Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection

Permanent URI for this collectionhttps://hdl.handle.net/11147/7148

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  • Article
    Citation - WoS: 8
    Citation - Scopus: 14
    An End-To Trainable Feature Selection-Forecasting Architecture Targeted at the Internet of Things
    (IEEE, 2021) Nakıp, Mert; Karakayalı, Kubilay; Güzeliş, Cüneyt; Rodoplu, Volkan
    We develop a novel end-to-end trainable feature selection-forecasting (FSF) architecture for predictive networks targeted at the Internet of Things (IoT). In contrast with the existing filter-based, wrapper-based and embedded feature selection methods, our architecture enables the automatic selection of features dynamically based on feature importance score calculation and gamma-gated feature selection units that are trained jointly and end-to-end with the forecaster. We compare the performance of our FSF architecture on the problem of forecasting IoT device traffic against the following existing (feature selection, forecasting) technique pairs: Autocorrelation Function (ACF), Analysis of Variance (ANOVA), Recurrent Feature Elimination (RFE) and Ridge Regression methods for feature selection, and Linear Regression, Multi-Layer Perceptron (MLP), Long Short Term Memory (LSTM), 1 Dimensional Convolutional Neural Network (1D CNN), Autoregressive Integrated Moving Average (ARIMA), and Logistic Regression for forecasting. We show that our FSF architecture achieves either the best or close to the best performance among all of the competing techniques by virtue of its dynamic, automatic feature selection capability. In addition, we demonstrate that both the training time and the execution time of FSF are reasonable for IoT applications. This work represents a milestone for the development of predictive networks for IoT in smart cities of the near future.
  • Article
    Citation - WoS: 560
    Citation - Scopus: 607
    A Community Effort To Assess and Improve Drug Sensitivity Prediction Algorithms
    (Nature Publishing Group, 2014) Costello, James C.; Heiser, Laura M.; Georgii, Elisabeth; Gönen, Mehmet; Menden, Michael P.; Wang, Nicholas J.; Bansal, Mukesh; Ammad-ud-din, Muhammad; Hintsanen, Petteri; Khan, Suleiman A.; Mpindi, John-Patrick; Kallioniemi, Olli; Honkela, Antti; Aittokallio, Tero; Wennerberg, Krister; NCI-DREAM Community; Karaçalı, Bilge; Collins, James J.; Gallahan, Dan; Singer, Dinah; Saez-Rodriguez, Julio; Kaski, Samuel; Gray, Joe W.; Stolovitzky, Gustavo
    Predicting the best treatment strategy from genomic information is a core goal of precision medicine. Here we focus on predicting drug response based on a cohort of genomic, epigenomic and proteomic profiling data sets measured in human breast cancer cell lines. Through a collaborative effort between the National Cancer Institute (NCI) and the Dialogue on Reverse Engineering Assessment and Methods (DREAM) project, we analyzed a total of 44 drug sensitivity prediction algorithms. The top-performing approaches modeled nonlinear relationships and incorporated biological pathway information. We found that gene expression microarrays consistently provided the best predictive power of the individual profiling data sets; however, performance was increased by including multiple, independent data sets. We discuss the innovations underlying the top-performing methodology, Bayesian multitask MKL, and we provide detailed descriptions of all methods. This study establishes benchmarks for drug sensitivity prediction and identifies approaches that can be leveraged for the development of new methods.
  • Article
    Citation - WoS: 240
    Citation - Scopus: 264
    A Community Computational Challenge To Predict the Activity of Pairs of Compounds
    (Nature Publishing Group, 2014) Bansal, Mukesh; Yang, Jichen; Karan, Charles; Menden, Michael P.; Costello, James C.; Tang, Hao; Xiao, Guanghua; Li, Yajuan; Allen, Jeffrey; Zhong, Rui; Chen, Beibei; Kim, Minsoo; Wang, Tao; Heiser, Laura M.; Realubit, Ronald; Mattioli, Michela; Alvarez, Mariano J.; Shen, Yao; NCI-DREAM Community; Karaçalı, Bilge; Gallahan, Daniel; Singer, Dinah; Saez-Rodriguez, Julio; Xie, Yang; Stolovitzky, Gustavo; Califano, Andrea
    Recent therapeutic successes have renewed interest in drug combinations, but experimental screening approaches are costly and often identify only small numbers of synergistic combinations. The DREAM consortium launched an open challenge to foster the development of in silico methods to computationally rank 91 compound pairs, from the most synergistic to the most antagonistic, based on gene-expression profiles of human B cells treated with individual compounds at multiple time points and concentrations. Using scoring metrics based on experimental dose-response curves, we assessed 32 methods (31 community-generated approaches and SynGen), four of which performed significantly better than random guessing. We highlight similarities between the methods. Although the accuracy of predictions was not optimal, we find that computational prediction of compound-pair activity is possible, and that community challenges can be useful to advance the field of in silico compound-synergy prediction.
  • Article
    Citation - WoS: 46
    Citation - Scopus: 49
    Predicting and Forecasting Flow Discharge at Sites Receiving Significant Lateral Inflow
    (John Wiley and Sons Inc., 2007) Tayfur, Gökmen; Moramarco, Tommaso; Singh, Vijay P.
    Two models, one linear and one non-linear, were employed for the prediction of flow discharge hydrographs at sites receiving significant lateral inflow. The linear model is based on a rating curve and permits a quick estimation of flow at a downstream site. The non-linear model is based on a multilayer feed-forward back propagation (FFBP) artificial neural network (ANN) and uses flow-stage data measured at the upstream and downstream stations. ANN predicted the real-time storm hydrographs satisfactorily and better than did the linear model. The results of sensitivity analysis indicated that when the lateral inflow contribution to the channel reach was insignificant, ANN, using only the flow-stage data at the upstream station, satisfactorily predicted the hydrograph at the downstream station. The prediction error of ANN increases exponentially with the difference between the peak discharge used in training and that used in testing. ANN was also employed for flood forecasting and was compared with the modified Muskingum model (MMM). For a 4-h lead time, MMM forecasts the floods reliably but could not be applied to reaches for lead times greater than the wave travel time. Although ANN and MMM had comparable performances for an 8-h lead time, ANN is capable of forecasting floods with lead times longer than the wave travel time.