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28
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Introduction
I am an assistant professor in Institute of Computing Science at PUT and Institute of Bioorganic Chemistry at Polish Academy of Sciences. Moreover, for over ten years I am a coach of teams participating in programming contests, and I am developing online judge systems supporting such competitions. I was PI on the project which objective was to develop Optil.io platform (a system that supports evaluation of optimization algorithms using an Evaluation as a Service scheme). My main areas of interest are operational research, optimization, bioinformatics and application of crowdsourcing.
Current institution
Additional affiliations
October 2008 - present
Publications
Publications (28)
This paper concludes the Brilliant Challenges contest. Participants had to design interesting optimization problems and publish them using the Optil.io platform. It was the first widely-advertised contest in the area of operational research where the objective was to submit the problem definition instead of the algorithmic solutions. Thus, it is a...
Chessboard and chess piece recognition is a computer vision problem that has not yet been efficiently solved. Digitization of a chess game state from a picture of a chessboard is a task typically performed by humans or with the aid of specialized chessboards and pieces. However, those solutions are neither easy nor convenient. To solve this problem...
The most plausible hypothesis for explaining the origins of life on earth is the RNA world hypothesis supported by a growing number of research results from various scientific areas. Frequently, the existence of a hypothetical species on earth is supposed, with a base RNA sequence probably dissimilar from any known genomes today. It is hard to dist...
Background
Open science is an emerging movement underlining the importance of transparent, high quality research where results can be verified and reused by others. However, one of the biggest problems in replicating experiments is the lack of access to the data used by the authors. This problem also occurs during mathematical modeling of a viral i...
The RNA World is currently the most plausible hypothesis for explaining the origins of life on Earth. The supporting body of evidence is growing and it comes from multiple areas, including astrobiology, chemistry, biology, mathematics, and, in particular, from computer simulations. Such methods frequently assume the existence of a hypothetical spec...
Chessboard and chess piece recognition is a computer vision problem that has not yet been efficiently solved. However, its solution is crucial for many experienced players who wish to compete against AI bots, but also prefer to make decisions based on the analysis of a physical chessboard. It is also important for organizers of chess tournaments wh...
Crowdsourcing is a very effective technique for outsourcing work to a vast network usually comprising anonymous people. In this study, we review the application of crowdsourcing to modeling systems originating from systems biology. We consider a variety of verified approaches, including well-known projects such as EyeWire, FoldIt, and DREAM Challen...
Reliable and trustworthy evaluation of algorithms is a challenging process. Firstly, each algorithm has its strengths and weaknesses, and the selection of test instances can significantly influence the assessment process. Secondly, the measured performance of the algorithm highly depends on the test environment architecture, i.e., CPU model, availa...
Reliable and trustworthy evaluation of algorithms is a challenging process. Firstly, each algorithm has its strengths and weaknesses, and the selection of test instances can significantly influence the assessment process. Secondly, the measured performance of the algorithm highly depends on the test environment architecture, i.e., CPU model, availa...
Online judges are systems designed for the reliable evaluation of algorithm source code submitted by users, which is next compiled and tested in a homogeneous environment. Online judges are becoming popular in various applications. Thus, we would like to review the state of the art for these systems. We classify them according to their principal ob...
Online judges are systems designed for the reliable evaluation of algorithm source code submitted by users, which is next compiled and tested in a homogeneous environment. Online judges are becoming popular in various applications. Thus, we would like to review the state of the art for these systems. We classify them according to their principal ob...
Despite years of study, it is still not clear how life emerged from inanimate matter and evolved into the complex forms that we observe today. One of the most recognized hypotheses for the origins of life, the RNA World hypothesis, assumes that life was sparked by prebiotic replicating RNA chains. In this paper, we address the problems caused by th...
Evaluation as a Service, in brief, is defined as a paradigm of keeping the evaluation data in the cloud and allowing to access them via dedicated interfaces. Here, we present Optil.io, an online platform that allows users to reliably evaluate metaheuristic-based algorithms, designed to solve complex optimization problems, in a secure cloud-based in...
According to some hypotheses, from a statistical perspective the origin of life seems to be a highly improbable event. Although there is no rigid definition of life itself, life as it is, is a fact. One of the most recognized hypotheses for the origins of life is the RNA world hypothesis. Laboratory experiments have been conducted to prove some ass...
Background: The choice of a bioinformatics tool that is used to design and analyse bioinformatics models is usually influenced by the choice of format used to store the models on the hard drive and vice versa and may seem irrelevant to researchers who design and analyse biological models using high-level computer software. However, the method for s...
In chemistry, a hypercycle is an abstract model of organization of self-replicating molecules connected in a cyclic, autocatalytic manner. It was introduced in an ordinary differential equation (ODE) form by the Nobel Prize winner Manfred Eigen in 1971 and subsequently further extended in collaboration with Peter Schuster. It was proposed as a solu...
The main objective of the presented research is to design a platform for continuous evaluation of optimization algorithms using crowdsourcing technique. The resulting platform, called Optil.io, runs in a cloud using platform as a service model and allows researchers from all over the world to collaboratively solve computational problems. This is th...
Crowdsourcing, understood as outsourcing work to a large network of people in the form of an open call, has been utilized successfully many times, including a very interesting concept involving the implementation of computer games with the objective of solving a scientific problem by employing users to play a game-so-called crowdsourced serious gam...
Chain of improvements.
Chain of improvements that lead to the best solution. It presents the sequence of solutions, each of which is based on the previous one with the value of the increment and id of the player.
(XLSX)
Example gameplay.
Video that demonstrates an example interaction with the game: construction of the spaceship, its flight and selecting another user’s solution as a starting solution to improve the spaceship.
(MP4)
Survey results.
The table contains all answers to the closed-ended questions inside the survey. It also contains the description of each question and possible answers. The information about the game was spread among our friends; that is why most of the open-ended questions were answered in Polish, so we do not include them. The analysis of answers...
Game results.
Game results generated during the first and the second iterations of tests. Each row presents the solution designed by the player, its value, the player’s id and the base solution that was used.
(XLSX)
The objective of this study is to design a method for modeling hepatitis C virus (HCV) infection using multi-agent simulation and to verify it in practice.
In this paper, first, the modeling of HCV infection using a multi-agent system is compared with the most commonly used model type, which is based on differential equations. Then, the implementat...
Computational modeling is an important element of systems biology. One of its important applications is modeling complex, dynamical, and biological systems, including viral infections. This type of modeling usually requires close cooperation between biologists and mathematicians. However, such cooperation often faces communication problems because...
We investigate a correlation between genetic diversity of hepatitis C virus population and the level of viral RNA accumulation in patient blood. Genetic diversity is defined as the mean Hamming distance between all pairs of virus RNA sequences representing the population. We have found that a low Hamming distance (i.e. low genetic diversity) correl...
Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two maj...
