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Biology subjects

Tavanaei, A.

Publications and source records attributed to Tavanaei, A..

2 recordsLinked to original sources

A novel data-driven model for real-time influenza forecasting

We provide data-driven machine learning methods that are capable of making real-time influenza forecasts that integrate the impacts of climatic factors and geographical proximity to achieve better forecasting performance. The key contributions of our approach are both applying deep learning methods and incorporation of environmental and spatio-temporal factors to improve the performance of the influenza forecasting models. We evaluate the method on Influenza Like Illness (ILI) counts and climatic data, both publicly available data sets. Our proposed method outperforms existing known influenza forecasting methods in terms of their Mean Absolute Percentage Error and Root Mean Square Error. The key advantages of the proposed data-driven methods are as following: (1) The deep-learning model was able to effectively capture the temporal dynamics of flu spread in different geographical regions, (2) The extensions to the deep-learning model capture the influence of external variables that include the geographical proximity and climatic variables such as humidity, temperature, precipitation and sun exposure in future stages, (3) The model consistently performs well for both the city scale and the regional scale on the Google Flu Trends (GFT) and Center for Disease Control (CDC) flu counts. The results offer a promising direction in terms of both data-driven forecasting methods and capturing the influence of spatio-temporal and environmental factors for influenza forecasting methods.

epidemiology

A Deep Learning Model for Predicting Tumor Suppressor Genes and Oncogenes from PDB Structure

While cancer is a heterogeneous complex of distinct diseases, the common underlying mechanism for uncontrolled tumor growth is due to mutations in proto-oncogenes and the loss of the regulatory function of tumor suppression genes. In this paper we propose a novel deep learning model for predicting tumor suppression genes (TSGs) and proto-oncogenes (OGs) from their Protein Data Bank (PDB) three dimensional structures. Specifically, we develop a convolutional neural network (CNN) to classify the feature map sets extracted from the tertiary protein structures. Each feature map set represents particular biological features associated with the atomic coordinates appearing on the outer surface of proteins three dimensional structure. The experimental results on the collected dataset for classifying TSGs and OGs demonstrate promising performance with 82.57% accuracy and 0.89 area under ROC curve. The initial success of the proposed model warrants further study to develop a comprehensive model to identify the cancer driver genes or events using the principle cancer genes (TSG and OG).

bioinformatics