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Efficient similarity search in sequence databases
, 1994
"... We propose an indexing method for time sequences for processing similarity queries. We use the Discrete Fourier Transform (DFT) to map time sequences to the frequency domain, the crucial observation being that, for most sequences of practical interest, only the first few frequencies are strong. Anot ..."
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Cited by 505 (21 self)
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. Another important observation is Parseval's theorem, which specifies that the Fourier transform preserves the Euclidean distance in the time or frequency domain. Having thus mapped sequences to a lowerdimensionality space by using only the first few Fourier coe cients, we use Rtrees to index
Searching in metric spaces
, 2001
"... The problem of searching the elements of a set that are close to a given query element under some similarity criterion has a vast number of applications in many branches of computer science, from pattern recognition to textual and multimedia information retrieval. We are interested in the rather gen ..."
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Cited by 432 (38 self)
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The problem of searching the elements of a set that are close to a given query element under some similarity criterion has a vast number of applications in many branches of computer science, from pattern recognition to textual and multimedia information retrieval. We are interested in the rather
Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. sect
 A
, 1991
"... Map interpretation remains a critical step in solving the structure of a macromolecule. Errors introduced at this early stage may persist throughout crystallographic refinement and result in an incorrect structure. The normally quoted crystallographic residual is often a poor description for the q ..."
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Cited by 1016 (9 self)
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for the quality of the model. Strategies and tools are described that help to alleviate this problem. These simplify the modelbuilding process, quantify the goodness of fit of the model on a perresidue basis and locate possible errors in peptide and sidechain conformations.
Mtree: An Efficient Access Method for Similarity Search in Metric Spaces
, 1997
"... A new access meth d, called Mtree, is proposed to organize and search large data sets from a generic "metric space", i.e. whE4 object proximity is only defined by a distance function satisfyingth positivity, symmetry, and triangle inequality postulates. We detail algorith[ for insertion o ..."
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Cited by 652 (38 self)
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A new access meth d, called Mtree, is proposed to organize and search large data sets from a generic "metric space", i.e. whE4 object proximity is only defined by a distance function satisfyingth positivity, symmetry, and triangle inequality postulates. We detail algorith[ for insertion
Spacetime Interest Points
 IN ICCV
, 2003
"... Local image features or interest points provide compact and abstract representations of patterns in an image. In this paper, we propose to extend the notion of spatial interest points into the spatiotemporal domain and show how the resulting features often reflect interesting events that can be use ..."
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Cited by 791 (22 self)
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Local image features or interest points provide compact and abstract representations of patterns in an image. In this paper, we propose to extend the notion of spatial interest points into the spatiotemporal domain and show how the resulting features often reflect interesting events that can be used for a compact representation of video data as well as for its interpretation.. To detect
Learning the Kernel Matrix with SemiDefinite Programming
, 2002
"... Kernelbased learning algorithms work by embedding the data into a Euclidean space, and then searching for linear relations among the embedded data points. The embedding is performed implicitly, by specifying the inner products between each pair of points in the embedding space. This information ..."
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Cited by 780 (22 self)
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is contained in the socalled kernel matrix, a symmetric and positive definite matrix that encodes the relative positions of all points. Specifying this matrix amounts to specifying the geometry of the embedding space and inducing a notion of similarity in the input spaceclassical model selection
Gapped Blast and PsiBlast: a new generation of protein database search programs
 NUCLEIC ACIDS RESEARCH
, 1997
"... The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while ..."
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Cited by 8393 (85 self)
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for automatically combining statistically significant alignments produced by BLAST into a positionspecific score matrix, and searching the database using this matrix. The resulting PositionSpecific Iterated BLAST (PSIBLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many
Probabilistic Roadmaps for Path Planning in HighDimensional Configuration Spaces
 IEEE INTERNATIONAL CONFERENCE ON ROBOTICS AND AUTOMATION
, 1996
"... A new motion planning method for robots in static workspaces is presented. This method proceeds in two phases: a learning phase and a query phase. In the learning phase, a probabilistic roadmap is constructed and stored as a graph whose nodes correspond to collisionfree configurations and whose edg ..."
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Cited by 1276 (124 self)
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edges correspond to feasible paths between these configurations. These paths are computed using a simple and fast local planner. In the query phase, any given start and goal configurations of the robot are connected to two nodes of the roadmap; the roadmap is then searched for a path joining these two
The FF planning system: Fast plan generation through heuristic search
 Journal of Artificial Intelligence Research
, 2001
"... We describe and evaluate the algorithmic techniques that are used in the FF planning system. Like the HSP system, FF relies on forward state space search, using a heuristic that estimates goal distances by ignoring delete lists. Unlike HSP's heuristic, our method does not assume facts to be ind ..."
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Cited by 822 (53 self)
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We describe and evaluate the algorithmic techniques that are used in the FF planning system. Like the HSP system, FF relies on forward state space search, using a heuristic that estimates goal distances by ignoring delete lists. Unlike HSP's heuristic, our method does not assume facts
Suffix arrays: A new method for online string searches
, 1991
"... A new and conceptually simple data structure, called a suffix array, for online string searches is introduced in this paper. Constructing and querying suffix arrays is reduced to a sort and search paradigm that employs novel algorithms. The main advantage of suffix arrays over suffix trees is that ..."
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Cited by 827 (0 self)
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is that, in practice, they use three to five times less space. From a complexity standpoint, suffix arrays permit online string searches of the type, "Is W a substring of A?" to be answered in time O(P + log N), where P is the length of W and N is the length of A, which is competitive with (and
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