search for: viterbi

Dear list, This question is about Hidden Markov Model. Given a transition matrix, an emission matrix and a sequence of observed symbols (actually, nucleotide sequences, A, T, C and G), I hope to predict the sequence of state by Viterbi algorithm. I searched R repository for related packages. msm package has function viterbi.msm (as well as very good document), but it only works for continuous-time condition. Other two HMM related packages, hmm.discnp and repeats, however, does not have such a function (similar to "hmmvite...

...uce a new package called ?aphid?, for analysis with profile hidden Markov models in R. The package contains functions for multiple and pairwise sequence alignment for both nucleic acids and proteins (preferably in the DNAbin or AAbin format), model building, parameter optimization (Baum Welch and Viterbi training), plotting, file import & export, tree-based sequence weighting, simulation, and implementation of the forward, backward and Viterbi algorithms for calculating sequence probabilities. Standard HMMs are also supported, with functions for building, training, plotting, sequence simulati...

...uce a new package called ?aphid?, for analysis with profile hidden Markov models in R. The package contains functions for multiple and pairwise sequence alignment for both nucleic acids and proteins (preferably in the DNAbin or AAbin format), model building, parameter optimization (Baum Welch and Viterbi training), plotting, file import & export, tree-based sequence weighting, simulation, and implementation of the forward, backward and Viterbi algorithms for calculating sequence probabilities. Standard HMMs are also supported, with functions for building, training, plotting, sequence simulati...

...n R. This is what I have so far. hmm <- initHMM(c("stay", "switch"), c("correct", "incorrect"), c(.5, .5), matrix(c(.9, .1, .1, .9),2), matrix(c(.2, .8, .8, .2), 2)) dat$test <- ifelse(dat$Slide1_ACC == 0, "incorrect", "correct") viterbi(hmm, dat$test) The sequence of observations I run through the model is the feedback the participant receives. Any help would be greatly appreciated. I think what I want to do is run the model on each participant to generate the most probable path and then compare that to the actual path to see...

...a simple discrete, two-state HMM, but my training data is irregularly shaped (i.e. the observation chains are of varying length). Additionally, I do not see how to label the state of the observations given to the hmm() function. Ultimately, I'd like to 1) train the hmm on labeled data, 2) use viterbi() to calculate optimal labeling of unlabeled observations. More concretely, I have labeled data that looks something like: 11212321221223121221112233222122112 AAAAAAAAABBBBBBBBBBBBBAAAAAAAAAAAAA 21221223121221112233222122112 AAAAAAAAABBBBBBBBBBBBBAAAAAAA 3121221112233222122112 B...

...quot;signature" and the values seem to be intuitive. My question is more a fundamental one in regards to understanding HMMs. I know I should use more examples of the above sequences to train the HMM in order to make it more robust. Assuming, that the HMM is trained good enough, I can use the viterbi algorithm to find the most probable sequence of hidden states. However, what I really want to find out is whether a particular observed sequence is modeled by my HMM (created above). There seems to be a viterbi() function in hmm.discnp and also mps() but both of them give them most probable hidden...

Dear R users, I am looking for the source code of the implementation of ppr (Projection Pursuit Regression) in R. It will be great if citations of the source papers on which the implementation is based, are also provided. Thank you, Arvind Iyer, Grad student, Deptt. of Biomedical Engineering Viterbi School of Engineering University of Southern California, Los Angeles [[alternative HTML version deleted]]

...gets. The idea is to turn: for (i = 0 .. 100) A[i] = 4; into: for (i = 100 .. 0) A[i] = 4; Another transform that needs dependence analysis which would be even more useful (but still very simple) is a "loops to memset/memcpy" pass. This optimization would speed up the 'viterbi' program in the test suite a *lot* for the various 'history' loops. A simple version of this is: for (i = 0 .. 100) A[i] = 0; -> memset(A, 0, sizeof(A[0])*100); >> I'd suggest looking at: >> >> Using the chains of recurrences algebra for data depend...

...167 6 37 1143 136 4 10 treecc 127 1 0 0 1 350 37 0 1 viterbi 7 0 1 0 1 1 0 0 0 Of these categories, the first 3 will become salvageable after this work is implemented, and Select Insts will also be salvageable...

...SC), founded in 1880, is the largest private employer in the City of Los Angeles and proud recipient of Time Magazine's College of the Year 2000. USC offers competitive pay and an outstanding benefits package. **PLEASE NOTE THAT THIS POSITION IS LOCATED IN Marina del Rey, California** The USC Viterbi School of Engineering's Information Sciences Institute (ISI) in Marina del Rey, California is one of the world's leading research centers in the fields of computer science and information technology. ISI is seeking a Network Operations Specialist for their Computer Networks Division, one o...

...xternal/SPEC/CINT2000/186.crafty/186.crafty -4.6% External/SPEC/CFP2000/188.ammp/188.ammp -4.5% SingleSource/Benchmarks/Misc/oourafft -4.5% MultiSource/Applications/sqlite3/sqlite3 -4.4% MultiSource/Applications/lua/lua -4.4% MultiSource/Benchmarks/Bullet/bullet -4.2% MultiSource/Applications/viterbi/viterbi -4.1% External/SPEC/CINT2006/403.gcc/403.gcc -4.0% External/SPEC/CINT2000/256.bzip2/256.bzip2 -3.9% MultiSource/Benchmarks/MallocBench/espresso/espresso -3.8% MultiSource/Benchmarks/tramp3d-v4/tramp3d-v4 -3.5% SingleSource/Benchmarks/Adobe-C++/simple_types_constant_folding -3.4% Multi...

...h spend lots of time accessing pointers off 'this'. 5. There are lots of ways to optimize out and improve handling of memcpy/memset (PR452) 6. It would be excellent to replace loops with scalar stores in them into memset/memcpy calls. This dramatically speeds up programs like 'viterbi' in the testsuite. 7. There may still be some ideas in PR1373 left. -Chris

...I'll have time for it in the nearest future. Maybe someone else is interested?:) > Another transform that needs dependence analysis which would be even > more useful (but still very simple) is a "loops to memset/memcpy" > pass. This optimization would speed up the 'viterbi' program in the > test suite a *lot* for the various 'history' loops. Ok, but, unfortunately, as above... Wojtek

Hello, all. To get my feet wet and hopefully make a small contribution, I was looking for something small to start with. I settled on one of the suggestions from the CodeGen readme: > Reassociate should turn things like: > > int factorial(int X) { > return X*X*X*X*X*X*X*X; > } > > into llvm.powi calls, allowing the code generator to > produce balanced multiplication

> Ok. I think the most important thing to keep in mind, if you want > this to be useful for LLVM, is for it to be sound in the presence of > incomplete programs. I think it would be very interesting to have a > BDD based analysis in LLVM, it would be useful for performance > comparisons and many other things, even if it isn't turned on by > default. However, it must

...ot.mspath pmatrix.mspath pmatrix.piecewise.mspath prevalence.mspath print.mspath print.summary.mspath qematrix.diagse.formstr qematrix.diagse.mspath qematrix.mspath qmatrix.mspath qratio.mspath qratio.se.mspath sojourn.mspath statetable.mspath summary.mspath totlos.mspath transient.mspath viterbi.mspath Undocumented data sets: e2 gold q2 All user-level objects in a package should have documentation entries. See chapter 'Writing R documentation files' in manual 'Writing R Extensions'. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK...

Hi all, I've started looking at the GlobalMerge pass, enabled by default on ARM and AArch64. I think we should reconsider that, at least for AArch64. As is, the pass just merges all globals together, in groups of 4KB (AArch64, 128B on ARM). At the time it was enabled, the general thinking was "it's almost free, it doesn't affect performance much, we might as well use it".

...ultiSource/Applications/aha/aha | * | * | MultiSource/Applications/lemon/lemon | * | * | MultiSource/Applications/Burg/burg | * | * | MultiSource/Applications/viterbi/viterbi | * | * | MultiSource/Applications/obsequi/Obsequi | * | * | MultiSource/Applications/spiff/spiff | * | * | MultiSource/Applications/hbd/hbd...

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Hi, > Cool! I think the most critical part of this is to get a good > interface for dependence analysis. There are lots of interesting > implementations that have various time/space tradeoffs. > > For example, it would be great if Omega was available as an option, > even if the compiler didn't use it by default. This argues for making > dependence analysis