Radiomics based likelihood functions for cancer diagnosis.
Ontology highlight
ABSTRACT:
SUBMITTER: Shakir H
PROVIDER: S-EPMC6603029 | biostudies-literature | 2019 Jul
REPOSITORIES: biostudies-literature
Publications
Radiomics based likelihood functions for cancer diagnosis.
Shakir Hina H Deng Yiming Y Rasheed Haroon H Khan Tariq Mairaj Rasool TMR
Scientific reports 20190701 1
Radiomic features based classifiers and neural networks have shown promising results in tumor classification. The classification performance can be further improved greatly by exploring and incorporating the discriminative features towards cancer into mathematical models. In this research work, we have developed two radiomics driven likelihood models in Computed Tomography(CT) images to classify lung, colon, head and neck cancer. Initially, two diagnostic radiomic signatures were derived by extr ...[more]
Similar Datasets
Project description:BackgroundEarly diagnosis of lung cancer is a key intervention for the treatment of lung cancer in which computer-aided diagnosis (CAD) can play a crucial role. Most published CAD methods perform lung cancer diagnosis by classifying each lung nodule in isolation. However, this does not reflect clinical practice, where clinicians diagnose a patient based on a set of images of nodules, instead of looking at one nodule at a time. Besides, the low interpretability of the output provided by these methods presents an important barrier for their adoption.MethodIn this article, we treat lung cancer diagnosis as a multiple instance learning (MIL) problem, which better reflects the diagnosis process in the clinical setting and provides higher interpretability of the output. We selected radiomics as the source of input features and deep attention-based MIL as the classification algorithm. The attention mechanism provides higher interpretability by estimating the importance of each instance in the set for the final diagnosis. To improve the model's performance in a small imbalanced dataset, we propose a new bag simulation method for MIL.Results and conclusionThe results show that our method can achieve a mean accuracy of 0.807 with a standard error of the mean (SEM) of 0.069, a recall of 0.870 (SEM 0.061), a positive predictive value of 0.928 (SEM 0.078), a negative predictive value of 0.591$0.591$ (SEM 0.155), and an area under the curve (AUC) of 0.842 (SEM 0.074), outperforming other MIL methods. Additional experiments show that the proposed oversampling strategy significantly improves the model's performance. In addition, experiments show that our method provides a good indication of the importance of each nodule in determining the diagnosis, which combined with the well-defined radiomic features, to make the results more interpretable and acceptable for doctors and patients.
| S-EPMC9310706 | biostudies-literature
Project description:MIXED MODELS: Models allowing for continuous heterogeneity by assuming that value of one or more parameters follow a specified distribution have become increasingly popular. This is known as 'mixing' parameters, and it is standard practice by researchers--and the default option in many statistical programs--to base test statistics for mixed models on simulations using asymmetric draws (e.g. Halton draws). PROBLEM 1: INCONSISTENT LR TESTS DUE TO ASYMMETRIC DRAWS: This paper shows that when the estimated likelihood functions depend on standard deviations of mixed parameters this practice is very likely to cause misleading test results for the number of draws usually used today. The paper illustrates that increasing the number of draws is a very inefficient solution strategy requiring very large numbers of draws to ensure against misleading test statistics. The main conclusion of this paper is that the problem can be solved completely by using fully antithetic draws, and that using one dimensionally antithetic draws is not enough to solve the problem. PROBLEM 2: MAINTAINING THE CORRECT DIMENSIONS WHEN REDUCING THE MIXING DISTRIBUTION: A second point of the paper is that even when fully antithetic draws are used, models reducing the dimension of the mixing distribution must replicate the relevant dimensions of the quasi-random draws in the simulation of the restricted likelihood. Again this is not standard in research or statistical programs. The paper therefore recommends using fully antithetic draws replicating the relevant dimensions of the quasi-random draws in the simulation of the restricted likelihood and that this should become the default option in statistical programs. JEL classification: C15; C25.
| S-EPMC4203670 | biostudies-literature
Project description:BackgroundBreast cancer consists not only of neoplastic cells but also of significant changes in the surrounding and parenchymal stroma, which can be reflected in radiomics. This study aimed to perform breast lesion classification through an ultrasound-based multiregional (intratumoral, peritumoral, and parenchymal) radiomic model.MethodsWe retrospectively reviewed ultrasound images of breast lesions from institution #1 (n=485) and institution #2 (n=106). Radiomic features were extracted from different regions (intratumoral, peritumoral, and ipsilateral breast parenchymal) and selected to train the random forest classifier with the training cohort (n=339, a subset of the institution #1 dataset). Then, the intratumoral, peritumoral, and parenchymal, intratumoral & peritumoral (In&Peri), intratumoral & parenchymal (In&P), and intratumoral & peritumoral & parenchymal (In&Peri&P) models were developed and validated on the internal (n=146, another subset of institution 1) and external (n=106, institution #2 dataset) test cohorts. Discrimination was evaluated using the area under the curve (AUC). Calibration curve and Hosmer-Lemeshow test assessed calibration. Integrated discrimination improvement (IDI) was used to assess performance improvement.ResultsThe performance of the In&Peri (AUC values 0.892 and 0.866), In&P (0.866 and 0.863), and In&Peri&P (0.929 and 0.911) models was significantly better than that of the intratumoral model (0.849 and 0.838) in the internal and external test cohorts (IDI test, all P<0.05). The intratumoral, In&Peri and In&Peri&P models showed good calibration (Hosmer-Lemeshow test, all P>0.05). The multiregional (In&Peri&P) model had the highest discrimination among the 6 radiomic models in the test cohorts, respectively.ConclusionsThe multiregional model combining radiomic information of intratumoral, peritumoral, and ipsilateral parenchymal regions yielded better performance than the intratumoral model in distinguishing malignant breast lesions from benign lesions.
| S-EPMC10167447 | biostudies-literature
Project description:BACKGROUND:This study aims to establish a radiomics analysis system for the diagnosis and clinical behaviour prediction of hepatocellular carcinoma (HCC) based on multi-parametric ultrasound imaging. METHODS:A total of 177 patients with focal liver lesions (FLLs) were included in the study. Every patient underwent multi-modal ultrasound examination, including B-mode ultrasound (BMUS), shear wave elastography (SWE), and shear wave viscosity (SWV) imaging. The radiomics analysis system was built on sparse representation theory (SRT) and support vector machine (SVM) for asymmetric data. Through the sparse regulation from the SRT, the proposed radiomics system can effectively avoid over-fitting issues that occur in regular radiomics analysis. The purpose of the proposed system includes differential diagnosis between benign and malignant FLLs, pathologic diagnosis of HCC, and clinical prognostic prediction. Three biomarkers, including programmed cell death protein 1 (PD-1), antigen Ki-67 (Ki-67) and microvascular invasion (MVI), were included and analysed. We calculated the accuracy (ACC), sensitivity (SENS), specificity (SPEC) and area under the receiver operating characteristic curve (AUC) to evaluate the performance of the radiomics models. RESULTS:A total of 2560 features were extracted from the multi-modal ultrasound images for each patient. Five radiomics models were built, and leave-one-out cross-validation (LOOCV) was used to evaluate the models. In LOOCV, the AUC was 0.94 for benign and malignant classification (95% confidence interval [CI]: 0.88 to 0.98), 0.97 for malignant subtyping (95% CI: 0.93 to 0.99), 0.97 for PD-1 prediction (95% CI: 0.89 to 0.98), 0.94 for Ki-67 prediction (95% CI: 0.87 to 0.97), and 0.98 for MVI prediction (95% CI: 0.93 to 0.99). The performance of each model improved when the viscosity modality was included. CONCLUSIONS:Radiomics analysis based on multi-modal ultrasound images could aid in comprehensive liver tumor evaluations, including diagnosis, differential diagnosis, and clinical prognosis.
| S-EPMC6233500 | biostudies-other
Project description:BACKGROUND:Frequent somatic mutations of BRAF and CTNNB1 were identified in both histological subtypes of craniopharyngioma (adamantinomatous and papillary) which shed light on target therapy to cure this oncogenic disease. The aim of this study was to investigate the noninvasive MRI-based radiomics diagnosis to detect BRAF and CTNNB1 mutations in craniopharyngioma patients. METHODS:Forty-four patients pathologically diagnosed as adamantinomatous craniopharyngioma (ACP) or papillary craniopharyngioma (PCP) were retrospectively studied. High-throughput features were extracted from manually segmented tumors in MR images of each case. The modifications-robustness in region of interests and Random Forest-based feature selection methods were adopted to select the most significant features. Random forest classifier with 10-fold cross-validation was applied to build our radiomics model. RESULTS:Four features were selected to make pathological diagnosis between ACP and PCP with area under the receiver operating characteristic curve (AUC) of 0.89, accurancy (ACC) of 0.86, sensitivity (SENS) of 0.89 and specificity (SPEC) of 0.85. The other two features were applied to estimate BRAF V600E mutation with AUC of 0.91, ACC of 0.93, SENS of 0.83 and SPEC of 0.97. Accurate predication of CTNNB1 mutation by three selected features was realized with AUC of 0.93, ACC of 0.86, SENS of 0.86 and SPEC of 0.86. CONCLUSIONS:We developed a reliable MRI-based radiomics approach to perform pathological and molecular diagnosis in craniopharyngioma patients with considerably accurate prediction, which could offer potential guidance for clinical decision-making.
| S-EPMC6322318 | biostudies-literature
Project description:PurposeTo evaluate the diagnostic accuracy of machine learning (ML) techniques applied to radiomic features extracted from OCT and OCT angiography (OCTA) images for diabetes mellitus (DM), diabetic retinopathy (DR), and referable DR (R-DR) diagnosis.DesignCross-sectional analysis of a retinal image dataset from a previous prospective OCTA study (ClinicalTrials.govNCT03422965).ParticipantsPatients with type 1 DM and controls included in the progenitor study.MethodsRadiomic features were extracted from fundus retinographies, OCT, and OCTA images in each study eye. Logistic regression, linear discriminant analysis, support vector classifier (SVC)-linear, SVC-radial basis function, and random forest models were created to evaluate their diagnostic accuracy for DM, DR, and R-DR diagnosis in all image types.Main outcome measuresArea under the receiver operating characteristic curve (AUC) mean and standard deviation for each ML model and each individual and combined image types.ResultsA dataset of 726 eyes (439 individuals) were included. For DM diagnosis, the greatest AUC was observed for OCT (0.82, 0.03). For DR detection, the greatest AUC was observed for OCTA (0.77, 0.03), especially in the 3 × 3 mm superficial capillary plexus OCTA scan (0.76, 0.04). For R-DR diagnosis, the greatest AUC was observed for OCTA (0.87, 0.12) and the deep capillary plexus OCTA scan (0.86, 0.08). The addition of clinical variables (age, sex, etc.) improved most models AUC for DM, DR and R-DR diagnosis. The performance of the models was similar in unilateral and bilateral eyes image datasets.ConclusionsRadiomics extracted from OCT and OCTA images allow identification of patients with DM, DR, and R-DR using standard ML classifiers. OCT was the best test for DM diagnosis, OCTA for DR and R-DR diagnosis and the addition of clinical variables improved most models. This pioneer study demonstrates that radiomics-based ML techniques applied to OCT and OCTA images may be an option for DR screening in patients with type 1 DM.Financial disclosuresProprietary or commercial disclosure may be found after the references.
| S-EPMC9791596 | biostudies-literature
Project description:PurposeLow-dose CT screening allows early lung cancer detection, but is affected by frequent false positive results, inter/intra observer variation and uncertain diagnoses of lung nodules. Radiomics-based models have recently been introduced to overcome these issues, but limitations in demonstrating their generalizability on independent datasets are slowing their introduction to clinic. The aim of this study is to evaluate two radiomics-based models to classify malignant pulmonary nodules in low-dose CT screening, and to externally validate them on an independent cohort. The effect of a radiomics features harmonization technique is also investigated to evaluate its impact on the classification of lung nodules from a multicenter data.MethodsPulmonary nodules from two independent cohorts were considered in this study; the first cohort (110 subjects, 113 nodules) was used to train prediction models, and the second cohort (72 nodules) to externally validate them. Literature-based radiomics features were extracted and, after feature selection, used as predictive variables in models for malignancy identification. An in-house prediction model based on artificial neural network (ANN) was implemented and evaluated, along with an alternative model from the literature, based on a support vector machine (SVM) classifier coupled with a least absolute shrinkage and selection operator (LASSO). External validation was performed on the second cohort to evaluate models' generalization ability. Additionally, the impact of the Combat harmonization method was investigated to compensate for multicenter datasets variabilities. A new training of the models based on harmonized features was performed on the first cohort, then tested separately on the harmonized and non-harmonized features of the second cohort.ResultsPreliminary results showed a good accuracy of the investigated models in distinguishing benign from malignant pulmonary nodules with both sets of radiomics features (i.e., non-harmonized and harmonized). The performance of the models, quantified in terms of Area Under the Curve (AUC), was > 0.89 in the training set and > 0.82 in the external validation set for all the investigated scenarios, outperforming the clinical standard (AUC of 0.76). Slightly higher performance was observed for the SVM-LASSO model than the ANN in the external dataset, although they did not result significantly different. For both harmonized and non-harmonized features, no statistical difference was found between Receiver operating characteristic (ROC) curves related to training and test set for both models.ConclusionsAlthough no significant improvements were observed when applying the Combat harmonization method, both in-house and literature-based models were able to classify lung nodules with good generalization to an independent dataset, thus showing their potential as tools for clinical decision-making in lung cancer screening.
| S-EPMC7708421 | biostudies-literature
Project description:Despite guidelines recommending against its routine use, perioperative imaging for distant metastases is frequently performed in newly diagnosed breast cancer patients, uncovering incidental findings of uncertain significance. We assessed the clinical significance of incidental findings by determining if their presence is associated with disease recurrence. A retrospective review of staging imaging was performed in patients with stage II or III invasive breast cancer diagnosed during 2008-2009 at a large academic medical center. Data related to perioperative imaging and disease recurrence were abstracted from the medical record. Kaplan-Meier curves and Cox proportional hazards models were used to assess the association between incidental findings and time to disease recurrence. A total of 169 of 340 patients (49.7 %) underwent staging evaluation for distant metastases (CT chest, abdomen, pelvis, bone scan, and/or PET-CT). Of these, 146 (86.4 %) had at least one suspicious or indeterminate finding. Follow-up studies were performed in 73 (43.2 %) patients. Nineteen patients were diagnosed with metastatic disease at diagnosis, 18 of whom had stage III disease. In patients without metastatic disease at diagnosis, 32 later developed recurrence. Non-calcified pulmonary nodules were associated with shorter time to disease recurrence (hazard ratio 2.51, 95 % CI 1.13-5.57, p = 0.02). Imaging for distant metastases frequently reveals indeterminate findings, most of which are not associated with disease recurrence. The association between pulmonary nodules and recurrence warrants validation in an independent cohort. Overall, these findings support current guidelines recommending against routine extent of disease evaluation in patients with newly diagnosed stage II breast cancer.
| S-EPMC4734930 | biostudies-literature
Project description:The authors developed scaling methods that monotonically transform the output of one classifier to the "scale" of another. Such transformations affect the distribution of classifier output while leaving the ROC curve unchanged. In particular, they investigated transformations between radiologists and computer classifiers, with the goal of addressing the problem of comparing and interpreting case-specific values of output from two classifiers.Using both simulated and radiologists' rating data of breast imaging cases, the authors investigated a likelihood-ratio-scaling transformation, based on "matching" classifier likelihood ratios. For comparison, three other scaling transformations were investigated that were based on matching classifier true positive fraction, false positive fraction, or cumulative distribution function, respectively. The authors explored modifying the computer output to reflect the scale of the radiologist, as well as modifying the radiologist's ratings to reflect the scale of the computer. They also evaluated how dataset size affects the transformations.When ROC curves of two classifiers differed substantially, the four transformations were found to be quite different. The likelihood-ratio scaling transformation was found to vary widely from radiologist to radiologist. Similar results were found for the other transformations. Our simulations explored the effect of database sizes on the accuracy of the estimation of our scaling transformations.The likelihood-ratio-scaling transformation that the authors have developed and evaluated was shown to be capable of transforming computer and radiologist outputs to a common scale reliably, thereby allowing the comparison of the computer and radiologist outputs on the basis of a clinically relevant statistic.
| S-EPMC3350543 | biostudies-other
Project description:BackgroundIndeterminate pulmonary nodules (IPN) are a diagnostic challenge in regions where pulmonary fungal disease and smoking prevalence are high. We aimed to determine the impact of a combined fungal and imaging biomarker approach compared with a validated prediction model (Mayo) to rule out benign disease and diagnose lung cancer.MethodsAdults ages 40 to 90 years with 6-30 mm IPNs were included from four sites. Serum samples were tested for histoplasmosis IgG and IgM antibodies by enzyme immunoassay and a CT-based risk score was estimated from a validated radiomic model. Multivariable logistic regression models including Mayo score, radiomics score, and IgG and IgM histoplasmosis antibody levels were estimated. The areas under the ROC curves (AUC) of the models were compared among themselves and to Mayo. Bias-corrected clinical net reclassification index (cNRI) was estimated to assess clinical reclassification using a combined biomarker model.ResultsWe included 327 patients; 157 from histoplasmosis-endemic regions. The combined biomarker model including radiomics, histoplasmosis serology, and Mayo score demonstrated improved diagnostic accuracy when endemic histoplasmosis was accounted for [AUC, 0.84; 95% confidence interval (CI), 0.79-0.88; P < 0.0001 compared with 0.73; 95% CI, 0.67-0.78 for Mayo]. The combined model demonstrated improved reclassification with cNRI of 0.18 among malignant nodules.ConclusionsFungal and imaging biomarkers may improve diagnostic accuracy and meaningfully reclassify IPNs. The endemic prevalence of histoplasmosis and cancer impact model performance when using disease related biomarkers.ImpactIntegrating a combined biomarker approach into the diagnostic algorithm of IPNs could decrease time to diagnosis.
| S-EPMC10128087 | biostudies-literature