT radiotherapy.

PMID:39024495 | DOI:10.1002/mp.17308