Interdiscip Sci. 2024 Mar 15. doi: 10.1007/s12539-024-00617-y. Online ahead of print.

ABSTRACT

Survival analysis, as a widely used method for analyzing and predicting the timing of event occurrence, plays a crucial role in the medicine field. Medical professionals utilize survival models to gain insight into the effects of patient covariates on the disease, and the correlation with the effectiveness of different treatment strategies. This knowledge is essential for the development of treatment plans and the enhancement of treatment approaches. Conventional survival models, such as the Cox proportional hazards model, require a significant amount of feature engineering or prior knowledge to facilitate personalized modeling. To address these limitations, we propose a novel residual-based self-attention deep neural network for survival modeling, called ResDeepSurv, which combines the benefits of neural networks and the Cox proportional hazards regression model. The model proposed in our study simulates the distribution of survival time and the correlation between covariates and outcomes, but does not impose strict assumptions on the basic distribution of survival data. This approach effectively accounts for both linear and nonlinear risk functions in survival data analysis. The performance of our model in analyzing survival data with various risk functions is on par with or even superior to that of other existing survival analysis methods. Furthermore, we validate the superior performance of our model in comparison to currently existing methods by evaluating multiple publicly available clinical datasets. Through this study, we prove the effectiveness of our proposed model in survival analysis, providing a promising alternative to traditional approaches. The application of deep learning techniques and the ability to capture complex relationships between covariates and survival outcomes without relying on extensive feature engineering make our model a valuable tool for personalized medicine and decision-making in clinical practice.

PMID:38489147 | DOI:10.1007/s12539-024-00617-y

Abdom Radiol (NY). 2024 Mar 15. doi: 10.1007/s00261-024-04232-9. Online ahead of print.

ABSTRACT

PURPOSE: To explore the value of deep learning-based multi-parametric magnetic resonance imaging (mp-MRI) nomogram in predicting the Ki-67 expression in rectal cancer.

METHODS: The data of 491 patients with rectal cancer from two centers were retrospectively analyzed and divided into training, internal validation, and external validation sets. They were categorized into high- and low-expression group based on postoperative pathological Ki-67 expression. Each patient's mp-MRI data were analyzed to extract and select the most relevant features of deep learning, and a deep learning model was constructed. Independent predictive risk factors were identified and incorporated into a clinical model, and the clinical and deep learning models were combined to obtain a nomogram for the prediction of Ki-67 expression. The performance characteristics of the DL-model, clinical model, and nomogram were assessed using ROCs, calibration curve, decision curve, and clinical impact curve analysis.

RESULTS: The strongest deep learning features were extracted and screened from mp-MRI data. Two independent predictive factors, namely Magnetic Resonance Imaging T (mrT) staging and differentiation degree, were identified through clinical feature selection. Three models were constructed: a deep learning (DL)-model, a clinical model, and a nomogram. The AUCs of clinical model in the training, internal validation, and external validation set were 0.69, 0.78, and 0.67, respectively. The AUCs of the deep model and nomogram ranged from 0.88 to 0.98. The prediction performance of the deep learning model and nomogram was significantly better than the clinical model (P < 0.001).

CONCLUSION: The nomogram based on deep learning can help clinicians accurately and conveniently predict the expression status of Ki-67 in rectal cancer.

PMID:38489038 | DOI:10.1007/s00261-024-04232-9

Sci China Life Sci. 2024 Mar 12. doi: 10.1007/s11427-023-2504-1. Online ahead of print.

ABSTRACT

Antimicrobial resistance (AMR) poses a critical threat to global health and development, with environmental factors-particularly in urban areas-contributing significantly to the spread of antibiotic resistance genes (ARGs). However, most research to date has been conducted at a local level, leaving significant gaps in our understanding of the global status of antibiotic resistance in urban environments. To address this issue, we thoroughly analyzed a total of 86,213 ARGs detected within 4,728 metagenome samples, which were collected by the MetaSUB International Consortium involving diverse urban environments in 60 cities of 27 countries, utilizing a deep-learning based methodology. Our findings demonstrated the strong geographical specificity of urban environmental resistome, and their correlation with various local socioeconomic and medical conditions. We also identified distinctive evolutionary patterns of ARG-related biosynthetic gene clusters (BGCs) across different countries, and discovered that the urban environment represents a rich source of novel antibiotics. Our study provides a comprehensive overview of the global urban environmental resistome, and fills a significant gap in our knowledge of large-scale urban antibiotic resistome analysis.

PMID:38489008 | DOI:10.1007/s11427-023-2504-1

Elife. 2024 Mar 15;12:RP92614. doi: 10.7554/eLife.92614.

ABSTRACT

Nondestructive pathology based on three-dimensional (3D) optical microscopy holds promise as a complement to traditional destructive hematoxylin and eosin (H&E) stained slide-based pathology by providing cellular information in high throughput manner. However, conventional techniques provided superficial information only due to shallow imaging depths. Herein, we developed open-top two-photon light sheet microscopy (OT-TP-LSM) for intraoperative 3D pathology. An extended depth of field two-photon excitation light sheet was generated by scanning a nondiffractive Bessel beam, and selective planar imaging was conducted with cameras at 400 frames/s max during the lateral translation of tissue specimens. Intrinsic second harmonic generation was collected for additional extracellular matrix (ECM) visualization. OT-TP-LSM was tested in various human cancer specimens including skin, pancreas, and prostate. High imaging depths were achieved owing to long excitation wavelengths and long wavelength fluorophores. 3D visualization of both cells and ECM enhanced the ability of cancer detection. Furthermore, an unsupervised deep learning network was employed for the style transfer of OT-TP-LSM images to virtual H&E images. The virtual H&E images exhibited comparable histological characteristics to real ones. OT-TP-LSM may have the potential for histopathological examination in surgical and biopsy applications by rapidly providing 3D information.

PMID:38488831 | DOI:10.7554/eLife.92614

Adv Sci (Weinh). 2024 Mar 15:e2307837. doi: 10.1002/advs.202307837. Online ahead of print.

ABSTRACT

Endo-microscopy is crucial for real-time 3D visualization of internal tissues and subcellular structures. Conventional methods rely on axial movement of optical components for precise focus adjustment, limiting miniaturization and complicating procedures. Meta-device, composed of artificial nanostructures, is an emerging optical flat device that can freely manipulate the phase and amplitude of light. Here, an intelligent fluorescence endo-microscope is developed based on varifocal meta-lens and deep learning (DL). The breakthrough enables in vivo 3D imaging of mouse brains, where varifocal meta-lens focal length adjusts through relative rotation angle. The system offers key advantages such as invariant magnification, a large field-of-view, and optical sectioning at a maximum focal length tuning range of ≈2 mm with 3 µm lateral resolution. Using a DL network, image acquisition time and system complexity are significantly reduced, and in vivo high-resolution brain images of detailed vessels and surrounding perivascular space are clearly observed within 0.1 s (≈50 times faster). The approach will benefit various surgical procedures, such as gastrointestinal biopsies, neural imaging, brain surgery, etc.

PMID:38488694 | DOI:10.1002/advs.202307837

J Appl Clin Med Phys. 2024 Mar 15:e14327. doi: 10.1002/acm2.14327. Online ahead of print.

ABSTRACT

PURPOSE: This study aimed to develop a hybrid multi-channel network to detect multileaf collimator (MLC) positional errors using dose difference (DD) maps and gamma maps generated from low-resolution detectors in patient-specific quality assurance (QA) for Intensity Modulated Radiation Therapy (IMRT).

METHODS: A total of 68 plans with 358 beams of IMRT were included in this study. The MLC leaf positions of all control points in the original IMRT plans were modified to simulate four types of errors: shift error, opening error, closing error, and random error. These modified plans were imported into the treatment planning system (TPS) to calculate the predicted dose, while the PTW seven29 phantom was utilized to obtain the measured dose distributions. Based on the measured and predicted dose, DD maps and gamma maps, both with and without errors, were generated, resulting in a dataset with 3222 samples. The network's performance was evaluated using various metrics, including accuracy, sensitivity, specificity, precision, F1-score, ROC curves, and normalized confusion matrix. Besides, other baseline methods, such as single-channel hybrid network, ResNet-18, and Swin-Transformer, were also evaluated as a comparison.

RESULTS: The experimental results showed that the multi-channel hybrid network outperformed other methods, demonstrating higher average precision, accuracy, sensitivity, specificity, and F1-scores, with values of 0.87, 0.89, 0.85, 0.97, and 0.85, respectively. The multi-channel hybrid network also achieved higher AUC values in the random errors (0.964) and the error-free (0.946) categories. Although the average accuracy of the multi-channel hybrid network was only marginally better than that of ResNet-18 and Swin Transformer, it significantly outperformed them regarding precision in the error-free category.

CONCLUSION: The proposed multi-channel hybrid network exhibits a high level of accuracy in identifying MLC errors using low-resolution detectors. The method offers an effective and reliable solution for promoting quality and safety of IMRT QA.

PMID:38488663 | DOI:10.1002/acm2.14327

J Phys Chem Lett. 2024 Mar 15:3238-3248. doi: 10.1021/acs.jpclett.4c00280. Online ahead of print.

ABSTRACT

It is crucial to unravel the structural factors influencing the dynamics of the amorphous solids. Deep learning aids in navigating these complexities, while transparency issues persist. Drawing inspiration from the successful application of prototype neural networks in image analysis, this study introduces a novel machine learning approach to address interpretability challenges in glassy research. Distinguishing from traditional machine learning models, the proposed neural network tries to learn distant structural motifs for solid-like atoms and liquid-like atoms. Such learned structural motifs constrain the underlying structural space and thus can serve as a breakthrough in explaining how structural differences impact dynamics. We further used the proposed model to explore the correlation between the local structure and activation energy in the CuZr alloys. Building upon this interpretable model, we demonstrated significant structural differences among atoms with different activation energies. Our interpretable model is a data-driven solution that provides a pathway to reveal the origin of structural heterogeneity in amorphous alloys.

PMID:38488506 | DOI:10.1021/acs.jpclett.4c00280

Transl Vis Sci Technol. 2024 Mar 1;13(3):12. doi: 10.1167/tvst.13.3.12.

ABSTRACT

PURPOSE: To evaluate the diagnostic performance of a robotically aligned optical coherence tomography (RAOCT) system coupled with a deep learning model in detecting referable posterior segment pathology in OCT images of emergency department patients.

METHODS: A deep learning model, RobOCTNet, was trained and internally tested to classify OCT images as referable versus non-referable for ophthalmology consultation. For external testing, emergency department patients with signs or symptoms warranting evaluation of the posterior segment were imaged with RAOCT. RobOCTNet was used to classify the images. Model performance was evaluated against a reference standard based on clinical diagnosis and retina specialist OCT review.

RESULTS: We included 90,250 OCT images for training and 1489 images for internal testing. RobOCTNet achieved an area under the curve (AUC) of 1.00 (95% confidence interval [CI], 0.99-1.00) for detection of referable posterior segment pathology in the internal test set. For external testing, RAOCT was used to image 72 eyes of 38 emergency department patients. In this set, RobOCTNet had an AUC of 0.91 (95% CI, 0.82-0.97), a sensitivity of 95% (95% CI, 87%-100%), and a specificity of 76% (95% CI, 62%-91%). The model's performance was comparable to two human experts' performance.

CONCLUSIONS: A robotically aligned OCT coupled with a deep learning model demonstrated high diagnostic performance in detecting referable posterior segment pathology in a cohort of emergency department patients.

TRANSLATIONAL RELEVANCE: Robotically aligned OCT coupled with a deep learning model may have the potential to improve emergency department patient triage for ophthalmology referral.

PMID:38488431 | DOI:10.1167/tvst.13.3.12

Cancer Med. 2024 Mar;13(5):e7104. doi: 10.1002/cam4.7104.

ABSTRACT

BACKGROUND: Microvascular invasion (MVI) is an independent prognostic factor that is associated with early recurrence and poor survival after resection of hepatocellular carcinoma (HCC). However, the traditional pathology approach is relatively subjective, time-consuming, and heterogeneous in the diagnosis of MVI. The aim of this study was to develop a deep-learning model that could significantly improve the efficiency and accuracy of MVI diagnosis.

MATERIALS AND METHODS: We collected H&E-stained slides from 753 patients with HCC at the First Affiliated Hospital of Zhejiang University. An external validation set with 358 patients was selected from The Cancer Genome Atlas database. The deep-learning model was trained by simulating the method used by pathologists to diagnose MVI. Model performance was evaluated with accuracy, precision, recall, F1 score, and the area under the receiver operating characteristic curve.

RESULTS: We successfully developed a MVI artificial intelligence diagnostic model (MVI-AIDM) which achieved an accuracy of 94.25% in the independent external validation set. The MVI positive detection rate of MVI-AIDM was significantly higher than the results of pathologists. Visualization results demonstrated the recognition of micro MVIs that were difficult to differentiate by the traditional pathology. Additionally, the model provided automatic quantification of the number of cancer cells and spatial information regarding MVI.

CONCLUSIONS: We developed a deep learning diagnostic model, which performed well and improved the efficiency and accuracy of MVI diagnosis. The model provided spatial information of MVI that was essential to accurately predict HCC recurrence after surgery.

PMID:38488408 | DOI:10.1002/cam4.7104

NMR Biomed. 2024 Mar 15:e5145. doi: 10.1002/nbm.5145. Online ahead of print.

ABSTRACT

Noninvasive extracellular pH (pHe ) mapping with Biosensor Imaging of Redundant Deviation in Shifts (BIRDS) using MR spectroscopic imaging (MRSI) has been demonstrated on 3T clinical MR scanners at 8 × 8 × 10 $$ \times 8\times 10 $$ mm3 spatial resolution and applied to study various liver cancer treatments. Although pHe imaging at higher resolution can be achieved by extending the acquisition time, a postprocessing method to increase the resolution is preferable, to minimize the duration spent by the subject in the MR scanner. In this work, we propose to improve the spatial resolution of pHe mapping with BIRDS by incorporating anatomical information in the form of multiparametric MRI and using an unsupervised deep-learning technique, Deep Image Prior (DIP). Specifically, we used high-resolution T 1 $$ {\mathrm{T}}_1 $$ , T 2 $$ {\mathrm{T}}_2 $$ , and diffusion-weighted imaging (DWI) MR images of rabbits with VX2 liver tumors as inputs to a U-Net architecture to provide anatomical information. U-Net parameters were optimized to minimize the difference between the output super-resolution image and the experimentally acquired low-resolution pHe image using the mean-absolute error. In this way, the super-resolution pHe image would be consistent with both anatomical MR images and the low-resolution pHe measurement from the scanner. The method was developed based on data from 49 rabbits implanted with VX2 liver tumors. For evaluation, we also acquired high-resolution pHe images from two rabbits, which were used as ground truth. The results indicate a good match between the spatial characteristics of the super-resolution images and the high-resolution ground truth, supported by the low pixelwise absolute error.

PMID:38488205 | DOI:10.1002/nbm.5145

Anal Chem. 2024 Mar 15. doi: 10.1021/acs.analchem.3c05019. Online ahead of print.

ABSTRACT

The rapid proliferation of new psychoactive substances (NPS) poses significant challenges to conventional mass-spectrometry-based identification methods due to the absence of reference spectra for these emerging substances. This paper introduces PS2MS, an AI-powered predictive system designed specifically to address the limitations of identifying the emergence of unidentified novel illicit drugs. PS2MS builds a synthetic NPS database by enumerating feasible derivatives of known substances and uses deep learning to generate mass spectra and chemical fingerprints. When the mass spectrum of an analyte does not match any known reference, PS2MS simultaneously examines the chemical fingerprint and mass spectrum against the putative NPS database using integrated metrics to deduce possible identities. Experimental results affirm the effectiveness of PS2MS in identifying cathinone derivatives within real evidence specimens, signifying its potential for practical use in identifying emerging drugs of abuse for researchers and forensic experts.

PMID:38488022 | DOI:10.1021/acs.analchem.3c05019

Health Data Sci. 2023 Nov 10;3:0098. doi: 10.34133/hds.0098. eCollection 2023.

ABSTRACT

Importance: Drug-likeness of a compound is an overall assessment of its potential to succeed in clinical trials, and is essential for economizing research expenditures by filtering compounds with unfavorable properties and poor development potential. To this end, a robust drug-likeness prediction method is indispensable. Various approaches, including discriminative rules, statistical models, and machine learning models, have been developed to predict drug-likeness based on physiochemical properties and structural features. Notably, recent advancements in novel deep learning techniques have significantly advanced drug-likeness prediction, especially in classification performance. Highlights: In this review, we addressed the evolving landscape of drug-likeness prediction, with emphasis on methods employing novel deep learning techniques, and highlighted the current challenges in drug-likeness prediction, specifically regarding the aspects of generalization and interpretability. Moreover, we explored potential remedies and outlined promising avenues for future research. Conclusion: Despite the hurdles of generalization and interpretability, novel deep learning techniques have great potential in drug-likeness prediction and are worthy of further research efforts.

PMID:38487200 | PMC:PMC10880170 | DOI:10.34133/hds.0098

Diagnosis (Berl). 2024 Mar 18. doi: 10.1515/dx-2024-0012. Online ahead of print.

ABSTRACT

OBJECTIVES: Early skin cancer diagnosis can save lives; however, traditional methods rely on expert knowledge and can be time-consuming. This calls for automated systems using machine learning and deep learning. However, existing datasets often focus on flat skin surfaces, neglecting more complex cases on organs or with nearby lesions.

METHODS: This work addresses this gap by proposing a skin cancer diagnosis methodology using a dataset named ASAN that covers diverse skin cancer cases but suffers from noisy features. To overcome the noisy feature problem, a segmentation dataset named SASAN is introduced, focusing on Region of Interest (ROI) extraction-based classification. This allows models to concentrate on critical areas within the images while ignoring learning the noisy features.

RESULTS: Various deep learning segmentation models such as UNet, LinkNet, PSPNet, and FPN were trained on the SASAN dataset to perform segmentation-based ROI extraction. Classification was then performed using the dataset with and without ROI extraction. The results demonstrate that ROI extraction significantly improves the performance of these models in classification. This implies that SASAN is effective in evaluating performance metrics for complex skin cancer cases.

CONCLUSIONS: This study highlights the importance of expanding datasets to include challenging scenarios and developing better segmentation methods to enhance automated skin cancer diagnosis. The SASAN dataset serves as a valuable tool for researchers aiming to improve such systems and ultimately contribute to better diagnostic outcomes.

PMID:38487874 | DOI:10.1515/dx-2024-0012

Brief Bioinform. 2024 Jan 22;25(2):bbae089. doi: 10.1093/bib/bbae089.

ABSTRACT

The screening of enzymes for catalyzing specific substrate-product pairs is often constrained in the realms of metabolic engineering and synthetic biology. Existing tools based on substrate and reaction similarity predominantly rely on prior knowledge, demonstrating limited extrapolative capabilities and an inability to incorporate custom candidate-enzyme libraries. Addressing these limitations, we have developed the Substrate-product Pair-based Enzyme Promiscuity Prediction (SPEPP) model. This innovative approach utilizes transfer learning and transformer architecture to predict enzyme promiscuity, thereby elucidating the intricate interplay between enzymes and substrate-product pairs. SPEPP exhibited robust predictive ability, eliminating the need for prior knowledge of reactions and allowing users to define their own candidate-enzyme libraries. It can be seamlessly integrated into various applications, including metabolic engineering, de novo pathway design, and hazardous material degradation. To better assist metabolic engineers in designing and refining biochemical pathways, particularly those without programming skills, we also designed EnzyPick, an easy-to-use web server for enzyme screening based on SPEPP. EnzyPick is accessible at http://www.biosynther.com/enzypick/.

PMID:38487850 | DOI:10.1093/bib/bbae089

Brief Bioinform. 2024 Jan 22;25(2):bbae088. doi: 10.1093/bib/bbae088.

ABSTRACT

Pharmacogenomics aims to provide personalized therapy to patients based on their genetic variability. However, accurate prediction of cancer drug response (CDR) is challenging due to genetic heterogeneity. Since clinical data are limited, most studies predicting drug response use preclinical data to train models. However, such models might not be generalizable to external clinical data due to differences between the preclinical and clinical datasets. In this study, a Precision Medicine Prediction using an Adversarial Network for Cancer Drug Response (PANCDR) model is proposed. PANCDR consists of two sub-models, an adversarial model and a CDR prediction model. The adversarial model reduces the gap between the preclinical and clinical datasets, while the CDR prediction model extracts features and predicts responses. PANCDR was trained using both preclinical data and unlabeled clinical data. Subsequently, it was tested on external clinical data, including The Cancer Genome Atlas and brain tumor patients. PANCDR outperformed other machine learning models in predicting external test data. Our results demonstrate the robustness of PANCDR and its potential in precision medicine by recommending patient-specific drug candidates. The PANCDR codes and data are available at https://github.com/DMCB-GIST/PANCDR.

PMID:38487849 | DOI:10.1093/bib/bbae088

Patterns (N Y). 2024 Feb 12;5(3):100932. doi: 10.1016/j.patter.2024.100932. eCollection 2024 Mar 8.

ABSTRACT

Along with propagating the input toward making a prediction, Bayesian neural networks also propagate uncertainty. This has the potential to guide the training process by rejecting predictions of low confidence, and recent variational Bayesian methods can do so without Monte Carlo sampling of weights. Here, we apply sample-free methods for wildlife call detection on recordings made via passive acoustic monitoring equipment in the animals' natural habitats. We further propose uncertainty-aware label smoothing, where the smoothing probability is dependent on sample-free predictive uncertainty, in order to downweigh data samples that should contribute less to the loss value. We introduce a bioacoustic dataset recorded in Malaysian Borneo, containing overlapping calls from 30 species. On that dataset, our proposed method achieves an absolute percentage improvement of around 1.5 points on area under the receiver operating characteristic (AU-ROC), 13 points in F1, and 19.5 points in expected calibration error (ECE) compared to the point-estimate network baseline averaged across all target classes.

PMID:38487806 | PMC:PMC10935495 | DOI:10.1016/j.patter.2024.100932

Patterns (N Y). 2024 Mar 1;5(3):100944. doi: 10.1016/j.patter.2024.100944. eCollection 2024 Mar 8.

ABSTRACT

The underrepresentation of gender, racial, and ethnic minorities in clinical trials is a problem undermining the efficacy of treatments on minorities and preventing precise estimates of the effects within these subgroups. We propose FRAMM, a deep reinforcement learning framework for fair trial site selection to help address this problem. We focus on two real-world challenges: the data modalities used to guide selection are often incomplete for many potential trial sites, and the site selection needs to simultaneously optimize for both enrollment and diversity. To address the missing data challenge, FRAMM has a modality encoder with a masked cross-attention mechanism for bypassing missing data. To make efficient trade-offs, FRAMM uses deep reinforcement learning with a reward function designed to simultaneously optimize for both enrollment and fairness. We evaluate FRAMM using real-world historical clinical trials and show that it outperforms the leading baseline in enrollment-only settings while also greatly improving diversity.

PMID:38487797 | PMC:PMC10935501 | DOI:10.1016/j.patter.2024.100944

Wearable Technol. 2023 Feb 20;4:e4. doi: 10.1017/wtc.2023.3. eCollection 2023.

ABSTRACT

The development of wearable technology, which enables motion tracking analysis for human movement outside the laboratory, can improve awareness of personal health and performance. This study used a wearable smart sock prototype to track foot-ankle kinematics during gait movement. Multivariable linear regression and two deep learning models, including long short-term memory (LSTM) and convolutional neural networks, were trained to estimate the joint angles in sagittal and frontal planes measured by an optical motion capture system. Participant-specific models were established for ten healthy subjects walking on a treadmill. The prototype was tested at various walking speeds to assess its ability to track movements for multiple speeds and generalize models for estimating joint angles in sagittal and frontal planes. LSTM outperformed other models with lower mean absolute error (MAE), lower root mean squared error, and higher R-squared values. The average MAE score was less than 1.138° and 0.939° in sagittal and frontal planes, respectively, when training models for each speed and 2.15° and 1.14° when trained and evaluated for all speeds. These results indicate wearable smart socks to generalize foot-ankle kinematics over various walking speeds with relatively low error and could consequently be used to measure gait parameters without the need for a lab-constricted motion capture system.

PMID:38487777 | PMC:PMC10936318 | DOI:10.1017/wtc.2023.3

Front Artif Intell. 2024 Feb 29;7:1331853. doi: 10.3389/frai.2024.1331853. eCollection 2024.

ABSTRACT

The application of artificial intelligence technology in the medical field has become increasingly prevalent, yet there remains significant room for exploration in its deep implementation. Within the field of orthopedics, which integrates closely with AI due to its extensive data requirements, rotator cuff injuries are a commonly encountered condition in joint motion. One of the most severe complications following rotator cuff repair surgery is the recurrence of tears, which has a significant impact on both patients and healthcare professionals. To address this issue, we utilized the innovative EV-GCN algorithm to train a predictive model. We collected medical records of 1,631 patients who underwent rotator cuff repair surgery at a single center over a span of 5 years. In the end, our model successfully predicted postoperative re-tear before the surgery using 62 preoperative variables with an accuracy of 96.93%, and achieved an accuracy of 79.55% on an independent external dataset of 518 cases from other centers. This model outperforms human doctors in predicting outcomes with high accuracy. Through this methodology and research, our aim is to utilize preoperative prediction models to assist in making informed medical decisions during and after surgery, leading to improved treatment effectiveness. This research method and strategy can be applied to other medical fields, and the research findings can assist in making healthcare decisions.

PMID:38487743 | PMC:PMC10938848 | DOI:10.3389/frai.2024.1331853

Front Oncol. 2024 Feb 29;14:1295251. doi: 10.3389/fonc.2024.1295251. eCollection 2024.

ABSTRACT

INTRODUCTION: Manual review of organ at risk (OAR) contours is crucial for creating safe radiotherapy plans but can be time-consuming and error prone. Statistical and deep learning models show the potential to automatically detect improper contours by identifying outliers using large sets of acceptable data (knowledge-based outlier detection) and may be able to assist human reviewers during review of OAR contours.

METHODS: This study developed an automated knowledge-based outlier detection method and assessed its ability to detect erroneous contours for all common head and neck (HN) OAR types used clinically at our institution. We utilized 490 accurate CT-based HN structure sets from unique patients, each with forty-two HN OAR contours when anatomically present. The structure sets were distributed as 80% for training, 10% for validation, and 10% for testing. In addition, 190 and 37 simulated contours containing errors were added to the validation and test sets, respectively. Single-contour features, including location, shape, orientation, volume, and CT number, were used to train three single-contour feature models (z-score, Mahalanobis distance [MD], and autoencoder [AE]). Additionally, a novel contour-to-contour relationship (CCR) model was trained using the minimum distance and volumetric overlap between pairs of OAR contours to quantify overlap and separation. Inferences from single-contour feature models were combined with the CCR model inferences and inferences evaluating the number of disconnected parts in a single contour and then compared.

RESULTS: In the test dataset, before combination with the CCR model, the area under the curve values were 0.922/0.939/0.939 for the z-score, MD, and AE models respectively for all contours. After combination with CCR model inferences, the z-score, MD, and AE had sensitivities of 0.838/0.892/0.865, specificities of 0.922/0.907/0.887, and balanced accuracies (BA) of 0.880/0.900/0.876 respectively. In the validation dataset, with similar overall performance and no signs of overfitting, model performance for individual OAR types was assessed. The combined AE model demonstrated minimum, median, and maximum BAs of 0.729, 0.908, and 0.980 across OAR types.

DISCUSSION: Our novel knowledge-based method combines models utilizing single-contour and CCR features to effectively detect erroneous OAR contours across a comprehensive set of 42 clinically used OAR types for HN radiotherapy.

PMID:38487718 | PMC:PMC10937434 | DOI:10.3389/fonc.2024.1295251