Gene Expression based Survival Prediction for Cancer Patients: A Topic Modeling Approach

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 GE data. There, a document is represented as a mixture over a relatively small number of topics, where each topic corresponds to a distribution over the words; here, to accommodate the heterogeneity of a patient's cancer, we represent each patient (~document) as a mixture over cancer-topics, where each cancer-topic is a mixture over GE values (~words). This required some extensions to the standard LDA model eg: to accommodate the "real-valued" expression values - leading to our novel "discretized" Latent Dirichlet Allocation (dLDA) procedure. We initially focus on the METABRIC dataset, which describes breast cancer patients using the r=49,576 GE values, from microarrays. Our results show that our approach provides survival estimates that are more accurate than standard models, in terms of the standard Concordance measure. We then validate this approach by running it on the Pan-kidney (KIPAN) dataset, over r=15,529 GE values - here using the mRNAseq modality - and find that it again achieves excellent results. In both cases, we also show that the resulting model is calibrated, using the recent "D-calibrated" measure. These successes, in two different cancer types and expression modalities, demonstrates the generality, and the effectiveness, of this approach

An Advanced Conceptual Diagnostic Healthcare Framework for Diabetes and Cardiovascular Disorders

The data mining along with emerging computing techniques have astonishingly influenced the healthcare industry. Researchers have used different Data Mining and Internet of Things (IoT) for enrooting a programmed solution for diabetes and heart patients. However, still, more advanced and united solution is needed that can offer a therapeutic opinion to individual diabetic and cardio patients. Therefore, here, a smart data mining and IoT (SMDIoT) based advanced healthcare system for proficient diabetes and cardiovascular diseases have been proposed. The hybridization of data mining and IoT with other emerging computing techniques is supposed to give an effective and economical solution to diabetes and cardio patients. SMDIoT hybridized the ideas of data mining, Internet of Things, chatbots, contextual entity search (CES), bio-sensors, semantic analysis and granular computing (GC). The bio-sensors of the proposed system assist in getting the current and precise status of the concerned patients so that in case of an emergency, the needful medical assistance can be provided. The novelty lies in the hybrid framework and the adequate support of chatbots, granular computing, context entity search and semantic analysis. The practical implementation of this system is very challenging and costly. However, it appears to be more operative and economical solution for diabetes and cardio patients.Comment: 11 PAGE