8613363
Mining Frequent Itemsets for Protein Kinase Regulation
Protein kinases, a family of enzymes, have been viewed as an important signaling intermediary by living organisms for regulating critical biological processes such as memory, hormone response and cell growth. The unbalanced kinases are known to cause cancer and other diseases. With the increasing efforts to collect, store and disseminate information about the entire kinase family, it not only leads to valuable data set to understand cell regulation but also poses a big challenge to extract valuable knowledge about metabolic pathway from the data. Data mining techniques that have been widely used to find frequent patterns in large datasets can be extended and adapted to kinase data as well. This paper proposes a framework for mining frequent itemsets from the collected kinase dataset. An experiment using AMPK regulation data demonstrates that our approaches are useful and efficient in analyzing kinase regulation data.
10107398
Yet Another Induction Algorithm
Inducing general functions from specific training examples is a central problem in the machine learning. Using sets of If-then rules is the most expressive and readable manner. To find If-then rules, many induction algorithms such as ID3, AQ, CN2 and their variants, were proposed. Sequential covering is the kernel technique of them. To avoid testing all possible selectors, Entropy gain is used to select the best attribute in ID3. Constraint of the size of star was introduced in AQ and beam search was adopted in CN2. These methods speed up their induction algorithms but many good selectors are filtered out. In this work, we introduce a new induction algorithm that is based on enumeration of all possible selectors. Contrary to the previous works, we use pruning power to reduce irrelative selectors. But we can guarantee that no good selectors are filtered out. Comparing with other techniques, the experiment results demonstrate that the rules produced by our induction algorithm have high consistency and simplicity.
12775848
Analyzing Inconsistency Toward Enhancing Integration of Biological Molecular Databases
The rapid growth of biological databases not only provides biologists with abundant data but also presents a big challenge in relation to the analysis of data. Many data analysis approaches such as data mining, information retrieval and machine learning have been used to extract frequent patterns from diverse biological databases. However, the discrepancies, due to the differences in the structure of databases and their terminologies, result in a significant lack of interoperability. Although ontology-based approaches have been used to integrate biological databases, the inconsistent analysis of biological databases has been greatly disregarded. This paper presents a method by which to measure the degree of inconsistency between biological databases. It not only presents a guideline for correct and efficient database integration, but also exposes high quality data for data mining and knowledge discovery.
6262105
A New Indexing Method for High Dimensional Dataset
Indexing high dimensional datasets has attracted extensive attention from many researchers in the last decade. Since R-tree type of index structures are known as suffering “curse of dimensionality” problems, Pyramid-tree type of index structures, which are based on the B-tree, have been proposed to break the curse of dimensionality. However, for high dimensional data, the number of pyramids is often insufficient to discriminate data points when the number of dimensions is high. Its effectiveness degrades dramatically with the increase of dimensionality. In this paper, we focus on one particular issue of “curse of dimensionality”; that is, the surface of a hypercube in a high dimensional space approaches 100% of the total hypercube volume when the number of dimensions approaches infinite. We propose a new indexing method based on the surface of dimensionality. We prove that the Pyramid tree technology is a special case of our method. The results of our experiments demonstrate clear priority of our novel method.
24794561
Finding Short Patterns to Classify Text Documents
Many classification methods have been proposed to find patterns in text documents. However, according to Occam's razor principle, "the explanation of any phenomenon should make as few assumptions as possible", short patterns usually have more explainable and meaningful for classifying text documents. In this paper, we propose a depth-first pattern generation algorithm, which can find out short patterns from text document more effectively, comparing with breadth-first algorithm
39700388
Surface Spatial Index Structure of High-Dimensional Space
This paper proposes a spatial index structure based on a new space-partitioning method. Previous research proposed various high dimensional index structures. However, when dimensionality becomes high, the effectiveness of the spatial index structure disappears. This problem is called the “curse of dimensionality”. This paper focuses on the fact that the volume of high dimensional space is mostly occupied by its surface and then proposes a new surface index structure. The utility of this new surface spatial index structure is illustrated through a series of experiments.
3257005
Voting multi-dimensional data with deviations for Web services under group testing
Web services (WS) need to be trustworthy to be used in critical applications. A technique called WS group testing has been proposed which can significantly reduce the cost of testing and ranking a large number of WS. A main feature of WS group testing is that it is able to establish the test oracles for the given test inputs from multiple WS and infer the oracles by plural voting. Efficient voting of complex and large number of data is critical to the success of group testing. Current voting techniques are not designed to deal with such a situation. This paper presents efficient voting algorithms that determine the plural value on multi-dimensional data and large number of data. The algorithm uses a clustering method to classify data into regions to identify the plural value. Experiments are designed and performed to concept-prove the algorithms and their applications with group testing.
16993982
Cache-conscious Frequent Pattern Mining on a Modern Processor
In this paper, we examine the performance of frequent pattern mining algorithms on a modern processor. A detailed performance study reveals that even the best frequent pattern mining implementations, with highly efficient memory managers, still grossly under-utilize a modern processor. The primary performance bottlenecks are poor data locality and low instruction level parallelism (ILP). We propose a cache-conscious prefix tree to address this problem. The resulting tree improves spatial locality and also enhances the benefits from hardware cache line prefetching. Furthermore, the design of this data structure allows the use of a novel tiling strategy to improve temporal locality. The result is an overall speedup of up to 3.2 when compared with state-of-the-art implementations. We then show how these algorithms can be improved further by realizing a non-naive thread-based decomposition that targets simultaneously multi-threaded processors. A key aspect of this decomposition is to ensure cache re-use between threads that are co-scheduled at a fine granularity. This optimization affords an additional speedup of 50%, resulting in an overall speedup of up to 4.8. To the best of our knowledge, this effort is the first to target cache-conscious data mining.
406686
Filtering of shrew DDoS attacks in frequency domain
The shrew distributed denial of service (DDoS) attacks are periodic, bursty, and stealthy in nature. They are also known as reduction of quality (RoQ) attacks. Such attacks could be even more detrimental than the widely known flooding DDoS attacks because they damage the victim servers for a long time without being noticed, thereby denying new visitors to the victim servers, which are mostly e-commerce sites. Thus, in order to minimize the huge monetary losses, there is a pressing need to effectively detect such attacks in real-time. Unfortunately, effective detection of shrew attacks remains an open problem. In this paper, we meet this challenge by proposing a new signal processing approach to identifying and detecting the attacks by examining the frequency-domain characteristics of incoming traffic flows to a server. A major strength of our proposed technique is that its detection time is less than a few seconds. Furthermore, the technique entails simple software or hardware implementations, making it easily deployable in a real-life network environment
669399
Camera Calibration: a USU Implementation
The task of camera calibration is to estimate the intrinsic and extrinsic parameters of a camera model. Though there are some restricted techniques to infer the 3-D information about the scene from uncalibrated cameras, effective camera calibration procedures will open up the possibility of using a wide range of existing algorithms for 3-D reconstruction and recognition. The applications of camera calibration include vision-based metrology, robust visual platooning and visual docking of mobile robots where the depth information is important.
5913277
OceanStore: an architecture for global-scale persistent storage
OceanStore is a utility infrastructure designed to span the globe and provide continuous access to persistent information. Since this infrastructure is comprised of untrusted servers, data is protected through redundancy and cryptographic techniques. To improve performance, data is allowed to be cached anywhere, anytime. Additionally, monitoring of usage patterns allows adaptation to regional outages and denial of service attacks; monitoring also enhances performance through pro-active movement of data. A prototype implementation is currently under development.