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1.
J Immunother Cancer ; 12(5)2024 05 15.
Article in English | MEDLINE | ID: mdl-38749538

ABSTRACT

BACKGROUND: Only a subset of patients with gastric cancer experience long-term benefits from immune checkpoint inhibitors (ICIs). Currently, there is a deficiency in precise predictive biomarkers for ICI efficacy. The aim of this study was to develop and validate a pathomics-driven ensemble model for predicting the response to ICIs in gastric cancer, using H&E-stained whole slide images (WSI). METHODS: This multicenter study retrospectively collected and analyzed H&E-stained WSIs and clinical data from 584 patients with gastric cancer. An ensemble model, integrating four classifiers: least absolute shrinkage and selection operator, k-nearest neighbors, decision trees, and random forests, was developed and validated using pathomics features, with the objective of predicting the therapeutic efficacy of immune checkpoint inhibition. Model performance was evaluated using metrics including the area under the curve (AUC), sensitivity, and specificity. Additionally, SHAP (SHapley Additive exPlanations) analysis was used to explain the model's predicted values as the sum of the attribution values for each input feature. Pathogenomics analysis was employed to explain the molecular mechanisms underlying the model's predictions. RESULTS: Our pathomics-driven ensemble model effectively stratified the response to ICIs in training cohort (AUC 0.985 (95% CI 0.971 to 0.999)), which was further validated in internal validation cohort (AUC 0.921 (95% CI 0.839 to 0.999)), as well as in external validation cohort 1 (AUC 0.914 (95% CI 0.837 to 0.990)), and external validation cohort 2 (0.927 (95% CI 0.802 to 0.999)). The univariate Cox regression analysis revealed that the prediction signature of pathomics-driven ensemble model was a prognostic factor for progression-free survival in patients with gastric cancer who underwent immunotherapy (p<0.001, HR 0.35 (95% CI 0.24 to 0.50)), and remained an independent predictor after multivariable Cox regression adjusted for clinicopathological variables, (including sex, age, carcinoembryonic antigen, carbohydrate antigen 19-9, therapy regime, line of therapy, differentiation, location and programmed death ligand 1 (PD-L1) expression in all patients (p<0.001, HR 0.34 (95% CI 0.24 to 0.50)). Pathogenomics analysis suggested that the ensemble model is driven by molecular-level immune, cancer, metabolism-related pathways, and was correlated with the immune-related characteristics, including immune score, Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data score, and tumor purity. CONCLUSIONS: Our pathomics-driven ensemble model exhibited high accuracy and robustness in predicting the response to ICIs using WSIs. Therefore, it could serve as a novel and valuable tool to facilitate precision immunotherapy.


Subject(s)
Immunotherapy , Stomach Neoplasms , Humans , Stomach Neoplasms/drug therapy , Stomach Neoplasms/immunology , Stomach Neoplasms/pathology , Stomach Neoplasms/therapy , Male , Female , Immunotherapy/methods , Retrospective Studies , Middle Aged , Immune Checkpoint Inhibitors/therapeutic use , Immune Checkpoint Inhibitors/pharmacology , Aged
2.
J Proteome Res ; 2024 May 07.
Article in English | MEDLINE | ID: mdl-38713528

ABSTRACT

The coevolution of liquid chromatography (LC) with mass spectrometry (MS) has shaped contemporary proteomics. LC hyphenated to MS now enables quantification of more than 10,000 proteins in a single injection, a number that likely represents most proteins in specific human cells or tissues. Separations by ion mobility spectrometry (IMS) have recently emerged to complement LC and further improve the depth of proteomics. Given the theoretical advantages in speed and robustness of IMS in comparison to LC, we envision that ongoing improvements to IMS paired with MS may eventually make LC obsolete, especially when combined with targeted or simplified analyses, such as rapid clinical proteomics analysis of defined biomarker panels. In this perspective, we describe the need for faster analysis that might drive this transition, the current state of direct infusion proteomics, and discuss some technical challenges that must be overcome to fully complete the transition to entirely gas phase proteomics.

3.
bioRxiv ; 2024 Feb 08.
Article in English | MEDLINE | ID: mdl-38370692

ABSTRACT

Non-invasive detection of protein biomarkers in plasma is crucial for clinical purposes. Liquid chromatography mass spectrometry (LC-MS) is the gold standard technique for plasma proteome analysis, but despite recent advances, it remains limited by throughput, cost, and coverage. Here, we introduce a new hybrid method, which integrates direct infusion shotgun proteome analysis (DISPA) with nanoparticle (NP) protein coronas enrichment for high throughput and efficient plasma proteomic profiling. We realized over 280 protein identifications in 1.4 minutes collection time, which enables a potential throughput of approximately 1,000 samples daily. The identified proteins are involved in valuable pathways and 44 of the proteins are FDA approved biomarkers. The robustness and quantitative accuracy of this method were evaluated across multiple NPs and concentrations with a mean coefficient of variation at 17%. Moreover, different protein corona profiles were observed among various nanoparticles based on their distinct surface modifications, and all NP protein profiles exhibited deeper coverage and better quantification than neat plasma. Our streamlined workflow merges coverage and throughput with precise quantification, leveraging both DISPA and NP protein corona enrichments. This underscores the significant potential of DISPA when paired with NP sample preparation techniques for plasma proteome studies.

4.
Comput Med Imaging Graph ; 112: 102336, 2024 03.
Article in English | MEDLINE | ID: mdl-38244280

ABSTRACT

Rigid pre-registration involving local-global matching or other large deformation scenarios is crucial. Current popular methods rely on unsupervised learning based on grayscale similarity, but under circumstances where different poses lead to varying tissue structures, or where image quality is poor, these methods tend to exhibit instability and inaccuracies. In this study, we propose a novel method for medical image registration based on arbitrary voxel point of interest matching, called query point quizzer (QUIZ). QUIZ focuses on the correspondence between local-global matching points, specifically employing CNN for feature extraction and utilizing the Transformer architecture for global point matching queries, followed by applying average displacement for local image rigid transformation.We have validated this approach on a large deformation dataset of cervical cancer patients, with results indicating substantially smaller deviations compared to state-of-the-art methods. Remarkably, even for cross-modality subjects, it achieves results surpassing the current state-of-the-art.


Subject(s)
Algorithms , Uterine Cervical Neoplasms , Female , Humans , Uterine Cervical Neoplasms/diagnostic imaging , Image Processing, Computer-Assisted/methods
5.
J Clin Invest ; 134(6)2024 Jan 25.
Article in English | MEDLINE | ID: mdl-38271117

ABSTRACT

BACKGROUNDThe tumor immune microenvironment can provide prognostic and therapeutic information. We aimed to develop noninvasive imaging biomarkers from computed tomography (CT) for comprehensive evaluation of immune context and investigate their associations with prognosis and immunotherapy response in gastric cancer (GC).METHODSThis study involved 2,600 patients with GC from 9 independent cohorts. We developed and validated 2 CT imaging biomarkers (lymphoid radiomics score [LRS] and myeloid radiomics score [MRS]) for evaluating the IHC-derived lymphoid and myeloid immune context respectively, and integrated them into a combined imaging biomarker [LRS/MRS: low(-) or high(+)] with 4 radiomics immune subtypes: 1 (-/-), 2 (+/-), 3 (-/+), and 4 (+/+). We further evaluated the imaging biomarkers' predictive values on prognosis and immunotherapy response.RESULTSThe developed imaging biomarkers (LRS and MRS) had a high accuracy in predicting lymphoid (AUC range: 0.765-0.773) and myeloid (AUC range: 0.736-0.750) immune context. Further, similar to the IHC-derived immune context, 2 imaging biomarkers (HR range: 0.240-0.761 for LRS; 1.301-4.012 for MRS) and the combined biomarker were independent predictors for disease-free and overall survival in the training and all validation cohorts (all P < 0.05). Additionally, patients with high LRS or low MRS may benefit more from immunotherapy (P < 0.001). Further, a highly heterogeneous outcome on objective response ​rate was observed in 4 imaging subtypes: 1 (-/-) with 27.3%, 2 (+/-) with 53.3%, 3 (-/+) with 10.2%, and 4 (+/+) with 30.0% (P < 0.0001).CONCLUSIONThe noninvasive imaging biomarkers could accurately evaluate the immune context and provide information regarding prognosis and immunotherapy for GC.


Subject(s)
Stomach Neoplasms , Humans , Stomach Neoplasms/diagnostic imaging , Stomach Neoplasms/therapy , Radiomics , Immunotherapy , Tomography, X-Ray Computed , Tumor Microenvironment , Biomarkers , Prognosis
6.
J Natl Cancer Inst ; 116(4): 555-564, 2024 Apr 05.
Article in English | MEDLINE | ID: mdl-37982756

ABSTRACT

BACKGROUND: Intratumor heterogeneity drives disease progression and treatment resistance, which can lead to poor patient outcomes. Here, we present a computational approach for quantification of cancer cell diversity in routine hematoxylin-eosin-stained histopathology images. METHODS: We analyzed publicly available digitized whole-slide hematoxylin-eosin images for 2000 patients. Four tumor types were included: lung, head and neck, colon, and rectal cancers, representing major histology subtypes (adenocarcinomas and squamous cell carcinomas). We performed single-cell analysis on hematoxylin-eosin images and trained a deep convolutional autoencoder to automatically learn feature representations of individual cancer nuclei. We then computed features of intranuclear variability and internuclear diversity to quantify tumor heterogeneity. Finally, we used these features to build a machine-learning model to predict patient prognosis. RESULTS: A total of 68 million cancer cells were segmented and analyzed for nuclear image features. We discovered multiple morphological subtypes of cancer cells (range = 15-20) that co-exist within the same tumor, each with distinct phenotypic characteristics. Moreover, we showed that a higher morphological diversity is associated with chromosome instability and genomic aneuploidy. A machine-learning model based on morphological diversity demonstrated independent prognostic values across tumor types (hazard ratio range = 1.62-3.23, P < .035) in validation cohorts and further improved prognostication when combined with clinical risk factors. CONCLUSIONS: Our study provides a practical approach for quantifying intratumor heterogeneity based on routine histopathology images. The cancer cell diversity score can be used to refine risk stratification and inform personalized treatment strategies.


Subject(s)
Carcinoma, Squamous Cell , Humans , Hematoxylin , Eosine Yellowish-(YS) , Prognosis , Carcinoma, Squamous Cell/genetics , Carcinoma, Squamous Cell/pathology , Disease Progression
7.
IEEE Trans Pattern Anal Mach Intell ; 46(5): 3692-3706, 2024 May.
Article in English | MEDLINE | ID: mdl-38147423

ABSTRACT

Facial editing is to manipulate the facial attributes of a given face image. Nowadays, with the development of generative models, users can easily generate 2D and 3D facial images with high fidelity and 3D-aware consistency. However, existing works are incapable of delivering a continuous and fine-grained editing mode (e.g., editing a slightly smiling face to a big laughing one) with natural interactions with users. In this work, we propose Talk-to-Edit, an interactive facial editing framework that performs fine-grained attribute manipulation through dialog between the user and the system. Our key insight is to model a continual "semantic field" in the GAN latent space. 1) Unlike previous works that regard the editing as traversing straight lines in the latent space, here the fine-grained editing is formulated as finding a curving trajectory that respects fine-grained attribute landscape on the semantic field. 2) The curvature at each step is location-specific and determined by the input image as well as the users' language requests. 3) To engage the users in a meaningful dialog, our system generates language feedback by considering both the user request and the current state of the semantic field. We demonstrate the effectiveness of our proposed framework on both 2D and 3D-aware generative models. We term the semantic field for the 3D-aware models as "tri-plane" flow, as it corresponds to the changes not only in the color space but also in the density space. We also contribute CelebA-Dialog, a visual-language facial editing dataset to facilitate large-scale study. Specifically, each image has manually annotated fine-grained attribute annotations as well as template-based textual descriptions in natural language. Extensive quantitative and qualitative experiments demonstrate the superiority of our framework in terms of 1) the smoothness of fine-grained editing, 2) the identity/attribute preservation, and 3) the visual photorealism and dialog fluency. Notably, the user study validates that our overall system is consistently favored by around 80% of the participants.

8.
Med Image Anal ; 91: 102984, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37837690

ABSTRACT

The accurate delineation of organs-at-risk (OARs) is a crucial step in treatment planning during radiotherapy, as it minimizes the potential adverse effects of radiation on surrounding healthy organs. However, manual contouring of OARs in computed tomography (CT) images is labor-intensive and susceptible to errors, particularly for low-contrast soft tissue. Deep learning-based artificial intelligence algorithms surpass traditional methods but require large datasets. Obtaining annotated medical images is both time-consuming and expensive, hindering the collection of extensive training sets. To enhance the performance of medical image segmentation, augmentation strategies such as rotation and Gaussian smoothing are employed during preprocessing. However, these conventional data augmentation techniques cannot generate more realistic deformations, limiting improvements in accuracy. To address this issue, this study introduces a statistical deformation model-based data augmentation method for volumetric medical image segmentation. By applying diverse and realistic data augmentation to CT images from a limited patient cohort, our method significantly improves the fully automated segmentation of OARs across various body parts. We evaluate our framework on three datasets containing tumor OARs from the head, neck, chest, and abdomen. Test results demonstrate that the proposed method achieves state-of-the-art performance in numerous OARs segmentation challenges. This innovative approach holds considerable potential as a powerful tool for various medical imaging-related sub-fields, effectively addressing the challenge of limited data access.


Subject(s)
Artificial Intelligence , Neoplasms , Humans , Algorithms , Neck , Tomography, X-Ray Computed/methods , Image Processing, Computer-Assisted/methods , Radiotherapy Planning, Computer-Assisted/methods
9.
Med Image Anal ; 91: 102998, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37857066

ABSTRACT

Radiotherapy serves as a pivotal treatment modality for malignant tumors. However, the accuracy of radiotherapy is significantly compromised due to respiratory-induced fluctuations in the size, shape, and position of the tumor. To address this challenge, we introduce a deep learning-anchored, volumetric tumor tracking methodology that employs single-angle X-ray projection images. This process involves aligning the intraoperative two-dimensional (2D) X-ray images with the pre-treatment three-dimensional (3D) planning Computed Tomography (CT) scans, enabling the extraction of the 3D tumor position and segmentation. Prior to therapy, a bespoke patient-specific tumor tracking model is formulated, leveraging a hybrid data augmentation, style correction, and registration network to create a mapping from single-angle 2D X-ray images to the corresponding 3D tumors. During the treatment phase, real-time X-ray images are fed into the trained model, producing the respective 3D tumor positioning. Rigorous validation conducted on actual patient lung data and lung phantoms attests to the high localization precision of our method at lowered radiation doses, thus heralding promising strides towards enhancing the precision of radiotherapy.


Subject(s)
Deep Learning , Neoplasms , Humans , Imaging, Three-Dimensional/methods , X-Rays , Tomography, X-Ray Computed/methods , Neoplasms/diagnostic imaging , Neoplasms/radiotherapy , Cone-Beam Computed Tomography/methods
11.
Sensors (Basel) ; 23(21)2023 Oct 24.
Article in English | MEDLINE | ID: mdl-37960379

ABSTRACT

Batch process monitoring datasets usually contain missing data, which decreases the performance of data-driven modeling for fault identification and optimal control. Many methods have been proposed to impute missing data; however, they do not fulfill the need for data quality, especially in sensor datasets with different types of missing data. We propose a hybrid missing data imputation method for batch process monitoring datasets with multi-type missing data. In this method, the missing data is first classified into five categories based on the continuous missing duration and the number of variables missing simultaneously. Then, different categories of missing data are step-by-step imputed considering their unique characteristics. A combination of three single-dimensional interpolation models is employed to impute transient isolated missing values. An iterative imputation based on a multivariate regression model is designed for imputing long-term missing variables, and a combination model based on single-dimensional interpolation and multivariate regression is proposed for imputing short-term missing variables. The Long Short-Term Memory (LSTM) model is utilized to impute both short-term and long-term missing samples. Finally, a series of experiments for different categories of missing data were conducted based on a real-world batch process monitoring dataset. The results demonstrate that the proposed method achieves higher imputation accuracy than other comparative methods.

12.
ArXiv ; 2023 Nov 13.
Article in English | MEDLINE | ID: mdl-38013887

ABSTRACT

Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods to aid the novice and experienced researcher. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this work to serve as a basic resource for new practitioners in the field of shotgun or bottom-up proteomics.

13.
Nat Commun ; 14(1): 5135, 2023 08 23.
Article in English | MEDLINE | ID: mdl-37612313

ABSTRACT

Substantial progress has been made in using deep learning for cancer detection and diagnosis in medical images. Yet, there is limited success on prediction of treatment response and outcomes, which has important implications for personalized treatment strategies. A significant hurdle for clinical translation of current data-driven deep learning models is lack of interpretability, often attributable to a disconnect from the underlying pathobiology. Here, we present a biology-guided deep learning approach that enables simultaneous prediction of the tumor immune and stromal microenvironment status as well as treatment outcomes from medical images. We validate the model for predicting prognosis of gastric cancer and the benefit from adjuvant chemotherapy in a multi-center international study. Further, the model predicts response to immune checkpoint inhibitors and complements clinically approved biomarkers. Importantly, our model identifies a subset of mismatch repair-deficient tumors that are non-responsive to immunotherapy and may inform the selection of patients for combination treatments.


Subject(s)
Brain Neoplasms , Deep Learning , Humans , Immunotherapy , Chemotherapy, Adjuvant , Biology , Tumor Microenvironment
14.
Cell Rep Med ; 4(8): 101146, 2023 08 15.
Article in English | MEDLINE | ID: mdl-37557177

ABSTRACT

The tumor microenvironment (TME) plays a critical role in disease progression and is a key determinant of therapeutic response in cancer patients. Here, we propose a noninvasive approach to predict the TME status from radiological images by combining radiomics and deep learning analyses. Using multi-institution cohorts of 2,686 patients with gastric cancer, we show that the radiological model accurately predicted the TME status and is an independent prognostic factor beyond clinicopathologic variables. The model further predicts the benefit from adjuvant chemotherapy for patients with localized disease. In patients treated with checkpoint blockade immunotherapy, the model predicts clinical response and further improves predictive accuracy when combined with existing biomarkers. Our approach enables noninvasive assessment of the TME, which opens the door for longitudinal monitoring and tracking response to cancer therapy. Given the routine use of radiologic imaging in oncology, our approach can be extended to many other solid tumor types.


Subject(s)
Deep Learning , Stomach Neoplasms , Humans , Stomach Neoplasms/diagnostic imaging , Stomach Neoplasms/therapy , Tumor Microenvironment , Immunotherapy , Chemotherapy, Adjuvant
15.
Radiother Oncol ; 186: 109793, 2023 09.
Article in English | MEDLINE | ID: mdl-37414254

ABSTRACT

BACKGROUND AND PURPOSE: Immunotherapy is a standard treatment for many tumor types. However, only a small proportion of patients derive clinical benefit and reliable predictive biomarkers of immunotherapy response are lacking. Although deep learning has made substantial progress in improving cancer detection and diagnosis, there is limited success on the prediction of treatment response. Here, we aim to predict immunotherapy response of gastric cancer patients using routinely available clinical and image data. MATERIALS AND METHODS: We present a multi-modal deep learning radiomics approach to predict immunotherapy response using both clinical data and computed tomography images. The model was trained using 168 advanced gastric cancer patients treated with immunotherapy. To overcome limitations of small training data, we leverage an additional dataset of 2,029 patients who did not receive immunotherapy in a semi-supervised framework to learn intrinsic imaging phenotypes of the disease. We evaluated model performance in two independent cohorts of 81 patients treated with immunotherapy. RESULTS: The deep learning model achieved area under receiver operating characteristics curve (AUC) of 0.791 (95% CI 0.633-0.950) and 0.812 (95% CI 0.669-0.956) for predicting immunotherapy response in the internal and external validation cohorts. When combined with PD-L1 expression, the integrative model further improved the AUC by 4-7% in absolute terms. CONCLUSION: The deep learning model achieved promising performance for predicting immunotherapy response from routine clinical and image data. The proposed multi-modal approach is general and can incorporate other relevant information to further improve prediction of immunotherapy response.


Subject(s)
Deep Learning , Stomach Neoplasms , Humans , Immunotherapy , Phenotype , ROC Curve , Retrospective Studies
16.
Sensors (Basel) ; 23(14)2023 Jul 19.
Article in English | MEDLINE | ID: mdl-37514811

ABSTRACT

As the development of the Internet of Things (IoT) continues, Federated Learning (FL) is gaining popularity as a distributed machine learning framework that does not compromise the data privacy of each participant. However, the data held by enterprises and factories in the IoT often have different distribution properties (Non-IID), leading to poor results in their federated learning. This problem causes clients to forget about global knowledge during their local training phase and then tends to slow convergence and degrades accuracy. In this work, we propose a method named FedRAD, which is based on relational knowledge distillation that further enhances the mining of high-quality global knowledge by local models from a higher-dimensional perspective during their local training phase to better retain global knowledge and avoid forgetting. At the same time, we devise an entropy-wise adaptive weights module (EWAW) to better regulate the proportion of loss in single-sample knowledge distillation versus relational knowledge distillation so that students can weigh losses based on predicted entropy and learn global knowledge more effectively. A series of experiments on CIFAR10 and CIFAR100 show that FedRAD has better performance in terms of convergence speed and classification accuracy compared to other advanced FL methods.

17.
bioRxiv ; 2023 Jun 29.
Article in English | MEDLINE | ID: mdl-37425781

ABSTRACT

Combined multi-omics analysis of proteomics, polar metabolomics, and lipidomics requires separate liquid chromatography-mass spectrometry (LC-MS) platforms for each omics layer. This requirement for different platforms limits throughput and increases costs, preventing the application of mass spectrometry-based multi-omics to large scale drug discovery or clinical cohorts. Here, we present an innovative strategy for simultaneous multi-omics analysis by direct infusion (SMAD) using one single injection without liquid chromatography. SMAD allows quantification of over 9,000 metabolite m/z features and over 1,300 proteins from the same sample in less than five minutes. We validated the efficiency and reliability of this method and then present two practical applications: mouse macrophage M1/M2 polarization and high throughput drug screening in human 293T cells. Finally, we demonstrate relationships between proteomic and metabolomic data are discovered by machine learning.

18.
J Am Soc Mass Spectrom ; 34(9): 1858-1867, 2023 Sep 06.
Article in English | MEDLINE | ID: mdl-37463334

ABSTRACT

Skeletal muscle is a major regulatory tissue of whole-body metabolism and is composed of a diverse mixture of cell (fiber) types. Aging and several diseases differentially affect the various fiber types, and therefore, investigating the changes in the proteome in a fiber-type specific manner is essential. Recent breakthroughs in isolated single muscle fiber proteomics have started to reveal heterogeneity among fibers. However, existing procedures are slow and laborious, requiring 2 h of mass spectrometry time per single muscle fiber; 50 fibers would take approximately 4 days to analyze. Thus, to capture the high variability in fibers both within and between individuals requires advancements in high throughput single muscle fiber proteomics. Here we use a single cell proteomics method to enable quantification of single muscle fiber proteomes in 15 min total instrument time. As proof of concept, we present data from 53 isolated skeletal muscle fibers obtained from two healthy individuals analyzed in 13.25 h. Adapting single cell data analysis techniques to integrate the data, we can reliably separate type 1 and 2A fibers. Ninety-four proteins were statistically different between clusters indicating alteration of proteins involved in fatty acid oxidation, oxidative phosphorylation, and muscle structure and contractile function. Our results indicate that this method is significantly faster than prior single fiber methods in both data collection and sample preparation while maintaining sufficient proteome depth. We anticipate this assay will enable future studies of single muscle fibers across hundreds of individuals, which has not been possible previously due to limitations in throughput.


Subject(s)
Proteome , Proteomics , Humans , Proteome/metabolism , Proteomics/methods , Workflow , Muscle Fibers, Skeletal/metabolism , Muscle, Skeletal
19.
Int J Surg ; 109(7): 2010-2024, 2023 Jul 01.
Article in English | MEDLINE | ID: mdl-37300884

ABSTRACT

BACKGROUND: Peritoneal recurrence (PR) is the predominant pattern of relapse after curative-intent surgery in gastric cancer (GC) and indicates a dismal prognosis. Accurate prediction of PR is crucial for patient management and treatment. The authors aimed to develop a noninvasive imaging biomarker from computed tomography (CT) for PR evaluation, and investigate its associations with prognosis and chemotherapy benefit. METHODS: In this multicenter study including five independent cohorts of 2005 GC patients, the authors extracted 584 quantitative features from the intratumoral and peritumoral regions on contrast-enhanced CT images. The artificial intelligence algorithms were used to select significant PR-related features, and then integrated into a radiomic imaging signature. And improvements of diagnostic accuracy for PR by clinicians with the signature assistance were quantified. Using Shapley values, the authors determined the most relevant features and provided explanations to prediction. The authors further evaluated its predictive performance in prognosis and chemotherapy response. RESULTS: The developed radiomics signature had a consistently high accuracy in predicting PR in the training cohort (area under the curve: 0.732) and internal and Sun Yat-sen University Cancer Center validation cohorts (0.721 and 0.728). The radiomics signature was the most important feature in Shapley interpretation. The diagnostic accuracy of PR with the radiomics signature assistance was improved by 10.13-18.86% for clinicians ( P <0.001). Furthermore, it was also applicable in the survival prediction. In multivariable analysis, the radiomics signature remained an independent predictor for PR and prognosis ( P <0.001 for all). Importantly, patients with predicting high risk of PR from radiomics signature could gain survival benefit from adjuvant chemotherapy. By contrast, chemotherapy had no impact on survival for patients with a predicted low risk of PR. CONCLUSION: The noninvasive and explainable model developed from preoperative CT images could accurately predict PR and chemotherapy benefit in patients with GC, which will allow the optimization of individual decision-making.


Subject(s)
Peritoneal Neoplasms , Stomach Neoplasms , Humans , Stomach Neoplasms/diagnostic imaging , Stomach Neoplasms/drug therapy , Stomach Neoplasms/surgery , Artificial Intelligence , Peritoneal Neoplasms/diagnostic imaging , Peritoneal Neoplasms/drug therapy , Retrospective Studies , Neoplasm Recurrence, Local/diagnostic imaging , Gastrectomy
20.
IEEE Trans Pattern Anal Mach Intell ; 45(7): 8874-8887, 2023 Jul.
Article in English | MEDLINE | ID: mdl-37015431

ABSTRACT

Reference-based Super-Resolution (Ref-SR) has recently emerged as a promising paradigm to enhance a low-resolution (LR) input image or video by introducing an additional high-resolution (HR) reference image. Existing Ref-SR methods mostly rely on implicit correspondence matching to borrow HR textures from reference images to compensate for the information loss in input images. However, performing local transfer is difficult because of two gaps between input and reference images: the transformation gap (e.g., scale and rotation) and the resolution gap (e.g., HR and LR). To tackle these challenges, we propose C2-Matching in this work, which performs explicit robust matching crossing transformation and resolution. 1) To bridge the transformation gap, we propose a contrastive correspondence network, which learns transformation-robust correspondences using augmented views of the input image. 2) To address the resolution gap, we adopt teacher-student correlation distillation, which distills knowledge from the easier HR-HR matching to guide the more ambiguous LR-HR matching. 3) Finally, we design a dynamic aggregation module to address the potential misalignment issue between input images and reference images. In addition, to faithfully evaluate the performance of Reference-based Image Super-Resolution (Ref Image SR) under a realistic setting, we contribute the Webly-Referenced SR (WR-SR) dataset, mimicking the practical usage scenario. We also extend C2-Matching to Reference-based Video Super-Resolution (Ref VSR) task, where an image taken in a similar scene serves as the HR reference image. Extensive experiments demonstrate that our proposed C2-Matching significantly outperforms state of the arts by up to 0.7 dB on the standard CUFED5 benchmark and also boosts the performance of video super-resolution by incorporating the C2-Matching component into Video SR pipelines. Notably, C2-Matching also shows great generalizability on WR-SR dataset as well as robustness across large scale and rotation transformations. Codes and datasets are available at https://github.com/yumingj/C2-Matching.

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