LPI-SKMSC: Predicting LncRNA-Protein Interactions with Segmented k-mer Frequencies and Multi-space Clustering.

 Long noncoding RNAs (lncRNAs) have significant regulatory roles in gene expression. Interactions with proteins are one of the ways lncRNAs play their roles. Since experiments to determine lncRNA-protein interactions (LPIs) are expensive and time-consuming, many computational methods for predicting LPIs have been proposed as alternatives. In the LPIs prediction problem, there commonly exists the imbalance in the distribution of positive and negative samples. However, there are few existing methods that give specific consideration to this problem. In this paper, we proposed a new clustering-based LPIs prediction method using segmented k-mer frequencies and multi-space clustering (LPI-SKMSC). It was dedicated to handling the imbalance of positive and negative samples. We constructed segmented k-mer frequencies to obtain global and local features of lncRNA and protein sequences. Then, the multi-space clustering was applied to LPI-SKMSC. The convolutional neural network (CNN)-based encoders were used to map different features of a sample to different spaces. It used multiple spaces to jointly constrain the classification of samples. Finally, the distances between the output features of the encoder and the cluster center in each space were calculated. The sum of distances in all spaces was compared with the cluster radius to predict the LPIs. We performed cross-validation on 3 public datasets and LPI-SKMSC showed the best performance compared to other existing methods. Experimental results showed that LPI-SKMSC could predict LPIs more effectively when faced with imbalanced positive and negative samples. In addition, we illustrated that our model was better at uncovering potential lncRNA-protein interaction pairs.

3D shape reconstruction with a multiple-constraint estimation approach.

In this study, a multiple-constraint estimation algorithm is presented to estimate the 3D shape of a 2D image sequence. Given the training data, a sparse representation model with an elastic net, i.e., l1-norm and l2-norm constraints, is devised to extract the shape bases. In the sparse model, the l1-norm and l2-norm constraints are enforced to regulate the sparsity and scale of coefficients, respectively. After obtaining the shape bases, a penalized least-square model is formulated to estimate 3D shape and motion, by considering the orthogonal constraint of the transformation matrix, and the similarity constraint between the 2D observations and the shape bases. Moreover, an Augmented Lagrange Multipliers (ALM) iterative algorithm is adopted to solve the optimization of the proposed approach. Experimental results on the well-known CMU image sequences demonstrate the effectiveness and feasibility of the proposed model.

CRBP-HFEF: Prediction of RBP-Binding Sites on circRNAs Based on Hierarchical Feature Expansion and Fusion.

Circular RNAs (circRNAs) participate in the regulation of biological processes by binding to specific proteins and thus influence transcriptional processes. In recent years, circRNAs have become an emerging hotspot in RNA research. Due to powerful learning ability, the various deep learning frameworks have been used to predict the binding sites of RNA-binding protein (RPB) on circRNAs. These methods usually perform only single-level feature extraction of sequence information. However, the feature acquisition may be inadequate for single-level extraction. Generally, the features of deep and shallow layers of neural network can complement each other and are both important for binding site prediction tasks. Based on this concept, we propose a method that combines deep and shallow features, namely CRBP-HFEF. Specifically, features are first extracted and expanded for different levels of network. Then, the expanded deep and shallow features are fused and fed into the classification network, which finally determines whether they are binding sites. Compared to several existing methods, the experimental results on multiple datasets show that the proposed method achieves significant improvements in a number of metrics (with an average AUC of 0.9855). Moreover, much sufficient ablation experiments are also performed to verify the effectiveness of the hierarchical feature expansion strategy.

PmliHFM: Predicting Plant miRNA-lncRNA Interactions with Hybrid Feature Mining Network.

Due to the crucial role of interactions between microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) in biological processes, the study of their biological functions is necessary. So far, the various computational methods have been employed to make predictions of the miRNA-lncRNA interaction, which compensate for the inadequacy of biological experiments. However, the existing methods do not consider the differences between miRNA and lncRNA in feature extraction. In this paper, we propose a hybrid feature mining network, named PmliHFM, for predicting plant miRNA-lncRNA interactions. Firstly, miRNA and lncRNA with different sequence lengths are encoded by different encodings, which can reduce the loss of information caused by using the same coding approach. Then, a hybrid feature mining network is designed to adapt to different encoding methods and extract more useful feature information than a single network. Finally, an ensemble module is utilized to integrate the training results of the hybrid feature mining network, while a prediction module is employed to determine whether there are interactions. By testing on multiple test sets, PmliHFM outperforms several state-of-the-art approaches. The results show that the AUC of PmliHFM achieves 0.8[Formula: see text], 3.1[Formula: see text] and 0.4[Formula: see text] improvement respectively on three balanced datasets, and achieves 2.1[Formula: see text] and 1.8[Formula: see text] improvement respectively on two imbalanced datasets. These experiments demonstrate the feasibility of the proposed method.

iDHS-FFLG: Identifying DNase I Hypersensitive Sites by Feature Fusion and Local-Global Feature Extraction Network.

The DNase I hypersensitive sites (DHSs) are active regions on chromatin that have been found to be highly sensitive to DNase I. These regions contain various cis-regulatory elements, including promoters, enhancers and silencers. Accurate identification of DHSs helps researchers better understand the transcriptional machinery of DNA and deepen the knowledge of functional DNA elements in non-coding sequences. Researchers have developed many methods based on traditional experiments and machine learning to identify DHSs. However, low prediction accuracy and robustness limit their application in genetics research. In this paper, a novel computational approach based on deep learning is proposed by feature fusion and local-global feature extraction network to identify DHSs in mouse, named iDHS-FFLG. First of all, multiple binary features of nucleotides are fused to better express sequence information. Then, a network consisting of the convolutional neural network (CNN), bidirectional long short-term memory (BiLSTM) and self-attention mechanism is designed to extract local features and global contextual associations. In the end, the prediction module is applied to distinguish between DHSs and non-DHSs. The results of several experiments demonstrate the superior performances of iDHS-FFLG compared to the latest methods.

Does Adoption of Honeybee Pollination Promote the Economic Value of Kiwifruit Farmers? Evidence from China.

Honeybee pollination plays a significant role in sustaining the balance and biodiversity of sustainable rural development, agricultural production, and environments. However, little research has been carried out on the agricultural and economic benefits of pollination, especially for small farmers. This study investigated the adoption of honeybee pollination and its impact on farmers' economic value using primary data from 186 kiwifruit farmers in three major producing districts, such as Pujiang, Cangxi, and Dujiangyan, in the Sichuan province of China. This study was conducted in two different steps: first, we used a bivariate probit model to estimate factors influencing honeybee pollination and artificial pollination adoption; second, we further used the Dynamic Research Assessment Management (DREAM) approach to analyze the influence of the adopted honeybee pollination economic impact. The results showed that: (1) growers with higher social capital, proxied by political affiliation, are more aware of quality-oriented products, and older growers tend to choose less labor-intensive pollination technology; (2) with the increase in labor costs, more kiwifruit growers would choose honeybee pollination, and more educated growers, measured by the number of training certificates, are more likely to adopt honeybee pollination; (3) the lack of awareness and access to commercial pollinating swarms hinders the adoption of honeybee pollination; (4) in addition to the economic benefit to producers, honey pollination also brings an even larger consumer surplus. This study suggests some policy recommendations for promoting bee pollination in China: raising farmers' awareness and understanding of bee pollination through training, promoting supply and demand in the pollination market, and optimizing the external environment through product standardization and certification.

MGF6mARice: prediction of DNA N6-methyladenine sites in rice by exploiting molecular graph feature and residual block.

DNA N6-methyladenine (6mA) is produced by the N6 position of the adenine being methylated, which occurs at the molecular level, and is involved in numerous vital biological processes in the rice genome. Given the shortcomings of biological experiments, researchers have developed many computational methods to predict 6mA sites and achieved good performance. However, the existing methods do not consider the occurrence mechanism of 6mA to extract features from the molecular structure. In this paper, a novel deep learning method is proposed by devising DNA molecular graph feature and residual block structure for 6mA sites prediction in rice, named MGF6mARice. Firstly, the DNA sequence is changed into a simplified molecular input line entry system (SMILES) format, which reflects chemical molecular structure. Secondly, for the molecular structure data, we construct the DNA molecular graph feature based on the principle of graph convolutional network. Then, the residual block is designed to extract higher level, distinguishable features from molecular graph features. Finally, the prediction module is used to obtain the result of whether it is a 6mA site. By means of 10-fold cross-validation, MGF6mARice outperforms the state-of-the-art approaches. Multiple experiments have shown that the molecular graph feature and residual block can promote the performance of MGF6mARice in 6mA prediction. To the best of our knowledge, it is the first time to derive a feature of DNA sequence by considering the chemical molecular structure. We hope that MGF6mARice will be helpful for researchers to analyze 6mA sites in rice.

Resource frontiers and agglomeration economies: The varied logics of transnational land-based investing in Southern and Eastern Africa.

Actor-level data on large-scale commercial agriculture in Sub-Saharan Africa are scarce. The peculiar choice of transnational investing in African land has, therefore, been subject to conjecture. Addressing this gap, we reconstructed the underlying logics of investment location choices in a Bayesian network, using firm- and actor-level interview and spatial data from 37 transnational agriculture and forestry investments across 121 sites in Mozambique, Zambia, Tanzania, and Ethiopia. We distinguish four investment locations across gradients of resource frontiers and agglomeration economies to derive the preferred locations of different investors with varied skillsets and market reach (i.e., track record). In contrast to newcomers, investors with extensive track records are more likely to expand the land use frontier, but they are also likely to survive the high transaction costs of the pre-commercial frontier. We highlight key comparative advantages of Southern and Eastern African frontiers and map the most probable categories of investment locations.

Managing nitrogen to restore water quality in China.

The nitrogen cycle has been radically changed by human activities1. China consumes nearly one third of the world's nitrogen fertilizers. The excessive application of fertilizers2,3 and increased nitrogen discharge from livestock, domestic and industrial sources have resulted in pervasive water pollution. Quantifying a nitrogen 'boundary'4 in heterogeneous environments is important for the effective management of local water quality. Here we use a combination of water-quality observations and simulated nitrogen discharge from agricultural and other sources to estimate spatial patterns of nitrogen discharge into water bodies across China from 1955 to 2014. We find that the critical surface-water quality standard (1.0 milligrams of nitrogen per litre) was being exceeded in most provinces by the mid-1980s, and that current rates of anthropogenic nitrogen discharge (14.5 ± 3.1 megatonnes of nitrogen per year) to fresh water are about 2.7 times the estimated 'safe' nitrogen discharge threshold (5.2 ± 0.7 megatonnes of nitrogen per year). Current efforts to reduce pollution through wastewater treatment and by improving cropland nitrogen management can partially remedy this situation. Domestic wastewater treatment has helped to reduce net discharge by 0.7 ± 0.1 megatonnes in 2014, but at high monetary and energy costs. Improved cropland nitrogen management could remove another 2.3 ± 0.3 megatonnes of nitrogen per year-about 25 per cent of the excess discharge to fresh water. Successfully restoring a clean water environment in China will further require transformational changes to boost the national nutrient recycling rate from its current average of 36 per cent to about 87 per cent, which is a level typical of traditional Chinese agriculture. Although ambitious, such a high level of nitrogen recycling is technologically achievable at an estimated capital cost of approximately 100 billion US dollars and operating costs of 18-29 billion US dollars per year, and could provide co-benefits such as recycled wastewater for crop irrigation and improved environmental quality and ecosystem services.

China's Land-Use Changes during the Past 300 Years: A Historical Perspective.

Understanding the processes of historical land-use change is crucial to the research of global environmental sustainability. Here we examine and attempt to disentangle the evolutionary interactions between land-use change and its underlying causes through a historical lens. We compiled and synthesized historical land-use change and various biophysical, political, socioeconomic, and technical datasets, from the Qing dynasty to modern China. The analysis reveals a clear transition period between the 1950s and the 1980s. Before the 1950s, cropland expanded while forested land diminished, which was also accompanied by increasing population; after the 1980s land-use change exhibited new characteristics: changes in cropland, and decoupling of forest from population as a result of agricultural intensification and globalization. Chinese political policies also played an important and complex role, especially during the 1950s-1980s transition periods. Overall, climate change plays an indirect but fundamental role in the dynamics of land use via a series of various cascading effects such as shrinking agricultural production proceeding to population collapse and outbreaks of war. The expected continuation of agricultural intensification this century should be able to support increasing domestic demand for richer diets, but may not be compatible with long-term environmental sustainability.

An Effective Approach for NRSFM of Small-Size Image Sequences.

In recent years, non-rigid structure from motion (NRSFM) has become one of the hottest issues in computer vision due to its wide applications. In practice, the number of available high-quality images may be limited in many cases. Under such a condition, the performances may not be satisfactory when existing NRSFM algorithms are applied directly to estimate the 3D coordinates of a small-size image sequence. In this paper, a sub-sequence-based integrated algorithm is proposed to deal with the NRSFM problem with small sequence sizes. In the proposed method, sub-sequences are first extracted from the original sequence. In order to obtain diversified estimations, multiple weaker estimators are constructed by applying the extracted sub-sequences to a recent NRSFM algorithm with a rotation-invariant kernel (RIK). Compared to other first-order statistics, the trimmed mean is a relatively robust statistic. Considering the fact that the estimations of some weaker estimators may have large errors, the trimmed means of the outputs for all the weaker estimators are computed to determine the final estimated 3D shapes. Compared to some existing methods, the proposed algorithm can achieve a higher estimation accuracy, and has better robustness. Experimental results on several widely used image sequences demonstrate the effectiveness and feasibility of the proposed algorithm.

Gene differential coexpression analysis based on biweight correlation and maximum clique.

Differential coexpression analysis usually requires the definition of 'distance' or 'similarity' between measured datasets. Until now, the most common choice is Pearson correlation coefficient. However, Pearson correlation coefficient is sensitive to outliers. Biweight midcorrelation is considered to be a good alternative to Pearson correlation since it is more robust to outliers. In this paper, we introduce to use Biweight Midcorrelation to measure 'similarity' between gene expression profiles, and provide a new approach for gene differential coexpression analysis. Firstly, we calculate the biweight midcorrelation coefficients between all gene pairs. Then, we filter out non-informative correlation pairs using the 'half-thresholding' strategy and calculate the differential coexpression value of gene, The experimental results on simulated data show that the new approach performed better than three previously published differential coexpression analysis (DCEA) methods. Moreover, we use the maximum clique analysis to gene subset included genes identified by our approach and previously reported T2D-related genes, many additional discoveries can be found through our method.

Low-rank and eigenface based sparse representation for face recognition.

In this paper, based on low-rank representation and eigenface extraction, we present an improvement to the well known Sparse Representation based Classification (SRC). Firstly, the low-rank images of the face images of each individual in training subset are extracted by the Robust Principal Component Analysis (Robust PCA) to alleviate the influence of noises (e.g., illumination difference and occlusions). Secondly, Singular Value Decomposition (SVD) is applied to extract the eigenfaces from these low-rank and approximate images. Finally, we utilize these eigenfaces to construct a compact and discriminative dictionary for sparse representation. We evaluate our method on five popular databases. Experimental results demonstrate the effectiveness and robustness of our method.

Microarray data classification using the spectral-feature-based TLS ensemble algorithm.

The reliable and accurate identification of cancer categories is crucial to a successful diagnosis and a proper treatment of the disease. In most existing work, samples of gene expression data are treated as one-dimensional signals, and are analyzed by means of some statistical signal processing techniques or intelligent computation algorithms. In this paper, from an image-processing viewpoint, a spectral-feature-based Tikhonov-regularized least-squares (TLS) ensemble algorithm is proposed for cancer classification using gene expression data. In the TLS model, a test sample is represented as a linear combination of the atoms of a dictionary. Two types of dictionaries, namely singular value decomposition (SVD)-based eigenassays and independent component analysis (ICA)-based eigenassays, are proposed for the TLS model, and both are extracted via a two-stage approach. The proposed algorithm is inspired by our finding that, among these eigenassays, the categories of some of the testing samples can be assigned correctly by using the TLS models formed from some of the spectral features, but not for those formed from the original samples only. In order to retain the positive characteristics of these spectral features in making correct category assignments, a strategy of classifier committee learning (CCL) is designed to combine the results obtained from the different spectral features. Experimental results on standard databases demonstrate the feasibility and effectiveness of the proposed method.

Face recognition with multi-resolution spectral feature images.

The one-sample-per-person problem has become an active research topic for face recognition in recent years because of its challenges and significance for real-world applications. However, achieving relatively higher recognition accuracy is still a difficult problem due to, usually, too few training samples being available and variations of illumination and expression. To alleviate the negative effects caused by these unfavorable factors, in this paper we propose a more accurate spectral feature image-based 2DLDA (two-dimensional linear discriminant analysis) ensemble algorithm for face recognition, with one sample image per person. In our algorithm, multi-resolution spectral feature images are constructed to represent the face images; this can greatly enlarge the training set. The proposed method is inspired by our finding that, among these spectral feature images, features extracted from some orientations and scales using 2DLDA are not sensitive to variations of illumination and expression. In order to maintain the positive characteristics of these filters and to make correct category assignments, the strategy of classifier committee learning (CCL) is designed to combine the results obtained from different spectral feature images. Using the above strategies, the negative effects caused by those unfavorable factors can be alleviated efficiently in face recognition. Experimental results on the standard databases demonstrate the feasibility and efficiency of the proposed method.

Depth estimation of face images using the nonlinear least-squares model.

In this paper, we propose an efficient algorithm to reconstruct the 3D structure of a human face from one or more of its 2D images with different poses. In our algorithm, the nonlinear least-squares model is first employed to estimate the depth values of facial feature points and the pose of the 2D face image concerned by means of the similarity transform. Furthermore, different optimization schemes are presented with regard to the accuracy levels and the training time required. Our algorithm also embeds the symmetrical property of the human face into the optimization procedure, in order to alleviate the sensitivities arising from changes in pose. In addition, the regularization term, based on linear correlation, is added in the objective function to improve the estimation accuracy of the 3D structure. Further, a model-integration method is proposed to improve the depth-estimation accuracy when multiple nonfrontal-view face images are available. Experimental results on the 2D and 3D databases demonstrate the feasibility and efficiency of the proposed methods.

A neuro-fuzzy inference system through integration of fuzzy logic and extreme learning machines.

This paper investigates the feasibility of applying a relatively novel neural network technique, i.e., extreme learning machine (ELM), to realize a neuro-fuzzy Takagi-Sugeno-Kang (TSK) fuzzy inference system. The proposed method is an improved version of the regular neuro-fuzzy TSK fuzzy inference system. For the proposed method, first, the data that are processed are grouped by the k-means clustering method. The membership of arbitrary input for each fuzzy rule is then derived through an ELM, followed by a normalization method. At the same time, the consequent part of the fuzzy rules is obtained by multiple ELMs. At last, the approximate prediction value is determined by a weight computation scheme. For the ELM-based TSK fuzzy inference system, two extensions are also proposed to improve its accuracy. The proposed methods can avoid the curse of dimensionality that is encountered in backpropagation and hybrid adaptive neuro-fuzzy inference system (ANFIS) methods. Moreover, the proposed methods have a competitive performance in training time and accuracy compared to three ANFIS methods.

MISEP method for postnonlinear blind source separation.

In this letter, a standard postnonlinear blind source separation algorithm is proposed, based on the MISEP method, which is widely used in linear and nonlinear independent component analysis. To best suit a wide class of postnonlinear mixtures, we adapt the MISEP method to incorporate a priori information of the mixtures. In particular, a group of three-layered perceptrons and a linear network are used as the unmixing system to separate sources in the postnonlinear mixtures, and another group of three-layered perceptron is used as the auxiliary network. The learning algorithm for the unmixing system is then obtained by maximizing the output entropy of the auxiliary network. The proposed method is applied to postnonlinear blind source separation of both simulation signals and real speech signals, and the experimental results demonstrate its effectiveness and efficiency in comparison with existing methods.