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| * Lecture 9 : Dynamic Programming -- [[Media:Biostat615-Fall2011-lecture09-handout.pdf | (Handout PDF)]] [[Media:Biostat615-Fall2011-lecture09-presentation.pdf | (Presentation PDF)]] | | * Lecture 9 : Dynamic Programming -- [[Media:Biostat615-Fall2011-lecture09-handout.pdf | (Handout PDF)]] [[Media:Biostat615-Fall2011-lecture09-presentation.pdf | (Presentation PDF)]] |
| * Review : Dynamic Programming & Midterm Review -- [[Media:Biostat615-Fall2011-midterm-2011-winter-.pdf | (PDF)]] | | * Review : Dynamic Programming & Midterm Review -- [[Media:Biostat615-Fall2011-midterm-2011-winter-.pdf | (PDF)]] |
− | * Lecture 10 : Hidden Markov Model-- [[Media:Biostat615-Fall2011-lecture10-handout.pdf | (Handout PDF)]] [[Media:Biostat615-Fall2011-lecture10-presentation.pdf | (Presentation PDF)]] | + | * Lecture 10 : Hidden Markov Model-- [[Media:Biostat615-Fall2011-lecture10-handout.pdf | (PDF)]] '''(UPDATED on Oct 29th at 12:51PM)''' |
− | * Lecture 11 : Hidden Markov Model (cont'd) -- [[Media:Biostat615-lecture11-2011-10-20.pdf | (Handout PDF)]] [[Media:Biostat615-lecture11-2011-10-20.pdf | (Presentation PDF)]] | + | * Lecture 11 : Hidden Markov Model (cont'd) -- [[Media:Biostat615-lecture11-2011-10-20.pdf | (PDF)]] '''(UPDATED on Oct 28th at 1:42PM)''' |
| * Lecture 12 : Boost Library & Random Numbers -- [[Media:Biostat615-lecture12-2011-10-25.pdf | (PDF)]] | | * Lecture 12 : Boost Library & Random Numbers -- [[Media:Biostat615-lecture12-2011-10-25.pdf | (PDF)]] |
| + | * Lecture 13 : Single dimensional optimization -- [[Media:Biostat615-lecture13-2011-10-27.pdf | (PDF)]] |
| + | * Lecture 14 : Single and multi dimensional optimizations -- [[Media:Biostat615-fall2011-lecture14.pdf | (PDF)]] (Updated on Nov 3rd 1:25AM) |
| + | * Lecture 15 : Multi dimensional optimizations -- [[Media:Biostat615-fall2011-lecture15.pdf | (PDF)]] (Updated Nov 8 10:35AM) |
| + | * Lecture 16 : E-M algorithm -- [[Media:Biostat615-fall2011-lecture16.pdf | (PDF)]] (Updated Nov 8 10:35AM) |
| + | * Lecture 17 : Simulated Annealing -- [[Media:Biostat615-fall2011-lecture17.pdf | (PDF)]] |
| + | * Lecture 18 : Gibbs Sampling -- [[Media:Biostat615-fall2011-lecture18.pdf | (PDF)]] (Updated Nov 16 10:00PM) |
| + | * Lecture 19 : Importace Sampling -- [[Media:Biostat615-fall2011-lecture19.pdf | (PDF)]] |
| + | * Lecture 20 : Advanced Hidden Markov Models -- [[Media:Biostat615-fall2011-lecture20.pdf | (PDF)]] |
| + | * Lecture 21 : Linear Algebra in C++ -- [[Media:Biostat615-fall2011-lecture21.pdf | (PDF)]] |
| + | * Lecture 22 : More Linear Algebra in C++ -- [[Media:Biostat615-fall2011-lecture22.pdf | (PDF)]] |
| + | * Lecture 23 : Interfacing between C++ and R -- [[Media:Biostat615-fall2011-lecture23.pdf | (PDF)]] |
| + | * Review : Final Review -- [[Media:Biostat615-winter2011-final.pdf | (PDF)]] [[Media:Biostat615-homework-review.pdf | (Homework)]] |
| | | |
| == Problem Sets == | | == Problem Sets == |
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| * Problem Set 1 -- Due on Tuesday September 27th, 2011 [[Media:Biostat615-Fall2011-homework01.pdf | (PDF)]] [[Media:Biostat615-Fall2011-homework01-solutions.pdf | (PDF-SOLUTIONS)]] | | * Problem Set 1 -- Due on Tuesday September 27th, 2011 [[Media:Biostat615-Fall2011-homework01.pdf | (PDF)]] [[Media:Biostat615-Fall2011-homework01-solutions.pdf | (PDF-SOLUTIONS)]] |
| * Problem Set 2 -- Due on Thursday October 6th, 2011 [[Media:Biostat615-Fall2011-homework02.pdf | (PDF)]] [[Media:Biostat615-Fall2011-homework02-solutions.pdf | (PDF-SOLUTIONS)]] | | * Problem Set 2 -- Due on Thursday October 6th, 2011 [[Media:Biostat615-Fall2011-homework02.pdf | (PDF)]] [[Media:Biostat615-Fall2011-homework02-solutions.pdf | (PDF-SOLUTIONS)]] |
| + | ** (Update Oct 2, 2011 : Note that the problem 1 and 3 are slightly updated for clarification) |
| + | ** (If you can't decompress the files above properly, use this alternative link by [http://dl.dropbox.com/u/1850834/biostat615-homework02-datasets.tar.gz CLICKING HERE] ) |
| + | * Problem Set 3 -- Due on Tuesday November 1st, 2011 [[Media:Biostat615-homework03.pdf | (PDF)]] (UPDATED on Oct 25th at 11:10AM) |
| + | * Problem Set 4 -- Due on Tuesday November 15th, 2011 [[Media:Biostat615-homework04.pdf | (PDF)]] |
| + | * Problem Set 5 -- Due on Tuesday November 29th, 2011 [[Media:Biostat615-fall2011-homework05.pdf | (PDF)]] |
| + | * Problem Set 6 -- Due on Tuesday December 13th, 2011 [[Media:Biostat615-fall2011-homework06.pdf | (PDF)]] |
| + | ** [http://www.sph.umich.edu/csg/abecasis/class/2006/ModelFittingData.txt DOWNLOAD DATA FOR PROBLEM 1] |
| + | ** [http://dl.dropbox.com/u/1850834/zip_01.zip DOWNLOAD DATA FOR PROBLEM 3] |
| + | |
| + | === Supplementary Data sets for Problem Sets === |
| + | * Problem Set 2 |
| ** [[Media:Shuf-1M.txt.gz| (Example data - shuf-1M.txt.gz)]] 1,000,000 randomly shuffled data (gzipped) | | ** [[Media:Shuf-1M.txt.gz| (Example data - shuf-1M.txt.gz)]] 1,000,000 randomly shuffled data (gzipped) |
| ** [[Media:Rand-1M-3digits.txt.gz| (Example data - Rand-1M-3digits.txt.gz)]] 1,000,000 random data from 1 to 1,000]] (gzipped) | | ** [[Media:Rand-1M-3digits.txt.gz| (Example data - Rand-1M-3digits.txt.gz)]] 1,000,000 random data from 1 to 1,000]] (gzipped) |
| ** [[Media:Rand-50k.txt.gz | (Example data - Rand-50k.txt.gz)]] 50,000 random data from 1 to 1,000,000)]] (gzippd) | | ** [[Media:Rand-50k.txt.gz | (Example data - Rand-50k.txt.gz)]] 50,000 random data from 1 to 1,000,000)]] (gzippd) |
− | ** (Update Oct 2, 2011 : Note that the problem 1 and 3 are slightly updated for clarification) | + | * Problem Set 3 |
− | ** (If you can't decompress the files above properly, use this alternative link by [http://dl.dropbox.com/u/1850834/biostat615-homework02-datasets.tar.gz CLICKING HERE] )
| + | ** Example output data for problem 3-1 (input is the second column) '''(NOTE : ADDED on Oct 25 11:45PM)''' -- This is also reflected in lecture 11 class note. |
− | * Problem Set 3 -- Due on Tuesday November 1st, 2011 [[Media:Biostat615-homework03.pdf | (PDF)]]
| + | TIME TOSS P(FAIR) P(BIAS) MLSTATE |
− | ** Example output data for problem 3-2 (input is the second column) | + | 1 H 0.5950 0.4050 FAIR |
| + | 2 T 0.8118 0.1882 FAIR |
| + | 3 H 0.8071 0.1929 FAIR |
| + | 4 T 0.8584 0.1416 FAIR |
| + | 5 H 0.7613 0.2387 FAIR |
| + | 6 H 0.7276 0.2724 FAIR |
| + | 7 T 0.7495 0.2505 FAIR |
| + | 8 H 0.5413 0.4587 BIASED |
| + | 9 H 0.4187 0.5813 BIASED |
| + | 10 H 0.3533 0.6467 BIASED |
| + | 11 H 0.3301 0.6699 BIASED |
| + | 12 H 0.3436 0.6564 BIASED |
| + | 13 H 0.3971 0.6029 BIASED |
| + | 14 T 0.5028 0.4972 BIASED |
| + | 15 H 0.3725 0.6275 BIASED |
| + | 16 H 0.2985 0.7015 BIASED |
| + | 17 H 0.2635 0.7365 BIASED |
| + | 18 H 0.2596 0.7404 BIASED |
| + | 19 H 0.2858 0.7142 BIASED |
| + | 20 H 0.3482 0.6518 BIASED |
| + | ** Example output data for problem 3-2 (input is the second column) '''(NOTE : UPDATED on Oct 25 11:23PM)''' |
| TIME TOSS Pr(F) Pr(HB) Pr(TB) MLSTATE | | TIME TOSS Pr(F) Pr(HB) Pr(TB) MLSTATE |
− | 1 T 0.8901 0.0308 0.0791 FAIR | + | 1 T 0.8844 0.0326 0.0830 FAIR |
− | 2 H 0.9084 0.0741 0.0175 FAIR | + | 2 H 0.9012 0.0791 0.0198 FAIR |
− | 3 H 0.9166 0.0682 0.0152 FAIR | + | 3 H 0.9075 0.0735 0.0189 FAIR |
− | 4 T 0.9238 0.0165 0.0597 FAIR | + | 4 T 0.9091 0.0145 0.0764 FAIR |
− | 5 T 0.9242 0.0165 0.0593 FAIR | + | 5 T 0.9068 0.0114 0.0818 FAIR |
− | 6 H 0.9182 0.0683 0.0135 FAIR | + | 6 H 0.9058 0.0440 0.0502 FAIR |
− | 7 H 0.9117 0.0746 0.0137 FAIR | + | 7 T 0.8834 0.0275 0.0891 FAIR |
− | 8 T 0.9008 0.0392 0.0600 FAIR | + | 8 H 0.8520 0.0698 0.0783 FAIR |
− | 9 H 0.8763 0.0692 0.0545 FAIR | + | 9 T 0.7713 0.0347 0.1940 FAIR |
− | 10 T 0.8139 0.0318 0.1543 FAIR | + | 10 T 0.6927 0.0823 0.2249 FAIR |
− | 11 T 0.7532 0.0680 0.1788 FAIR | + | 11 H 0.4730 0.4984 0.0286 HEAD-BIASED |
− | 12 H 0.5835 0.3935 0.0230 HEAD-BIASED | + | 12 H 0.3227 0.6706 0.0066 HEAD-BIASED |
− | 13 H 0.4680 0.5265 0.0054 HEAD-BIASED | + | 13 H 0.2236 0.7726 0.0037 HEAD-BIASED |
− | 14 H 0.3947 0.6022 0.0031 HEAD-BIASED | + | 14 H 0.1589 0.8381 0.0031 HEAD-BIASED |
− | 15 H 0.3514 0.6460 0.0027 HEAD-BIASED | + | 15 H 0.1169 0.8803 0.0028 HEAD-BIASED |
− | 16 H 0.3305 0.6670 0.0025 HEAD-BIASED | + | 16 H 0.0902 0.9072 0.0026 HEAD-BIASED |
− | 17 H 0.3283 0.6692 0.0025 HEAD-BIASED | + | 17 H 0.0740 0.9235 0.0025 HEAD-BIASED |
− | 18 H 0.3443 0.6527 0.0030 HEAD-BIASED | + | 18 H 0.0654 0.9321 0.0025 HEAD-BIASED |
− | 19 H 0.3812 0.6124 0.0064 HEAD-BIASED | + | 19 H 0.0630 0.9346 0.0025 HEAD-BIASED |
− | 20 H 0.4434 0.5207 0.0359 HEAD-BIASED | + | 20 H 0.0661 0.9314 0.0025 HEAD-BIASED |
− | 21 T 0.5248 0.1730 0.3022 TAIL-BASED | + | 21 H 0.0755 0.9219 0.0026 HEAD-BIASED |
− | 22 T 0.5382 0.1658 0.2960 TAIL-BASED | + | 22 H 0.0926 0.9038 0.0036 HEAD-BIASED |
− | 23 H 0.5073 0.4574 0.0353 HEAD-BIASED | + | 23 H 0.1204 0.8684 0.0113 HEAD-BIASED |
− | 24 H 0.4768 0.5171 0.0061 HEAD-BIASED | + | 24 H 0.1603 0.7586 0.0811 HEAD-BIASED |
− | 25 H 0.4652 0.5320 0.0028 HEAD-BIASED | + | 25 T 0.1904 0.0858 0.7238 TAIL-BASED |
− | 26 H 0.4739 0.5236 0.0025 HEAD-BIASED | + | 26 T 0.1819 0.0118 0.8063 TAIL-BASED |
− | 27 H 0.5046 0.4916 0.0037 HEAD-BIASED | + | 27 T 0.1797 0.0036 0.8167 TAIL-BASED |
− | 28 H 0.5622 0.4244 0.0134 HEAD-BIASED | + | 28 T 0.1894 0.0028 0.8077 TAIL-BASED |
− | 29 T 0.6503 0.2511 0.0986 HEAD-BIASED | + | 29 T 0.2136 0.0038 0.7826 TAIL-BASED |
− | 30 H 0.6628 0.2956 0.0417 HEAD-BIASED | + | 30 T 0.2561 0.0123 0.7317 TAIL-BASED |
| + | ** Example input/output data for problem 3-3 (Applying 2-state HMM in Problem 3-1): Download using [http://dl.dropbox.com/u/1850834/biostat615-homework3-3-20k-examples.zip THIS LINK] |
| | | |
| == Office Hours == | | == Office Hours == |