Annotation of OpenXM/src/hgm/doc/ref-hgm.html, Revision 1.31
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10: <body>
11:
12: <h1> References for the Holonomic Gradient Method (HGM) and
13: the Holonomic Gradient Descent Method (HGD) </h1>
14:
15: <h2> Papers and Tutorials</h2>
16: <ol>
1.30 takayama 17: <li> M.Adamer, A.Lorincz, A.L.Sattelberger, B.Sturmfels, Algebraic Analysis of Rotation Data
18: <a href="https://arxiv.org/abs/1912.00396"> arxiv: 1912.00396 </a>
1.28 takayama 19: <li>
1.29 takayama 20: Anna-Laura Sattelberger, Bernd Sturmfels,
21: D-Modules and Holonomic Functions
22: <a href="https://arxiv.org/abs/1910.01395"> arxiv:1910.01395 </a>
23: <li>
1.28 takayama 24: N.Takayama, L.Jiu, S.Kuriki, Y.Zhang,
25: Computations of the Expected Euler Characteristic for the Largest Eigenvalue of a Real Wishart Matrix,
1.31 ! takayama 26: <!--
! 27: <a href="https://arxiv.org/abs/1903.10099"> arxiv:1903.10099 </a> -->
! 28: <a href="https://doi.org/10.1016/j.jmva.2020.104642"> jmva </a>
1.27 takayama 29: <li> M.Harkonen, T.Sei, Y.Hirose,
30: Holonomic extended least angle regression,
31: <a href="https://arxiv.org/abs/1809.08190"> arxiv:1809.08190 </a>
32: <li> S.Mano,
33: Partitions, Hypergeometric Systems, and Dirichlet Processes in Statistics,
34: <a href="https://www.springer.com/jp/book/9784431558866">
35: JSS Research Series in Statistics</a>, 2018.
1.26 takayama 36: <li> A.Kume, T.Sei,
37: On the exact maximum likelihood inference of Fisher–Bingham distributions using an adjusted holonomic gradient method,
38: <a href="https://doi.org/10.1007/s11222-017-9765-3"> doi </a> (2018)
1.24 takayama 39: <li> Yoshihito Tachibana, Yoshiaki Goto, Tamio Koyama, Nobuki Takayama,
40: Holonomic Gradient Method for Two Way Contingency Tables,
1.25 takayama 41: <a href="https://arxiv.org/abs/1803.04170"> arxiv:1803.04170 </a>
42: <li> F.H.Danufane, K.Ohara, N.Takayama, C.Siriteanu,
43: Holonomic Gradient Method-Based CDF Evaluation for the Largest Eigenvalue of a Complex Noncentral Wishart Matrix
44: (Title of the version 1: Holonomic Gradient Method for the Distribution Function of the Largest Root of Complex Non-central Wishart Matrices),
1.23 takayama 45: <a href="https://arxiv.org/abs/1707.02564"> arxiv:1707.02564 </a>
46: <li> T.Koyama,
47: An integral formula for the powered sum of the independent, identically and normally distributed random variables,
48: <a href="https://arxiv.org/abs/1706.03989"> arxiv:1706.03989 </a>
1.21 takayama 49: <li> H.Hashiguchi, N.Takayama, A.Takemura,
50: Distribution of Ratio of two Wishart Matrices and Evaluation of Cumulative Probability
51: by Holonomic Gradient Method,
52: <a href="https://arxiv.org/abs/1610.09187"> arxiv:1610.09187 </a>
53:
1.18 takayama 54: <li> R.Vidunas, A.Takemura,
55: Differential relations for the largest root distribution
56: of complex non-central Wishart matrices,
57: <a href="http://arxiv.org/abs/1609.01799"> arxiv:1609.01799 </a>
58:
1.20 takayama 59: <li> S.Mano,
60: The A-hypergeometric System Associated with the Rational Normal Curve and
61: Exchangeable Structures,
62: <a href="http://arxiv.org/abs/1607.03569"> arxiv:1607.03569 </a>
63:
1.19 takayama 64: <li> M.Noro,
65: System of Partial Differential Equations for the Hypergeometric Function 1F1 of a Matrix Argument on Diagonal Regions,
66: <a href="http://dl.acm.org/citation.cfm?doid=2930889.2930905"> ACM DL </a>
67:
1.12 takayama 68: <li> Y.Goto, K.Matsumoto,
69: Pfaffian equations and contiguity relations of the hypergeometric function of type (k+1,k+n+2) and their applications,
1.13 takayama 70: <a href="http://arxiv.org/abs/1602.01637"> arxiv:1602.01637 </a>
71:
72: <li> T.Koyama,
73: Holonomic gradient method for the probability content of a simplex
74: region
75: with a multivariate normal distribution,
76: <a href="http://arxiv.org/abs/1512.06564"> arxiv:1512.06564 </a>
77:
78:
79: <li> N.Takayama, S.Kuriki, A.Takemura,
80: A-Hpergeometric Distributions and Newton Polytopes,
81: <a href="http://arxiv.org/abs/1510.02269"> arxiv:1510.02269 </a>
82:
83: <li> G.Weyenberg, R.Yoshida, D.Howe,
84: Normalizing Kernels in the Billera-Holmes-Vogtmann Treespace,
85: <a href="http://arxiv.org/abs/1506.00142"> arxiv:1506.00142 </a>
86:
1.17 takayama 87: <li> C.Siriteanu, A.Takemura, C.Koutschan, S.Kuriki, D.St.P.Richards, H.Sin,
88: Exact ZF Analysis and Computer-Algebra-Aided Evaluation
89: in Rank-1 LoS Rician Fading,
90: <a href="http://arxiv.org/abs/1507.07056"> arxiv:1507.07056 </a>
91:
1.13 takayama 92: <li> K.Ohara, N.Takayama,
93: Pfaffian Systems of A-Hypergeometric Systems II ---
94: Holonomic Gradient Method,
95: <a href="http://arxiv.org/abs/1505.02947"> arxiv:1505.02947 </a>
96:
97: <li> T.Koyama,
98: The Annihilating Ideal of the Fisher Integral,
99: <a href="http://arxiv.org/abs/1503.05261"> arxiv:1503.05261 </a>
100:
101: <li> T.Koyama, A.Takemura,
102: Holonomic gradient method for distribution function of a weighted sum
103: of noncentral chi-square random variables,
104: <a href="http://arxiv.org/abs/1503.00378"> arxiv:1503.00378 </a>
105:
106: <li> Y.Goto,
107: Contiguity relations of Lauricella's F_D revisited,
108: <a href="http://arxiv.org/abs/1412.3256"> arxiv:1412.3256 </a>
1.12 takayama 109:
1.15 takayama 110: <li>
111: T.Koyama, H.Nakayama, K.Ohara, T.Sei, N.Takayama,
112: Software Packages for Holonomic Gradient Method,
113: Mathematial Software --- ICMS 2014,
114: 4th International Conference, Proceedings.
115: Edited by Hoon Hong and Chee Yap,
116: Springer lecture notes in computer science 8592,
117: 706--712.
118: <a href="http://link.springer.com/chapter/10.1007%2F978-3-662-44199-2_105">
119: DOI
120: </a>
121:
1.11 takayama 122: <li>N.Marumo, T.Oaku, A.Takemura,
123: Properties of powers of functions satisfying second-order linear differential equations with applications to statistics,
124: <a href="http://arxiv.org/abs/1405.4451"> arxiv:1405.4451</a>
125:
1.8 takayama 126: <li> J.Hayakawa, A.Takemura,
127: Estimation of exponential-polynomial distribution by holonomic gradient descent
128: <a href="http://arxiv.org/abs/1403.7852"> arxiv:1403.7852</a>
129:
130: <li> C.Siriteanu, A.Takemura, S.Kuriki,
131: MIMO Zero-Forcing Detection Performance Evaluation by Holonomic Gradient Method
132: <a href="http://arxiv.org/abs/1403.3788"> arxiv:1403.3788</a>
133:
1.4 takayama 134: <li> T.Koyama,
1.1 takayama 135: Holonomic Modules Associated with Multivariate Normal Probabilities of Polyhedra,
136: <a href="http://arxiv.org/abs/1311.6905"> arxiv:1311.6905 </a>
137:
138: <li> T.Hibi, K.Nishiyama, N.Takayama,
139: Pfaffian Systems of A-Hypergeometric Equations I,
140: Bases of Twisted Cohomology Groups,
141: <a href="http://arxiv.org/abs/1212.6103"> arxiv:1212.6103 </a>
1.22 takayama 142: (major revision v2 of arxiv:1212.6103).
143: Accepted version is at
144: <a href="http://dx.doi.org/10.1016/j.aim.2016.10.021"> DOI </a>
1.1 takayama 145:
146: <li> <img src="./wakaba01.png" alt="Intro">
147: <a href="http://link.springer.com/book/10.1007/978-4-431-54574-3">
148: T.Hibi et al, Groebner Bases : Statistics and Software Systems </a>, Springer, 2013.
149:
150: <li> <img src="./wakaba01.png" alt="Intro">
151: Introduction to the Holonomic Gradient Method (movie), 2013.
152: <a href="http://www.youtube.com/watch?v=SgyDDLzWTyI"> movie at youtube </a>
153:
1.2 takayama 154:
1.1 takayama 155: <li> T.Sei, A.Kume,
1.2 takayama 156: Calculating the Normalising Constant of the Bingham Distribution on the Sphere using the Holonomic Gradient Method,
1.1 takayama 157: Statistics and Computing, 2013,
158: <a href="http://dx.doi.org/10.1007/s11222-013-9434-0">DOI</a>
159:
1.4 takayama 160: <li> T.Koyama, A.Takemura,
1.2 takayama 161: Calculation of Orthant Probabilities by the Holonomic Gradient Method,
162: <a href="http://arxiv.org/abs/1211.6822"> arxiv:1211.6822</a>
163:
1.1 takayama 164: <li>T. Koyama, H. Nakayama, K. Nishiyama, N. Takayama,
165: Holonomic Rank of the Fisher-Bingham System of Differential Equations,
166: <!-- <a href="http://arxiv.org/abs/1205.6144"> arxiv:1205.6144 </a>-->
1.11 takayama 167: Journal of Pure and Applied Algebra (online),
168: <a href="http://dx.doi.org/10.1016/j.jpaa.2014.03.004"> DOI </a>
1.1 takayama 169:
170: <li>
171: T. Koyama, H. Nakayama, K. Nishiyama, N. Takayama,
172: Holonomic Gradient Descent for the Fisher-Bingham Distribution on the d-dimensional Sphere,
173: <!-- <a href="http://arxiv.org/abs/1201.3239"> 1201.3239 </a> -->
174: Computational Statistics (2013)
175: <a href="http://dx.doi.org/10.1007/s00180-013-0456-z"> DOI </a>
176:
177: <li> Hiroki Hashiguchi, Yasuhide Numata, Nobuki Takayama, Akimichi Takemura,
178: Holonomic gradient method for the distribution function of the largest root of a Wishart matrix,
179: <!-- <a href="http://arxiv.org/abs/1201.0472"> 1201.0472 </a> -->
180: Journal of Multivariate Analysis, 117, (2013) 296-312,
181: <a href="http://dx.doi.org/10.1016/j.jmva.2013.03.011"> DOI </a>
182:
183: <li> Tomonari Sei, Hiroki Shibata, Akimichi Takemura, Katsuyoshi Ohara, Nobuki Takayama,
184: Properties and applications of Fisher distribution on the rotation group,
185: <!-- <a href="http://arxiv.org/abs/1110.0721"> 1110.0721 </a> -->
186: Journal of Multivariate Analysis, 116 (2013), 440--455,
187: <a href="http://dx.doi.org/10.1016/j.jmva.2013.01.010">DOI</a>
188:
189: <li>T.Koyama, A Holonomic Ideal which Annihilates the Fisher-Bingham Integral,
190: Funkcialaj Ekvacioj 56 (2013), 51--61.
1.11 takayama 191: <a href="http://dx.doi.org/10.1619/fesi.56.51">DOI</a>
192: <!-- <a href="https://www.jstage.jst.go.jp/article/fesi/56/1/56_51/_article">jstage</a> -->
1.1 takayama 193:
194: <li>
195: Hiromasa Nakayama, Kenta Nishiyama, Masayuki Noro, Katsuyoshi Ohara,
196: Tomonari Sei, Nobuki Takayama, Akimichi Takemura ,
197: Holonomic Gradient Descent and its Application to Fisher-Bingham Integral,
198: <!-- <a href="http://arxiv.org/abs//1005.5273"> arxiv:1005.5273 </a> -->
199: Advances in Applied Mathematics 47 (2011), 639--658,
200: <a href="http://dx.doi.org/10.1016/j.aam.2011.03.001"> DOI </a>
1.13 takayama 201:
1.1 takayama 202: </ol>
203:
1.13 takayama 204: Early papers related to HGM. <br>
205: <ol>
206: <li>
207: H.Dwinwoodie, L.Matusevich, E. Mosteig,
208: Transform methods for the hypergeometric distribution,
209: Statistics and Computing 14 (2004), 287--297.
210: </ol>
211:
212:
213:
1.2 takayama 214: <h2> Three Steps of HGM </h2>
215: <ol>
1.10 takayama 216: <li> Finding a holonomic system satisfied by the normalizing constant.
1.2 takayama 217: We may use computational or theoretical methods to find it.
218: Groebner basis and related methods are used.
1.10 takayama 219: <li> Finding an initial value vector for the holonomic system.
1.2 takayama 220: This is equivalent to evaluating the normalizing constant and its derivatives
221: at a point.
222: This step is usually performed by a series expansion.
1.10 takayama 223: <li> Solving the holonomic system numerically. We use several methods
1.2 takayama 224: in numerical analysis such as the Runge-Kutta method of solving
225: ordinary differential equations and efficient solvers of systems of linear
226: equations.
227: </ol>
228:
1.1 takayama 229: <h2> Software Packages for HGM</h2>
1.14 takayama 230:
1.15 takayama 231: <ul>
232: <li>
1.16 takayama 233: CRAN package <a href="https://cran.r-project.org/web/packages/hgm/index.html"> hgm </a> (for R).
1.14 takayama 234:
1.15 takayama 235: <li>
1.14 takayama 236: Some software packages are experimental and temporary documents are found in
1.6 takayama 237: "asir-contrib manual" (auto-autogenerated part), or
238: "Experimental Functions in Asir", or "miscellaneous and other documents"
239: of the
240: <a href="http://www.math.kobe-u.ac.jp/OpenXM/Current/doc/index-doc.html">
1.7 takayama 241: OpenXM documents</a>
1.8 takayama 242: or in <a href="./"> this folder</a>.
1.10 takayama 243: The nightly snapshot of the asir-contrib can be found in the asir page below,
1.6 takayama 244: or look up our <a href="http://www.math.sci.kobe-u.ac.jp/cgi/cvsweb.cgi/">
1.8 takayama 245: cvsweb page</a>.
1.1 takayama 246: <ol>
1.9 takayama 247: <li> Command line interfaces are in the folder OpenXM/src/hgm
248: in the OpenXM source tree. See <a href="http://www.math.kobe-u.ac.jp/OpenXM">
249: OpenXM distribution page </a>.
1.14 takayama 250: <li> Experimental version of <a href="http://www.math.kobe-u.ac.jp/OpenXM/Math/hgm/"> hgm package for R </a> (hgm_*tar.gz, hgm-manual.pdf) for the step 3.
1.11 takayama 251: To install this package in R, type in
252: <pre>
253: R CMD install hgm_*.tar.gz
254: </pre>
1.10 takayama 255: <li> The following packages are
256: for the computer algebra system
257: <a href="http://www.math.kobe-u.ac.jp/Asir"> Risa/Asir</a>.
258: They are in the asir-contrib collection.
259: <ul>
260: <li> yang.rr (for Pfaffian systems) ,
261: nk_restriction.rr (for D-module integrations),
262: tk_jack.rr (for Jack polynomials),
263: ko_fb_pfaffian.rr (Pfaffian system for the Fisher-Bingham system),
264: are for the steps 1 or 2.
265: <li> nk_fb_gen_c.rr is a package to generate a C program to perform
1.7 takayama 266: maximal Likehood estimates for the Fisher-Bingham distribution by HGD (holonomic gradient descent).
1.10 takayama 267: <li> ot_hgm_ahg.rr (HGM for A-distributions, very experimental).
268: </ul>
1.1 takayama 269: </ol>
270:
1.15 takayama 271: </ul>
272:
1.1 takayama 273: <h2> Programs to try examples of our papers </h2>
274: <ol>
275: <li> <a href="http://www.math.kobe-u.ac.jp/OpenXM/Math/Fisher-Bingham-2"> d-dimensional Fisher-Bingham System </a>
276: </ol>
277:
1.31 ! takayama 278: <pre> $OpenXM: OpenXM/src/hgm/doc/ref-hgm.html,v 1.30 2019/12/03 23:19:40 takayama Exp $ </pre>
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