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1.
Artif Intell Med ; 151: 102828, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38564879

RESUMO

Reliable large-scale cell detection and segmentation is the fundamental first step to understanding biological processes in the brain. The ability to phenotype cells at scale can accelerate preclinical drug evaluation and system-level brain histology studies. The impressive advances in deep learning offer a practical solution to cell image detection and segmentation. Unfortunately, categorizing cells and delineating their boundaries for training deep networks is an expensive process that requires skilled biologists. This paper presents a novel self-supervised Dual-Loss Adaptive Masked Autoencoder (DAMA) for learning rich features from multiplexed immunofluorescence brain images. DAMA's objective function minimizes the conditional entropy in pixel-level reconstruction and feature-level regression. Unlike existing self-supervised learning methods based on a random image masking strategy, DAMA employs a novel adaptive mask sampling strategy to maximize mutual information and effectively learn brain cell data. To the best of our knowledge, this is the first effort to develop a self-supervised learning method for multiplexed immunofluorescence brain images. Our extensive experiments demonstrate that DAMA features enable superior cell detection, segmentation, and classification performance without requiring many annotations. In addition, to examine the generalizability of DAMA, we also experimented on TissueNet, a multiplexed imaging dataset comprised of two-channel fluorescence images from six distinct tissue types, captured using six different imaging platforms. Our code is publicly available at https://github.com/hula-ai/DAMA.


Assuntos
Encéfalo , Encéfalo/diagnóstico por imagem , Processamento de Imagem Assistida por Computador/métodos , Aprendizado de Máquina Supervisionado , Humanos , Aprendizado Profundo , Animais , Algoritmos , Neuroimagem/métodos
2.
BMC Bioinformatics ; 25(1): 155, 2024 Apr 20.
Artigo em Inglês | MEDLINE | ID: mdl-38641616

RESUMO

BACKGROUND: Classification of binary data arises naturally in many clinical applications, such as patient risk stratification through ICD codes. One of the key practical challenges in data classification using machine learning is to avoid overfitting. Overfitting in supervised learning primarily occurs when a model learns random variations from noisy labels in training data rather than the underlying patterns. While traditional methods such as regularization and early stopping have demonstrated effectiveness in interpolation tasks, addressing overfitting in the classification of binary data, in which predictions always amount to extrapolation, demands extrapolation-enhanced strategies. One such approach is hybrid mechanistic/data-driven modeling, which integrates prior knowledge on input features into the learning process, enhancing the model's ability to extrapolate. RESULTS: We present NoiseCut, a Python package for noise-tolerant classification of binary data by employing a hybrid modeling approach that leverages solutions of defined max-cut problems. In a comparative analysis conducted on synthetically generated binary datasets, NoiseCut exhibits better overfitting prevention compared to the early stopping technique employed by different supervised machine learning algorithms. The noise tolerance of NoiseCut stems from a dropout strategy that leverages prior knowledge of input features and is further enhanced by the integration of max-cut problems into the learning process. CONCLUSIONS: NoiseCut is a Python package for the implementation of hybrid modeling for the classification of binary data. It facilitates the integration of mechanistic knowledge on the input features into learning from data in a structured manner and proves to be a valuable classification tool when the available training data is noisy and/or limited in size. This advantage is especially prominent in medical and biomedical applications where data scarcity and noise are common challenges. The codebase, illustrations, and documentation for NoiseCut are accessible for download at https://pypi.org/project/noisecut/ . The implementation detailed in this paper corresponds to the version 0.2.1 release of the software.


Assuntos
Algoritmos , Software , Humanos , Aprendizado de Máquina Supervisionado , Aprendizado de Máquina
3.
Bioinformatics ; 40(4)2024 Mar 29.
Artigo em Inglês | MEDLINE | ID: mdl-38588559

RESUMO

MOTIVATION: Supervised deep learning is used to model the complex relationship between genomic sequence and regulatory function. Understanding how these models make predictions can provide biological insight into regulatory functions. Given the complexity of the sequence to regulatory function mapping (the cis-regulatory code), it has been suggested that the genome contains insufficient sequence variation to train models with suitable complexity. Data augmentation is a widely used approach to increase the data variation available for model training, however current data augmentation methods for genomic sequence data are limited. RESULTS: Inspired by the success of comparative genomics, we show that augmenting genomic sequences with evolutionarily related sequences from other species, which we term phylogenetic augmentation, improves the performance of deep learning models trained on regulatory genomic sequences to predict high-throughput functional assay measurements. Additionally, we show that phylogenetic augmentation can rescue model performance when the training set is down-sampled and permits deep learning on a real-world small dataset, demonstrating that this approach improves data efficiency. Overall, this data augmentation method represents a solution for improving model performance that is applicable to many supervised deep-learning problems in genomics. AVAILABILITY AND IMPLEMENTATION: The open-source GitHub repository agduncan94/phylogenetic_augmentation_paper includes the code for rerunning the analyses here and recreating the figures.


Assuntos
Aprendizado Profundo , Genômica , Filogenia , Genômica/métodos , Aprendizado de Máquina Supervisionado , Humanos
4.
Sci Rep ; 14(1): 9080, 2024 04 20.
Artigo em Inglês | MEDLINE | ID: mdl-38643324

RESUMO

In developing countries, one-quarter of young women have suffered from anemia. However, the available studies in Ethiopia have been usually used the traditional stastical methods. Therefore, this study aimed to employ multiple machine learning algorithms to identify the most effective model for the prediction of anemia among youth girls in Ethiopia. A total of 5642 weighted samples of young girls from the 2016 Ethiopian Demographic and Health Survey dataset were utilized. The data underwent preprocessing, with 80% of the observations used for training the model and 20% for testing. Eight machine learning algorithms were employed to build and compare models. The model performance was assessed using evaluation metrics in Python software. Various data balancing techniques were applied, and the Boruta algorithm was used to select the most relevant features. Besides, association rule mining was conducted using the Apriori algorithm in R software. The random forest classifier with an AUC value of 82% outperformed in predicting anemia among all the tested classifiers. Region, poor wealth index, no formal education, unimproved toilet facility, rural residence, not used contraceptive method, religion, age, no media exposure, occupation, and having more than 5 family size were the top attributes to predict anemia. Association rule mining was identified the top seven best rules that most frequently associated with anemia. The random forest classifier is the best for predicting anemia. Therefore, making it potentially valuable as decision-support tools for the relevant stakeholders and giving emphasis for the identified predictors could be an important intervention to halt anemia among youth girls.


Assuntos
Algoritmos , Anemia , Humanos , Adolescente , Feminino , Etiópia/epidemiologia , Aprendizado de Máquina Supervisionado , Software , Anemia/diagnóstico , Anemia/epidemiologia
5.
Comput Methods Programs Biomed ; 249: 108141, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38574423

RESUMO

BACKGROUND AND OBJECTIVE: Lung tumor annotation is a key upstream task for further diagnosis and prognosis. Although deep learning techniques have promoted automation of lung tumor segmentation, there remain challenges impeding its application in clinical practice, such as a lack of prior annotation for model training and data-sharing among centers. METHODS: In this paper, we use data from six centers to design a novel federated semi-supervised learning (FSSL) framework with dynamic model aggregation and improve segmentation performance for lung tumors. To be specific, we propose a dynamically updated algorithm to deal with model parameter aggregation in FSSL, which takes advantage of both the quality and quantity of client data. Moreover, to increase the accessibility of data in the federated learning (FL) network, we explore the FAIR data principle while the previous federated methods never involve. RESULT: The experimental results show that the segmentation performance of our model in six centers is 0.9348, 0.8436, 0.8328, 0.7776, 0.8870 and 0.8460 respectively, which is superior to traditional deep learning methods and recent federated semi-supervised learning methods. CONCLUSION: The experimental results demonstrate that our method is superior to the existing FSSL methods. In addition, our proposed dynamic update strategy effectively utilizes the quality and quantity information of client data and shows efficiency in lung tumor segmentation. The source code is released on (https://github.com/GDPHMediaLab/FedDUS).


Assuntos
Algoritmos , Neoplasias Pulmonares , Humanos , Automação , Neoplasias Pulmonares/diagnóstico por imagem , Software , Aprendizado de Máquina Supervisionado , Tomografia Computadorizada por Raios X , Processamento de Imagem Assistida por Computador
6.
Int J Mol Sci ; 25(7)2024 Mar 28.
Artigo em Inglês | MEDLINE | ID: mdl-38612602

RESUMO

Molecular property prediction is an important task in drug discovery, and with help of self-supervised learning methods, the performance of molecular property prediction could be improved by utilizing large-scale unlabeled dataset. In this paper, we propose a triple generative self-supervised learning method for molecular property prediction, called TGSS. Three encoders including a bi-directional long short-term memory recurrent neural network (BiLSTM), a Transformer, and a graph attention network (GAT) are used in pre-training the model using molecular sequence and graph structure data to extract molecular features. The variational auto encoder (VAE) is used for reconstructing features from the three models. In the downstream task, in order to balance the information between different molecular features, a feature fusion module is added to assign different weights to each feature. In addition, to improve the interpretability of the model, atomic similarity heat maps were introduced to demonstrate the effectiveness and rationality of molecular feature extraction. We demonstrate the accuracy of the proposed method on chemical and biological benchmark datasets by comparative experiments.


Assuntos
Benchmarking , Descoberta de Drogas , Animais , Fontes de Energia Elétrica , Estro , Aprendizado de Máquina Supervisionado
7.
Brief Bioinform ; 25(3)2024 Mar 27.
Artigo em Inglês | MEDLINE | ID: mdl-38605640

RESUMO

Language models pretrained by self-supervised learning (SSL) have been widely utilized to study protein sequences, while few models were developed for genomic sequences and were limited to single species. Due to the lack of genomes from different species, these models cannot effectively leverage evolutionary information. In this study, we have developed SpliceBERT, a language model pretrained on primary ribonucleic acids (RNA) sequences from 72 vertebrates by masked language modeling, and applied it to sequence-based modeling of RNA splicing. Pretraining SpliceBERT on diverse species enables effective identification of evolutionarily conserved elements. Meanwhile, the learned hidden states and attention weights can characterize the biological properties of splice sites. As a result, SpliceBERT was shown effective on several downstream tasks: zero-shot prediction of variant effects on splicing, prediction of branchpoints in humans, and cross-species prediction of splice sites. Our study highlighted the importance of pretraining genomic language models on a diverse range of species and suggested that SSL is a promising approach to enhance our understanding of the regulatory logic underlying genomic sequences.


Assuntos
Splicing de RNA , Vertebrados , Animais , Humanos , Sequência de Bases , Vertebrados/genética , RNA , Aprendizado de Máquina Supervisionado
8.
Sensors (Basel) ; 24(7)2024 Mar 29.
Artigo em Inglês | MEDLINE | ID: mdl-38610406

RESUMO

Wearable sensors could be beneficial for the continuous quantification of upper limb motor symptoms in people with Parkinson's disease (PD). This work evaluates the use of two inertial measurement units combined with supervised machine learning models to classify and predict a subset of MDS-UPDRS III subitems in PD. We attached the two compact wearable sensors on the dorsal part of each hand of 33 people with PD and 12 controls. Each participant performed six clinical movement tasks in parallel with an assessment of the MDS-UPDRS III. Random forest (RF) models were trained on the sensor data and motor scores. An overall accuracy of 94% was achieved in classifying the movement tasks. When employed for classifying the motor scores, the averaged area under the receiver operating characteristic values ranged from 68% to 92%. Motor scores were additionally predicted using an RF regression model. In a comparative analysis, trained support vector machine models outperformed the RF models for specific tasks. Furthermore, our results surpass the literature in certain cases. The methods developed in this work serve as a base for future studies, where home-based assessments of pharmacological effects on motor function could complement regular clinical assessments.


Assuntos
Doença de Parkinson , Humanos , Doença de Parkinson/diagnóstico , Aprendizado de Máquina , Movimento , Aprendizado de Máquina Supervisionado , Mãos
9.
PLoS Comput Biol ; 20(4): e1012006, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38578796

RESUMO

Single-cell RNA sequencing (scRNASeq) data plays a major role in advancing our understanding of developmental biology. An important current question is how to classify transcriptomic profiles obtained from scRNASeq experiments into the various cell types and identify the lineage relationship for individual cells. Because of the fast accumulation of datasets and the high dimensionality of the data, it has become challenging to explore and annotate single-cell transcriptomic profiles by hand. To overcome this challenge, automated classification methods are needed. Classical approaches rely on supervised training datasets. However, due to the difficulty of obtaining data annotated at single-cell resolution, we propose instead to take advantage of partial annotations. The partial label learning framework assumes that we can obtain a set of candidate labels containing the correct one for each data point, a simpler setting than requiring a fully supervised training dataset. We study and extend when needed state-of-the-art multi-class classification methods, such as SVM, kNN, prototype-based, logistic regression and ensemble methods, to the partial label learning framework. Moreover, we study the effect of incorporating the structure of the label set into the methods. We focus particularly on the hierarchical structure of the labels, as commonly observed in developmental processes. We show, on simulated and real datasets, that these extensions enable to learn from partially labeled data, and perform predictions with high accuracy, particularly with a nonlinear prototype-based method. We demonstrate that the performances of our methods trained with partially annotated data reach the same performance as fully supervised data. Finally, we study the level of uncertainty present in the partially annotated data, and derive some prescriptive results on the effect of this uncertainty on the accuracy of the partial label learning methods. Overall our findings show how hierarchical and non-hierarchical partial label learning strategies can help solve the problem of automated classification of single-cell transcriptomic profiles, interestingly these methods rely on a much less stringent type of annotated datasets compared to fully supervised learning methods.


Assuntos
Perfilação da Expressão Gênica , Aprendizado de Máquina Supervisionado , Incerteza , Modelos Logísticos
10.
J Neural Eng ; 21(2)2024 Apr 17.
Artigo em Inglês | MEDLINE | ID: mdl-38588700

RESUMO

Objective. The instability of the EEG acquisition devices may lead to information loss in the channels or frequency bands of the collected EEG. This phenomenon may be ignored in available models, which leads to the overfitting and low generalization of the model.Approach. Multiple self-supervised learning tasks are introduced in the proposed model to enhance the generalization of EEG emotion recognition and reduce the overfitting problem to some extent. Firstly, channel masking and frequency masking are introduced to simulate the information loss in certain channels and frequency bands resulting from the instability of EEG, and two self-supervised learning-based feature reconstruction tasks combining masked graph autoencoders (GAE) are constructed to enhance the generalization of the shared encoder. Secondly, to take full advantage of the complementary information contained in these two self-supervised learning tasks to ensure the reliability of feature reconstruction, a weight sharing (WS) mechanism is introduced between the two graph decoders. Thirdly, an adaptive weight multi-task loss (AWML) strategy based on homoscedastic uncertainty is adopted to combine the supervised learning loss and the two self-supervised learning losses to enhance the performance further.Main results. Experimental results on SEED, SEED-V, and DEAP datasets demonstrate that: (i) Generally, the proposed model achieves higher averaged emotion classification accuracy than various baselines included in both subject-dependent and subject-independent scenarios. (ii) Each key module contributes to the performance enhancement of the proposed model. (iii) It achieves higher training efficiency, and significantly lower model size and computational complexity than the state-of-the-art (SOTA) multi-task-based model. (iv) The performances of the proposed model are less influenced by the key parameters.Significance. The introduction of the self-supervised learning task helps to enhance the generalization of the EEG emotion recognition model and eliminate overfitting to some extent, which can be modified to be applied in other EEG-based classification tasks.


Assuntos
Eletroencefalografia , Emoções , Aprendizado de Máquina Supervisionado , Aprendizado de Máquina Supervisionado/normas , Conjuntos de Dados como Assunto , Humanos
12.
Med Image Anal ; 94: 103150, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38574545

RESUMO

Self-supervised representation learning can boost the performance of a pre-trained network on downstream tasks for which labeled data is limited. A popular method based on this paradigm, known as contrastive learning, works by constructing sets of positive and negative pairs from the data, and then pulling closer the representations of positive pairs while pushing apart those of negative pairs. Although contrastive learning has been shown to improve performance in various classification tasks, its application to image segmentation has been more limited. This stems in part from the difficulty of defining positive and negative pairs for dense feature maps without having access to pixel-wise annotations. In this work, we propose a novel self-supervised pre-training method that overcomes the challenges of contrastive learning in image segmentation. Our method leverages Information Invariant Clustering (IIC) as an unsupervised task to learn a local representation of images in the decoder of a segmentation network, but addresses three important drawbacks of this approach: (i) the difficulty of optimizing the loss based on mutual information maximization; (ii) the lack of clustering consistency for different random transformations of the same image; (iii) the poor correspondence of clusters obtained by IIC with region boundaries in the image. Toward this goal, we first introduce a regularized mutual information maximization objective that encourages the learned clusters to be balanced and consistent across different image transformations. We also propose a boundary-aware loss based on cross-correlation, which helps the learned clusters to be more representative of important regions in the image. Compared to contrastive learning applied in dense features, our method does not require computing positive and negative pairs and also enhances interpretability through the visualization of learned clusters. Comprehensive experiments involving four different medical image segmentation tasks reveal the high effectiveness of our self-supervised representation learning method. Our results show the proposed method to outperform by a large margin several state-of-the-art self-supervised and semi-supervised approaches for segmentation, reaching a performance close to full supervision with only a few labeled examples.


Assuntos
Processamento de Imagem Assistida por Computador , Aprendizagem , Humanos , Aprendizado de Máquina Supervisionado
13.
BMC Bioinformatics ; 25(1): 103, 2024 Mar 08.
Artigo em Inglês | MEDLINE | ID: mdl-38459463

RESUMO

BACKGROUND: Blood test is extensively performed for screening, diagnoses and surveillance purposes. Although it is possible to automatically evaluate the raw blood test data with the advanced deep self-supervised machine learning approaches, it has not been profoundly investigated and implemented yet. RESULTS: This paper proposes deep machine learning algorithms with multi-dimensional adaptive feature elimination, self-feature weighting and novel feature selection approaches. To classify the health risks based on the processed data with the deep layers, four machine learning algorithms having various properties from being utterly model free to gradient driven are modified. CONCLUSIONS: The results show that the proposed deep machine learning algorithms can remove the unnecessary features, assign self-importance weights, selects their most informative ones and classify the health risks automatically from the worst-case low to worst-case high values.


Assuntos
Algoritmos , Aprendizado de Máquina , Aprendizado de Máquina Supervisionado
14.
Artif Intell Med ; 149: 102778, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38462280

RESUMO

Many computational methods have been proposed to identify potential drug-target interactions (DTIs) to expedite drug development. Graph neural network (GNN) methods are considered to be one of the most effective approaches. However, shallow GNN methods can only aggregate local information from nodes. Also, deep GNN methods may result in over-smoothing while obtaining long-distance neighbourhood information. As a result, existing GNN methods struggle to extract the complete features of the graph. Additionally, the number of known DTIs is insufficient, and there are far more unknown drug-target pairs than known DTIs, leading to class imbalance. This article proposes a model that combines graph autoencoder and self-supervised learning to accurately encode multilevel features of graphs using only a small number of labelled samples. We introduce a positive sample compensation coefficient to the objective function to mitigate the impact of class imbalance. Experiments on two datasets demonstrated that our model outperforms the four baseline methods, and the new DTIs predicted by the SSLDTI model were verified by the DrugBank database.


Assuntos
Desenvolvimento de Medicamentos , Redes Neurais de Computação , Bases de Dados Factuais , Aprendizado de Máquina Supervisionado
15.
Biometrics ; 80(1)2024 Jan 29.
Artigo em Inglês | MEDLINE | ID: mdl-38465982

RESUMO

In many modern machine learning applications, changes in covariate distributions and difficulty in acquiring outcome information have posed challenges to robust model training and evaluation. Numerous transfer learning methods have been developed to robustly adapt the model itself to some unlabeled target populations using existing labeled data in a source population. However, there is a paucity of literature on transferring performance metrics, especially receiver operating characteristic (ROC) parameters, of a trained model. In this paper, we aim to evaluate the performance of a trained binary classifier on unlabeled target population based on ROC analysis. We proposed Semisupervised Transfer lEarning of Accuracy Measures (STEAM), an efficient three-step estimation procedure that employs (1) double-index modeling to construct calibrated density ratio weights and (2) robust imputation to leverage the large amount of unlabeled data to improve estimation efficiency. We establish the consistency and asymptotic normality of the proposed estimator under the correct specification of either the density ratio model or the outcome model. We also correct for potential overfitting bias in the estimators in finite samples with cross-validation. We compare our proposed estimators to existing methods and show reductions in bias and gains in efficiency through simulations. We illustrate the practical utility of the proposed method on evaluating prediction performance of a phenotyping model for rheumatoid arthritis (RA) on a temporally evolving EHR cohort.


Assuntos
Aprendizado de Máquina , Aprendizado de Máquina Supervisionado , Humanos , Curva ROC , Projetos de Pesquisa , Viés
16.
J Assist Reprod Genet ; 41(4): 967-978, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38470553

RESUMO

PURPOSE: To study the effectiveness of whole-scenario embryo identification using a self-supervised learning encoder (WISE) in in vitro fertilization (IVF) on time-lapse, cross-device, and cryo-thawed scenarios. METHODS: WISE was based on the vision transformer (ViT) architecture and masked autoencoders (MAE), a self-supervised learning (SSL) method. To train WISE, we prepared three datasets including the SSL pre-training dataset, the time-lapse identification dataset, and the cross-device identification dataset. To identify whether pairs of images were from the same embryos in different scenarios in the downstream identification tasks, embryo images including time-lapse and microscope images were first pre-processed through object detection, cropping, padding, and resizing, and then fed into WISE to get predictions. RESULTS: WISE could accurately identify embryos in the three scenarios. The accuracy was 99.89% on the time-lapse identification dataset, and 83.55% on the cross-device identification dataset. Besides, we subdivided a cryo-thawed evaluation set from the cross-device test set to have a better estimation of how WISE performs in the real-world, and it reached an accuracy of 82.22%. There were approximately 10% improvements in cross-device and cryo-thawed identification tasks after the SSL method was applied. Besides, WISE demonstrated improvements in the accuracy of 9.5%, 12%, and 18% over embryologists in the three scenarios. CONCLUSION: SSL methods can improve embryo identification accuracy even when dealing with cross-device and cryo-thawed paired images. The study is the first to apply SSL in embryo identification, and the results show the promise of WISE for future application in embryo witnessing.


Assuntos
Fertilização In Vitro , Imagem com Lapso de Tempo , Humanos , Fertilização In Vitro/métodos , Feminino , Imagem com Lapso de Tempo/métodos , Aprendizado de Máquina Supervisionado , Embrião de Mamíferos , Gravidez , Processamento de Imagem Assistida por Computador/métodos , Blastocisto/citologia , Blastocisto/fisiologia , Transferência Embrionária/métodos , Criopreservação/métodos
17.
Med Image Anal ; 94: 103086, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38537414

RESUMO

Discriminative, restorative, and adversarial learning have proven beneficial for self-supervised learning schemes in computer vision and medical imaging. Existing efforts, however, fail to capitalize on the potentially synergistic effects these methods may offer in a ternary setup, which, we envision can significantly benefit deep semantic representation learning. Towards this end, we developed DiRA, the first framework that unites discriminative, restorative, and adversarial learning in a unified manner to collaboratively glean complementary visual information from unlabeled medical images for fine-grained semantic representation learning. Our extensive experiments demonstrate that DiRA: (1) encourages collaborative learning among three learning ingredients, resulting in more generalizable representation across organs, diseases, and modalities; (2) outperforms fully supervised ImageNet models and increases robustness in small data regimes, reducing annotation cost across multiple medical imaging applications; (3) learns fine-grained semantic representation, facilitating accurate lesion localization with only image-level annotation; (4) improves reusability of low/mid-level features; and (5) enhances restorative self-supervised approaches, revealing that DiRA is a general framework for united representation learning. Code and pretrained models are available at https://github.com/JLiangLab/DiRA.


Assuntos
Doenças Hereditárias Autoinflamatórias , Humanos , Semântica , Aprendizado de Máquina Supervisionado , Proteína Antagonista do Receptor de Interleucina 1
18.
Med Image Anal ; 94: 103151, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38527405

RESUMO

Self-supervised learning has emerged as a powerful tool for pretraining deep networks on unlabeled data, prior to transfer learning of target tasks with limited annotation. The relevance between the pretraining pretext and target tasks is crucial to the success of transfer learning. Various pretext tasks have been proposed to utilize properties of medical image data (e.g., three dimensionality), which are more relevant to medical image analysis than generic ones for natural images. However, previous work rarely paid attention to data with anatomy-oriented imaging planes, e.g., standard cardiac magnetic resonance imaging views. As these imaging planes are defined according to the anatomy of the imaged organ, pretext tasks effectively exploiting this information can pretrain the networks to gain knowledge on the organ of interest. In this work, we propose two complementary pretext tasks for this group of medical image data based on the spatial relationship of the imaging planes. The first is to learn the relative orientation between the imaging planes and implemented as regressing their intersecting lines. The second exploits parallel imaging planes to regress their relative slice locations within a stack. Both pretext tasks are conceptually straightforward and easy to implement, and can be combined in multitask learning for better representation learning. Thorough experiments on two anatomical structures (heart and knee) and representative target tasks (semantic segmentation and classification) demonstrate that the proposed pretext tasks are effective in pretraining deep networks for remarkably boosted performance on the target tasks, and superior to other recent approaches.


Assuntos
Coração , Articulação do Joelho , Humanos , Coração/diagnóstico por imagem , Semântica , Aprendizado de Máquina Supervisionado , Processamento de Imagem Assistida por Computador
19.
Neural Netw ; 174: 106262, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38547803

RESUMO

In machine learning it is often necessary to assume or know the distribution of the data, however it is difficult to do so in practical applications. Aiming to this problem, this work, we propose a novel distribution-free Bayesian regularized learning framework for semi-supervised learning, which is called Hessian regularized twin minimax probability extreme learning machine (HRTMPELM). In this framework, we attempt to construct two non-parallel hyperplanes by introducing the high separation probability assumption, such that each hyperplane separates samples from one class with maximum probability while moving away from samples from the other class. Subsidiently, the framework can be utilized to construct reasonable semi-supervised classifiers by using the information of the inherent geometric distribution of the samples through the Hessian regularization term. Additionally, the proposed framework controls the misclassification error of samples by minimizing the upper limit of the worst-case misclassification probability, and improves the generalization performance of the model by introducing the idea of regularization to avoid the occurrence of ill-posedness and overfitting problems. More importantly, the framework has no hyperparameters, making the learning process very simplified and efficient. Finally, a simple and reliable algorithm with globally optimal solutions via multivariate Chebyshev inequalities is designed for solving the proposed learning framework. Experiments on multiple datasets demonstrate the reliability and effectiveness of the proposed learning framework compared to other methods. Especially, we applied the framework to Ningxia wolfberry quality detection, which greatly enriches and facilitates the application of machine learning algorithms in the agricultural field.


Assuntos
Algoritmos , Aprendizado de Máquina Supervisionado , Teorema de Bayes , Reprodutibilidade dos Testes , Aprendizado de Máquina
20.
Radiol Artif Intell ; 6(3): e230077, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38446043

RESUMO

Purpose To develop and evaluate a semi-supervised learning model for intracranial hemorrhage detection and segmentation on an out-of-distribution head CT evaluation set. Materials and Methods This retrospective study used semi-supervised learning to bootstrap performance. An initial "teacher" deep learning model was trained on 457 pixel-labeled head CT scans collected from one U.S. institution from 2010 to 2017 and used to generate pseudo labels on a separate unlabeled corpus of 25 000 examinations from the Radiological Society of North America and American Society of Neuroradiology. A second "student" model was trained on this combined pixel- and pseudo-labeled dataset. Hyperparameter tuning was performed on a validation set of 93 scans. Testing for both classification (n = 481 examinations) and segmentation (n = 23 examinations, or 529 images) was performed on CQ500, a dataset of 481 scans performed in India, to evaluate out-of-distribution generalizability. The semi-supervised model was compared with a baseline model trained on only labeled data using area under the receiver operating characteristic curve, Dice similarity coefficient, and average precision metrics. Results The semi-supervised model achieved a statistically significant higher examination area under the receiver operating characteristic curve on CQ500 compared with the baseline (0.939 [95% CI: 0.938, 0.940] vs 0.907 [95% CI: 0.906, 0.908]; P = .009). It also achieved a higher Dice similarity coefficient (0.829 [95% CI: 0.825, 0.833] vs 0.809 [95% CI: 0.803, 0.812]; P = .012) and pixel average precision (0.848 [95% CI: 0.843, 0.853]) vs 0.828 [95% CI: 0.817, 0.828]) compared with the baseline. Conclusion The addition of unlabeled data in a semi-supervised learning framework demonstrates stronger generalizability potential for intracranial hemorrhage detection and segmentation compared with a supervised baseline. Keywords: Semi-supervised Learning, Traumatic Brain Injury, CT, Machine Learning Supplemental material is available for this article. Published under a CC BY 4.0 license. See also the commentary by Swimburne in this issue.


Assuntos
Hemorragias Intracranianas , Aprendizado de Máquina Supervisionado , Humanos , Estudos Retrospectivos , Hemorragias Intracranianas/diagnóstico , Aprendizado de Máquina , Benchmarking
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