scholarly journals Two-stage Neural-network based Prognosis Models using Pathological Image and Transcriptomic Data: An Application in Hepatocellular Carcinoma Patient Survival Prediction

2020 ◽  
Author(s):  
Zhucheng Zhan ◽  
Noshad Hosseni ◽  
Olivier Poirion ◽  
Maria Westerhoff ◽  
Eun-Young Choi ◽  
...  
Keyword(s):  
Neural Network ◽  
Hepatocellular Carcinoma ◽  
Patient Survival ◽  
Survival Prediction ◽  
Two Stage ◽  
Transcriptomic Data ◽  
Carcinoma Patient ◽  
Pathological Image

scholarly journals Two-stage neural-network based prognosis models using pathological image and transcriptomic data: An application in hepatocellular carcinoma patient survival prediction

2020 ◽  
Author(s):  
Zhucheng Zhan ◽  
Noshad Hossenei ◽  
Olivier Poirion ◽  
Maria Westerhoff ◽  
Eun-Young Choi ◽  
...  
Keyword(s):  
Neural Network ◽  
Hepatocellular Carcinoma ◽  
Proportional Hazards Model ◽  
Patient Survival ◽  
Complex Model ◽  
Cox Proportional Hazards ◽  
Cox Proportional Hazards Model ◽  
P Value ◽  
Survival Prediction ◽  
Two Stage

AbstractPathological images are easily accessible data type with potential as prognostic biomarkers. Here we extend Cox-nnet, a neural network based prognosis method previously used for transcriptomics data, to predict patient survival using hepatocellular carcinoma (HCC) pathological images. Cox-nnet based imaging predictions are more robust and accurate than Cox proportional hazards model. Moreover, using a novel two-stage Cox-nnet complex model, we are able to combine histopathology image and transcriptomics RNA-Seq data to make impressively accurate prognosis predictions, with C-index close to 0.90 and log-ranked p-value of 4e-21 in the testing dataset. This work provides a new, biologically relevant and relatively interpretable solution to the challenge of integrating multi-modal and multiple types of data, particularly for survival prediction.

scholarly journals Survival prediction for oral tongue cancer patients via probabilistic genetic algorithm optimized neural network models

2020 ◽  
Vol 93 (1112) ◽  
pp. 20190825
Author(s):  
Xiaoying Pan ◽  
Ting Zhang ◽  
QingPing Yang ◽  
Di Yang ◽  
Jean-Claude Rwigema ◽  
...  
Keyword(s):  
Neural Network ◽  
Genetic Algorithm ◽  
Patient Survival ◽  
Back Propagation ◽  
Network Models ◽  
Image Features ◽  
Survival Prediction ◽  
Reduction Algorithm ◽  
Neural Network Models ◽  
Pre Treatment

Objectives: High throughput pre-treatment imaging features may predict radiation treatment outcome and guide individualized treatment in radiotherapy (RT). Given relatively small patient sample (as compared with high dimensional imaging features), identifying potential prognostic imaging biomarkers is typically challenging. We aimed to develop robust machine learning methods for patient survival prediction using pre-treatment quantitative CT image features for a subgroup of head-and-neck cancer patients. Methods: Three neural network models, including back propagation (BP), Genetic Algorithm-Back Propagation (GA-BP), and Probabilistic Genetic Algorithm-Back Propagation (PGA-BP) neural networks were trained to simulate association between patient survival and radiomics data in radiotherapy. To evaluate the models, a subgroup of 59 head-and-neck patients with primary cancers in oral tongue area were utilized. Quantitative image features were extracted from planning CT images, a novel t-Distributed Stochastic Neighbor Embedding (t-SNE) method was used to remove irrelevant and redundant image features before fed into the network models. 80% patients were used to train the models, and remaining 20% were used for evaluation. Results: Of the three supervised machine-learning methods studied, PGA-BP yielded the best predictive performance. The reported actual patient survival interval of 30.5 ± 21.3 months, the predicted survival times were 47.3 ± 38.8, 38.5 ± 13.5 and 29.9 ± 15.3 months using the traditional PCA. Combining with the novel t-SNE dimensionality reduction algorithm, the predicted survival intervals are 35.8 ± 15.2, 32.3 ± 13.1 and 31.6 ± 15.8 months for the BP, GA-BP and PGA-BP neural network models, respectively. Conclusion: The work demonstrated that the proposed probabilistic genetic algorithm optimized neural network models, integrating with the t-SNE dimensionality reduction algorithm, achieved accurate prediction of patient survival. Advances in knowledge: The proposed PGA-BP neural network, integrating with an advanced dimensionality reduction algorithm (t-SNE), improved patient survival prediction accuracy using pre-treatment quantitative CT image features of head-and-neck cancer patients.

scholarly journals Two-stage Cox-nnet: biologically interpretable neural-network model for prognosis prediction and its application in liver cancer survival using histopathology and transcriptomic data

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Zhucheng Zhan ◽  
Zheng Jing ◽  
Bing He ◽  
Noshad Hosseini ◽  
Maria Westerhoff ◽  
...  
Keyword(s):  
Neural Network ◽  
Gene Expression ◽  
Image Features ◽  
P Value ◽  
Imaging Features ◽  
Two Stage ◽  
Prognosis Prediction ◽  
Random Survival Forests ◽  
Survival Forests ◽  
Pathological Image

Abstract Pathological images are easily accessible data with the potential of prognostic biomarkers. Moreover, integration of heterogeneous data types from multi-modality, such as pathological image and gene expression data, is invaluable to help predicting cancer patient survival. However, the analytical challenges are significant. Here, we take the hepatocellular carcinoma (HCC) pathological image features extracted by CellProfiler, and apply them as the input for Cox-nnet, a neural network-based prognosis prediction model. We compare this model with the conventional Cox proportional hazards (Cox-PH) model, CoxBoost, Random Survival Forests and DeepSurv, using C-index and log-rank P-values. The results show that Cox-nnet is significantly more accurate than Cox-PH and Random Survival Forests models and comparable with CoxBoost and DeepSurv models, on pathological image features. Further, to integrate pathological image and gene expression data of the same patients, we innovatively construct a two-stage Cox-nnet model, and compare it with another complex neural-network model called PAGE-Net. The two-stage Cox-nnet complex model combining histopathology image and transcriptomic RNA-seq data achieves much better prognosis prediction, with a median C-index of 0.75 and log-rank P-value of 6e−7 in the testing datasets, compared to PAGE-Net (median C-index of 0.68 and log-rank P-value of 0.03). Imaging features present additional predictive information to gene expression features, as the combined model is more accurate than the model with gene expression alone (median C-index 0.70). Pathological image features are correlated with gene expression, as genes correlated to top imaging features present known associations with HCC patient survival and morphogenesis of liver tissue. This work proposes two-stage Cox-nnet, a new class of biologically relevant and interpretable models, to integrate multiple types of heterogenous data for survival prediction.

scholarly journals Tailored Prediction Model of Survival after Liver Transplantation for Hepatocellular Carcinoma

2021 ◽  
Vol 10 (13) ◽  
pp. 2869
Author(s):  
Indah Jamtani ◽  
Kwang-Woong Lee ◽  
Yun-Hee Choi ◽  
Young-Rok Choi ◽  
Jeong-Moo Lee ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Liver Transplantation ◽  
Prediction Model ◽  
Risk Group ◽  
Significant Risk ◽  
Risk Scores ◽  
Accurate Information ◽  
Survival Prediction ◽  
Good Prediction ◽  
Recurrence Rates

This study aimed to create a tailored prediction model of hepatocellular carcinoma (HCC)-specific survival after transplantation based on pre-transplant parameters. Data collected from June 2006 to July 2018 were used as a derivation dataset and analyzed to create an HCC-specific survival prediction model by combining significant risk factors. Separate data were collected from January 2014 to June 2018 for validation. The prediction model was validated internally and externally. The data were divided into three groups based on risk scores derived from the hazard ratio. A combination of patient demographic, laboratory, radiological data, and tumor-specific characteristics that showed a good prediction of HCC-specific death at a specific time (t) were chosen. Internal and external validations with Uno’s C-index were 0.79 and 0.75 (95% confidence interval (CI) 0.65–0.86), respectively. The predicted survival after liver transplantation for HCC (SALT) at a time “t” was calculated using the formula: [1 − (HCC-specific death(t’))] × 100. The 5-year HCC-specific death and recurrence rates in the low-risk group were 2% and 5%; the intermediate-risk group was 12% and 14%, and in the high-risk group were 71% and 82%. Our HCC-specific survival predictor named “SALT calculator” could provide accurate information about expected survival tailored for patients undergoing transplantation for HCC.

scholarly journals A Two-Stage Neural Network-Based Cold Start Item Recommender

2021 ◽  
Vol 11 (9) ◽  
pp. 4243
Author(s):  
Chieh-Yuan Tsai ◽  
Yi-Fan Chiu ◽  
Yu-Jen Chen
Keyword(s):  
Neural Network ◽  
Recommendation System ◽  
Service Providers ◽  
Cold Start ◽  
Computational Time ◽  
Two Stage ◽  
The Neural Network ◽  
Textual Description ◽  
Recommendation Algorithms ◽  
Content Information

Nowadays, recommendation systems have been successfully adopted in variant online services such as e-commerce, news, and social media. The recommenders provide users a convenient and efficient way to find their exciting items and increase service providers’ revenue. However, it is found that many recommenders suffered from the cold start (CS) problem where only a small number of ratings are available for some new items. To conquer the difficulties, this research proposes a two-stage neural network-based CS item recommendation system. The proposed system includes two major components, which are the denoising autoencoder (DAE)-based CS item rating (DACR) generator and the neural network-based collaborative filtering (NNCF) predictor. In the DACR generator, a textual description of an item is used as auxiliary content information to represent the item. Then, the DAE is applied to extract the content features from high-dimensional textual vectors. With the compact content features, a CS item’s rating can be efficiently derived based on the ratings of similar non-CS items. Second, the NNCF predictor is developed to predict the ratings in the sparse user–item matrix. In the predictor, both spare binary user and item vectors are projected to dense latent vectors in the embedding layer. Next, latent vectors are fed into multilayer perceptron (MLP) layers for user–item matrix learning. Finally, appropriate item suggestions can be accurately obtained. The extensive experiments show that the DAE can significantly reduce the computational time for item similarity evaluations while keeping the original features’ characteristics. Besides, the experiments show that the proposed NNCF predictor outperforms several popular recommendation algorithms. We also demonstrate that the proposed CS item recommender can achieve up to 8% MAE improvement compared to adding no CS item rating.

scholarly journals A Real-time Driver Fatigue Detection Method Based on Two-Stage Convolutional Neural Network

2020 ◽  
Vol 53 (2) ◽  
pp. 15374-15379
Author(s):  
Hu He ◽  
Xiaoyong Zhang ◽  
Fu Jiang ◽  
Chenglong Wang ◽  
Yingze Yang ◽  
...  
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Real Time ◽  
Detection Method ◽  
Driver Fatigue ◽  
Two Stage ◽  
Fatigue Detection
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