Time-series forecasting is an important research and application area. Much effort has been devoted over the past several decades to develop and improve the time-series forecasting models. This paper introduces a new time-series forecasting model based on the flexible neural tree (FNT). The FNT model is generated initially as a flexible multi-layer feed-forward neural network and evolved using an evolutionary procedure. Very often it is a difficult task to select the proper input variables or time-lags for constructing a time-series model. Our research demonstrates that the FNT model is capable of handing the task automatically. The performance and effectiveness of the proposed method are evaluated using time series prediction problems and compared with those of related methods.

Time-series forecasting using flexible neural tree model

DNNAce: Prediction of prokaryote lysine acetylation sites through deep neural networks with multi-information fusion

With the advent of array-based techniques to measure methylation levels in primary tumor samples, systematic investigations of methylomes have widely been performed on a large number of tumor entities. Most of these approaches are not based on measuring individual cell methylation but rather the bulk tumor sample DNA, which contains a mixture of tumor cells, infiltrating immune cells and other stromal components. This raises questions about the purity of a certain tumor sample, given the varying degrees of stromal infiltration in different entities. Previous methods to infer tumor purity require or are based on the use of matching control samples which are rarely available. Here we present a novel, reference free method to quantify tumor purity, based on two Random Forest classifiers, which were trained on ABSOLUTE as well as ESTIMATE purity values from TCGA tumor samples. We subsequently apply this method to a previously published, large dataset of brain tumors, proving that these models perform well in datasets that have not been characterized with respect to tumor purity . Using two gold standard methods to infer purity – the ABSOLUTE score based on whole genome sequencing data and the ESTIMATE score based on gene expression data- we have optimized Random Forest classifiers to predict tumor purity in entities that were contained in the TCGA project. We validated these classifiers using an independent test data set and cross-compared it to other methods which have been applied to the TCGA datasets (such as ESTIMATE and LUMP). Using Illumina methylation array data of brain tumor entities (as published in Capper et al. (Nature 555:469-474,2018)) we applied this model to estimate tumor purity and find that subgroups of brain tumors display substantial differences in tumor purity. Random forest- based tumor purity prediction is a well suited tool to extrapolate gold standard measures of purity to novel methylation array datasets. In contrast to other available methylation based tumor purity estimation methods, our classifiers do not need a priori knowledge about the tumor entity or matching control tissue to predict tumor purity.

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RF_Purify: a novel tool for comprehensive analysis of tumor-purity in methylation array data based on random forest regression

Faced with the avalanche of genomic sequences and data on messenger RNA expression, biological scientists are confronting a frightening prospect: piles of information but only flakes of knowledge. How can the thousands of sequences being determined and deposited, and the thousands of expression profiles being generated by the new array methods, be synthesized into useful knowledge? What form will this knowledge take? These are questions being addressed by scientists in the field known as ‘functional genomics’.

Protein Function in the Post-Genomic Era

DeepMal: Accurate prediction of protein malonylation sites by deep neural networks

CMSENN: Computational Modification Sites with Ensemble Neural Network

Post-translational modification plays a key role in the field of biology. Experimental identification methods are time-consuming and expensive. Therefore, computational methods to deal with such issues overcome these shortcomings and limitations. In this article, we propose a lysine acetylation site identification with polynomial tree method (LAIPT), making use of the polynomial style to demonstrate amino-acid residue relationships in peptide segments. This polynomial style was enriched by the physical and chemical properties of amino-acid residues. Then, these reconstructed features were input into the employed classification model, named the flexible neural tree. Finally, some effect evaluation measurements were employed to test the model's performance.

Bin Yang

Papers

CMSENN: Computational Modification Sites with Ensemble Neural Network

LAIPT: Lysine Acetylation Site Identification with Polynomial Tree.