KLÍMOVÁ, L. Automatové techniky v analýze DNA [online]. Brno: Vysoké učení technické v Brně. Fakulta informačních technologií. 2025.
The work and results deserve to be priced by themselves, but the students tenacity and overall ability to conduct all kinds of research task highly independently stands out even among the best students.
| Kritérium | Známka | Body | Slovní hodnocení |
|---|---|---|---|
| Informace k zadání | An extremely difficult research assignment. It combines a research on advanced automata-based pattern matching with advanced technology of gene annotations. The assignment is even more difficult due to the supervisor's illiteracy in gene annotation and computational biology. It is also very ambitious, aiming at outperforming state-of-the-art tools in gene annotation. | ||
| Práce s literaturou | Exceptional. The student has compensated for my lack of knowledge in computational biology and studied on need literature form that field by herself, and generally worked with the literature competently and efficiently. | ||
| Aktivita během řešení, konzultace, komunikace | This project has been going on for several years, starting by an experimental collaboration and slowly evolving into a serious research endevour with a high potential to generate publications. Most of the credit for this goes to the student, who compensated for my lack of knowledge in computational biology, carried on with tenacity even after major setbacks (we run into several dead ends on the way, for instance with the Alergia learning approach), solved technical problems, understood quickly her advisor's half baked ideas and turned them into meaningful conversations and later solutions, and came up with very good and fresh ideas by herself. She has shown an exceptional abilities in theory and algorithm design as well as in implementation. The amount of work actually exceeds an excellent diploma thesis. | ||
| Aktivita při dokončování | I was able to review the entire text before it was handed in. | ||
| Publikační činnost, ocenění | The work is almost ready for publication, it may even turn into a research direction. |
The student presented two novel techniques for the detection of structural domains of transposons. The first approach, based on learning automata, did not yield competitive results. The second one is based on splitting profile hidden Markov models and turning them into deterministic finite automata which are then used for fast matching. The results show that it can outcompete the state-of-the-art tool BLAST. Considering the quality and scope of the work, I believe it would be suitable even for a master's thesis. Therefore, I recommend awarding the grade A .
| Kritérium | Známka | Body | Slovní hodnocení |
|---|---|---|---|
| Náročnost zadání | I find the assignment quite difficult, as it required the student to study advanced methods of biological sequence alignment along with related topics in automata theory. | ||
| Rozsah splnění požadavků zadání | |||
| Rozsah technické zprávy | Even though the thesis is longer than usual, it contains no unnecessary information. The length is justified and reflects the substantial amount of work the student has completed. | ||
| Prezentační úroveň technické zprávy | 98 | The thesis is very well written, with a good number of examples showing how the proposed algorithm works. | |
| Formální úprava technické zprávy | 95 | The report is written in solid English, with only very minor problems. | |
| Práce s literaturou | 97 | The thesis contains an extensive overview of existing methods, with appropriate selection and citation of relevant sources. The student’s own work is clearly distinguished from existing approaches. | |
| Realizační výstup | 93 | The proposed algorithm was implemented in a new tool named DUCK. The tool is properly documented and was extensively compared with existing tools BLAST and HMMER. | |
| Využitelnost výsledků | I think that the work could lead to a publication. |
eVSKP id 164168