StackACPred: Prediction of anticancer peptides by integrating optimized multiple feature descriptors with stacked ensemble approach

Author(s):  
Muhammad Arif ◽  
Saeed Ahmed ◽  
Fang Ge ◽  
Muhammad Kabir ◽  
Yaser Daanial Khan ◽  
...  
2019 ◽  
Vol 21 (5) ◽  
pp. 1846-1855 ◽  
Author(s):  
Bing Rao ◽  
Chen Zhou ◽  
Guoying Zhang ◽  
Ran Su ◽  
Leyi Wei

Abstract Fast and accurate identification of the peptides with anticancer activity potential from large-scale proteins is currently a challenging task. In this study, we propose a new machine learning predictor, namely, ACPred-Fuse, that can automatically and accurately predict protein sequences with or without anticancer activity in peptide form. Specifically, we establish a feature representation learning model that can explore class and probabilistic information embedded in anticancer peptides (ACPs) by integrating a total of 29 different sequence-based feature descriptors. In order to make full use of various multiview information, we further fused the class and probabilistic features with handcrafted sequential features and then optimized the representation ability of the multiview features, which are ultimately used as input for training our prediction model. By comparing the multiview features and existing feature descriptors, we demonstrate that the fused multiview features have more discriminative ability to capture the characteristics of ACPs. In addition, the information from different views is complementary for the performance improvement. Finally, our benchmarking comparison results showed that the proposed ACPred-Fuse is more precise and promising in the identification of ACPs than existing predictors. To facilitate the use of the proposed predictor, we built a web server, which is now freely available via http://server.malab.cn/ACPred-Fuse.


2018 ◽  
Vol 10 (03) ◽  
pp. 3864-3879
Author(s):  
Sunil Swamilingappa Harakannanavar ◽  
Prashanth Chikkanayakanahalli Renukamurthy ◽  
Sapna Patil ◽  
Kori Basava Raja

2009 ◽  
Vol 03 (02) ◽  
pp. 183-208 ◽  
Author(s):  
CARLOS N. SILLA ◽  
ALESSANDRO L. KOERICH ◽  
CELSO A. A. KAESTNER

In this paper we present an analysis of the suitability of four different feature sets which are currently employed to represent music signals in the context of the automatic music genre classification. To such an aim, feature selection is carried out through genetic algorithms, and it is applied to multiple feature vectors generated from different segments of the music signal. The feature sets used in this paper, which encompass time-domain and frequency-domain characteristics of the music signal, comprise: short-time Fourier transform, Mel frequency cepstral coefficient, beat-related features, pitch-related features, inter-onset interval histogram coefficients, rhythm histograms and statistical spectrum descriptors. The classification is based on the use of multiple feature vectors and an ensemble approach, according to time and space decomposition strategies. Feature vectors are extracted from music segments from the beginning, middle and end parts of the music signal (time-decomposition). Despite music genre classification being a multi-class problem, we accomplish the task using a combination of binary classifiers, whose results are merged to produce the final music genre label (space decomposition). Experiments were carried out on two databases: the Latin Music Database, which contains 3,227 music pieces categorized into ten musical genres; the ISMIR'2004 genre contest database which contains 1,458 music pieces categorized into six popular western musical genres. The experimental results have shown that the feature sets have different importance according to the part of the music signal from where the feature vectors are extracted. Furthermore, the ensemble approach provides better results than the individual segments in most cases. For high-dimensional feature sets, the feature selection provides a compact but discriminative feature subset which has an interesting trade-off between classification accuracy and computational effort.


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