IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, 1990
Most RC simulators handle only tree networks, not arbitrary networks. We present an algorithm for... more Most RC simulators handle only tree networks, not arbitrary networks. We present an algorithm for computing signal delays in general RC networks using the RC-tree computation as the primary operation. We partition a given network into a spanning tree and links. Then we compute the signal delay of the spanning tree, and update the signal delay as we incrementally add the links back to reconstruct the original network. If rn is the number of links, this algorithm requires m ( r i i + 1)/2 updates and !ti + 1 tree delay evaluations. All the tree delay evaluations involve computing signal delays with the same resistive spanning tree, but with different values for the capacitors.
This is a draft of the report of the Accreditation Task Force. It is nearing the final form, but ... more This is a draft of the report of the Accreditation Task Force. It is nearing the final form, but there are still big holes in it where volunteers did not follow through on their promises. Accreditation means different things in different parts of the world and in different academic cultures even within one country. It is difficult to come up with a meaningful world-wide accreditation system or set of standards for our field.
Journal of the Acoustical Society of America, Sep 1, 1987
BACKGROUND OF THE INVENTION ral the filtering method requires a large number of multiplication st... more BACKGROUND OF THE INVENTION ral the filtering method requires a large number of multiplication steps which are economically expen-This invention relates to musical instruments and srve^ 0 achieve, more specifically to digitally controlled electronic in-In a typical example of a filter technique, a wavestruments and methods for generating musical sound. 15 shape memory provides digital samples of one cycle of Digitally controlled methods of generating musical a waveshape to a loop circuit which includes a filter and ...
This paper makes a quantitative comparison of different methods, called regularizers, for estimat... more This paper makes a quantitative comparison of different methods, called regularizers, for estimating the distribution of amino acids in a specific context, given a very small sample of amino acids from that distribution. The regularizers considered here are zero-offsets, pseudocounts, substitution matrices (with several variants), and Dirichlet mixture regularizers. Each regularizer is evaluated based on how well it estimates the distributions of the columns of a multiple alignment--specifically, the expected encoding cost per amino acid using the regularizer and all possible samples from each column. In general, pseudocounts give the lowest encoding costs for samples of size zero, substitution matrices give the lowest encoding costs for samples of size one, and Dirichlet mixtures give the lowest for larger samples. One of the substitution matrix variants, which added pseudocounts and scaled counts, does almost as well as the best known Dirichlet mixtures, but with a lower computation cost.
Motivation: SAM-T99 is an iterative hidden Markov model-based method for finding proteins similar... more Motivation: SAM-T99 is an iterative hidden Markov model-based method for finding proteins similar to a single target sequence and aligning them. One of its main uses is to produce multiple alignments of homologs of the target sequence. Previous tests of SAM-T99 and its predecessors have concentrated on the quality of the searches performed, not on the quality of the multiple alignment. In this paper we report on tests of multiple alignment quality, comparing SAM-T99 to the standard multiple aligner, CLUSTALW. Results: The paper evaluates the multiple-alignment aspect of the SAM-T99 protocol, using the BAliBASE benchmark alignment database. On these benchmarks, SAM-T99 is comparable in accuracy with ClustalW.
Protein Engineering Design & Selection, Oct 24, 2005
This paper proposes a strategy to translate experimental 1 H NMR proton distance restraints into ... more This paper proposes a strategy to translate experimental 1 H NMR proton distance restraints into their corresponding heavy atom distance restraints for the purpose of protein structure prediction. The relationships between interproton distances and the corresponding heavy atom distances are determined by studying well-resolved X-ray protein structures. The data from the interproton distances of amide protons, a-protons, b-protons and side chain methyl protons are plotted against the corresponding heavy atoms in scatter plots and then fitted with linear equations for lower bounds, upper bounds and optimal fits. We also transform the scatter plots into two-dimensional heat maps and three-dimensional histograms, which identify the regions where data points concentrate. The common interproton distances between amide protons, a-protons, b-protons in a-helices, antiparallel b-sheets and parallel b-sheets are also tabulated. We have found several patterns emerging from the distance relationships between heavy atom pairs and their corresponding proton pairs. All our upper bound, lower bound and optimal fit results for translating the interproton distance into their corresponding heavy atom distances are tabulated.
Our group tested three quality assessment functions in CASP8: a function which used only distance... more Our group tested three quality assessment functions in CASP8: a function which used only distance constraints derived from alignments (SAM-T08-MQAO), a function which added other single-model terms to the distance constraints (SAM-T08-MQAU), and a function which used both single-model and consensus terms (SAM-T08-MQAC). We analyzed the functions both for ranking models for a single target and for producing an accurate estimate of GDT TS. Our functions were optimized for the ranking problem, so are perhaps more appropriate for metaserver applications than for providing a trustworthiness estimate for single models. On the CASP8 test, the functions with more terms performed better. The MQAC consensus method was substantially better than either single-model function, and the MQAU function was substantially better than the MQAO function that used only constraints from alignments.
Motivation: Our focus has been on detecting topological properties that are rare in real proteins... more Motivation: Our focus has been on detecting topological properties that are rare in real proteins, but occur more frequently in models generated by protein structure prediction methods such as Rosetta. We previously created the Knotfind algorithm, successfully decreasing the frequency of knotted Rosetta models during CASP6. We observed an additional class of knot-like loops that appeared to be equally un-protein-like and yet do not contain a mathematical knot. These topological features are commonly referred to as slipknots and are caused by the same mechanisms that result in knotted models. Slip-knots are undetectable by the original Knotfind algorithm. We have generalized our algorithm to detect them, and analyzed CASP6 models built using the Rosetta loop modeling method. Results: After analyzing known protein structures in the PDB, we found that slip-knots do occur in certain proteins, but are rare and fall into a small number of specific classes. Our group used this new Pokefind algorithm to distinguish between these rare real slip-knots and the numerous classes of slip-knots that we discovered in Rosetta models and models submitted by the various CASP7 servers. The goal of this work is to improve future models created by protein structure prediction methods. Both algorithms are able to detect unprotein-like features that current metrics such as GDT are unable to identify, so these topological filters can also be used as additional assessment tools.
This article describes the use of binary decision diagrams (BDDs) and if-then-else dags for repre... more This article describes the use of binary decision diagrams (BDDs) and if-then-else dags for representing and manipulating Boolean functions. Two-cuts are de ned for binary decision diagrams, and a relationship is exhibited between general if-then-else expressions and the two-cuts of a BDD for the same function. An algorithm for computing all two-cuts of a BDD in O(n 2 ) time is given. A new canonical form for if-then-else dags, analogous to Bryant's canonical form for BDDs, is introduced. The canonical form is based on representing the lowest non-trivial two-cut in the corresponding BDD, while Bryant's canonical form represents the highest two-cut. Expressions in Bryant's canonical form or in the new canonical form are shown to be prime and irredundant. Some applications of if-then-else dags to multi-level logic minimization are given, and the Printform transformations for reducing the complexity of if-then-else dags are presented. This research was partially supported by an IBM Faculty Development Award and by NSF grant DCR-8503262.
This paper presents a new algorithm, Xmap, for doing mapping from multi-level logic to field-prog... more This paper presents a new algorithm, Xmap, for doing mapping from multi-level logic to field-programmable gate arrays based on table-lookup gates, such as those used in the Xilinx chip. The algorithm is baaed on an if-then-else DAG representation for the functions. The technology mapper differs from previous mappers in that the circuit is not decomposed into fan-out-free trees. The Xmap algorithm uses 7% fewer cells than Chortle, 1170 fewer than misII, and 14~0 fewer than mis-pga, and is 4.5 times faster than Chortle, 17 times faster than misII, and at least 150 times faster than mis-pga.
SPrCY is a web-accessible database which provides comparison of structure prediction results for ... more SPrCY is a web-accessible database which provides comparison of structure prediction results for the Saccharomyces cerevisiae genome. This web service offers the ability to search, analyze and compare the yeast structural predictions from sequence-only (Superfamily, PDBAA BLAST and Pfam) and sequence-structure-based (SAM-T02, 3D-PSSM, mGenTHREADER) methods.
IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, 1990
Most RC simulators handle only tree networks, not arbitrary networks. We present an algorithm for... more Most RC simulators handle only tree networks, not arbitrary networks. We present an algorithm for computing signal delays in general RC networks using the RC-tree computation as the primary operation. We partition a given network into a spanning tree and links. Then we compute the signal delay of the spanning tree, and update the signal delay as we incrementally add the links back to reconstruct the original network. If rn is the number of links, this algorithm requires m ( r i i + 1)/2 updates and !ti + 1 tree delay evaluations. All the tree delay evaluations involve computing signal delays with the same resistive spanning tree, but with different values for the capacitors.
This is a draft of the report of the Accreditation Task Force. It is nearing the final form, but ... more This is a draft of the report of the Accreditation Task Force. It is nearing the final form, but there are still big holes in it where volunteers did not follow through on their promises. Accreditation means different things in different parts of the world and in different academic cultures even within one country. It is difficult to come up with a meaningful world-wide accreditation system or set of standards for our field.
Journal of the Acoustical Society of America, Sep 1, 1987
BACKGROUND OF THE INVENTION ral the filtering method requires a large number of multiplication st... more BACKGROUND OF THE INVENTION ral the filtering method requires a large number of multiplication steps which are economically expen-This invention relates to musical instruments and srve^ 0 achieve, more specifically to digitally controlled electronic in-In a typical example of a filter technique, a wavestruments and methods for generating musical sound. 15 shape memory provides digital samples of one cycle of Digitally controlled methods of generating musical a waveshape to a loop circuit which includes a filter and ...
This paper makes a quantitative comparison of different methods, called regularizers, for estimat... more This paper makes a quantitative comparison of different methods, called regularizers, for estimating the distribution of amino acids in a specific context, given a very small sample of amino acids from that distribution. The regularizers considered here are zero-offsets, pseudocounts, substitution matrices (with several variants), and Dirichlet mixture regularizers. Each regularizer is evaluated based on how well it estimates the distributions of the columns of a multiple alignment--specifically, the expected encoding cost per amino acid using the regularizer and all possible samples from each column. In general, pseudocounts give the lowest encoding costs for samples of size zero, substitution matrices give the lowest encoding costs for samples of size one, and Dirichlet mixtures give the lowest for larger samples. One of the substitution matrix variants, which added pseudocounts and scaled counts, does almost as well as the best known Dirichlet mixtures, but with a lower computation cost.
Motivation: SAM-T99 is an iterative hidden Markov model-based method for finding proteins similar... more Motivation: SAM-T99 is an iterative hidden Markov model-based method for finding proteins similar to a single target sequence and aligning them. One of its main uses is to produce multiple alignments of homologs of the target sequence. Previous tests of SAM-T99 and its predecessors have concentrated on the quality of the searches performed, not on the quality of the multiple alignment. In this paper we report on tests of multiple alignment quality, comparing SAM-T99 to the standard multiple aligner, CLUSTALW. Results: The paper evaluates the multiple-alignment aspect of the SAM-T99 protocol, using the BAliBASE benchmark alignment database. On these benchmarks, SAM-T99 is comparable in accuracy with ClustalW.
Protein Engineering Design & Selection, Oct 24, 2005
This paper proposes a strategy to translate experimental 1 H NMR proton distance restraints into ... more This paper proposes a strategy to translate experimental 1 H NMR proton distance restraints into their corresponding heavy atom distance restraints for the purpose of protein structure prediction. The relationships between interproton distances and the corresponding heavy atom distances are determined by studying well-resolved X-ray protein structures. The data from the interproton distances of amide protons, a-protons, b-protons and side chain methyl protons are plotted against the corresponding heavy atoms in scatter plots and then fitted with linear equations for lower bounds, upper bounds and optimal fits. We also transform the scatter plots into two-dimensional heat maps and three-dimensional histograms, which identify the regions where data points concentrate. The common interproton distances between amide protons, a-protons, b-protons in a-helices, antiparallel b-sheets and parallel b-sheets are also tabulated. We have found several patterns emerging from the distance relationships between heavy atom pairs and their corresponding proton pairs. All our upper bound, lower bound and optimal fit results for translating the interproton distance into their corresponding heavy atom distances are tabulated.
Our group tested three quality assessment functions in CASP8: a function which used only distance... more Our group tested three quality assessment functions in CASP8: a function which used only distance constraints derived from alignments (SAM-T08-MQAO), a function which added other single-model terms to the distance constraints (SAM-T08-MQAU), and a function which used both single-model and consensus terms (SAM-T08-MQAC). We analyzed the functions both for ranking models for a single target and for producing an accurate estimate of GDT TS. Our functions were optimized for the ranking problem, so are perhaps more appropriate for metaserver applications than for providing a trustworthiness estimate for single models. On the CASP8 test, the functions with more terms performed better. The MQAC consensus method was substantially better than either single-model function, and the MQAU function was substantially better than the MQAO function that used only constraints from alignments.
Motivation: Our focus has been on detecting topological properties that are rare in real proteins... more Motivation: Our focus has been on detecting topological properties that are rare in real proteins, but occur more frequently in models generated by protein structure prediction methods such as Rosetta. We previously created the Knotfind algorithm, successfully decreasing the frequency of knotted Rosetta models during CASP6. We observed an additional class of knot-like loops that appeared to be equally un-protein-like and yet do not contain a mathematical knot. These topological features are commonly referred to as slipknots and are caused by the same mechanisms that result in knotted models. Slip-knots are undetectable by the original Knotfind algorithm. We have generalized our algorithm to detect them, and analyzed CASP6 models built using the Rosetta loop modeling method. Results: After analyzing known protein structures in the PDB, we found that slip-knots do occur in certain proteins, but are rare and fall into a small number of specific classes. Our group used this new Pokefind algorithm to distinguish between these rare real slip-knots and the numerous classes of slip-knots that we discovered in Rosetta models and models submitted by the various CASP7 servers. The goal of this work is to improve future models created by protein structure prediction methods. Both algorithms are able to detect unprotein-like features that current metrics such as GDT are unable to identify, so these topological filters can also be used as additional assessment tools.
This article describes the use of binary decision diagrams (BDDs) and if-then-else dags for repre... more This article describes the use of binary decision diagrams (BDDs) and if-then-else dags for representing and manipulating Boolean functions. Two-cuts are de ned for binary decision diagrams, and a relationship is exhibited between general if-then-else expressions and the two-cuts of a BDD for the same function. An algorithm for computing all two-cuts of a BDD in O(n 2 ) time is given. A new canonical form for if-then-else dags, analogous to Bryant's canonical form for BDDs, is introduced. The canonical form is based on representing the lowest non-trivial two-cut in the corresponding BDD, while Bryant's canonical form represents the highest two-cut. Expressions in Bryant's canonical form or in the new canonical form are shown to be prime and irredundant. Some applications of if-then-else dags to multi-level logic minimization are given, and the Printform transformations for reducing the complexity of if-then-else dags are presented. This research was partially supported by an IBM Faculty Development Award and by NSF grant DCR-8503262.
This paper presents a new algorithm, Xmap, for doing mapping from multi-level logic to field-prog... more This paper presents a new algorithm, Xmap, for doing mapping from multi-level logic to field-programmable gate arrays based on table-lookup gates, such as those used in the Xilinx chip. The algorithm is baaed on an if-then-else DAG representation for the functions. The technology mapper differs from previous mappers in that the circuit is not decomposed into fan-out-free trees. The Xmap algorithm uses 7% fewer cells than Chortle, 1170 fewer than misII, and 14~0 fewer than mis-pga, and is 4.5 times faster than Chortle, 17 times faster than misII, and at least 150 times faster than mis-pga.
SPrCY is a web-accessible database which provides comparison of structure prediction results for ... more SPrCY is a web-accessible database which provides comparison of structure prediction results for the Saccharomyces cerevisiae genome. This web service offers the ability to search, analyze and compare the yeast structural predictions from sequence-only (Superfamily, PDBAA BLAST and Pfam) and sequence-structure-based (SAM-T02, 3D-PSSM, mGenTHREADER) methods.
Uploads
Papers by Kevin Karplus