Survival prediction is an important branch of cancer prognosis analysis. The model that predicts survival risk through TCGA genomics data can discover genes related to cancer and provide diagnosis and treatment recommendations based on patient characteristics. We found that deep learning models based on Cox proportional hazards often suffer from overfitting when dealing with high-throughput data. Moreover, we found that as the number of network layers increases, the experimental results will not get better, and network degradation will occur. Based on this problem, we propose a new framework based on Deep Residual Learning. Combine the ideas of Cox proportional hazards and Residual. And name it ResSurv. First, ResSurv is a feed-forward deep learning network stacked by multiple basic ResNet Blocks. In each ResNet Block, we add a Normalization Layer to prevent gradient disappearance and gradient explosion. Secondly, for the loss function of the neural network, we inherited the Cox proportional hazards methods, applied the semi-parametric of the CPH model to the neural network, combined with the partial likelihood model, established the loss function, and performed backpropagation and gradient update. Finally, we compared ResSurv networks of different depths and found that we can effectively extract high-dimensional features. Ablation experiments and comparative experiments prove that our model has reached SOTA(state of the art) in the field of deep learning, and our network can effectively extract deep information.
Progress in immunotherapy revolutionized the treatment landscape for advanced lung cancer, raising survival expectations beyond those that were historically anticipated with this disease. In the present study, we describe the methods for the adjustment of mixture parametric models of two populations for survival analysis in the presence of long survivors. A methodology is proposed in several five steps: first, it is proposed to use the multimodality test to decide the number of subpopulations to be considered in the model, second to adjust simple parametric survival models and mixture distribu…
The Cox proportional hazard model is one of the most popular tools in analyzing time-to-event data in public health studies. When outcomes observed in clinical data from different regions yield a varying pattern correlated with location, it is often of great interest to investigate spatially varying effects of covariates. In this paper, we propose a geographically weighted Cox regression model for sparse spatial survival data. In addition, a stochastic neighborhood weighting scheme is introduced at the county level. Theoretical properties of the proposed geographically weighted estimators are …
In medical research, it is often needed to obtain subgroups with heterogeneous survivals, which have been predicted from a prognostic factor. For this purpose, a binary split has often been used once or recursively; however, binary partitioning may not provide an optimal set of well separated subgroups. We propose a multi-way partitioning algorithm, which divides the data into K heterogeneous subgroups based on the information from a prognostic factor. The resulting subgroups show significant differences in survival. Such a multi-way partition is found by maximizing the minimum of the subgroup…
Understanding the factors that explain differences in survival times is an important issue for establishing policies to improve national health systems. Motivated by breast cancer data arising from the Surveillance Epidemiology and End Results program, we propose a covariate-adjusted proportional hazards frailty model for the analysis of clustered right-censored data. Rather than incorporating exchangeable frailties in the linear predictor of commonly-used survival models, we allow the frailty distribution to flexibly change with both continuous and categorical cluster-level covariates and mod…
Lung cancer is among the most common cancers in the United States, in terms of incidence and mortality. In 2009, it is estimated that more than 150,000 deaths will result from lung cancer alone. Genetic information is an extremely valuable data source in characterizing the personal nature of cancer. Over the past several years, investigators have conducted numerous association studies where intensive genetic data is collected on relatively few patients compared to the numbers of gene predictors, with one scientific goal being to identify genetic features associated with cancer recurrence or su…
Survival analysis has been developed and applied in the number of areas including manufacturing, finance, economics and healthcare. In healthcare domain, usually clinical data are high-dimensional, sparse and complex and sometimes there exists few amount of time-to-event (labeled) instances. Therefore building an accurate survival model from electronic health records is challenging. With this motivation, we address this issue and provide a new survival analysis framework using deep learning and active learning with a novel sampling strategy. First, our approach provides better representation w…
Memorial Sloan Kettering Cancer Center（纪念斯隆·凯特琳癌症中心）
Accurate and robust cell nuclei classification is the cornerstone for a wider range of tasks in digital and Computational Pathology. However, most machine learning systems require extensive labeling from expert pathologists for each individual problem at hand, with no or limited abilities for knowledge transfer between datasets and organ sites. In this paper we implement and evaluate a variety of deep neural network models and model ensembles for nuclei classification in renal cell cancer (RCC) and prostate cancer (PCa). We propose a convolutional neural network system based on residual learni…
University of Alberta（阿尔伯塔大学）；Alberta Machine Intelligence Institute (Amii)（阿尔伯塔机器智能研究所（Amii））
Cancer is one of the leading cause of death, worldwide. Many believe that genomic data will enable us to better predict the survival time of these patients, which will lead to better, more personalized treatment options and patient care. As standard survival prediction models have a hard time coping with the high-dimensionality of such gene expression (GE) data, many projects use some dimensionality reduction techniques to overcome this hurdle. We introduce a novel methodology, inspired by topic modeling from the natural language domain, to derive expressive features from the high-dimensional …
In epidemiology research with cancer registry data, it is often of primary interest to make inference on cancer death, not overall survival. Since cause of death is not easy to collect or is not necessarily reliable in cancer registries, some special methodologies have been introduced and widely used by using the concepts of the relative survival ratio and the net survival. In making inference of those measures, external life tables of the general population are utilized to adjust the impact of non-cancer death on overall survival. The validity of this adjustment relies on the assumption that …
Tianjin University（天津大学）；CSIRO Data61（澳大利亚联邦科学与工业研究组织Data61）；Agency for Science, Technology and Research (A*STAR)（新加坡科技研究局）；Shandong University（山东大学）
Ovarian cancer is one of the most serious cancers that threaten women around the world. Epithelial ovarian cancer (EOC), as the most commonly seen subtype of ovarian cancer, has rather high mortality rate and poor prognosis among various gynecological cancers. Survival analysis outcome is able to provide treatment advices to doctors. In recent years, with the development of medical imaging technology, survival prediction approaches based on pathological images have been proposed. In this study, we designed a deep framework named EOCSA which analyzes the prognosis of EOC patients based on patho…
Unobserved individual heterogeneity is a common challenge in population cancer survival studies. This heterogeneity is usually associated with the combination of model misspecification and the failure to record truly relevant variables. We investigate the effects of unobserved individual heterogeneity in the context of excess hazard models, one of the main tools in cancer epidemiology. We propose an individual excess hazard frailty model to account for individual heterogeneity. This represents an extension of frailty modelling to the relative survival framework. In order to facilitate the infe…
Southern Methodist University（南卫理公会大学）；University of Texas at Dallas（德克萨斯大学达拉斯分校）；University of Texas Southwestern Medical Center（德克萨斯大学西南医学中心）
Tumor shape is a key factor that affects tumor growth and metastasis. This paper proposes a topological feature computed by persistent homology to characterize tumor progression from digital pathology and radiology images and examines its effect on the time-to-event data. The proposed topological features are invariant to scale-preserving transformation and can summarize various tumor shape patterns. The topological features are represented in functional space and used as functional predictors in a functional Cox proportional hazards model. The proposed model enables interpretable inference ab…
Two challenging problems in the clinical study of cancer are the characterization of cancer subtypes and the classification of individual patients according to those subtypes. Statistical approaches addressing these problems are hampered by population heterogeneity and challenges inherent in data integration across high-dimensional, diverse covariates. We have developed a survival-supervised latent Dirichlet allocation (survLDA) modeling framework to address these concerns. LDA models have proven extremely effective at identifying themes common across large collections of text, but application…
Indian Institute of Technology Kharagpur（印度理工学院卡拉格普尔分校）；Tata Medical Center（塔塔医学中心）；Arden Cancer Centre（雅顿癌症中心）；University Hospitals Coventry and Warwickshire（考文垂与沃里克郡大学医院）
Prediction of survivability in a patient for tumor progression is useful to estimate the effectiveness of a treatment protocol. In our work, we present a model to take into account the heterogeneous nature of a tumor to predict survival. The tumor heterogeneity is measured in terms of its mass by combining information regarding the radiodensity obtained in images with the gross tumor volume (GTV). We propose a novel feature called Tumor Mass within a GTV (TMG), that improves the prediction of survivability, compared to existing models which use GTV. Weekly variation in TMG of a patient is comp…
School of Electrical and Computer Engineering, Purdue University（普渡大学电气与计算机工程学院）；Department of Medicine, Indiana University School of Medicine（印第安纳大学医学院医学系）；School of Electrical and Computer Engineering, Indiana University - Purdue University Indianapolis（印第安纳大学-普渡大学印第安纳波利斯分校电气与计算机工程学院）
One of the central goals in precision health is the understanding and interpretation of high-dimensional biological data to identify genes and markers associated with disease initiation, development, and outcomes. Though significant effort has been committed to harness gene expression data for multiple analyses while accounting for time-to-event modeling by including survival times, many traditional analyses have focused separately on non-negative matrix factorization (NMF) of the gene expression data matrix and survival regression with Cox proportional hazards model. In this work, Cox proport…
With known cause of death (CoD), competing risk survival methods are applicable in estimating disease-specific survival. Relative survival analysis may be used to estimate disease-specific survival when cause of death is either unknown or subject to misspecification and not reliable for practical usage. This method is popular for population-based cancer survival studies using registry data and does not require CoD information. The standard estimator is the ratio of all-cause survival in the cancer cohort group to the known expected survival from a general reference population. Disease-specific…
Colorectal cancer (CRC) is the third most frequent malignant disease in the world. In some countries with established screening programs, its incidence and mortality have decreased, and survival has improved. AIMS: To obtain reliable data about the epidemiology of CRC in Chile, we analyzed the trends in the last ten years and the influence of observable factors on survival, including explicit guarantees in CRC treatment access (GES program). Publicly available data published by the Health Ministry and National Institute of Statistics were used. Data were obtained from registries of mortality a…
Tree-based methods for length-biased survival data
National Cancer Center（韩国国立癌症中心）；Yonsei University（延世大学）；Seoul National University College of Medicine（首尔大学医学院）；Seoul Metropolitan Government-Seoul National University Boramae Medical Center（首尔市政府-首尔大学八良医疗中心）；Ewha Womans University（梨花女子大学）
Methods for the evaluation of the predictive accuracy of biomarkers with respect to survival outcomes subject to right censoring have been discussed extensively in the literature. In cancer and other diseases, survival outcomes are commonly subject to interval censoring by design or due to the follow up schema. In this paper, we present an estimator for the area under the time-dependent receiver operating characteristic ROC curve for interval censored data based on a nonparametric sieve maximum likelihood approach. We establish the asymptotic properties of the proposed estimator, and illustrat…
Cancer survival prediction is important for developing personalized treatments and inducing disease-causing mechanisms. Multi-omics data integration is attracting widespread interest in cancer research for providing information for understanding cancer progression at multiple genetic levels. Many works, however, are limited because of the high dimensionality and heterogeneity of multi-omics data. In this paper, we propose a novel method to integrate multi-omics data for cancer survival prediction, called Stacked AutoEncoder-based Survival Prediction Neural Network (SAEsurv-net). In the cancer …
Georgia Institute of Technology（佐治亚理工学院）；Emory University（埃默里大学）
Prediction of survival for cancer patients is an open area of research. However, many of these studies focus on datasets with a large number of patients. We present a novel method that is specifically designed to address the challenge of data scarcity, which is often the case for cancer datasets. Our method is able to use unlabeled data to improve classification by adopting a semi-supervised training approach to learn an ensemble classifier. The results of applying our method to three cancer datasets show the promise of semi-supervised learning for prediction of cancer survival.
Guiding Treatment Strategies: The Role of Adjuvant Anti-Her2 Neu Therapy and Skin/Nipple Involvement in Local Recurrence-Free Survival in Breast Cancer Patients
University of Toronto（多伦多大学）；University Health Network（大学健康网络）；Princess Margaret Cancer Centre（玛格丽特公主癌症中心）
Accurate survival prediction is crucial for development of precision cancer medicine, creating the need for new sources of prognostic information. Recently, there has been significant interest in exploiting routinely collected clinical and medical imaging data to discover new prognostic markers in multiple cancer types. However, most of the previous studies focus on individual data modalities alone and do not make use of recent advances in machine learning for survival prediction. We present Deep-CR MTLR -- a novel machine learning approach for accurate cancer survival prediction from multi-mo…
Indian Institute of Technology Bombay（印度理工学院孟买分校）；Case Western Reserve University（凯斯西储大学）；University of Illinois at Chicago（伊利诺伊大学芝加哥分校）
Survival models are used in various fields, such as the development of cancer treatment protocols. Although many statistical and machine learning models have been proposed to achieve accurate survival predictions, little attention has been paid to obtain well-calibrated uncertainty estimates associated with each prediction. The currently popular models are opaque and untrustworthy in that they often express high confidence even on those test cases that are not similar to the training samples, and even when their predictions are wrong. We propose a Bayesian framework for survival models that no…
Neural networks are capable of learning rich, nonlinear feature representations shown to be beneficial in many predictive tasks. In this work, we use these models to explore the use of geographical features in predicting colorectal cancer survival curves for patients in the state of Iowa, spanning the years 1989 to 2012. Specifically, we compare model performance using a newly defined metric -- area between the curves (ABC) -- to assess (a) whether survival curves can be reasonably predicted for colorectal cancer patients in the state of Iowa, (b) whether geographical features improve predicti…
Tongue cancer is a common oral cavity malignancy that originates in the mouth and throat. Much effort has been invested in improving its diagnosis, treatment, and management. Surgical removal, chemotherapy, and radiation therapy remain the major treatment for tongue cancer. The survival of patients determines the treatment effect. Previous studies have identified certain survival and risk factors based on descriptive statistics, ignoring the complex, nonlinear relationship among clinical and demographic variables. In this study, we utilize five cutting-edge machine learning models and clinical…
Predicting Breast Cancer Survival: A Survival Analysis Approach Using Log Odds and Clinical Variables
Federal College of Animal Health and Production Technology（联邦动物卫生与生产技术学院）；Universidad Mayor de San Andres（圣安德烈斯大学）；National University of Computer & Emerging Sciences-FAST（国立计算机与新兴科学大学（FAST大学））；University of Khartoum（喀土穆大学）；University of Jazan（贾赞大学）；New York Institute of Technology（纽约理工学院）；Khalifa Gull Nawaz Teaching Hospital（哈利法·古尔·纳瓦兹教学医院）
University of Illinois at Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）；IBM Research（IBM研究院）；VinUniversity（文大）
Effective understanding of a disease such as cancer requires fusing multiple sources of information captured across physical scales by multimodal data. In this work, we propose a novel feature embedding module that derives from canonical correlation analyses to account for intra-modality and inter-modality correlations. Experiments on simulated and real data demonstrate how our proposed module can learn well-correlated multi-dimensional embeddings. These embeddings perform competitively on one-year survival classification of TCGA-BRCA breast cancer patients, yielding average F1 scores up to 58…
University of Birmingham（伯明翰大学）；University of Melbourne（墨尔本大学）；RMIT University（皇家墨尔本理工大学）
Survival risk prediction using gene expression data is important in making treatment decisions in cancer. Standard neural network (NN) survival analysis models are black boxes with lack of interpretability. More interpretable visible neural network (VNN) architectures are designed using biological pathway knowledge. But they do not model how pathway structures can change for particular cancer types. We propose a novel Mutated Pathway VNN or MPVNN architecture, designed using prior signaling pathway knowledge and gene mutation data-based edge randomization simulating signal flow disruption. As …
University of Science and Technology of China（中国科学技术大学）；UNSW Sydney（悉尼新南威尔士大学）；Genmab Inc.（Genmab公司）
Most early-stage colorectal cancer (CRC) patients can be cured by surgery alone, and only certain high-risk early-stage CRC patients benefit from adjuvant chemotherapies. However, very few validated biomarkers are available to accurately predict survival benefit from postoperative chemotherapy. We developed a novel deep-learning algorithm (CRCNet) using whole-slide images from Molecular and Cellular Oncology (MCO) to predict survival benefit of adjuvant chemotherapy in stage II/III CRC. We validated CRCNet both internally through cross-validation and externally using an independent cohort from…
Breast cancer is the most frequently reported cancer type among the women around the globe and beyond that it has the second highest female fatality rate among all cancer types. Despite all the progresses made in prevention and early intervention, early prognosis and survival prediction rates are still unsatisfactory. In this paper, we propose a novel type of perceptron called L-Perceptron which outperforms all the previous supervised learning methods by reaching 97.42 \% and 98.73 \% in terms of accuracy and sensitivity, respectively in Wisconsin Breast Cancer dataset. Experimental results on…
Vanderbilt University（范德堡大学）；Vanderbilt University Medical Center（范德堡大学医学中心）
Integrating cross-department multi-modal data (e.g., radiological, pathological, genomic, and clinical data) is ubiquitous in brain cancer diagnosis and survival prediction. To date, such an integration is typically conducted by human physicians (and panels of experts), which can be subjective and semi-quantitative. Recent advances in multi-modal deep learning, however, have opened a door to leverage such a process to a more objective and quantitative manner. Unfortunately, the prior arts of using four modalities on brain cancer survival prediction are limited by a "complete modalities" settin…
More than 144 000 Australians were diagnosed with cancer in 2019. The majority will first present to their GP symptomatically, even for cancer for which screening programs exist. Diagnosing cancer in primary care is challenging due to the non-specific nature of cancer symptoms and its low prevalence. Understanding the epidemiology of cancer symptoms and patterns of presentation in patient's medical history from primary care data could be important to improve earlier detection and cancer outcomes. As past medical data about a patient can be incomplete, irregular or missing, this creates additio…
Google Health（谷歌健康）；Advanced Clinical；Tempus Labs Inc（Tempus实验室公司）
Prognostic information at diagnosis has important implications for cancer treatment and monitoring. Although cancer staging, histopathological assessment, molecular features, and clinical variables can provide useful prognostic insights, improving risk stratification remains an active research area. We developed a deep learning system (DLS) to predict disease specific survival across 10 cancer types from The Cancer Genome Atlas (TCGA). We used a weakly-supervised approach without pixel-level annotations, and tested three different survival loss functions. The DLS was developed using 9,086 slid…
In this study, we present a hybrid CNN-RNN approach to investigate long-term survival of subjects in a lung cancer screening study. Subjects who died of cardiovascular and respiratory causes were identified whereby the CNN model was used to capture imaging features in the CT scans and the RNN model was used to investigate time series and thus global information. The models were trained on subjects who underwent cardiovascular and respiratory deaths and a control cohort matched to participant age, gender, and smoking history. The combined model can achieve an AUC of 0.76 which outperforms human…
Georgia Institute of Technology（佐治亚理工学院）；Emory University（埃默里大学）
Cancer survival prediction is an active area of research that can help prevent unnecessary therapies and improve patient's quality of life. Gene expression profiling is being widely used in cancer studies to discover informative biomarkers that aid predict different clinical endpoint prediction. We use multiple modalities of data derived from RNA deep-sequencing (RNA-seq) to predict survival of cancer patients. Despite the wealth of information available in expression profiles of cancer tumors, fulfilling the aforementioned objective remains a big challenge, for the most part, due to the pauci…
