Search

Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary tree-child networks is one of the most studied ones. However, very little is known about the combinatorial structure of these networks. In this paper we address the problem of generating all possible binary tree-child (BTC) networks with a given number of leaves in an efficient way via reduction/augmentation operations that extend and generalize analogous operations for phylogenetic trees, and are biologically relevant. Since our solution is recursive, this also provides us with a recurrence relation giving an upper bound on the number of such networks. We also show how the operations introduced in this paper can be employed to extend the evolutive history of a set of sequences, represented by a BTC network, to include a new sequence. An implementation in python of the algorithms described in this paper, along with some computational experiments, can be downloaded from . [ABSTRACT FROM AUTHOR]

Since 1997 a considerable effort has been spent on the study of the swap (switch) Markov chains on graphic degree sequences. All of these results assume some kind of regularity in the corresponding degree sequences. Recently, Greenhill and Sfragara published a breakthrough paper about irregular normal and directed degree sequences for which rapid mixing of the swap Markov chain is proved. In this paper we present two groups of results. An example from the first group is the following theorem: let be a directed degree sequence on n vertices. Denote by Δ the maximum value among all in- and out-degrees and denote by the number of edges in the realization. Assume furthermore that . Then the swap Markov chain on the realizations of is rapidly mixing. This result is a slight improvement on one of the results of Greenhill and Sfragara. An example from the second group is the following: let d be a bipartite degree sequence on the vertex set U ⊎ V, and let 0 < c1 ≤ c2 < |U| and 0 < d1 ≤ d2 < |V| be integers, where c1 ≤ d(v) ≤ c2: ∀v ∈ V and d1 ≤ d(u) ≤ d2: ∀u ∈ U. Furthermore assume that (c2 − c1 − 1)(d2 − d1 − 1) < max{c1(|V| − d2), d1(|U| − c2)}. Then the swap Markov chain on the realizations of d is rapidly mixing. A straightforward application of this latter result shows that when a random bipartite or directed graph is generated under the Erdős—Rényi G(n, p) model with mild assumptions on n and p then the degree sequence of the generated graph has, with high probability, a rapidly mixing swap Markov chain on its realizations. [ABSTRACT FROM AUTHOR]

Due to continuous evolution of biomedical data, biomedical ontologies are becoming larger and more complex, which leads to the existence of many overlapping information. To support semantic inter-operability between ontology-based biomedical systems, it is necessary to identify the correspondences between these information, which is commonly known as biomedical ontology matching. However, it is a challenge to match biomedical ontologies, which dues to: (1) biomedical ontologies often possess tens of thousands of entities, (2) biomedical terminologies are complex and ambiguous. To efficiently match biomedical ontologies, in this paper, an interactive biomedical ontology matching approach is proposed, which utilizes the Evolutionary Algorithm (EA) to implement the automatic matching process, and gets a user involved in the evolving process to improve the matching efficiency. In particular, we propose an Evolutionary Tabu Search (ETS) algorithm, which can improve EA’s performance by introducing the tabu search algorithm as a local search strategy into the evolving process. On this basis, we further make the ETS-based ontology matching technique cooperate with the user in a reasonable amount of time to efficiently create high quality alignments, and make use of EA’s survival of the fittest to eliminate the wrong correspondences brought by erroneous user validations. The experiment is conducted on the Anatomy track and Large Biomedic track that are provided by the Ontology Alignment Evaluation Initiative (OAEI), and the experimental results show that our approach is able to efficiently exploit the user intervention to improve its non-interactive version, and the performance of our approach outperforms the state-of-the-art semi-automatic ontology matching systems. [ABSTRACT FROM AUTHOR]

We generalize the notion of λ-superstrings, presented in a previous paper, to the notion of weighted λ-superstrings. This generalization entails an important improvement in the applications to vaccine designs, as it allows epitopes to be weighted by their immunogenicities. Motivated by these potential applications of constructing short weighted λ-superstrings to vaccine design, we approach this problem in two ways. First, we formalize the problem as a combinatorial optimization problem (in fact, as two polynomially equivalent problems) and develop an integer programming (IP) formulation for solving it optimally. Second, we describe a model that also takes into account good pairwise alignments of the obtained superstring with the input strings, and present a genetic algorithm that solves the problem approximately. We apply both algorithms to a set of 169 strings corresponding to the Nef protein taken from patiens infected with HIV-1. In the IP-based algorithm, we take the epitopes and the estimation of the immunogenicities from databases of experimental epitopes. In the genetic algorithm we take as candidate epitopes all 9-mers present in the 169 strings and estimate their immunogenicities using a public bioinformatics tool. Finally, we used several bioinformatic tools to evaluate the properties of the candidates generated by our method, which indicated that we can score high immunogenic λ-superstrings that at the same time present similar conformations to the Nef virus proteins. [ABSTRACT FROM AUTHOR]

This paper presents a lightweight synthesis algorithm, named adaptive region segmentation based piecewise linear (ARSPL) algorithm, for reconstructing standard 12-lead electrocardiogram (ECG) signals from a 3-lead subset (I, II and V2). Such a lightweight algorithm is particularly suitable for healthcare mobile devices with limited resources for computing, communication and data storage. After detection of R-peaks, the ECGs are segmented by cardiac cycles. Each cycle is further divided into four regions according to different cardiac electrical activity stages. A personalized linear regression algorithm is then applied to these regions respectively for improved ECG synthesis. The proposed ARSPL method has been tested on 39 subjects randomly selected from the PTB diagnostic ECG database and achieved accurate synthesis of remaining leads with an average correlation coefficient of 0.947, an average root-mean-square error of 55.4μV, and an average runtime performance of 114ms. Overall, these results are significantly better than those of the common linear regression method, the back propagation (BP) neural network and the BP optimized using the genetic algorithm. We have also used the reconstructed ECG signals to evaluate the denivelation of ST segment, which is a potential symptom of intrinsic myocardial disease. After ARSPL, only 10.71% of the synthesized ECG cycles are with a ST-level synthesis error larger than 0.1mV, which is also better than those of the three above-mentioned methods. [ABSTRACT FROM AUTHOR]

To predict what products customers will buy in next transaction is an important task. Existing work in next-basket prediction can be summarized into two paradigms. One is the item-centric paradigm, where sequential patterns are mined from customers’ transactional data and leveraged for prediction. However, these approaches usually suffer from the data sparseness problem. The other is the user-centric paradigm, where collaborative filtering techniques have been applied on customers’ historical data. However, these methods ignore the sequential behaviors of customers which is often crucial for next-basket prediction. In this paper, we introduce a hybrid method, namely the Co-Factorization model over Sequential and Historical purchase data (CFSH for short) for next-basket recommendation. Compared with existing methods, our approach conveys the following merits: 1) By mining global sequential patterns, we can avoid the sparseness problem in traditional item-centric methods; 2) By factorizing product-product and customer-product matrices simultaneously, we can fully exploit both sequential and historical behaviors to learn customer and product representations better; 3) By using a hybrid recommendation method, we can achieve better performance in next-basket prediction. Experimental results on three real-world purchase datasets demonstrated the effectiveness of our approach as compared with the state-of-the-art methods. [ABSTRACT FROM AUTHOR]

Web service has become irreplaceable for service-oriented application in both academia and industry in recent years. Quality of Service (QoS) is used to describe the nonfunctional characteristics of Web service. Identifying Web service QoS is crucial for service-oriented application designers because service users may obtain very different QoS performance of the same service in the client-side due to dynamic changes of Internet environment as well as user context. However, evaluating QoS performance of a large scale of Web services requires considerable time and resources in real-world. Existing methods can make a personalized prediction for average QoS values by employing historical data but fail to take into consideration the fluctuation feature of Web service QoS values. To address this issue, this paper proposes a novel method for personalized QoS prediction of dynamic Web Services. First, a novel approach is used to extract feature points of QoS sequences and dynamic time warping distance is used to compute the similarity instead of Euclidean distance. By finding the most similar QoS sequences of the target QoS sequence, the missing QoS values can be predicted without extra Web services invoking. To validate our method, we conduct a large number of experiments based on real-world Web service QoS data set. The experimental studies show that our method has higher accuracy rate compared with the existing methods. [ABSTRACT FROM AUTHOR]

As an important factor for improving recommendations, time information has been introduced to model users’ dynamic preferences in many papers. However, the sequence of users’ behaviour is rarely studied in recommender systems. Due to the users’ unique behavior evolution patterns and personalized interest transitions among items, users’ similarity in sequential dimension should be introduced to further distinguish users’ preferences and interests. In this paper, we propose a new collaborative filtering recommendation method based on users’ interest sequences (IS) that rank users’ ratings or other online behaviors according to the timestamps when they occurred. This method extracts the semantics hidden in the interest sequences by the length of users’ longest common sub-IS (LCSIS) and the count of users’ total common sub-IS (ACSIS). Then, these semantics are utilized to obtain users’ IS-based similarities and, further, to refine the similarities acquired from traditional collaborative filtering approaches. With these updated similarities, transition characteristics and dynamic evolution patterns of users’ preferences are considered. Our new proposed method was compared with state-of-the-art time-aware collaborative filtering algorithms on datasets MovieLens, Flixster and Ciao. The experimental results validate that the proposed recommendation method is effective and outperforms several existing algorithms in the accuracy of rating prediction. [ABSTRACT FROM AUTHOR]

Motion capture allows accurate recording of human motion, with applications in many fields, including entertainment, medicine, sports science and human computer interaction. A common difficulty with this technology is the occurrence of missing data, due to occlusions, or recording conditions. Various models have been proposed to estimate missing data. Some are based on interpolation, low-rank properties or inter-correlations. Others involve dataset matching or skeleton constraints. While the latter have the advantage of promoting a realistic motion estimation, they require prior knowledge of skeleton constraints, or the availability of a prerecorded dataset. In this article, we propose a probabilistic averaging method of several recovery models (referred to as Probabilistic Model Averaging (PMA) in this paper), based on the likelihoods of the distances between body points. This method has the advantage of being automatic, while allowing an efficient gap data recovery. To support and validate the proposed method, we use a set of four individual recovery models, based on linear/nonlinear regression in local coordinate systems. Finally, we propose two heuristic algorithms to enforce skeleton constraints in the reconstructed motion, which can be used on any individual recovery model. For validation purposes, random gaps were introduced into motion-capture sequences, and the effects of factors such as the number of simultaneous gaps, gap length and sequence duration were analyzed. Results show that the proposed probabilistic averaging method yields better recovery than (i) each of the four individual models and (ii) two recent state-of-the-art models, regardless of gap length, sequence duration and number of simultaneous gaps. Moreover, both of our heuristic skeleton-constraint algorithms significantly improve the recovery for 7 out of 8 tested motion-capture sequences (p < 0.05), for 10 simultaneous gaps of 5 seconds. The code is available for free download at: . [ABSTRACT FROM AUTHOR]

Both in DNA and protein contexts, an important method for modelling motifs is to utilize position weight matrix (PWM) in biological sequences. With the development of genome sequencing technology, the quantity of the sequence data is increasing explosively, so the faster searching algorithms which have the ability to meet the increasingly need are desired to develop. In this paper, we proposed a method for speeding up the searching process of candidate transcription factor binding sites (TFBS), and the users can be allowed to specify p threshold to get the desired trade-off between speed and sensitivity for a particular sequence analysis. Moreover, the proposed method can also be generalized to large-scale annotation and sequence projects. [ABSTRACT FROM AUTHOR]

The query-template alignment of proteins is one of the most critical steps of template-based modeling methods used to predict the 3D structure of a query protein. This alignment can be interpreted as a temporal classification or structured prediction task and first order Conditional Random Fields have been proposed for protein alignment and proven to be rather successful. Some other popular structured prediction problems, such as speech or image classification, have gained from the use of higher order Conditional Random Fields due to the well known higher order correlations that exist between their labels and features. In this paper, we propose and describe the use of higher order Conditional Random Fields for query-template protein alignment. The experiments carried out on different public datasets validate our proposal, especially on distantly-related protein pairs which are the most difficult to align. [ABSTRACT FROM AUTHOR]

A significant approach for the discovery of biological regulatory rules of genes, protein and their inheritance relationships is the extraction of meaningful patterns from biological sequence data. The existing algorithms of sequence pattern discovery, like MSPM and FBSB, suffice their low efficiency and accuracy. In order to deal with this issue, this paper presents a new algorithm for biological sequence pattern mining abbreviated MpBsmi based on the data index structure. The MpBsmi algorithm employs a sequence position table abbreviated ST and a sequence database index structure named DB-Index for data storing, mining and pattern expansion. The ST and DB-Index of single items are firstly obtained through scanning sequence database once. Then a new algorithm for fast support counting is developed to mine the table ST to identify the frequent single items. Based on a connection strategy, the frequent patterns are expanded and the expanded table ST is updated by scanning the DB-Index. The fast support counting algorithm is used for obtaining the frequent expansion patterns. Finally, a new pruning technique is developed for extended pattern to avoid the generation of unnecessarily large number of candidate patterns. The experiments results on multiple classical protein sequences from the Pfam database validate the performance of the proposed algorithm including the accuracy, stability and scalability. It is showed that the proposed algorithm has achieved the better space efficiency, stability and scalability comparing with MSPM, FBSB which are the two main algorithms for biological sequence mining. [ABSTRACT FROM AUTHOR]

RNA-protein binding is critical to gene regulation, controlling fundamental processes including splicing, translation, localization and stability, and aberrant RNA-protein interactions are known to play a role in a wide variety of diseases. However, molecular understanding of RNA-protein interactions remains limited; in particular, identification of RNA motifs that bind proteins has long been challenging, especially when such motifs depend on both sequence and structure. Moreover, although RNA binding proteins (RBPs) often contain more than one binding domain, algorithms capable of identifying more than one binding motif simultaneously have not been developed. In this paper we present a novel pipeline to determine binding peaks in crosslinking immunoprecipitation (CLIP) data, to discover multiple possible RNA sequence/structure motifs among them, and to experimentally validate such motifs. At the core is a new semi-automatic algorithm SARNAclust, the first unsupervised method to identify and deconvolve multiple sequence/structure motifs simultaneously. SARNAclust computes similarity between sequence/structure objects using a graph kernel, providing the ability to isolate the impact of specific features through the bulge graph formalism. Application of SARNAclust to synthetic data shows its capability of clustering 5 motifs at once with a V-measure value of over 0.95, while GraphClust achieves only a V-measure of 0.083 and RNAcontext cannot detect any of the motifs. When applied to existing eCLIP sets, SARNAclust finds known motifs for SLBP and HNRNPC and novel motifs for several other RBPs such as AGGF1, AKAP8L and ILF3. We demonstrate an experimental validation protocol, a targeted Bind-n-Seq-like high-throughput sequencing approach that relies on RNA inverse folding for oligo pool design, that can validate the components within the SLBP motif. Finally, we use this protocol to experimentally interrogate the SARNAclust motif predictions for protein ILF3. Our results support a newly identified partially double-stranded UUUUUGAGA motif similar to that known for the splicing factor HNRNPC. [ABSTRACT FROM AUTHOR]

In this paper, we propose a connectivity-preserving flocking algorithm for multi-agent systems in which the neighbor set of each agent is determined by the hybrid metric-topological distance so that the interaction topology can be represented as the range-limited Delaunay graph, which combines the properties of the commonly used disk graph and Delaunay graph. As a result, the proposed flocking algorithm has the following advantages over the existing ones. First, range-limited Delaunay graph is sparser than the disk graph so that the information exchange among agents is reduced significantly. Second, some links irrelevant to the connectivity can be dynamically deleted during the evolution of the system. Thus, the proposed flocking algorithm is more flexible than existing algorithms, where links are not allowed to be disconnected once they are created. Finally, the multi-agent system spontaneously generates a regular quasi-lattice formation without imposing the constraint on the ratio of the sensing range of the agent to the desired distance between two adjacent agents. With the interaction topology induced by the hybrid distance, the proposed flocking algorithm can still be implemented in a distributed manner. We prove that the proposed flocking algorithm can steer the multi-agent system to a stable flocking motion, provided the initial interaction topology of multi-agent systems is connected and the hysteresis in link addition is smaller than a derived upper bound. The correctness and effectiveness of the proposed algorithm are verified by extensive numerical simulations, where the flocking algorithms based on the disk and Delaunay graph are compared. [ABSTRACT FROM AUTHOR]

In this paper, we introduce sequence-based multiscale modeling for biomolecular data analysis. We employ spectral clustering method in our modeling and reveal the difference between sequence-based global scale clustering and local scale clustering. Essentially, two types of distances, i.e., Euclidean (or spatial) distance and genomic (or sequential) distance, can be used in data clustering. Clusters from sequence-based global scale models optimize spatial distances, meaning spatially adjacent loci are more likely to be assigned into the same cluster. Sequence-based local scale models, on the other hand, result in clusters that optimize genomic distances. That is to say, in these models, sequentially adjoining loci tend to be cluster together. We propose two sequence-based multiscale models (SeqMMs) for the study of chromosome hierarchical structures, including genomic compartments and topological associated domains (TADs). We find that genomic compartments are determined only by global scale information in the Hi-C data. The removal of all the local interactions within a band region as large as 10 Mb in genomic distance has almost no significant influence on the final compartment results. Further, in TAD analysis, we find that when the sequential scale is small, a tiny variation of diagonal band region in a contact map will result in a great change in the predicted TAD boundaries. When the scale value is larger than a threshold value, the TAD boundaries become very consistent. This threshold value is highly related to TAD sizes. By the comparison of our results with those previously obtained using a spectral clustering model, we find that our method is more robust and reliable. Finally, we demonstrate that almost all TAD boundaries from both clustering methods are local minimum of a TAD summation function. [ABSTRACT FROM AUTHOR]

DNA-binding proteins play pivotal roles in alternative splicing, RNA editing, methylating and many other biological functions for both eukaryotic and prokaryotic proteomes. Predicting the functions of these proteins from primary amino acids sequences is becoming one of the major challenges in functional annotations of genomes. Traditional prediction methods often devote themselves to extracting physiochemical features from sequences but ignoring motif information and location information between motifs. Meanwhile, the small scale of data volumes and large noises in training data result in lower accuracy and reliability of predictions. In this paper, we propose a deep learning based method to identify DNA-binding proteins from primary sequences alone. It utilizes two stages of convolutional neutral network to detect the function domains of protein sequences, and the long short-term memory neural network to identify their long term dependencies, an binary cross entropy to evaluate the quality of the neural networks. When the proposed method is tested with a realistic DNA binding protein dataset, it achieves a prediction accuracy of 94.2% at the Matthew’s correlation coefficient of 0.961. Compared with the LibSVM on the arabidopsis and yeast datasets via independent tests, the accuracy raises by 9% and 4% respectively. Comparative experiments using different feature extraction methods show that our model performs similar accuracy with the best of others, but its values of sensitivity, specificity and AUC increase by 27.83%, 1.31% and 16.21% respectively. Those results suggest that our method is a promising tool for identifying DNA-binding proteins. [ABSTRACT FROM AUTHOR]

Approximate string matching with k-differences has a number of practical applications, ranging from pattern recognition to computational biology. This paper proposes an efficient memory-access algorithm for parallel approximate string matching with k-differences on Graphics Processing Units (GPUs). In the proposed algorithm, all threads in the same GPUs warp share data using warp-shuffle operation instead of accessing the shared memory. Moreover, we implement the proposed algorithm by exploiting the memory structure of GPUs to optimize its performance. Experiment results for real DNA packages revealed that the performance of the proposed algorithm and its implementation archived up to 122.64 and 1.53 times compared to that of sequential algorithm on CPU and previous parallel approximate string matching algorithm on GPUs, respectively. [ABSTRACT FROM AUTHOR]

High-utility sequential pattern mining (HUSPM) has become an important issue in the field of data mining. Several HUSPM algorithms have been designed to mine high-utility sequential patterns (HUPSPs). They have been applied in several real-life situations such as for consumer behavior analysis and event detection in sensor networks. Nonetheless, most studies on HUSPM have focused on mining HUPSPs in precise data. But in real-life, uncertainty is an important factor as data is collected using various types of sensors that are more or less accurate. Hence, data collected in a real-life database can be annotated with existing probabilities. This paper presents a novel pattern mining framework called high utility-probability sequential pattern mining (HUPSPM) for mining high utility-probability sequential patterns (HUPSPs) in uncertain sequence databases. A baseline algorithm with three optional pruning strategies is presented to mine HUPSPs. Moroever, to speed up the mining process, a projection mechanism is designed to create a database projection for each processed sequence, which is smaller than the original database. Thus, the number of unpromising candidates can be greatly reduced, as well as the execution time for mining HUPSPs. Substantial experiments both on real-life and synthetic datasets show that the designed algorithm performs well in terms of runtime, number of candidates, memory usage, and scalability for different minimum utility and minimum probability thresholds. [ABSTRACT FROM AUTHOR]

Double cycling is an efficient tool to increase the efficiency of quay crane (QC) in container terminals. In this paper, an optimization model for double cycling is developed to optimize the operation sequence of multiple QCs. The objective is to minimize the makespan of the ship handling operation considering the ship balance constraint. To solve the model, an algorithm based on Lagrangian relaxation is designed. Finally, we compare the efficiency of the Lagrangian relaxation based heuristic with the branch-and-bound method and a genetic algorithm using instances of different sizes. The results of numerical experiments indicate that the proposed model can effectively reduce the unloading and loading times of QCs. The effects of the ship balance constraint are more notable when the number of QCs is high. [ABSTRACT FROM AUTHOR]

Latent Semantic Analysis (LSA) is widely used for finding the documents whose semantic is similar to the query of keywords. Although LSA yield promising similar results, the existing LSA algorithms involve lots of unnecessary operations in similarity computation and candidate check during on-line query processing, which is expensive in terms of time cost and cannot efficiently response the query request especially when the dataset becomes large. In this paper, we study the efficiency problem of on-line query processing for LSA towards efficiently searching the similar documents to a given query. We rewrite the similarity equation of LSA combined with an intermediate value called partial similarity that is stored in a designed index called partial index. For reducing the searching space, we give an approximate form of similarity equation, and then develop an efficient algorithm for building partial index, which skips the partial similarities lower than a given threshold θ. Based on partial index, we develop an efficient algorithm called ILSA for supporting fast on-line query processing. The given query is transformed into a pseudo document vector, and the similarities between query and candidate documents are computed by accumulating the partial similarities obtained from the index nodes corresponds to non-zero entries in the pseudo document vector. Compared to the LSA algorithm, ILSA reduces the time cost of on-line query processing by pruning the candidate documents that are not promising and skipping the operations that make little contribution to similarity scores. Extensive experiments through comparison with LSA have been done, which demonstrate the efficiency and effectiveness of our proposed algorithm. [ABSTRACT FROM AUTHOR]

This paper presents a method for classifying the ancestry of Brazilian surnames based on historical sources. The information obtained forms the basis for applying fuzzy matching and machine learning classification algorithms to more than 46 million workers in 5 categories: Iberian, Italian, Japanese, German and East European. The vast majority (96.7%) of the single surnames were identified using a fuzzy matching and the rest using a method proposed by Cavnar and Trenkle (1994). A comparison of the results of the procedures with data on foreigners in the 1920 Census and with the geographic distribution of non-Iberian surnames underscores the accuracy of the procedure. The study shows that surname ancestry is associated with significant differences in wages and schooling. [ABSTRACT FROM AUTHOR]

This paper describes the design, acquisition process and baseline evaluation of the new e-BioSign database, which includes dynamic signature and handwriting information. Data is acquired from 5 different COTS devices: three Wacom devices (STU-500, STU-530 and DTU-1031) specifically designed to capture dynamic signatures and handwriting, and two general purpose tablets (Samsung Galaxy Note 10.1 and Samsung ATIV 7). For the two Samsung tablets, data is collected using both pen stylus and also the finger in order to study the performance of signature verification in a mobile scenario. Data was collected in two sessions for 65 subjects, and includes dynamic information of the signature, the full name and alpha numeric sequences. Skilled forgeries were also performed for signatures and full names. We also report a benchmark evaluation based on e-BioSign for person verification under three different real scenarios: 1) intra-device, 2) inter-device, and 3) mixed writing-tool. We have experimented the proposed benchmark using the main existing approaches for signature verification: feature- and time functions-based. As a result, new insights into the problem of signature biometrics in sensor-interoperable scenarios have been obtained, namely: the importance of specific methods for dealing with device interoperability, and the necessity of a deeper analysis on signatures acquired using the finger as the writing tool. This e-BioSign public database allows the research community to: 1) further analyse and develop signature verification systems in realistic scenarios, and 2) investigate towards a better understanding of the nature of the human handwriting when captured using electronic COTS devices in realistic conditions. [ABSTRACT FROM AUTHOR]

Human endogenous retroviruses (HERVs) encode active retroviral proteins, which may be involved in the progression of cancer and other diseases. Matrix protein (MA), in group-specific antigen genes (gag) of retroviruses, is associated with the virus envelope glycoproteins in most mammalian retroviruses and may be involved in virus particle assembly, transport and budding. However, the amount of annotated MAs in ERVs is still at a low level so far. No computational method to predict the exact start and end coordinates of MAs in gags has been proposed yet. In this paper, a computational method to identify MAs in ERVs is proposed. A divide and conquer technique was designed and applied to the conventional prediction model to acquire better results when dealing with gene sequences with various lengths. Initiation sites and termination sites were predicted separately and then combined according to their intervals. Three different algorithms were applied and compared: weighted support vector machine (WSVM), weighted extreme learning machine (WELM) and random forest (RF). G − mean (geometric mean of sensitivity and specificity) values of initiation sites and termination sites under 5-fold cross validation generated by random forest models are 0.9869 and 0.9755 respectively, highest among the algorithms applied. Our prediction models combine RF & WSVM algorithms to achieve the best prediction results. 98.4% of all the collected ERV sequences with complete MAs (125 in total) could be predicted exactly correct by the models. 94,671 HERV sequences from 118 families were scanned by the model, 104 new putative MAs were predicted in human chromosomes. Distributions of the putative MAs and optimizations of model parameters were also analyzed. The usage of our predicting method was also expanded to other retroviruses and satisfying results were acquired. [ABSTRACT FROM AUTHOR]

The rapid development of sequencing technology has led to an explosive accumulation of genomic sequence data. Clustering is often the first step to perform in sequence analy- sis, and hierarchical clustering is one of the most commonly used approaches for this purpose. However, it is currently computationally expensive to perform hierarchical clustering of extremely large sequence datasets due to its quadratic time and space complexities. In this paper we developed a new algorithm called ESPRIT-Forest for parallel hierarchical clustering of sequences. The algorithm achieves subquadratic time and space complexity and maintains a high clustering accuracy comparable to the standard method. The basic idea is to organize sequences into a pseudo-metric based partitioning tree for sub-linear time searching of nearest neighbors, and then use a new multiple-pair merging criterion to construct clusters in parallel using multiple threads. The new algorithm was tested on the human microbiome project (HMP) dataset, currently one of the largest published microbial 16S rRNA sequence dataset. Our experiment demonstrated that with the power of parallel computing it is now compu- tationally feasible to perform hierarchical clustering analysis of tens of millions of sequences. The software is available at . [ABSTRACT FROM AUTHOR]

As the quality of crucial entities can directly affect that of software, their identification and protection become an important premise for effective software development, management, maintenance and testing, which thus contribute to improving the software quality and its attack-defending ability. Most analysis and evaluation on important entities like codes-based static structure analysis are on the destruction of the actual software running. In this paper, from the perspective of software execution process, we proposed an approach to mine dynamic noteworthy functions (DNFM)in software execution sequences. First, according to software decompiling and tracking stack changes, the execution traces composed of a series of function addresses were acquired. Then these traces were modeled as execution sequences and then simplified so as to get simplified sequences (SFS), followed by the extraction of patterns through pattern extraction (PE) algorithm from SFS. After that, evaluating indicators inner-importance and inter-importance were designed to measure the noteworthiness of functions in DNFM algorithm. Finally, these functions were sorted by their noteworthiness. Comparison and contrast were conducted on the experiment results from two traditional complex network-based node mining methods, namely PageRank and DegreeRank. The results show that the DNFM method can mine noteworthy functions in software effectively and precisely. [ABSTRACT FROM AUTHOR]

The 3D High Efficiency Video Coding (3D-HEVC) standard aims to code 3D videos that usually contain multi-view texture videos and its corresponding depth information. It inherits the same quadtree prediction structure of HEVC to code both texture videos and depth maps. Each coding unit (CU) allows recursively splitting into four equal sub-CUs. At each CU depth level, it enables 10 types of inter modes and 35 types of intra modes in inter frames. Furthermore, the inter-view prediction tools are applied to each view in the test model of 3D-HEVC (HTM), which uses variable size disparity-compensated prediction to exploit inter-view correlation within neighbor views. It also exploits redundancies between a texture video and its associated depth using inter-component coding tools. These achieve the highest coding efficiency to code 3D videos but require a very high computational complexity. In this paper, we propose a context-adaptive based fast CU processing algorithm to jointly optimize the most complex components of HTM including CU depth level decision, mode decision, motion estimation (ME) and disparity estimation (DE) processes. It is based on the hypothesis that the optimal CU depth level, prediction mode and motion vector of a CU are correlated with those from spatiotemporal, inter-view and inter-component neighboring CUs. We analyze the video content based on coding information from neighboring CUs and early predict each CU into one of five categories i.e., DE-omitted CU, ME-DE-omitted CU, SPLIT CU, Non-SPLIT CU and normal CU, and then each type of CU adaptively adopts different processing strategies. Experimental results show that the proposed algorithm saves 70% encoder runtime on average with only a 0.1% BD-rate increase on coded views and 0.8% BD-rate increase on synthesized views. Our algorithm outperforms the state-of-the-art algorithms in terms of coding time saving or with better RD performance. [ABSTRACT FROM AUTHOR]

Data compression and encryption are key components of commonly deployed platforms such as Hadoop. Numerous data compression and encryption tools are presently available on such platforms and the tools are characteristically applied in sequence, i.e., compression followed by encryption or encryption followed by compression. This paper focuses on the open-source Hadoop framework and proposes a data storage method that efficiently couples data compression with encryption. A simultaneous compression and encryption scheme is introduced that addresses an important implementation issue of source coding based on Tent Map and Piece-wise Linear Chaotic Map (PWLM), which is the infinite precision of real numbers that result from their long products. The approach proposed here solves the implementation issue by removing fractional components that are generated by the long products of real numbers. Moreover, it incorporates a stealth key that performs a cyclic shift in PWLM without compromising compression capabilities. In addition, the proposed approach implements a masking pseudorandom keystream that enhances encryption quality. The proposed algorithm demonstrated a congruent fit within the Hadoop framework, providing robust encryption security and compression. [ABSTRACT FROM AUTHOR]

Background: Identifying conserved regions in protein sequences is a fundamental operation, occurring in numerous sequence-driven analysis pipelines. It is used as a way to decode domain-rich regions within proteins, to compute protein clusters, to annotate sequence function, and to compute evolutionary relationships among protein sequences. A number of approaches exist for identifying and characterizing protein families based on their domains, and because domains represent conserved portions of a protein sequence, the primary computation involved in protein family characterization is identification of such conserved regions. However, identifying conserved regions from large collections (millions) of protein sequences presents significant challenges. Methods: In this paper we present a new, alignment-free method for detecting conserved regions in protein sequences called NADDA (No-Alignment Domain Detection Algorithm). Our method exploits the abundance of exact matching short subsequences (k-mers) to quickly detect conserved regions, and the power of machine learning is used to improve the prediction accuracy of detection. We present a parallel implementation of NADDA using the MapReduce framework and show that our method is highly scalable. Results: We have compared NADDA with Pfam and InterPro databases. For known domains annotated by Pfam, accuracy is 83%, sensitivity 96%, and specificity 44%. For sequences with new domains not present in the training set an average accuracy of 63% is achieved when compared to Pfam. A boost in results in comparison with InterPro demonstrates the ability of NADDA to capture conserved regions beyond those present in Pfam. We have also compared NADDA with ADDA and MKDOM2, assuming Pfam as ground-truth. On average NADDA shows comparable accuracy, more balanced sensitivity and specificity, and being alignment-free, is significantly faster. Excluding the one-time cost of training, runtimes on a single processor were 49s, 10,566s, and 456s for NADDA, ADDA, and MKDOM2, respectively, for a data set comprised of approximately 2500 sequences. [ABSTRACT FROM AUTHOR]

Spatial-temporal k-anonymity has become a mainstream approach among techniques for protection of users’ privacy in location-based services (LBS) applications, and has been applied to several variants such as LBS snapshot queries and continuous queries. Analyzing large-scale spatial-temporal anonymity sets may benefit several LBS applications. In this paper, we propose two location prediction methods based on transition probability matrices constructing from sequential rules for spatial-temporal k-anonymity dataset. First, we define single-step sequential rules mined from sequential spatial-temporal k-anonymity datasets generated from continuous LBS queries for multiple users. We then construct transition probability matrices from mined single-step sequential rules, and normalize the transition probabilities in the transition matrices. Next, we regard a mobility model for an LBS requester as a stationary stochastic process and compute the n-step transition probability matrices by raising the normalized transition probability matrices to the power n. Furthermore, we propose two location prediction methods: rough prediction and accurate prediction. The former achieves the probabilities of arriving at target locations along simple paths those include only current locations, target locations and transition steps. By iteratively combining the probabilities for simple paths with n steps and the probabilities for detailed paths with n-1 steps, the latter method calculates transition probabilities for detailed paths with n steps from current locations to target locations. Finally, we conduct extensive experiments, and correctness and flexibility of our proposed algorithm have been verified. [ABSTRACT FROM AUTHOR]

We introduce a fast error-free tracking method applicable to sequences of two and three dimensional images. The core idea is to use Quadtree (resp. Octree) data structures for representing the spatial discretization of an image in two (resp. three) spatial dimensions. This representation enables one to merge into large computational cells the regions that can be faithfully described with such a coarse representation, thus significantly reducing the total number of degrees of freedom that are processed, without compromising accuracy. This encoding is particularly effective in the case of algorithms based on moving fronts, since the adaptive refinement provides a natural means to focus the processing resources on information near the moving front. In this paper, we use an existing contour based tracker and reformulate it to the case of Quad-/Oc-tree data structures. Relevant mathematical assumptions and derivations are presented for this purpose. We then demonstrate that, on standard bio-medical image sequences, a speed up of 5X is easily achieved in 2D and about 10X in 3D. [ABSTRACT FROM AUTHOR]