Semi-supervised machine learning method for predicting homogeneous ancestry groups to assess Hardy-Weinberg equilibrium in diverse whole-genome sequencing studies.

Large-scale, multi-ethnic whole-genome sequencing (WGS) studies, such as the National Human Genome Research Institute Genome Sequencing Program's Centers for Common Disease Genomics (CCDG), play an important role in increasing diversity for genetic research. Before performing association analyses, assessing Hardy-Weinberg equilibrium (HWE) is a crucial step in quality control procedures to remove low quality variants and ensure valid downstream analyses. Diverse WGS studies contain ancestrally heterogeneous samples; however, commonly used HWE methods assume that the samples are homogeneous. Therefore, directly applying these to the whole dataset can yield statistically invalid results. To account for this heterogeneity, HWE can be tested on subsets of samples that have genetically homogeneous ancestries and the results aggregated at each variant. To facilitate valid HWE subset testing, we developed a semi-supervised learning approach that predicts homogeneous ancestries based on the genotype. This method provides a convenient tool for estimating HWE in the presence of population structure and missing self-reported race and ethnicities in diverse WGS studies. In addition, assessing HWE within the homogeneous ancestries provides reliable HWE estimates that will directly benefit downstream analyses, including association analyses in WGS studies. We applied our proposed method on the CCDG dataset, predicting homogeneous genetic ancestry groups for 60,545 multi-ethnic WGS samples to assess HWE within each group.

GLDADec: marker-gene guided LDA modeling for bulk gene expression deconvolution.

Inferring cell type proportions from bulk transcriptome data is crucial in immunology and oncology. Here, we introduce guided LDA deconvolution (GLDADec), a bulk deconvolution method that guides topics using cell type-specific marker gene names to estimate topic distributions for each sample. Through benchmarking using blood-derived datasets, we demonstrate its high estimation performance and robustness. Moreover, we apply GLDADec to heterogeneous tissue bulk data and perform comprehensive cell type analysis in a data-driven manner. We show that GLDADec outperforms existing methods in estimation performance and evaluate its biological interpretability by examining enrichment of biological processes for topics. Finally, we apply GLDADec to The Cancer Genome Atlas tumor samples, enabling subtype stratification and survival analysis based on estimated cell type proportions, thus proving its practical utility in clinical settings. This approach, utilizing marker gene names as partial prior information, can be applied to various scenarios for bulk data deconvolution. GLDADec is available as an open-source Python package at https://github.com/mizuno-group/GLDADec.

TransGCN: a semi-supervised graph convolution network-based framework to infer protein translocations in spatio-temporal proteomics.

Protein subcellular localization (PSL) is very important in order to understand its functions, and its movement between subcellular niches within cells plays fundamental roles in biological process regulation. Mass spectrometry-based spatio-temporal proteomics technologies can help provide new insights of protein translocation, but bring the challenge in identifying reliable protein translocation events due to the noise interference and insufficient data mining. We propose a semi-supervised graph convolution network (GCN)-based framework termed TransGCN that infers protein translocation events from spatio-temporal proteomics. Based on expanded multiple distance features and joint graph representations of proteins, TransGCN utilizes the semi-supervised GCN to enable effective knowledge transfer from proteins with known PSLs for predicting protein localization and translocation. Our results demonstrate that TransGCN outperforms current state-of-the-art methods in identifying protein translocations, especially in coping with batch effects. It also exhibited excellent predictive accuracy in PSL prediction. TransGCN is freely available on GitHub at https://github.com/XuejiangGuo/TransGCN.

Breaking the barriers of data scarcity in drug-target affinity prediction.

Accurate prediction of drug-target affinity (DTA) is of vital importance in early-stage drug discovery, facilitating the identification of drugs that can effectively interact with specific targets and regulate their activities. While wet experiments remain the most reliable method, they are time-consuming and resource-intensive, resulting in limited data availability that poses challenges for deep learning approaches. Existing methods have primarily focused on developing techniques based on the available DTA data, without adequately addressing the data scarcity issue. To overcome this challenge, we present the Semi-Supervised Multi-task training (SSM) framework for DTA prediction, which incorporates three simple yet highly effective strategies: (1) A multi-task training approach that combines DTA prediction with masked language modeling using paired drug-target data. (2) A semi-supervised training method that leverages large-scale unpaired molecules and proteins to enhance drug and target representations. This approach differs from previous methods that only employed molecules or proteins in pre-training. (3) The integration of a lightweight cross-attention module to improve the interaction between drugs and targets, further enhancing prediction accuracy. Through extensive experiments on benchmark datasets such as BindingDB, DAVIS and KIBA, we demonstrate the superior performance of our framework. Additionally, we conduct case studies on specific drug-target binding activities, virtual screening experiments, drug feature visualizations and real-world applications, all of which showcase the significant potential of our work. In conclusion, our proposed SSM-DTA framework addresses the data limitation challenge in DTA prediction and yields promising results, paving the way for more efficient and accurate drug discovery processes.

Segmentation of supragranular and infragranular layers in ultra-high-resolution 7T ex vivo MRI of the human cerebral cortex.

Accurate labeling of specific layers in the human cerebral cortex is crucial for advancing our understanding of neurodevelopmental and neurodegenerative disorders. Building on recent advancements in ultra-high-resolution ex vivo MRI, we present a novel semi-supervised segmentation model capable of identifying supragranular and infragranular layers in ex vivo MRI with unprecedented precision. On a dataset consisting of 17 whole-hemisphere ex vivo scans at 120 $\mu $m, we propose a Multi-resolution U-Nets framework that integrates global and local structural information, achieving reliable segmentation maps of the entire hemisphere, with Dice scores over 0.8 for supra- and infragranular layers. This enables surface modeling, atlas construction, anomaly detection in disease states, and cross-modality validation while also paving the way for finer layer segmentation. Our approach offers a powerful tool for comprehensive neuroanatomical investigations and holds promise for advancing our mechanistic understanding of progression of neurodegenerative diseases.

Cellograph: a semi-supervised approach to analyzing multi-condition single-cell RNA-sequencing data using graph neural networks.

With the growing number of single-cell datasets collected under more complex experimental conditions, there is an opportunity to leverage single-cell variability to reveal deeper insights into how cells respond to perturbations. Many existing approaches rely on discretizing the data into clusters for differential gene expression (DGE), effectively ironing out any information unveiled by the single-cell variability across cell-types. In addition, DGE often assumes a statistical distribution that, if erroneous, can lead to false positive differentially expressed genes. Here, we present Cellograph: a semi-supervised framework that uses graph neural networks to quantify the effects of perturbations at single-cell granularity. Cellograph not only measures how prototypical cells are of each condition but also learns a latent space that is amenable to interpretable data visualization and clustering. The learned gene weight matrix from training reveals pertinent genes driving the differences between conditions. We demonstrate the utility of our approach on publicly-available datasets including cancer drug therapy, stem cell reprogramming, and organoid differentiation. Cellograph outperforms existing methods for quantifying the effects of experimental perturbations and offers a novel framework to analyze single-cell data using deep learning.

A semi-supervised approach for the integration of multi-omics data based on transformer multi-head self-attention mechanism and graph convolutional networks.

BACKGROUND AND OBJECTIVES: Comprehensive analysis of multi-omics data is crucial for accurately formulating effective treatment plans for complex diseases. Supervised ensemble methods have gained popularity in recent years for multi-omics data analysis. However, existing research based on supervised learning algorithms often fails to fully harness the information from unlabeled nodes and overlooks the latent features within and among different omics, as well as the various associations among features. Here, we present a novel multi-omics integrative method MOSEGCN, based on the Transformer multi-head self-attention mechanism and Graph Convolutional Networks(GCN), with the aim of enhancing the accuracy of complex disease classification. MOSEGCN first employs the Transformer multi-head self-attention mechanism and Similarity Network Fusion (SNF) to separately learn the inherent correlations of latent features within and among different omics, constructing a comprehensive view of diseases. Subsequently, it feeds the learned crucial information into a self-ensembling Graph Convolutional Network (SEGCN) built upon semi-supervised learning methods for training and testing, facilitating a better analysis and utilization of information from multi-omics data to achieve precise classification of disease subtypes. RESULTS: The experimental results show that MOSEGCN outperforms several state-of-the-art multi-omics integrative analysis approaches on three types of omics data: mRNA expression data, microRNA expression data, and DNA methylation data, with accuracy rates of 83.0% for Alzheimer's disease and 86.7% for breast cancer subtyping. Furthermore, MOSEGCN exhibits strong generalizability on the GBM dataset, enabling the identification of important biomarkers for related diseases. CONCLUSION: MOSEGCN explores the significant relationship information among different omics and within each omics' latent features, effectively leveraging labeled and unlabeled information to further enhance the accuracy of complex disease classification. It also provides a promising approach for identifying reliable biomarkers, paving the way for personalized medicine.

Development of an Interpretable Deep Learning Model for Pathological Tumor Response Assessment After Neoadjuvant Therapy.

BACKGROUND: Neoadjuvant therapy followed by surgery has become the standard of care for locally advanced esophageal squamous cell carcinoma (ESCC) and accurate pathological response assessment is critical to assess the therapeutic efficacy. However, it can be laborious and inconsistency between different observers may occur. Hence, we aim to develop an interpretable deep-learning model for efficient pathological response assessment following neoadjuvant therapy in ESCC. METHODS: This retrospective study analyzed 337 ESCC resection specimens from 2020-2021 at the Pudong-Branch (Cohort 1) and 114 from 2021-2022 at the Puxi-Branch (External Cohort 2) of Fudan University Shanghai Cancer Center. Whole slide images (WSIs) from these two cohorts were generated using different scanning machines to test the ability of the model in handling color variations. Four pathologists independently assessed the pathological response. The senior pathologists annotated tumor beds and residual tumor percentages on WSIs to determine consensus labels. Furthermore, 1850 image patches were randomly extracted from Cohort 1 WSIs and binarily classified for tumor viability. A deep-learning model employing knowledge distillation was developed to automatically classify positive patches for each WSI and estimate the viable residual tumor percentages. Spatial heatmaps were output for model explanations and visualizations. RESULTS: The approach achieved high concordance with pathologist consensus, with an R^2 of 0.8437, a RAcc_0.1 of 0.7586, a RAcc_0.3 of 0.9885, which were comparable to two senior pathologists (R^2 of 0.9202/0.9619, RAcc_0.1 of 8506/0.9425, RAcc_0.3 of 1.000/1.000) and surpassing two junior pathologists (R^2 of 0.5592/0.5474, RAcc_0.1 of 0.5287/0.5287, RAcc_0.3 of 0.9080/0.9310). Visualizations enabled the localization of residual viable tumor to augment microscopic assessment. CONCLUSION: This work illustrates deep learning's potential for assisting pathological response assessment. Spatial heatmaps and patch examples provide intuitive explanations of model predictions, engendering clinical trust and adoption (Code and data will be available at https://github.com/WinnieLaugh/ESCC_Percentage once the paper has been conditionally accepted). Integrating interpretable computational pathology could help enhance the efficiency and consistency of tumor response assessment and empower precise oncology treatment decisions.

FCCCSR_Glu: a semi-supervised learning model based on FCCCSR algorithm for prediction of glutarylation sites.

Glutarylation is a post-translational modification which plays an irreplaceable role in various functions of the cell. Therefore, it is very important to accurately identify the glutarylation substrates and its corresponding glutarylation sites. In recent years, many computational methods of glutarylation sites have emerged one after another, but there are still many limitations, among which noisy data and the class imbalance problem caused by the uncertainty of non-glutarylation sites are great challenges. In this study, we propose a new semi-supervised learning algorithm, named FCCCSR, to identify reliable non-glutarylation lysine sites from unlabeled samples as negative samples. FCCCSR first finds core objects from positive samples according to reverse nearest neighbor information, and then clusters core objects based on natural neighbor structure. Finally, reliable negative samples are selected according to clustering result. With FCCCSR algorithm, we propose a new method named FCCCSR_Glu for glutarylation sites identification. In this study, multi-view features are extracted and fused to describe peptides, including amino acid composition, BLOSUM62, amino acid factors and composition of k-spaced amino acid pairs. Then, reliable negative samples selected by FCCCSR and positive samples are combined to establish models and XGBoost optimized by differential evolution algorithm is used as the classifier. On the independent testing dataset, FCCCSR_Glu achieves 85.18%, 98.36%, 94.31% and 0.8651 in sensitivity, specificity, accuracy and Matthew's Correlation Coefficient, respectively, which is superior to state-of-the-art methods in predicting glutarylation sites. Therefore, FCCCSR_Glu can be a useful tool for glutarylation sites prediction and FCCCSR algorithm can effectively select reliable negative samples from unlabeled samples. The data and code are available on https://github.com/xbbxhbc/FCCCSR_Glu.git.

Positive-unlabeled learning in bioinformatics and computational biology: a brief review.

Conventional supervised binary classification algorithms have been widely applied to address significant research questions using biological and biomedical data. This classification scheme requires two fully labeled classes of data (e.g. positive and negative samples) to train a classification model. However, in many bioinformatics applications, labeling data is laborious, and the negative samples might be potentially mislabeled due to the limited sensitivity of the experimental equipment. The positive unlabeled (PU) learning scheme was therefore proposed to enable the classifier to learn directly from limited positive samples and a large number of unlabeled samples (i.e. a mixture of positive or negative samples). To date, several PU learning algorithms have been developed to address various biological questions, such as sequence identification, functional site characterization and interaction prediction. In this paper, we revisit a collection of 29 state-of-the-art PU learning bioinformatic applications to address various biological questions. Various important aspects are extensively discussed, including PU learning methodology, biological application, classifier design and evaluation strategy. We also comment on the existing issues of PU learning and offer our perspectives for the future development of PU learning applications. We anticipate that our work serves as an instrumental guideline for a better understanding of the PU learning framework in bioinformatics and further developing next-generation PU learning frameworks for critical biological applications.

A review of self-supervised, generative, and few-shot deep learning methods for data-limited magnetic resonance imaging segmentation.

Magnetic resonance imaging (MRI) is a ubiquitous medical imaging technology with applications in disease diagnostics, intervention, and treatment planning. Accurate MRI segmentation is critical for diagnosing abnormalities, monitoring diseases, and deciding on a course of treatment. With the advent of advanced deep learning frameworks, fully automated and accurate MRI segmentation is advancing. Traditional supervised deep learning techniques have advanced tremendously, reaching clinical-level accuracy in the field of segmentation. However, these algorithms still require a large amount of annotated data, which is oftentimes unavailable or impractical. One way to circumvent this issue is to utilize algorithms that exploit a limited amount of labeled data. This paper aims to review such state-of-the-art algorithms that use a limited number of annotated samples. We explain the fundamental principles of self-supervised learning, generative models, few-shot learning, and semi-supervised learning and summarize their applications in cardiac, abdomen, and brain MRI segmentation. Throughout this review, we highlight algorithms that can be employed based on the quantity of annotated data available. We also present a comprehensive list of notable publicly available MRI segmentation datasets. To conclude, we discuss possible future directions of the field-including emerging algorithms, such as contrastive language-image pretraining, and potential combinations across the methods discussed-that can further increase the efficacy of image segmentation with limited labels.

Soft phenotyping for sepsis via EHR time-aware soft clustering.

OBJECTIVE: Sepsis is one of the most serious hospital conditions associated with high mortality. Sepsis is the result of a dysregulated immune response to infection that can lead to multiple organ dysfunction and death. Due to the wide variability in the causes of sepsis, clinical presentation, and the recovery trajectories, identifying sepsis sub-phenotypes is crucial to advance our understanding of sepsis characterization, to choose targeted treatments and optimal timing of interventions, and to improve prognostication. Prior studies have described different sub-phenotypes of sepsis using organ-specific characteristics. These studies applied clustering algorithms to electronic health records (EHRs) to identify disease sub-phenotypes. However, prior approaches did not capture temporal information and made uncertain assumptions about the relationships among the sub-phenotypes for clustering procedures. METHODS: We developed a time-aware soft clustering algorithm guided by clinical variables to identify sepsis sub-phenotypes using data available in the EHR. RESULTS: We identified six novel sepsis hybrid sub-phenotypes and evaluated them for medical plausibility. In addition, we built an early-warning sepsis prediction model using logistic regression. CONCLUSION: Our results suggest that these novel sepsis hybrid sub-phenotypes are promising to provide more accurate information on sepsis-related organ dysfunction and sepsis recovery trajectories which can be important to inform management decisions and sepsis prognosis.

Semi-supervised Double Deep Learning Temporal Risk Prediction (SeDDLeR) with Electronic Health Records.

BACKGROUND: Risk prediction plays a crucial role in planning for prevention, monitoring, and treatment. Electronic Health Records (EHRs) offer an expansive repository of temporal medical data encompassing both risk factors and outcome indicators essential for effective risk prediction. However, challenges emerge due to the lack of readily available gold-standard outcomes and the complex effects of various risk factors. Compounding these challenges are the false positives in diagnosis codes, and formidable task of pinpointing the onset timing in annotations. OBJECTIVE: We develop a Semi-supervised Double Deep Learning Temporal Risk Prediction (SeDDLeR) algorithm based on extensive unlabeled longitudinal Electronic Health Records (EHR) data augmented by a limited set of gold standard labels on the binary status information indicating whether the clinical event of interest occurred during the follow-up period. METHODS: The SeDDLeR algorithm calculates an individualized risk of developing future clinical events over time using each patient's baseline EHR features via the following steps: (1) construction of an initial EHR-derived surrogate as a proxy for the onset status; (2) deep learning calibration of the surrogate along gold-standard onset status; and (3) semi-supervised deep learning for risk prediction combining calibrated surrogates and gold-standard onset status. To account for missing onset time and heterogeneous follow-up, we introduce temporal kernel weighting. We devise a Gated Recurrent Units (GRUs) module to capture temporal characteristics. We subsequently assess our proposed SeDDLeR method in simulation studies and apply the method to the Massachusetts General Brigham (MGB) Biobank to predict type 2 diabetes (T2D) risk. RESULTS: SeDDLeR outperforms benchmark risk prediction methods, including Semi-parametric Transformation Model (STM) and DeepHit, with consistently best accuracy across experiments. SeDDLeR achieved the best C-statistics ( 0.815, SE 0.023; vs STM +.084, SE 0.030, P-value .004; vs DeepHit +.055, SE 0.027, P-value .024) and best average time-specific AUC (0.778, SE 0.022; vs STM + 0.059, SE 0.039, P-value .067; vs DeepHit + 0.168, SE 0.032, P-value <0.001) in the MGB T2D study. CONCLUSION: SeDDLeR can train robust risk prediction models in both real-world EHR and synthetic datasets with minimal requirements of labeling event times. It holds the potential to be incorporated for future clinical trial recruitment or clinical decision-making.

Enhancing identification performance of cognitive impairment high-risk based on a semi-supervised learning method.

BACKGROUND: Cognitive assessment plays a pivotal role in the early detection of cognitive impairment, particularly in the prevention and management of cognitive diseases such as Alzheimer's and Lewy body dementia. Large-scale screening relies heavily on cognitive assessment scales as primary tools, with some low sensitivity and others expensive. Despite significant progress in machine learning for cognitive function assessment, its application in this particular screening domain remains underexplored, often requiring labor-intensive expert annotations. AIMS: This paper introduces a semi-supervised learning algorithm based on pseudo-label with putback (SS-PP), aiming to enhance model efficiency in predicting the high risk of cognitive impairment (HR-CI) by utilizing the distribution of unlabeled samples. DATA: The study involved 189 labeled samples and 215,078 unlabeled samples from real world. A semi-supervised classification algorithm was designed and evaluated by comparison with supervised methods composed by 14 traditional machine-learning methods and other advanced semi-supervised algorithms. RESULTS: The optimal SS-PP model, based on GBDT, achieved an AUC of 0.947. Comparative analysis with supervised learning models and semi-supervised methods demonstrated an average AUC improvement of 8% and state-of-art performance, repectively. CONCLUSION: This study pioneers the exploration of utilizing limited labeled data for HR-CI predictions and evaluates the benefits of incorporating physical examination data, holding significant implications for the development of cost-effective strategies in relevant healthcare domains.

al-BERT: a semi-supervised denoising technique for disease prediction.

BACKGROUND: Medical records are a valuable source for understanding patient health conditions. Doctors often use these records to assess health without solely depending on time-consuming and complex examinations. However, these records may not always be directly relevant to a patient's current health issue. For instance, information about common colds may not be relevant to a more specific health condition. While experienced doctors can effectively navigate through unnecessary details in medical records, this excess information presents a challenge for machine learning models in predicting diseases electronically. To address this, we have developed 'al-BERT', a new disease prediction model that leverages the BERT framework. This model is designed to identify crucial information from medical records and use it to predict diseases. 'al-BERT' operates on the principle that the structure of sentences in diagnostic records is similar to regular linguistic patterns. However, just as stuttering in speech can introduce 'noise' or irrelevant information, similar issues can arise in written records, complicating model training. To overcome this, 'al-BERT' incorporates a semi-supervised layer that filters out irrelevant data from patient visitation records. This process aims to refine the data, resulting in more reliable indicators for disease correlations and enhancing the model's predictive accuracy and utility in medical diagnostics. METHOD: To discern noise diseases within patient records, especially those resembling influenza-like illnesses, our approach employs a customized semi-supervised learning algorithm equipped with a focused attention mechanism. This mechanism is specifically calibrated to enhance the model's sensitivity to chronic conditions while concurrently distilling salient features from patient records, thereby augmenting the predictive accuracy and utility of the model in clinical settings. We evaluate the performance of al-BERT using real-world health insurance data provided by Taiwan's National Health Insurance. RESULT: In our study, we evaluated our model against two others: one based on BERT that uses complete disease records, and another variant that includes extra filtering techniques. Our findings show that models incorporating filtering mechanisms typically perform better than those using the entire, unfiltered dataset. Our approach resulted in improved outcomes across several key measures: AUC-ROC (an indicator of a model's ability to distinguish between classes), precision (the accuracy of positive predictions), recall (the model's ability to find all relevant cases), and overall accuracy. Most notably, our model showed a 15% improvement in recall compared to the current best-performing method in the field of disease prediction. CONCLUSION: The conducted ablation study affirms the advantages of our attention mechanism and underscores the crucial role of the selection module within al-BERT.

Employing Constrained Nonnegative Matrix Factorization for Microstructure Segmentation.

Materials characterization using electron backscatter diffraction (EBSD) requires indexing the orientation of the measured region from Kikuchi patterns. The quality of Kikuchi patterns can degrade due to pattern overlaps arising from two or more orientations, in the presence of defects or grain boundaries. In this work, we employ constrained nonnegative matrix factorization to segment a microstructure with small grain misorientations, (<1∘), and predict the amount of pattern overlap. First, we implement the method on mixed simulated patterns-that replicates a pattern overlap scenario, and demonstrate the resolution limit of pattern mixing or factorization resolution using a weight metric. Subsequently, we segment a single-crystal dendritic microstructure and compare the results with high-resolution EBSD. By utilizing weight metrics across a low-angle grain boundary, we demonstrate how very small misorientations/low-angle grain boundaries can be resolved at a pixel level. Our approach constitutes a versatile and robust tool, complementing other fast indexing methods for microstructure characterization.

Semi-supervised auto-segmentation method for pelvic organ-at-risk in magnetic resonance images based on deep-learning.

BACKGROUND AND PURPOSE: In radiotherapy, magnetic resonance (MR) imaging has higher contrast for soft tissues compared to computed tomography (CT) scanning and does not emit radiation. However, manual annotation of the deep learning-based automatic organ-at-risk (OAR) delineation algorithms is expensive, making the collection of large-high-quality annotated datasets a challenge. Therefore, we proposed the low-cost semi-supervised OAR segmentation method using small pelvic MR image annotations. METHODS: We trained a deep learning-based segmentation model using 116 sets of MR images from 116 patients. The bladder, femoral heads, rectum, and small intestine were selected as OAR regions. To generate the training set, we utilized a semi-supervised method and ensemble learning techniques. Additionally, we employed a post-processing algorithm to correct the self-annotation data. Both 2D and 3D auto-segmentation networks were evaluated for their performance. Furthermore, we evaluated the performance of semi-supervised method for 50 labeled data and only 10 labeled data. RESULTS: The Dice similarity coefficient (DSC) of the bladder, femoral heads, rectum and small intestine between segmentation results and reference masks is 0.954, 0.984, 0.908, 0.852 only using self-annotation and post-processing methods of 2D segmentation model. The DSC of corresponding OARs is 0.871, 0.975, 0.975, 0.783, 0.724 using 3D segmentation network, 0.896, 0.984, 0.890, 0.828 using 2D segmentation network and common supervised method. CONCLUSION: The outcomes of our study demonstrate that it is possible to train a multi-OAR segmentation model using small annotation samples and additional unlabeled data. To effectively annotate the dataset, ensemble learning and post-processing methods were employed. Additionally, when dealing with anisotropy and limited sample sizes, the 2D model outperformed the 3D model in terms of performance.

Dual-branch Transformer for semi-supervised medical image segmentation.

PURPOSE: In recent years, the use of deep learning for medical image segmentation has become a popular trend, but its development also faces some challenges. Firstly, due to the specialized nature of medical data, precise annotation is time-consuming and labor-intensive. Training neural networks effectively with limited labeled data is a significant challenge in medical image analysis. Secondly, convolutional neural networks commonly used for medical image segmentation research often focus on local features in images. However, the recognition of complex anatomical structures or irregular lesions often requires the assistance of both local and global information, which has led to a bottleneck in its development. Addressing these two issues, in this paper, we propose a novel network architecture. METHODS: We integrate a shift window mechanism to learn more comprehensive semantic information and employ a semi-supervised learning strategy by incorporating a flexible amount of unlabeled data. Specifically, a typical U-shaped encoder-decoder structure is applied to obtain rich feature maps. Each encoder is designed as a dual-branch structure, containing Swin modules equipped with windows of different size to capture features of multiple scales. To effectively utilize unlabeled data, a level set function is introduced to establish consistency between the function regression and pixel classification. RESULTS: We conducted experiments on the COVID-19 CT dataset and DRIVE dataset and compared our approach with various semi-supervised and fully supervised learning models. On the COVID-19 CT dataset, we achieved a segmentation accuracy of up to 74.56%. Our segmentation accuracy on the DRIVE dataset was 79.79%. CONCLUSIONS: The results demonstrate the outstanding performance of our method on several commonly used evaluation metrics. The high segmentation accuracy of our model demonstrates that utilizing Swin modules with different window sizes can enhance the feature extraction capability of the model, and the level set function can enable semi-supervised models to more effectively utilize unlabeled data. This provides meaningful insights for the application of deep learning in medical image segmentation. Our code will be released once the manuscript is accepted for publication.

Semi-Supervised Informer for the Compound Fault Diagnosis of Industrial Robots.

The increasing deployment of industrial robots in manufacturing requires accurate fault diagnosis. Online monitoring data typically consist of a large volume of unlabeled data and a small quantity of labeled data. Conventional intelligent diagnosis methods heavily rely on supervised learning with abundant labeled data. To address this issue, this paper presents a semi-supervised Informer algorithm for fault diagnosis modeling, leveraging the Informer model's long- and short-term memory capabilities and the benefits of semi-supervised learning to handle the diagnosis of a small amount of labeled data alongside a substantial amount of unlabeled data. An experimental study is conducted using real-world industrial robot monitoring data to assess the proposed algorithm's effectiveness, demonstrating its ability to deliver accurate fault diagnosis despite limited labeled samples.

Optimizing Automated Optical Inspection: An Adaptive Fusion and Semi-Supervised Self-Learning Approach for Elevated Accuracy and Efficiency in Scenarios with Scarce Labeled Data.

In the field of automatic optical inspection (AOI), this study presents innovative strategies to enhance object detection accuracy while minimizing dependence on large annotated datasets. We initially developed a defect detection model using a dataset of 3579 images across 32 categories, created in collaboration with a major Taiwanese panel manufacturer. This model was evaluated using 12,000 ambiguously labeled images, with improvements achieved through data augmentation and annotation refinement. To address the challenges of limited labeled data, we proposed the Adaptive Fused Semi-Supervised Self-Learning (AFSL) method. This approach, designed for anchor-based object detection models, leverages a small set of labeled data alongside a larger pool of unlabeled data to enable continuous model optimization. Key components of AFSL include the Bounding Box Assigner, Adaptive Training Scheduler, and Data Allocator, which together facilitate dynamic threshold adjustments and balanced training, significantly enhancing the model's performance on AOI datasets. The AFSL method improved the mean average precision (mAP) from 43.5% to 57.1% on the COCO dataset and by 2.6% on the AOI dataset, demonstrating its effectiveness in achieving high levels of precision and efficiency in AOI with minimal labeled data.