GMTKJT(1)

NAME
gmtkJT - a Graphical Models Toolkit (GMTK) 1.4.4 program

SYNOPSIS
gmtkJT [[[-flag] [option]] ...]

DESCRIPTION
This program computes the probability of evidence, and can also compute the posterior distributions of the hidden variables

OPTIONS
Required: <>; Optional: []; Flagless arguments must be in order.

Observation input file handling:

<-ofX str>
    Observation File. Replace X with the file number {null}

[-nfX unsigned]
    Number of floats in observation file X {0}

[-niX unsigned]
    Number of ints in observation file X {0}

[-fmtX str]
    Format (htk,binary,ascii,flatascii,hdf5,pfile) for observation file X {pfile}

[-fileBufferSize unsigned]
    Size in MB of the file observation frame buffer {16}

[-constantSpace bool]
    Use only fileBufferSize memory to hold the observation data {F}

[-fileWindowSize unsigned]
    Size in MB to load at once if constantSpace is active {4}

[-fileWindowDelta unsigned]
    How close (in frames) from the edge of the current window triggers loading more frames {100}

[-iswpX bool]
    Endian swap condition for observation file X {T}

[-prefrX str]
    Float range for observation file X (before transforms) {all}

[-preirX str]
    Int range for observation file X {all}

[-frX str]
    Float range for observation file X (after transforms) {all}

[-irX str]
    Int range for observation file X {all}

[-srX str]
    Segment range for observation file X {all}

[-leftPadX unsigned]
    Prepend padding frames to file X {0}

[-rightPadX unsigned]
    Append padding frames to file X {0}

[-preprX str]
    Pre Per-segment frame Range for obs file X before any transforms are applied {null}

[-postprX str]
    Post Per-segment frame Range for obs file X after per-stream transforms are applied {null}

[-gpr str]
    Global Per-segment final frame Range {null}

[-justification str]
    Justification of usable frames (left, center, right) {left}

[-obsNAN bool]
    True if observation files allow FP NAN values {F}

File range options:

[-dcdrng str]
    Range to decode over segment file {all}

[-startSkip integer]
    Frames to skip at beginning (i.e., first frame is buff[startSkip]) {0}

[-endSkip integer]
    Frames to skip at end (i.e., last frame is buff[len-1-endSkip]) {0}

Help options:

[-help [unsigned]]
    Print this message. Add an argument from 1 to 5 for increasing help info. {1}

[-version bool]
    Print GMTK version number and exit. {F}

Observation matrix transformation options:

[-fdiffactX str]
    Action if different number of frames in streams: error (er), repeat last frame (rl), first frame (rf), segmentally expand (se), truncate from start (ts), truncate from end (te) {er}

[-sdiffactX str]
    Action if different number of segments in streams: error (er), truncate from end (te), repeat last sent (rl), and wrap around (wa). {te}

[-cppifascii bool]
    Pre-process ASCII files using CPP {F}

[-transX str]
    per stream transformations string {null}

[-posttrans str]
    Final global transformations string {null}

[-comb str]
    Combine float features (none: no combination, add, sub, mul,div {none}

[-cppCommandOptions str]
    Command line options to give to 'cpp' {null}

Input trainable parameter file handling:

<-inputMasterFile str>
    Input file of multi-level master CPP processed GM input parameters {null}

[-mapX str]
    Deterministic mapping dynamic library file. Replace X with the file number {null}

[-inputTrainableParameters str]
    File of only and all trainable parameters {null}

[-binInputTrainableParameters bool]
    Binary condition of trainable parameters file {F}

[-allocateDenseCpts integer]
    Automatically allocate undefined CPTs. (-1) = don't read params, (0) = don't allocate, (1) = use random initial CPT values, (2) = use uniform values {0}

[-cptNormThreshold double]
    Read error if |Sum-1.0|/card > norm_threshold {1.000000e-02}

Input model file handling:

<-strFile str>
    Graphical Model Structure File {null}

[-checkTriFileCards bool]
    Verify rv cardinalities in triangulation file match .str file {T}

[-triFile str]
    Triangulation file for strFile {null}

[-jtFile str]
    Name of file to write junction tree information {jt_info.txt}

[-jtwUB bool]
    True means jtWeight is allways an upper bound on true JT weight, false means jtWeight is estimate {F}

Continuous random variable options:

[-varFloor double]
    Variance Floor (variances can't fall below this value) {1.000000e-10}

[-floorVarOnRead bool]
    Floor the variances to varFloor when they are read in {F}

Beam pruning options:

[-cbeam double]
    Clique beam width to prune clique (log value) {1.000000e+17}

[-cpbeam double]
    Clique beam width while building cliques (log value) {1.000000e+17}

[-cpfilter str]
    Adaptive filter to use for clique bild pruning {}

[-cpch bool]
    For clique beam build pruning, use a continuation heurisic within the rest of the clique {T}

[-cpef double]
    For clique beam build pruning, the amount that the beam expands each time we find a zero clique {1.000000e+00}

[-cpme unsigned]
    For clique beam build pruning, the maximum number of expansions before we fail and exit {1}

[-ckbeam unsigned]
    Prune to this clique max state space (0 = no pruning) {0}

[-cusample double]
    Uniformly sample pruned clique (0<v=<=1 fraction, > 1 number) {0.000000e+00}

[-ccclusters unsigned]
    Number of clusters to use in cluster pruning {0}

[-ccbeam double]
    Clique cluster beam width to prune clique clusters (log value) {1.000000e+17}

[-cckbeam unsigned]
    Max number of states in each cluster in cluster pruning {4294967295}

[-ccrbeam float]
    Fraction of in-cluster clique state space to retain. Range: 0 < v <= 1. {1.000000e+00}

[-ccmbeam double]
    Percentage of clique cluster mass to retain. Range: 0 < v <= 1. v = 1.0 means no pruning {1.000000e+00}

[-ccmexp double]
    Exponent to apply to clique cluster scores when doing mass pruning. Must be non-negative. {1.000000e+00}

[-ccmmin unsigned]
    When using -cmbeam, min possible resulting clique cluster state size (>= 1) {1}

[-ccmfurther double]
    When using -ccmbeam, additional beam to use after mass has been acounted for (>= 0) {0.000000e+00}

[-crbeam float]
    Fraction of clique state space to retain. Range: 0 < v <= 1. v = 1 means no pruning {1.000000e+00}

[-cmbeam double]
    Percentage of clique mass to relinquish. Range: 0 < v <= 1. v = 1.0 means no pruning {1.000000e+00}

[-cmexp double]
    Exponent to apply to clique scores when doing mass pruning. Must be non-negative. {1.000000e+00}

[-cmmin unsigned]
    When using -cmbeam, min possible resulting clique state size (>= 1) {1}

[-cmfurther double]
    When using -cmbeam, additional beam to use after mass has been acounted for (>= 0) {0.000000e+00}

[-sbeam double]
    Separator beam width pruning log value {1.000000e+17}

Memory management options:

[-memoryGrowth str]
    Rate to grow data structures (conservative, default, aggressive) {default}

[-hashLoadFactor float]
    Hash table load factor, in range 0.05 <= lf <= 1.0 {5.000000e-01}

[-deterministicChildrenStore bool]
    Store deterministic children in clique memory {T}

[-clearCliqueValMem bool]
    Free clique/separator value cache for each segment {T}

[-mmapViterbiValues bool]
    Use mmap() to get memory to hold Viterbi values {T}

General options:

[-seed bool]
    Seed the random number generator {F}

[-skipStartupChecks bool]
    Skip expensive model validity checks performed at GMTK startup {F}

[-verbosity str]
    Verbosity - coma separated list of m=v, where m is all, default, inference, inference-memory, training, triangulation, boundary, unrolling, printing, modelinfo, obsfile, obsstream; 0 <= v <= 100 {null}

[-printIntValues bool]
    Always print rv values as integer rather than symbols {F}

Clique posterior output options:

[-pCliquePrintRange str]
    With CE/DE, print range cliques from P section. {null}

[-cCliquePrintRange str]
    With CE/DE, print range cliques from C section. {null}

[-eCliquePrintRange str]
    With CE/DE, print range cliques from E section. {null}

[-cliquePrintOnlyEntropy bool]
    With CE/DE, print only clique entropies. {F}

[-cliquePosteriorNormalize bool]
    Normalize posterior probabilities to sum to 1. {T}

[-cliquePosteriorUnlog bool]
    Output probabilities instead of log probabilities. {T}

[-cliqueOutputFileName str]
    Output filename for clique posteriors. {null}

[-cliqueListFileName str]
    Output list filename for clique posteriors (HDF5, HTK, ASCII, Binary). {null}

[-cliquePrintSeparator str]
    String to use as separator when outputting HTK, ASCII, or binary clique posteriors. {_}

[-cliquePrintSwap bool]
    Do byte swapping when outputting PFile, HTK, or binary clique posteriors. {F}

[-cliquePrintFormat str]
    Output file format for clique posteriors (hdf5,htk,binary,ascii,flatascii,pfile). {pfile}

Inference options:

[-island bool]
    Run island algorithm {F}

[-base str]
    Island algorithm logarithm base (integer or 'root') {3}

[-root float]
    use T^r as the island logarithm base, where T is the number of frames {5.000000e-01}

[-lst unsigned]
    Island algorithm linear segment threshold {100}

[-debugSections str]
    Section range to generate debug output {all}

[-debugIncrement integer]
    Increment to adjust inference verbosity on USR1/2 signals {1}

[-componentCache bool]
    Cache mixture probabilities, faster but uses more memory. {T}

[-vsap str]
    Variable section assignment priority. Sequence of chars in set [C,D,O,B,S,I,A,F,N] {COI}

[-vcap str]
    Variable clique sorting priority. Sequence of chars in set [C,D,O,B,S,I,A,F,N,T,M,+,.] {COT}

[-jcap str]
    Junction Tree Clique MST Sorting Priority. From Set: [D,E,S,U,V,W,H,O,L,Q] {DSU}

[-icap str]
    Interface Clique Priority Determiner Priority. From Set: [W,D,H,O,I] {W}

[-useVESeparators unsigned]
    Use Virtual Evidence (VE) Separators (if any are available) during inference (Bitwise or of 0x1 (PC) or PCG (0x2) {3}

[-veSepWhere unsigned]
    Where to use VE seps. Bitwise or of 0x1 (P), 0x2 (C), 0x4 (E) {0}

[-veSepFileName str]
    Name of VE separators file to store VE sep/read previous VE sep info {veSeparatorFile.dat}

[-veSepRecompute bool]
    Force a re-compute of VE separator information {F}

[-veSepLogProdCardLimit float]
    The log (base 10) upper limit on a VE sep variable cardinality product {7.000000e+00}

[-viterbiScore bool]
    Compute p(o,h_max) (rather than sum_h p(o,h)) {F}

[-doDistributeEvidence bool]
    Also run distribute-evidence {F}

[-sectionPartialDoDist bool]
    Compute P(Q_t|X_{0:t}), where Q_t are the hidden variables in modified section t and X_{0:t} is the evidence observed up to modified section t {F}

[-keepOnlyInterfaceSeparatorMemory bool]
    Use a slower but more memory efficient inference implementation {F}

[-failOnZeroClique bool]
    abort GMTK program on zero clique errors {T}

[-probE bool]
    Run the constant memory prob(evidence) function {F}

[-cliqueTableNormalize float]
    Normalize scores of each clique right after its creation (increases dynamic range). {1.000000e+00}

Lattice options:

[-latticeDefaultFrameRate double]
    Lattice, default frame rate (if negative, compute from file) {-1.000000e+02}

[-latticeUseMaxScore bool]
    Lattice, use max edge score for node CPT {T}

[-latticeIgnoreNodeTimeMarks bool]
    Lattice, ignore lattice node time marks in all lattices {F}

Additional arguments:

[-argsFile <str>]
    File to obtain additional arguments from {}

Mercurial id: 2e685b02ff37 checkin date: Fri Dec 04 02:13:34 2015 -0800

ENVIRONMENT

GMTKTMPDIR
    Temporary directory gmtkDMLPtrain uses to store neural network parameters

GMTK_CPP_CMD
    Command GMTK programs use to preprocess ASCII input files

GMTK_GZIP_CMD
    Command GMTK programs use to uncompress ASCII input files with ".gz" extensions

GMTK_BZIP2_CMD
    Command GMTK programs ue to uncompress ASCII input files with ".bz2" extensions

REPORTING BUGS
Report bugs to http://j.ee.washington.edu/trac/gmtk

COPYRIGHT
Copyright © 2001-2015 Jeff Bilmes

Licensed under the Open Software License version 3.0
See COPYING or http://opensource.org/licenses/OSL-3.0

SEE ALSO
The GMTK source code and full documentation is available at
http://melodi.ee.washington.edu/gmtk

Support is availabe via the GMTK Users' mailing list
gmtk-users@u.washington.edu

Subscribe at
http://mailman.u.washington.edu/mailman/listinfo/gmtk-users