35361263
Reducing Overfitting in Predicting Intrinsically Unstructured Proteins
Intrinsically unstructured or disordered proteins are proteins that lack fixed 3-D structure globally or contain long disordered regions. Predicting disordered regions has attracted significant research recently. In developing a decision tree based disordered region predictor, we note that many previous predictors applying 20 amino acid compositions as training parameter tend to overfit the data. In this paper we propose to alleviate overfitting in prediction of intrinsically unstructured proteins by reducing input parameters. We also compare this approach with the random forest model, which is inherently tolerant to overfitting. Our experiments suggest that reducing 20 amino acid compositions into 4 groups according to amino acid property can reduce the overfitting in decision tree model. Alternatively, ensemble-learning techniques like random forest is inherently more tolerant to this kind of overfitting and can be a promising candidate in disordered region prediction.
11532289
Computing Complex Iceberg Cubes by Multiway Aggregation and Bounding
Iceberg cubing is a valuable technique in data warehouses. The efficiency of iceberg cube computation comes from efficient aggregation and effective pruning for constraints. In advanced applications, iceberg constraints are often non-monotone and complex, for example, “Average cost in the range [δ 1, δ 2] and standard deviation of cost less than β”. The current cubing algorithms either are efficient in aggregation but weak in pruning for such constraints, or can prune for non-monotone constraints but are inefficient in aggregation. The best algorithm of the former, Star-cubing, computes aggregations of cuboids simultaneously but its pruning is specific to only monotone constraints such as “COUNT(*) ≥ δ”. In the latter case, the Divide and Approximate pruning technique can prune for non-monotone constraints but is limited to bottom-up single-group aggregation. We propose a solution that exhibits both efficiency in aggregation and generality and effectiveness in pruning for complex constraints. Our bounding techniques are as general as the Divide and Approximate pruning techniques for complex constraints and yet our multiway aggregation is as efficient as Star-cubing.
30931074
A Distributed Object Database's Basic Design Issues
750246
Noise Tolerance of EP-Based Classifiers
Emerging Pattern (EP)-based classifiers are a type of new classifiers based on itemsets whose occurrence in one dataset varies significantly from that of another. These classifiers are very promising and have shown to perform comparably with some popular classifiers. In this paper, we conduct two experiments to study the noise tolerance of EP-based classifiers. A primary concern is to ascertain if overfitting occurs in them. Our results highlight the fact that the aggregating approach in constructing EP-based classifiers prevents them from overfitting. We further conclude that perfect training accuracy does not necessarily lead to overfitting of a classifier as long as there exists a suitable mechanism, such as an aggregating approach, to counterbalance any propensity to overfit.
37955611
Transforming RDB schema into well-structured OODB schema
Abstract When transforming relational database (RDB) schema into object-oriented database(OODB) schema, much effort was put on examining key and inclusion dependency (ID) constraints to identify class and establish inheritance and association between classes. However, in order to further remove the original data redundancy and update anomaly, multi-valued dependency (MVD) should also be examined. In this paper, we discuss class structures and define well-structured classes. Based on MVDs, a theorem is given transforming a relation schema into a well-structured class. To transform RDB schema into OODB schema, a composition process simplifying the input RDB schema and an algorithm transforming the simplified RDB schema into well-structured OODB classes are developed.
2953976
A performance study of monitoring and information services for distributed systems
Monitoring and information services form a key component of a distributed system, or Grid. A quantitative study of such services can aid in understanding the performance limitations, advise in the deployment of the monitoring system, and help evaluate future development work. To this end, we study the performance of three monitoring and information services for distributed systems: the Globus Toolkit/spl reg/ Monitoring and Discovery Service (MDS2), the European Data Grid Relational Grid Monitoring Architecture (R-GMA) and Hawkeye, part of the Condor project. We perform experiments to test their scalability with respect to number of users, number of resources and amount of data collected. Our study shows that each approach has different behaviors, often due to their different design goals. In the four sets of experiments we conducted to evaluate the performance of the service components under different circumstances, we found a strong advantage to caching or pre-fetching the data, as well as the need to have primary components at well-connected sites because of the high load seen by all systems.
3577423
Locating faulty code using failure-inducing chops
Software debugging is the process of locating and correcting faulty code. Prior techniques to locate faulty code either use program analysis techniques such as backward dynamic program slicing or exclusively use delta debugging to analyze the state changes during program execution. In this paper, we present a new approach that integrates the potential of delta debugging algorithm with the benefit of forward and backward dynamic program slicing to narrow down the search for faulty code. Our approach is to use delta debugging algorithm to identify a minimal failure-inducing input, use this input to compute a forward dynamic slice and then intersect the statements in this forward dynamic slice with the statements in the backward dynamic slice of the erroneous output to compute a failure-inducing chop. We implemented our technique and conducted experiments with faulty versions of several programs from the Siemens suite to evaluate our technique. Our experiments show that failure-inducing chops can greatly reduce the size of search space compared to the dynamic slices without significantly compromising the capability to locate the faulty code. We also applied our technique to several programs with known memory related bugs such as buffer overflow bugs. The failure-inducing chop in several of these cases contained only 2 to 4 statements which included the code causing memory corruption.
8353152
An Efficient Algorithm for Mining Coherent Patterns from Heterogeneous Microarrays
DNA microarray techniques present a novel way for geneticists to monitor interactions among tens of thousands of genes simultaneously, and have become standard lab routines in gene discovery, disease diagnosis, and drug design. There has been extensive research on coherent subspace clustering of gene expressions measured under consistent experimental settings. This implies that all experiments are run using the same batch of microarray chips with similar characteristics of noise. Algorithms developed under this assumption may not be applicable for analyzing data collected from heterogeneous settings, where the set of genes being monitored may be different and expression levels may be not directly comparable even for the same gene. In this paper, we propose a model, F-cluster, for mining subspace coherent patterns from heterogeneous gene expression data, which is shown effective for revealing truthful patterns and reducing spurious ones. We also develop an efficient and scalable hybrid approach that combines gene-pair based and sample-pair based pruning to generate F-clusters from multiple gene expression matrices simultaneously. The experimental results demonstrate that our model can discover significant clusters that may not be identified by previous models.
5639888
Strategies for using additional resources in parallel hash-based join algorithms
Hash-based join is a compute- and memory-intensive algorithm. It achieves good performance and scales well to large datasets, if sufficient memory is available to hold the hash table and the distribution of computing had across nodes is balanced. We compare three adaptive algorithms that start with a partitioning of the hash table across a group of nodes and expand during the hash table building phase to additional resources, when memory on a node is used up. The split-based algorithm partitions the hash table range assigned to the node, on which memory is full, into two segments and assigns one of the segments to a new node in the system. The replication-based algorithm replicates the hash table range on a new node. The hybrid algorithm combines the first and second strategies in order to address each strategy's short comings. We perform an experimental performance evaluation of these algorithms on a PC cluster. Our results show that among the three algorithms, in most cases the hybrid algorithm either performs close to the better of the two or is the best algorithm.
9586691
A New Approach for Alignment of Multiple Proteins
We introduce a new graph-based multiple sequence alignment method for protein sequences. We name our method HSA (Horizontal Sequence Alignment) for it horizontally slides a window on the protein sequences simultaneously. Current progressive alignment tools build up final alignment by adding sequences one by one to existing alignment. Thus, they have the shortcoming of order-dependent alignment. In contrast, HSA considers all the proteins at once. It obtains final alignment by concatenating cliques of graph. In order to find a biologically relevant alignment, HSA takes secondary structure information as well as amino acid sequences into account. The experimental results show that HSA achieves higher accuracy compared to existing tools on BAliBASE benchmarks. The improvement is more significant for proteins with low similarity.