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1.
PLoS Pathog ; 20(6): e1011915, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38861581

RESUMEN

Mycobacterium tuberculosis infects two billion people across the globe, and results in 8-9 million new tuberculosis (TB) cases and 1-1.5 million deaths each year. Most patients have no known genetic basis that predisposes them to disease. Here, we investigate the complex genetic basis of pulmonary TB by modelling human genetic diversity with the Diversity Outbred mouse population. When infected with M. tuberculosis, one-third develop early onset, rapidly progressive, necrotizing granulomas and succumb within 60 days. The remaining develop non-necrotizing granulomas and survive longer than 60 days. Genetic mapping using immune and inflammatory mediators; and clinical, microbiological, and granuloma correlates of disease identified five new loci on mouse chromosomes 1, 2, 4, 16; and three known loci on chromosomes 3 and 17. Further, multiple positively correlated traits shared loci on chromosomes 1, 16, and 17 and had similar patterns of allele effects, suggesting these loci contain critical genetic regulators of inflammatory responses to M. tuberculosis. To narrow the list of candidate genes, we used a machine learning strategy that integrated gene expression signatures from lungs of M. tuberculosis-infected Diversity Outbred mice with gene interaction networks to generate scores representing functional relationships. The scores were used to rank candidates for each mapped trait, resulting in 11 candidate genes: Ncf2, Fam20b, S100a8, S100a9, Itgb5, Fstl1, Zbtb20, Ddr1, Ier3, Vegfa, and Zfp318. Although all candidates have roles in infection, inflammation, cell migration, extracellular matrix remodeling, or intracellular signaling, and all contain single nucleotide polymorphisms (SNPs), SNPs in only four genes (S100a8, Itgb5, Fstl1, Zfp318) are predicted to have deleterious effects on protein functions. We performed methodological and candidate validations to (i) assess biological relevance of predicted allele effects by showing that Diversity Outbred mice carrying PWK/PhJ alleles at the H-2 locus on chromosome 17 QTL have shorter survival; (ii) confirm accuracy of predicted allele effects by quantifying S100A8 protein in inbred founder strains; and (iii) infection of C57BL/6 mice deficient for the S100a8 gene. Overall, this body of work demonstrates that systems genetics using Diversity Outbred mice can identify new (and known) QTLs and functionally relevant gene candidates that may be major regulators of complex host-pathogens interactions contributing to granuloma necrosis and acute inflammation in pulmonary TB.


Asunto(s)
Mycobacterium tuberculosis , Animales , Mycobacterium tuberculosis/genética , Mycobacterium tuberculosis/patogenicidad , Ratones , Sitios de Carácter Cuantitativo , Tuberculosis Pulmonar/genética , Tuberculosis Pulmonar/microbiología , Tuberculosis Pulmonar/patología , Modelos Animales de Enfermedad , Animales no Consanguíneos , Humanos , Mapeo Cromosómico , Biología de Sistemas
2.
Artículo en Inglés | MEDLINE | ID: mdl-38756441

RESUMEN

Current deep learning methods in histopathology are limited by the small amount of available data and time consumption in labeling the data. Colorectal cancer (CRC) tumor budding quantification performed using H&E-stained slides is crucial for cancer staging and prognosis but is subject to labor-intensive annotation and human bias. Thus, acquiring a large-scale, fully annotated dataset for training a tumor budding (TB) segmentation/detection system is difficult. Here, we present a DatasetGAN-based approach that can generate essentially an unlimited number of images with TB masks from a moderate number of unlabeled images and a few annotated images. The images generated by our model closely resemble the real colon tissue on H&E-stained slides. We test the performance of this model by training a downstream segmentation model, UNet++, on the generated images and masks. Our results show that the trained UNet++ model can achieve reasonable TB segmentation performance, especially at the instance level. This study demonstrates the potential of developing an annotation-efficient segmentation model for automatic TB detection and quantification.

3.
Artículo en Inglés | MEDLINE | ID: mdl-38752165

RESUMEN

Tumor budding refers to a cluster of one to four tumor cells located at the tumor-invasive front. While tumor budding is a prognostic factor for colorectal cancer, counting and grading tumor budding are time consuming and not highly reproducible. There could be high inter- and intra-reader disagreement on H&E evaluation. This leads to the noisy training (imperfect ground truth) of deep learning algorithms, resulting in high variability and losing their ability to generalize on unseen datasets. Pan-cytokeratin staining is one of the potential solutions to enhance the agreement, but it is not routinely used to identify tumor buds and can lead to false positives. Therefore, we aim to develop a weakly-supervised deep learning method for tumor bud detection from routine H&E-stained images that does not require strict tissue-level annotations. We also propose Bayesian Multiple Instance Learning (BMIL) that combines multiple annotated regions during the training process to further enhance the generalizability and stability in tumor bud detection. Our dataset consists of 29 colorectal cancer H&E-stained images that contain 115 tumor buds per slide on average. In six-fold cross-validation, our method demonstrated an average precision and recall of 0.94, and 0.86 respectively. These results provide preliminary evidence of the feasibility of our approach in improving the generalizability in tumor budding detection using H&E images while avoiding the need for non-routine immunohistochemical staining methods.

4.
Artículo en Inglés | MEDLINE | ID: mdl-38765185

RESUMEN

Colorectal cancer (CRC) is the third most common cancer in the United States. Tumor Budding (TB) detection and quantification are crucial yet labor-intensive steps in determining the CRC stage through the analysis of histopathology images. To help with this process, we adapt the Segment Anything Model (SAM) on the CRC histopathology images to segment TBs using SAM-Adapter. In this approach, we automatically take task-specific prompts from CRC images and train the SAM model in a parameter-efficient way. We compare the predictions of our model with the predictions from a trained-from-scratch model using the annotations from a pathologist. As a result, our model achieves an intersection over union (IoU) of 0.65 and an instance-level Dice score of 0.75, which are promising in matching the pathologist's TB annotation. We believe our study offers a novel solution to identify TBs on H&E-stained histopathology images. Our study also demonstrates the value of adapting the foundation model for pathology image segmentation tasks.

5.
J Surg Oncol ; 130(1): 93-101, 2024 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-38712939

RESUMEN

BACKGROUND AND OBJECTIVES: Deep learning models (DLMs) are applied across domains of health sciences to generate meaningful predictions. DLMs make use of neural networks to generate predictions from discrete data inputs. This study employs DLM on prechemotherapy cross-sectional imaging to predict patients' response to neoadjuvant chemotherapy. METHODS: Adult patients with colorectal liver metastasis who underwent surgery after neoadjuvant chemotherapy were included. A DLM was trained on computed tomography images using attention-based multiple-instance learning. A logistic regression model incorporating clinical parameters of the Fong clinical risk score was used for comparison. Both model performances were benchmarked against the Response Evaluation Criteria in Solid Tumors criteria. A receiver operating curve was created and resulting area under the curve (AUC) was determined. RESULTS: Ninety-five patients were included, with 33,619 images available for study inclusion. Ninety-five percent of patients underwent 5-fluorouracil-based chemotherapy with oxaliplatin and/or irinotecan. Sixty percent of the patients were categorized as chemotherapy responders (30% reduction in tumor diameter). The DLM had an AUC of 0.77. The AUC for the clinical model was 0.41. CONCLUSIONS: Image-based DLM for prediction of response to neoadjuvant chemotherapy in patients with colorectal cancer liver metastases was superior to a clinical-based model. These results demonstrate potential to identify nonresponders to chemotherapy and guide select patients toward earlier curative resection.


Asunto(s)
Protocolos de Quimioterapia Combinada Antineoplásica , Neoplasias Colorrectales , Aprendizaje Profundo , Neoplasias Hepáticas , Terapia Neoadyuvante , Humanos , Neoplasias Colorrectales/patología , Neoplasias Colorrectales/tratamiento farmacológico , Neoplasias Colorrectales/diagnóstico por imagen , Neoplasias Hepáticas/secundario , Neoplasias Hepáticas/diagnóstico por imagen , Neoplasias Hepáticas/tratamiento farmacológico , Neoplasias Hepáticas/cirugía , Masculino , Femenino , Persona de Mediana Edad , Anciano , Protocolos de Quimioterapia Combinada Antineoplásica/uso terapéutico , Tomografía Computarizada por Rayos X , Fluorouracilo/administración & dosificación , Fluorouracilo/uso terapéutico , Quimioterapia Adyuvante , Oxaliplatino/administración & dosificación , Oxaliplatino/uso terapéutico , Adulto , Estudios de Seguimiento , Estudios Retrospectivos
6.
Front Neurosci ; 18: 1331677, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38384484

RESUMEN

Background: Frontotemporal dementia (FTD) represents a collection of neurobehavioral and neurocognitive syndromes that are associated with a significant degree of clinical, pathological, and genetic heterogeneity. Such heterogeneity hinders the identification of effective biomarkers, preventing effective targeted recruitment of participants in clinical trials for developing potential interventions and treatments. In the present study, we aim to automatically differentiate patients with three clinical phenotypes of FTD, behavioral-variant FTD (bvFTD), semantic variant PPA (svPPA), and nonfluent variant PPA (nfvPPA), based on their structural MRI by training a deep neural network (DNN). Methods: Data from 277 FTD patients (173 bvFTD, 63 nfvPPA, and 41 svPPA) recruited from two multi-site neuroimaging datasets: the Frontotemporal Lobar Degeneration Neuroimaging Initiative and the ARTFL-LEFFTDS Longitudinal Frontotemporal Lobar Degeneration databases. Raw T1-weighted MRI data were preprocessed and parcellated into patch-based ROIs, with cortical thickness and volume features extracted and harmonized to control the confounding effects of sex, age, total intracranial volume, cohort, and scanner difference. A multi-type parallel feature embedding framework was trained to classify three FTD subtypes with a weighted cross-entropy loss function used to account for unbalanced sample sizes. Feature visualization was achieved through post-hoc analysis using an integrated gradient approach. Results: The proposed differential diagnosis framework achieved a mean balanced accuracy of 0.80 for bvFTD, 0.82 for nfvPPA, 0.89 for svPPA, and an overall balanced accuracy of 0.84. Feature importance maps showed more localized differential patterns among different FTD subtypes compared to groupwise statistical mapping. Conclusion: In this study, we demonstrated the efficiency and effectiveness of using explainable deep-learning-based parallel feature embedding and visualization framework on MRI-derived multi-type structural patterns to differentiate three clinically defined subphenotypes of FTD: bvFTD, nfvPPA, and svPPA, which could help with the identification of at-risk populations for early and precise diagnosis for intervention planning.

7.
Diagn Pathol ; 19(1): 17, 2024 Jan 19.
Artículo en Inglés | MEDLINE | ID: mdl-38243330

RESUMEN

BACKGROUND: c-MYC and BCL2 positivity are important prognostic factors for diffuse large B-cell lymphoma. However, manual quantification is subject to significant intra- and inter-observer variability. We developed an automated method for quantification in whole-slide images of tissue sections where manual quantification requires evaluating large areas of tissue with possibly heterogeneous staining. We train this method using annotations of tumor positivity in smaller tissue microarray cores where expression and staining are more homogeneous and then translate this model to whole-slide images. METHODS: Our method applies a technique called attention-based multiple instance learning to regress the proportion of c-MYC-positive and BCL2-positive tumor cells from pathologist-scored tissue microarray cores. This technique does not require annotation of individual cell nuclei and is trained instead on core-level annotations of percent tumor positivity. We translate this model to scoring of whole-slide images by tessellating the slide into smaller core-sized tissue regions and calculating an aggregate score. Our method was trained on a public tissue microarray dataset from Stanford and applied to whole-slide images from a geographically diverse multi-center cohort produced by the Lymphoma Epidemiology of Outcomes study. RESULTS: In tissue microarrays, the automated method had Pearson correlations of 0.843 and 0.919 with pathologist scores for c-MYC and BCL2, respectively. When utilizing standard clinical thresholds, the sensitivity/specificity of our method was 0.743 / 0.963 for c-MYC and 0.938 / 0.951 for BCL2. For double-expressors, sensitivity and specificity were 0.720 and 0.974. When translated to the external WSI dataset scored by two pathologists, Pearson correlation was 0.753 & 0.883 for c-MYC and 0.749 & 0.765 for BCL2, and sensitivity/specificity was 0.857/0.991 & 0.706/0.930 for c-MYC, 0.856/0.719 & 0.855/0.690 for BCL2, and 0.890/1.00 & 0.598/0.952 for double-expressors. Survival analysis demonstrates that for progression-free survival, model-predicted TMA scores significantly stratify double-expressors and non double-expressors (p = 0.0345), whereas pathologist scores do not (p = 0.128). CONCLUSIONS: We conclude that proportion of positive stains can be regressed using attention-based multiple instance learning, that these models generalize well to whole slide images, and that our models can provide non-inferior stratification of progression-free survival outcomes.


Asunto(s)
Aprendizaje Profundo , Linfoma de Células B Grandes Difuso , Humanos , Pronóstico , Proteínas Proto-Oncogénicas c-myc/metabolismo , Proteínas Proto-Oncogénicas c-bcl-2/metabolismo , Protocolos de Quimioterapia Combinada Antineoplásica
8.
Semin Cancer Biol ; 97: 70-85, 2023 12.
Artículo en Inglés | MEDLINE | ID: mdl-37832751

RESUMEN

Artificial Intelligence (AI)-enhanced histopathology presents unprecedented opportunities to benefit oncology through interpretable methods that require only one overall label per hematoxylin and eosin (H&E) slide with no tissue-level annotations. We present a structured review of these methods organized by their degree of verifiability and by commonly recurring application areas in oncological characterization. First, we discuss morphological markers (tumor presence/absence, metastases, subtypes, grades) in which AI-identified regions of interest (ROIs) within whole slide images (WSIs) verifiably overlap with pathologist-identified ROIs. Second, we discuss molecular markers (gene expression, molecular subtyping) that are not verified via H&E but rather based on overlap with positive regions on adjacent tissue. Third, we discuss genetic markers (mutations, mutational burden, microsatellite instability, chromosomal instability) that current technologies cannot verify if AI methods spatially resolve specific genetic alterations. Fourth, we discuss the direct prediction of survival to which AI-identified histopathological features quantitatively correlate but are nonetheless not mechanistically verifiable. Finally, we discuss in detail several opportunities and challenges for these one-label-per-slide methods within oncology. Opportunities include reducing the cost of research and clinical care, reducing the workload of clinicians, personalized medicine, and unlocking the full potential of histopathology through new imaging-based biomarkers. Current challenges include explainability and interpretability, validation via adjacent tissue sections, reproducibility, data availability, computational needs, data requirements, domain adaptability, external validation, dataset imbalances, and finally commercialization and clinical potential. Ultimately, the relative ease and minimum upfront cost with which relevant data can be collected in addition to the plethora of available AI methods for outcome-driven analysis will surmount these current limitations and achieve the innumerable opportunities associated with AI-driven histopathology for the benefit of oncology.


Asunto(s)
Inteligencia Artificial , Inestabilidad Cromosómica , Humanos , Reproducibilidad de los Resultados , Eosina Amarillenta-(YS) , Oncología Médica
9.
Artículo en Inglés | MEDLINE | ID: mdl-37538448

RESUMEN

Obstructive sleep apnea (OSA) is a prevalent disease affecting 10 to 15% of Americans and nearly one billion people worldwide. It leads to multiple symptoms including daytime sleepiness; snoring, choking, or gasping during sleep; fatigue; headaches; non-restorative sleep; and insomnia due to frequent arousals. Although polysomnography (PSG) is the gold standard for OSA diagnosis, it is expensive, not universally available, and time-consuming, so many patients go undiagnosed due to lack of access to the test. Given the incomplete access and high cost of PSG, many studies are seeking alternative diagnosis approaches based on different data modalities. Here, we propose a machine learning model to predict OSA severity from 2D frontal view craniofacial images. In a cross-validation study of 280 patients, our method achieves an average AUC of 0.780. In comparison, the craniofacial analysis model proposed by a recent study only achieves 0.638 AUC on our dataset. The proposed model also outperforms the widely used STOP-BANG OSA screening questionnaire, which achieves an AUC of 0.52 on our dataset. Our findings indicate that deep learning has the potential to significantly reduce the cost of OSA diagnosis.

10.
Photoacoustics ; 32: 100531, 2023 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-37485041

RESUMEN

Clinical tools for measuring tumor vascular hemodynamics, such as dynamic contrast-enhanced MRI, are clinically important to assess tumor properties. Here we explored the use of multispectral optoacoustic tomography (MSOT), which has a high spatial and temporal resolution, to measure the intratumoral pharmacokinetics of a near-infrared-dye-labeled 2-Deoxyglucose, 2-DG-800, in orthotropic 2-LMP breast tumors in mice. As uptake of 2-DG-800 is dependent on both vascular properties, and glucose transporter activity - a widely-used surrogate for metabolism, we evaluate hemodynamics of 2-DG-MP by fitting the dynamic MSOT signal of 2-DG-800 into two-compartment models including the extended Tofts model (ETM) and reference region model (RRM). We showed that dynamic 2-DG-enhanced MSOT (DGE-MSOT) is powerful in acquiring hemodynamic rate constants, including Ktrans and Kep, via systemically injecting a low dose of 2-DG-800 (0.5 µmol/kg b.w.). In our study, both ETM and RRM are efficient in deriving hemodynamic parameters in the tumor. Area-under-curve (AUC) values (which correlate to metabolism), and Ktrans and Kep values, can effectively distinguish tumor from muscle. Hemodynamic parameters also demonstrated correlations to hemoglobin, oxyhemoglobin, and blood oxygen level (SO2) measurements by spectral unmixing of the MSOT data. Together, our study for the first time demonstrated the capability of DGE-MSOT in assessing vascular hemodynamics of tumors.

11.
Cancers (Basel) ; 15(13)2023 Jun 30.
Artículo en Inglés | MEDLINE | ID: mdl-37444538

RESUMEN

The early diagnosis of lymph node metastasis in breast cancer is essential for enhancing treatment outcomes and overall prognosis. Unfortunately, pathologists often fail to identify small or subtle metastatic deposits, leading them to rely on cytokeratin stains for improved detection, although this approach is not without its flaws. To address the need for early detection, multiple-instance learning (MIL) has emerged as the preferred deep learning method for automatic tumor detection on whole slide images (WSIs). However, existing methods often fail to identify some small lesions due to insufficient attention to small regions. Attention-based multiple-instance learning (ABMIL)-based methods can be particularly problematic because they may focus too much on normal regions, leaving insufficient attention for small-tumor lesions. In this paper, we propose a new ABMIL-based model called normal representative keyset ABMIL (NRK-ABMIL), which addresseses this issue by adjusting the attention mechanism to give more attention to lesions. To accomplish this, the NRK-ABMIL creates an optimal keyset of normal patch embeddings called the normal representative keyset (NRK). The NRK roughly represents the underlying distribution of all normal patch embeddings and is used to modify the attention mechanism of the ABMIL. We evaluated NRK-ABMIL on the publicly available Camelyon16 and Camelyon17 datasets and found that it outperformed existing state-of-the-art methods in accurately identifying small tumor lesions that may spread over a few patches. Additionally, the NRK-ABMIL also performed exceptionally well in identifying medium/large tumor lesions.

12.
Clin Breast Cancer ; 23(8): 775-783, 2023 12.
Artículo en Inglés | MEDLINE | ID: mdl-37179225

RESUMEN

Metaplastic breast cancers (MBC) encompass a group of highly heterogeneous tumors which share the ability to differentiate into squamous, mesenchymal or neuroectodermal components. While often termed rare breast tumors, given the relatively high prevalence of breast cancer, they are seen with some frequency. Depending upon the definition applied, MBC represents 0.2% to 1% of breast cancers diagnosed in the United States. Less is known about the epidemiology of MBC globally, though a growing number of reports are providing information on this. These tumors are often more advanced at presentation relative to breast cancer broadly. While more indolent subtypes exist, the majority of MBC subtypes are associated with inferior survival. MBC is most commonly of triple-negative phenotype. In less common hormone receptor positive MBCs, hormone receptor status appears not to be prognostic. In contrast, relatively rare HER2-positive MBCs are associated with superior outcomes. Multiple potentially targetable molecular features are overrepresented in MBC including DNA repair deficiency signatures and PIK3/AKT/mTOR and WNT pathways alterations. Data on the prevalence of targets for novel antibody-drug conjugates is also emerging. While chemotherapy appears to be less active in MBC than in other breast cancer subtypes, efficacy is seen in some MBCs. Disease-specific trials, as well as reports of exceptional responses, may provide clues for novel approaches to this often hard-to-treat breast cancer. Strategies which harness newer research tools, such as large data and artificial intelligence hold the promise of overcoming historic barriers to the study of uncommon tumors and could markedly advance disease-specific understanding in MBC.


Asunto(s)
Neoplasias de la Mama , Humanos , Femenino , Neoplasias de la Mama/epidemiología , Neoplasias de la Mama/terapia , Neoplasias de la Mama/genética , Inteligencia Artificial , Biomarcadores de Tumor/metabolismo , Pronóstico , Vía de Señalización Wnt
13.
Nanoscale ; 15(21): 9390-9402, 2023 Jun 01.
Artículo en Inglés | MEDLINE | ID: mdl-37184508

RESUMEN

DNA-modified nanoparticles enable DNA sensing and therapeutics in nanomedicine and are also crucial for nanoparticle self-assembly with DNA-based materials. However, methods to conjugate DNA to nanoparticle surfaces are limited, inefficient, and lack control. Inspired by DNA tile nanotechnology, we demonstrate a new approach to nanoparticle modification based on electrostatic attraction between negatively charged DNA tiles and positively charged nanoparticles. This approach does not disrupt nanoparticle surfaces and leverages the programmability of DNA nanotechnology to control DNA presentation. We demonstrated this approach using a vareity of nanoparticles, including polymeric micelles, polystyrene beads, gold nanoparticles, and superparamagnetic iron oxide nanoparticles with sizes ranging from 5-20 nm in diameter. DNA cage formation was confirmed through transmission electron microscopy (TEM), neutralization of zeta potential, and a series of fluorescence experiments. DNA cages present "handle" sequences that can be used for reversible target attachment or self-assembly. Handle functionality was verified in solution, at the solid-liquid interface, and inside fixed cells, corresponding to applications in biosensing, DNA microarrays, and erasable immunocytochemistry. These experiments demonstrate the versatility of the electrostatic DNA caging approach and provide a new pathway to nanoparticle modification with DNA that will empower further applications of these materials in medicine and materials science.


Asunto(s)
Nanopartículas del Metal , Nanopartículas , Electricidad Estática , Oro , ADN , Nanotecnología
14.
PLoS One ; 18(4): e0283562, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37014891

RESUMEN

Breast cancer is the most common malignancy in women, with over 40,000 deaths annually in the United States alone. Clinicians often rely on the breast cancer recurrence score, Oncotype DX (ODX), for risk stratification of breast cancer patients, by using ODX as a guide for personalized therapy. However, ODX and similar gene assays are expensive, time-consuming, and tissue destructive. Therefore, developing an AI-based ODX prediction model that identifies patients who will benefit from chemotherapy in the same way that ODX does would give a low-cost alternative to the genomic test. To overcome this problem, we developed a deep learning framework, Breast Cancer Recurrence Network (BCR-Net), which automatically predicts ODX recurrence risk from histopathology slides. Our proposed framework has two steps. First, it intelligently samples discriminative features from whole-slide histopathology images of breast cancer patients. Then, it automatically weights all features through a multiple instance learning model to predict the recurrence score at the slide level. On a dataset of H&E and Ki67 breast cancer resection whole slides images (WSIs) from 99 anonymized patients, the proposed framework achieved an overall AUC of 0.775 (68.9% and 71.1% accuracies for low and high risk) on H&E WSIs and overall AUC of 0.811 (80.8% and 79.2% accuracies for low and high risk) on Ki67 WSIs of breast cancer patients. Our findings provide strong evidence for automatically risk-stratify patients with a high degree of confidence. Our experiments reveal that the BCR-Net outperforms the state-of-the-art WSI classification models. Moreover, BCR-Net is highly efficient with low computational needs, making it practical to deploy in limited computational settings.


Asunto(s)
Neoplasias de la Mama , Aprendizaje Profundo , Femenino , Humanos , Neoplasias de la Mama/patología , Antígeno Ki-67 , Mama/patología , Riesgo
15.
J Am Coll Surg ; 236(4): 884-893, 2023 04 01.
Artículo en Inglés | MEDLINE | ID: mdl-36727981

RESUMEN

BACKGROUND: Surgical intervention remains the cornerstone of a multidisciplinary approach in the treatment of colorectal liver metastases (CLM). Nevertheless, patient outcomes vary greatly. While predictive tools can assist decision-making and patient counseling, decades of efforts have yet to result in generating a universally adopted tool in clinical practice. STUDY DESIGN: An international collaborative database of CLM patients who underwent surgical therapy between 2000 and 2018 was used to select 1,004 operations for this study. Two different machine learning methods were applied to construct 2 predictive models for recurrence and death, using 128 clinicopathologic variables: gradient-boosted trees (GBTs) and logistic regression with bootstrapping (LRB) in a leave-one-out cross-validation. RESULTS: Median survival after resection was 47.2 months, and disease-free survival was 19.0 months, with a median follow-up of 32.0 months in the cohort. Both models had good predictive power, with GBT demonstrating a superior performance in predicting overall survival (area under the receiver operating curve [AUC] 0.773, 95% CI 0.743 to 0.801 vs LRB: AUC 0.648, 95% CI 0.614 to 0.682) and recurrence (AUC 0.635, 95% CI 0.599 to 0.669 vs LRB: AUC 0.570, 95% CI 0.535 to 0.601). Similarly, better performances were observed predicting 3- and 5-year survival, as well as 3- and 5-year recurrence, with GBT methods generating higher AUCs. CONCLUSIONS: Machine learning provides powerful tools to create predictive models of survival and recurrence after surgery for CLM. The effectiveness of both machine learning models varies, but on most occasions, GBT outperforms LRB. Prospective validation of these models lays the groundwork to adopt them in clinical practice.


Asunto(s)
Neoplasias Colorrectales , Aprendizaje Automático , Humanos , Modelos Logísticos
16.
Otolaryngol Head Neck Surg ; 168(4): 635-642, 2023 04.
Artículo en Inglés | MEDLINE | ID: mdl-35290142

RESUMEN

OBJECTIVE: Otitis media (OM) is a model disease for developing, validating, and implementing artificial intelligence (AI) techniques. We aim to review the state of the art applications of AI used to diagnose OM in pediatric and adult populations. DATA SOURCES: Several comprehensive databases were searched to identify all articles that applied AI technologies to diagnose OM. REVIEW METHODS: Relevant articles from January 2010 through May 2021 were identified by title and abstract. Articles were excluded if they did not discuss AI in conjunction with diagnosing OM. References of included studies and relevant review articles were cross-referenced to identify any additional studies. CONCLUSION: Title and abstract screening resulted in full-text retrieval of 40 articles that met initial screening parameters. Of this total, secondary review articles (n = 7) and commentary-based articles (n = 2) were removed, as were articles that did not specifically discuss AI and OM diagnosis (n = 5), leaving 25 articles for review. Applications of AI technologies specific to diagnosing OM included machine learning and natural language processing (n = 23) and prototype approaches (n = 2). IMPLICATIONS FOR PRACTICE: This review emphasizes the utility of AI techniques to automate and aid in diagnosing OM. Although these techniques are still in the development and testing stages, AI has the potential to improve the practice of otolaryngologists and primary care clinicians by increasing the efficiency and accuracy of diagnoses.


Asunto(s)
Inteligencia Artificial , Otitis Media , Adulto , Humanos , Niño , Otitis Media/diagnóstico , Otitis Media/complicaciones , Aprendizaje Automático , Otorrinolaringólogos
17.
Cancers (Basel) ; 14(23)2022 Nov 24.
Artículo en Inglés | MEDLINE | ID: mdl-36497258

RESUMEN

Recent methods in computational pathology have trended towards semi- and weakly-supervised methods requiring only slide-level labels. Yet, even slide-level labels may be absent or irrelevant to the application of interest, such as in clinical trials. Hence, we present a fully unsupervised method to learn meaningful, compact representations of WSIs. Our method initially trains a tile-wise encoder using SimCLR, from which subsets of tile-wise embeddings are extracted and fused via an attention-based multiple-instance learning framework to yield slide-level representations. The resulting set of intra-slide-level and inter-slide-level embeddings are attracted and repelled via contrastive loss, respectively. This resulted in slide-level representations with self-supervision. We applied our method to two tasks- (1) non-small cell lung cancer subtyping (NSCLC) as a classification prototype and (2) breast cancer proliferation scoring (TUPAC16) as a regression prototype-and achieved an AUC of 0.8641 ± 0.0115 and correlation (R2) of 0.5740 ± 0.0970, respectively. Ablation experiments demonstrate that the resulting unsupervised slide-level feature space can be fine-tuned with small datasets for both tasks. Overall, our method approaches computational pathology in a novel manner, where meaningful features can be learned from whole-slide images without the need for annotations of slide-level labels. The proposed method stands to benefit computational pathology, as it theoretically enables researchers to benefit from completely unlabeled whole-slide images.

18.
Patterns (N Y) ; 3(11): 100613, 2022 Nov 11.
Artículo en Inglés | MEDLINE | ID: mdl-36419451

RESUMEN

Treatment decisions for brain metastatic disease rely on knowledge of the primary organ site and are currently made with biopsy and histology. Here, we develop a deep-learning approach for accurate non-invasive digital histology with whole-brain magnetic resonance imaging (MRI) data. Contrast-enhanced T1-weighted and fast spoiled gradient echo brain MRI exams (n = 1,582) were preprocessed and input to the proposed deep-learning workflow for tumor segmentation, modality transfer, and primary site classification into one of five classes. Tenfold cross-validation generated an overall area under the receiver operating characteristic curve (AUC) of 0.878 (95% confidence interval [CI]: 0.873,0.883). These data establish that whole-brain imaging features are discriminative enough to allow accurate diagnosis of the primary organ site of malignancy. Our end-to-end deep radiomic approach has great potential for classifying metastatic tumor types from whole-brain MRI images. Further refinement may offer an invaluable clinical tool to expedite primary cancer site identification for precision treatment and improved outcomes.

19.
Med Image Anal ; 79: 102462, 2022 07.
Artículo en Inglés | MEDLINE | ID: mdl-35512532

RESUMEN

Deep learning consistently demonstrates high performance in classifying and segmenting medical images like CT, PET, and MRI. However, compared to these kinds of images, whole slide images (WSIs) of stained tissue sections are huge and thus much less efficient to process, especially for deep learning algorithms. To overcome these challenges, we present attention2majority, a weak multiple instance learning model to automatically and efficiently process WSIs for classification. Our method initially assigns exhaustively sampled label-free patches with the label of the respective WSIs and trains a convolutional neural network to perform patch-wise classification. Then, an intelligent sampling method is performed in which patches with high confidence are collected to form weak representations of WSIs. Lastly, we apply a multi-head attention-based multiple instance learning model to do slide-level classification based on high-confidence patches (intelligently sampled patches). Attention2majority was trained and tested on classifying the quality of 127 WSIs (of regenerated kidney sections) into three categories. On average, attention2majority resulted in 97.4%±2.4 AUC for the four-fold cross-validation. We demonstrate that the intelligent sampling module within attention2majority is superior to the current state-of-the-art random sampling method. Furthermore, we show that the replacement of random sampling with intelligent sampling in attention2majority results in its performance boost (from 94.9%±3.1 to 97.4%±2.4 average AUC for the four-fold cross-validation). We also tested a variation of attention2majority on the famous Camelyon16 dataset, which resulted in 89.1%±0.8 AUC1. When compared to random sampling, the attention2majority demonstrated excellent slide-level interpretability. It also provided an efficient framework to arrive at a multi-class slide-level prediction.


Asunto(s)
Algoritmos , Redes Neurales de la Computación , Humanos , Riñón/diagnóstico por imagen
20.
J Med Imaging (Bellingham) ; 9(Suppl 1): 012203, 2022 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-35233437

RESUMEN

The term "digital pathology" (DP) broadly refers to the process of digitizing glass whole-slide images (WSIs) using a digital whole-slide scanner as these WSIs are also used to render a diagnosis. Artificial intelligence (AI), on the other hand, is broadly defined as the application of machine-based algorithms to make a prediction, just like an intelligent human who has access to the necessary knowledge to make said prediction. Deep learning is a specific type of AI that has become very popular for the analysis and interpretation of DP images over the last decade because of the recent increase in computational power and advancements in whole-slide scanning. AI-enabled DP analysis of routine hematoxylin and eosin-stained tissues has shown increasing utility in characterizing complex tissue architecture to render disease diagnoses, prognoses, and predicting therapeutic response. A PubMed search for "digital pathology" yielded 310 hits in articles published in 2020; for those published in 2010, the same search yielded only 12 hits. The Digital Pathology Conference was initiated in 2011 by the authors (Drs. Madabhushi and Gurcan), two early pioneers in computational pathology, in anticipation of the expected explosion of research and clinical interest in this space.

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