• Beginning the Ph.D. study
• Mandatory and recommended things to do during the study
• Individual study plan
• Yearly evaluation
• Doctoral exam
• Thesis defense
• Grants and finances

A checklist for advisors of prospective students. Often these are master's students from MFF who would like to continue doing their Ph.D. here, but students coming from other universities are common and welcome. The procedure is almost the same in both cases, the external students may need more guidance throughout it. Please also check the official admissions information to make sure the information below is up-to-date.

1. You agree with a prospective student on a focus of their study, which should be reflected in the topic of their thesis. You enter the topic in SIS, with thesis subject area P4I4 (Czech language program) or P4I4A (English language program). The student will also need one (in the Czech language program) or two (English language program) letters of recommendation, usually the prospective advisor writes one of them. Do not put too much effort into these letters, for students whom an advisor agreed to take they are just a formality.
2. The student applies to the program Computer Science - Theory of Computing, Discrete Models and Optimization; there are two admission dates, with deadlines at the end of April and end of December.
3. As part of the application process, the student selects the thesis topic you entered into SIS (occasionally, there may be issues with this, if the student is not able to do so, contact the study affairs department) and submits all required documents, including the recommendation letters.
4. The student may need to pass the English exam (waived for MFF students who passed an English exam during their studies, or students from English-speaking countries, or subject to various certifications).
5. There is also a subject examination, which is usually waived (for MFF students based on grades, for others based on having a publication or other results testifying their ability for doctoral studies).
6. Non-EU students may need to obtain a long-term residence permit and go through other formalities; consult with the secretaries, who should be familiar with the most common cases and be able to point you to other resources if necessary.
7. After the student is accepted, they are hired as research assistants for the regular duration of their studies (four years); see the finances section for more details. A separate application is needed; this is coordinated by the deparment chair, but please pay attention to the e-mails from the secretaries around the admissions.
8. Together with your student, you need to fill in the Individual Study Plan in SIS.

To receive Ph.D., you need to fulfill the following requirements:

• Pass the English exam (for the students of the P4I4A English language program, the exam is not mandatory, but it can be included in their Individual Study Plan if the advisor thinks they will benefit from it). The written part can be waived based on other certifications, but the oral part (including the discussion of your own professional publications and other specialized text your field of study) is obligatory.
• Pass the doctoral exam.
• Write and defend a dissertation thesis. Of course, you also need to obtain the original research results on which this thesis is based.

Usually, the students also participate in some of the following activities. These may be assigned to you as duties in your Individual Study Plan:

• Do research. You will regularly meet with your advisor and get assigned papers to read and open problems to think about; later in your study, you are expected to become more independent and set your own agenda. You will discuss your findings and your advisor may give you suggestions about ways to solve the problems, the relevant techniques and related results you may not be aware of.
• Publish your results in journals and present them at workshops and conferences. During Ph.D. study, you are expected to learn the ways the results are disseminated in your field. Your advisor will help you prepare the results for publication, give you an overview of journals and conferences relevant in your field and some idea of their relative prestige, and guide you in selecting the right venue for your work. They will also help you with obtaining a funding for the travel costs and conference fees.
• Solve grant projects. You will likely participate in solving a grant project of your advisor or one of their colleagues, giving you an opportunity to learn to work in a group and obtain results relevant for your thesis, as well as an access to additional funding. You may also apply by yourself for some of the grants offered by the university, giving you an experience with the grant application and management process. For more details, see the section on grants and funding.
• Participate in workshops and summer schools. These are specialized events focusing on presentation of recent results from some field, intensive courses on particular topics or techniques, or group research on interesting open problems. These events are helpful in obtaining original results, but even more importantly, they will enable you to work and establish contacts with other researchers in your area. Your advisor may help you to find and apply for suitable events, recommend you for invitation-only events, and assist you with obtaining the necessary funding.
• Take part in or help organize the departmental events:
  • Spring school: A one-week school held in April.
  • Midsummer Combinatorial Workshop: a workshop held at the end of July or the beginning of August
  • KAMAK: A research workshop held in September.
  The departments also regularly host other events and conferences, and you may be asked to help and to learn how to organize them.
• Visit other universities and researchers abroad. During a visit lasting a few weeks or months, you may be able to do research with established researchers from other universities, in order to give you new ideas and broaden your interests, and to establish contacts that will be useful to you later in your career. Your job applications will require letters of recommendation, and this is a great way to make sure you will know who to ask for them. You will also learn about the differences between the university culture and organization in different countries. Your advisor should be able to help you with the introductions, ask a colleague to host you, and potentially assist with funding.
• Take some courses. MFF offers a number of specialized courses designed for doctoral students, but you can also take more general courses (depending on your educational history, these may be recommended to you by your advisor). The courses generally end by an exam, which for Ph.D. students is only graded pass or fail (failing an exam does not have any immeditate consequences, but it may be a contributing factor in your yearly evaluation). The availability of the courses changes each year (some are only taught every second year, or when a guest lecturer stays for the term); you can learn about most of the relevant ones during the scheduling event held by our departments at the beginning of each term. Taking these courses may be your last opportunity to conveniently learn new topics and broaden your perspective; however, especially later in your study, the courses should account for only a small amount of your time.
• Participate in seminars. Many of the research groups at our departments organize seminars focusing on their particular topic, where the participants read and present recent papers or learn about new ideas and specialized techniques. You can also learn about them during the scheduling event. Furthermore, all doctoral students are recommended to attend the doctoral seminar, where they can practice presenting advanced papers and learn about the topics that interest other doctoral students.
• Teach. Having a teaching experience is helpful when searching for a job at a university. Tutorials for most courses at MFF are lead by doctoral students, and you will be expected to take part; 1-2 months before the start of each term you will be contacted to sign up. Later in your study, you may also get involved with organization of one of the seminars or help teaching some of the advanced courses related to your specialization.

The ISP needs to be filled at the beginning of the study (roughly during the first month of the term). The goal of ISP should be to help the student and their advisor to plan the course of the study. It also lets the advisory board track your progress and possibly give you a feedback in case there appears to be a substantial deviation. The two fields that are helpful in this aspect and that you should pay attention to are:

• Course of study (průběh studia): An overview of the planned course of the whole study and expected duties. The first year can be more detailed, while for the later years should specify the major duties and describe the general focus at the given stage. The course of study must include all mandatory duties, i.e., the doctoral exam, the English language exam (except for the the students of the P4I4A English language program), and the defense of the dissertation thesis. Example:

    1st year:
      * survey of the literature relating to the thesis topic
      * the student attends the following courses and seminars: ...
      * research and preparation of the results for publication
      * presentation of the results at the conference ...
      * leading of tutorials on (subject)
  
    2nd year:
      * the doctoral exam
      * the student applies for a GAUK grant on the topic ...
      * research and publications on the topics arising from the survey
      * student attends seminars ... related to the thesis topic
      * leading of tutorials
  
    3rd year:
      * the English exam
      * research and publication, with focus on finishing the started
        projects related to the dissertation
      * 3-month stay at ...
      * start of the work on the thesis
  
    4th year:
      * the student takes active part in organization of the seminar ...
      * finishing the thesis and its defense
  

• "progress on the doctoral dissertation" field of "Dissertation and progress on the dissertation" (postup v přípravě disertační práce / Disertační práce a postup v přípravě disertační práce): This should include more details on the scientific aspects, to the foreseeable extent. Example:

    1st year:
      * the student surveys the series of papers by ... and learns the
        following methods ...
      * the student applies these methods in an attempt to obtain new results
        on ..., and prepares the results for publication
    2nd year:
      * student considers (among other topics possibly arising from the survey)
        the open problems regarding ...
    3rd year:
      * during the 3-month stay at ..., student works on the topics suggested
        by ...
      * the student writes an outline of the thesis and focuses on resolving the
        loose ends that become apparent in the process
    4th year:
      * the student finishes and defends the thesis
  

On the other hand, I do not recommend spending too much time on the "itemized" duties (list of duties/přehled povinností). You can input the courses that the student plans to attend, but it rarely makes sense to write specific publications/conferences/… in advance.

You will be able to amend the ISP during the yearly evaluation.

During the yearly evaluation, after consulting with their advisor, the student fills in a report in SIS detailing their progress over the last year and possibly suggesting amendments to the ISP. The advisor then fills in their own recommendation.

Afterwards, the reports are evaluated by the advisory board. The board gives feedback to the students and advisors in case the progress deviates from the ISP. In exceptional cases where the student clearly does not fulfill the goals set in the ISP and is not likely to be able to obtain the Ph.D. degree, the advisory board may terminate study.

The evaluation is on a three-grade scale:

• A: Everything seems to be in order. Check the text evaluation for possible suggestions from the advisory board.
• B: The boards is concerned. Pay close attention to the text evaluation, and possibly contact the program coordinator (currently Zdeněk Dvořák) to discuss the situation.
• C: The board decided to terminate the study.

Overall, we encourage the students to finish their study within the standard duration (four years) and with several publications. To this end, we in general follow the evaluation guidelines given below. When considering these guidelines, the board of course takes into account the individual circumstances of each student (the previous education, any long-term interruptions of the study, ...) and the information from their supervisor.

• It is desirable to have at least one result submitted for publication by the end of the second year of the study. This not being the case does not necessarily lead to a reduced grade, but the board will carefully evaluate the circumstances and possibly discuss the situation with the student and their advisor.
• Students not having any results submitted for publication after the third year will receive the B grade.
• Students not having any results submitted for publication after the fourth year will receive the C grade and their study will be terminated.
• The doctoral exam should be taken at latest in the third year. Students who have not passed the doctoral exam by the end of the third year will receive the B grade.
• After the fifth year of study, only B or C grades are possible; the student should demonstrate a tangible progress towards fulfilling their obligatory duties (passing the doctoral exam and defending the thesis).

The doctoral exam is an in-depth exam from several fields, usually taken in the second or third year of study. In theory:

• Choose two of the following fields: Discrete Mathematics; Logic; Computational Complexity; Design and Analysis of Algorithms.
• Choose two of the following fields: Optimization; Combinatorics; Structure Theory; Probabilistic Method; Topological Methods and Discrete Geometry; Cryptography; Data Structures; Algorithmic Game Theory.
• After consulting with your advisor, choose another field (which also may be one of the 8 listed in the previous point).

In practice, rather than studying the whole field, the student and their advisor agree with the examiner on a more focused topic and are assigned specific study materials (several chapters from a book, a series of papers, …). Often, this is taken as an opportunity to obtain an in-depth understanding of a particular topic or to learn a generally useful technique. While the selected topics must adhere to the formal rules outlined above, the fields are quite broad (and we are flexible in interpreting them), so any reasonable choice can be accommodated. Moreover, to keep the study load manageable, from one of the topics (usually the one closest to the student's specialization), the student is examined only on their broad overview (their knowledge of the most important results and research directions in the field and the relationships between them).

How to proceed:

• Together with your advisor, agree on the five topics that you would like to be examined from and on four examiners for the focused topics. The examiners can be from other departments, other universities, or even from abroad (especially for the topics that are not well represented here); in fact, this is desirable, as at least one member of the exam committee must be from outside of MFF.
• Consult the topics and examiners with the program coordinator (currently Zdeněk Dvořák). Generally, he will just confirm that the formal criteria are met; in more complicated cases, he will discuss the proposal with the whole program advisory board. The examiners who are not docents or professors must be confirmed by the scientific board, unless they already are on the list of approved examiners (the program coordinator will arrange this and it is generally just a formality, there is no need to wait for this confirmation).
• Agree with each of the four examiners on the topic and material to study.
• Prepare for the exam (this usually takes several months).
• At least a month in advance, contact the program coordinator and ask them to organize the exam. They will agree with you and the committee members on an exact date and time.
• Take the exam. The examiners will ask you questions from the selected topics; after a preparation time, you will be asked to present your answers to the committee, who can have some additional questions. The committee will also ask general question from your broad overview topic.

The last part of your study, which can only be undertaken after you have passed the doctoral exam and fulfilled all other duties specified in your ISP. The thesis must in a significant part contain your own original research and it is expected that it will be at least partially based on results published in journals or at refereed conferences. Note that the writing of the thesis is a significant undertaking, takes at least several months, and involves multiple rounds of revisions based on your advisor's feedback. The thesis is usually written in English (though Czech and Slovak are allowed). See also more info on the formatting of the thesis and LaTeX templates.

How to proceed once you are ready to defend the thesis:

• After consulting with your advisor, contact two suitable opponents for your thesis and obtain their preliminary agreement; at least one of them must be from outside of the university, and they should not have any conflict of interest.
• At least two months in advance contact the program coordinator (currently Zdeněk Dvořák) and inform him on your intention and your suggestions for opponents. He will propose a committee for the defense, and the committee then agrees on the suggested opponents (or selects different ones, in case they do not consider them suitable). The program coordinator will also agree with you and the committee on the date and time of the defense.
• At least 6 weeks before this date submit your thesis in SIS (along with your cv, the list of accepted and submitted publications including the citation counts, and 10-20 page extended abstract of your thesis) and inform the study affairs department.
• You also need to submit 3 printed copies of the thesis at the study affairs department.
• The program coordinator will then formally contact the opponents and ask them for their evaluations. Your advisor also needs to submit their evaluation (commenting both on the thesis and the student in general). The evaluations will be made available to you at least five days before the defense date.
• The defense is public. During the defense, you will give a 30-minute presentation of your thesis, followed by a discussion in which the audience members can as additional questions. In your presentation, you should also address the concerns raised in the opponents evaluations (if any).

During your first four years of study, you are guaranteed an income of at least 25500 CZK/month:

Year	State-guaranteed stipend	School of Computer Science salary	Total
1st	11000 CZK/month	16000 CZK/month	27000 CZK/month
2nd till 4th	12500 CZK/month	13000 CZK/month	25500 CZK/month

The stipend further increases by

• 2000 CZK/month after you pass the doctoral exam
• 1000 CZK/month for publication activity. This is roughly defined as having papers accepted for publication in journals or presented at refereed computer science conferences on which your total contribution is at least 100% (e.g., two papers with one additional co-author), though the program advisory board can also take the quality of the publications into account. Once you pass this criterion, contact the program coordinator to apply for the stipend increase.

Your income will also increase in case you work on a grant project (as a team member, or in case of the university GAUK projects, as its principal investigator). Such an extra income will be used to cover a part of the School of Computer Science salary contribution, but always in such a way that your total income increases. You will usually be included in the project team of your advisor's grant (if they have one), or possibly of one of their colleagues if you show interest in a relevant topic.

After the 4th year (beyond the standard length of the study), you may still receive salary from from grants in case you substantially contribute to them, but this needs to be discussed with your advisor and the department chair at an individual basis.

The department budget and the grant projects will also be used to fund the travel and conference costs essential for your study. As a general rule, we will be able to arrange funding in case your paper is accepted for a presentation at a refereed conference or you get an invitation to attend an invitation-only event. In other cases (workshops, schools, research visits, …), discuss the possibilities with your advisor, who will likely be able to obtain a funding for you in case the event advances your study.

Ways to obtain additional funding:

• GAUK (university grant agency) runs a full-fledged grant program for the university students. In addition to possibly gaining more independence with your own funding, this gives you a chance to gain experience with grant applications and (if you succeed in obtaining the grant) with the grant management. Hence, we encourage all doctoral students to participate. The applications are submitted in October each year, and the projects typically last 2-3 years.
• The university has a number of bilateral agreements with other institutions, and some of them include funding for various-length stays at the partner institutions. In case you are interested in visiting one of your contacts at these institutions, ask the Research & International Affairs Department for details.
• Many conferences offer funding for students; see the web pages of the conference you consider attending for more details.