IEEE J Biomed Health Inform. 2024 Jul 10;PP. doi: 10.1109/JBHI.2024.3426068. Online ahead of print.

ABSTRACT

Congenital heart disease (CHD) is the most common congenital disability affecting healthy development and growth, even resulting in pregnancy termination or fetal death. Recently, deep learning techniques have made remarkable progress to assist in diagnosing CHD. One very popular method is directly classifying fetal ultrasound images, recognized as abnormal and normal, which tends to focus more on global features and neglects semantic knowledge of anatomical structures. The other approach is segmentation-based diagnosis, which requires a large number of pixel-level annotation masks for training. However, the detailed pixel-level segmentation annotation is costly or even unavailable. Based on the above analysis, we propose SKGC, a universal framework to identify normal or abnormal four-chamber heart (4CH) images, guided by a few annotation masks, while improving accuracy remarkably. SKGC consists of a semantic-level knowledge extraction module (SKEM), a multi-knowledge fusion module (MFM), and a classification module (CM). SKEM is responsible for obtaining high-level semantic knowledge, serving as an abstract representation of the anatomical structures that obstetricians focus on. MFM is a lightweight but efficient module that fuses semantic-level knowledge with the original specific knowledge in ultrasound images. CM classifies the fused knowledge and can be replaced by any advanced classifier. Moreover, we design a new loss function that enhances the constraint between the foreground and background predictions, improving the quality of the semantic-level knowledge. Experimental results on the collected real-world NA-4CH and the publicly FEST datasets show that SKGC achieves impressive performance with the best accuracy of 99.68% and 95.40%, respectively. Notably, the accuracy improves from 74.68% to 88.14% using only 10 labeled masks.

PMID:38985556 | DOI:10.1109/JBHI.2024.3426068

IEEE Trans Neural Netw Learn Syst. 2024 Jul 10;PP. doi: 10.1109/TNNLS.2024.3409573. Online ahead of print.

ABSTRACT

Low-dose computed tomography (LDCT) image reconstruction techniques can reduce patient radiation exposure while maintaining acceptable imaging quality. Deep learning (DL) is widely used in this problem, but the performance of testing data (also known as target domain) is often degraded in clinical scenarios due to the variations that were not encountered in training data (also known as source domain). Unsupervised domain adaptation (UDA) of LDCT reconstruction has been proposed to solve this problem through distribution alignment. However, existing UDA methods fail to explore the usage of uncertainty quantification, which is crucial for reliable intelligent medical systems in clinical scenarios with unexpected variations. Moreover, existing direct alignment for different patients would lead to content mismatch issues. To address these issues, we propose to leverage a probabilistic reconstruction framework to conduct a joint discrepancy minimization between source and target domains in both the latent and image spaces. In the latent space, we devise a Bayesian uncertainty alignment to reduce the epistemic gap between the two domains. This approach reduces the uncertainty level of target domain data, making it more likely to render well-reconstructed results on target domains. In the image space, we propose a sharpness-aware distribution alignment (SDA) to achieve a match of second-order information, which can ensure that the reconstructed images from the target domain have similar sharpness to normal-dose CT (NDCT) images from the source domain. Experimental results on two simulated datasets and one clinical low-dose imaging dataset show that our proposed method outperforms other methods in quantitative and visualized performance.

PMID:38985555 | DOI:10.1109/TNNLS.2024.3409573

JMIR AI. 2024 Jul 10;3:e51118. doi: 10.2196/51118.

ABSTRACT

BACKGROUND: Abdominal auscultation (i.e., listening to bowel sounds (BSs)) can be used to analyze digestion. An automated retrieval of BS would be beneficial to assess gastrointestinal disorders noninvasively.

OBJECTIVE: This study aims to develop a multiscale spotting model to detect BSs in continuous audio data from a wearable monitoring system.

METHODS: We designed a spotting model based on the Efficient-U-Net (EffUNet) architecture to analyze 10-second audio segments at a time and spot BSs with a temporal resolution of 25 ms. Evaluation data were collected across different digestive phases from 18 healthy participants and 9 patients with inflammatory bowel disease (IBD). Audio data were recorded in a daytime setting with a smart T-Shirt that embeds digital microphones. The data set was annotated by independent raters with substantial agreement (Cohen κ between 0.70 and 0.75), resulting in 136 hours of labeled data. In total, 11,482 BSs were analyzed, with a BS duration ranging between 18 ms and 6.3 seconds. The share of BSs in the data set (BS ratio) was 0.0089. We analyzed the performance depending on noise level, BS duration, and BS event rate. We also report spotting timing errors.

RESULTS: Leave-one-participant-out cross-validation of BS event spotting yielded a median F1-score of 0.73 for both healthy volunteers and patients with IBD. EffUNet detected BSs under different noise conditions with 0.73 recall and 0.72 precision. In particular, for a signal-to-noise ratio over 4 dB, more than 83% of BSs were recognized, with precision of 0.77 or more. EffUNet recall dropped below 0.60 for BS duration of 1.5 seconds or less. At a BS ratio greater than 0.05, the precision of our model was over 0.83. For both healthy participants and patients with IBD, insertion and deletion timing errors were the largest, with a total of 15.54 minutes of insertion errors and 13.08 minutes of deletion errors over the total audio data set. On our data set, EffUNet outperformed existing BS spotting models that provide similar temporal resolution.

CONCLUSIONS: The EffUNet spotter is robust against background noise and can retrieve BSs with varying duration. EffUNet outperforms previous BS detection approaches in unmodified audio data, containing highly sparse BS events.

PMID:38985504 | DOI:10.2196/51118

EJNMMI Phys. 2024 Jul 10;11(1):60. doi: 10.1186/s40658-024-00651-1.

ABSTRACT

PURPOSE: 123I-Ioflupane SPECT is an effective tool for the diagnosis and progression assessment of Parkinson's disease (PD). Radiomics and deep learning (DL) can be used to track and analyze the underlying image texture and features to predict the Hoehn-Yahr stages (HYS) of PD. In this study, we aim to predict HYS at year 0 and year 4 after the first diagnosis with combined imaging, radiomics and DL-based features using 123I-Ioflupane SPECT images at year 0.

METHODS: In this study, 161 subjects from the Parkinson's Progressive Marker Initiative database underwent baseline 3T MRI and 123I-Ioflupane SPECT, with HYS assessment at years 0 and 4 after first diagnosis. Conventional imaging features (IF) and radiomic features (RaF) for striatum uptakes were extracted from SPECT images using MRI- and SPECT-based (SPECT-V and SPECT-T) segmentations respectively. A 2D DenseNet was used to predict HYS of PD, and simultaneously generate deep features (DF). The random forest algorithm was applied to develop models based on DF, RaF, IF and combined features to predict HYS (stage 0, 1 and 2) at year 0 and (stage 0, 1 and ≥ 2) at year 4, respectively. Model predictive accuracy and receiver operating characteristic (ROC) analysis were assessed for various prediction models.

RESULTS: For the diagnostic accuracy at year 0, DL (0.696) outperformed most models, except DF + IF in SPECT-V (0.704), significantly superior based on paired t-test. For year 4, accuracy of DF + RaF model in MRI-based method is the highest (0.835), significantly better than DF + IF, IF + RaF, RaF and IF models. And DL (0.820) surpassed models in both SPECT-based methods. The area under the ROC curve (AUC) highlighted DF + RaF model (0.854) in MRI-based method at year 0 and DF + RaF model (0.869) in SPECT-T method at year 4, outperforming DL models, respectively. And then, there was no significant differences between SPECT-based and MRI-based segmentation methods except for the imaging feature models.

CONCLUSION: The combination of radiomic and deep features enhances the prediction accuracy of PD HYS compared to only radiomics or DL. This suggests the potential for further advancements in predictive model performance for PD HYS at year 0 and year 4 after first diagnosis using 123I-Ioflupane SPECT images at year 0, thereby facilitating early diagnosis and treatment for PD patients. No significant difference was observed in radiomics results obtained between MRI- and SPECT-based striatum segmentations for radiomic and deep features.

PMID:38985382 | DOI:10.1186/s40658-024-00651-1

Osteoporos Int. 2024 Jul 10. doi: 10.1007/s00198-024-07179-1. Online ahead of print.

ABSTRACT

PURPOSE: This scoping review aimed to assess the current research on artificial intelligence (AI)--enhanced opportunistic screening approaches for stratifying osteoporosis and osteopenia risk by evaluating vertebral trabecular bone structure in CT scans.

METHODS: PubMed, Scopus, and Web of Science databases were systematically searched for studies published between 2018 and December 2023. Inclusion criteria encompassed articles focusing on AI techniques for classifying osteoporosis/osteopenia or determining bone mineral density using CT scans of vertebral bodies. Data extraction included study characteristics, methodologies, and key findings.

RESULTS: Fourteen studies met the inclusion criteria. Three main approaches were identified: fully automated deep learning solutions, hybrid approaches combining deep learning and conventional machine learning, and non-automated solutions using manual segmentation followed by AI analysis. Studies demonstrated high accuracy in bone mineral density prediction (86-96%) and classification of normal versus osteoporotic subjects (AUC 0.927-0.984). However, significant heterogeneity was observed in methodologies, workflows, and ground truth selection.

CONCLUSIONS: The review highlights AI's promising potential in enhancing opportunistic screening for osteoporosis using CT scans. While the field is still in its early stages, with most solutions at the proof-of-concept phase, the evidence supports increased efforts to incorporate AI into radiologic workflows. Addressing knowledge gaps, such as standardizing benchmarks and increasing external validation, will be crucial for advancing the clinical application of these AI-enhanced screening methods. Integration of such technologies could lead to improved early detection of osteoporotic conditions at a low economic cost.

PMID:38985200 | DOI:10.1007/s00198-024-07179-1

Eur Radiol. 2024 Jul 10. doi: 10.1007/s00330-024-10907-0. Online ahead of print.

ABSTRACT

OBJECTIVES: The accurate detection and precise segmentation of lung nodules on computed tomography are key prerequisites for early diagnosis and appropriate treatment of lung cancer. This study was designed to compare detection and segmentation methods for pulmonary nodules using deep-learning techniques to fill methodological gaps and biases in the existing literature.

METHODS: This study utilized a systematic review with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, searching PubMed, Embase, Web of Science Core Collection, and the Cochrane Library databases up to May 10, 2023. The Quality Assessment of Diagnostic Accuracy Studies 2 criteria was used to assess the risk of bias and was adjusted with the Checklist for Artificial Intelligence in Medical Imaging. The study analyzed and extracted model performance, data sources, and task-focus information.

RESULTS: After screening, we included nine studies meeting our inclusion criteria. These studies were published between 2019 and 2023 and predominantly used public datasets, with the Lung Image Database Consortium Image Collection and Image Database Resource Initiative and Lung Nodule Analysis 2016 being the most common. The studies focused on detection, segmentation, and other tasks, primarily utilizing Convolutional Neural Networks for model development. Performance evaluation covered multiple metrics, including sensitivity and the Dice coefficient.

CONCLUSIONS: This study highlights the potential power of deep learning in lung nodule detection and segmentation. It underscores the importance of standardized data processing, code and data sharing, the value of external test datasets, and the need to balance model complexity and efficiency in future research.

CLINICAL RELEVANCE STATEMENT: Deep learning demonstrates significant promise in autonomously detecting and segmenting pulmonary nodules. Future research should address methodological shortcomings and variability to enhance its clinical utility.

KEY POINTS: Deep learning shows potential in the detection and segmentation of pulmonary nodules. There are methodological gaps and biases present in the existing literature. Factors such as external validation and transparency affect the clinical application.

PMID:38985185 | DOI:10.1007/s00330-024-10907-0

Radiol Artif Intell. 2024 Jul 10:e230254. doi: 10.1148/ryai.230254. Online ahead of print.

ABSTRACT

"Just Accepted" papers have undergone full peer review and have been accepted for publication in Radiology: Artificial Intelligence. This article will undergo copyediting, layout, and proof review before it is published in its final version. Please note that during production of the final copyedited article, errors may be discovered which could affect the content. Purpose To develop, externally test, and evaluate clinical acceptability of a deep learning (DL) pediatric brain tumor segmentation model using stepwise transfer learning. Materials and Methods In this retrospective study, the authors leveraged two T2-weighted MRI datasets (May 2001-December 2015) from a national brain tumor consortium (n = 184; median age, 7 years (range: 1-23 years); 94 male) and a pediatric cancer center (n = 100; median age, 8 years (range: 1-19 years); 47 male) to develop and evaluate DL neural networks for pediatric low-grade glioma segmentation using a novel stepwise transfer learning approach to maximize performance in a limited data scenario. The best model was externally-tested on an independent test set and subjected to randomized, blinded evaluation by three clinicians, wherein they assessed clinical acceptability of expert- and artificial intelligence (AI)-generated segmentations via 10-point Likert scales and Turing tests. Results The best AI model used in-domain, stepwise transfer learning (median DSC: 0.88 [IQR 0.72-0.91] versus 0.812 [0.56-0.89] for baseline model; P = .049). On external testing, AI model yielded excellent accuracy using reference standards from three clinical experts (Expert-1: 0.83 [0.75-0.90]; Expert-2: 0.81 [0.70-0.89]; Expert-3: 0.81 [0.68-0.88]; mean accuracy: 0.82)). On clinical benchmarking (n = 100 scans), experts rated AI-based segmentations higher on average compared with other experts (median Likert score: median 9 [IQR 7-9]) versus 7 [IQR 7-9]) and rated more AI segmentations as clinically acceptable (80.2% versus 65.4%). Experts correctly predicted the origin of AI segmentations in an average of 26.0% of cases. Conclusion Stepwise transfer learning enabled expert-level, automated pediatric brain tumor auto-segmentation and volumetric measurement with a high level of clinical acceptability. ©RSNA, 2024.

PMID:38984985 | DOI:10.1148/ryai.230254

Radiol Artif Intell. 2024 Jul 10:e240076. doi: 10.1148/ryai.240076. Online ahead of print.

ABSTRACT

"Just Accepted" papers have undergone full peer review and have been accepted for publication in Radiology: Artificial Intelligence. This article will undergo copyediting, layout, and proof review before it is published in its final version. Please note that during production of the final copyedited article, errors may be discovered which could affect the content. Purpose To develop a deep learning algorithm to predict 2-year neurodevelopmental outcomes in neonates with hypoxic-ischemic encephalopathy (HIE) using MRI and basic clinical data. Materials and Methods In this study, MRI data of term neonates with encephalopathy in the High Dose Erythropoietin for Asphyxia (HEAL) trial (ClinicalTrials.gov: NCT02811263), who were enrolled from 17 institutions between January 25th, 2017 and October ninth, 2019, were retrospectively analyzed. The harmonized MRI protocol included T1-weighted, T2-weighted, and diffusion tensor imaging. Deep learning classifiers were trained to predict the primary outcome of the HEAL trial (death or any neurodevelopmental impairment [NDI] at 2 years) using multisequence MRI and basic clinical variables, including sex and gestational age at birth. Model performance was evaluated on a test sets comprising 10% of cases from 15 institutions (in-distribution test set, n = 41) and 100% of cases from 2 institutions (out-of-distribution test set, n = 41). Model performance in predicting additional secondary outcomes, including death alone, was also assessed. Results For the 414 neonates (mean gestational age, 39 weeks ± 1.4, 232 males, 182 females), in the study cohort, 198 (48%) died or had any NDI at 2 years. The deep learning model achieved an area under the receiver operating characteristic curve (AUC) of 0.74 (95% CI: 0.60-0.86) and 63% accuracy on the in-distribution test set and an AUC of 0.77 (95% CI: 0.63-0.90) and 78% accuracy on the out-of-distribution test set. Performance was similar or better for predicting secondary outcomes. Conclusion Deep learning analysis of neonatal brain MRI yielded high performance for predicting 2-year neurodevelopmental outcomes. ©RSNA, 2024.

PMID:38984984 | DOI:10.1148/ryai.240076

Transl Vis Sci Technol. 2024 Jul 1;13(7):10. doi: 10.1167/tvst.13.7.10.

ABSTRACT

PURPOSE: The purpose of this study was to establish and validate a deep learning model to screen vascular aging using retinal fundus images. Although vascular aging is considered a novel cardiovascular risk factor, the assessment methods are currently limited and often only available in developed regions.

METHODS: We used 8865 retinal fundus images and clinical parameters of 4376 patients from two independent datasets for training a deep learning algorithm. The gold standard for vascular aging was defined as a pulse wave velocity ≥1400 cm/s. The probability of the presence of vascular aging was defined as deep learning retinal vascular aging score, the Reti-aging score. We compared the performance of the deep learning model and clinical parameters by calculating the area under the receiver operating characteristics curve (AUC). We recruited clinical specialists, including ophthalmologists and geriatricians, to assess vascular aging in patients using retinal fundus images, aiming to compare the diagnostic performance between deep learning models and clinical specialists. Finally, the potential of Reti-aging score for identifying new-onset hypertension (NH) and new-onset carotid artery plaque (NCP) in the subsequent three years was examined.

RESULTS: The Reti-aging score model achieved an AUC of 0.826 (95% confidence interval [CI] = 0.793-0.855) and 0.779 (95% CI = 0.765-0.794) in the internal and external dataset. It showed better performance in predicting vascular aging compared with the prediction with clinical parameters. The average accuracy of ophthalmologists (66.3%) was lower than that of the Reti-aging score model, whereas geriatricians were unable to make predictions based on retinal fundus images. The Reti-aging score was associated with the risk of NH and NCP (P < 0.05).

CONCLUSIONS: The Reti-aging score model might serve as a novel method to predict vascular aging through analysis of retinal fundus images. Reti-aging score provides a novel indicator to predict new-onset cardiovascular diseases.

TRANSLATIONAL RELEVANCE: Given the robust performance of our model, it provides a new and reliable method for screening vascular aging, especially in undeveloped areas.

PMID:38984914 | DOI:10.1167/tvst.13.7.10

Med Phys. 2024 Jul 10. doi: 10.1002/mp.17297. Online ahead of print.

ABSTRACT

BACKGROUND: Positron emission tomography (PET) has been investigated for its ability to reconstruct proton-induced positron activity distributions in proton therapy. This technique holds potential for range verification in clinical practice. Recently, deep learning-based dose estimation from positron activity distributions shows promise for in vivo proton dose monitoring and guided proton therapy.

PURPOSE: This study evaluates the effectiveness of three classical neural network models, recurrent neural network (RNN), U-Net, and Transformer, for proton dose estimating. It also investigates the characteristics of these models, providing valuable insights for selecting the appropriate model in clinical practice.

METHODS: Proton dose calculations for spot beams were simulated using Geant4. Computed tomography (CT) images from four head cases were utilized, with three for training neural networks and the remaining one for testing. The neural networks were trained with one-dimensional (1D) positron activity distributions as inputs and generated 1D dose distributions as outputs. The impact of the number of training samples on the networks was examined, and their dose prediction performance in both homogeneous brain and heterogeneous nasopharynx sites was evaluated. Additionally, the effect of positron activity distribution uncertainty on dose prediction performance was investigated. To quantitatively evaluate the models, mean relative error (MRE) and absolute range error (ARE) were used as evaluation metrics.

RESULTS: The U-Net exhibited a notable advantage in range verification with a smaller number of training samples, achieving approximately 75% of AREs below 0.5 mm using only 500 training samples. The networks performed better in the homogeneous brain site compared to the heterogeneous nasopharyngeal site. In the homogeneous brain site, all networks exhibited small AREs, with approximately 90% of the AREs below 0.5 mm. The Transformer exhibited the best overall dose distribution prediction, with approximately 92% of MREs below 3%. In the heterogeneous nasopharyngeal site, all networks demonstrated acceptable AREs, with approximately 88% of AREs below 3 mm. The Transformer maintained the best overall dose distribution prediction, with approximately 85% of MREs below 5%. The performance of all three networks in dose prediction declined as the uncertainty of positron activity distribution increased, and the Transformer consistently outperformed the other networks in all cases.

CONCLUSIONS: Both the U-Net and the Transformer have certain advantages in the proton dose estimation task. The U-Net proves well suited for range verification with a small training sample size, while the Transformer outperforms others at dose-guided proton therapy.

PMID:38984805 | DOI:10.1002/mp.17297

Bioinformatics. 2024 Jul 10:btae405. doi: 10.1093/bioinformatics/btae405. Online ahead of print.

ABSTRACT

MOTIVATION: Identifying the binding sites of antibodies is essential for developing vaccines and synthetic antibodies. In this paper, we investigate the optimal representation for predicting the binding sites in the two molecules and emphasize the importance of geometric information.

RESULTS: Specifically, we compare different geometric deep learning methods applied to proteins' inner (I-GEP) and outer (O-GEP) structures. We incorporate 3D coordinates and spectral geometric descriptors as input features to fully leverage the geometric information. Our research suggests that different geometrical representation information are useful for different tasks. Surface-based models are more efficient in predicting the binding of the epitope, while graph models are better in paratope prediction, both achieving significant performance improvements. Moreover we analyse the impact of structural changes in antibodies and antigens resulting from conformational rearrangements or reconstruction errors. Through this investigation, we showcase the robustness of geometric deep learning methods and spectral geometric descriptors to such perturbations.

AVAILABILITY AND IMPLEMENTATION: The python code for the models and the processing pipeline is open-source and available at https://github.com/Marco-Peg/GEP.

SUPPLEMENTARY INFORMATION: The supplementary material includes comprehensive details about the proposed method and additional results.

PMID:38984742 | DOI:10.1093/bioinformatics/btae405

Front Ophthalmol (Lausanne). 2024 Mar 6;4:1368081. doi: 10.3389/fopht.2024.1368081. eCollection 2024.

ABSTRACT

With advancements in the implementation of artificial intelligence (AI) in different ophthalmology disciplines, it continues to have a significant impact on glaucoma diagnosis and screening. This article explores the distinct roles of AI in specialized ophthalmology clinics and general practice, highlighting the critical balance between sensitivity and specificity in diagnostic and screening models. Screening models prioritize sensitivity to detect potential glaucoma cases efficiently, while diagnostic models emphasize specificity to confirm disease with high accuracy. AI applications, primarily using machine learning (ML) and deep learning (DL), have been successful in detecting glaucomatous optic neuropathy from colored fundus photographs and other retinal imaging modalities. Diagnostic models integrate data extracted from various forms of modalities (including tests that assess structural optic nerve damage as well as those evaluating functional damage) to provide a more nuanced, accurate and thorough approach to diagnosing glaucoma. As AI continues to evolve, the collaboration between technology and clinical expertise should focus more on improving specificity of glaucoma diagnostic models to assess ophthalmologists to revolutionize glaucoma diagnosis and improve patients care.

PMID:38984126 | PMC:PMC11182276 | DOI:10.3389/fopht.2024.1368081

Front Ophthalmol (Lausanne). 2024 May 17;4:1380701. doi: 10.3389/fopht.2024.1380701. eCollection 2024.

ABSTRACT

INTRODUCTION: The application of artificial intelligence (AI) systems in ophthalmology is rapidly expanding. Early detection and management of keratoconus is important for preventing disease progression and the need for corneal transplant. We review studies regarding the utility of AI in the diagnosis and management of keratoconus and other corneal ectasias.

METHODS: We conducted a systematic search for relevant original, English-language research studies in the PubMed, Web of Science, Embase, and Cochrane databases from inception to October 31, 2023, using a combination of the following keywords: artificial intelligence, deep learning, machine learning, keratoconus, and corneal ectasia. Case reports, literature reviews, conference proceedings, and editorials were excluded. We extracted the following data from each eligible study: type of AI, input used for training, output, ground truth or reference, dataset size, availability of algorithm/model, availability of dataset, and major study findings.

RESULTS: Ninety-three original research studies were included in this review, with the date of publication ranging from 1994 to 2023. The majority of studies were regarding the use of AI in detecting keratoconus or subclinical keratoconus (n=61). Among studies regarding keratoconus diagnosis, the most common inputs were corneal topography, Scheimpflug-based corneal tomography, and anterior segment-optical coherence tomography. This review also summarized 16 original research studies regarding AI-based assessment of severity and clinical features, 7 studies regarding the prediction of disease progression, and 6 studies regarding the characterization of treatment response. There were only three studies regarding the use of AI in identifying susceptibility genes involved in the etiology and pathogenesis of keratoconus.

DISCUSSION: Algorithms trained on Scheimpflug-based tomography seem promising tools for the early diagnosis of keratoconus that can be particularly applied in low-resource communities. Future studies could investigate the application of AI models trained on multimodal patient information for staging keratoconus severity and tracking disease progression.

PMID:38984114 | PMC:PMC11182163 | DOI:10.3389/fopht.2024.1380701

Adv Neural Inf Process Syst. 2023 Dec;36:79376-79398.

ABSTRACT

Neuroprostheses show potential in restoring lost sensory function and enhancing human capabilities, but the sensations produced by current devices often seem unnatural or distorted. Exact placement of implants and differences in individual perception lead to significant variations in stimulus response, making personalized stimulus optimization a key challenge. Bayesian optimization could be used to optimize patient-specific stimulation parameters with limited noisy observations, but is not feasible for high-dimensional stimuli. Alternatively, deep learning models can optimize stimulus encoding strategies, but typically assume perfect knowledge of patient-specific variations. Here we propose a novel, practically feasible approach that overcomes both of these fundamental limitations. First, a deep encoder network is trained to produce optimal stimuli for any individual patient by inverting a forward model mapping electrical stimuli to visual percepts. Second, a preferential Bayesian optimization strategy utilizes this encoder to optimize patient-specific parameters for a new patient, using a minimal number of pairwise comparisons between candidate stimuli. We demonstrate the viability of this approach on a novel, state-of-the-art visual prosthesis model. We show that our approach quickly learns a personalized stimulus encoder, leads to dramatic improvements in the quality of restored vision, and is robust to noisy patient feedback and misspecifications in the underlying forward model. Overall, our results suggest that combining the strengths of deep learning and Bayesian optimization could significantly improve the perceptual experience of patients fitted with visual prostheses and may prove a viable solution for a range of neuroprosthetic technologies.

PMID:38984104 | PMC:PMC11232484

JACC Basic Transl Sci. 2024 May 27;9(5):674-686. doi: 10.1016/j.jacbts.2024.02.007. eCollection 2024 May.

ABSTRACT

The adult mammalian heart harbors minute levels of cycling cardiomyocytes (CMs). Large numbers of images are needed to accurately quantify cycling events using microscopy-based methods. CardioCount is a new deep learning-based pipeline to rigorously score nuclei in microscopic images. When applied to a repository of 368,434 human microscopic images, we found evidence of coupled growth between CMs and cardiac endothelial cells in the adult human heart. Additionally, we found that vascular rarefaction and CM hypertrophy are interrelated in end-stage heart failure. CardioCount is available for use via GitHub and via Google Colab for users with minimal machine learning experience.

PMID:38984052 | PMC:PMC11228115 | DOI:10.1016/j.jacbts.2024.02.007

JACC Basic Transl Sci. 2024 May 27;9(5):687-688. doi: 10.1016/j.jacbts.2024.04.002. eCollection 2024 May.

NO ABSTRACT

PMID:38984048 | PMC:PMC11228390 | DOI:10.1016/j.jacbts.2024.04.002

Biol Methods Protoc. 2024 Jun 18;9(1):bpae043. doi: 10.1093/biomethods/bpae043. eCollection 2024.

ABSTRACT

Proteins are complex biomolecules essential for numerous biological processes, making them crucial targets for advancements in molecular biology, medical research, and drug design. Understanding their intricate, hierarchical structures, and functions is vital for progress in these fields. To capture this complexity, we introduce Multimodal Protein Representation Learning (MPRL), a novel framework for symmetry-preserving multimodal pretraining that learns unified, unsupervised protein representations by integrating primary and tertiary structures. MPRL employs Evolutionary Scale Modeling (ESM-2) for sequence analysis, Variational Graph Auto-Encoders (VGAE) for residue-level graphs, and PointNet Autoencoder (PAE) for 3D point clouds of atoms, each designed to capture the spatial and evolutionary intricacies of proteins while preserving critical symmetries. By leveraging Auto-Fusion to synthesize joint representations from these pretrained models, MPRL ensures robust and comprehensive protein representations. Our extensive evaluation demonstrates that MPRL significantly enhances performance in various tasks such as protein-ligand binding affinity prediction, protein fold classification, enzyme activity identification, and mutation stability prediction. This framework advances the understanding of protein dynamics and facilitates future research in the field. Our source code is publicly available at https://github.com/HySonLab/Protein_Pretrain.

PMID:38983679 | PMC:PMC11233121 | DOI:10.1093/biomethods/bpae043

Front Surg. 2024 Jun 25;11:1418679. doi: 10.3389/fsurg.2024.1418679. eCollection 2024.

ABSTRACT

OBJECTIVE: The development of surgical microscope-associated cameras has given rise to a new operating style embodied by hybrid microsurgical and exoscopic operative systems. These platforms utilize specialized camera systems to visualize cranial neuroanatomy at various depths. Our study aims to understand how different camera settings in a novel hybrid exoscope system influence image quality in the context of neurosurgical procedures.

METHODS: We built an image database using captured cadaveric dissection images obtained with a prototype version of a hybrid (microsurgical/exoscopic) operative platform. We performed comprehensive 4K-resolution image capture using 76 camera settings across three magnification levels and two working distances. Computer algorithms such as structural similarity (SSIM) and mean squared error (MSE) were used to measure image distortion across different camera settings. We utilized a Laplacian filter to compute the overall sharpness of the acquired images. Additionally, a monocular depth estimation deep learning model was used to examine the image's capability to visualize the depth of deeper structures accurately.

RESULTS: A total of 1,368 high-resolution pictures were captured. The SSIM index ranged from 0.63 to 0.85. The MSE was nearly zero for all image batches. It was determined that the exoscope could accurately detect both the sharpness and depth based on the Laplacian filter and depth maps, respectively. Our findings demonstrate that users can utilize the full range of camera settings available on the exoscope, including adjustments to aperture, color saturation, contrast, sharpness, and brilliance, without introducing significant image distortions relative to the standard mode.

CONCLUSION: The evolution of the camera incorporated into a surgical microscope enables exoscopic visualization during cranial base surgery. Our result should encourage surgeons to take full advantage of the exoscope's extensive range of camera settings to match their personal preferences or specific clinical requirements of the surgical scenario. This places the exoscope as an invaluable asset in contemporary surgical practice, merging high-definition imaging with ergonomic design and adaptable operability.

PMID:38983589 | PMC:PMC11231637 | DOI:10.3389/fsurg.2024.1418679

Front Ophthalmol (Lausanne). 2022 Sep 21;2:937205. doi: 10.3389/fopht.2022.937205. eCollection 2022.

ABSTRACT

Glaucoma is a leading cause of progressive blindness and visual impairment worldwide. Microstructural evidence of glaucomatous damage to the optic nerve head and associated tissues can be visualized using optical coherence tomography (OCT). In recent years, development of novel deep learning (DL) algorithms has led to innovative advances and improvements in automated detection of glaucomatous damage and progression on OCT imaging. DL algorithms have also been trained utilizing OCT data to improve detection of glaucomatous damage on fundus photography, thus improving the potential utility of color photos which can be more easily collected in a wider range of clinical and screening settings. This review highlights ten years of contributions to glaucoma detection through advances in deep learning models trained utilizing OCT structural data and posits future directions for translation of these discoveries into the field of aging and the basic sciences.

PMID:38983522 | PMC:PMC11182271 | DOI:10.3389/fopht.2022.937205

World J Clin Cases. 2024 Jun 26;12(18):3340-3350. doi: 10.12998/wjcc.v12.i18.3340.

ABSTRACT

BACKGROUND: Enhanced magnetic resonance imaging (MRI) is widely used in the diagnosis, treatment and prognosis of hepatocellular carcinoma (HCC), but it can not effectively reflect the heterogeneity within the tumor and evaluate the effect after treatment. Preoperative imaging analysis of voxel changes can effectively reflect the internal heterogeneity of the tumor and evaluate the progression-free survival (PFS).

AIM: To predict the PFS of patients with HCC before operation by building a model with enhanced MRI images.

METHODS: Delineate the regions of interest (ROI) in arterial phase, portal venous phase and delayed phase of enhanced MRI. After extracting the combinatorial features of ROI, the features are fused to obtain deep learning radiomics (DLR)_Sig. DeLong's test was used to evaluate the diagnostic performance of different typological features. K-M analysis was applied to assess PFS in different risk groups, and the discriminative ability of the model was evaluated using the C-index.

RESULTS: Tumor diameter and diolame were independent factors influencing the prognosis of PFS. Delong's test revealed multi-phase combined radiomic features had significantly greater area under the curve values than did those of the individual phases (P < 0.05).In deep transfer learning (DTL) and DLR, significant differences were observed between the multi-phase and individual phases feature sets (P < 0.05). K-M survival analysis revealed a median survival time of high risk group and low risk group was 12.8 and 14.2 months, respectively, and the predicted probabilities of 6 months, 1 year and 2 years were 92%, 60%, 40% and 98%, 90%,73%, respectively. The C-index was 0.764, indicating relatively good consistency between the predicted and observed results. DTL and DLR have higher predictive value for 2-year PFS in nomogram.

CONCLUSION: Based on the multi-temporal characteristics of enhanced MRI and the constructed Nomograph, it provides a new strategy for predicting the PFS of transarterial chemoembolization treatment of HCC.

PMID:38983440 | PMC:PMC11229926 | DOI:10.12998/wjcc.v12.i18.3340