Anand Mahendran

Matrix insertion-deletion systems for bio-molecular structures

Insertion and deletion are considered to be the basic operations in Biology, more specifically in DNA processing and RNA editing. Based on these evolutionary transformations, a computing model has been formulated in formal language theory known as insertion-deletion systems. Since the biological macromolecules can be viewed as symbols, the gene sequences can be represented as strings. This suggests that the molecular representations can be theoretically analyzed if a biologically inspired computing model recognizes various bio-molecular structures like pseudoknot, hairpin, stem and loop, cloverleaf and dumbbell. In this paper, we introduce a simple grammar system that encompasses many bio-molecular structures including the above mentioned structures. This new grammar system is based on insertion-deletion and matrix grammar systems and is called Matrix insertion-deletion grammars. Finally, we discuss how the ambiguity levels defined for insertion-deletion grammar systems can be realized in bio-molecular structures, thus the ambiguity issues in gene sequences can be studied in terms of grammar systems.

Comment spam classification in blogs through comment analysis and comment-blog post relationships

Spamming refers to the process of providing unwanted and irrelevant information to the users. It is a widespread phenomenon that is often noticed in e-mails, instant messages, blogs and forums. In our paper, we consider the problem of spamming in blogs. In blogs, spammers usually target commenting systems which are provided by the authors to facilitate interaction with the readers. Unfortunately, spammers abuse these commenting systems by posting irrelevant and unsolicited content in the form of spam comments. Thus, we propose a novel methodology to classify comments into spam and non-spam using previously-undescribed features including certain blog post-comment relationships. Experiments conducted using our methodology produced a spam detection accuracy of 94.82% with a precision of 96.50% and a recall of 95.80%.

On the study of ambiguity and the trade-off between measures and ambiguity in insertion–deletion languages☆

Abstract Gene insertion and deletion are the operations that occur commonly in DNA processing and RNA editing. Based on these operations, a computing model has been formulated in formal language theory known as insertion–deletion systems. In this paper we study about ambiguity issues of these systems. First, we define six levels of ambiguity for insertion–deletion systems that are based on the components used in the derivation such as axiom , contexts and strings . Next, we show that there are inherently i -ambiguous insertion–deletion languages which are j -unambiguous for the combinations ( i , j ) ∈ { ( 5 , 4 ) , ( 4 , 3 ) , ( 4 , 2 ) , ( 3 , 1 ) , ( 2 , 1 ) , ( 1 , 0 ) , ( 0 , 1 ) } . As an application, we discuss with an example that how some of these ambiguity levels can be interpreted in gene sequences. Further, we prove an important result that the ambiguity problem of insertion–deletion systems is undecidable. Then, we define six new measures for insertion–deletion systems based on used contexts and strings. Finally, we analyze the trade-off between ambiguity levels and measures. We note that there are languages which are inherently i -ambiguous (for i = 5 , 4 , 2 , 0 ) when a measure M is minimal for the languages but they are i -unambiguous otherwise.

Secured E-commerce transactions through choatic map

Internet has become widespread, and is used for all transactions to support client and server services. E-commerce is also one of the services to sell the goods using the Internet. E-Transaction has becomes more important, security for E-transaction is a important work because of the insecure communication channel. In this paper, we have proposed a new algorithm for a secure e-transaction using chaos.

Formal Language Representation and Modelling Structures Underlying RNA Folding Process

The biological sequences that occur in DNA, RNA and proteins can be considered as strings formed over the well defined chemical alphabets. Such gene sequences form structure based on the complementary pair and the structures can be interpreted as languages. Matrix insertion-deletion system has been introduced a few years back that modelled several bio-molecular structures occur at intramolecular and intermolecular level. In this paper, we identify some structures that are frequently noticed during RNA folding process such as double bulge loop, extended internal loop, triple stem and loop and we give the corresponding formal language representation to such structures. Further, we model the structures using Matrix insertion-deletion systems. This work is pioneering to give the language representation and modelling the structures of RNA folding process using formal grammar.

On the Trade-off Between Ambiguity and Complexity in Contextual Languages

Contextual grammars are introduced by Solomon Marcus in 1969 based on the fundamental concept of descriptive linguistics of insertion of strings in given contexts. Internal contextual grammars are introduced by Păun and Nguyen in 1980. For contextual grammars several descriptional complexity measures and levels of ambiguity have been defined. In this paper, we analyze the trade-off between ambiguity and complexity of languages generated by internal contextual grammars. The notion of a pseudo inherently ambiguous language with respect to two complexity measures is introduced and investigated. These languages can be generated by unambiguous grammars which are minimal with respect to one measure and ambiguous if they are minimal with respect to the other measure. An open problem from [15] is solved in this framework.

ON THE AMBIGUITY OF INSERTION SYSTEMS

Gene insertion and deletion are the operations that occur commonly in DNA processing and RNA editing. Based on these evolutionary transformations, a computing model has been formulated in formal language theory known as insertion-deletion systems. In this paper, we study about the ambiguity issues of insertion systems. First, we define six levels of ambiguity for insertion systems based on the components used in the derivation such as axiom, contexts and strings. Next, we show that there are inherently i-ambiguous insertion languages which are j-unambiguous for the combinations (i, j) ∈ {(5,0), (5,4), (4,3), (4,2), (3,1),(2,1), (1,0), (0,1)}. Finally, we prove an important result that the ambiguity problem of insertion systems is undecidable.

On the Ambiguity and Complexity Measures of Insertion-Deletion Systems

In DNA processing and RNA editing, gene insertion and deletion are considered as the basic operations. Based on the above evolutionary transformations, a computing model has been formulated in formal language theory known as insertion-deletion systems. In this paper we study about ambiguity and complexity measures of these systems. First, we define the various levels of ambiguity (i = 0,1,2,3,4,5) for insertion-deletion systems. Next, we show that there are inherently i-ambiguous insertion-deletion languages which are j-unambiguous for the combinations (i, j) ∈ {(5,4), (4,2), (3,1), (3,2), (2,1),(0,1)}. Further, We prove an important result that the ambiguity problem of insertion-deletion system is undecidable. Finally, we define three new complexity measures TLength − Con, TLength − Ins, TLength − Del for insertion-deletion systems and analyze the trade-off between the newly defined ambiguity levels and complexity measures.