Connectivity and diagnosability are important parameters in measuring the fault tolerance and reliability of interconnection networks. The Rg-vertex-connectivity of a connected graph G is the minimum cardinality of a faulty set X⊆V(G) such that G−X is disconnected and every fault-free vertex has at least g fault-free neighbors. The g-good-neighbor conditional diagnosability is defined as the maximum cardinality of a g-good-neighbor conditional faulty set that the system can guarantee to identify. The interconnection network considered here is the locally exchanged twisted cube LeTQ(s,t)⁠. For 1≤s≤t and 0≤g≤s⁠, we first determine the Rg-vertex-connectivity of LeTQ(s,t)⁠, then establish the g-good-neighbor conditional diagnosability of LeTQ(s,t) under the PMC model and MM* model, respectively.

BACKGROUND: Protein secondary structure (PSS) is critical to further predict the tertiary structure, understand protein function and design drugs. However, experimental techniques of PSS are time consuming and expensive, and thus it's very urgent to develop efficient computational approaches for predicting PSS based on sequence information alone. Moreover, the feature matrix of a protein contains two dimensions: the amino-acid residue dimension and the feature vector dimension. Existing deep learning based methods have achieved remarkable performances of PSS prediction, but the methods often utilize the features from the amino-acid dimension. Thus, there is still room to improve computational methods of PSS prediction. RESULTS: We propose a novel deep neural network method, called DeepACLSTM, to predict 8-category PSS from protein sequence features and profile features. Our method efficiently applies asymmetric convolutional neural networks (ACNNs) combined with bidirectional long short-term memory (BLSTM) neural networks to predict PSS, leveraging the feature vector dimension of the protein feature matrix. In DeepACLSTM, the ACNNs extract the complex local contexts of amino-acids; the BLSTM neural networks capture the long-distance interdependencies between amino-acids. Furthermore, the prediction module predicts the category of each amino-acid residue based on both local contexts and long-distance interdependencies. To evaluate performances of DeepACLSTM, we conduct experiments on three publicly available datasets: CB513, CASP10 and CASP12. Results indicate that the performance of our method is superior to the state-of-the-art baselines on three publicly datasets. CONCLUSIONS: Experiments demonstrate that DeepACLSTM is an efficient predication method for predicting 8-category PSS and has the ability to extract more complex sequence-structure relationships between amino-acid residues. Moreover, experiments also indicate the feature vector dimension contains the useful information for improving PSS prediction.

The tradeoff in remote sensing instruments that balances the spatial resolution and temporal frequency limits our capacity to monitor spatial and temporal dynamics effectively. The spatiotemporal data fusion technique is considered as a cost-effective way to obtain remote sensing data with both high spatial resolution and high temporal frequency, by blending observations from multiple sensors with different advantages or characteristics. In this paper, we develop the spatial and temporal nonlocal filter-based fusion model (STNLFFM) to enhance the prediction capacity and accuracy, especially for complex changed landscapes. The STNLFFM method provides a new transformation relationship between the fine-resolution reflectance images acquired from the same sensor at different dates with the help of coarse-resolution reflectance data, and makes full use of the high degree of spatiotemporal redundancy in the remote sensing image sequence to produce the final prediction. The proposed method was tested over both the Coleambally Irrigation Area study site and the Lower Gwydir Catchment study site. The results show that the proposed method can provide a more accurate and robust prediction, especially for heterogeneous landscapes and temporally dynamic areas.

BACKGROUND: Understanding the constituent domains of oncogenes, their origins and their fusions may shed new light about the initiation and the development of cancers. RESULTS: We have developed a computational pipeline for identification of functional domains of human genes, prediction of the origins of these domains and their major fusion events during evolution through integration of existing and new tools of our own. An application of the pipeline to 124 well-characterized human oncogenes has led to the identification of a collection of domains and domain pairs that occur substantially more frequently in oncogenes than in human genes on average. Most of these enriched domains and domain pairs are related to tyrosine kinase activities. In addition, our analyses indicate that a substantial portion of the domain-fusion events of oncogenes took place in metazoans during evolution. CONCLUSION: We expect that the computational pipeline for domain identification, domain origin and domain fusion prediction will prove to be useful for studying other groups of genes.

We introduce a new ensemble method based on decision tree to discover significant and diversified rules for subtype classification of childhood acute lymphoblastic leukemia, a heterogeneous disease with individual subtypes differing in their response to chemotherapy. Our approach simply uses each of top-ranked features as root node to build up different trees in the ensemble. Since these trees are all generated from original training samples, rules derived by our algorithm are true and reliable. This is a characteristic of our method contrast to state-of-the-art methods such as Bagging, Boosting and Random Forest which may produce false rules. Experimental results on a large gene expression profiling data set of childhood leukemia patients demonstrate that our proposed method is not only superior to other classifiers' performance, but also can identify a small subset of genes for biomarker analysis.

UNLABELLED: DNAFSMiner (DNA Functional Sites Miner) is a web-based software toolbox to recognize functional sites in nucleic acid sequences. Currently in this toolbox, we provide two software: TIS Miner and Poly(A) Signal Miner. The TIS Miner can be used to predict translation initiation sites in vertebrate DNA/mRNA/cDNA sequences, and the Poly(A) Signal Miner can be used to predict polyadenylation [poly(A)] signals in human DNA sequences. The prediction results are better than those by literature methods on two benchmark applications. This good performance is mainly attributable to our unique learning method. DNAFSMiner is available free of charge for academic and non-profit organizations. AVAILABILITY: http://research.i2r.a-star.edu.sg/DNAFSMiner/ CONTACT: [email protected].

MOTIVATION: Patient outcome prediction using microarray technologies is an important application in bioinformatics. Based on patients' genotypic microarray data, predictions are made to estimate patients' survival time and their risk of tumor metastasis or recurrence. So, accurate prediction can potentially help to provide better treatment for patients. RESULTS: We present a new computational method for patient outcome prediction. In the training phase of this method, we make use of two types of extreme patient samples: short-term survivors who got an unfavorable outcome within a short period and long-term survivors who were maintaining a favorable outcome after a long follow-up time. These extreme training samples yield a clear platform for us to identify relevant genes whose expression is closely related to the outcome. The selected extreme samples and the relevant genes are then integrated by a support vector machine to build a prediction model, by which each validation sample is assigned a risk score that falls into one of the special pre-defined risk groups. We apply this method to several public datasets. In most cases, patients in high and low risk groups stratified by our method have clearly distinguishable outcome status as seen in their Kaplan-Meier curves. We also show that the idea of selecting only extreme patient samples for training is effective for improving the prediction accuracy when different gene selection methods are used.

We introduce a new method, called CS4, to construct committees of decision trees for classification. The method considers different top-ranked features as the root nodes of member trees. This idea is particularly suitable for dealing with high-dimensional bio-medical data as top-ranked features in this type of data usually possess similar merits for classification. To make a decision, the committee combines the power of individual trees in a weighted manner. Unlike Bagging or Boosting which uses bootstrapped training data, our method builds all the member trees of a committee using exactly the same set of training data. We have tested these ideas on UCI data sets as well as recent bio-medical data sets of gene expression or proteomic profiles that are usually described by more than 10,000 features. All the experimental results show that our method is efficient and that the classification performance are superior to C4.5 family algorithms.

MOTIVATIONS AND RESULTS: For classifying gene expression profiles or other types of medical data, simple rules are preferable to non-linear distance or kernel functions. This is because rules may help us understand more about the application in addition to performing an accurate classification. In this paper, we discover novel rules that describe the gene expression profiles of more than six subtypes of acute lymphoblastic leukemia (ALL) patients. We also introduce a new classifier, named PCL, to make effective use of the rules. PCL is accurate and can handle multiple parallel classifications. We evaluate this method by classifying 327 heterogeneous ALL samples. Our test error rate is competitive to that of support vector machines, and it is 71% better than C4.5, 50% better than Naive Bayes, and 43% better than k-nearest neighbour. Experimental results on another independent data sets are also presented to show the strength of our method. AVAILABILITY: Under http://sdmc.lit.org.sg/GEDatasets/, click on Supplementary Information.

Many semistructured objects are similarly, though not identically structured. We study the problem of discovering "typical" substructures of a collection of semistructured objects. The discovered structures can serve the following purposes: 1) the "table-of-contents" for gaining general information of a source, 2) a road map for browsing and querying information sources, 3) a basis for clustering documents, 4) partial schemas for providing standard database access methods, and 5) user/customer interests and browsing patterns. The discovery task is affected by structural features of semistructured data in a nontrivial way and traditional data mining frameworks are inapplicable. We define this discovery problem and propose a solution.

Article Discovering typical structures of documents: a road map approach Share on Authors: Ke Wang Department of Information Systems and Computer Science, National University of Singapore Department of Information Systems and Computer Science, National University of SingaporeView Profile , Huiqing Liu BioInformatics Center, National University of Singapore BioInformatics Center, National University of SingaporeView Profile Authors Info & Claims SIGIR '98: Proceedings of the 21st annual international ACM SIGIR conference on Research and development in information retrievalAugust 1998 Pages 146–154https://doi.org/10.1145/290941.290982Online:01 August 1998Publication History 82citation642DownloadsMetricsTotal Citations82Total Downloads642Last 12 Months9Last 6 weeks2 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access