scholarly journals Discrimination Between Invasive and In Situ Melanomas Using Clinical Close-Up Images and a De Novo Convolutional Neural Network

2021 ◽  
Vol 8 ◽  
Author(s):  
Sam Polesie ◽  
Martin Gillstedt ◽  
Gustav Ahlgren ◽  
Hannah Ceder ◽  
Johan Dahlén Gyllencreutz ◽  
...  
Keyword(s):  
De Novo ◽  
Area Under The Curve ◽  
Classification Problem ◽  
Dense Layer ◽  
Training Set ◽  
Clinical Images ◽  
Test Set ◽  
Time Period ◽  
Validation Set

Background: Melanomas are often easy to recognize clinically but determining whether a melanoma is in situ (MIS) or invasive is often more challenging even with the aid of dermoscopy. Recently, convolutional neural networks (CNNs) have made significant and rapid advances within dermatology image analysis. The aims of this investigation were to create a de novo CNN for differentiating between MIS and invasive melanomas based on clinical close-up images and to compare its performance on a test set to seven dermatologists.Methods: A retrospective study including clinical images of MIS and invasive melanomas obtained from our department during a five-year time period (2016–2020) was conducted. Overall, 1,551 images [819 MIS (52.8%) and 732 invasive melanomas (47.2%)] were available. The images were randomized into three groups: training set (n = 1,051), validation set (n = 200), and test set (n = 300). A de novo CNN model with seven convolutional layers and a single dense layer was developed.Results: The area under the curve was 0.72 for the CNN (95% CI 0.66–0.78) and 0.81 for dermatologists (95% CI 0.76–0.86) (P < 0.001). The CNN correctly classified 208 out of 300 lesions (69.3%) whereas the corresponding number for dermatologists was 216 (72.0%). When comparing the CNN performance to each individual reader, three dermatologists significantly outperformed the CNN.Conclusions: For this classification problem, the CNN was outperformed by the dermatologist. However, since the algorithm was only trained and validated on 1,251 images, future refinement and development could make it useful for dermatologists in a real-world setting.

Discriminating Malignancy in Thyroid Nodules: The Nomogram Versus the Kwak and ACR TI-RADS

2020 ◽  
Vol 163 (6) ◽  
pp. 1156-1165
Author(s):  
Juan Xiao ◽  
Qiang Xiao ◽  
Wei Cong ◽  
Ting Li ◽  
Shouluan Ding ◽  
...  
Keyword(s):  
Thyroid Nodules ◽  
Characteristic Curve ◽  
Area Under The Curve ◽  
Diagnostic Study ◽  
Diagnostic Efficiency ◽  
Training Set ◽  
Multivariable Logistic Regression Model ◽  
Predictive Values ◽  
Validation Set ◽  
Sensitivity Specificity

Objective To develop an easy-to-use nomogram for discrimination of malignant thyroid nodules and to compare diagnostic efficiency with the Kwak and American College of Radiology (ACR) Thyroid Imaging, Reporting and Data System (TI-RADS). Study Design Retrospective diagnostic study. Setting The Second Hospital of Shandong University. Subjects and Methods From March 2017 to April 2019, 792 patients with 1940 thyroid nodules were included into the training set; from May 2019 to December 2019, 174 patients with 389 nodules were included into the validation set. Multivariable logistic regression model was used to develop a nomogram for discriminating malignant nodules. To compare the diagnostic performance of the nomogram with the Kwak and ACR TI-RADS, the area under the receiver operating characteristic curve, sensitivity, specificity, and positive and negative predictive values were calculated. Results The nomogram consisted of 7 factors: composition, orientation, echogenicity, border, margin, extrathyroidal extension, and calcification. In the training set, for all nodules, the area under the curve (AUC) for the nomogram was 0.844, which was higher than the Kwak TI-RADS (0.826, P = .008) and the ACR TI-RADS (0.810, P < .001). For the 822 nodules >1 cm, the AUC of the nomogram was 0.891, which was higher than the Kwak TI-RADS (0.852, P < .001) and the ACR TI-RADS (0.853, P < .001). In the validation set, the AUC of the nomogram was also higher than the Kwak and ACR TI-RADS ( P < .05), each in the whole series and separately for nodules >1 or ≤1 cm. Conclusions When compared with the Kwak and ACR TI-RADS, the nomogram had a better performance in discriminating malignant thyroid nodules.

scholarly journals A MYC-Driven Plasma Polyamine Signature for Early Detection of Ovarian Cancer

Cancers ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 913
Author(s):  
Johannes Fahrmann ◽  
Ehsan Irajizad ◽  
Makoto Kobayashi ◽  
Jody Vykoukal ◽  
Jennifer Dennison ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Early Stage ◽  
Area Under The Curve ◽  
Polyamine Metabolism ◽  
Healthy Controls ◽  
Test Set ◽  
Exact Test ◽  
Oncogenic Driver ◽  
Characteristic Area ◽  
Validation Set

MYC is an oncogenic driver in the pathogenesis of ovarian cancer. We previously demonstrated that MYC regulates polyamine metabolism in triple-negative breast cancer (TNBC) and that a plasma polyamine signature is associated with TNBC development and progression. We hypothesized that a similar plasma polyamine signature may associate with ovarian cancer (OvCa) development. Using mass spectrometry, four polyamines were quantified in plasma from 116 OvCa cases and 143 controls (71 healthy controls + 72 subjects with benign pelvic masses) (Test Set). Findings were validated in an independent plasma set from 61 early-stage OvCa cases and 71 healthy controls (Validation Set). Complementarity of polyamines with CA125 was also evaluated. Receiver operating characteristic area under the curve (AUC) of individual polyamines for distinguishing cases from healthy controls ranged from 0.74–0.88. A polyamine signature consisting of diacetylspermine + N-(3-acetamidopropyl)pyrrolidin-2-one in combination with CA125 developed in the Test Set yielded improvement in sensitivity at >99% specificity relative to CA125 alone (73.7% vs 62.2%; McNemar exact test 2-sided P: 0.019) in the validation set and captured 30.4% of cases that were missed with CA125 alone. Our findings reveal a MYC-driven plasma polyamine signature associated with OvCa that complemented CA125 in detecting early-stage ovarian cancer.

scholarly journals Application of Multi-Scale Fusion Attention U-Net to Segment the Thyroid Gland on CT Localization Images for Radiotherapy

2021 ◽  
Author(s):  
Xiaobo Wen ◽  
Biao Zhao ◽  
Meifang Yuan ◽  
Jinzhi Li ◽  
Mengzhen Sun ◽  
...  
Keyword(s):  
Thyroid Gland ◽  
Clinical Work ◽  
Similarity Coefficient ◽  
Dice Similarity Coefficient ◽  
Training Set ◽  
Data Set ◽  
Test Set ◽  
Noise Interference ◽  
Multi Scale ◽  
Validation Set

Abstract Objectives: To explore the performance of Multi-scale Fusion Attention U-net (MSFA-U-net) in thyroid gland segmentation on CT localization images for radiotherapy. Methods: CT localization images for radiotherapy of 80 patients with breast cancer or head and neck tumors were selected; label images were manually delineated by experienced radiologists. The data set was randomly divided into the training set (n=60), the validation set (n=10), and the test set (n=10). Data expansion was performed in the training set, and the performance of the MSFA-U-net model was evaluated using the evaluation indicators Dice similarity coefficient (DSC), Jaccard similarity coefficient (JSC), positive predictive value (PPV), sensitivity (SE), and Hausdorff distance (HD). Results: With the MSFA-U-net model, the DSC, JSC, PPV, SE, and HD indexes of the segmented thyroid gland in the test set were 0.8967±0.0935, 0.8219±0.1115, 0.9065±0.0940, 0.8979±0.1104, and 2.3922±0.5423, respectively. Compared with U-net, HR-net, and Attention U-net, MSFA-U-net showed that DSC increased by 0.052, 0.0376, and 0.0346 respectively; JSC increased by 0.0569, 0.0805, and 0.0433, respectively; SE increased by 0.0361, 0.1091, and 0.0831, respectively; and HD increased by −0.208, −0.1952, and −0.0548, respectively. The test set image results showed that the thyroid edges segmented by the MSFA-U-net model were closer to the standard thyroid delineated by the experts, in comparison with those segmented by the other three models. Moreover, the edges were smoother, over-anti-noise interference was stronger, and oversegmentation and undersegmentation were reduced. Conclusion: The MSFA-U-net model can meet basic clinical requirements and improve the efficiency of physicians' clinical work.

scholarly journals The role of red cell distribution width in the differential diagnosis of iron deficiency anemia and non-transfusion dependent thalassemia patients

2018 ◽  
Vol 10 (3) ◽  
Author(s):  
Pokpong Piriyakhuntorn ◽  
Adisak Tantiworawit ◽  
Thanawat Rattanathammethee ◽  
Chatree Chai-Adisaksopha ◽  
Ekarat Rattarittamrong ◽  
...  
Keyword(s):  
Diagnostic Accuracy ◽  
Predictive Value ◽  
Area Under The Curve ◽  
Microcytic Anemia ◽  
Deficiency Anemia ◽  
Operating Characteristics ◽  
Training Set ◽  
Distribution Width ◽  
Validation Set ◽  
Sensitivity Specificity

This study aims to find the cut-off value and diagnostic accuracy of the use of RDW as initial investigation in enabling the differentiation between IDA and NTDT patients. Patients with microcytic anemia were enrolled in the training set and used to plot a receiving operating characteristics (ROC) curve to obtain the cut-off value of RDW. A second set of patients were included in the validation set and used to analyze the diagnostic accuracy. We recruited 94 IDA and 64 NTDT patients into the training set. The area under the curve of the ROC in the training set was 0.803. The best cut-off value of RDW in the diagnosis of NTDT was 21.0% with a sensitivity and specificity of 81.3% and 55.3% respectively. In the validation set, there were 34 IDA and 58 NTDT patients using the cut-off value of >21.0% to validate. The sensitivity, specificity, positive predictive value and negative predictive value were 84.5%, 70.6%, 83.1% and 72.7% respectively. We can therefore conclude that RDW >21.0% is useful in differentiating between IDA and NTDT patients with high diagnostic accuracy

scholarly journals Use of serum biomarkers in staging of canine hepatic fibrosis

2019 ◽  
Vol 31 (5) ◽  
pp. 665-673 ◽  
Author(s):  
Maud Menard ◽  
Alexis Lecoindre ◽  
Jean-Luc Cadoré ◽  
Michèle Chevallier ◽  
Aurélie Pagnon ◽  
...  
Keyword(s):  
Liver Biopsy ◽  
Hepatic Fibrosis ◽  
External Validation ◽  
Model Performance ◽  
Area Under The Curve ◽  
Gamma Glutamyl Transferase ◽  
Training Set ◽  
Internal Validation ◽  
Validation Set ◽  
Glutamyl Transferase

Accurate staging of hepatic fibrosis (HF) is important for treatment and prognosis of canine chronic hepatitis. HF scores are used in human medicine to indirectly stage and monitor HF, decreasing the need for liver biopsy. We developed a canine HF score to screen for moderate or greater HF. We included 96 dogs in our study, including 5 healthy dogs. A liver biopsy for histologic examination and a biochemistry profile were performed on all dogs. The dogs were randomly split into a training set of 58 dogs and a validation set of 38 dogs. A HF score that included alanine aminotransferase, alkaline phosphatase, total bilirubin, potassium, and gamma-glutamyl transferase was developed in the training set. Model performance was confirmed using the internal validation set, and was similar to the performance in the training set. The overall sensitivity and specificity for the study group were 80% and 70% respectively, with an area under the curve of 0.80 (0.71–0.90). This HF score could be used for indirect diagnosis of canine HF when biochemistry panels are performed on the Konelab 30i (Thermo Scientific), using reagents as in our study. External validation is required to determine if the score is sufficiently robust to utilize biochemical results measured in other laboratories with different instruments and methodologies.

scholarly journals Multiclass Classifier for P-Glycoprotein Substrates, Inhibitors, and Non-Active Compounds

Molecules ◽  
2019 ◽  
Vol 24 (10) ◽  
pp. 2006 ◽  
Author(s):  
Liadys Mora Lagares ◽  
Nikola Minovski ◽  
Marjana Novič
Keyword(s):  
In Silico ◽  
Transmembrane Protein ◽  
External Validation ◽  
Assessment Process ◽  
Classification Model ◽  
Training Set ◽  
Test Set ◽  
Active Compounds ◽  
P Glycoprotein ◽  
Validation Set

P-glycoprotein (P-gp) is a transmembrane protein that actively transports a wide variety of chemically diverse compounds out of the cell. It is highly associated with the ADMET (absorption, distribution, metabolism, excretion and toxicity) properties of drugs/drug candidates and contributes to decreasing toxicity by eliminating compounds from cells, thereby preventing intracellular accumulation. Therefore, in the drug discovery and toxicological assessment process it is advisable to pay attention to whether a compound under development could be transported by P-gp or not. In this study, an in silico multiclass classification model capable of predicting the probability of a compound to interact with P-gp was developed using a counter-propagation artificial neural network (CP ANN) based on a set of 2D molecular descriptors, as well as an extensive dataset of 2512 compounds (1178 P-gp inhibitors, 477 P-gp substrates and 857 P-gp non-active compounds). The model provided a good classification performance, producing non error rate (NER) values of 0.93 for the training set and 0.85 for the test set, while the average precision (AvPr) was 0.93 for the training set and 0.87 for the test set. An external validation set of 385 compounds was used to challenge the model’s performance. On the external validation set the NER and AvPr values were 0.70 for both indices. We believe that this in silico classifier could be effectively used as a reliable virtual screening tool for identifying potential P-gp ligands.

scholarly journals Dataset Splitting Techniques Comparison For Face Classification on CCTV Images

2020 ◽  
Vol 14 (4) ◽  
pp. 341
Author(s):  
Ade Nurhopipah ◽  
Uswatun Hasanah
Keyword(s):  
Splitting Method ◽  
Machine Learning Algorithms ◽  
Support Vector ◽  
Training Set ◽  
Test Set ◽  
Face Classification ◽  
Lower Accuracy ◽  
Svm Algorithm ◽  
Stable Performance ◽  
Validation Set

The performance of classification models in machine learning algorithms is influenced by many factors, one of which is dataset splitting method. To avoid overfitting, it is important to apply a suitable dataset splitting strategy. This study presents comparison of four dataset splitting techniques, namely Random Sub-sampling Validation (RSV), k-Fold Cross Validation (k-FCV), Bootstrap Validation (BV) and Moralis Lima Martin Validation (MLMV). This comparison is done in face classification on CCTV images using Convolutional Neural Network (CNN) algorithm and Support Vector Machine (SVM) algorithm. This study is also applied in two image datasets. The results of the comparison are reviewed by using model accuracy in training set, validation set and test set, also bias and variance of the model. The experiment shows that k-FCV technique has more stable performance and provide high accuracy on training set as well as good generalizations on validation set and test set. Meanwhile, data splitting using MLMV technique has lower performance than the other three techniques since it yields lower accuracy. This technique also shows higher bias and variance values and it builds overfitting models, especially when it is applied on validation set.

scholarly journals An Early Biomarker Algorithm Predicts Lethal Graft-Versus-Host Disease and Survival after Allogeneic Hematopoietic Cell Transplantation

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 509-509 ◽  
Author(s):  
Matthew J Hartwell ◽  
Umut Ozbek ◽  
Ernst Holler ◽  
Anne S. Renteria ◽  
Pavan R. Reddy ◽  
...  
Keyword(s):  
High Risk ◽  
Research Funding ◽  
Acute Gvhd ◽  
Conditioning Regimen ◽  
Training Set ◽  
Test Set ◽  
Graft Versus Host ◽  
Independent Validation ◽  
Blood Biomarker ◽  
Validation Set

Abstract No laboratory test can predict non-relapse mortality (NRM) after hematopoietic cellular transplantation (HCT) prior to the onset graft-versus-host disease (GVHD). Recently, we have shown that a signature of three GVHD plasma biomarkers (TNFR1, ST2, and REG3α) can predict response to GVHD therapy and NRM at the onset of clinical GVHD (Levine, Lancet Haem, 2015). Our goal in the current study was to identify a blood biomarker signature that could predict lethal GVHD and six-month NRM well in advance of the onset of GVHD symptoms. Patient samples on day +7 after HCT were obtained from 1,287 patients from 11 HCT centers in the Mount Sinai Acute GVHD International Consortium (MAGIC). Samples from two large centers (n = 929) were combined and randomly assigned to a training set (n = 620) and test set (n = 309). 358 patients from nine others centers constituted an independent validation set. The overall cumulative incidences of 6-month NRM were 11%, 12%, and 13% for the training, test, and validation sets respectively. The incidence of lethal GVHD, defined as death without preceding relapse while under steroid treatment for acute GVHD, were 18%, 24%, and 14% in the same groups, respectively. The median day of GVHD onset was 28 days in the training set and 29 days in the test and validation sets. We measured four GVHD related biomarkers [ST2, REG3α, TNFR1, and IL2Rα] in all samples and used the training set alone to develop competing risks regression models that used all 13 possible combinations of one to four biomarkers to predict 6-month NRM. The best algorithm, which we rigorously confirmed through Monte Carlo cross-validation of 75 different combinations of training sets, included ST2 and REG3α. No combination of one, three, or four biomarkers was superior to the combination of these two biomarkers. The day 7 algorithm identified high risk (HR) and low risk (LR) groups with 6-month NRMs of 28% and 7%, respectively (p<0.001) (Fig 1A). The relapse rates did not differ between risk groups so that overall survival (OS) was 60% for HR and 84% for LR (p<0.001) (Fig 1B). When applied to the test set (Fig 1C/D), the algorithm identified 54/309 (17%) of the patients as HR with an NRM of 33% vs 7% for LR patients (p<0.001) and 6-month OS of 57% and 81% for HR and LR patients, respectively (p<0.001). In the independent validation set (Fig 1 E/F), the algorithm identified 72/358 (20%) of the patients as HR with an NRM of 26% vs 10% for LR patients (p<0.001) and OS of 68% and 85% for HR and LR patients, respectively (p<0.001). High risk patients were three times more likely to die from GVHD than LR patients in each cohort (p<0.001) (Fig 2). The GI tract is the GVHD target organ that is most resistant to treatment and represents a major cause of NRM, and we observed twice as much severe GI GVHD (stage 3 or 4) in HR patients as in LR patients (p<0.001, data not shown). The algorithm successfully separated HR and LR strata for 6 month NRM in several groups with differing risks for GVHD and NRM, including donor type, degree. of HLA-match, age group, and conditioning regimen intensity (Fig 3). In conclusion, we have developed a blood biomarker algorithm that predicts the development of lethal GVHD seven days after HCT, which performed successfully in large multicenter validation sets. The GVH reaction is already in progress by day +7, even though clinical symptoms may not occur until days or weeks later. We speculate that the blood biomarker concentrations at this early time point reflect subclinical GI pathology, a notion that is reinforced by the fact that ST2 and REG3α, the two biomarkers in the algorithm, are closely associated with GI GVHD. The algorithm identified HR and LR strata in several patient groups with different overall risk for lethal GVHD (donor, HLA match, conditioning regimen intensity, age). This day +7 algorithm should prove useful in clinical BMT research by identifying patients at high risk for lethal GVHD who might benefit from aggressive preemptive treatment strategies. Disclosures Chen: Novartis: Research Funding; Incyte Corporation: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding. Jagasia:Therakos: Consultancy. Kitko:Therakos: Honoraria, Speakers Bureau. Kroeger:Novartis: Honoraria, Research Funding. Levine:Viracor: Patents & Royalties: GVHD biomarkers patent. Ferrara:Viracor: Patents & Royalties: GVHD biomarkers patent.

scholarly journals Identification of 5 Gene Signatures in Survival Prediction for Patients with Lung Squamous Cell Carcinoma Based on Integrated Multiomics Data Analysis

2020 ◽  
Vol 2020 ◽  
pp. 1-19
Author(s):  
Hongxia Ma ◽  
Lihong Tong ◽  
Qian Zhang ◽  
Wenjun Chang ◽  
Fengsen Li
Keyword(s):  
Squamous Cell Carcinoma ◽  
Data Analysis ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Lung Squamous Cell Carcinoma ◽  
Training Set ◽  
Test Set ◽  
Gene Signatures ◽  
Genomic Variants ◽  
Validation Set

Background. Lung squamous cell carcinoma (LSCC) is a frequently diagnosed cancer worldwide, and it has a poor prognosis. The current study is aimed at developing the prediction of LSCC prognosis by integrating multiomics data including transcriptome, copy number variation data, and mutation data analysis, so as to predict patients’ survival and discover new therapeutic targets. Methods. RNASeq, SNP, CNV data, and LSCC patients’ clinical follow-up information were downloaded from The Cancer Genome Atlas (TCGA), and the samples were randomly divided into two groups, namely, the training set and the validation set. In the training set, the genes related to prognosis and those with different copy numbers or with different SNPs were integrated to extract features using random forests, and finally, robust biomarkers were screened. In addition, a gene-related prognostic model was established and further verified in the test set and GEO validation set. Results. We obtained a total of 804 prognostic-related genes and 535 copy amplification genes, 621 copy deletions genes, and 388 significantly mutated genes in genomic variants; noticeably, these genomic variant genes were found closely related to tumor development. A total of 51 candidate genes were obtained by integrating genomic variants and prognostic genes, and 5 characteristic genes (HIST1H2BH, SERPIND1, COL22A1, LCE3C, and ADAMTS17) were screened through random forest feature selection; we found that many of those genes had been reported to be related to LSCC progression. Cox regression analysis was performed to establish 5-gene signature that could serve as an independent prognostic factor for LSCC patients and can stratify risk samples in training set, test set, and external validation set (p<0.01), and the 5-year survival areas under the curve (AUC) of both training set and validation set were > 0.67. Conclusion. In the current study, 5 gene signatures were constructed as novel prognostic markers to predict the survival of LSCC patients. The present findings provide new diagnostic and prognostic biomarkers and therapeutic targets for LSCC treatment.

Identification of predictive biomarkers of overall survival (OS) in patients (pts) with advanced renal cell carcinoma (RCC) treated with interferon alpha (I) with or without bevacizumab (B): Results from CALGB 90206 (Alliance).

2013 ◽  
Vol 31 (15_suppl) ◽  
pp. 4520-4520 ◽  
Author(s):  
Andrew B. Nixon ◽  
Susan Halabi ◽  
Ivo Shterev ◽  
Mark Starr ◽  
John C Brady ◽  
...  
Keyword(s):  
Proportional Hazards ◽  
Proportional Hazards Model ◽  
Predictive Accuracy ◽  
Area Under The Curve ◽  
Predictive Biomarkers ◽  
Risk Groups ◽  
Phase Iii ◽  
Plasma Samples ◽  
Training Set ◽  
Validation Set

4520 Background: CALGB 90206 was a phase III trial of 732 pts with RCC comparing B+I versus I alone demonstrating no difference in OS. To date, there are no validated predictive biomarkers for B in RCC. For this reason, baseline plasma samples from CALGB 90206 pts were analyzed to identify and test predictive markers for B+I in RCC pts. Methods: Baseline EDTA plasma samples from 424 consenting pts were analyzed using an optimized multiplex ELISA platform for 32 candidate factors related to tumor growth, angiogenesis, and inflammation. The data were randomly split into training (n=286) and validation (n=138) sets. The proportional hazards model was used to test for treatment-marker interactions of OS. The estimated coefficients from the training set were used to compute a risk score (RS) for each pt in the validation set. The RS classified pts by risk in the validation set. The model was assessed for its predictive accuracy using area under the curve (AUC). Results: A statistically significant 3-way interaction between interleukin-6 (IL-6), hepatocyte growth factor (HGF) and treatment was observed in the training set (p<0.0001). The median levels of IL-6 and HGF in the training set were 8.4 pg/ml and 89 pg/ml, respectively. In the validation set, the RS was predictive of OS (p<0.001) with the high and low risk groups having a median OS of 10 months and 32 months, respectively. The AUC in the validation set was 0.82 (95% CI=0.77-0.88). The median OS (in months) by median levels of IL-6 and HGF stratified by treatment arm in the validation set is presented in the table with associated 95% CI (NR=not reached). Conclusions: IL-6 and HGF are predictive for OS in RCC patients treated with B+I and a RS based on these factors identified patients who benefitted most from B. If independently validated, this novel RS could guide clinical decisions and pt selection in future RCC trials. [Table: see text]

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