Mehmet Dalkilic, PhD


Current PhD and Masters students Former PhD students

(the students themselves selected their own pictures. MMD)

February 27, 2014
Exam, Classes, Papers Sent
We had our exam in H212. I'll post it soon. Latest topic is Classes II. We submitted a paper last week to KDD and to VLDB this week. There was an interesting article in Nature on inauthentic texts. I commented about our paper Using Compression to Identify Classes of Inauthentic Texts. I've had many requests for this paper, but the links don't seem to work; I'm posting it here An Approximate de Bruijn Graph Approach to Multiple Local Alignment and Motif Discovery in Protein Sequences - (edited February 27, 2014, 12:33 PM)
February 13, 2014
Met Barclay's yesterday -- wonderful presentation. Working on submitting to KDD two papers -- exciting! Gave last assignment before first exam in C++. Received the kinects from Microsoft. Hard to not explore that right now, since the papers are due by the 21st. Paper to Computer was accepted on mining the milky way. From a letter to WSJ, "... To paraphrase Margaret Thatcher, the problem with demand-side economics is that eventually you run out of other people's productivity." - (edited February 13, 2014, 3:46 PM)
January 30, 2014
This week, we worked on arrays and simulations. Met with FAC to begin evaluating faculty reports. Met with Chris to discuss summer teaching. I received two kinects from Microsoft to begin work on a project for the athletic department. Here's homework on Newton-Raphson for root-finding for financial engineering. - 5:55 PM
January 27, 2014
We have four lectures now on C++. I'll post them later. - (edited January 30, 2014, 6:00 PM)
January 24, 2014
Met with Hani Dawoud about IS. We'll be working on some kind of data-driven ontology related to crowd sourcing. Met with Hussein Mohsen. We'll be working on random forests -- another idea about improving the method. I met with Alex Christou. We'll be doing something in Med* fraud. Meeting Creighton Helms (Class '17 Kelley SoB) to discuss financial engineering on Sunday. This was initiated by a talk by Goldman Sachs. Kaylan Tildsley spoke on January 14th at 3PM about the securities industry as a whole to a packed CG1050. For students looking for PhD qualifier forms, they are here. Having dinner with guest speaker Andrew McGregor from UMass who works on algorithms and complexity. Bryce Ogden and students are touring natatorium for software systems project. Writing three letters of recommendation. - (edited January 24, 2014, 1:45 PM)
January 22, 2014
Second Week of Classes
Met with 12 students who are continuing with Android OS Tablets from honors data structures. We had pizza and discussed several exciting projects. Met with Hani Dawoud for IS. We're reading this paper:

Jonathan A. Silva, Elaine R. Faria, Rodrigo C. Barros, Eduardo R. Hruschka, André C. P. L. F. de Carvalho, and João Gama. 2013. Data stream clustering: A survey. ACM Comput. Surv. 46, 1, Article 13 (July 2013)

In H212 we began reviewing logic and wrote C++ for the material implication operator. We reviewed Syllogistic arguments, A,E,I,O, and created an algorithm that establishes whether an argument is valid or not. The algorithm iterates over the subject and predicates using the two premises to remove possible valuations. The conclusion is the iterated over the remaining truths--stopping if an invalid truth is found. I'll show this tomorrow.

Received a card from Fuxio Xin and Yong Li -- they're in the Bay. - (edited January 22, 2014, 3:41 PM)

June 21, 2011
Yesterday I gave the first of three Professor's Perspectives to a couple of hundred people--a mix of students and parents. From the feedback I received, the talk went well. I accompanied the parents and students to Wright Quad for "dinner", though I didn't eat anything--just water. I met some marvelous parets and students.

In the talk I promised that I would post whether I'd be giving a seminar on how to study--so visit this page to find out.

I have a policy committee meeting tomorrow with the Dean.

The details of the Golfing tournament my niece is playing in Thursday, June 23

My niece is quite the golfer--first place in her age group this week in the Girls PGA

larger view

By next week I will have submitted two small NIH grants with Dr. Brown from the UV Medical School.

With several other authors, I've submitted a paper to ICDM

The word of the day is pullulate--which effloresce in a sence--copiousness--increase quickly. It's a good word. This is from One of the quotations is by Borges, "...and heads monstrously pullulate in mutual conjunction..."

A former, talented student of mine is living in France--making music I believe Brandon

Completed the survey from Indiana CTSI (Clinical and Translation Science Institute)

Answered query about the MS program from Colin who has done work in MEL (Maya's scripting language).

Of significant importance is NSF's proposed revisions in review criteria. In particular, the "broadening of broader impact" will likely affect proposals the most.

Please read NSF changes

From a colleague who will remain nameless unless I am otherwise instructed: 21

Finished reading Lies! Lies! Lies! The Psychology of Deceit by C.V. Ford, M.D. I'll post notes soon. - (edited June 21, 2011, 10:54 AM)

March 7, 2011
March 5-7
NSF Panel review

Grading Android

Letters of recommendation - 12:55 PM

March 4, 2011
March 3
Judged OWA science competition

Dear Staff Letter

Met with K.S. and discussed awesome future

Withdrew name from Div C Chair

Met Dr. Feresu in School of Health—she does epidemiology—will discuss project

Program Computer Science Meeting

Complete CS MS admissions

- 12:58 PM

March 2, 2011
March 2
Received materials for WISP competition--I will be judging posters.

I will speak with Pedro Villurruel on Tuesday at 1:00pm about the mobile device classes I've been teaching.

CACR Talk Tuesday:


abhi shelat Assistant Professor of Computer Science School of Engineering and Applied Science University of Virginia


TITLE: The Price of Secure Collaboration

We frame the notion of secure collaboration as one about the ability for several parties p1,...,pn, who privately hold inputs x1,...,xn respectively, to jointly compute some function f(x1,...,xn).

In this talk, we discuss two aspects about the *price* of security. How much extra communication and computation are necessary? What extra assumptions about ``parties following the instructions" need to be made? We partially answer these questions by Presenting recent work that addresses these factors.

For the two-party case, we first present a recently designed system that achieves security against a malicious adversaries with the lowest communication and computation among all known solutions.

For the multi-party case, we introduce a new threshold fully homomorphic encryption scheme. This system allows a set of players to generate a public key pk for which each party has a share sk_i of the secret key. We also develop a proof of knowledge of plaintext and a collaborative decryption procedure for this system. By combining these methods, we construct the first secure multi-party computation protocol that allows evaluation of a function $f$ using communication that is independent of the circuit description of $f$.

The talk covers joint work with Chih-hao Shen, and with Steve Myers and Mona Sergi.

- 2:26 PM

March 1, 2011
March 1
March 1 I've been blogging/web building/working on another site--I will keep this site for most academic activities. Monday: Last full class on Android Development The class worked on one of three Android Projects, 2.2. I will discuss only two of the projects, since the third might be offered as a real game. The class is bimodal in its abilities: paucity of programming experience, abundance of experience. For the former, students are working one of two projects: an app to help finite math students multiple matrices; an app to assess body language using The Definite Book of Body Language by Pease and Pease. The app allows the assessment of body language. The app for the advanced programmers deals with extending Soduku. I can't discuss this in detail.

Youtube for c290

Working on admissions for CS MS

Answered T.G. on program

Repy to NSF review panel inquiry

Submitted admission information for MS in Bioinformatics

Sought help for minority student M.R.--funding

Completed Athletic Dept's Kiosk with Jayce

Spoke with student from India about MS CS program

Watch sponsored intramural (we won!)

Meet T.G. for three letters for overseas study

Will call WFIU’s Pedro Villarruel who is writing an article on Application for mobile devices. - (edited March 2, 2011, 11:49 AM)

July 26, 2010
Nearing the end of the excluded middle


Centocor, Inc., a member of Johnson and Johnson's family of companies, is recruiting. Please visit for

(1) Principal Research Scientist, Network Pharmacology

(2) Associate Director, Molecular Profiling

MS Advising Tip

One can use any course with a middle digit of 0/1 to fulfill the foundations requirements, e.g., B501 or B503. In some very rare cases, it would be possible to use the undergraduate versions of B501 and B503 but that would require special permission from the Director.


The Unit for Natural Language Processing at the Digital Enterprise Research Institute (DERI: of the National University of Ireland, Galway invites applications for an internship in information mining. The successful applicant will have the following responsibilities:

1. Research: topic clustering. We are currently extracting over 27,000 topics from scientific publications using NLP techniques, and need a reliable and efficient technique to cluster these so that they are more manageable in our expert-finding application’s user interface. This could be hierarchical topic clustering (super topics and sub topics in a tree structure) or some other suitable way determined by research.

2. Development: crawling. We are currently identifying further sources of both documents and metadata describing the documents, and need infrastructure to be setup and run to effectively crawl this information for subsequent information extraction. This will involve the setting up and administration of databases, metadata stores and open source crawling tools, as well as the development of some custom screen-scraping tools.

3. Any other tasks required of them.

The work will be carried out in the context of an ongoing industrial research collaboration, and internally with DERI's Unit for Information Mining and Retrieval. Internships are aimed at undergraduate and postgraduate students, with a duration of 3-12 months and will be remunerated at EUR 1000 per month (EUR 1200 for postgraduate students).

DERI is a leading research institute in semantic technologies that offers a stimulating, dynamic and multi-cultural research environment, excellent ties to research-groups worldwide, close collaboration with industrial partners and up-to-date infrastructure and resources. The DERI Unit for Natural Language Processing ( has a focus on applied research in ontology-based information extraction, semantic-level text mining and the use of linguistic and semantic methods in information retrieval. The unit develops methods for the efficient application of NLP tools in combination with domain semantics as specified in ontologies, thesauri and other knowledge organisation systems for relevant use cases. Research is carried out in close cooperation with the DERI Unit for Information Mining and Retrieval ( in the context of the DERI Semantic Information Mining stream ( as well as with other DERI units.

Please send an expression of interest, preferably with links to relevant previous study and/or research experience, by August 1st to: - (edited July 26, 2010, 4:43 PM)

July 23, 2010
Nice ...
One incoming student has already finished "The Stranger" are her thoughts: I just finished it! The way its written reminds me of Catcher in the Rye, or I guess it would be the other way around since this book is older. But the writing is really precise and short, and then in the second half he gets so much more emotional and long-winded. I think this is a book I'd have to read a few times to really understand, because I'm not sure I understand exactly the point Camus was trying to make. But it was a pretty good book. My opinion of Meursault changed a few times. I liked him at the very beginning, and then when he helped Raymond write the letter to his mistress, which led to her being beaten, I kind of hated him. When he first went to prison, I felt bad again, because he was alone and he was thinking about Marie and wondering if she had found someone else. Maybe that was the point, to see how quickly and easily your opinion of a person can change. What really struck me is how little emotion Meursault shows. When his mother dies, when Marie wants to marry him, HE KILLED A GUY! and he didn't show feeling for any of it. If this was a book report I would definitely fail, but I just wanted to share my thoughts -Tessa

She got the point!

My niece's results for Indiana's Golf Foundation Course: Crestview Golf Course(Muncie , IN)

Results for contest Girls 10-11:


1 Claire Cameron Martinsville, IN 32 -4

2 Reece Malapit Muncie, IN 39 +3

3 Alexis Miestowski Schererville, IN 40 +4

Lexie's 1st hole put up a challenge--but she came back to third!

Nathan's band--please view: tenstrikemusic - (edited July 23, 2010, 2:59 PM)

July 20, 2010
Start of the new academic year
Send fix to our website folks--my website URL isn't working correctly

Reply to John M.

Reply to Suzanne. M

Average salaries of School of Informatics and Computing undergraduates...

Meeting Gregory, Jim, and Lisa at LH 215 3:00pm

Create oncourse site for CS (Andrew)

Emipire to fix my airconditioning and heater

CS Program MS requirements

MS issue from Jenny

Name of my second semester graduate class:Fundamentals and Applications of Information Theory

Discuss with Anoop last part of Algorithms

Fetal Blood presence in maternal blood paper--Greg

During my Professor's Perspective, I wrote down some thoughts about Some Suggestions

Here's one of the requests:

Sent: Sunday, July 18, 2010 6:42 PM To: Dalkilic, Mehmet M. Subject:

Dr. Dalkilic, I was at the July 15th & 16th orientation and did not recieve one the the papers that you were passing around the crowd. Could you please send me the PDF file if it is not too much trouble. I would also like to thank you for the Border's Books gift card and for making Orientation enjoyable.

Thank you, Lucas H.

Met with Kalpana

Another nice email:

Hello, my name is Nathan K* and I attended the orientation meeting you gave in the auditorium a couple days ago. I accepted the offer for the gift card and am emailing you concerning what book I should get. My friend and coworkers pursuaded me into starting Dharma Bums by Jack Kerouac a few weeks ago and I've grown to really enjoy the adventurous stories and the views he has of life and religion. I'm almost finished reading it and was planning on reading either more Kerouac or start branching out to books by other poets that he knew and was friends with. I'm hoping that you encouage this choice, or if you have any other suggestions, I'm open to those as well. I'd also like to thank you for the gift card. It's extremely generous of you and I'm hoping to continue reading and talking about books with you! Sincerly, Nathan K

Chris Myle's resume

Kevin K.'s travels in China:

Dr. Dalkilic, so now i'm currently in the shandong province, which is north of beijing . I have some differences/quirkes now. my friends and I have compiled a decent list. here are the first of them. if it is hot, men just roll their shirts up above their nipples, they don't take them off they just roll them high. if you are a tall-ish white blonde man, you are a hot commodity and everyone wants pictures with you. i have taken at least two dozen pictures with asian people. ... - (edited July 20, 2010, 10:42 AM)

April 13, 2010
More Digging
Meet Chris

Meet Cuifang

Work on NIH reviews

Taxes - 2:39 PM

April 9, 2010
End of week
Hiring meeting with Jiong

Dinner with Jiong and Lee and Scott

Hiring Talk

Hiring committee

Meet with Ron at Athletics

Meet Informatics Program

Meet Lightening talk

Meet guest of Center - 2:46 PM

April 6, 2010
Meet with Sun

Attend Hiring Talk

Meet with Linda

Meet with Biogroup + Esfan - (edited April 6, 2010, 1:08 PM)

April 1, 2010
The Deluge
Finishing admissions for PhD and MS degrees

Sat in for Pedja for space committee

Meeting every Thursday (even spring break) for PC

Working on Capstones

Preparing PhD qualifiers

Dealing with machines digging a hole

Midcareer Faculty Workshop, tomorrow, Friday, April 2, in the Georgian Room of the IMU, 9 – 11 am. - 3:26 PM

February 21, 2010
At the University on a Sunday
This is pretty cool: Cell Landscape

Policy Committee x 10

Promotion and Tenure

Meet with Simo

Meet with Visual Studio C#/iPhone Development Group


larger view

Working on large graphs

Working on intentional logic for ontologies

PhD Admissions / Masters Admissions

Director of Bioinformatics

- (edited February 21, 2010, 11:37 AM)

January 12, 2010
10:54 a.m.EST, Tue January 12, 2010
Spoke to Sam about letters of recommendation

Answer email 14143 Center for Bioinformatics Research Special Talk Thursday, January 14, 2010 Dogwood Room, Indiana Memorial Union 3:00-4:00 p.m. Admission Free

Yaoqi Zhou
IUPUI-School of Informatics Director & Professor Bioinformatics
From sequence to structure, to function, and back again: Integrating knowledge-based approaches with physical intuitions for protein folding, binding, and design

The Algorithms Reading Group is a group of graduate students and faculty members who meet weekly to discuss topics related to algorithms and algorithm theory. The topics covered are fairly broad, and assume a general CS background.
Our first talk of the semester is Tuesday, Jan. 12 in LH101 from 5 p.m. to ~6 p.m.,
Jeff Johnson ( Coordinator
Working on meeting times with Bobak and Justen

Meet with Paul and Dirk
Meet with PC and Bobby 11a IE210

Reference for Austin Buono

A memorial service to celebrate the life of Professor Belton will take place on Friday January 15, at 5 p.m. at the Unitarian Universalist Church on Fee Lane in Bloomington.
- (edited January 12, 2010, 12:17 PM)

November 29, 2009
So long--too long
I apologize for not keeping up--but I've purchased a couple of other personal domains that I'll be using to disentangle personal from professional discussions. I don't believe this blog should be too garish in its politics.

I met with Billy about his internships--I suggested the difficult one. We'll see what he does. He did nominate me for Distinguished Professor in Teaching--I was very touched, but to my chagrin, a dossier is required. Having completed work on P & T (maybe a dozen) and the dossier being required in a few days, it was suggested that I try again next year. I cannot decide if it's [application process] like a water slide or a Sisyphean exercise.

I met with Bobak and Justen several times

I picked up Jim at the airport and dropped him off around 5:00am. He wanted to leave at 4:00am, because his flight was at 11:00am.

P & T writing

My sister was kind enough to make arrangements for our family for Thanks-giving, but I was encouraged not to spend 9 hours on the road for a meal at 11:30am. I miss seeing them, but Kan has no keeper.

I took my entire H101 class to Mozart's Die Zauberflöte. We were written up by the IDS by Lindsey Ferguson . I recommend Peter Branscombe's W.A. Mozort Die Zauberöte. larger view

If this link is stale, I found it at The site has a synopsis of the book:

Few operas have had more written about them than Die Zauberflote, yet few are as often exposed to misguided comment--or to idiosyncratic productions. This book sets out to provide a straightforward account of Mozart's most beloved opera, exposing the half-truths and legends that have proliferated since its first production in 1791. The sources for the opera are discussed, and there are chapters devoted to composition of the work, the authorship and qualities of the libretto, the music (analyzed by Erik Smith), early productions and performance history, and the practical problems of directing a production (examined by Anthony Besch). The book contains illustrations, a synopsis, bibliography, and discography and will be of interest to music students, scholars and operagoers.

UT edged one step closer to the championship game. A&M always plays tough, but our team prevailed. larger viewJordan and Colt strollin'. I looking forward to the championship game, though we still have the Big 12 Championship.

For all you creationists out there, I secretly photographed the heart of the beast that is evolution larger view. Yes, it's devoid of anything.

The cosmos did decide to reward me with an inability to go not only faster than the speed limit down Indiana, but not even 1/2 the speed.larger view and of course, the helpful Bloomington signs larger view

Chris Paulson, a student from some time ago, sent me this nice message:

Hey Dr. D, Long time no talk to, this is Chris Paulson(from class of '04) and I got an informatics booklet in the mail today and it made me think of you and I wanted to shoot you an email to see how things are going? I follow the website some and also get updates from Matt Hottell on facebook and its amazing how much things are growing around there! I would love to catch up with you and I will be down at IU sometime in the next couple months visiting my sister(shes a sophmore) and am hoping to catch a basketball game, so I will let you know when I'm gonna be there and hopefully we could meet up for a bit if you have the time. I am living in Wisconsin these days, married(no kids) and I work for GlaxoSmithKline in the Vaccines division selling to hospitals/clinics covering SW Wisconsin. Well I hope things are going well for you as I'm sure they are, and I hope to catch up with you soon. Chris

Jim explained "metrotextual" to me. Evidently, it's OK to end one's text with 'xoxox...' (how ever many are deserved, etc.) without exposing oneself--you can finish this this though.

I'm stealing this from Chelsea Lately, but when she remarked, "Do you remember when 'twilight' just meant dark outside?" I was thinking some hollywooden tax on usurping words.

Another study session of KAN for textbooks

I guess the lesson for the day is "postponed prepositions." This grammatical form is only for informal writing (that's what's believed). For example, "The paper that I was asking about is late." In this case, 'about' is the preposition, and its object is 'that'. Which is correct? "I concur (with or in or to) that proposal? The correct answer is 'in'. Prepositions are pesky elements! I've been working on my dad (whose mother tongue is not English) to rid himself of superfluous prepositions. "Where are you at?" (remove the 'at'); "Is the game over with?" (remove the 'with'). I was going to end with a passage from Voltaire's Philosphical Dictionary. Evidently I can download it for free on my unused KindleDX. Let's see how it goes. - (edited November 29, 2009, 2:50 PM)

November 23, 2009
Two Weeks---Yikes
I'll be posting soon. I finished The Golden Ratio by Livio. I'll discuss it later. Working on Golgi with Haixu, Justen, and Bobak. Very weak posting--forgive me, Edith. - 8:04 AM
October 16, 2009
Monday - Friday
Read with Justen and Bob Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network by Linghu et al. The linkage network is interesting--I suggest reading it.

Handed back Exam I in H101

Creating revisions for homework--this weekend.

Worked on P & T

Got Altas Shrugged, The Stranger, Pride and Prejudice, In the President's Secret Service: Behind the Scenes with Agents in the Line of Fire and the Presidents They Protect, The Lost Symbol books for students, and various music too, Brahms, Prokofiev, Mozart, Gregorian Chants; sheet music (Suites from Debussy)

Instruments of Hell

While at one of the entrances of Hell (I was able to shoot two pictures before the forces of evil disabled my phone) The rolodex to the right are the souls of produce.

Portal of Hell

I was accosted by a young man who found a young praying mantis (the color and texture of grayish tree bark), distressed what to do. I promptly offered to take the mantis to somewhere safe.

He's bewildered

and placed him in one of the trees on the west side of Kroger. Bloomington is "Tree USA", after all.

I also watched nearly half a dozen brave souls, of a larger contingent, creating The School of Informatics and Computing - Bloomington, Bloomington, Indiana's float Pulchritude.

This is homecoming week--and although I like the weather, it's not conducive to crepe paper.

I must show Kan's disdain for my having to do work at home--the laptop is at the left. Punkinbutter

I will eventually show what he does inbetween these misleading cute, passive poses. The last thing to say is that I must be a luddite.

Bad TV! No!

The last image is of my television informing me I should pay my television...What happens when the house is eventually tethered electronically, and your electric toothbrush flashes, "Pay the TV--and buy more Crest?" I'm glad I've kept the clock I had in high school--no electronic soul or enough silicon to give messages other than static or an annoying beep to rouse me from sleep. I know it's probably paranoid, but I could swear the television was trying to turn-off the other electrical devices in the room until I looked at it squarely and performed what is asked.

Meet Miles.

Let's hope for a blowout in the Red River Shoot Out. I'm looking for Colt and Shipley to have a great game, dispensing with OU. Go Horns

- (edited October 16, 2009, 5:20 PM)

October 11, 2009
Friday - Sunday
larger view It was a closer game than I would have liked, but Texas beat Colorado handily in the third and fourth quarters. For any who watched the game, Shipley and the great defense was the answer.

Completed grading H101 Exam and gave an exciting homework III.

Ordered books and more music for Honors students.

Odious, necessary errands today too. I am looking forward to my new website. - (edited October 16, 2009, 4:11 PM)

October 8, 2009
Meet with Honors and Graduate classes. In honors we worked on inferencing. Graduate class will be how to deal with getting a job--guest speaker Scott Beason.

Our Drosophila paper in Genome Biology has been accessed 1938 times so far and is now designated in Genome Biology as "highly accessed". Please visit Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function

Beginning the onslaught of P&T cases.

Attended Life Sciences Reception Faculty/Employers/Students Wednesday, October 7th, 7:00 p.m., President’s Room- Indiana Memorial Union. - 4:56 PM

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