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Planted Motif Search
In the field of computational biology, a planted motif search (PMS) also known as a (''l, d'')-motif search (LDMS) is a method for identifying conserved motifs within a set of nucleic acid or peptide sequences. PMS is known to be NP-complete. The time complexities of most of the planted motif search algorithms depend exponentially on the alphabet size and ''l''. The PMS problem was first introduced by Keich and Pevzner. The problem of identifying meaningful patterns (e.g., motifs) from biological data has been studied extensively since they play a vital role in understanding gene function, human disease, and may serve as therapeutic drug targets. Description The search problem may be summarized as follows: ''Input are n strings (s1, s2, ... , sn) of length m each from an alphabet Σ and two integers l and d. Find all strings x such that , x, = l and every input string contains at least one variant of x at a Hamming distance of at most d. Each such x is referred to as an ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computational Biology
Computational biology refers to the use of data analysis, mathematical modeling and computational simulations to understand biological systems and relationships. An intersection of computer science, biology, and big data, the field also has foundations in applied mathematics, chemistry, and genetics. It differs from biological computing, a subfield of computer engineering which uses bioengineering to build computers. History Bioinformatics, the analysis of informatics processes in biological systems, began in the early 1970s. At this time, research in artificial intelligence was using network models of the human brain in order to generate new algorithms. This use of biological data pushed biological researchers to use computers to evaluate and compare large data sets in their own field. By 1982, researchers shared information via punch cards. The amount of data grew exponentially by the end of the 1980s, requiring new computational methods for quickly interpreting ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Approximation Algorithms
In computer science and operations research, approximation algorithms are efficient algorithms that find approximate solutions to optimization problems (in particular NP-hard problems) with provable guarantees on the distance of the returned solution to the optimal one. Approximation algorithms naturally arise in the field of theoretical computer science as a consequence of the widely believed P ≠ NP conjecture. Under this conjecture, a wide class of optimization problems cannot be solved exactly in polynomial time. The field of approximation algorithms, therefore, tries to understand how closely it is possible to approximate optimal solutions to such problems in polynomial time. In an overwhelming majority of the cases, the guarantee of such algorithms is a multiplicative one expressed as an approximation ratio or approximation factor i.e., the optimal solution is always guaranteed to be within a (predetermined) multiplicative factor of the returned solution. However, there are ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Integer Linear Program
An integer programming problem is a mathematical optimization or feasibility program in which some or all of the variables are restricted to be integers. In many settings the term refers to integer linear programming (ILP), in which the objective function and the constraints (other than the integer constraints) are linear. Integer programming is NP-complete. In particular, the special case of 0-1 integer linear programming, in which unknowns are binary, and only the restrictions must be satisfied, is one of Karp's 21 NP-complete problems. If some decision variables are not discrete, the problem is known as a mixed-integer programming problem. Canonical and standard form for ILPs In integer linear programming, the ''canonical form'' is distinct from the ''standard form''. An integer linear program in canonical form is expressed thus (note that it is the \mathbf vector which is to be decided): : \begin & \text && \mathbf^\mathrm \mathbf\\ & \text && A \mathbf \le \mathbf, \ ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Subtree
In computer science, a tree is a widely used abstract data type that represents a hierarchical tree structure with a set of connected nodes. Each node in the tree can be connected to many children (depending on the type of tree), but must be connected to exactly one parent, except for the ''root'' node, which has no parent. These constraints mean there are no cycles or "loops" (no node can be its own ancestor), and also that each child can be treated like the root node of its own subtree, making recursion a useful technique for tree traversal. In contrast to linear data structures, many trees cannot be represented by relationships between neighboring nodes in a single straight line. Binary trees are a commonly used type, which constrain the number of children for each parent to exactly two. When the order of the children is specified, this data structure corresponds to an ordered tree in graph theory. A value or pointer to other data may be associated with every node in the tr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Tree Traversal
In computer science, tree traversal (also known as tree search and walking the tree) is a form of graph traversal and refers to the process of visiting (e.g. retrieving, updating, or deleting) each node in a tree data structure, exactly once. Such traversals are classified by the order in which the nodes are visited. The following algorithms are described for a binary tree, but they may be generalized to other trees as well. Types Unlike linked lists, one-dimensional arrays and other linear data structures, which are canonically traversed in linear order, trees may be traversed in multiple ways. They may be traversed in depth-first or breadth-first order. There are three common ways to traverse them in depth-first order: in-order, pre-order and post-order. Beyond these basic traversals, various more complex or hybrid schemes are possible, such as depth-limited searches like iterative deepening depth-first search. The latter, as well as breadth-first search, can also be ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Subroutine
In computer programming, a function or subroutine is a sequence of program instructions that performs a specific task, packaged as a unit. This unit can then be used in programs wherever that particular task should be performed. Functions may be defined within programs, or separately in libraries that can be used by many programs. In different programming languages, a function may be called a routine, subprogram, subroutine, method, or procedure. Technically, these terms all have different definitions, and the nomenclature varies from language to language. The generic umbrella term ''callable unit'' is sometimes used. A function is often coded so that it can be started several times and from several places during one execution of the program, including from other functions, and then branch back ('' return'') to the next instruction after the ''call'', once the function's task is done. The idea of a subroutine was initially conceived by John Mauchly during his work on ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Depth-first Search
Depth-first search (DFS) is an algorithm for traversing or searching tree or graph data structures. The algorithm starts at the root node (selecting some arbitrary node as the root node in the case of a graph) and explores as far as possible along each branch before backtracking. Extra memory, usually a stack, is needed to keep track of the nodes discovered so far along a specified branch which helps in backtracking of the graph. A version of depth-first search was investigated in the 19th century by French mathematician Charles Pierre Trémaux as a strategy for solving mazes. Properties The time and space analysis of DFS differs according to its application area. In theoretical computer science, DFS is typically used to traverse an entire graph, and takes time where , V, is the number of vertices and , E, the number of edges. This is linear in the size of the graph. In these applications it also uses space O(, V, ) in the worst case to store the stack of vertices on the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Branch-and-bound Algorithm
Branch and bound (BB, B&B, or BnB) is an algorithm algorithmic paradigm, design paradigm for discrete optimization, discrete and combinatorial optimization problems, as well as mathematical optimization. A branch-and-bound algorithm consists of a systematic enumeration of candidate solutions by means of state space search: the set of candidate solutions is thought of as forming a Tree (graph theory), rooted tree with the full set at the root. The algorithm explores ''branches'' of this tree, which represent subsets of the solution set. Before enumerating the candidate solutions of a branch, the branch is checked against upper and lower estimated ''bounds'' on the optimal solution, and is discarded if it cannot produce a better solution than the best one found so far by the algorithm. The algorithm depends on efficient estimation of the lower and upper bounds of regions/branches of the search space. If no bounds are available, the algorithm degenerates to an exhaustive search. The ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Tree (data Structure)
In computer science, a tree is a widely used abstract data type that represents a hierarchical tree structure with a set of connected nodes. Each node in the tree can be connected to many children (depending on the type of tree), but must be connected to exactly one parent, except for the ''root'' node, which has no parent. These constraints mean there are no cycles or "loops" (no node can be its own ancestor), and also that each child can be treated like the root node of its own subtree, making recursion a useful technique for tree traversal. In contrast to linear data structures, many trees cannot be represented by relationships between neighboring nodes in a single straight line. Binary trees are a commonly used type, which constrain the number of children for each parent to exactly two. When the order of the children is specified, this data structure corresponds to an ordered tree in graph theory. A value or pointer to other data may be associated with every node in the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Radix Sorting
In computer science, radix sort is a non- comparative sorting algorithm. It avoids comparison by creating and distributing elements into buckets according to their radix. For elements with more than one significant digit, this bucketing process is repeated for each digit, while preserving the ordering of the prior step, until all digits have been considered. For this reason, radix sort has also been called bucket sort and digital sort. Radix sort can be applied to data that can be sorted lexicographically, be they integers, words, punch cards, playing cards, or the mail. History Radix sort dates back as far as 1887 to the work of Herman Hollerith on tabulating machines. Radix sorting algorithms came into common use as a way to sort punched cards as early as 1923. Donald Knuth. ''The Art of Computer Programming'', Volume 3: ''Sorting and Searching'', Third Edition. Addison-Wesley, 1997. . Section 5.2.5: Sorting by Distribution, pp. 168–179. The first memory-eff ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Intractability (complexity)
In theoretical computer science and mathematics, computational complexity theory focuses on classifying computational problems according to their resource usage, and relating these classes to each other. A computational problem is a task solved by a computer. A computation problem is solvable by mechanical application of mathematical steps, such as an algorithm. A problem is regarded as inherently difficult if its solution requires significant resources, whatever the algorithm used. The theory formalizes this intuition, by introducing mathematical models of computation to study these problems and quantifying their computational complexity, i.e., the amount of resources needed to solve them, such as time and storage. Other measures of complexity are also used, such as the amount of communication (used in communication complexity), the number of gates in a circuit (used in circuit complexity) and the number of processors (used in parallel computing). One of the roles of computational ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Clique (graph Theory)
In the mathematical area of graph theory, a clique ( or ) is a subset of vertices of an undirected graph such that every two distinct vertices in the clique are adjacent. That is, a clique of a graph G is an induced subgraph of G that is complete. Cliques are one of the basic concepts of graph theory and are used in many other mathematical problems and constructions on graphs. Cliques have also been studied in computer science: the task of finding whether there is a clique of a given size in a graph (the clique problem) is NP-complete, but despite this hardness result, many algorithms for finding cliques have been studied. Although the study of complete subgraphs goes back at least to the graph-theoretic reformulation of Ramsey theory by , the term ''clique'' comes from , who used complete subgraphs in social networks to model cliques of people; that is, groups of people all of whom know each other. Cliques have many other applications in the sciences and particularly in b ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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