Autumn 2019 Program

This is the programme of the Sitola seminar in autumn 2019. Presentations for the current semester are available here.

• 12.9.2019
  SitSem: materials from Jana Hozzová
  Basic statistics for scientists
  • Online course containing all this and much more, including our and other examples of concepts in R
  • Visualization of the impact of the effect size (Cohen’s d)
  • Visualization of the impact of the correlation
  • Why most studies are false?

• 18.9.2019
  CESNET seminar (no presentation)
• 25.9.2019
  doc. Mgr. Hana Rudová, Ph.D.
  Adaptive large neighborhood search for scheduling of mobile robots
  Abstract: The talk addresses the scheduling of mobile robots for transportation and processing of operations on machines in a flexible manufacturing system. Both mobile robots and automated guided vehicles (AGVs) can transport components among machines in the working space. Nevertheless, the difference is that mobile robots considered in this work can process specific value-added operations, which is not possible for AGVs. This new feature increases complexity as well as computational demands. To summarize, we need to compute a sequence of operations on machines, the robot assignments for transportation, and the robot assignments for processing. The main contribution is the proposal of an adaptive large neighborhood search algorithm with the sets of exploration and exploitation heuristics to solve the problem considering makespan minimization. Experimental evaluation is presented on the existing benchmarks. The quality of our solutions is compared to a heuristic based on genetic algorithm and mixed-integer programming proposed recently. The comparison shows that our approach can achieve comparable results in real-time which is in order of magnitude faster than the earlier heuristic.
  The talk is an extended version of the presentation at GECCO 2019, see the paper here.

• 2.10.2019
  Ing. Jana Hozzová, Ph.D.
  Improved search heuristics in molecular docking
  Abstract: Before the drug binds into the active site of the protein, it may need to pass through the tunnel within the protein. Molecular docking, a computer simulation, looks for a specific position of the drug so that it fits into the tunnel at the current spot. In collaboration with Loschmidt Laboratories in Faculty of Science at Masaryk University, we have developed a software tool CaverDock which applies a modified docking to construct a complete, smooth trajectory of the drug passing through the tunnel. From the point of computer science, the process of construction of the trajectory includes searching in a vast space of all possible conformations of the molecule. In this talk, we show our improved search heuristics of that search and back it up with a carefully done statistical evaluation.
• 9.10.2019
  RNDr. Tomáš Raček
  DSL for computing partial atomic charges
  Abstract: While programming languages like C or Java can be used for any task, some applications might benefit from using more specialized solutions – domain specific languages (DSL). Compared to the general-purpose ones, languages like SQL, DOT, or CSS might offer several advantages – from the simplicity of use, meaningful error reporting to type safety.
  In this talk, we outline the design and the implementation of a simple DSL for computing partial atomic charges. Specifically, we cover all the aspects needed to translate a program in this DSL into a language like C++, i.e., grammar design, building a parser, abstract-syntax tree traversal, type checking, and code generation. Although the DSL in question is designed for computational chemists, no a priori chemical knowledge is required for this talk.
• 16.10.2019
  ing. Michal Bidlo, Ph.D.
  Advances in evolutionary design of cellular automata
  The talk will be devoted to the latest research results regarding an evolutionary design of complex multi-state cellular automata (CA). In particular, two-dimensional cellular automata will be considered in combination with a pattern development problem as a case study. An advanced representation technique for designing transitions functions for CA, called Conditionally Matching Rules, will be briefly introduced and its abilities compared to the conventional table-based representation. It will be demonstrated that the representation significantly influences both the quality of results and the way of their functioning. Interactive visualizations of selected results will also be included.
• 23.10.2019
  RNDr. Dalibor Klusáček, Ph.D.
  Improving fairness in a large scale HTC system through workload analysis and simulation
  In this talk, we present an example of a real-life scheduling problem coming from one of the largest academic computing centers in France. This high throughput computing (HTC) center serves as one of the main facilities to analyze data produced by the Large Hadron Collider (LHC) at CERN. These high energy physics computations utilize nearly two-thirds of available resources while the remaining part is used by local users. By analyzing these two different user groups and their workloads, we identify some problems related to the overall fairness of the existing scheduling scheme. Importantly, the scale and complexity of these large workloads composed of millions of jobs per month require special efforts when trying to improve the existing scheduler. Using real-life data and detailed simulations, we evaluate newly proposed scheduling setups that aim at improving fairness between various user groups. The results show that the existing scheduling setup can be enhanced, significantly improving the quality of service experienced by formerly unfavored users.
• 30.10.2019
  Soumen Atta, Ph.D.
  Solving maximal covering location problem using a genetic algorithm with local refinement
  Maximal covering location problem (MCLP) is one of the well-studied facility location problems. MCLP deals with the problem of finding an optimal placement of a given number of facilities within a set of customers. Each customer has a specific demand and the facilities should be placed in such a way that the total demand of the customers served by the facilities is maximized.
  In this talk, a new approach based on the genetic algorithm (GA) is discussed to solve MCLP. The approach utilizes a local refinement strategy for faster convergence. It is applied to several MCLP instances of sizes up to 2,500 customers from literature, and it is demonstrated that the proposed GA with local refinement gives better results in terms of percentage of coverage and computation time to find the solutions in almost all the cases.
• 6.11.2019
  prof. Mgr. Jiří Damborský, Dr.
  25 years of research experience in Loschmidt Laboratories
  Abstract: The research group, which became later known as Loschmidt Laboratories, has been started in 1994 by two people in a single laboratory (12 m²), equipped with a fridge, a shaker bath, and old spectrophotometer. We published the first article in the local journal Scripta Medica. Today, the group comprises of >40 members, facilities worth 100 mils. CZK, 350 m² of laboratories and publishes papers in visible journals, like Nature Chemical Biology, Angewandte Chemie, Nucleic Acids Research, The Journal of American Chemical Society, ACS Catalysis and PNAS. In this interactive seminar, we will discuss critical elements of running an academic group. Selected topics to be covered: (i) recruitment, (ii) publishing strategies, (iii) group meetings, journal clubs, outreach seminars, (iv) bilateral meetings, and (v) project management, reporting. The topics will be introduced by 5-10 min description of practices in Loschmidt Laboratories, which will be followed by questions and discussion. 
• 13.11.2019
  doc. Mgr. Radek Pelánek, Ph.D.
  Simulated data in adaptive learning research
  Abstract: Adaptive Learning group has developed several widely used learning systems and used them to collect extensive data. Yet, in our research, we often use simulated data. I will describe the motivation for using simulated data and examples of specific research studies that we have done using simulated data, particularly for the analysis of the impact of biases in data collection.
• 20.11.2019
  Ing. Tomáš Košňar
  Network & Network Traffic Monitoring
  Abstract: Computer networks as general purpose communication facilities represent a basic platform for global information exchange in the current world altogether. Monitoring is, therefore, a necessary activity to maintain this complex technical environment in an operating state, fully functional and secure. In this talk, we will discuss and summarise basic and most common approaches to large scale and continuous infrastructure and traffic monitoring in wide area networks. We will show an example from real monitoring systems and finally highlight challenges for the future.
• 27.11.2019
  Štěpán Balážik
  Testing server selection algorithms in DNS resolvers
  Abstract: Different implementations of DNS resolvers take different approaches to the authoritative server selection problem, i.e., resolvers are faced with the question „Which authoritative server should I ask now?“. This presentation introduces a new tool for testing server selection strategies implemented in DNS resolvers called DNS Maze. DNS Maze runs DNS resolvers inside a simulated environment containing various authoritative server configurations (good and lame delegations, invalid signatures, …) and also network parameters (latency, packet loss, …), and gathers statistical data about communication between the resolver and authoritative servers. Using Maze, we can expose multiple versions of different implementations to various scenarios and get a better understanding of their performance, and thus make informed decisions refactoring/rewriting/configuring server selection part of DNS resolvers. We will also present our findings about various resolver implementations.
• 4.12.2019
  Mgr. Břetislav Regner
  Office 365 Overview (presentation for 40 minutes, survey talk)
  Abstract: Office 365 is a suite of tools intended to facilitate daily work and collaboration, as well as a platform on which more complex systems can be built. In the talk, we will introduce some of the available tools and their intended usage – document storage, sharing and co-authoring, working with calendars and mailboxes, team communication and collaboration tools, planning, and task management. We will also mention some advanced data visualization, integration, automation, and development tools. Considering the audience – mainly IT pros, we will focus on tips, tricks, and known issues, instead of on detailed description of basic functions.
• 11.12.2019
  Mgr. Petra Hrozková
  Towards CaverDock 2.0.
  CaverDock is a tool for modeling the transport process in protein tunnels. These processes are hard to measure, and in some cases, it is impossible. The course of tunnel transport is indispensable for studying protein reactions, and it is essential for detection whether the ligand will be able to go through the tunnel and react with an active center. The limitation of the CaverDock approach is a rigid structure of protein -CaverDock assumes there is almost no flexibility of protein, while in reality, the protein is, of course, quite flexible. These factors could be added to CaverDock from an external source, e.g., by an iterative refinement of CaverDock structures by minimization using the Amber force field. Another challenging task is to explore possible pathways through the tunnel rapidly: in our case, we decided to use a combination of the original CaverDock heuristics with algorithms used for motion planning in robotics.
• Tuesday 17.12.2019 16:00
  Discussion about future Sitola and
  Christmas meeting

• Examination period 2.1. – 12.2.2020
  Meetings devoted to state exam training are scheduled mostly. State exam training are in Czech mostly. More days can be added if needed by students.

• 27.1.2021
  State exam training (master)
  State exam rehearsals (master)
  Dávid Horov: Veřejná data a nové aplikace o chytrých městech
  Vedoucí: Hana Rudová
  Oponent: Barbora Bühnová
• 5.2.2020 State exam rehearsals (bachelor)
  Andrej Betík: Visualization of tree search algorithms
  Vedoucí: Hana Rudová
  Oponent: Stanislav Murín

  Samuel Gorta: Detekce kortikálních vrstev v signálech magnetické rezonance nízkého rozlišení
  Vedoucí: Aleš Křenek
  Oponent: Jan Fousek

Contact: Hana Rudová