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| MOED BET checked and graded | Hello all,
MOED BET exams were all checked and graded. Grades are available in GR++ (not submitted yet to the secretariat).
We applied a small factor on the grades as follows: factored_grade = Round(100*((grade*0.01)^0.75)).
Appeals will be accepted until next Thursday (Nov 15) at 14:00, to Ilan's mailbox through the usual protocol. After that, grades will be submitted to the secretariat.
We wish you good luck with the rest of your studies,
--course staff |
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| Created on 7/11/2007, 16:58:45 |
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| Reception hour for MOED BET | Hi all,
This Thursday (1.11.07) we will hold special reception hours before the exam.
Shlomo will give his reception hours between 13:00 and 14:30.
Ilan will give his reception hours between 14:30 and 16:00.
You are welcome to come with questions. We also added the MOED ALEPH exam to the exam database (under 'material' section). FYI, the MOED BET exam will be more-or-less in the same format.
Good luck,
--course staff |
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| Created on 28/10/2007, 15:45:38 |
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| MOED BET - more details | Hi all,
MOED BET will take place on Sunday, November 4th, 16:30 in Taub 4. The exam format and regulations will be the same as in MOED ALEPH. We will soon publish special reception hours for the exam.
--course staff |
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| Created on 21/10/2007, 10:04:01 |
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| MOED BET | Hi all,
The MOED BET exam will take place on Sunday, November 4 (and not in the preceeding week as published earlier). The exact time and classroom will be published later on.
The appeal period is therefore being extended until Monday, October 15. Make sure to fill in an appeal form and put it (toxether with a copy of the exam) in Ilan's mailbaox (5th floor).
We will not be able to deal with late appeals. Make sure to submit appeals by the deadline !!
HAG SAMEAH,
--course staff |
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| Created on 3/10/2007, 10:30:50 |
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| Grades are in | Hello all,
The exams were checked and graded. The grades, together with final grades, are available through GR++. The hard-copies will be handed in to the secreteriate tomorrow morning. The final grades were calculated according to the following scheme:
If a student got a passing grade in the exam (>=55), the homework was calculated as 25% MAGEN. Otherwise, the exam grade is the final grade.
We will submit final grades to LIMUDEI HASMACHA only after the appeal period. Appeals should be submitted with the proper forms to Ilan's mail box (now #110 at 5th floor) until Thursday, October 11. The very tight deadline is there to accommodate the close date of MOED BET.
We will publish a final date for MOED BET soon. It will most probably be between 21.10 - 25.10.
Good luck with the rest of your studies,
--course staff |
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| Last updated on 1/10/2007, 14:19:14 |
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| Reception hours on Sunday | Hi all,
Shlomo will not be able to hold reception hours on Sunday. Instead, I will give my reception hours from 14:00.
If you intend on coming, please make sure to do so between 14:00 and 14:30, so that you may have enough time to have all your questions answered. You may benefit from other people's questions as well. If ou think of coming in another time, let me know to see if that can be arranged.
--Ilan. |
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| Created on 21/9/2007, 09:35:16 |
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| Cover page for exam | Hi all,
Under "course material" you can find the cover page of the exam containing the rules and regulations (so that you come prepared on Monday).
Good luck,
--course staff |
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| Created on 21/9/2007, 09:15:17 |
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| New "old" exams on the web site | I added several exams from previous years to the ones already existing on the course' web site.
--Ilan. |
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| Created on 18/9/2007, 10:15:58 |
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| MOED A' exam - cont | Hi all,
For your information, the exam will be written in English. Your answers, of course, can be written in Hebrew.
Again, HAG SAMEAH,
--course staff |
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| Created on 11/9/2007, 15:39:49 |
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| MOED A' exam | Hello all,
MOED A' exam will take place on Monday, Sept 24, 13:00, in Taub 5.
We will hold reception hours on the preceeding Sunday (Sept 23):
- Shlomo: 13:00 - 14:30
- Ilan: 14:30 - 16:00.
Let us know if you wish to set a meeting at a different time. If enough demmand is raised, we will move one of the reception hours accordingly.
Good luck in your studies, and SHANA TOVA.
--course staff |
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| Created on 11/9/2007, 13:03:42 |
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| HW hard copies | Hi all,
The hard copies are still with me. If you want them, you can come and collect them this week until Wednesday. You may want to make sure I'm in my office before you come. Next week I am away, and on September 10th I will put them in their boxes.
--Ilan. |
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| Created on 27/8/2007, 10:46:07 |
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| HW 5 checked and graded | Grades are already online. The hard copies will be returned to your boxes tomorrow. Note that the Technion is closed next week, so they may have to wait there until September.
We have a month or so before MOED ALEPH. We will put some partially solved exams from previous years online. If you bump into a question you think is interesting let me know. I may publish a solution so that the all students can see as well.
Have a nice vacation,
Ilan. |
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| Created on 22/8/2007, 19:04:14 |
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| Extension in the deadline for HW 5 | Hi all,
Due to repeated requests of many students, the deadline for submission of HW 5 is extended in a week to August 12. Of course, you may submit it earlier if you wish.
Good luck,
--course staff. |
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| Created on 2/8/2007, 11:10:28 |
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| Tutorial 13 is online | see "course material" section.
--course staff |
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| Created on 31/7/2007, 16:25:37 |
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| Material for next tutorial | Hello all,
Next week I plan to do a bit of a HAZARA on various topics covered by this course. I plan to solve question 2 of HW 3, and an EM question. If any of you suggestions for other topics (covered in the lectures/tutorials/hw), I'd be glad to make the necessary adjustments. Just make sure to let me know by Sunday (29.7) afternoon.
--Ilan. |
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| Last updated on 25/7/2007, 11:17:31 |
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| Tutorial 12 is online | See "course material" section.
--course staff
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| Created on 24/7/2007, 18:32:18 |
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| HW 5 is online | The assignment is due Sunday, August 5th, at noon.
Good luck!
--course staff |
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| Last updated on 22/7/2007, 11:33:03 |
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| This week lecture will be held as usual on Tuesday | This Tuesday is Tisha Be'Av.
Few weeks ago an announcement concerning Tisha Be'Av lecture was published in the course site (you can see it below).
Following this anouncement, none of you have asked not to make a lecure on Tisha Be'Av (this Tuesday).
Hence this week lecture will be held on Tuesday 24.7, regular time and place.
--Shlomo
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| Last updated on 22/7/2007, 09:29:34 |
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| Clarification regarding Fitch's algorithm | Hi all,
In today's tutorial I may have made a misleading statement when discussing the state-subsets R(v) computed by Fitch's algorithm. I said that R(v) is a _subset_ of states which appear in optimal assignments for the subtree rooted at vertex v. This is true, but R(v) actually contains _all_ such states. This is proved in the last two slides of lecture 11.
Note that still there may be an optimal assignment to the _entire_tree_ which assigns to v a state which is not in R(v). In other words, the subtrees of a maximum parsimony tree do not have to be the most parsimonious themselves.
I hope this clarifies things,
Ilan. |
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| Last updated on 18/7/2007, 12:42:42 |
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| HW 4 checked and graded | The hard-copies will be rerturned tomorrow in the tutorial.
The presentation of tutorial 11 will be available online later today.
--course staff
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| Last updated on 17/7/2007, 12:16:21 |
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| Tutorial 10 is online | See "course material" section.
--course staff |
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| Created on 10/7/2007, 17:59:51 |
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| HW 3 finally checked and graded | The hard-copies will be rerturned in this week's classes. You are urged to go over my comments, and if you have any questions you can come to reception hours.
Ilan. |
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| Created on 10/7/2007, 10:25:52 |
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| An updated version of Lecture 11 is online | | see "Course Material" Section. |
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| Last updated on 9/7/2007, 12:24:25 |
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| Lecture 9 is online | | See "course material" section. |
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| Last updated on 3/7/2007, 17:57:22 |
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| Clarification regarding q1 of HW 4 | Hello all,
The first question of the exercise discusses the general formulation of EM as shown in the lecture. Note that x1 and x2 correspond to observations and y1, y2 correspond to the hidden data "behind" these observations. The entire analysis depens on the fact that each observation corresponds to a set of possible assignments to the "hidden variables". This is why we say that x1,x2 denote sets of "hidden data".
Good luck,
--course staff |
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| Created on 1/7/2007, 15:54:19 |
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| HW 4 is online | The assignment is due July 12 at noon.
Good luck!
--course staff |
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| Last updated on 27/6/2007, 17:08:39 |
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| Clarification regarding today's tutorial | Hello all,
There was some confusion (caused by me) regarding the approximation ration of Lifted-Tree-Alignments. It had to do with the last inequality in the slide before last. The approximation ration remains 2 (as stated there).
The triangle inequality states that D(a,c) <= D(a,b) + D(b,c). This may be extended to a path of arbitrary length a1,...,ak. By induction you can show (using the original triangle inequality) that D(a1,ak) <= D(a1,a2)+D(a2,a3)+...D(ak-1,ak). Notice you do not loose an extra factor of 2 here, so the last ineaulity holds.
Sorry for the mix-up,
Ilan.
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| Created on 27/6/2007, 10:36:42 |
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| Tomorrow's tutorial | Tomorrow we will return to tutorial 4 which was lost due to the strike. The slides are already online.
--course staff |
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| Created on 26/6/2007, 19:07:51 |
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| Checking possibility of changing the date of Moed A | The current date for Moed A exam is 24.9.07.
We are checking the possibility of moving it to August.
This will be possible only if all students registered to the course will agree on an alternative date.
Lena (slenakl@t2) agreed to coordinate this checking.
--Shlomo |
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| Last updated on 26/6/2007, 15:24:53 |
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| This week's lecture and tutorial are online | See "course material" section.
--course staff |
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| Last updated on 19/6/2007, 12:23:25 |
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| Tutorial #7 is online | See "course material" section.
--course staff |
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| Last updated on 12/6/2007, 20:13:07 |
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| HW 3 is online | The assignment is due June 21 at noon.
Also note that Tutorial 6 is online as well.
--course staff |
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| Last updated on 5/6/2007, 15:18:30 |
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| Tisha Be'av lecture | The lecture of 24.7.07 (Tisha Be'av) was rescheduled to 26.7.07 (ie, Thursday of the same week) at 18:30.
It is possible to keep the original schedule (i.e., lecture on Tisha Be'av), provided none of the students registered to the course will object.
Thus, any of you who prefers NOT to have a lecture on Tisha Be'av (i.e., move it to 26.7 at 18:30), should inform me. If none is interested in moving the lecture, we will have it in Tisha Be'av.
--Shlomo |
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| Last updated on 22/7/2007, 09:32:59 |
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| This week's lecture and tutorial | Hello all,
This week we will skip to the fifth lecture and tutorial (already online). The fourth lecture and tutorial discussing 'multiple sequence alignment' will not be presented at this time. The presentations are, however, online, for your general reference.
Welcome back,
--course staff. |
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| Created on 29/5/2007, 10:36:07 |
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| HW2 checked and graded | Hard-copies will be returned next tutorial/lecture.
--course staff
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| Created on 8/5/2007, 10:58:34 |
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| Lecture 5 is online | | for the case that classes resume by Tuesday. A slightly updated version will be uploaded tomorrow. |
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| Last updated on 6/5/2007, 11:02:45 |
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| Tutorial 4 online | Please make sure to review the star algorithm (end of tutorial 3) before tomorrow's class. We'll start with the proof of approximation-ratio, which I owe you from before Pessach.
--Ilan |
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| Created on 1/5/2007, 18:10:23 |
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| Annoncement concerning the strike | Due to the prolonged strike, lecture 4 (whose presentation was uploaded few weeks ago) will not be given in class.
Please note that the material in this lecture includes two parts:
1. Description of statistical aprproach to define scoring function for pairwise alignment, and PAM scoring matrices.
2. Multiple sequence alignment.
This material is not used or assumed in rest of the course, and part of it was or will be covered in the tutorials. Nevertheless, you should study that presentation if you didn't do it so far. |
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| Created on 1/5/2007, 08:37:55 |
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| Additional clarification regarding HW 2 | Hi all,
The homework assignment was specifically designed so that its solution will not require any material not presented in class (lectures and tutorials). This also goes for question 4. The generalized DP algorithm was discussed in Tutorial 3, and all necessary definitions appear in the question itself.
Good luck,
--course staff |
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| Created on 25/4/2007, 12:06:03 |
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| Clarifications regarding HW 2 | In question 1, the algorithm you propose in part (b) should solve the formal search problem you define in part (a). Part (c) is somewhat separate from (a) and (b).
Note that no special extension of the deadline is expected due to the strike.
Good luck,
--course staff |
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| Created on 17/4/2007, 15:18:52 |
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| HW2 published | The homeowrk assignmnet is online, and is due Thursday, April 26 by noon.
Note that question 4 deals with material discussed in lecture 4 (which is postponed due to the strike).
Good luck,
--course staff |
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| Last updated on 12/4/2007, 14:29:48 |
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| HW1 checked and graded | Hard-copies will be returned next tutorial/lecture (after the strike).
--course staff |
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| Created on 11/4/2007, 19:30:38 |
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| Modifications in Tutorial #3 | Some minor modifications were made in the last part of the tutorial ('star alignment'). The files were changed accordingly.
--course staff |
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| Created on 28/3/2007, 10:37:42 |
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| Lecture and tutorial #3 are online | See 'material' section.
--course staff
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| Created on 26/3/2007, 11:28:28 |
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| This week's lecture and tutorial are online | See 'material' section.
--course staff |
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| Created on 19/3/2007, 19:05:24 |
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| Some openning announcements | Welcome all to 'Algorithms in Computational Biology - 236522'.
Due to students' requests, course presentations (lectures and tutorials) will be available also in pdf format (2 slides per page). The lecture power-point slides will be available in 'read-only' format (choose 'read-only' when opening the file).
In order to allow easier access to material necessary for the first homework assignment, we scanned the first chapter in Setubal's book and made it available in the course' site under 'assignments' section. This section will temporarily be restricted only to students registered to the course (due to copyright issues). If you have any problems accessing this section, contact me and I'll make the necessary arrangements.
Regards,
Ilan. |
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| Created on 15/3/2007, 11:47:27 |
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Technion - Israel Institute of Technology 
