13799231
Improving molecular cancer class discovery through sparse non-negative matrix factorization
MOTIVATION
Identifying different cancer classes or subclasses with similar morphological appearances presents a challenging problem and has important implication in cancer diagnosis and treatment. Clustering based on gene-expression data has been shown to be a powerful method in cancer class discovery. Non-negative matrix factorization is one such method and was shown to be advantageous over other clustering techniques, such as hierarchical clustering or self-organizing maps. In this paper, we investigate the benefit of explicitly enforcing sparseness in the factorization process.


RESULTS
We report an improved unsupervised method for cancer classification by the use of gene-expression profile via sparse non-negative matrix factorization. We demonstrate the improvement by direct comparison with classic non-negative matrix factorization on the three well-studied datasets. In addition, we illustrate how to identify a small subset of co-expressed genes that may be directly involved in cancer.
11110395
In Vitro Implementation of Finite-State Machines
We explore the information processing capabilities and efficiency of DNA computations by giving two different types of implementations of finite-state machines. A ligation-based approach allows input of arbitrary length and can be readily implemented with current biotechnology, but requires sequential input feed and different molecules for different machines. In a second implementation not based on ligation, transitions are represented by reusable molecules, and the input, coded as a molecule, can be introduced at once. We extend the technique for programmable fault-tolerant implementation of nondeterministic finite-state machines by enforcings the basic conditions in the subset constructions that permit efficient computation. All implementations allow optical extraction of the status of the machine.
16609037
DELPHI: A pattern-based method for detecting sequence similarity
We describe DELPHI, a new computational tool for identifying sequence similarity between a query sequence and a database of proteins. Use is made of a set of patterns obtained from the underlying database through a one-time computation. The patterns are subsequently matched against every query sequence presented to the system. A pattern matched by a region of the query pinpoints a potential local similarity between that region and all of the database sequences also matching that pattern. In a final step, all such local similarities are examined more closely by aligning and scoring the corresponding query and database regions. By prudently choosing a set of patterns, the method can be used to discover weak but biologically important similarities. We provide a number of examples using both classified and unclassified proteins that corroborate this claim.
18106801
Mining Protein Sequences for Motifs
We use methods from Data Mining and Knowledge Discovery to design an algorithm for detecting motifs in protein sequences. The algorithm assumes that a motif is constituted by the presence of a "good" combination of residues in appropriate locations of the motif. The algorithm attempts to compile such good combinations into a "pattern dictionary" by processing an aligned training set of protein sequences. The dictionary is subsequently used to detect motifs in new protein sequences. Statistical significance of the detection results are ensured by statistically determining the various parameters of the algorithm. Based on this approach, we have implemented a program called GYM. The Helix-Turn-Helix motif was used as a model system on which to test our program. The program was also extended to detect Homeodomain motifs. The detection results for the two motifs compare favorably with existing programs. In addition, the GYM program provides a lot of useful information about a given protein sequence.
17160551
Pattern discovery on character sets and real-valued data: linear bound on irredundant motifs and an efficient polynomial time algorithm
Given an input sequence of data, a motif is a repeating pattern, possibly interspersed with "dont care" characters. The data could be a sequence of characters or sets of characters or even real values. In the first two cases, the number of motifs could potentially be exponential in the size of the input sequence and in the third case there could be infinite number of motifs (assuming two real numbers are equal if they are within some specified 5 > 0 of each other). However, it has been shown in some motif based applications, such as multiple sequence aligz~nent [Par98, PFR99], that a small subset of these motifs capture all the relevant information. Also, from an information-theoretic viewpoint, the special motifs represent the sets with low co-relation, hence of higher informational value. In this paper, we show, for any sequence with n characters, there exists only a linear (or no more than 3n) number of these special motifs and every other motif can be constructed from this set. We term these special motifs as irredundant motifs. We also present an efficient polynomial time algorithm to generate these motifs. This bound on the number of useful motifs ~ves validation to motif-based approaches, since the total number of irredundant motifs does not explode. This result is potentially of significance to most applications that use pattern discovery as the basic engine such as data mining, clustering, matching and others.
28841129
Believability Based Iterated Belief Revision
Classical iterated belief revision methods rarely take into account the impact of the uncertain information. In this paper, an approach of believability based iterated belief revision(BIBR) is presented. BIBR relates the belief revision in the multi-agent system to the believability of information, which plays an important role in the revision process. Based on the Dempster-Shafer theory of evidence and believability function formalism, the believability of information can be obtained. The revised belief set by BIBR is dependent on the history of revision, namely, on the information received prior to the current belief set. It is proved that the BIBR operation meets the AGM postulates for belief revision and the Darwiche and Pearl postulates for iterated belief revision.
20003562
Mapping Web Usage Patterns to MDP Model and Mining with Reinforcement Learning
For many web usage mining applications, it is crucial to compare navigation paths of different users. This paper presents a reinforcement learning based method for mining the sequential usage patterns of user behaviors. In detail, the temporal data set about every user is constructed from the web log file, and then the navigation paths of the users are modelled using the extended Markov decision process. The proposed method could learn the dynamical sequential usage patterns on-line.
41738297
Human face profile recognition using attributed string
A new attributed string matching method for human face profile recognition is proposed in this work. It is a novel idea to apply structural and syntactic technique on face profile matching. The approach works on a chain of profile line segments and highlights the favor of curve matching by suppressing the operations of insert and delete. The technique relies mainly on the merge and change operations of string to tackle the inconsistency problem of feature point detection. A quadratic penalty function is proposed to prohibit large angle changes and overmerging. The method produces very encouraging results and is found to be suitable for similar shape classification.
23206649
Learning classifier system ensemble for data mining
This paper proposes LCSE, a learning classifier system ensemble, which is an extension of the classical learning classifier system(LCS). The classical LCS includes two major modules, a genetic algorithm module used to facilitate rule discovery, and a reinforcement learning module used to adjust the strength of the corresponding rules while it receives the rewards from the environment. In LCSE we build a two-level ensemble architecture to enhance the generalization of LCS. In the first-level, new instances are first bootstrapped and sent to several LCSs for classification. Then, in the second-level, a plurality-vote method is used to combine the classification results of individual LCSs into a final decision. Experiments on some benchmark data sets from the UCI repository have shown that LCSE has better generalization ability than the single LCS and other supervised learning methods.
15420304
Incremental gradient descent imputation method for missing data in learning classifier systems
Learning with incomplete or missing data has been a major challenge in learning classifier system. One method for covering missing data is imputing missing values based on the statistic of known values. Another is marking them matching arbitrary case. A new approach using incremental gradient descent imputation model is proposed in this paper, which use the relationship among variables to estimate the missing value. And, some experiments are conducted in order to compare the performance of new approach and other classical covering methods.