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1.
Nat Commun ; 15(1): 4973, 2024 Jun 26.
Artigo em Inglês | MEDLINE | ID: mdl-38926357

RESUMO

Endometrial cancer (EC) has four molecular subtypes with strong prognostic value and therapeutic implications. The most common subtype (NSMP; No Specific Molecular Profile) is assigned after exclusion of the defining features of the other three molecular subtypes and includes patients with heterogeneous clinical outcomes. In this study, we employ artificial intelligence (AI)-powered histopathology image analysis to differentiate between p53abn and NSMP EC subtypes and consequently identify a sub-group of NSMP EC patients that has markedly inferior progression-free and disease-specific survival (termed 'p53abn-like NSMP'), in a discovery cohort of 368 patients and two independent validation cohorts of 290 and 614 from other centers. Shallow whole genome sequencing reveals a higher burden of copy number abnormalities in the 'p53abn-like NSMP' group compared to NSMP, suggesting that this group is biologically distinct compared to other NSMP ECs. Our work demonstrates the power of AI to detect prognostically different and otherwise unrecognizable subsets of EC where conventional and standard molecular or pathologic criteria fall short, refining image-based tumor classification. This study's findings are applicable exclusively to females.


Assuntos
Inteligência Artificial , Neoplasias do Endométrio , Humanos , Feminino , Neoplasias do Endométrio/patologia , Neoplasias do Endométrio/genética , Pessoa de Meia-Idade , Idoso , Processamento de Imagem Assistida por Computador/métodos , Prognóstico , Variações do Número de Cópias de DNA , Sequenciamento Completo do Genoma , Proteína Supressora de Tumor p53/genética , Estudos de Coortes
2.
Int J Comput Assist Radiol Surg ; 19(5): 841-849, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38704793

RESUMO

PURPOSE: Deep learning-based analysis of micro-ultrasound images to detect cancerous lesions is a promising tool for improving prostate cancer (PCa) diagnosis. An ideal model should confidently identify cancer while responding with appropriate uncertainty when presented with out-of-distribution inputs that arise during deployment due to imaging artifacts and the biological heterogeneity of patients and prostatic tissue. METHODS: Using micro-ultrasound data from 693 patients across 5 clinical centers who underwent micro-ultrasound guided prostate biopsy, we train and evaluate convolutional neural network models for PCa detection. To improve robustness to out-of-distribution inputs, we employ and comprehensively benchmark several state-of-the-art uncertainty estimation methods. RESULTS: PCa detection models achieve performance scores up to 76 % average AUROC with a 10-fold cross validation setup. Models with uncertainty estimation obtain expected calibration error scores as low as 2 % , indicating that confident predictions are very likely to be correct. Visualizations of the model output demonstrate that the model correctly identifies healthy versus malignant tissue. CONCLUSION: Deep learning models have been developed to confidently detect PCa lesions from micro-ultrasound. The performance of these models, determined from a large and diverse dataset, is competitive with visual analysis of magnetic resonance imaging, the clinical benchmark to identify PCa lesions for targeted biopsy. Deep learning with micro-ultrasound should be further studied as an avenue for targeted prostate biopsy.


Assuntos
Aprendizado Profundo , Neoplasias da Próstata , Humanos , Masculino , Neoplasias da Próstata/diagnóstico por imagem , Neoplasias da Próstata/patologia , Neoplasias da Próstata/diagnóstico , Biópsia Guiada por Imagem/métodos , Ultrassonografia/métodos , Redes Neurais de Computação , Ultrassonografia de Intervenção/métodos
3.
Int J Comput Assist Radiol Surg ; 19(6): 1121-1128, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38598142

RESUMO

PURPOSE: The standard of care for prostate cancer (PCa) diagnosis is the histopathological analysis of tissue samples obtained via transrectal ultrasound (TRUS) guided biopsy. Models built with deep neural networks (DNNs) hold the potential for direct PCa detection from TRUS, which allows targeted biopsy and subsequently enhances outcomes. Yet, there are ongoing challenges with training robust models, stemming from issues such as noisy labels, out-of-distribution (OOD) data, and limited labeled data. METHODS: This study presents LensePro, a unified method that not only excels in label efficiency but also demonstrates robustness against label noise and OOD data. LensePro comprises two key stages: first, self-supervised learning to extract high-quality feature representations from abundant unlabeled TRUS data and, second, label noise-tolerant prototype-based learning to classify the extracted features. RESULTS: Using data from 124 patients who underwent systematic prostate biopsy, LensePro achieves an AUROC, sensitivity, and specificity of 77.9%, 85.9%, and 57.5%, respectively, for detecting PCa in ultrasound. Our model shows it is effective for detecting OOD data in test time, critical for clinical deployment. Ablation studies demonstrate that each component of our method improves PCa detection by addressing one of the three challenges, reinforcing the benefits of a unified approach. CONCLUSION: Through comprehensive experiments, LensePro demonstrates its state-of-the-art performance for TRUS-based PCa detection. Although further research is necessary to confirm its clinical applicability, LensePro marks a notable advancement in enhancing automated computer-aided systems for detecting prostate cancer in ultrasound.


Assuntos
Redes Neurais de Computação , Neoplasias da Próstata , Humanos , Masculino , Neoplasias da Próstata/diagnóstico por imagem , Neoplasias da Próstata/patologia , Neoplasias da Próstata/diagnóstico , Biópsia Guiada por Imagem/métodos , Sensibilidade e Especificidade , Ultrassonografia/métodos , Aprendizado Profundo , Ultrassonografia de Intervenção/métodos
4.
Int J Comput Assist Radiol Surg ; 19(6): 1129-1136, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38600411

RESUMO

PURPOSE: Real-time assessment of surgical margins is critical for favorable outcomes in cancer patients. The iKnife is a mass spectrometry device that has demonstrated potential for margin detection in cancer surgery. Previous studies have shown that using deep learning on iKnife data can facilitate real-time tissue characterization. However, none of the existing literature on the iKnife facilitate the use of publicly available, state-of-the-art pretrained networks or datasets that have been used in computer vision and other domains. METHODS: In a new framework we call ImSpect, we convert 1D iKnife data, captured during basal cell carcinoma (BCC) surgery, into 2D images in order to capitalize on state-of-the-art image classification networks. We also use self-supervision to leverage large amounts of unlabeled, intraoperative data to accommodate the data requirements of these networks. RESULTS: Through extensive ablation studies, we show that we can surpass previous benchmarks of margin evaluation in BCC surgery using iKnife data, achieving an area under the receiver operating characteristic curve (AUC) of 81%. We also depict the attention maps of the developed DL models to evaluate the biological relevance of the embedding space CONCLUSIONS: We propose a new method for characterizing tissue at the surgical margins, using mass spectrometry data from cancer surgery.


Assuntos
Carcinoma Basocelular , Margens de Excisão , Espectrometria de Massas , Neoplasias Cutâneas , Humanos , Espectrometria de Massas/métodos , Carcinoma Basocelular/cirurgia , Carcinoma Basocelular/diagnóstico por imagem , Carcinoma Basocelular/patologia , Neoplasias Cutâneas/cirurgia , Neoplasias Cutâneas/diagnóstico por imagem , Aprendizado de Máquina Supervisionado , Aprendizado Profundo
5.
Artigo em Inglês | MEDLINE | ID: mdl-37478033

RESUMO

Deep learning-based analysis of high-frequency, high-resolution micro-ultrasound data shows great promise for prostate cancer (PCa) detection. Previous approaches to analysis of ultrasound data largely follow a supervised learning (SL) paradigm. Ground truth labels for ultrasound images used for training deep networks often include coarse annotations generated from the histopathological analysis of tissue samples obtained via biopsy. This creates inherent limitations on the availability and quality of labeled data, posing major challenges to the success of SL methods. However, unlabeled prostate ultrasound data are more abundant. In this work, we successfully apply self-supervised representation learning to micro-ultrasound data. Using ultrasound data from 1028 biopsy cores of 391 subjects obtained in two clinical centers, we demonstrate that feature representations learned with this method can be used to classify cancer from noncancer tissue, obtaining an AUROC score of 91% on an independent test set. To the best of our knowledge, this is the first successful end-to-end self-SL (SSL) approach for PCa detection using ultrasound data. Our method outperforms baseline SL approaches, generalizes well between different data centers, and scales well in performance as more unlabeled data are added, making it a promising approach for future research using large volumes of unlabeled data. Our code is publicly available at https://www.github.com/MahdiGilany/SSL_micro_ultrasound.


Assuntos
Próstata , Neoplasias da Próstata , Masculino , Humanos , Próstata/diagnóstico por imagem , Neoplasias da Próstata/diagnóstico por imagem , Ultrassonografia/métodos , Aprendizado de Máquina Supervisionado
6.
Int J Comput Assist Radiol Surg ; 18(7): 1193-1200, 2023 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-37217768

RESUMO

PURPOSE: A large body of previous machine learning methods for ultrasound-based prostate cancer detection classify small regions of interest (ROIs) of ultrasound signals that lie within a larger needle trace corresponding to a prostate tissue biopsy (called biopsy core). These ROI-scale models suffer from weak labeling as histopathology results available for biopsy cores only approximate the distribution of cancer in the ROIs. ROI-scale models do not take advantage of contextual information that are normally considered by pathologists, i.e., they do not consider information about surrounding tissue and larger-scale trends when identifying cancer. We aim to improve cancer detection by taking a multi-scale, i.e., ROI-scale and biopsy core-scale, approach. METHODS: Our multi-scale approach combines (i) an "ROI-scale" model trained using self-supervised learning to extract features from small ROIs and (ii) a "core-scale" transformer model that processes a collection of extracted features from multiple ROIs in the needle trace region to predict the tissue type of the corresponding core. Attention maps, as a by-product, allow us to localize cancer at the ROI scale. RESULTS: We analyze this method using a dataset of micro-ultrasound acquired from 578 patients who underwent prostate biopsy, and compare our model to baseline models and other large-scale studies in the literature. Our model shows consistent and substantial performance improvements compared to ROI-scale-only models. It achieves [Formula: see text] AUROC, a statistically significant improvement over ROI-scale classification. We also compare our method to large studies on prostate cancer detection, using other imaging modalities. CONCLUSIONS: Taking a multi-scale approach that leverages contextual information improves prostate cancer detection compared to ROI-scale-only models. The proposed model achieves a statistically significant improvement in performance and outperforms other large-scale studies in the literature. Our code is publicly available at www.github.com/med-i-lab/TRUSFormer .


Assuntos
Próstata , Neoplasias da Próstata , Masculino , Humanos , Próstata/diagnóstico por imagem , Próstata/patologia , Biópsia Guiada por Imagem/métodos , Neoplasias da Próstata/diagnóstico por imagem , Neoplasias da Próstata/patologia , Ultrassonografia/métodos , Pelve
7.
Int J Comput Assist Radiol Surg ; 17(12): 2305-2313, 2022 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-36175747

RESUMO

PURPOSE: Rapid evaporative ionization mass spectrometry (REIMS) is an emerging technology for clinical margin detection. Deployment of REIMS depends on construction of reliable deep learning models that can categorize tissue according to its metabolomic signature. Challenges associated with developing these models include the presence of noise during data acquisition and the variance in tissue signatures between patients. In this study, we propose integration of uncertainty estimation in deep models to factor predictive confidence into margin detection in cancer surgery. METHODS: iKnife is used to collect 693 spectra of cancer and healthy samples acquired from 91 patients during basal cell carcinoma resection. A Bayesian neural network and two baseline models are trained on these data to perform classification as well as uncertainty estimation. The samples with high estimated uncertainty are then removed, and new models are trained using the clean data. The performance of proposed and baseline models, with different ratios of filtered data, is then compared. RESULTS: The data filtering does not improve the performance of the baseline models as they cannot provide reliable estimations of uncertainty. In comparison, the proposed model demonstrates a statistically significant improvement in average balanced accuracy (75.2%), sensitivity (74.1%) and AUC (82.1%) after removing uncertain training samples. We also demonstrate that if highly uncertain samples are predicted and removed from the test data, sensitivity further improves to 88.2%. CONCLUSIONS: This is the first study that applies uncertainty estimation to inform model training and deployment for tissue recognition in cancer surgery. Uncertainty estimation is leveraged in two ways: by factoring a measure of input noise in training the models and by including predictive confidence in reporting the outputs. We empirically show that considering uncertainty for model development can help improve the overall accuracy of a margin detection system using REIMS.


Assuntos
Margens de Excisão , Neoplasias , Humanos , Incerteza , Teorema de Bayes , Espectrometria de Massas/métodos , Neoplasias/diagnóstico , Neoplasias/cirurgia
8.
Int J Comput Assist Radiol Surg ; 17(9): 1697-1705, 2022 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-35881210

RESUMO

PURPOSE: Ultrasound is the standard-of-care to guide the systematic biopsy of the prostate. During the biopsy procedure, up to 12 biopsy cores are randomly sampled from six zones within the prostate, where the histopathology of those cores is used to determine the presence and grade of the cancer. Histopathology reports only provide statistical information on the presence of cancer and do not normally contain fine-grain information of cancer distribution within each core. This limitation hinders the development of machine learning models to detect the presence of cancer in ultrasound so that biopsy can be more targeted to highly suspicious prostate regions. METHODS: In this paper, we tackle this challenge in the form of training with noisy labels derived from histopathology. Noisy labels often result in the model overfitting to the training data, hence limiting its generalizability. To avoid overfitting, we focus on the generalization of the features of the model and present an iterative data label refinement algorithm to amend the labels gradually. We simultaneously train two classifiers, with the same structure, and automatically stop the training when we observe any sign of overfitting. Then, we use a confident learning approach to clean the data labels and continue with the training. This process is iteratively applied to the training data and labels until convergence. RESULTS: We illustrate the performance of the proposed method by classifying prostate cancer using a dataset of ultrasound images from 353 biopsy cores obtained from 90 patients. We achieve area under the curve, sensitivity, specificity, and accuracy of 0.73, 0.80, 0.63, and 0.69, respectively. CONCLUSION: Our approach is able to provide clinicians with a visualization of regions that likely contain cancerous tissue to obtain more accurate biopsy samples. The results demonstrate that our proposed method produces superior accuracy compared to the state-of-the-art methods.


Assuntos
Biópsia Guiada por Imagem , Neoplasias da Próstata , Biópsia com Agulha de Grande Calibre , Humanos , Biópsia Guiada por Imagem/métodos , Masculino , Redes Neurais de Computação , Próstata/diagnóstico por imagem , Próstata/patologia , Neoplasias da Próstata/diagnóstico por imagem , Neoplasias da Próstata/patologia
9.
Int J Comput Assist Radiol Surg ; 17(5): 841-847, 2022 May.
Artigo em Inglês | MEDLINE | ID: mdl-35344123

RESUMO

PURPOSE: Ultrasound-guided biopsy plays a major role in prostate cancer (PCa) detection, yet is limited by a high rate of false negatives and low diagnostic yield of the current systematic, non-targeted approaches. Developing machine learning models for accurately identifying cancerous tissue in ultrasound would help sample tissues from regions with higher cancer likelihood. A plausible approach for this purpose is to use individual ultrasound signals corresponding to a core as inputs and consider the histopathology diagnosis for the entire core as labels. However, this introduces significant amount of label noise to training and degrades the classification performance. Previously, we suggested that histopathology-reported cancer involvement can be a reasonable approximation for the label noise. METHODS: Here, we propose an involvement-based label refinement (iLR) method to correct corrupted labels and improve cancer classification. The difference between predicted and true cancer involvements is used to guide the label refinement process. We further incorporate iLR into state-of-the-art methods for learning with noisy labels and predicting cancer involvement. RESULTS: We use 258 biopsy cores from 70 patients and demonstrate that our proposed label refinement method improves the performance of multiple noise-tolerant approaches and achieves a balanced accuracy, correlation coefficient, and mean absolute error of 76.7%, 0.68, and 12.4, respectively. CONCLUSIONS: Our key contribution is to leverage a data-centric method to deal with noisy labels using histopathology reports, and improve the performance of prostate cancer diagnosis through a hierarchical training process with label refinement.


Assuntos
Próstata , Neoplasias da Próstata , Humanos , Biópsia Guiada por Imagem/métodos , Aprendizado de Máquina , Masculino , Próstata/diagnóstico por imagem , Próstata/patologia , Neoplasias da Próstata/diagnóstico por imagem , Neoplasias da Próstata/patologia , Ultrassonografia/métodos
10.
Int J Comput Assist Radiol Surg ; 17(1): 121-128, 2022 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-34783976

RESUMO

PURPOSE: Systematic prostate biopsy is widely used for cancer diagnosis. The procedure is blind to underlying prostate tissue micro-structure; hence, it can lead to a high rate of false negatives. Development of a machine-learning model that can reliably identify suspicious cancer regions is highly desirable. However, the models proposed to-date do not consider the uncertainty present in their output or the data to benefit clinical decision making for targeting biopsy. METHODS: We propose a deep network for improved detection of prostate cancer in systematic biopsy considering both the label and model uncertainty. The architecture of our model is based on U-Net, trained with temporal enhanced ultrasound (TeUS) data. We estimate cancer detection uncertainty using test-time augmentation and test-time dropout. We then use uncertainty metrics to report the cancer probability for regions with high confidence to help the clinical decision making during the biopsy procedure. RESULTS: Experiments for prostate cancer classification includes data from 183 prostate biopsy cores of 41 patients. We achieve an area under the curve, sensitivity, specificity and balanced accuracy of 0.79, 0.78, 0.71 and 0.75, respectively. CONCLUSION: Our key contribution is to automatically estimate model and label uncertainty towards enabling targeted ultrasound-guided prostate biopsy. We anticipate that such information about uncertainty can decrease the number of unnecessary biopsy with a higher rate of cancer yield.


Assuntos
Próstata , Neoplasias da Próstata , Humanos , Biópsia Guiada por Imagem , Imageamento por Ressonância Magnética , Masculino , Próstata/diagnóstico por imagem , Neoplasias da Próstata/diagnóstico por imagem , Ultrassonografia de Intervenção , Incerteza
12.
J Imaging ; 7(8)2021 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-34460790

RESUMO

This paper presents the design of NaviPBx, an ultrasound-navigated prostate cancer biopsy system. NaviPBx is designed to support an affordable and sustainable national healthcare program in Senegal. It uses spatiotemporal navigation and multiparametric transrectal ultrasound to guide biopsies. NaviPBx integrates concepts and methods that have been independently validated previously in clinical feasibility studies and deploys them together in a practical prostate cancer biopsy system. NaviPBx is based entirely on free open-source software and will be shared as a free open-source program with no restriction on its use. NaviPBx is set to be deployed and sustained nationwide through the Senegalese Military Health Service. This paper reports on the results of the design process of NaviPBx. Our approach concentrates on "frugal technology", intended to be affordable for low-middle income (LMIC) countries. Our project promises the wide-scale application of prostate biopsy and will foster time-efficient development and programmatic implementation of ultrasound-guided diagnostic and therapeutic interventions in Senegal and beyond.

13.
Proc IEEE Int Symp Biomed Imaging ; 2021: 443-447, 2021 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-36225596

RESUMO

Prostate cancer is the second most prevalent cancer in men worldwide. Deep neural networks have been successfully applied for prostate cancer diagnosis in magnetic resonance images (MRI). Pathology results from biopsy procedures are often used as ground truth to train such systems. There are several sources of noise in creating ground truth from biopsy data including sampling and registration errors. We propose: 1) A fully convolutional neural network (FCN) to produce cancer probability maps across the whole prostate gland in MRI; 2) A Gaussian weighted loss function to train the FCN with sparse biopsy locations; 3) A probabilistic framework to model biopsy location uncertainty and adjust cancer probability given the deep model predictions. We assess the proposed method on 325 biopsy locations from 203 patients. We observe that the proposed loss improves the area under the receiver operating characteristic curve and the biopsy location adjustment improves the sensitivity of the models.

14.
Ann Biomed Eng ; 49(2): 573-584, 2021 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-32779056

RESUMO

Prostate cancer (PCa) is a common, serious form of cancer in men that is still prevalent despite ongoing developments in diagnostic oncology. Current detection methods lead to high rates of inaccurate diagnosis. We present a method to directly model and exploit temporal aspects of temporal enhanced ultrasound (TeUS) for tissue characterization, which improves malignancy prediction. We employ a probabilistic-temporal framework, namely, hidden Markov models (HMMs), for modeling TeUS data obtained from PCa patients. We distinguish malignant from benign tissue by comparing the respective log-likelihood estimates generated by the HMMs. We analyze 1100 TeUS signals acquired from 12 patients. Our results show improved malignancy identification compared to previous results, demonstrating over 85% accuracy and AUC of 0.95. Incorporating temporal information directly into the models leads to improved tissue differentiation in PCa. We expect our method to generalize and be applied to other types of cancer in which temporal-ultrasound can be recorded.


Assuntos
Modelos Teóricos , Próstata/diagnóstico por imagem , Neoplasias da Próstata/diagnóstico , Humanos , Masculino , Cadeias de Markov , Ultrassonografia
15.
Ann Biomed Eng ; 48(12): 3025, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-32901381

RESUMO

The authors have noted an omission in the original acknowledgements. The correct acknowledgements are as follows: Acknowledgements: This work was partially supported by Grants from NSERC Discovery to Hagit Shatkay and Parvin Mousavi, NSERC and CIHR CHRP to Parvin Mousavi and NIH R01 LM012527, NIH U54 GM104941, NSF IIS EAGER #1650851 & NSF HDR #1940080 to Hagit Shatkay.

16.
Int J Comput Assist Radiol Surg ; 15(7): 1215-1223, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32372384

RESUMO

PURPOSE: The detection of clinically significant prostate cancer (PCa) is shown to greatly benefit from MRI-ultrasound fusion biopsy, which involves overlaying pre-biopsy MRI volumes (or targets) with real-time ultrasound images. In previous literature, machine learning models trained on either MRI or ultrasound data have been proposed to improve biopsy guidance and PCa detection. However, quantitative fusion of information from MRI and ultrasound has not been explored in depth in a large study. This paper investigates information fusion approaches between MRI and ultrasound to improve targeting of PCa foci in biopsies. METHODS: We build models of fully convolutional networks (FCN) using data from a newly proposed ultrasound modality, temporal enhanced ultrasound (TeUS), and apparent diffusion coefficient (ADC) from 107 patients with 145 biopsy cores. The architecture of our models is based on U-Net and U-Net with attention gates. Models are built using joint training through intermediate and late fusion of the data. We also build models with data from each modality, separately, to use as baseline. The performance is evaluated based on the area under the curve (AUC) for predicting clinically significant PCa. RESULTS: Using our proposed deep learning framework and intermediate fusion, integration of TeUS and ADC outperforms the individual modalities for cancer detection. We achieve an AUC of 0.76 for detection of all PCa foci, and 0.89 for PCa with larger foci. Results indicate a shared representation between multiple modalities outperforms the average unimodal predictions. CONCLUSION: We demonstrate the significant potential of multimodality integration of information from MRI and TeUS to improve PCa detection, which is essential for accurate targeting of cancer foci during biopsy. By using FCNs as the architecture of choice, we are able to predict the presence of clinically significant PCa in entire imaging planes immediately, without the need for region-based analysis. This reduces the overall computational time and enables future intra-operative deployment of this technology.


Assuntos
Imageamento por Ressonância Magnética/métodos , Neoplasias da Próstata/diagnóstico por imagem , Ultrassonografia/métodos , Humanos , Biópsia Guiada por Imagem/métodos , Masculino , Modelos Teóricos , Neoplasias da Próstata/patologia
17.
Int J Comput Assist Radiol Surg ; 15(6): 1023-1031, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32356095

RESUMO

PURPOSE: Ultrasound imaging is routinely used in prostate biopsy, which involves obtaining prostate tissue samples using a systematic, yet, non-targeted approach. This approach is blinded to individual patient intraprostatic pathology, and unfortunately, has a high rate of false negatives. METHODS: In this paper, we propose a deep network for improved detection of prostate cancer in systematic biopsy. We address several challenges associated with training such network: (1) Statistical labels: Since biopsy core's pathology report only represents a statistical distribution of cancer within the core, we use multiple instance learning (MIL) networks to enable learning from ultrasound image regions associated with those data; (2) Limited labels: The number of biopsy cores are limited to at most 12 per patient. As a result, the number of samples available for training a deep network is limited. We alleviate this issue by effectively combining Independent Conditional Variational Auto Encoders (ICVAE) with MIL. We train ICVAE to learn label-invariant features of RF data, which is subsequently used to generate synthetic data for improved training of the MIL network. RESULTS: Our in vivo study includes data from 339 prostate biopsy cores of 70 patients. We achieve an area under the curve, sensitivity, specificity, and balanced accuracy of 0.68, 0.77, 0.55 and 0.66, respectively. CONCLUSION: The proposed approach is generic and can be applied to several other scenarios where unlabeled data and noisy labels in training samples are present.


Assuntos
Biópsia Guiada por Imagem/métodos , Próstata/patologia , Neoplasias da Próstata/patologia , Ultrassonografia de Intervenção/métodos , Estudos de Viabilidade , Humanos , Masculino , Redes Neurais de Computação , Próstata/diagnóstico por imagem , Neoplasias da Próstata/diagnóstico por imagem , Sensibilidade e Especificidade
18.
Int J Comput Assist Radiol Surg ; 15(5): 877-886, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32314226

RESUMO

PURPOSE:  The emerging market of cardiac handheld ultrasound (US) is on the rise. Despite the advantages in ease of access and the lower cost, a gap in image quality can still be observed between the echocardiography (echo) data captured by point-of-care ultrasound (POCUS) compared to conventional cart-based US, which limits the further adaptation of POCUS. In this work, we aim to present a machine learning solution based on recent advances in adversarial training to investigate the feasibility of translating POCUS echo images to the quality level of high-end cart-based US systems. METHODS:  We propose a constrained cycle-consistent generative adversarial architecture for unpaired translation of cardiac POCUS to cart-based US data. We impose a structured shape-wise regularization via a critic segmentation network to preserve the underlying shape of the heart during quality translation. The proposed deep transfer model is constrained to the anatomy of the left ventricle (LV) in apical two-chamber (AP2) echo views. RESULTS:  A total of 1089 echo studies from 841 patients are used in this study. The AP2 frames are captured by POCUS (Philips Lumify and Clarius) and cart-based (Philips iE33 and Vivid E9) US machines. The dataset of quality translation comprises a total of 441 echo studies from 395 patients. Data from both POCUS and cart-based systems of the same patient were available in 122 cases. The deep-quality transfer model is integrated into a pipeline for an automated cardiac evaluation task, namely segmentation of LV in AP2 view. By transferring the low-quality POCUS data to the cart-based US, a significant average improvement of 30% and 34 mm is obtained in the LV segmentation Dice score and Hausdorff distance metrics, respectively. CONCLUSION:  This paper presents the feasibility of a machine learning solution to transform the image quality of POCUS data to that of high-quality high-end cart-based systems. The experiments show that by leveraging the quality translation through the proposed constrained adversarial training, the accuracy of automatic segmentation with POCUS data could be improved.


Assuntos
Ecocardiografia/métodos , Coração/diagnóstico por imagem , Sistemas Automatizados de Assistência Junto ao Leito , Humanos , Aprendizado de Máquina
19.
Med Image Anal ; 57: 186-196, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31325722

RESUMO

The goal of this work was to develop a method for accurate and robust automatic segmentation of the prostate clinical target volume in transrectal ultrasound (TRUS) images for brachytherapy. These images can be difficult to segment because of weak or insufficient landmarks or strong artifacts. We devise a method, based on convolutional neural networks (CNNs), that produces accurate segmentations on easy and difficult images alike. We propose two strategies to achieve improved segmentation accuracy on difficult images. First, for CNN training we adopt an adaptive sampling strategy, whereby the training process is encouraged to pay more attention to images that are difficult to segment. Secondly, we train a CNN ensemble and use the disagreement among this ensemble to identify uncertain segmentations and to estimate a segmentation uncertainty map. We improve uncertain segmentations by utilizing the prior shape information in the form of a statistical shape model. Our method achieves Hausdorff distance of 2.7 ±â€¯2.3 mm and Dice score of 93.9 ±â€¯3.5%. Comparisons with several competing methods show that our method achieves significantly better results and reduces the likelihood of committing large segmentation errors. Furthermore, our experiments show that our approach to estimating segmentation uncertainty is better than or on par with recent methods for estimation of prediction uncertainty in deep learning models. Our study demonstrates that estimation of model uncertainty and use of prior shape information can significantly improve the performance of CNN-based medical image segmentation methods, especially on difficult images.


Assuntos
Aprendizado Profundo , Processamento de Imagem Assistida por Computador/métodos , Reconhecimento Automatizado de Padrão/métodos , Neoplasias da Próstata/diagnóstico por imagem , Ultrassonografia , Pontos de Referência Anatômicos , Artefatos , Braquiterapia , Humanos , Masculino , Redes Neurais de Computação , Próstata/diagnóstico por imagem , Neoplasias da Próstata/radioterapia
20.
Biomed Opt Express ; 10(5): 2588-2605, 2019 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-31143504

RESUMO

In vivo imaging of prostate cancer with photoacoustic tomography is currently limited by the lack of sufficient local fluence for deep tissue penetration and the risk of over-irradiation near the laser-tissue contact surface. We propose the design of a transurethral illumination probe that addresses those limitations. A high energy of 50 mJ/pulse is coupled into a 1000-µm-core diameter multimode fiber. A 2 cm diffusing end is fabricated, which delivers light in radial illumination. The radial illumination is then reflected and reshaped by a parabolic cylindrical mirror to obtain nearly parallel side illumination with a doubled fluence. The fiber assembly is housed in a 25 Fr cystoscope sheath to provide protection of the fiber and maintain a minimal laser-tissue contact distance of 5 mm. A large laser-tissue contact surface area of 4 cm2 is obtained and the fluence on the tissue surface is kept below the maximum permissible exposure. By imaging a prostate mimicking phantom, a penetration depth of 3.5 cm at 10 mJ/cm2 fluence and 700 nm wavelength is demonstrated. The results indicate that photoacoustic tomography with the proposed transurethral probe has the potential to image the entire prostate while satisfying the fluence maximum permissible exposure and delivering a high power to the tissue.

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