BMC Bioinformatics. 2024 May 3;25(1):175. doi: 10.1186/s12859-024-05799-2.

ABSTRACT

BACKGROUD: Modelling discrete-time cause-specific hazards in the presence of competing events and non-proportional hazards is a challenging task in many domains. Survival analysis in longitudinal cohorts often requires such models; notably when the data is gathered at discrete points in time and the predicted events display complex dynamics. Current models often rely on strong assumptions of proportional hazards, that is rarely verified in practice; or do not handle sequential data in a meaningful way. This study proposes a Transformer architecture for the prediction of cause-specific hazards in discrete-time competing risks. Contrary to Multilayer perceptrons that were already used for this task (DeepHit), the Transformer architecture is especially suited for handling complex relationships in sequential data, having displayed state-of-the-art performance in numerous tasks with few underlying assumptions on the task at hand.

RESULTS: Using synthetic datasets of 2000-50,000 patients, we showed that our Transformer model surpassed the CoxPH, PyDTS, and DeepHit models for the prediction of cause-specific hazard, especially when the proportional assumption did not hold. The error along simulated time outlined the ability of our model to anticipate the evolution of cause-specific hazards at later time steps where few events are observed. It was also superior to current models for prediction of dementia and other psychiatric conditions in the English longitudinal study of ageing cohort using the integrated brier score and the time-dependent concordance index. We also displayed the explainability of our model's prediction using the integrated gradients method.

CONCLUSIONS: Our model provided state-of-the-art prediction of cause-specific hazards, without adopting prior parametric assumptions on the hazard rates. It outperformed other models in non-proportional hazards settings for both the synthetic dataset and the longitudinal cohort study. We also observed that basic models such as CoxPH were more suited to extremely simple settings than deep learning models. Our model is therefore especially suited for survival analysis on longitudinal cohorts with complex dynamics of the covariate-to-outcome relationship, which are common in clinical practice. The integrated gradients provided the importance scores of input variables, which indicated variables guiding the model in its prediction. This model is ready to be utilized for time-to-event prediction in longitudinal cohorts.

PMID:38702609 | DOI:10.1186/s12859-024-05799-2

Sci Bull (Beijing). 2024 Mar 29:S2095-9273(24)00217-2. doi: 10.1016/j.scib.2024.03.061. Online ahead of print.

ABSTRACT

An intraoperative diagnosis is critical for precise cancer surgery. However, traditional intraoperative assessments based on hematoxylin and eosin (H&E) histology, such as frozen section, are time-, resource-, and labor-intensive, and involve specimen-consuming concerns. Here, we report a near-real-time automated cancer diagnosis workflow for breast cancer that combines dynamic full-field optical coherence tomography (D-FFOCT), a label-free optical imaging method, and deep learning for bedside tumor diagnosis during surgery. To classify the benign and malignant breast tissues, we conducted a prospective cohort trial. In the modeling group (n = 182), D-FFOCT images were captured from April 26 to June 20, 2018, encompassing 48 benign lesions, 114 invasive ductal carcinoma (IDC), 10 invasive lobular carcinoma, 4 ductal carcinoma in situ (DCIS), and 6 rare tumors. Deep learning model was built up and fine-tuned in 10,357 D-FFOCT patches. Subsequently, from June 22 to August 17, 2018, independent tests (n = 42) were conducted on 10 benign lesions, 29 IDC, 1 DCIS, and 2 rare tumors. The model yielded excellent performance, with an accuracy of 97.62%, sensitivity of 96.88% and specificity of 100%; only one IDC was misclassified. Meanwhile, the acquisition of the D-FFOCT images was non-destructive and did not require any tissue preparation or staining procedures. In the simulated intraoperative margin evaluation procedure, the time required for our novel workflow (approximately 3 min) was significantly shorter than that required for traditional procedures (approximately 30 min). These findings indicate that the combination of D-FFOCT and deep learning algorithms can streamline intraoperative cancer diagnosis independently of traditional pathology laboratory procedures.

PMID:38702279 | DOI:10.1016/j.scib.2024.03.061

J Formos Med Assoc. 2024 May 2:S0929-6646(24)00216-X. doi: 10.1016/j.jfma.2024.04.016. Online ahead of print.

ABSTRACT

The purpose of this study is to establish a deep learning automatic assistance diagnosis system for benign and malignant classification of mediastinal lesions in endobronchial ultrasound (EBUS) images. EBUS images are in the form of video and contain multiple imaging modes. Different imaging modes and different frames can reflect the different characteristics of lesions. Compared with previous studies, the proposed model can efficiently extract and integrate the spatiotemporal relationships between different modes and does not require manual selection of representative frames. In recent years, Vision Transformer has received much attention in the field of computer vision. Combined with convolutional neural networks, hybrid transformers can also perform well on small datasets. This study designed a novel deep learning architecture based on hybrid transformer called TransEBUS. By adding learnable parameters in the temporal dimension, TransEBUS was able to extract spatiotemporal features from insufficient data. In addition, we designed a two-stream module to integrate information from three different imaging modes of EBUS. Furthermore, we applied contrastive learning when training TransEBUS, enabling it to learn discriminative representation of benign and malignant mediastinal lesions. The results show that TransEBUS achieved a diagnostic accuracy of 82% and an area under the curve of 0.8812 in the test dataset, outperforming other methods. It also shows that several models can improve performance by incorporating two-stream module. Our proposed system has shown its potential to help physicians distinguishing benign and malignant mediastinal lesions, thereby ensuring the accuracy of EBUS examination.

PMID:38702216 | DOI:10.1016/j.jfma.2024.04.016

Acad Radiol. 2024 May 2:S1076-6332(24)00221-6. doi: 10.1016/j.acra.2024.04.012. Online ahead of print.

ABSTRACT

RATIONALE AND OBJECTIVES: To develop and validate a deep learning radiomics (DLR) model based on contrast-enhanced computed tomography (CT) to identify the primary source of liver metastases.

MATERIALS AND METHODS: In total, 657 liver metastatic lesions, including breast cancer (BC), lung cancer (LC), colorectal cancer (CRC), gastric cancer (GC), and pancreatic cancer (PC), from 428 patients were collected at three clinical centers from January 2018 to October 2023 series. The lesions were randomly assigned to the training and validation sets in a 7:3 ratio. An additional 112 lesions from 61 patients at another clinical center served as an external test set. A DLR model based on contrast-enhanced CT of the liver was developed to distinguish the five pathological types of liver metastases. Stepwise classification was performed to improve the classification efficiency of the model. Lesions were first classified as digestive tract cancer (DTC) and non-digestive tract cancer (non-DTC). DTCs were divided into CRC, GC, and PC and non-DTCs were divided into LC and BC. To verify the feasibility of the DLR model, we trained classical machine learning (ML) models as comparison models. Model performance was evaluated using accuracy (ACC) and area under the receiver operating characteristic curve (AUC).

RESULTS: The classification model constructed by the DLR algorithm showed excellent performance in the classification task compared to ML models. Among the five categories task, highest ACC and average AUC were achieved at 0.563 and 0.796 in the validation set, respectively. In the DTC and non-DTC and the LC and BC classification tasks, AUC was achieved at 0.907 and 0.809 and ACC was achieved at 0.843 and 0.772, respectively. In the CRC, GC, and PC classification task, ACC and average AUC were the highest, at 0.714 and 0.811, respectively.

CONCLUSION: The DLR model is an effective method for identifying the primary source of liver metastases.

PMID:38702214 | DOI:10.1016/j.acra.2024.04.012

Acad Radiol. 2024 May 2:S1076-6332(24)00219-8. doi: 10.1016/j.acra.2024.03.044. Online ahead of print.

ABSTRACT

RATIONALE AND OBJECTIVES: We present a machine learning and computer vision approach for a localized, automated, and standardized scoring of Crohn's disease (CD) severity in the small bowel, overcoming the current limitations of manual measurements CT enterography (CTE) imaging and qualitative assessments, while also considering the complex anatomy and distribution of the disease.

MATERIALS AND METHODS: Two radiologists introduced a severity score and evaluated disease severity at 7.5 mm intervals along the curved planar reconstruction of the distal and terminal ileum using 236 CTE scans. A hybrid model, combining deep-learning, 3-D CNN, and Random Forest model, was developed to classify disease severity at each mini-segment. Precision, sensitivity, weighted Cohen's score, and accuracy were evaluated on a 20% hold-out test set.

RESULTS: The hybrid model achieved precision and sensitivity ranging from 42.4% to 84.1% for various severity categories (normal, mild, moderate, and severe) on the test set. The model's Cohen's score (κ = 0.83) and accuracy (70.7%) were comparable to the inter-observer agreement between experienced radiologists (κ = 0.87, accuracy = 76.3%). The model accurately predicted disease length, correlated with radiologist-reported disease length (r = 0.83), and accurately identified the portion of total ileum containing moderate-to-severe disease with an accuracy of 91.51%.

CONCLUSION: The proposed automated hybrid model offers a standardized, reproducible, and quantitative local assessment of small bowel CD severity and demonstrates its value in CD severity assessment.

PMID:38702212 | DOI:10.1016/j.acra.2024.03.044

J Neurointerv Surg. 2024 May 3:jnis-2024-021718. doi: 10.1136/jnis-2024-021718. Online ahead of print.

ABSTRACT

BACKGROUND: In mechanical thrombectomy (MT), extracranial vascular tortuosity is among the main determinants of procedure duration and success. Currently, no rapid and reliable method exists to identify the anatomical features precluding fast and stable access to the cervical vessels.

METHODS: A retrospective sample of 513 patients were included in this study. Patients underwent first-line transfemoral MT following anterior circulation large vessel occlusion stroke. Difficult transfemoral access (DTFA) was defined as impossible common carotid catheterization or time from groin puncture to first carotid angiogram >30 min. A machine learning model based on 29 anatomical features automatically extracted from head-and-neck computed tomography angiography (CTA) was developed to predict DTFA. Three experienced raters independently assessed the likelihood of DTFA on a reduced cohort of 116 cases using a Likert scale as benchmark for the model, using preprocedural CTA as well as automatic 3D vascular segmentation separately.

RESULTS: Among the study population, 11.5% of procedures (59/513) presented DTFA. Six different features from the aortic, supra-aortic, and cervical regions were included in the model. Cross-validation resulted in an area under the receiver operating characteristic (AUROC) curve of 0.76 (95% CI 0.75 to 0.76) for DTFA prediction, with high sensitivity for impossible access identification (0.90, 95% CI 0.81 to 0.94). The model outperformed human assessment in the reduced cohort [F1-score (95% CI) by experts with CTA: 0.43 (0.37 to 0.50); experts with 3D segmentation: 0.50 (0.46 to 0.54); and model: 0.70 (0.65 to 0.75)].

CONCLUSIONS: A fully automatic model for DTFA prediction was developed and validated. The presented method improved expert assessment of difficult access prediction in stroke MT. Derived information could be used to guide decisions regarding arterial access for MT.

PMID:38702182 | DOI:10.1136/jnis-2024-021718

JMIR Public Health Surveill. 2024 May 3;10:e52691. doi: 10.2196/52691.

ABSTRACT

BACKGROUND: Structural racism produces mental health disparities. While studies have examined the impact of individual factors such as poverty and education, the collective contribution of these elements, as manifestations of structural racism, has been less explored. Milwaukee County, Wisconsin, with its racial and socioeconomic diversity, provides a unique context for this multifactorial investigation.

OBJECTIVE: This research aimed to delineate the association between structural racism and mental health disparities in Milwaukee County, using a combination of geospatial and deep learning techniques. We used secondary data sets where all data were aggregated and anonymized before being released by federal agencies.

METHODS: We compiled 217 georeferenced explanatory variables across domains, initially deliberately excluding race-based factors to focus on nonracial determinants. This approach was designed to reveal the underlying patterns of risk factors contributing to poor mental health, subsequently reintegrating race to assess the effects of racism quantitatively. The variable selection combined tree-based methods (random forest) and conventional techniques, supported by variance inflation factor and Pearson correlation analysis for multicollinearity mitigation. The geographically weighted random forest model was used to investigate spatial heterogeneity and dependence. Self-organizing maps, combined with K-means clustering, were used to analyze data from Milwaukee communities, focusing on quantifying the impact of structural racism on the prevalence of poor mental health.

RESULTS: While 12 influential factors collectively accounted for 95.11% of the variability in mental health across communities, the top 6 factors-smoking, poverty, insufficient sleep, lack of health insurance, employment, and age-were particularly impactful. Predominantly, African American neighborhoods were disproportionately affected, which is 2.23 times more likely to encounter high-risk clusters for poor mental health.

CONCLUSIONS: The findings demonstrate that structural racism shapes mental health disparities, with Black community members disproportionately impacted. The multifaceted methodological approach underscores the value of integrating geospatial analysis and deep learning to understand complex social determinants of mental health. These insights highlight the need for targeted interventions, addressing both individual and systemic factors to mitigate mental health disparities rooted in structural racism.

PMID:38701436 | DOI:10.2196/52691

Brief Bioinform. 2024 Mar 27;25(3):bbae226. doi: 10.1093/bib/bbae226.

NO ABSTRACT

PMID:38701423 | DOI:10.1093/bib/bbae226

Brief Bioinform. 2024 Mar 27;25(3):bbae042. doi: 10.1093/bib/bbae042.

ABSTRACT

In this review article, we explore the transformative impact of deep learning (DL) on structural bioinformatics, emphasizing its pivotal role in a scientific revolution driven by extensive data, accessible toolkits and robust computing resources. As big data continue to advance, DL is poised to become an integral component in healthcare and biology, revolutionizing analytical processes. Our comprehensive review provides detailed insights into DL, featuring specific demonstrations of its notable applications in bioinformatics. We address challenges tailored for DL, spotlight recent successes in structural bioinformatics and present a clear exposition of DL-from basic shallow neural networks to advanced models such as convolution, recurrent, artificial and transformer neural networks. This paper discusses the emerging use of DL for understanding biomolecular structures, anticipating ongoing developments and applications in the realm of structural bioinformatics.

PMID:38701422 | DOI:10.1093/bib/bbae042

Brief Bioinform. 2024 Mar 27;25(3):bbae191. doi: 10.1093/bib/bbae191.

ABSTRACT

The relationship between genotype and fitness is fundamental to evolution, but quantitatively mapping genotypes to fitness has remained challenging. We propose the Phenotypic-Embedding theorem (P-E theorem) that bridges genotype-phenotype through an encoder-decoder deep learning framework. Inspired by this, we proposed a more general first principle for correlating genotype-phenotype, and the P-E theorem provides a computable basis for the application of first principle. As an application example of the P-E theorem, we developed the Co-attention based Transformer model to bridge Genotype and Fitness model, a Transformer-based pre-train foundation model with downstream supervised fine-tuning that can accurately simulate the neutral evolution of viruses and predict immune escape mutations. Accordingly, following the calculation path of the P-E theorem, we accurately obtained the basic reproduction number (${R}_0$) of SARS-CoV-2 from first principles, quantitatively linked immune escape to viral fitness and plotted the genotype-fitness landscape. The theoretical system we established provides a general and interpretable method to construct genotype-phenotype landscapes, providing a new paradigm for studying theoretical and computational biology.

PMID:38701420 | DOI:10.1093/bib/bbae191

Brief Bioinform. 2024 Mar 27;25(3):bbae195. doi: 10.1093/bib/bbae195.

ABSTRACT

Transcription factors (TFs) are proteins essential for regulating genetic transcriptions by binding to transcription factor binding sites (TFBSs) in DNA sequences. Accurate predictions of TFBSs can contribute to the design and construction of metabolic regulatory systems based on TFs. Although various deep-learning algorithms have been developed for predicting TFBSs, the prediction performance needs to be improved. This paper proposes a bidirectional encoder representations from transformers (BERT)-based model, called BERT-TFBS, to predict TFBSs solely based on DNA sequences. The model consists of a pre-trained BERT module (DNABERT-2), a convolutional neural network (CNN) module, a convolutional block attention module (CBAM) and an output module. The BERT-TFBS model utilizes the pre-trained DNABERT-2 module to acquire the complex long-term dependencies in DNA sequences through a transfer learning approach, and applies the CNN module and the CBAM to extract high-order local features. The proposed model is trained and tested based on 165 ENCODE ChIP-seq datasets. We conducted experiments with model variants, cross-cell-line validations and comparisons with other models. The experimental results demonstrate the effectiveness and generalization capability of BERT-TFBS in predicting TFBSs, and they show that the proposed model outperforms other deep-learning models. The source code for BERT-TFBS is available at https://github.com/ZX1998-12/BERT-TFBS.

PMID:38701417 | DOI:10.1093/bib/bbae195

Brief Bioinform. 2024 Mar 27;25(3):bbae196. doi: 10.1093/bib/bbae196.

ABSTRACT

Predicting protein function is crucial for understanding biological life processes, preventing diseases and developing new drug targets. In recent years, methods based on sequence, structure and biological networks for protein function annotation have been extensively researched. Although obtaining a protein in three-dimensional structure through experimental or computational methods enhances the accuracy of function prediction, the sheer volume of proteins sequenced by high-throughput technologies presents a significant challenge. To address this issue, we introduce a deep neural network model DeepSS2GO (Secondary Structure to Gene Ontology). It is a predictor incorporating secondary structure features along with primary sequence and homology information. The algorithm expertly combines the speed of sequence-based information with the accuracy of structure-based features while streamlining the redundant data in primary sequences and bypassing the time-consuming challenges of tertiary structure analysis. The results show that the prediction performance surpasses state-of-the-art algorithms. It has the ability to predict key functions by effectively utilizing secondary structure information, rather than broadly predicting general Gene Ontology terms. Additionally, DeepSS2GO predicts five times faster than advanced algorithms, making it highly applicable to massive sequencing data. The source code and trained models are available at https://github.com/orca233/DeepSS2GO.

PMID:38701416 | DOI:10.1093/bib/bbae196

Brief Bioinform. 2024 Mar 27;25(3):bbae200. doi: 10.1093/bib/bbae200.

ABSTRACT

N4-acetylcytidine (ac4C) is a modification found in ribonucleic acid (RNA) related to diseases. Expensive and labor-intensive methods hindered the exploration of ac4C mechanisms and the development of specific anti-ac4C drugs. Therefore, an advanced prediction model for ac4C in RNA is urgently needed. Despite the construction of various prediction models, several limitations exist: (1) insufficient resolution at base level for ac4C sites; (2) lack of information on species other than Homo sapiens; (3) lack of information on RNA other than mRNA; and (4) lack of interpretation for each prediction. In light of these limitations, we have reconstructed the previous benchmark dataset and introduced a new dataset including balanced RNA sequences from multiple species and RNA types, while also providing base-level resolution for ac4C sites. Additionally, we have proposed a novel transformer-based architecture and pipeline for predicting ac4C sites, allowing for highly accurate predictions, visually interpretable results and no restrictions on the length of input RNA sequences. Statistically, our work has improved the accuracy of predicting specific ac4C sites in multiple species from less than 40% to around 85%, achieving a high AUC > 0.9. These results significantly surpass the performance of all existing models.

PMID:38701415 | DOI:10.1093/bib/bbae200

Medicine (Baltimore). 2024 May 3;103(18):e37943. doi: 10.1097/MD.0000000000037943.

ABSTRACT

BACKGROUND: Lumbar disc herniation was regarded as an age-related degenerative disease. Nevertheless, emerging reports highlight a discernible shift, illustrating the prevalence of these conditions among younger individuals.

METHODS: This study introduces a novel deep learning methodology tailored for spinal canal segmentation and disease diagnosis, emphasizing image processing techniques that delve into essential image attributes such as gray levels, texture, and statistical structures to refine segmentation accuracy.

RESULTS: Analysis reveals a progressive increase in the size of vertebrae and intervertebral discs from the cervical to lumbar regions. Vertebrae, bearing weight and safeguarding the spinal cord and nerves, are interconnected by intervertebral discs, resilient structures that counteract spinal pressure. Experimental findings demonstrate a lack of pronounced anteroposterior bending during flexion and extension, maintaining displacement and rotation angles consistently approximating zero. This consistency maintains uniform anterior and posterior vertebrae heights, coupled with parallel intervertebral disc heights, aligning with theoretical expectations.

CONCLUSIONS: Accuracy assessment employs 2 methods: IoU and Dice, and the average accuracy of IoU is 88% and that of Dice is 96.4%. The proposed deep learning-based system showcases promising results in spinal canal segmentation, laying a foundation for precise stenosis diagnosis in computed tomography images. This contributes significantly to advancements in spinal pathology understanding and treatment.

PMID:38701305 | DOI:10.1097/MD.0000000000037943

Microsc Microanal. 2024 May 3:ozae033. doi: 10.1093/mam/ozae033. Online ahead of print.

ABSTRACT

Automated image acquisition can significantly improve the throughput of serial section scanning electron microscopy (ssSEM). However, image quality can vary from image to image depending on autofocusing and beam stigmation. Automatically evaluating the quality of images is, therefore, important for efficiently generating high-quality serial section scanning electron microscopy (ssSEM) datasets. We tested several convolutional neural networks for their ability to reproduce user-generated evaluations of ssSEM image quality. We found that a modification of ResNet-50 that we term quality evaluation Network (QEN) reliably predicts user-generated quality scores. Running QEN in parallel to ssSEM image acquisition therefore allows users to quickly identify imaging problems and flag images for retaking. We have publicly shared the Python code for evaluating images with QEN, the code for training QEN, and the training dataset.

PMID:38701183 | DOI:10.1093/mam/ozae033

J Xray Sci Technol. 2024 Apr 28. doi: 10.3233/XST-230429. Online ahead of print.

ABSTRACT

BACKGROUND: The emergence of deep learning (DL) techniques has revolutionized tumor detection and classification in medical imaging, with multimodal medical imaging (MMI) gaining recognition for its precision in diagnosis, treatment, and progression tracking.

OBJECTIVE: This review comprehensively examines DL methods in transforming tumor detection and classification across MMI modalities, aiming to provide insights into advancements, limitations, and key challenges for further progress.

METHODS: Systematic literature analysis identifies DL studies for tumor detection and classification, outlining methodologies including convolutional neural networks (CNNs), recurrent neural networks (RNNs), and their variants. Integration of multimodality imaging enhances accuracy and robustness.

RESULTS: Recent advancements in DL-based MMI evaluation methods are surveyed, focusing on tumor detection and classification tasks. Various DL approaches, including CNNs, YOLO, Siamese Networks, Fusion-Based Models, Attention-Based Models, and Generative Adversarial Networks, are discussed with emphasis on PET-MRI, PET-CT, and SPECT-CT.

FUTURE DIRECTIONS: The review outlines emerging trends and future directions in DL-based tumor analysis, aiming to guide researchers and clinicians toward more effective diagnosis and prognosis. Continued innovation and collaboration are stressed in this rapidly evolving domain.

CONCLUSION: Conclusions drawn from literature analysis underscore the efficacy of DL approaches in tumor detection and classification, highlighting their potential to address challenges in MMI analysis and their implications for clinical practice.

PMID:38701131 | DOI:10.3233/XST-230429

Int J Cardiovasc Imaging. 2024 May 3. doi: 10.1007/s10554-024-03080-4. Online ahead of print.

ABSTRACT

Almost 35 years after its introduction, coronary artery calcium score (CACS) not only survived technological advances but became one of the cornerstones of contemporary cardiovascular imaging. Its simplicity and quantitative nature established it as one of the most robust approaches for atherosclerotic cardiovascular disease risk stratification in primary prevention and a powerful tool to guide therapeutic choices. Groundbreaking advances in computational models and computer power translated into a surge of artificial intelligence (AI)-based approaches directly or indirectly linked to CACS analysis. This review aims to provide essential knowledge on the AI-based techniques currently applied to CACS, setting the stage for a holistic analysis of the use of these techniques in coronary artery calcium imaging. While the focus of the review will be detailing the evidence, strengths, and limitations of end-to-end CACS algorithms in electrocardiography-gated and non-gated scans, the current role of deep-learning image reconstructions, segmentation techniques, and combined applications such as simultaneous coronary artery calcium and pulmonary nodule segmentation, will also be discussed.

PMID:38700819 | DOI:10.1007/s10554-024-03080-4

Med Biol Eng Comput. 2024 May 3. doi: 10.1007/s11517-024-03096-x. Online ahead of print.

ABSTRACT

Neurodegenerative diseases often exhibit a strong link with sleep disruption, highlighting the importance of effective sleep stage monitoring. In this light, automatic sleep stage classification (ASSC) plays a pivotal role, now more streamlined than ever due to the advancements in deep learning (DL). However, the opaque nature of DL models can be a barrier in their clinical adoption, due to trust concerns among medical practitioners. To bridge this gap, we introduce SleepBoost, a transparent multi-level tree-based ensemble model specifically designed for ASSC. Our approach includes a crafted feature engineering block (FEB) that extracts 41 time and frequency domain features, out of which 23 are selected based on their high mutual information score (> 0.23). Uniquely, SleepBoost integrates three fundamental linear models into a cohesive multi-level tree structure, further enhanced by a novel reward-based adaptive weight allocation mechanism. Tested on the Sleep-EDF-20 dataset, SleepBoost demonstrates superior performance with an accuracy of 86.3%, F1-score of 80.9%, and Cohen kappa score of 0.807, outperforming leading DL models in ASSC. An ablation study underscores the critical role of our selective feature extraction in enhancing model accuracy and interpretability, crucial for clinical settings. This innovative approach not only offers a more transparent alternative to traditional DL models but also extends potential implications for monitoring and understanding sleep patterns in the context of neurodegenerative disorders. The open-source availability of SleepBoost's implementation at https://github.com/akibzaman/SleepBoost can further facilitate its accessibility and potential for widespread clinical adoption.

PMID:38700613 | DOI:10.1007/s11517-024-03096-x

Graefes Arch Clin Exp Ophthalmol. 2024 May 3. doi: 10.1007/s00417-024-06501-1. Online ahead of print.

ABSTRACT

PURPOSE: To investigate the possibility of distinguishing between IgG4-related ophthalmic disease (IgG4-ROD) and orbital MALT lymphoma using artificial intelligence (AI) and hematoxylin-eosin (HE) images.

METHODS: After identifying a total of 127 patients from whom we were able to procure tissue blocks with IgG4-ROD and orbital MALT lymphoma, we performed histological and molecular genetic analyses, such as gene rearrangement. Subsequently, pathological HE images were collected from these patients followed by the cutting out of 10 different image patches from the HE image of each patient. A total of 970 image patches from the 97 patients were used to construct nine different models of deep learning, and the 300 image patches from the remaining 30 patients were used to evaluate the diagnostic performance of the models. Area under the curve (AUC) and accuracy (ACC) were used for the performance evaluation of the deep learning models. In addition, four ophthalmologists performed the binary classification between IgG4-ROD and orbital MALT lymphoma.

RESULTS: EVA, which is a vision-centric foundation model to explore the limits of visual representation, was the best deep learning model among the nine models. The results of EVA were ACC = 73.3% and AUC = 0.807. The ACC of the four ophthalmologists ranged from 40 to 60%.

CONCLUSIONS: It was possible to construct an AI software based on deep learning that was able to distinguish between IgG4-ROD and orbital MALT. This AI model may be useful as an initial screening tool to direct further ancillary investigations.

PMID:38700592 | DOI:10.1007/s00417-024-06501-1

Radiol Med. 2024 May 3. doi: 10.1007/s11547-024-01820-z. Online ahead of print.

ABSTRACT

PURPOSE: High PSMA expression might be correlated with structural characteristics such as growth patterns on histopathology, not recognized by the human eye on MRI images. Deep structural image analysis might be able to detect such differences and therefore predict if a lesion would be PSMA positive. Therefore, we aimed to train a neural network based on PSMA PET/MRI scans to predict increased prostatic PSMA uptake based on the axial T2-weighted sequence alone.

MATERIAL AND METHODS: All patients undergoing simultaneous PSMA PET/MRI for PCa staging or biopsy guidance between April 2016 and December 2020 at our institution were selected. To increase the specificity of our model, the prostatic beds on PSMA PET scans were dichotomized in positive and negative regions using an SUV threshold greater than 4 to generate a PSMA PET map. Then, a C-ENet was trained on the T2 images of the training cohort to generate a predictive prostatic PSMA PET map.

RESULTS: One hundred and fifty-four PSMA PET/MRI scans were available (133 [68Ga]Ga-PSMA-11 and 21 [18F]PSMA-1007). Significant cancer was present in 127 of them. The whole dataset was divided into a training cohort (n = 124) and a test cohort (n = 30). The C-ENet was able to predict the PSMA PET map with a dice similarity coefficient of 69.5 ± 15.6%.

CONCLUSION: Increased prostatic PSMA uptake on PET might be estimated based on T2 MRI alone. Further investigation with larger cohorts and external validation is needed to assess whether PSMA uptake can be predicted accurately enough to help in the interpretation of mpMRI.

PMID:38700556 | DOI:10.1007/s11547-024-01820-z