Efficient Truss Maintenance in Evolving Networks

Truss was proposed to study social network data represented by graphs. A k-truss of a graph is a cohesive subgraph, in which each edge is contained in at least k-2 triangles within the subgraph. While truss has been demonstrated as superior to model the close relationship in social networks and efficient algorithms for finding trusses have been extensively studied, very little attention has been paid to truss maintenance. However, most social networks are evolving networks. It may be infeasible to recompute trusses from scratch from time to time in order to find the up-to-date $k$-trusses in the evolving networks. In this paper, we discuss how to maintain trusses in a graph with dynamic updates. We first discuss a set of properties on maintaining trusses, then propose algorithms on maintaining trusses on edge deletions and insertions, finally, we discuss truss index maintenance. We test the proposed techniques on real datasets. The experiment results show the promise of our work

Design of an energy supply and demand forecasting system based on web crawler and a grey dynamic model

An energy supply and demand forecasting system can help decision-makers grasp more comprehensive information, make accurate decisions and even plan a carbon-neutral future when adjusting energy structure, developing alternative energy resources and so on. This paper presents a hierarchical design of an energy supply and demand forecasting system based on web crawler and a grey dynamic model called GM(1,1) which covers all the process of data collection, data analysis and data prediction. It mainly consists of three services, namely Crawler Service (CS), Algorithm Service (AS), Data Service (DS). The architecture of multiple loose coupling services makes the system flexible in more data, and more advanced prediction algorithms for future energy forecasting works. In order to make higher prediction accuracy based on GM(1,1), this paper illustrates some basic enhanced methods and their combinations with adaptable variable weights. An implementation for testing the system was applied, where the model was set up for coal, oil and natural gas separately, and the enhanced GM was better with relative error about 9.18% than original GM on validation data between 2010 and 2020. All results are available for reference on adjusting of energy structure and developing alternative energy resources.This research was funded by NSFC grant number 61972174, Guangdong Science and Technology Planning Project grant number 2020A0505100018, Guangdong Universities’ Innovation Team Project grant number 2021KCXTD015, Guangdong Key Disciplines Project grant number 2021ZDJS138, and 2021 University-level Teaching Quality Project grant number ZLGC20210203

Warburg Effects in Cancer and Normal Proliferating Cells: Two Tales of the Same Name

It has been observed that both cancer tissue cells and normal proliferating cells (NPCs) have the Warburg effect. Our goal here is to demonstrate that they do this for different reasons. To accomplish this, we have analyzed the transcriptomic data of over 7000 cancer and control tissues of 14 cancer types in TCGA and data of five NPC types in GEO. Our analyses reveal that NPCs accumulate large quantities of ATPs produced by the respiration process before starting the Warburg effect, to raise the intracellular pH from ∼6.8 to ∼7.2 and to prepare for cell division energetically. Once cell cycle starts, the cells start to rely on glycolysis for ATP generation followed by ATP hydrolysis and lactic acid release, to maintain the elevated intracellular pH as needed by cell division since together the three processes are pH neutral. The cells go back to the normal respiration-based ATP production once the cell division phase ends. In comparison, cancer cells have reached their intracellular pH at ∼7.4 from top down as multiple acid-loading transporters are up-regulated and most acid-extruding ones except for lactic acid exporters are repressed. Cancer cells use continuous glycolysis for ATP production as way to acidify the intracellular space since the lactic acid secretion is decoupled from glycolysis-based ATP generation and is pH balanced by increased expressions of acid-loading transporters. Co-expression analyses suggest that lactic acid secretion is regulated by external, non-pH related signals. Overall, our data strongly suggest that the two cell types have the Warburg effect for very different reasons

PUEPro : A Computational Pipeline for Prediction of Urine Excretory Proteins

This work is supported by the National Natural Science Foundation of China (Grant Nos. 81320108025, 61402194, 61572227), Development Project of Jilin Province of China (20140101180JC) and China Postdoctoral Science Foundation (2014T70291).Postprin

Efficient Empirical Likelihood Inference for recovery rate of COVID-19 under Double-Censoring

Doubly censored data are very common in epidemiology studies. Ignoring censorship in the analysis may lead to biased parameter estimation. In this paper, we highlight that the publicly available COVID19 data may involve high percentage of double-censoring and point out the importance of dealing with such missing information in order to achieve better forecasting results. Existing statistical methods for doubly censored data may suffer from the convergence problems of the EM algorithms or may not be good enough for small sample sizes. This paper develops a new empirical likelihood method to analyse the recovery rate of COVID19 based on a doubly censored dataset. The efficient influence function of the parameter of interest is used to define the empirical likelihood (EL) ratio. We prove that $-2\log$(EL-ratio) asymptotically follows a standard $\chi^2$ distribution. This new method does not require any scale parameter adjustment for the log-likelihood ratio and thus does not suffer from the convergence problems involved in traditional EM-type algorithms. Finite sample simulation results show that this method provides much less biased estimate than existing methods, when censoring percentage is large. The method application to the COVID19 data will help researchers in other field to achieve better estimates and forecasting results

An ant colony optimization method for generalized TSP problem

Focused on a variation of the euclidean traveling salesman problem (TSP), namely, the generalized traveling salesman problem (GTSP), this paper extends the ant colony optimization method from TSP to this field. By considering the group influence, an improved method is further improved. To avoid locking into local minima, a mutation process and a local searching technique are also introduced into this method. Numerical results show that the proposed method can deal with the GTSP problems fairly well, and the developed mutation process and local search technique are effective

The chemical composition of a mild barium star HD202109

We present the result of chemical abundances of a mild barium star HD202109 (zeta Cyg) determined from the analysis of spectrum obtained by using a 2-m telescope at the Peak Terskol Observatory and a high-resolution spectrometer with R=80,000, signal to noise ratio >100. We also present the atmospheric parameters of the star determined by using various methods including iron-line abundance analysis. For line identifications, we use whole-range synthetic spectra computed by using the Kurucz database and the latest lists of spectral lines. Among the determined abundances of 51 elements, those of P, S, K, Cu, Zn, Ge, Rb, Sr, Nb, Mo, Ru, Rh, Pd, In, Sm, Gd, Tb, Dy, Er, Tm, Hf, Os, Ir, Pt, Tl, and Pb have not been previously known. Under the assumption that the overabundance pattern of Ba stars is due to wind-accretion process, adding information of more element abundances enables one to show that the heavy element overabundances of HD202109 can be explained with the wind accretion scenario model.Comment: 10 pages, Accepted by Astronomy and Astrophysic

Multilayer perceptron network optimization for chaotic time series modeling

Chaotic time series are widely present in practice, but due to their characteristics—such as internal randomness, nonlinearity, and long-term unpredictability—it is difficult to achieve high-precision intermediate or long-term predictions. Multi-layer perceptron (MLP) networks are an effective tool for chaotic time series modeling. Focusing on chaotic time series modeling, this paper presents a generalized degree of freedom approximation method of MLP. We then obtain its Akachi information criterion, which is designed as the loss function for training, hence developing an overall framework for chaotic time series analysis, including phase space reconstruction, model training, and model selection. To verify the effectiveness of the proposed method, it is applied to two artificial chaotic time series and two real-world chaotic time series. The numerical results show that the proposed optimized method is effective to obtain the best model from a group of candidates. Moreover, the optimized models perform very well in multi-step prediction tasks.This research was funded in part by the NSFC grant numbers 61972174 and 62272192, the Science-Technology Development Plan Project of Jilin Province grant number 20210201080GX, the Jilin Province Development and Reform Commission grant number 2021C044-1, the Guangdong Universities’ Innovation Team grant number 2021KCXTD015, and Key Disciplines Projects grant number 2021ZDJS138

An entropy-based improved k-top scoring pairs (TSP) method for classifying human cancers

Classification and prediction of different cancers based on gene-expression profiles are important for cancer diagnosis, cancer treatment and medication discovery. However, most data in the gene expression profile are not able to make a contribution to cancer classification and prediction. Hence, it is important to find the key genes that are relevant. An entropy-based improved k-top scoring pairs (TSP) (Ik-TSP) method was presented in this study for the classification and prediction of human cancers based on gene-expression data. We compared Ik-TSP classifiers with 5 different machine learning methods and the k-TSP method based on 3 different feature selection methods on 9 binary class gene expression datasets and 10 multi-class gene expression datasets involving human cancers. Experimental results showed that the Ik-TSP method had higher accuracy. The experimental results also showed that the proposed method can effectively find genes that are important for distinguishing different cancer and cancer subtype.Key words: Cancer classification, gene expression, k-TSP, information entropy, gene selection

Clustering Single-cell RNA-sequencing Data based on Matching Clusters Structures

Single-cell sequencing technology can generate RNA-sequencing data at the single cell level, and one important single-cell RNA-sequencing data analysis method is to identify their cell types without supervised information. Clustering is an unsupervised approach that can help find new insights into biology especially for exploring the biological functions of specific cell type. However, it is challenging for traditional clustering methods to obtain high-quality cell type recognition results. In this research, we propose a novel Clustering method based on Matching Clusters Structures (MCSC) for identifying cell types among single-cell RNA-sequencing data. Firstly, MCSC obtains two different groups of clustering results from the same K-means algorithm because its initial centroids are randomly selected. Then, for one group, MCSC uses shared nearest neighbour information to calculate a label transition matrix, which denotes label transition probability between any two initial clusters. Each initial cluster may be reassigned if merging results after label transition satisfy a consensus function that maximizes structural matching degree of two different groups of clustering results. In essence, the MCSC may be interpreted as a label training process. We evaluate the proposed MCSC with five commonly used datasets and compare MCSC with several classical and state-of-the-art algorithms. The experimental results show that MCSC outperform other algorithms